https://newweb.sudoroom.org/mediawiki/api.php?action=feedcontributions&feedformat=atom&user=208.87.217.74Sudo Room - User contributions [en]2026-10-30T00:56:34ZUser contributionsMediaWiki 1.43.11https://newweb.sudoroom.org/mediawiki/index.php?title=ATX_PSU&diff=6956ATX PSU2014-01-11T01:18:14Z<p>208.87.217.74: </p>
<hr />
<div>Readily hackable power supplies, 3.3v, 5v, +/-12v.<br />
<br />
Minimum steps to power up a PSU<br />
Jump the Green (Power On) wire to a Black (ground) wire.<br />
<br />
To indicate power on state, connect LED with resistor to Grey and Black.<br />
<br />
Units contain a typically variable speed cooling fan.<br />
Standard PC cable power port.<br />
Some units have power switch on back, some have on indicator LED as well.<br />
Usually a switch for 120v/240v supplies.<br />
Generally requires at least one external load drawing current to power on.<br />
<br />
General Wire color coding:<br />
<br />
Black = Ground<br />
Orange = 3.3v Max 10A 33w<br />
Red = 5v Max 20A 100w<br />
Purple = 5v (standby)<br />
Yellow = 12v Max 12A 144w <br />
Blue = -12v Shared with 12v+<br />
<br />
Green = Power On<br />
Grey = Power OK<br />
<br />
<br />
http://en.wikipedia.org/wiki/Power_supply_unit_(computer)</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=5896Phage therapy2013-10-30T03:00:04Z<p>208.87.217.74: /* The Gonorrhea Eradication Team and Integration Taskforce (GETit!) */</p>
<hr />
<div>==Contribute To Our Pilot Program!==<br />
<br />
If you have time or resources to contribute to this project, we urge you to attend our bi-weekly meetings or donate to our Pilot Program WePay Campaign [https://wepay.com/donations/gonorrhea-eradication-team here!]<br />
<br />
==The Gonorrhea Eradication Team and Integration Taskforce (GETit!) ==<br />
We are a volunteer group of experienced citizen scientists working to foster healthy communities through innovative medical research. Our team includes PhD-, Master- and Bachelor-level scientists. Together, we are taking on our first major project: the eradication of antibiotic resistant gonorrhea using Phage Therapy! We are asking for support in launching our Pilot Program which aims to: (1) Isolate and Characterize Bacteriophage from 10 patients, and (2) create a proof-of-concept bacteriophage cocktail to be tested ''in vitro''.<br />
<br />
''Our team:''<br />
<br />
:'''Craig Rouskey''', MSc in Molecular Biology, Biochemistry, Microbiology and Immunology<br />
:'''Ami Knop Ullrich''', MSc in Medical Microbiology and Immunology<br />
:'''Marc Juul''', MSc in Biotechnology Engineering<br />
:'''Jenny Ryan''', MA in Anthropology, MA in Communication<br />
:'''Ianto Lin Xi''', BSc Molecular Biology<br />
<br />
== Introduction ==<br />
Neisseria gonorrhoeae, the sexually transmitted pathogen that causes Gonorrhea, has progressively developed resistance to the antibiotic drugs used to treat it. Within the past 40 years, this pathogen has developed resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Neisseria gonorrhoeae (ARNG) is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. These treatments have been mostly successful, but given the ability of ARNG to develop antibiotic resistance, it is critical to continuously research and develop new treatment regimens for gonorrhea<ref>http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>. <br />
<br />
To meet the needs of a rapidly changing public health field in which traditional antibiotic-based therapies are becoming ineffective, the Gonorrhea Eradication Team and Integration Task-force (GETit) was created. This organization was created to conduct research into bacteriophage associated with Neisseria gonorrhoeae. Bacteriophage are viruses that infect bacterial hosts and can induce lysis upon infection. Ultimately, our goal is to identify and characterize bacteriophage from wild type ARNG and use a composite cocktail of ARNG-associated phage as therapy to treat hosts infected with this pathogen.<br />
<br />
'''During our pilot program, we plan to''': <br />
# isolate ''N. gonorrhoeae'' from 10 patients<br />
# isolate bacteriophage from 10 clinical samples of ARNG <br />
# characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae'', and <br />
# conduct proof-of-concept experiments in which ARNG-derived phage cocktails are used to lyse cultures of ARNG ''in vitro''.<br />
:<br />
<br /><br />
: '''This project is in its early stages. Our longer-term goals are to''':<br />
# Begin a free-Gonorrhea screening program on the streets of Oakland and San Francisco;<br />
# Enhance the Center for Disease Control's Surveillance of antibiotic-resistant gonorrheal infections;<br />
# Develop assays for the rapid detection of ''N. gonorrhoeae.''<br />
# Develop methods by which bacteriophages can be cultured and used as prophylaxis and therapy for gonoccocal infections;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research;<br />
# Develop a community education program to bring science to underrepresented cultural groups.<br />
<br />
:<br />
: <br /><br />
<br />
:'''''If you would like to help with any of these project goals, please contact Craig (contact [at] craigrouskey [dot] com).'''''<br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections == <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the facultative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Symptoms of Gonorrhea ==<br />
== Antibiotic Resistant Gonorrhea ==<br />
:Until recently, gonorrhea treatment was simply a matter of picking the right antibiotics; however, that is quickly ceasing to be the case. Gonorrhea is currently one of the most common treatable STDs in the United States, but soon it may be just one of the most common STDs. The number of gonorrhea cases resistant to treatment with antibiotics has continued to rise, and scientists are quickly running out of options. Single-dose antibiotics for gonorrhea treatment are quickly becoming a thing of the past.<br />
<br />
:Gonorrhea, otherwise known as the clap, often seems like nothing more than a nuisance, particularly since it is so frequently asymptomatic, but that won't continue to be the case if we run out of antibiotics to treat it. Left untreated, gonorrhea can lead to serious problems. It is, for example, a major cause of pelvic inflammatory disease and infertility. Gonorrhea can also lead to an infection known as disseminated gonorrhea and cause problems in pregnant women and infants.<br />
<br />
:Because gonorrhea is so common, doctors would like to be able to treat it with a single, effective dose of medication. Single-dose gonorrhea antibiotics reduce problems with drug compliance that can increase the prevalence of antibiotic resistance, and also decrease the need for follow-up. Unfortunately, one-dose regimens may soon no longer be an option. The affordable antibiotics that have been widely used to treat gonorrhea in the past are losing effectiveness against a growing number of strains. Although it is still possible to find an antibiotic that can treat individual cases of gonorrhea, the choices are narrowing as multi-drug-resistant strains of the bacteria continue to appear. At this point, American doctors have been recommended to stop giving oral antibiotics as a primary treatment and switch over to an injectable cocktail.<br />
<br />
:The specific types of antibiotic-resistant gonorrhea strains seen in the U.S. and around the world vary from year to year, city to city, and population to population. Some scientists hope that by eliminating use of gonorrhea antibiotics that are becoming ineffective, strains that are resistant to those drugs will decrease in prevalence so that the drugs will become useful once again. Scientists have to hope, because they are quickly running out of drugs. In late 2012, the scientists reported that the last, effective oral antibiotic used to treat gonorrhea had begun to fail. In one clinic in Ontario, up to 7 percent of patients were not effectively treated with cephalosporins.<br />
<br />
:In a few years, gonorrhea treatment will cease to be a simple process. Kicking an infection may require course after course of antibiotics, followed by repeated testing to see which, if any, of the antibiotics have worked. At that point, your best option will be one that you also have right now -- consistently practicing safe sex to avoid getting infected in the first place.<br />
<br />
'''Antibiotics That Are No Longer Recommended For Gonorrhea Treatment'''<br />
:'''Sulfonamides''' - Over a period of only 9 years, 30 percent of gonorrhea strains became resistant to treatment with sulfonamides. They stopped being used in the mid-1940s and were replaced by penicillin.<br />
<br />
:'''Penicillin''' - Although initially quite effective, required penicillin doses for gonorrhea treatment climbed significantly over time, until eventually, in the 1980s, U.S. doctors stopped using penicillin to treat gonorrhea.<br />
<br />
:'''Tetracycline''' - In the 1980s, tetracycline also ceased being a first-line treatment option due to the spread of treatment-resistant gonorrhea strains.<br />
<br />
:'''Fluoroquinolones''' (ciprofloxacin, ofloxacin, levofloxacin) - In 2007, the CDC changed their gonorrhea treatment guidelines to remove single-dose fluoroquinolones from the recommended list. Fluoroquinolone-resistant strains have been identified around the world, including in many areas of the U.S. The prevalence of fluoroquinolone-resistant gonorrhea in California went from less than one percent of infections in 1999 to over 20 percent in 2003.<br />
<br />
:'''Oral Cephalosporins''' (ceftriaxone, cefixime) - Cephalosporin-resistant gonorrhea strains were first identified in Asia and Australia and have been slowly becoming more common around the globe. As of August 2012, oral cephalosporins are no longer recommended for the treatment of gonorrhea in the United States. Between 2006 and 2011, the percentage of gonorrhea strains resistant to these drugs went up more than ten-fold in many areas of the U.S. Cefixime is no longer recommended for gonorrhea treatment at all, except in cases where ceftriaxone can not be used. <br />
<br />
'''Antibiotics Currently Used to Treat Gonorrhea'''<br />
<br />
:Combination Treatment with Injectable Cephalosporins - As of August, 2012, the recommended treatment for gonorrhea is one injection of 250 mg ceftriaxone. This is combined with either a single oral dose of 1 g azithromycin or a week of taking 100 mg oral doxycycline twice a day. To date, few gonorrhea strains are resistant to both types of antibiotic. However, this will not be true forever. There are alternate treatment regimens available for people allergic to ceftriaxone, but they require patients to return for a second test to make certain they have been cured.<br />
<br />
== Bacteriophages ==<br />
:Bacteriophage (phage) is a virus that infects bacteria host cells. Viruses are acellular microbes that are obligate intracellular pathogens; requiring living cell hosts to carry out metabolic and reproductive needs. Bacteriophages carry with them a protein coat called a capsid that surrounds a small amount of DNA genetic material. The size of the DNA can vary from 5 genes to over 100 genes (3). The majority of the genes on phage DNA code for capsid proteins, proteins to protect viral DNA from degradation, and proteins used in the release from the host cell (3, 4). Because phage cannot reproduce or undergo metabolism on their own, they must infect living bacteria cells in order to reproduce. As part of their reproductive cycle, phages kill the bacteria cell they are infecting. There are two main types of reproductive cycles that a phage can use: the lytic cycle and the lysogenic cycle. A typical phage lytic cycle consists of five main steps. The first step is attachment. The attachment occurs between the phage and a receptor or structure on the surface of the bacterial cell. Attachment is very specific for the bacteriophage, with each phage being able to only infect one species of bacteria. After attachment is entry and this is where the phage DNA enters into the cytoplasm of the bacteria cell. Once inside the bacteria cell, the phage takes over the metabolic machinery of the cell, degrades the bacteria DNA, and changes the cell into a phage producing factory. The viral DNA is translated and viral proteins are made in the synthesis part of the viral cycle. In addition to translation, viral DNA is also being replicated to produce more viral DNA. Once enough viral capsid proteins and viral DNA are synthesized, the assembly part of the cycle occurs. During assembly, the viral capsid proteins surround the viral DNA to build more bacteriophage. When enough bacteriophage particles have been assembled, the release phase occurs. During the release phase, the host cell lysis open, releasing numerous bacteriophage into the environment. The bacteriophage can then go and attach to another bacteria host cell to repeat the lytic cycle over and over again until no bacteria are available for attachment.<br />
<br/><br />
:Although the lytic cycle can occur with all bacteriophage, some phage can enter a dormant cycle called the lysogenic cycle. In the lysogenic cycle, attachment and entry still occur but the host cell DNA is not degraded upon entrance. Instead, the phage DNA incorporates into the host cell DNA to form a prophage. A prophage implies that a bacteriophage has infected the host cell and is in a dormant cycle. The length of this dormant cycle depends on a number of parameters such as, the specific bacteriophage, the host cell, and the stress of the environment. Most bacteria that enter this dormant stage never re-enter the lytic cycle. Each time the bacterial cell divides and replicates its DNA, the prophage DNA is also being replicated. Eventually induction occurs which is when the prophage excises out of the host DNA and re-enters the lytic cycle at the synthesis stage. During the synthesis phase, the host cell DNA is degraded and viral proteins are translated. The assembly and release phases will follow. Many things can trigger induction such as nutrient depletion, UV damage to host cell, or any change in environment temperature or pH (5).<br />
<br/><br />
:Bacteriophages provide a selective method for targeting and destroying specific bacteria. In addition, because bacteriophage cannot replicate without the presence of their host bacteria, once the bacteria have been eliminated, the viral particles will soon degrade and also be eliminated. For each bacteria that exists, there is at least one bacteriophage specifically able to attach and infect it. This makes bacteriophage the most abundant entity on earth an estimated 1x10^31 present on Earth (3). With such an abundance, this makes bacteriophage an excellent candidate for eliminating bacterial infections.<br />
<br />
<br />
== History of Phage Therapy ==<br />
:The initial discovery bacteriophage has been subject to speculation to who was the first. In the western world, Ernest Hankin, a British bacteriologist, first reported observing unidentified antibacterial preventing the spread of cholera (Vibrio cholerae) in the rivers Ganges and Jumna in India in 1896 [mini]. These unidentified antibacterial remained of unknown origin until bacteriologist Frederick Twort hypothesized that the cause of inhibition of bacterial growth was from viruses [M13] in 1915. Twort would be unable to continue pursuing his findings due to various reasons. <br />
<br />
:D'Herelle first observed bacteriophages as 2-3mm "clear spots" which was a pathogenic agent to coccobacillus bacteria cultures studying locusts in South America and Africa in the early 1900s [M18]. He would use his observations of bacteriophages to perform one of the first phage therapy techniques on severe hemorrhagic dysentery outbreaks among French soldiers stationed at Maisons-Laffitte in the summer of 1915 [M18, Mini]. On September 15, 1917 Felix d'Herelle would present his findings in the Academy of Sciences naming this phenomena 'Bacteriophage' after the Greek words "bacteria" and "phagein", which means to devour [M18]. <br />
<br />
:Continuing on the study of bacteriophages, d'Herelle starts researching on the effects of phage therapy on a 12-year-old boy with severe dysentery in 1919 at the Hôpital des Enfants-Malades in Paris, under the hospital's Chief of Pediatrics, Victor-Henri Hutinel. The patient's symptoms ceased after a single administration of d'Herelle's anti-dysentery phage, and the boy fully recovered within a few days [DHERELLE-BOOK]. Phage therapy was accept as the reason for cure after three more patients having bacterial dysentery were each treated with one dose of the preparation and started to recover within 24 hours of treatment.<br />
<br />
:Due to poor scientific experimentation, understanding of pathogenesis, phage-host interactions, and pharmacokinetics knowledge, bacteriophages soon lost interest in the western world as antibiotics and penicillin was discovered. However research continued in the eastern Europe in the Soviet era where two prominent research centers established, The Eliava Institute (EIBMV) in 1923 and The Hirszfeld Institute (HIIET) in 1952. Both continue to research bacteriophages presently. With new knowledge bacteriophages properties and due to increasingly drug resistant bacteria, bacteriophages has been brought to light again in the fight against disease.<br />
<br />
<br />
== Present Day Phage Therapy in Animals ==<br />
<br />
:Present day research on phage therapy in gram negative bacteria in animals have been very extensive and promising. <br />
<br />
:With a better understanding of phage therapy and more advanced equipment, modern day phage therapy can close the gaps in experimental accuracy and knowledge that was missing in the past. Using blood culture machines and better filtration methods, such as caesium chloride density centrifugation, have lead the better understanding of host-phage relationships such as longer-circulating strains of phage [nih11]. This has led to more efficient phage therapy techniques. With the knowledge of heat effects on phages, control groups observe differences in bacteriophage effect, therefore eliminating immunologic response variation in experiments. The National Institute of Health has done extensive controls on phage therapy on Vancomycin-Resistant Enterococcus faecium in mice, where single injection of phage administered 45 min after bacterium contact rescued 100% of mice compared to 100% fatality when no phage was administered [m10]. Numerous studies have shown substantial efficacy of phage on gram negative bacteria in calves, pigs, mice, and lamb[soothill01]. <br />
<br />
:Extensive studies of phage therapy on gram negative bacteria have already been proved extremely effective [soothill, smith hw]. Experimentation of E. coli done on in vivo mice showed that bacteriophages were more efficient in vivo experimenation than in vitro. [59] Research on calves showed that one injection of specific phage strain 8 hours after contact with E coli protected the calves from death and diarrhoea, and again the in vitro experimentation underestimated the virulence of phage. Futhermore, different strains of phage were tested for efficiency in isolated does and cocktail formulas [60]. Some strains were proven more effective than leading antibiotics []. [soothill experiments needed].<br />
<br />
<br />
== Questions and Specific Aims ==<br />
:'''Pilot Project Aims'''<br />
<br /><br />
:'''Isolate N. gonorrhoeae from 10 patients'''. <br />
:''Acquiring samples''. We are currently in negotiations with local clinics (ie. Berkeley Free Clinic, Magnet, City Clinic :of San Francisco and St. James Infirmary) to enroll patients in our pilot study. Briefly, patients who are screened by :these clinics and test positive for oropharyngeal N. gonorrhoeae will be provided with information on our study. Within :the informational packet, patients will find their assigned Patient ID and use this number to schedule an in-house visit. :The Patient ID allows the patient to remain anonymous during our screening process. During their primary visit, patients :will provide their consent, sign liability waivers, fill out our surveillance survey, and provide us with an :oropharyngeal specimen. Patients can then use their Patient ID to track the results from their specimen using our :anonymous web tracking system.<br />
<br />
:''Primary isolation of N. gonorrhoeae''. Primary gonococcal cultures will be grown on Modified Thayer-Martin (MTM) medium containing chocolate agar (5% SRBC), Vancomycin, Colistin, Nystatin and SXT. This medium allows selective growth of Neisseria species. Primary cultures will be propagated in tryptic soy broth (TSB) according to the standards set forth by the Centers for Disease Control (REF). <br />
<br />
:''Confirmation of N. gonorrhoeae''. Upon primary culture and propagation, N. gonorrhoeae samples will be confirmed using nucleic acid testing. A panel of polymerase chain reactions will be performed on DNA isolated from bacterial cultures. These panels will be performed to (1) identify genes responsible for 1st-, 2nd- and 3rd-generation antibiotic resistance, (2) differentiate N. gonorrhoeae from other Neisseria species. The differentiation PCR will be confirmed using CTA sugar growth testing as described by the CDC (REF). Briefly, isolates will be assessed for their ability to grow in Glucose, Maltose, Lactose and Sucrose. N. gonorrhoeae is positive for glucose metabolism, but not maltose or lactose metablism.<br />
<br /><br />
:'''Isolate ARNG-derived bacteriophage from 10 patients'''. <br />
:''Bacteriophage Isolation''. Bacteriophage will be isolated from 10 clinical samples as previously described (REF). Briefly, isolated colonies will be selected and cultured in 5 mL TPY broth (trypticase, phytone, and yeast extract) and cultued for 24 hours at 37oC in 5% CO2.<br />
<br /><br />
:After culture, 1500 µL of broth will be transferred to Trypticase Soy Agar (TSA) plates in triplicate (500uL each). One plate will be used for harvesting bacteriophage, a second plate will be used for propagating bacteriophage, and a third plate used for storing cultures. The remaining culture (3500uL) will be centrifuged for 10min at 2500 RPM. The supernatant will be removed and filtered through a 0.22 µm syringe filter. The syringe filters removes all cellular debris resulting in a pure bacteriophage culture. Bacteriopahge cultures will then be added to a bacterial lawns using 10-fold titrations to determine titers. Positive titers will result in plaque formation.<br />
<br /><br />
:'''Characterize ARNG-derived bacteriophage from 10 patients'''.<br />
<br />
:''Genomic Molecular Weight Analysis''. Bacteriophage genomes will be extracted as previously described (REF). The genomes :will then be analyzed via gel-electrophoresis to determine approximate molecular weight(REF).<br />
<br />
:''SDS-PAGE''. Purified bacteriophage lysates will be analyzed by denaturing SDS-PAGE as previously described. The SDS-:PAGE characterization assays will determine the molecular weight of proteins and assess their relative abundance. All :samples will be compared to positive control T4-phage panels.<br />
<br />
:''Host Range Studies''. Host range studies will be performed as previously described (REF). The purpose of this assay is :to determine the ability of ARNG-associated phage to infect different Neisseria species, bacterial from different genii :(I.e gram positive, and coliforms), and alternate clinical N. gonorrhoeae samples. Briefly, bacterial lawns of varying :host bacteria will be created and phage will be drop-tested and assessed for their ability to produce plaques in :different genii, species, or isolates cultures. We also propose a novel broth-culture assay in which OD readings are :taken before and after bacteriophage infection. Should our bacteriophage isolates maintain their capacity for lysis, OD :culture readings should drop significantly. <br />
<br />
:'''Conduct proof-of-concept lysis experiments'''.<br />
:''Infection Assay''. Following testing of each individual phage, a 10-sample phage cocktail will be generated and tested :for its ability to lyse clinical samples of N. gonorrhoeae. These methods are similar to "Host Range Studies," the only :difference being that instead of using single-phage samples, the proof-of-concept treatment will be a 10-phage cocktail :in which all bacteriophage samples are combined at (a) the same titer, and (b) in the same proportions. These assays are :previously described (REF).<br />
<br />
== Anticipated Challenges to Our Approach ==<br />
<br />
#rapid clearance of phages by human host and bacteria: bacterial strain resistance / anti-phage antibodies.<br />
#patient safety: altering phage to prevent lysis of gram negative species.<br />
#bacterium targeting and optimization: altering the binding kinetics of Phage adherence.<br />
#narrow range of hosts<br />
#achieving phage purity: while administering directly may be hazardous if bacteria is not removed.<br />
#poor stability of phage: how do we preserve phage ex vivo and ensure that is viable upon administration?<br />
#Addressing previous citizen science failures and conducting research with a greater adherence to quality.<br />
#Preventing Lysogeny.<br />
<br />
===Protocol Documentation===<br />
http://aegia.nu/folder/getitproject/130721_prephage-protocols.txt<br />
<br />
== Laboratory Needs ==<br />
:[https://www.wepay.com/donations/gonorrhea-eradication-team Your Financial Support]<br />
:CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
:Benchtop butane torches.<br />
:Sterilized toothpicks.<br />
:MTM agar plates '''(ordered!)'''<br />
:Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
:Glass test-tubes.<br />
:Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
:Rayon Swabs and tongue depressors ('''ordered!''')<br />
:-80c Freezer to store glycerol stocks of clinical samples. <br />
:Ultracentrifuge<br />
:SDS-PAGE gel electrophoresis equipment and reagents.<br />
:Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br /><br />
==Guiding Principles==<br />
<br />
: <br />
''We believe in building egalitarian networks'': <br />
: Hierarchy, privilege and discrimination have the potential to repress creative thought in science, deny access to science, and as a result, hold back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to listening to, hearing and acknowledging the diverse voices that make our community great! <br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, decision making is made by consensus. Proposals are brought to weekly meetings and offered to the group. The group develops and integrates proposals into organizational policy and scientific research aims.<br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We desire to collectively answer questions and serve our communities. We believe that all knowledge must be '''free''' and '''accessible''' and will continue to work to maintain that openness.<br />
<br />
''We believe in equal access to healthcare.''<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 8/4/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=5895Phage therapy2013-10-30T02:59:40Z<p>208.87.217.74: /* The Gonorrhea Eradication Team and Integration Taskforce (GETit!) */</p>
<hr />
<div>==Contribute To Our Pilot Program!==<br />
<br />
If you have time or resources to contribute to this project, we urge you to attend our bi-weekly meetings or donate to our Pilot Program WePay Campaign [https://wepay.com/donations/gonorrhea-eradication-team here!]<br />
<br />
==The Gonorrhea Eradication Team and Integration Taskforce (GETit!) ==<br />
We are a volunteer group of experienced citizen scientists working to foster healthy communities through innovative medical research. Our team includes PhD-, Master- and Bachelor-level scientists. Together, we are taking on our first major project: the eradication of antibiotic resistant gonorrhea using Phage Therapy! We are asking for support in launching our Pilot Program which aims to: (1) Isolate and Characterize Bacteriophage from 10 patients, and (2) create a proof-of-concept bacteriophage cocktail to be tested ''in vitro''.<br />
<br />
''Our team:''<br />
<br />
:'''Craig Rouskey''', MSc in Molecular Biology, Biochemistry, Microbiology and Immunology<br />
:'''Ami Knop Ullrich''', MSc in Medical Microbiology and Immunology<br />
:'''Nina DiPrimio''', PhD in Pharmacology<br />
:'''Marc Juul''', MSc in Biotechnology Engineering<br />
:'''Jenny Ryan''', MA in Anthropology, MA in Communication<br />
:'''Tess Westbrook''', BSc Biology, MBA<br />
:'''Ianto Lin Xi''', BSc Molecular Biology<br />
<br />
== Introduction ==<br />
Neisseria gonorrhoeae, the sexually transmitted pathogen that causes Gonorrhea, has progressively developed resistance to the antibiotic drugs used to treat it. Within the past 40 years, this pathogen has developed resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Neisseria gonorrhoeae (ARNG) is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. These treatments have been mostly successful, but given the ability of ARNG to develop antibiotic resistance, it is critical to continuously research and develop new treatment regimens for gonorrhea<ref>http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>. <br />
<br />
To meet the needs of a rapidly changing public health field in which traditional antibiotic-based therapies are becoming ineffective, the Gonorrhea Eradication Team and Integration Task-force (GETit) was created. This organization was created to conduct research into bacteriophage associated with Neisseria gonorrhoeae. Bacteriophage are viruses that infect bacterial hosts and can induce lysis upon infection. Ultimately, our goal is to identify and characterize bacteriophage from wild type ARNG and use a composite cocktail of ARNG-associated phage as therapy to treat hosts infected with this pathogen.<br />
<br />
'''During our pilot program, we plan to''': <br />
# isolate ''N. gonorrhoeae'' from 10 patients<br />
# isolate bacteriophage from 10 clinical samples of ARNG <br />
# characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae'', and <br />
# conduct proof-of-concept experiments in which ARNG-derived phage cocktails are used to lyse cultures of ARNG ''in vitro''.<br />
:<br />
<br /><br />
: '''This project is in its early stages. Our longer-term goals are to''':<br />
# Begin a free-Gonorrhea screening program on the streets of Oakland and San Francisco;<br />
# Enhance the Center for Disease Control's Surveillance of antibiotic-resistant gonorrheal infections;<br />
# Develop assays for the rapid detection of ''N. gonorrhoeae.''<br />
# Develop methods by which bacteriophages can be cultured and used as prophylaxis and therapy for gonoccocal infections;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research;<br />
# Develop a community education program to bring science to underrepresented cultural groups.<br />
<br />
:<br />
: <br /><br />
<br />
:'''''If you would like to help with any of these project goals, please contact Craig (contact [at] craigrouskey [dot] com).'''''<br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections == <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the facultative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Symptoms of Gonorrhea ==<br />
== Antibiotic Resistant Gonorrhea ==<br />
:Until recently, gonorrhea treatment was simply a matter of picking the right antibiotics; however, that is quickly ceasing to be the case. Gonorrhea is currently one of the most common treatable STDs in the United States, but soon it may be just one of the most common STDs. The number of gonorrhea cases resistant to treatment with antibiotics has continued to rise, and scientists are quickly running out of options. Single-dose antibiotics for gonorrhea treatment are quickly becoming a thing of the past.<br />
<br />
:Gonorrhea, otherwise known as the clap, often seems like nothing more than a nuisance, particularly since it is so frequently asymptomatic, but that won't continue to be the case if we run out of antibiotics to treat it. Left untreated, gonorrhea can lead to serious problems. It is, for example, a major cause of pelvic inflammatory disease and infertility. Gonorrhea can also lead to an infection known as disseminated gonorrhea and cause problems in pregnant women and infants.<br />
<br />
:Because gonorrhea is so common, doctors would like to be able to treat it with a single, effective dose of medication. Single-dose gonorrhea antibiotics reduce problems with drug compliance that can increase the prevalence of antibiotic resistance, and also decrease the need for follow-up. Unfortunately, one-dose regimens may soon no longer be an option. The affordable antibiotics that have been widely used to treat gonorrhea in the past are losing effectiveness against a growing number of strains. Although it is still possible to find an antibiotic that can treat individual cases of gonorrhea, the choices are narrowing as multi-drug-resistant strains of the bacteria continue to appear. At this point, American doctors have been recommended to stop giving oral antibiotics as a primary treatment and switch over to an injectable cocktail.<br />
<br />
:The specific types of antibiotic-resistant gonorrhea strains seen in the U.S. and around the world vary from year to year, city to city, and population to population. Some scientists hope that by eliminating use of gonorrhea antibiotics that are becoming ineffective, strains that are resistant to those drugs will decrease in prevalence so that the drugs will become useful once again. Scientists have to hope, because they are quickly running out of drugs. In late 2012, the scientists reported that the last, effective oral antibiotic used to treat gonorrhea had begun to fail. In one clinic in Ontario, up to 7 percent of patients were not effectively treated with cephalosporins.<br />
<br />
:In a few years, gonorrhea treatment will cease to be a simple process. Kicking an infection may require course after course of antibiotics, followed by repeated testing to see which, if any, of the antibiotics have worked. At that point, your best option will be one that you also have right now -- consistently practicing safe sex to avoid getting infected in the first place.<br />
<br />
'''Antibiotics That Are No Longer Recommended For Gonorrhea Treatment'''<br />
:'''Sulfonamides''' - Over a period of only 9 years, 30 percent of gonorrhea strains became resistant to treatment with sulfonamides. They stopped being used in the mid-1940s and were replaced by penicillin.<br />
<br />
:'''Penicillin''' - Although initially quite effective, required penicillin doses for gonorrhea treatment climbed significantly over time, until eventually, in the 1980s, U.S. doctors stopped using penicillin to treat gonorrhea.<br />
<br />
:'''Tetracycline''' - In the 1980s, tetracycline also ceased being a first-line treatment option due to the spread of treatment-resistant gonorrhea strains.<br />
<br />
:'''Fluoroquinolones''' (ciprofloxacin, ofloxacin, levofloxacin) - In 2007, the CDC changed their gonorrhea treatment guidelines to remove single-dose fluoroquinolones from the recommended list. Fluoroquinolone-resistant strains have been identified around the world, including in many areas of the U.S. The prevalence of fluoroquinolone-resistant gonorrhea in California went from less than one percent of infections in 1999 to over 20 percent in 2003.<br />
<br />
:'''Oral Cephalosporins''' (ceftriaxone, cefixime) - Cephalosporin-resistant gonorrhea strains were first identified in Asia and Australia and have been slowly becoming more common around the globe. As of August 2012, oral cephalosporins are no longer recommended for the treatment of gonorrhea in the United States. Between 2006 and 2011, the percentage of gonorrhea strains resistant to these drugs went up more than ten-fold in many areas of the U.S. Cefixime is no longer recommended for gonorrhea treatment at all, except in cases where ceftriaxone can not be used. <br />
<br />
'''Antibiotics Currently Used to Treat Gonorrhea'''<br />
<br />
:Combination Treatment with Injectable Cephalosporins - As of August, 2012, the recommended treatment for gonorrhea is one injection of 250 mg ceftriaxone. This is combined with either a single oral dose of 1 g azithromycin or a week of taking 100 mg oral doxycycline twice a day. To date, few gonorrhea strains are resistant to both types of antibiotic. However, this will not be true forever. There are alternate treatment regimens available for people allergic to ceftriaxone, but they require patients to return for a second test to make certain they have been cured.<br />
<br />
== Bacteriophages ==<br />
:Bacteriophage (phage) is a virus that infects bacteria host cells. Viruses are acellular microbes that are obligate intracellular pathogens; requiring living cell hosts to carry out metabolic and reproductive needs. Bacteriophages carry with them a protein coat called a capsid that surrounds a small amount of DNA genetic material. The size of the DNA can vary from 5 genes to over 100 genes (3). The majority of the genes on phage DNA code for capsid proteins, proteins to protect viral DNA from degradation, and proteins used in the release from the host cell (3, 4). Because phage cannot reproduce or undergo metabolism on their own, they must infect living bacteria cells in order to reproduce. As part of their reproductive cycle, phages kill the bacteria cell they are infecting. There are two main types of reproductive cycles that a phage can use: the lytic cycle and the lysogenic cycle. A typical phage lytic cycle consists of five main steps. The first step is attachment. The attachment occurs between the phage and a receptor or structure on the surface of the bacterial cell. Attachment is very specific for the bacteriophage, with each phage being able to only infect one species of bacteria. After attachment is entry and this is where the phage DNA enters into the cytoplasm of the bacteria cell. Once inside the bacteria cell, the phage takes over the metabolic machinery of the cell, degrades the bacteria DNA, and changes the cell into a phage producing factory. The viral DNA is translated and viral proteins are made in the synthesis part of the viral cycle. In addition to translation, viral DNA is also being replicated to produce more viral DNA. Once enough viral capsid proteins and viral DNA are synthesized, the assembly part of the cycle occurs. During assembly, the viral capsid proteins surround the viral DNA to build more bacteriophage. When enough bacteriophage particles have been assembled, the release phase occurs. During the release phase, the host cell lysis open, releasing numerous bacteriophage into the environment. The bacteriophage can then go and attach to another bacteria host cell to repeat the lytic cycle over and over again until no bacteria are available for attachment.<br />
<br/><br />
:Although the lytic cycle can occur with all bacteriophage, some phage can enter a dormant cycle called the lysogenic cycle. In the lysogenic cycle, attachment and entry still occur but the host cell DNA is not degraded upon entrance. Instead, the phage DNA incorporates into the host cell DNA to form a prophage. A prophage implies that a bacteriophage has infected the host cell and is in a dormant cycle. The length of this dormant cycle depends on a number of parameters such as, the specific bacteriophage, the host cell, and the stress of the environment. Most bacteria that enter this dormant stage never re-enter the lytic cycle. Each time the bacterial cell divides and replicates its DNA, the prophage DNA is also being replicated. Eventually induction occurs which is when the prophage excises out of the host DNA and re-enters the lytic cycle at the synthesis stage. During the synthesis phase, the host cell DNA is degraded and viral proteins are translated. The assembly and release phases will follow. Many things can trigger induction such as nutrient depletion, UV damage to host cell, or any change in environment temperature or pH (5).<br />
<br/><br />
:Bacteriophages provide a selective method for targeting and destroying specific bacteria. In addition, because bacteriophage cannot replicate without the presence of their host bacteria, once the bacteria have been eliminated, the viral particles will soon degrade and also be eliminated. For each bacteria that exists, there is at least one bacteriophage specifically able to attach and infect it. This makes bacteriophage the most abundant entity on earth an estimated 1x10^31 present on Earth (3). With such an abundance, this makes bacteriophage an excellent candidate for eliminating bacterial infections.<br />
<br />
<br />
== History of Phage Therapy ==<br />
:The initial discovery bacteriophage has been subject to speculation to who was the first. In the western world, Ernest Hankin, a British bacteriologist, first reported observing unidentified antibacterial preventing the spread of cholera (Vibrio cholerae) in the rivers Ganges and Jumna in India in 1896 [mini]. These unidentified antibacterial remained of unknown origin until bacteriologist Frederick Twort hypothesized that the cause of inhibition of bacterial growth was from viruses [M13] in 1915. Twort would be unable to continue pursuing his findings due to various reasons. <br />
<br />
:D'Herelle first observed bacteriophages as 2-3mm "clear spots" which was a pathogenic agent to coccobacillus bacteria cultures studying locusts in South America and Africa in the early 1900s [M18]. He would use his observations of bacteriophages to perform one of the first phage therapy techniques on severe hemorrhagic dysentery outbreaks among French soldiers stationed at Maisons-Laffitte in the summer of 1915 [M18, Mini]. On September 15, 1917 Felix d'Herelle would present his findings in the Academy of Sciences naming this phenomena 'Bacteriophage' after the Greek words "bacteria" and "phagein", which means to devour [M18]. <br />
<br />
:Continuing on the study of bacteriophages, d'Herelle starts researching on the effects of phage therapy on a 12-year-old boy with severe dysentery in 1919 at the Hôpital des Enfants-Malades in Paris, under the hospital's Chief of Pediatrics, Victor-Henri Hutinel. The patient's symptoms ceased after a single administration of d'Herelle's anti-dysentery phage, and the boy fully recovered within a few days [DHERELLE-BOOK]. Phage therapy was accept as the reason for cure after three more patients having bacterial dysentery were each treated with one dose of the preparation and started to recover within 24 hours of treatment.<br />
<br />
:Due to poor scientific experimentation, understanding of pathogenesis, phage-host interactions, and pharmacokinetics knowledge, bacteriophages soon lost interest in the western world as antibiotics and penicillin was discovered. However research continued in the eastern Europe in the Soviet era where two prominent research centers established, The Eliava Institute (EIBMV) in 1923 and The Hirszfeld Institute (HIIET) in 1952. Both continue to research bacteriophages presently. With new knowledge bacteriophages properties and due to increasingly drug resistant bacteria, bacteriophages has been brought to light again in the fight against disease.<br />
<br />
<br />
== Present Day Phage Therapy in Animals ==<br />
<br />
:Present day research on phage therapy in gram negative bacteria in animals have been very extensive and promising. <br />
<br />
:With a better understanding of phage therapy and more advanced equipment, modern day phage therapy can close the gaps in experimental accuracy and knowledge that was missing in the past. Using blood culture machines and better filtration methods, such as caesium chloride density centrifugation, have lead the better understanding of host-phage relationships such as longer-circulating strains of phage [nih11]. This has led to more efficient phage therapy techniques. With the knowledge of heat effects on phages, control groups observe differences in bacteriophage effect, therefore eliminating immunologic response variation in experiments. The National Institute of Health has done extensive controls on phage therapy on Vancomycin-Resistant Enterococcus faecium in mice, where single injection of phage administered 45 min after bacterium contact rescued 100% of mice compared to 100% fatality when no phage was administered [m10]. Numerous studies have shown substantial efficacy of phage on gram negative bacteria in calves, pigs, mice, and lamb[soothill01]. <br />
<br />
:Extensive studies of phage therapy on gram negative bacteria have already been proved extremely effective [soothill, smith hw]. Experimentation of E. coli done on in vivo mice showed that bacteriophages were more efficient in vivo experimenation than in vitro. [59] Research on calves showed that one injection of specific phage strain 8 hours after contact with E coli protected the calves from death and diarrhoea, and again the in vitro experimentation underestimated the virulence of phage. Futhermore, different strains of phage were tested for efficiency in isolated does and cocktail formulas [60]. Some strains were proven more effective than leading antibiotics []. [soothill experiments needed].<br />
<br />
<br />
== Questions and Specific Aims ==<br />
:'''Pilot Project Aims'''<br />
<br /><br />
:'''Isolate N. gonorrhoeae from 10 patients'''. <br />
:''Acquiring samples''. We are currently in negotiations with local clinics (ie. Berkeley Free Clinic, Magnet, City Clinic :of San Francisco and St. James Infirmary) to enroll patients in our pilot study. Briefly, patients who are screened by :these clinics and test positive for oropharyngeal N. gonorrhoeae will be provided with information on our study. Within :the informational packet, patients will find their assigned Patient ID and use this number to schedule an in-house visit. :The Patient ID allows the patient to remain anonymous during our screening process. During their primary visit, patients :will provide their consent, sign liability waivers, fill out our surveillance survey, and provide us with an :oropharyngeal specimen. Patients can then use their Patient ID to track the results from their specimen using our :anonymous web tracking system.<br />
<br />
:''Primary isolation of N. gonorrhoeae''. Primary gonococcal cultures will be grown on Modified Thayer-Martin (MTM) medium containing chocolate agar (5% SRBC), Vancomycin, Colistin, Nystatin and SXT. This medium allows selective growth of Neisseria species. Primary cultures will be propagated in tryptic soy broth (TSB) according to the standards set forth by the Centers for Disease Control (REF). <br />
<br />
:''Confirmation of N. gonorrhoeae''. Upon primary culture and propagation, N. gonorrhoeae samples will be confirmed using nucleic acid testing. A panel of polymerase chain reactions will be performed on DNA isolated from bacterial cultures. These panels will be performed to (1) identify genes responsible for 1st-, 2nd- and 3rd-generation antibiotic resistance, (2) differentiate N. gonorrhoeae from other Neisseria species. The differentiation PCR will be confirmed using CTA sugar growth testing as described by the CDC (REF). Briefly, isolates will be assessed for their ability to grow in Glucose, Maltose, Lactose and Sucrose. N. gonorrhoeae is positive for glucose metabolism, but not maltose or lactose metablism.<br />
<br /><br />
:'''Isolate ARNG-derived bacteriophage from 10 patients'''. <br />
:''Bacteriophage Isolation''. Bacteriophage will be isolated from 10 clinical samples as previously described (REF). Briefly, isolated colonies will be selected and cultured in 5 mL TPY broth (trypticase, phytone, and yeast extract) and cultued for 24 hours at 37oC in 5% CO2.<br />
<br /><br />
:After culture, 1500 µL of broth will be transferred to Trypticase Soy Agar (TSA) plates in triplicate (500uL each). One plate will be used for harvesting bacteriophage, a second plate will be used for propagating bacteriophage, and a third plate used for storing cultures. The remaining culture (3500uL) will be centrifuged for 10min at 2500 RPM. The supernatant will be removed and filtered through a 0.22 µm syringe filter. The syringe filters removes all cellular debris resulting in a pure bacteriophage culture. Bacteriopahge cultures will then be added to a bacterial lawns using 10-fold titrations to determine titers. Positive titers will result in plaque formation.<br />
<br /><br />
:'''Characterize ARNG-derived bacteriophage from 10 patients'''.<br />
<br />
:''Genomic Molecular Weight Analysis''. Bacteriophage genomes will be extracted as previously described (REF). The genomes :will then be analyzed via gel-electrophoresis to determine approximate molecular weight(REF).<br />
<br />
:''SDS-PAGE''. Purified bacteriophage lysates will be analyzed by denaturing SDS-PAGE as previously described. The SDS-:PAGE characterization assays will determine the molecular weight of proteins and assess their relative abundance. All :samples will be compared to positive control T4-phage panels.<br />
<br />
:''Host Range Studies''. Host range studies will be performed as previously described (REF). The purpose of this assay is :to determine the ability of ARNG-associated phage to infect different Neisseria species, bacterial from different genii :(I.e gram positive, and coliforms), and alternate clinical N. gonorrhoeae samples. Briefly, bacterial lawns of varying :host bacteria will be created and phage will be drop-tested and assessed for their ability to produce plaques in :different genii, species, or isolates cultures. We also propose a novel broth-culture assay in which OD readings are :taken before and after bacteriophage infection. Should our bacteriophage isolates maintain their capacity for lysis, OD :culture readings should drop significantly. <br />
<br />
:'''Conduct proof-of-concept lysis experiments'''.<br />
:''Infection Assay''. Following testing of each individual phage, a 10-sample phage cocktail will be generated and tested :for its ability to lyse clinical samples of N. gonorrhoeae. These methods are similar to "Host Range Studies," the only :difference being that instead of using single-phage samples, the proof-of-concept treatment will be a 10-phage cocktail :in which all bacteriophage samples are combined at (a) the same titer, and (b) in the same proportions. These assays are :previously described (REF).<br />
<br />
== Anticipated Challenges to Our Approach ==<br />
<br />
#rapid clearance of phages by human host and bacteria: bacterial strain resistance / anti-phage antibodies.<br />
#patient safety: altering phage to prevent lysis of gram negative species.<br />
#bacterium targeting and optimization: altering the binding kinetics of Phage adherence.<br />
#narrow range of hosts<br />
#achieving phage purity: while administering directly may be hazardous if bacteria is not removed.<br />
#poor stability of phage: how do we preserve phage ex vivo and ensure that is viable upon administration?<br />
#Addressing previous citizen science failures and conducting research with a greater adherence to quality.<br />
#Preventing Lysogeny.<br />
<br />
===Protocol Documentation===<br />
http://aegia.nu/folder/getitproject/130721_prephage-protocols.txt<br />
<br />
== Laboratory Needs ==<br />
:[https://www.wepay.com/donations/gonorrhea-eradication-team Your Financial Support]<br />
:CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
:Benchtop butane torches.<br />
:Sterilized toothpicks.<br />
:MTM agar plates '''(ordered!)'''<br />
:Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
:Glass test-tubes.<br />
:Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
:Rayon Swabs and tongue depressors ('''ordered!''')<br />
:-80c Freezer to store glycerol stocks of clinical samples. <br />
:Ultracentrifuge<br />
:SDS-PAGE gel electrophoresis equipment and reagents.<br />
:Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br /><br />
==Guiding Principles==<br />
<br />
: <br />
''We believe in building egalitarian networks'': <br />
: Hierarchy, privilege and discrimination have the potential to repress creative thought in science, deny access to science, and as a result, hold back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to listening to, hearing and acknowledging the diverse voices that make our community great! <br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, decision making is made by consensus. Proposals are brought to weekly meetings and offered to the group. The group develops and integrates proposals into organizational policy and scientific research aims.<br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We desire to collectively answer questions and serve our communities. We believe that all knowledge must be '''free''' and '''accessible''' and will continue to work to maintain that openness.<br />
<br />
''We believe in equal access to healthcare.''<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 8/4/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Cool_Projects&diff=5890Cool Projects2013-10-28T01:55:16Z<p>208.87.217.74: </p>
<hr />
<div>Please add links to pages for any active projects here.<br />
<br />
''See also'' [[:Category:Projects]]<br />
<br />
==Regular Meetups==<br />
*[[Mesh]]<br />
*[[Kopimism]]<br />
*[[Oakland Wiki]]<br />
*[[Javascript Mondayz]]<br />
<br />
==Sudo Room Room Projects==<br />
These are projects related to the infrastructure and community of Sudo Room.<br />
<br />
===Electronics at SudoRoom===<br />
* [[RackHacks]]<br />
* [[Router Reuse | Router Reuse]]<br />
* [[MicroControllerHackNight]] Tuesday nights and including other cool wearable electronics, raspberry pi hacks as well!<br />
* [[Projects/SudoRoom Computer Terminal]] a computer terminal on wheels hacked by matt Senate!<br />
<br />
====Door Access====<br />
We are currently working on creating a system for access to Sudo Room via some kind of websitey thingamajig. <br />
* [[Door Access|Door Access]]<br />
**[[Door Access#Sudo Door Intercom|Sudo Door Intercom]]<br />
**[[Door Access#Door Open Indicator|Door Open Indicator]]<br />
**[[Door Access#Outside Facing Door|Outside Facing Door Access]]<br />
**[[Door Access#Inside Door|Inside Door Access]]<br />
* * [[DefensiveHacking]] - How do we keep SudoRoom Secure?<br />
<br />
===3D Printing===<br />
*[[3DPrinting|3D Printing at SudoRoom]] or [http://sembly.net:8080/mediawiki 3D Printers]<br />
<br />
===Programming at SudoRoom===<br />
*[[Sudo API]]<br />
*[[SudoLearningProgramming]] Learn Python, Ruby, Node.JS and other languages! Maybe even Prolog!<br />
* Lone wolf iOS developer group - we are outcasts in the hacker community. people get paid to pester us to developer for the latest a* product. let's cling together and try not to get split up<br />
<br />
===Music at SudoRoom=== <br />
*[[Audio]] includes the SudoRoom music channel<br />
* [[DanceSound]]<br />
* [[Sudo Radio|Sudo Radio]] the SudoRoom radio station, includes little kids on Tuesdays!<br />
* [[East Bay Sound Art Music Meetup]] lots of experimental music and stuff that crosses the line between electronic music, sculpture and performance art<br />
<br />
===Biology Projects===<br />
*[[Bio-LoaD|Biotech Lab-on-a-Desk (Bio-LoaD)]]<br />
*[[Phage_therapy|Phage Therapy]]<br />
*[[Sudoshroom]]<br />
*[[Beer brewing]]<br />
*[[Cider]]<br />
<br />
More info on the [[biohacking]] page.<br />
<br />
===Sudo Space Program===<br />
*[[3D Printed Aerodynamic Parts]]<br />
*[[Payload Adapters]]<br />
*[[Propulsion]]<br />
*[[Avionics]]<br />
*[[Science Payloads]]<br />
<br />
===Other cool stuff===<br />
<br />
*[[HackDrawing|HackDrawing]]<br />
*[[McHawking Robot Hacking]]<br />
<br />
==See also==<br />
See our [http://sudoroom.org/category/Projects Projects page] on the main Sudo Room website.<br />
===Non SudoRoom Projects that are Cool===<br />
====Sudo Space Program====<br />
These are neat but are these projects that anyone at SudoRoom works on? If not then they should be moved into another page outside of SudoRoom projects (Romy)<br />
*[[3D Printed Aerodynamic Parts]]<br />
*[[Payload Adapters]]<br />
*[[Propulsion]]<br />
*[[Avionics]]<br />
*[[Science Payloads]]<br />
<br />
===Other cool stuff===<br />
*[[Projects/self-driving_car_conversion_kits|self-driving car conversion kits]]<br />
* [[Projects/VirtualReality]]<br />
<br />
<br />
====Ideas====<br />
<br />
Ideas don't mean nothing until you do stuff.<br />
* [[GameHacking]]<br />
*[[Projects/HackDrawing|HackDrawing]]<br />
* [[SudoBook]] - we make our own SudoBook together collaboratively over git<br />
* [[food|Food Hacking]]<br />
* Make a video for [[Sudo room/funding opportunities#Crowd-funding|crowd-funding opportunities]]<br />
* Library Catalog - [[https://github.com/jnny/sudolib_app.git github]] OR [[Sudo Library]]<br />
*[[Inventory]]<br />
*[[Sudobot]]<br />
*[[Inclusivity]]<br />
*[[Education]]<br />
*[[Wikitown]]<br />
*[[Energy]]<br />
* [[BitcoinSudoRoom]]</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Cool_Projects&diff=5889Cool Projects2013-10-28T01:54:56Z<p>208.87.217.74: </p>
<hr />
<div>Please add links to pages for any active projects here..<br />
<br />
''See also'' [[:Category:Projects]]<br />
<br />
==Regular Meetups==<br />
*[[Mesh]]<br />
*[[Kopimism]]<br />
*[[Oakland Wiki]]<br />
*[[Javascript Mondayz]]<br />
<br />
==Sudo Room Room Projects==<br />
These are projects related to the infrastructure and community of Sudo Room.<br />
<br />
===Electronics at SudoRoom===<br />
* [[RackHacks]]<br />
* [[Router Reuse | Router Reuse]]<br />
* [[MicroControllerHackNight]] Tuesday nights and including other cool wearable electronics, raspberry pi hacks as well!<br />
* [[Projects/SudoRoom Computer Terminal]] a computer terminal on wheels hacked by matt Senate!<br />
<br />
====Door Access====<br />
We are currently working on creating a system for access to Sudo Room via some kind of websitey thingamajig. <br />
* [[Door Access|Door Access]]<br />
**[[Door Access#Sudo Door Intercom|Sudo Door Intercom]]<br />
**[[Door Access#Door Open Indicator|Door Open Indicator]]<br />
**[[Door Access#Outside Facing Door|Outside Facing Door Access]]<br />
**[[Door Access#Inside Door|Inside Door Access]]<br />
* * [[DefensiveHacking]] - How do we keep SudoRoom Secure?<br />
<br />
===3D Printing===<br />
*[[3DPrinting|3D Printing at SudoRoom]] or [http://sembly.net:8080/mediawiki 3D Printers]<br />
<br />
===Programming at SudoRoom===<br />
*[[Sudo API]]<br />
*[[SudoLearningProgramming]] Learn Python, Ruby, Node.JS and other languages! Maybe even Prolog!<br />
* Lone wolf iOS developer group - we are outcasts in the hacker community. people get paid to pester us to developer for the latest a* product. let's cling together and try not to get split up<br />
<br />
===Music at SudoRoom=== <br />
*[[Audio]] includes the SudoRoom music channel<br />
* [[DanceSound]]<br />
* [[Sudo Radio|Sudo Radio]] the SudoRoom radio station, includes little kids on Tuesdays!<br />
* [[East Bay Sound Art Music Meetup]] lots of experimental music and stuff that crosses the line between electronic music, sculpture and performance art<br />
<br />
===Biology Projects===<br />
*[[Bio-LoaD|Biotech Lab-on-a-Desk (Bio-LoaD)]]<br />
*[[Phage_therapy|Phage Therapy]]<br />
*[[Sudoshroom]]<br />
*[[Beer brewing]]<br />
*[[Cider]]<br />
<br />
More info on the [[biohacking]] page.<br />
<br />
===Sudo Space Program===<br />
*[[3D Printed Aerodynamic Parts]]<br />
*[[Payload Adapters]]<br />
*[[Propulsion]]<br />
*[[Avionics]]<br />
*[[Science Payloads]]<br />
<br />
===Other cool stuff===<br />
<br />
*[[HackDrawing|HackDrawing]]<br />
*[[McHawking Robot Hacking]]<br />
<br />
==See also==<br />
See our [http://sudoroom.org/category/Projects Projects page] on the main Sudo Room website.<br />
===Non SudoRoom Projects that are Cool===<br />
====Sudo Space Program====<br />
These are neat but are these projects that anyone at SudoRoom works on? If not then they should be moved into another page outside of SudoRoom projects (Romy)<br />
*[[3D Printed Aerodynamic Parts]]<br />
*[[Payload Adapters]]<br />
*[[Propulsion]]<br />
*[[Avionics]]<br />
*[[Science Payloads]]<br />
<br />
===Other cool stuff===<br />
*[[Projects/self-driving_car_conversion_kits|self-driving car conversion kits]]<br />
* [[Projects/VirtualReality]]<br />
<br />
<br />
====Ideas====<br />
<br />
Ideas don't mean nothing until you do stuff.<br />
* [[GameHacking]]<br />
*[[Projects/HackDrawing|HackDrawing]]<br />
* [[SudoBook]] - we make our own SudoBook together collaboratively over git<br />
* [[food|Food Hacking]]<br />
* Make a video for [[Sudo room/funding opportunities#Crowd-funding|crowd-funding opportunities]]<br />
* Library Catalog - [[https://github.com/jnny/sudolib_app.git github]] OR [[Sudo Library]]<br />
*[[Inventory]]<br />
*[[Sudobot]]<br />
*[[Inclusivity]]<br />
*[[Education]]<br />
*[[Wikitown]]<br />
*[[Energy]]<br />
* [[BitcoinSudoRoom]]</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Subiir/Third_Brew&diff=4090Subiir/Third Brew2013-04-28T09:10:22Z<p>208.87.217.74: /* In turkey fryer */</p>
<hr />
<div>= Subiir 2 =<br />
<br />
The third subiir (sudo beer). A nice and hoppy American Pale Ale.<br />
<br />
*Brewed 17th of April 2013.<br />
*To be bottled 8th of May.<br />
*To be drunk 29th of May.<br />
<br />
== Ethanol ==<br />
<br />
Specific gravity measured to 1.050 at 20 degrees C at start of fermentation, meaning a potential alcohol percentage of 6.4%.<br />
<br />
== Recipe ==<br />
<br />
=== Small pot on stove ===<br />
<br />
*1 pound carapils<br />
*1 pound crystal 45<br />
*Bit more than 1 pound sugar.<br />
*In the big pot in the kitchen almost full (3 gallons?)<br />
*Went straight to 65-67 degrees C for 1 hour.<br />
<br />
=== In turkey fryer ===<br />
<br />
2.6 gallons of two row domestic<br />
<br />
Tried to do:<br />
<br />
*50 for 30 mins.<br />
*60 for 30 mins.<br />
*<70 for 1 hour.<br />
<br />
But difficult because the liquid near the sides keeps getting really hot.<br />
<br />
Drained and let it run through all of the malt (including carapils and crystal) together with the kitchen pot mash.<br />
<br />
Let it drain through the bag (this is brewing in a bag) and into the brewpot once again, this time squeezing the bag quite a lot to get more mash out.<br />
<br />
Started heating towards boil.<br />
<br />
Once boil was achieved:<br />
<br />
90 minutes:<br />
<br />
*2 oz Columbus 15.4% (pellet)<br />
*2 oz Simcoe 14.1% (non-pellet)<br />
<br />
0 minutes:<br />
<br />
*2 oz Cascade 6.5% (pellet)<br />
<br />
5 mins to steep 0 min hops, then continue to steep while counter-flow chilling the wort.<br />
<br />
Yeast: GigaYeast Gold Pitch.<br />
<br />
=== Fermentation ===<br />
<br />
Three weeks on top of sudo room fridge. Approximate temperature 22 C.<br />
<br />
=== Dry hopping ===<br />
<br />
A jar (maybe 35 cl) stuffed full of donated mystery hops was added to the fermenters on the eighth day after fermentation was started. It looked home-grown and smelled very aromatic. It did not smell at all like the bitter columbus or simcoe hops, but smelled much fruitier / more flowery.<br />
<br />
== Prep work ==<br />
<br />
Drilled top hole for airlock in home depot food safe bucket:<br />
<br />
3/4" hole drill (ryobi forstner 8 pcs bit set). A bit tricky to drill. Need smallish rounded file to clean up the hole.</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Subiir/Third_Brew&diff=4089Subiir/Third Brew2013-04-28T09:05:22Z<p>208.87.217.74: /* In turkey fryer */</p>
<hr />
<div>= Subiir 2 =<br />
<br />
The third subiir (sudo beer). A nice and hoppy American Pale Ale.<br />
<br />
*Brewed 17th of April 2013.<br />
*To be bottled 8th of May.<br />
*To be drunk 29th of May.<br />
<br />
== Ethanol ==<br />
<br />
Specific gravity measured to 1.050 at 20 degrees C at start of fermentation, meaning a potential alcohol percentage of 6.4%.<br />
<br />
== Recipe ==<br />
<br />
=== Small pot on stove ===<br />
<br />
*1 pound carapils<br />
*1 pound crystal 45<br />
*Bit more than 1 pound sugar.<br />
*In the big pot in the kitchen almost full (3 gallons?)<br />
*Went straight to 65-67 degrees C for 1 hour.<br />
<br />
=== In turkey fryer ===<br />
<br />
2.6 gallons of two row domestic<br />
<br />
Tried to do:<br />
<br />
*50 for 30 mins.<br />
*60 for 30 mins.<br />
*<70 for 1 hour.<br />
<br />
But difficult because the liquid near the sides keeps getting really hot.<br />
<br />
Drained and let it run through all of the malt (including carapils and crystal) together with the kitchen pot mash.<br />
<br />
Let it drain through the bag (this is brewing in a bag) and into the brewpot once again, this time squeezing the bag quite a lot to get more mash out.<br />
<br />
Started heating towards boil.<br />
<br />
Once boil was achieved:<br />
<br />
90 minutes:<br />
<br />
*2 oz Columbus 15.4% (pellet)<br />
*2 oz Simcoe 14.1% (non-pellet)<br />
<br />
0 minutes:<br />
<br />
*2 oz Cascade 6.5% (pellet)<br />
<br />
5 mins to steep 0 min hops, then continue to steep while counter-flow chilling the wort|<br />
<br />
Yeast: GigaYeast Gold Pitch.<br />
<br />
== Prep work ==<br />
<br />
Drilled top hole for airlock in home depot food safe bucket:<br />
<br />
3/4" hole drill (ryobi forstner 8 pcs bit set). A bit tricky to drill. Need smallish rounded file to clean up the hole.</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Subiir/Third_Brew&diff=3976Subiir/Third Brew2013-04-18T07:08:56Z<p>208.87.217.74: /* In turkey fryer */</p>
<hr />
<div>= Subiir 2 =<br />
<br />
The third subiir (sudo beer). A nice and hoppy American Pale Ale.<br />
<br />
*Brewed 17th of April 2013.<br />
*To be bottled 8th of May.<br />
*To be drunk 29th of May.<br />
<br />
== Ethanol ==<br />
<br />
Specific gravity measured to 1.050 at 20 degrees C at start of fermentation, meaning a potential alcohol percentage of 6.4%.<br />
<br />
== Recipe ==<br />
<br />
=== Small pot on stove ===<br />
<br />
*1 pound carapils<br />
*1 pound crystal 45<br />
*Bit more than 1 pound sugar.<br />
*In the big pot in the kitchen almost full (3 gallons?)<br />
*Went straight to 65-67 degrees C for 1 hour.<br />
<br />
=== In turkey fryer ===<br />
<br />
2.6 gallons of two row domestic<br />
<br />
Tried to do:<br />
<br />
*50 for 30 mins.<br />
*60 for 30 mins.<br />
*<70 for 1 hour.<br />
<br />
But difficult because the liquid near the sides keeps getting really hot.<br />
<br />
Drained and let it run through all of the malt (including carapils and crystal) together with the kitchen pot mash.<br />
<br />
Let it drain through the bag (this is brewing in a bag) and into the brewpot once again, this time squeezing the bag quite a lot to get more mash out.<br />
<br />
Started heating towards boil.<br />
<br />
Once boil was achieved:<br />
<br />
90 minutes:<br />
<br />
*2 oz Columbus 15.4% (pellet)<br />
*2 oz Simcoe 14.1% (non-pellet)<br />
<br />
0 minutes:<br />
<br />
*2 oz Cascade 6.5% (pellet)<br />
<br />
5 mins to steep 0 min hops, then continue to steep while counter-flow chilling the wort|<br />
<br />
== Prep work ==<br />
<br />
Drilled top hole for airlock in home depot food safe bucket:<br />
<br />
3/4" hole drill (ryobi forstner 8 pcs bit set). A bit tricky to drill. Need smallish rounded file to clean up the hole.</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Subiir/Third_Brew&diff=3975Subiir/Third Brew2013-04-18T07:08:43Z<p>208.87.217.74: /* Small pot on stove */</p>
<hr />
<div>= Subiir 2 =<br />
<br />
The third subiir (sudo beer). A nice and hoppy American Pale Ale.<br />
<br />
*Brewed 17th of April 2013.<br />
*To be bottled 8th of May.<br />
*To be drunk 29th of May.<br />
<br />
== Ethanol ==<br />
<br />
Specific gravity measured to 1.050 at 20 degrees C at start of fermentation, meaning a potential alcohol percentage of 6.4%.<br />
<br />
== Recipe ==<br />
<br />
=== Small pot on stove ===<br />
<br />
*1 pound carapils<br />
*1 pound crystal 45<br />
*Bit more than 1 pound sugar.<br />
*In the big pot in the kitchen almost full (3 gallons?)<br />
*Went straight to 65-67 degrees C for 1 hour.<br />
<br />
=== In turkey fryer ===<br />
<br />
2.6 gallons of two row domestic<br />
<br />
Tried to do:<br />
<br />
*50 for 30 mins.<br />
*60 for 30 mins.<br />
*<70 for 1 hour.<br />
<br />
But difficult because the liquid near the sides keeps getting really hot.<br />
<br />
Drained and let it run through all of the malt (including carapils and crystal) together with the kitchen pot mash.<br />
<br />
Let it drain through the bag (this is brewing in a bag) and into the brewpot once again, this time squeezing the bag quite a lot to get more mash out.<br />
<br />
Started heating towards boil.<br />
<br />
Once boil was achieved:<br />
<br />
90 minutes:<br />
<br />
*2 oz Columbus 15.4% (pellet)<br />
*2 oz Simcoe 14.1% (non-pellet)<br />
<br />
0 minutes:<br />
<br />
*2 oz Cascade 6.5% (pellet)<br />
<br />
5 mins to steep 0 min hops, then continue to steep while counter-flow chilling the wort|<br />
<br />
== Prep work<br />
<br />
Drilled top hole for airlock in home depot food safe bucket:<br />
<br />
3/4" hole drill (ryobi forstner 8 pcs bit set). A bit tricky to drill. Need smallish rounded file to clean up the hole.</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Subiir/Third_Brew&diff=3974Subiir/Third Brew2013-04-18T07:08:20Z<p>208.87.217.74: </p>
<hr />
<div>= Subiir 2 =<br />
<br />
The third subiir (sudo beer). A nice and hoppy American Pale Ale.<br />
<br />
*Brewed 17th of April 2013.<br />
*To be bottled 8th of May.<br />
*To be drunk 29th of May.<br />
<br />
== Ethanol ==<br />
<br />
Specific gravity measured to 1.050 at 20 degrees C at start of fermentation, meaning a potential alcohol percentage of 6.4%.<br />
<br />
== Recipe ==<br />
<br />
=== Small pot on stove ===<br />
<br />
*1 pound carapils<br />
*1 pound crystal 45<br />
*Bit more than 1 pound sugar.<br />
*In the big pot in the kitchen almost full (3 gallons?)<br />
*Went straight to 65-67 degrees C for 1 hour.<br />
Poured on top of semi-drained bag of other two-row malt.<br />
<br />
=== In turkey fryer ===<br />
<br />
2.6 gallons of two row domestic<br />
<br />
Tried to do:<br />
<br />
*50 for 30 mins.<br />
*60 for 30 mins.<br />
*<70 for 1 hour.<br />
<br />
But difficult because the liquid near the sides keeps getting really hot.<br />
<br />
Drained and let it run through all of the malt (including carapils and crystal) together with the kitchen pot mash.<br />
<br />
Let it drain through the bag (this is brewing in a bag) and into the brewpot once again, this time squeezing the bag quite a lot to get more mash out.<br />
<br />
Started heating towards boil.<br />
<br />
Once boil was achieved:<br />
<br />
90 minutes:<br />
<br />
*2 oz Columbus 15.4% (pellet)<br />
*2 oz Simcoe 14.1% (non-pellet)<br />
<br />
0 minutes:<br />
<br />
*2 oz Cascade 6.5% (pellet)<br />
<br />
5 mins to steep 0 min hops, then continue to steep while counter-flow chilling the wort|<br />
<br />
== Prep work<br />
<br />
Drilled top hole for airlock in home depot food safe bucket:<br />
<br />
3/4" hole drill (ryobi forstner 8 pcs bit set). A bit tricky to drill. Need smallish rounded file to clean up the hole.</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3043Phage therapy2013-03-19T07:04:20Z<p>208.87.217.74: /* Questions and Specific Aims */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
:<br /><br />
: This project is in its early stages. We are working to:<br />
# Begin a free-Gonorrhea screening program on the streets of Oakland and San Francisco;<br />
# Enhance the Center for Disease Control's Surveillance of antibiotic-resistant gonorrheal infections;<br />
# Develop an intern program for Oakland teens;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research;<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested;<br />
# Identify the first known bacteriophages from ''N. gonorrhoeae;''<br />
# Develop methods by which bacteriophages can be cultured and used as prophylaxis and therapy for gonoccocal infections;<br />
:<br />
: <br /><br />
<br />
:'''''If you would like to help with any of these project goals, please contact Craig (moleculararts [at] riseup [dot] net).'''''<br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
<br /><br />
1. Begin a long-term mobile screening program for antibiotic resistant gonorrhea on the streets of Oakland and San Francisco.<br /><br />
:a. Develop a website through which patients, after being provided a patient number can retrieve their results with a full analysis of their strain.<br />
:b. Compose and deploy a mobile screening unit at various locations throughout Oakland and San Francisco.<br />
<br /><br />
2. Support the Center for Disease Control's efforts to monitor the emergence of antibiotic resistant gonorrhea.<br />
:a. Compile data from the mobile screening program and report it (anonymously) to the CDC.<br />
:b. Send antibiotic-resistant gonorrhea samples to the center for disease control according to the Instructions for Submitting Specimens to CDC Gonorrhea Laboratory for Confirmation Testing and/or Testing of Clinical Treatment Failures. <br />
<br /><br />
3. Develop a community laboratory space in Oakland, CA that has the equipment (acquired or built) we need in which we can conduct our research.<br />
:a. Procure capital equipment and reagents needed for this project. <br />
:b. Procure reagents and equipment to begin molecular microbiological research.<br />
:c. Open space up to provide education for Oakland teens.<br />
<br /><br />
4. Isolate, identify and characterize the first known bacteriophages from '''N. gonorrhoeae.'''<br />
:a. Swab patients, grow samples on Modified Thayer Martin medium, broth cultures grown in Trypticase Soy Broth.<br />
:b. Supernatants harvested and filtered through a 0.2um filter and analyzed by SDS-PAGE.<br />
:c. <br />
<br /><br />
5.Develop methods by which bacteriophages can be cultured and used as prophylaxis and therapy for gonoccocal infections.<br />
<br />
== Experiments and Anticipated Problems ==<br />
:We plan to begin acquiring clinical samples in April, 2013. Samples will be grown on Modified Thayer Martin agar supplemented with antibiotics. Colonies will '''(1)'''be stored in glycerol at -80oC, '''(2)'''grown in liquid culture for the assessment of bacteriophage production, '''(3)'''grown in Maltose to ensure we have cultured ''N. gonorrhoeae,'' and '''(4)'''grown in Fastidious Broth with 3rd-generation antibiotics to assess antibiotic resistance.<br />
:<br />
:Following growth in FB, supernatants will be analyzed for the presence of bacteriophage using SDS-PAGE electrophoresis.<br />
:<br />
:If bacteriophage proteins are present in the supernatants, these cultures will be re-grown in bulk and bacteriophage-containing sups will be stored at -80oC.<br />
:<br />
:All clinical screening data will be available to patients online through our website. If patients are positive, they will be asked to fill out a form on their results page that will detail their risk level. This data is important in the surveillance of antibiotic-resistant ''N. gonorrhoeae'' emergence. '''''All screening procedures and results are anonymous.'''''<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Rayon Swabs and tongue depressors ('''ordered!''')<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3042Phage therapy2013-03-19T06:29:33Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
:<br /><br />
: This project is in its early stages. We are working to:<br />
# Begin a free-Gonorrhea screening program on the streets of Oakland and San Francisco;<br />
# Enhance the Center for Disease Control's Surveillance of antibiotic-resistant gonorrheal infections;<br />
# Develop an intern program for Oakland teens;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research;<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested;<br />
# Identify the first known bacteriophages from ''N. gonorrhoeae;''<br />
# Develop methods by which bacteriophages can be cultured and used as prophylaxis and therapy for gonoccocal infections;<br />
:<br />
: <br /><br />
<br />
:'''''If you would like to help with any of these project goals, please contact Craig (moleculararts [at] riseup [dot] net).'''''<br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
# Provide surveillance data on the emergence of antibiotic-resistant ''N. gonorrhoeae.''<br />
# Uncover lytic bacteriophages from clinical strains of ''N. gonorrhoeae.''<br />
# Characterize lytic pathways of novel ''N. gonorrhoeae'' bacteriophage.<br />
#<br />
<br />
== Experiments and Anticipated Problems ==<br />
:We plan to begin acquiring clinical samples in April, 2013. Samples will be grown on Modified Thayer Martin agar supplemented with antibiotics. Colonies will '''(1)'''be stored in glycerol at -80oC, '''(2)'''grown in liquid culture for the assessment of bacteriophage production, '''(3)'''grown in Maltose to ensure we have cultured ''N. gonorrhoeae,'' and '''(4)'''grown in Fastidious Broth with 3rd-generation antibiotics to assess antibiotic resistance.<br />
:<br />
:Following growth in FB, supernatants will be analyzed for the presence of bacteriophage using SDS-PAGE electrophoresis.<br />
:<br />
:If bacteriophage proteins are present in the supernatants, these cultures will be re-grown in bulk and bacteriophage-containing sups will be stored at -80oC.<br />
:<br />
:All clinical screening data will be available to patients online through our website. If patients are positive, they will be asked to fill out a form on their results page that will detail their risk level. This data is important in the surveillance of antibiotic-resistant ''N. gonorrhoeae'' emergence. '''''All screening procedures and results are anonymous.'''''<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Rayon Swabs and tongue depressors ('''ordered!''')<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3041Phage therapy2013-03-19T06:28:22Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
:<br />
: This project is in its early stages. We are working to:<br />
# Begin a free-Gonorrhea screening program on the streets of San Francisco;<br />
# Enhance the Center for Disease Control's Surveillance of antibiotic-resistant gonorrheal infections;<br />
# Develop an intern program for Oakland teens;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research;<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested;<br />
# Identify the first known bacteriophages from ''N. gonorrhoeae;''<br />
# Develop methods by which bacteriophages can be cultured and used as prophylaxis and therapy for gonoccocal infections;<br />
:<br />
: <br /><br />
<br />
:'''''If you would like to help with any of these project goals, please contact Craig (moleculararts [at] riseup [dot] net).'''''<br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
# Provide surveillance data on the emergence of antibiotic-resistant ''N. gonorrhoeae.''<br />
# Uncover lytic bacteriophages from clinical strains of ''N. gonorrhoeae.''<br />
# Characterize lytic pathways of novel ''N. gonorrhoeae'' bacteriophage.<br />
#<br />
<br />
== Experiments and Anticipated Problems ==<br />
:We plan to begin acquiring clinical samples in April, 2013. Samples will be grown on Modified Thayer Martin agar supplemented with antibiotics. Colonies will '''(1)'''be stored in glycerol at -80oC, '''(2)'''grown in liquid culture for the assessment of bacteriophage production, '''(3)'''grown in Maltose to ensure we have cultured ''N. gonorrhoeae,'' and '''(4)'''grown in Fastidious Broth with 3rd-generation antibiotics to assess antibiotic resistance.<br />
:<br />
:Following growth in FB, supernatants will be analyzed for the presence of bacteriophage using SDS-PAGE electrophoresis.<br />
:<br />
:If bacteriophage proteins are present in the supernatants, these cultures will be re-grown in bulk and bacteriophage-containing sups will be stored at -80oC.<br />
:<br />
:All clinical screening data will be available to patients online through our website. If patients are positive, they will be asked to fill out a form on their results page that will detail their risk level. This data is important in the surveillance of antibiotic-resistant ''N. gonorrhoeae'' emergence. '''''All screening procedures and results are anonymous.'''''<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Rayon Swabs and tongue depressors ('''ordered!''')<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3040Phage therapy2013-03-19T06:27:07Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
:<br />
: This project is in its early stages. We are working to:<br />
# Begin a free-Gonorrhea screening program on the streets of San Francisco;<br />
# Enhance the Center for Disease Control's Surveillance of antibiotic-resistant gonorrheal infections;<br />
# Develop an intern program for Oakland teens;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research;<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested;<br />
# Identify the first known bacteriophages from ''N. gonorrhoeae;''<br />
# Develop methods by which bacteriophages can be cultured and used as prophylaxis and therapy for gonoccocal infections;<br />
:<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
# Provide surveillance data on the emergence of antibiotic-resistant ''N. gonorrhoeae.''<br />
# Uncover lytic bacteriophages from clinical strains of ''N. gonorrhoeae.''<br />
# Characterize lytic pathways of novel ''N. gonorrhoeae'' bacteriophage.<br />
#<br />
<br />
== Experiments and Anticipated Problems ==<br />
:We plan to begin acquiring clinical samples in April, 2013. Samples will be grown on Modified Thayer Martin agar supplemented with antibiotics. Colonies will '''(1)'''be stored in glycerol at -80oC, '''(2)'''grown in liquid culture for the assessment of bacteriophage production, '''(3)'''grown in Maltose to ensure we have cultured ''N. gonorrhoeae,'' and '''(4)'''grown in Fastidious Broth with 3rd-generation antibiotics to assess antibiotic resistance.<br />
:<br />
:Following growth in FB, supernatants will be analyzed for the presence of bacteriophage using SDS-PAGE electrophoresis.<br />
:<br />
:If bacteriophage proteins are present in the supernatants, these cultures will be re-grown in bulk and bacteriophage-containing sups will be stored at -80oC.<br />
:<br />
:All clinical screening data will be available to patients online through our website. If patients are positive, they will be asked to fill out a form on their results page that will detail their risk level. This data is important in the surveillance of antibiotic-resistant ''N. gonorrhoeae'' emergence. '''''All screening procedures and results are anonymous.'''''<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Rayon Swabs and tongue depressors ('''ordered!''')<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3039Phage therapy2013-03-19T06:03:09Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to:<br />
# Begin a free-Gonorrhea screening program on the streets of San Francisco;<br />
# Develop an intern program for Oakland teens,<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested.<br />
# Identify the first known bacteriophages from ''N. gonorrhoeae.''<br />
# Develop methods by which bacteriophages can be cultured and used as prophylaxis and therapy for gonoccocal infections.<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
# Provide surveillance data on the emergence of antibiotic-resistant ''N. gonorrhoeae.''<br />
# Uncover lytic bacteriophages from clinical strains of ''N. gonorrhoeae.''<br />
# Characterize lytic pathways of novel ''N. gonorrhoeae'' bacteriophage.<br />
#<br />
<br />
== Experiments and Anticipated Problems ==<br />
:We plan to begin acquiring clinical samples in April, 2013. Samples will be grown on Modified Thayer Martin agar supplemented with antibiotics. Colonies will '''(1)'''be stored in glycerol at -80oC, '''(2)'''grown in liquid culture for the assessment of bacteriophage production, '''(3)'''grown in Maltose to ensure we have cultured ''N. gonorrhoeae,'' and '''(4)'''grown in Fastidious Broth with 3rd-generation antibiotics to assess antibiotic resistance.<br />
:<br />
:Following growth in FB, supernatants will be analyzed for the presence of bacteriophage using SDS-PAGE electrophoresis.<br />
:<br />
:If bacteriophage proteins are present in the supernatants, these cultures will be re-grown in bulk and bacteriophage-containing sups will be stored at -80oC.<br />
:<br />
:All clinical screening data will be available to patients online through our website. If patients are positive, they will be asked to fill out a form on their results page that will detail their risk level. This data is important in the surveillance of antibiotic-resistant ''N. gonorrhoeae'' emergence. '''''All screening procedures and results are anonymous.'''''<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Rayon Swabs and tongue depressors ('''ordered!''')<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3037Phage therapy2013-03-18T17:44:19Z<p>208.87.217.74: /* Experiments and Anticipated Problems */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
# Provide surveillance data on the emergence of antibiotic-resistant ''N. gonorrhoeae.''<br />
# Uncover lytic bacteriophages from clinical strains of ''N. gonorrhoeae.''<br />
# Characterize lytic pathways of novel ''N. gonorrhoeae'' bacteriophage.<br />
#<br />
<br />
== Experiments and Anticipated Problems ==<br />
:We plan to begin acquiring clinical samples in April, 2013. Samples will be grown on Modified Thayer Martin agar supplemented with antibiotics. Colonies will '''(1)'''be stored in glycerol at -80oC, '''(2)'''grown in liquid culture for the assessment of bacteriophage production, '''(3)'''grown in Maltose to ensure we have cultured ''N. gonorrhoeae,'' and '''(4)'''grown in Fastidious Broth with 3rd-generation antibiotics to assess antibiotic resistance.<br />
:<br />
:Following growth in FB, supernatants will be analyzed for the presence of bacteriophage using SDS-PAGE electrophoresis.<br />
:<br />
:If bacteriophage proteins are present in the supernatants, these cultures will be re-grown in bulk and bacteriophage-containing sups will be stored at -80oC.<br />
:<br />
:All clinical screening data will be available to patients online through our website. If patients are positive, they will be asked to fill out a form on their results page that will detail their risk level. This data is important in the surveillance of antibiotic-resistant ''N. gonorrhoeae'' emergence. '''''All screening procedures and results are anonymous.'''''<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Rayon Swabs and tongue depressors ('''ordered!''')<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3036Phage therapy2013-03-18T17:43:51Z<p>208.87.217.74: /* Experiments and Anticipated Problems */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
# Provide surveillance data on the emergence of antibiotic-resistant ''N. gonorrhoeae.''<br />
# Uncover lytic bacteriophages from clinical strains of ''N. gonorrhoeae.''<br />
# Characterize lytic pathways of novel ''N. gonorrhoeae'' bacteriophage.<br />
#<br />
<br />
== Experiments and Anticipated Problems ==<br />
:We plan to begin acquiring clinical samples in April, 2013. Samples will be grown on Modified Thayer Martin agar supplemented with antibiotics. Colonies will '''(1)'''be stored in glycerol at -80oC, '''(2)'''grown in liquid culture for the assessment of bacteriophage production, '''(3)'''grown in Maltose to ensure we have cultured ''N. gonorrhoeae,'' and '''(4)'''grown in Fastidious Broth with 3rd-generation antibiotics to assess antibiotic resistance.<br />
:<br />
:Following growth in FB, supernatants will be analyzed for the presence of bacteriophage using SDS-PAGE electrophoresis.<br />
:<br />
:If bacteriophage proteins are present in the supernatants, these cultures will be re-grown in bulk and bacteriophage-containing sups will be stored at -80oC.<br />
:<br />
:All clinical screening data will be available to patients online through our website. If patients are positive, they will be asked to fill out a form on their results page that will detail their risk level. This data is important in the surveillance of antibiotic-resistant ''N. gonorrhoeae'' emergence. ''All screening procedures and results are anonymous.''<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Rayon Swabs and tongue depressors ('''ordered!''')<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3035Phage therapy2013-03-18T17:40:21Z<p>208.87.217.74: /* Experiments and Anticipated Problems */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
# Provide surveillance data on the emergence of antibiotic-resistant ''N. gonorrhoeae.''<br />
# Uncover lytic bacteriophages from clinical strains of ''N. gonorrhoeae.''<br />
# Characterize lytic pathways of novel ''N. gonorrhoeae'' bacteriophage.<br />
#<br />
<br />
== Experiments and Anticipated Problems ==<br />
:We plan to begin acquiring clinical samples in April, 2013. Samples will be grown on Modified Thayer Martin agar supplemented with antibiotics. Colonies will '''(1)'''be stored in glycerol at -80oC, '''(2)'''grown in liquid culture for the assessment of bacteriophage production, '''(3)'''grown in Maltose to ensure we have cultured ''N. gonorrhoeae,'' and '''(4)'''grown in Fastidious Broth with 3rd-generation antibiotics to assess antibiotic resistance.<br />
:<br />
:Following growth in FB, supernatants will be analyzed for the presence of bacteriophage using SDS-PAGE electrophoresis.<br />
:If bacteriophage proteins are present in the supernatants, these cultures will be re-grown in bulk and bacteriophage-containing sups will be stored at -80oC.<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Rayon Swabs and tongue depressors ('''ordered!''')<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3034Phage therapy2013-03-18T17:34:23Z<p>208.87.217.74: /* Laboratory Needs */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
# Provide surveillance data on the emergence of antibiotic-resistant ''N. gonorrhoeae.''<br />
# Uncover lytic bacteriophages from clinical strains of ''N. gonorrhoeae.''<br />
# Characterize lytic pathways of novel ''N. gonorrhoeae'' bacteriophage.<br />
#<br />
<br />
== Experiments and Anticipated Problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Rayon Swabs and tongue depressors ('''ordered!''')<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
:<br />
: '''''much much much more'''''.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3033Phage therapy2013-03-18T05:20:24Z<p>208.87.217.74: /* Questions and Specific Aims */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
:<br />
:<br />
:'''Specific Aims'''<br />
# Provide surveillance data on the emergence of antibiotic-resistant ''N. gonorrhoeae.''<br />
# Uncover lytic bacteriophages from clinical strains of ''N. gonorrhoeae.''<br />
# Characterize lytic pathways of novel ''N. gonorrhoeae'' bacteriophage.<br />
#<br />
<br />
== Experiments and Anticipated Problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Swabs and tongue depressors (we can use regular cotton swabs, though previous research indicates cotton swabs may not be the most effective)<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
<br />
: much much much more.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3032Phage therapy2013-03-18T05:11:47Z<p>208.87.217.74: /* Laboratory Needs */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
== Experiments and Anticipated Problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
#CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
#Benchtop butane torches.<br />
#Sterilized toothpicks.<br />
#MTM agar plates '''(ordered!)'''<br />
#Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
#Glass test-tubes.<br />
#Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
#Swabs and tongue depressors (we can use regular cotton swabs, though previous research indicates cotton swabs may not be the most effective)<br />
#-80c Freezer to store glycerol stocks of clinical samples. <br />
#Ultracentrifuge<br />
#SDS-PAGE gel electrophoresis equipment and reagents.<br />
#Autoclave<br />
<br />
: much much much more.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3031Phage therapy2013-03-18T05:10:53Z<p>208.87.217.74: /* Laboratory Needs */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
== Experiments and Anticipated Problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
:CO2 incubator (we've built a prototype incubator but it has no CO2 component). We can grow these organisms in candle jars inside the incubator which means we need candle jars and candles.<br />
:Benchtop butane torches.<br />
:Sterilized toothpicks.<br />
:MTM agar plates '''(ordered!)'''<br />
:Fastidious Broth <ref>Cultivation of Neisseria gonorrhoeae in Liquid Media and Determination of Its In Vitro Susceptibilities to Quinolones. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234085/</ref><br />
:Glass test-tubes.<br />
:Maltose for differentiation of N. meningiditis vs. N. gonorrhoeae.<br />
:Swabs and tongue depressors (we can use regular cotton swabs, though previous research indicates cotton swabs may not be the most effective)<br />
:-80c Freezer to store glycerol stocks of clinical samples. <br />
:Ultracentrifuge<br />
:SDS-PAGE gel electrophoresis equipment and reagents.<br />
:Autoclave<br />
<br />
: much much much more.<br />
<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3029Phage therapy2013-03-18T05:00:07Z<p>208.87.217.74: /* Meeting Announcements and Contact Information */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
== Experiments and Anticipated Problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 3/24/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3028Phage therapy2013-03-18T04:47:28Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is exacerbated by the fact that primary treatments for gonorrheal infections are solely antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
== Experiments and Anticipated Problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3027Phage therapy2013-03-18T04:45:48Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: ''Neisseria gonorrhoeae'' has progressively developed resistance to the antibiotic drugs used to treat it. Since the late 1970's, Gonorrhea has shown signs of developing resistance to 3rd-generation, cephalosporin antibiotics which are ultimately the last line of defense against this bacterial pathogen <ref>Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/default.htm</ref>. Antibiotic resistant Gonorrhea is therefore a growing public health concern. In the United States, this concern is greater since primary treatments for gonorrheal infections are antibiotic-based. Currently, CDC STD treatment guidelines recommend dual therapy with the injectable cephalosporin ceftriaxone and either azithromycin or doxycycline to treat all uncomplicated gonococcal infections among adults and adolescents in the United States. Dual therapy is recommended to address the potential emergence of gonococcal cephalosporin resistance. Given the ability of ''N. gonorrhoeae'' to develop antibiotic resistance, it is critical to continuously monitor gonococcal antibiotic resistance and encourage research and development of new treatment regimens for gonorrhea <ref> Basic Information about Antibiotic Resistant Gonorrhea. http://www.cdc.gov/std/Gonorrhea/arg/basic.htm</ref>.<br />
<br />
: This project was established to (1) Provide surveillance insight into the emergence of antibiotic resistant gonorrhea, (2) better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae,'' and (3) develop phage-based prophylaxis and therapy to stop prevent further emergence of antibiotic-resistant gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Update this wiki with background research and a literature review so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge about the project;<br />
# Develop a space that has the equipment (acquired or built) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
== Experiments and Anticipated Problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3026Phage therapy2013-03-18T04:33:51Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: This project was established to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae'' with the aim of developing prophylactics and therapies to stop the emergence of non-treatable gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
# Acquire culture materials, and clinical specimen from which bacteriophages can be harvested<br />
<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
== Experiments and Anticipated Problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3025Phage therapy2013-03-18T04:09:53Z<p>208.87.217.74: /* Experiments and anticipated problems */</p>
<hr />
<div>== Introduction ==<br />
: This project was established to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae'' with the hope of developing prophylactics and therapies to stop the emergence of non-treatable gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
== Experiments and Anticipated Problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=3024Phage therapy2013-03-18T04:09:27Z<p>208.87.217.74: /* Experiments */</p>
<hr />
<div>== Introduction ==<br />
: This project was established to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseria gonorrhoeae'' with the hope of developing prophylactics and therapies to stop the emergence of non-treatable gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases of gonorrhea nationally each year. Of these, 0.5-3% of cases develop into disseminated, systemic infection where the falcutative intracellular diplococci induce more serious illness such as pelvic inflammatory disease.<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions and Specific Aims ==<br />
:<br />
== Experiments and anticipated problems ==<br />
:<br />
<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Open_Biotech/PCR&diff=2518Open Biotech/PCR2013-02-18T10:33:47Z<p>208.87.217.74: /* Discussion */</p>
<hr />
<div><br />
The goal of this project is to build a PCR machine as part of the open biolab. The device should be simple enough that people with a basic skillset can build it on their own while being cheap and simple to produce in a 100x to 500x quantity.<br />
<br />
The current target for the entire kit is $300 (PCR, centrifuge, shaking incubator, gel electrophoresis box, micropipette + chemistry/biology/plastics for 3+ experiments). This may turn out to be too low for the first run, but we're aiming at making this as affordable as possible while maintaining a quality that's good enough for day-to-day citizen science work.<br />
<br />
= Bill of materials and pricing =<br />
<br />
*[https://docs.google.com/spreadsheet/ccc?key=0Akog0JI0-bB9dDA0cTRLWFhlTkVOdGdhSUN4SE5NVEE&usp=sharing#gid=2 Order list for prototype materials]<br />
:Our initial prototype order. Based on aluminum block PCR tube holder. Does not include case.<br />
*[https://docs.google.com/spreadsheet/ccc?key=0Akog0JI0-bB9dDA0cTRLWFhlTkVOdGdhSUN4SE5NVEE&usp=sharing#gid=1 Pricing for between 100 and 500 units unit].<br />
:Some prices estimated. Not including taxes and shipping.<br />
<br />
= PCR tube holder =<br />
<br />
This is what will hold the PCR tubes. In commercial machines this is usually a block of with holes for the PCR tubes. The holes are usually only deep enough for about 50% of the PCR tube.<br />
<br />
Some examples:<br />
<br />
*[http://i.istockimg.com/file_thumbview_approve/8677256/2/stock-photo-8677256-pcr-machine.jpg Holy block type]<br />
*[http://thumbs.dreamstime.com/x/polymerase-chain-reaction-%28pcr%29-machine-28261032.jpg Connected cylinders type]<br />
<br />
PCR Tube dimensions:<br />
<br />
*Height: 20.81 (± 0.07) to 20.93 (± 0.08) mm<br />
*Diameter: 5.95 (± 0.04) to 6.07 (± 0.03) mm<br />
:Source: [http://www.spartanbio.com/wp-content/themes/spartan/assets/application_notes/17.pdf Dimensions and thermal property of different PCR tubes]<br />
<br />
Note that many PCR machines have PCR tube holes that are much shallower than the height of a PCR tube. <br />
<br />
The curvature/slant of the bottom runs to about half-way up the tube.<br />
<br />
Three strategies for the PCR tube holder are being investigated:<br />
<br />
*Milled aluminum<br />
*Cast pewter<br />
*Air cooling<br />
:Where the PCR tubes are held in a holed piece of wood/plastic/metal.<br />
<br />
== Milled aluminum ==<br />
<br />
Aluminum has a high thermal conductivity and is easy to machine. Adding a chunk of metal will slow temperature change. This is not desirable for rapid cycling, but it will make it easier to ensure that the temperature at the temperature probe and the temperature in all of the the PCR tubes is the same. <br />
<br />
Using a holed sheet of metal and air heating/cooling would be cheaper but may be more difficult to control accurately.<br />
<br />
*[http://www.mcmaster.com/#standard-aluminum-sheets/=lfqnfz Aluminum bars from McMaster-Carr]<br />
:1 cm x 4 cm x 6 feet for $35 (enough for 45 4x4 cm tube holders)<br />
:1 cm x 5 cm x 6 feet for $44 (enough for 36 5x5 cm tube holders)<br />
:1 cm x 2.5 cm x 6 feet for $23<br />
<br />
Milled aluminum has the problem that a custom-made drill-bit is needed to drill the holes for the PCR tubes. Hackteria has had a few of these made, and will send them to people to loan, but that's not quite as accessible as we would want. Another option is that people can just drill normal holes for the home-made version of the kit and then add a bit of mineral oil to the bottom of the holes to make contact between the PCR tubes and the block of aluminum. We should test how well this works.<br />
<br />
== Cast pewter ==<br />
<br />
Pros:<br />
<br />
*No special drill bit needed (more DIY friendly).<br />
*Metal can be melted on a normal stove.<br />
*RTV silicone mold is re-usable.<br />
<br />
Cons:<br />
<br />
*Lower heat conductivity than aluminum.<br />
*Molten metal is dangerous.<br />
*RTV silicone mold supplies are expensive.<br />
<br />
Supplies needed:<br />
<br />
*[http://www.amazon.com/Lyman-Big-Dipper-Casting-Furnace/dp/B0037NA7ZA/ref=sr_1_6?ie=UTF8&qid=1360652567&sr=8-6&keywords=pewter+casting electric casting furnace] $43<br />
*[http://www.amazon.com/Lee-LP90026-Precision-Lead-Ladle/dp/B000LN12Y4/ref=sr_1_1?s=sporting-goods&ie=UTF8&qid=1360653015&sr=1-1&keywords=casting+ladle casting ladle] $12<br />
*high temperature RTV silicone mold kit<br />
*oil-based clay (e.g. chavant)<br />
*lead-free pewter pieces / small ingots<br />
<br />
Safety supplies:<br />
<br />
*gloves for casting<br />
*face shield<br />
*goggles<br />
<br />
= Air cooling =<br />
<br />
A sheet of metal with holes in it and a fan to circulate the air. <br />
<br />
Controlling the temperature accurately will require more dynamic control but we should try it and see what kind of temperature stability and ramp times we can get.<br />
<br />
= Microcontroller =<br />
<br />
*Atmega 328<br />
:Same as the standard Arduino<br />
:DIP (through-hole) version is $2.88 but only $1.60 at 100x [http://www.digikey.com/product-detail/en/ATMEGA328-PU/ATMEGA328-PU-ND/2271026 via digikey].<br />
*Atmega 32u4 which has built in USB (meaning that we don't have to include a serial to usb cable) <br />
:No DIP version exists, but QFP version exists which sorta kinda is hand-solderable but not by noobs.<br />
:Price is $3.37 at 100x [http://www.digikey.com/product-search/en/integrated-circuits-ics/embedded-microcontrollers/2556109?k=atmega32u4&quantity=100&ColumnSort=1000011&fid=0 via digikey].<br />
<br />
== USB to serial cable ==<br />
<br />
*Cables based on the PL2303HX chip can be had for [https://www.google.com/search?q=usb+serial+3.3&hl=en&biw=1024&bih=613&sa=X&ei=8eAaUaiMBMnmiwKd7IHoBQ&ved=0CDIQpwUoAA&tbs=%2Cprice%3A1%2Cppr_min%3A1%2Cppr_max%3A5&tbm=shop&tbo= $3]. Maybe slightly less if we buy in bulk.<br />
<br />
<br />
= Temperature control =<br />
<br />
== Temperature sensing ==<br />
<br />
It would be nice to have minimum plus/minus 0.5 C accurate sensors.<br />
<br />
Digital is more expensive than analog for an equivalent accuracy, and prohibitively expensive at high accuracy. If we go with the cheaper analog solution then we may have to individually calibrate the sensors.<br />
<br />
Arduino ADC resolution is 10 bit, so if hooked up correctly we should be able to get better than 0.2 C accuracy in sampling.<br />
<br />
=== Analog ===<br />
<br />
*2k ohm NTC thermistor [http://www.digikey.com/product-detail/en/NTSD1XM202FPB50/490-4665-ND/1203944 via digikey] for $0.72 at 1x or $0.37 at 100x.<br />
:About +/- 0.5 C accurate from 0 to 50 C.<br />
:+/- 1.0 C at 75 C.<br />
:+/- 1.5 C at 100 C.<br />
:7.198 k ohm at -5 C.<br />
:0.111 k ohm at 120 C.<br />
*1k ohm NTC thermistor [http://www.digikey.com/product-detail/en/PT103G2/PT103G2-ND/2242426 via digikey] for $1.06 at 100x.<br />
:+/- 0.2 C from 0 to 70 C.<br />
:Min order is 100x.<br />
:Rather minimal datasheet.<br />
<br />
We can likely get much better prices for high accuracy thermistors if we are willing to work with SMD components.<br />
<br />
=== Digital ===<br />
<br />
*Analog Devices TMP36 at [http://www.digikey.com/product-detail/en/TMP36GT9Z/TMP36GT9Z-ND/820404 at digikey] for $1.42 or $1.00 at 100x <br />
:+/- 1.0 at 25 C.<br />
:+/- 2.0 from -40 to 125 C.<br />
*Maxim DS18B20 [https://www.sparkfun.com/products/245 at sparkfun] for $4.25 or $3.40 at 100x.<br />
:1-wire digital sensor. <br />
:+/- 0.5 C accuracy from -55 to 85 C. <br />
:Range is -55 to 125 C. <br />
:12 bit resolution.<br />
<br />
== Cooling ==<br />
<br />
*Peltier element 40x40 mm [https://www.sparkfun.com/products/10080 at sparkfun] for $15 or $12 at 100x.<br />
:Could not find anything cheaper on digikey.<br />
:It looks like searching for '12709 Tec' can yield small lots of a very very similar device for $5 a piece.<br />
<br />
=== Discussion ===<br />
<br />
I've been looking at the specs of some Peltier chips (see https://docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem to be designed for lower temperature operation and the lifetime of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly. I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this out for a temperature controlled minielectrophoresis unit that I am designing (to be open source). [[User:Hbergeronx|Hbergeronx]].<br />
<br />
:Yeah. The temperature sensor + MOSFET + microcontroller allows us this dynamic control :-) (also, please put three tilde characters to tag comments with your name) - [[User:Juul|Juul]]<br />
::A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention. [[User:Hbergeronx|Hbergeronx]]<br />
:::My apologies for the brief comment before. I was in a hurry. Interesting information indeed! One solution would be to just not switch them on at the higher temperatures. We can see how much of an effect the peltier will have above 80 C. My guess is that it will be fairly small. Another solution is to either PWM control the MOSFET, perhaps through a capacitor, or even better, to use the analog output of the microcontroller and a non-charge-pumped MOSFET to gradually control the peltier based on the temperature. We may want to do this with the heating element as well. [[User:Juul|Juul]]<br />
<br />
= Heating =<br />
<br />
[http://hydraraptor.blogspot.com/2009/01/yet-another-quick-heater-hack.html Using vitreous enamel wire wound resistor]<br />
<br />
Use "fire cement diluted with a little water" to hold the power resistor in place. [http://reprap.org/wiki/Geared_extruder_nozzle source].<br />
<br />
Maybe use a NIF5003 MOSFET connected to insulated nichrome? [http://forums.reprap.org/read.php?13,51178,55089 source]<br />
<br />
Look at extruder controllers:<br />
<br />
*[http://reprap.org/wiki/Extruder_Controller_2.2 reprap 2.2 controller]<br />
:Specifically the [http://reprap.org/wiki/Extruder_Controller_2.2#MOSFETS mosfets]<br />
<br />
Example [http://energeticforum.com/inductive-resistor/5359-mosfet-heating-circuits.html MOSFET heating circuit].<br />
<br />
== Resistors ==<br />
<br />
*[http://www.digikey.com/product-detail/en/RS0101R000FE73/RSD-1.0RCT-ND/1166575 10 watt wire wound resistor] at $1.56 or $1.25<br />
*[http://www.digikey.com/scripts/dksearch/dksus.dll?FV=ffec4985%2Cfff40001%2Cfff80482%2C8000a%2C80010%2C8004c%2C8004d%2C80068%2C8006a%2C8006d%2C80075%2C800bc%2C8022a%2C8022b%2C2b8001a&k=resistor&mnonly=0&newproducts=0&ColumnSort=1000011&page=1&stock=1&pbfree=0&rohs=0&quantity=0&ptm=0&fid=0 search for RWM series 8+ watt wirewound resistors] a bit expensive at $4<br />
<br />
<br />
== MOSFETs ==<br />
<br />
*The RFP30N06LE or FQP30N06L [https://www.sparkfun.com/products/10213? from sparkfun] for $1 or $0.76 at 100x. Same price at digikey.<br />
:This has a built in charge pump, which allows it to trigger fully from 3.3v.<br />
<br />
Alternatives:<br />
<br />
*Digikey page for NIF5003 at $1.37 [http://www.digikey.com/product-detail/en/NIF5003NT1G/NIF5003NT1GOSCT-ND/1967238 here]<br />
:Used in some of the 3D printers for nozzle heater control, but not fully triggerable from 3.3v.<br />
*Jake says, if we want to use "normal" FETs then we can try IXDD604PI <br />
<br />
For the simple solution (no heating/cooling in the lid) we need:<br />
<br />
*1 MOSFET for regulating heating element.<br />
*1 MOSFET for regulating peltier element.<br />
<br />
Each MOSFET needs a [https://www.sparkfun.com/products/11508 10k resistor] and a [https://www.sparkfun.com/products/8589 1N4001 diode] for about $0.30.<br />
<br />
== Fans and heatsinks ==<br />
<br />
Should be 5 or 12 vdc 5x5 cm. We should use standard CPU coolers since they are cheap an easy to find, which is important since this is the only moving part in the PCR machine and will likely need to be replaced at some point by the user.<br />
<br />
*[http://www.digikey.com/product-detail/en/KDE1205PHV2%20MS.A.GN/259-1357-ND/1021206 $4 fan from digikey] - no heatsink included (drops to $2.90 for 100).<br />
*[https://www.sparkfun.com/products/9648 $5 fan from sparkfun] - no heatsink.<br />
*Fan with built in heatsink for $6.20 [http://www.google.com/shopping/product/13394255327842041335?q=cpu%20fan&hl=en&psj=1&bav=on.2,or.r_gc.r_pw.r_qf.&bvm=bv.42261806,d.cGE&biw=1024&bih=613&sa=X&ei=SvkZUamMBaKsjAKMhYDwAQ&ved=0CH8Q8wIwAA&prds=scoring:tp via google]<br />
*Fan with built in heatsink, but a bit too big for $5.00 [http://www.outletpc.com/c1987.html?utm_source=c1987&utm_medium=shopping%2Bengine&utm_campaign=googleproducts via outletpc.com]<br />
<br />
We also need a transistor to control the fan. The digikey fan uses 0.8 watt and the sparkfun fan uses 1 watt.<br />
<br />
Assuming the fans are 12 volts, the NPN 2N3904 can be used (but it's max 200 mA) [https://www.sparkfun.com/products/521 via sparkfun] at $0.75 but they're less than 10 cents at 100x.<br />
<br />
= Power supply =<br />
<br />
*12v 10amp [http://www.amazon.com/Logisys-Corp-Bearing-Supply-PS550E12BK/dp/B004MU8VCS/ref=sr_1_2?ie=UTF8&qid=1360655541&sr=8-2&keywords=atx+power+supply power supply] $24, but can be used for centrifuge and incubator as well.<br />
<br />
*24-pin ATX PSU female [https://www.sparkfun.com/products/9498 connector] and [https://www.sparkfun.com/products/9558 breakout-board] for $7 total.<br />
<br />
*[http://www.mouser.com/ProductDetail/Molex/44206-0007/?qs=g5f4E6w8l8gzEjxCgQ0R8g%3D%3D&gclid=CJar6Je-srUCFeeDQgodPBYAgA via mouser] for $0.74 or x100 for $0.65<br />
<br />
<br />
= Previous work =<br />
<br />
== Existing DIY cyclers ==<br />
<br />
*[http://openpcr.org/ openpcr]<br />
*[http://russelldurrett.com/lightbulbpcr.html lightbulb pcr]<br />
*[http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS Arduino PCR]<br />
*griessen pcr<br />
*[http://pimm.wordpress.com/2009/10/31/lavaamp-cheapest-pocket-pcr-thermocycler-dreamed-for-diy-biologists/ lava-amp]<br />
<br />
*[http://diyhpl.us/~bryan/papers2/microfluidics/2010-01-20/Petri%20dish%20PCR%20-%20laser-heated%20reactions%20in%20nanoliter%20droplet%20arrays.pdf laser-heated petri dish PCR]<br />
*[http://144.206.159.178/ft/943/73743/1264824.pdf A portable battery-operated chip thermocycler based on induction heating]<br />
<br />
== Useful links ==<br />
<br />
* [http://hackteria.org/wiki/index.php/Jugaad_PCR_Thermocyclers Hackteria PCR notes]<br />
* [http://openwetware.org/wiki/DIYbio:Notebook/Open_Thermal_Cycler DIYbio:Notebook/Open Thermal Cycler]<br />
* [http://russelldurrett.com/lightbulbpcr.html The Light Bulb PCR Machine]<br />
* [http://groups.google.com/d/topic/diybio/XqIJ3l-IHZ8/discussion $10 buck thermocycler design work]<br />
* [http://groups.google.com/d/msg/diybio/r7opEnSApkU/arffsaDtv_oJ Re: inexpensive PCR designs UnBlockedâ„¢]<br />
* [http://groups.google.com/d/topic/diybio/ZzMZohMpgB8/discussion The open-source Pacer PCR]<br />
* [http://groups.google.com/d/topic/diybio/tlPUBoCTf-Q/discussion Cheaper OpenPCR]<br />
<br />
= Documentation =<br />
<br />
== Peltier ==<br />
Note: Comments moved to different section of this page: Temperature control -> Cooling.<br />
<br />
== MOSFETs ==<br />
<br />
*[http://bildr.org/2012/03/rfp30n06le-arduino/ bildr tutorial]<br />
*[http://www.sparkfun.com/news/819 20 min video about MOSFETs]<br />
<br />
= Protocols =<br />
<br />
== DNA extraction ==<br />
<br />
http://www.scq.ubc.ca/the-macgyver-project-genomic-dna-extraction-and-gel-electrophoresis-experiments-using-everyday-materials/<br />
<br />
== Transformation ==<br />
<br />
[http://hackteria.org/wiki/index.php/GFP_Protocol_Jugaad GFP]<br />
<br />
== Electrophoresis ==<br />
<br />
[http://learn.genetics.utah.edu/content/labs/gel/electrophoresis/ University of utah's guide]<br />
[http://www.instructables.com/id/How-to-Prepare-an-Electrophoresis-Argarose-Gel/step3/Cast-the-Gel/ How to prepare a gel]</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Open_Biotech/PCR&diff=2517Open Biotech/PCR2013-02-18T10:29:53Z<p>208.87.217.74: </p>
<hr />
<div><br />
The goal of this project is to build a PCR machine as part of the open biolab. The device should be simple enough that people with a basic skillset can build it on their own while being cheap and simple to produce in a 100x to 500x quantity.<br />
<br />
The current target for the entire kit is $300 (PCR, centrifuge, shaking incubator, gel electrophoresis box, micropipette + chemistry/biology/plastics for 3+ experiments). This may turn out to be too low for the first run, but we're aiming at making this as affordable as possible while maintaining a quality that's good enough for day-to-day citizen science work.<br />
<br />
= Bill of materials and pricing =<br />
<br />
*[https://docs.google.com/spreadsheet/ccc?key=0Akog0JI0-bB9dDA0cTRLWFhlTkVOdGdhSUN4SE5NVEE&usp=sharing#gid=2 Order list for prototype materials]<br />
:Our initial prototype order. Based on aluminum block PCR tube holder. Does not include case.<br />
*[https://docs.google.com/spreadsheet/ccc?key=0Akog0JI0-bB9dDA0cTRLWFhlTkVOdGdhSUN4SE5NVEE&usp=sharing#gid=1 Pricing for between 100 and 500 units unit].<br />
:Some prices estimated. Not including taxes and shipping.<br />
<br />
= PCR tube holder =<br />
<br />
This is what will hold the PCR tubes. In commercial machines this is usually a block of with holes for the PCR tubes. The holes are usually only deep enough for about 50% of the PCR tube.<br />
<br />
Some examples:<br />
<br />
*[http://i.istockimg.com/file_thumbview_approve/8677256/2/stock-photo-8677256-pcr-machine.jpg Holy block type]<br />
*[http://thumbs.dreamstime.com/x/polymerase-chain-reaction-%28pcr%29-machine-28261032.jpg Connected cylinders type]<br />
<br />
PCR Tube dimensions:<br />
<br />
*Height: 20.81 (± 0.07) to 20.93 (± 0.08) mm<br />
*Diameter: 5.95 (± 0.04) to 6.07 (± 0.03) mm<br />
:Source: [http://www.spartanbio.com/wp-content/themes/spartan/assets/application_notes/17.pdf Dimensions and thermal property of different PCR tubes]<br />
<br />
Note that many PCR machines have PCR tube holes that are much shallower than the height of a PCR tube. <br />
<br />
The curvature/slant of the bottom runs to about half-way up the tube.<br />
<br />
Three strategies for the PCR tube holder are being investigated:<br />
<br />
*Milled aluminum<br />
*Cast pewter<br />
*Air cooling<br />
:Where the PCR tubes are held in a holed piece of wood/plastic/metal.<br />
<br />
== Milled aluminum ==<br />
<br />
Aluminum has a high thermal conductivity and is easy to machine. Adding a chunk of metal will slow temperature change. This is not desirable for rapid cycling, but it will make it easier to ensure that the temperature at the temperature probe and the temperature in all of the the PCR tubes is the same. <br />
<br />
Using a holed sheet of metal and air heating/cooling would be cheaper but may be more difficult to control accurately.<br />
<br />
*[http://www.mcmaster.com/#standard-aluminum-sheets/=lfqnfz Aluminum bars from McMaster-Carr]<br />
:1 cm x 4 cm x 6 feet for $35 (enough for 45 4x4 cm tube holders)<br />
:1 cm x 5 cm x 6 feet for $44 (enough for 36 5x5 cm tube holders)<br />
:1 cm x 2.5 cm x 6 feet for $23<br />
<br />
Milled aluminum has the problem that a custom-made drill-bit is needed to drill the holes for the PCR tubes. Hackteria has had a few of these made, and will send them to people to loan, but that's not quite as accessible as we would want. Another option is that people can just drill normal holes for the home-made version of the kit and then add a bit of mineral oil to the bottom of the holes to make contact between the PCR tubes and the block of aluminum. We should test how well this works.<br />
<br />
== Cast pewter ==<br />
<br />
Pros:<br />
<br />
*No special drill bit needed (more DIY friendly).<br />
*Metal can be melted on a normal stove.<br />
*RTV silicone mold is re-usable.<br />
<br />
Cons:<br />
<br />
*Lower heat conductivity than aluminum.<br />
*Molten metal is dangerous.<br />
*RTV silicone mold supplies are expensive.<br />
<br />
Supplies needed:<br />
<br />
*[http://www.amazon.com/Lyman-Big-Dipper-Casting-Furnace/dp/B0037NA7ZA/ref=sr_1_6?ie=UTF8&qid=1360652567&sr=8-6&keywords=pewter+casting electric casting furnace] $43<br />
*[http://www.amazon.com/Lee-LP90026-Precision-Lead-Ladle/dp/B000LN12Y4/ref=sr_1_1?s=sporting-goods&ie=UTF8&qid=1360653015&sr=1-1&keywords=casting+ladle casting ladle] $12<br />
*high temperature RTV silicone mold kit<br />
*oil-based clay (e.g. chavant)<br />
*lead-free pewter pieces / small ingots<br />
<br />
Safety supplies:<br />
<br />
*gloves for casting<br />
*face shield<br />
*goggles<br />
<br />
= Air cooling =<br />
<br />
A sheet of metal with holes in it and a fan to circulate the air. <br />
<br />
Controlling the temperature accurately will require more dynamic control but we should try it and see what kind of temperature stability and ramp times we can get.<br />
<br />
= Microcontroller =<br />
<br />
*Atmega 328<br />
:Same as the standard Arduino<br />
:DIP (through-hole) version is $2.88 but only $1.60 at 100x [http://www.digikey.com/product-detail/en/ATMEGA328-PU/ATMEGA328-PU-ND/2271026 via digikey].<br />
*Atmega 32u4 which has built in USB (meaning that we don't have to include a serial to usb cable) <br />
:No DIP version exists, but QFP version exists which sorta kinda is hand-solderable but not by noobs.<br />
:Price is $3.37 at 100x [http://www.digikey.com/product-search/en/integrated-circuits-ics/embedded-microcontrollers/2556109?k=atmega32u4&quantity=100&ColumnSort=1000011&fid=0 via digikey].<br />
<br />
== USB to serial cable ==<br />
<br />
*Cables based on the PL2303HX chip can be had for [https://www.google.com/search?q=usb+serial+3.3&hl=en&biw=1024&bih=613&sa=X&ei=8eAaUaiMBMnmiwKd7IHoBQ&ved=0CDIQpwUoAA&tbs=%2Cprice%3A1%2Cppr_min%3A1%2Cppr_max%3A5&tbm=shop&tbo= $3]. Maybe slightly less if we buy in bulk.<br />
<br />
<br />
= Temperature control =<br />
<br />
== Temperature sensing ==<br />
<br />
It would be nice to have minimum plus/minus 0.5 C accurate sensors.<br />
<br />
Digital is more expensive than analog for an equivalent accuracy, and prohibitively expensive at high accuracy. If we go with the cheaper analog solution then we may have to individually calibrate the sensors.<br />
<br />
Arduino ADC resolution is 10 bit, so if hooked up correctly we should be able to get better than 0.2 C accuracy in sampling.<br />
<br />
=== Analog ===<br />
<br />
*2k ohm NTC thermistor [http://www.digikey.com/product-detail/en/NTSD1XM202FPB50/490-4665-ND/1203944 via digikey] for $0.72 at 1x or $0.37 at 100x.<br />
:About +/- 0.5 C accurate from 0 to 50 C.<br />
:+/- 1.0 C at 75 C.<br />
:+/- 1.5 C at 100 C.<br />
:7.198 k ohm at -5 C.<br />
:0.111 k ohm at 120 C.<br />
*1k ohm NTC thermistor [http://www.digikey.com/product-detail/en/PT103G2/PT103G2-ND/2242426 via digikey] for $1.06 at 100x.<br />
:+/- 0.2 C from 0 to 70 C.<br />
:Min order is 100x.<br />
:Rather minimal datasheet.<br />
<br />
We can likely get much better prices for high accuracy thermistors if we are willing to work with SMD components.<br />
<br />
=== Digital ===<br />
<br />
*Analog Devices TMP36 at [http://www.digikey.com/product-detail/en/TMP36GT9Z/TMP36GT9Z-ND/820404 at digikey] for $1.42 or $1.00 at 100x <br />
:+/- 1.0 at 25 C.<br />
:+/- 2.0 from -40 to 125 C.<br />
*Maxim DS18B20 [https://www.sparkfun.com/products/245 at sparkfun] for $4.25 or $3.40 at 100x.<br />
:1-wire digital sensor. <br />
:+/- 0.5 C accuracy from -55 to 85 C. <br />
:Range is -55 to 125 C. <br />
:12 bit resolution.<br />
<br />
== Cooling ==<br />
<br />
*Peltier element 40x40 mm [https://www.sparkfun.com/products/10080 at sparkfun] for $15 or $12 at 100x.<br />
:Could not find anything cheaper on digikey.<br />
:It looks like searching for '12709 Tec' can yield small lots of a very very similar device for $5 a piece.<br />
<br />
=== Discussion ===<br />
<br />
I've been looking at the specs of some Peltier chips (see https://docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem to be designed for lower temperature operation and the lifetime of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly. I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this out for a temperature controlled minielectrophoresis unit that I am designing (to be open source). [[User:Hbergeronx|Hbergeronx]].<br />
<br />
:Interesting information! I knew there was some problems with the peltier elements at higher temperatures but it's good to have some numbers. One solution would be to just not switch them on at the higher temperatures. We can see how much of an effect the peltier will have above 80 C. My guess is that it will be fairly small. Another solution is to either PWM control the MOSFET, perhaps through a capacitor, or even better, to use the analog output of the microcontroller and a non-charge-pumped MOSFET to gradually control the peltier based on the temperature. We may want to do this with the heating element as well. [[User:Juul|Juul]]<br />
<br />
<br />
A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention.<br />
<br />
= Heating =<br />
<br />
[http://hydraraptor.blogspot.com/2009/01/yet-another-quick-heater-hack.html Using vitreous enamel wire wound resistor]<br />
<br />
Use "fire cement diluted with a little water" to hold the power resistor in place. [http://reprap.org/wiki/Geared_extruder_nozzle source].<br />
<br />
Maybe use a NIF5003 MOSFET connected to insulated nichrome? [http://forums.reprap.org/read.php?13,51178,55089 source]<br />
<br />
Look at extruder controllers:<br />
<br />
*[http://reprap.org/wiki/Extruder_Controller_2.2 reprap 2.2 controller]<br />
:Specifically the [http://reprap.org/wiki/Extruder_Controller_2.2#MOSFETS mosfets]<br />
<br />
Example [http://energeticforum.com/inductive-resistor/5359-mosfet-heating-circuits.html MOSFET heating circuit].<br />
<br />
== Resistors ==<br />
<br />
*[http://www.digikey.com/product-detail/en/RS0101R000FE73/RSD-1.0RCT-ND/1166575 10 watt wire wound resistor] at $1.56 or $1.25<br />
*[http://www.digikey.com/scripts/dksearch/dksus.dll?FV=ffec4985%2Cfff40001%2Cfff80482%2C8000a%2C80010%2C8004c%2C8004d%2C80068%2C8006a%2C8006d%2C80075%2C800bc%2C8022a%2C8022b%2C2b8001a&k=resistor&mnonly=0&newproducts=0&ColumnSort=1000011&page=1&stock=1&pbfree=0&rohs=0&quantity=0&ptm=0&fid=0 search for RWM series 8+ watt wirewound resistors] a bit expensive at $4<br />
<br />
<br />
== MOSFETs ==<br />
<br />
*The RFP30N06LE or FQP30N06L [https://www.sparkfun.com/products/10213? from sparkfun] for $1 or $0.76 at 100x. Same price at digikey.<br />
:This has a built in charge pump, which allows it to trigger fully from 3.3v.<br />
<br />
Alternatives:<br />
<br />
*Digikey page for NIF5003 at $1.37 [http://www.digikey.com/product-detail/en/NIF5003NT1G/NIF5003NT1GOSCT-ND/1967238 here]<br />
:Used in some of the 3D printers for nozzle heater control, but not fully triggerable from 3.3v.<br />
*Jake says, if we want to use "normal" FETs then we can try IXDD604PI <br />
<br />
For the simple solution (no heating/cooling in the lid) we need:<br />
<br />
*1 MOSFET for regulating heating element.<br />
*1 MOSFET for regulating peltier element.<br />
<br />
Each MOSFET needs a [https://www.sparkfun.com/products/11508 10k resistor] and a [https://www.sparkfun.com/products/8589 1N4001 diode] for about $0.30.<br />
<br />
== Fans and heatsinks ==<br />
<br />
Should be 5 or 12 vdc 5x5 cm. We should use standard CPU coolers since they are cheap an easy to find, which is important since this is the only moving part in the PCR machine and will likely need to be replaced at some point by the user.<br />
<br />
*[http://www.digikey.com/product-detail/en/KDE1205PHV2%20MS.A.GN/259-1357-ND/1021206 $4 fan from digikey] - no heatsink included (drops to $2.90 for 100).<br />
*[https://www.sparkfun.com/products/9648 $5 fan from sparkfun] - no heatsink.<br />
*Fan with built in heatsink for $6.20 [http://www.google.com/shopping/product/13394255327842041335?q=cpu%20fan&hl=en&psj=1&bav=on.2,or.r_gc.r_pw.r_qf.&bvm=bv.42261806,d.cGE&biw=1024&bih=613&sa=X&ei=SvkZUamMBaKsjAKMhYDwAQ&ved=0CH8Q8wIwAA&prds=scoring:tp via google]<br />
*Fan with built in heatsink, but a bit too big for $5.00 [http://www.outletpc.com/c1987.html?utm_source=c1987&utm_medium=shopping%2Bengine&utm_campaign=googleproducts via outletpc.com]<br />
<br />
We also need a transistor to control the fan. The digikey fan uses 0.8 watt and the sparkfun fan uses 1 watt.<br />
<br />
Assuming the fans are 12 volts, the NPN 2N3904 can be used (but it's max 200 mA) [https://www.sparkfun.com/products/521 via sparkfun] at $0.75 but they're less than 10 cents at 100x.<br />
<br />
= Power supply =<br />
<br />
*12v 10amp [http://www.amazon.com/Logisys-Corp-Bearing-Supply-PS550E12BK/dp/B004MU8VCS/ref=sr_1_2?ie=UTF8&qid=1360655541&sr=8-2&keywords=atx+power+supply power supply] $24, but can be used for centrifuge and incubator as well.<br />
<br />
*24-pin ATX PSU female [https://www.sparkfun.com/products/9498 connector] and [https://www.sparkfun.com/products/9558 breakout-board] for $7 total.<br />
<br />
*[http://www.mouser.com/ProductDetail/Molex/44206-0007/?qs=g5f4E6w8l8gzEjxCgQ0R8g%3D%3D&gclid=CJar6Je-srUCFeeDQgodPBYAgA via mouser] for $0.74 or x100 for $0.65<br />
<br />
<br />
= Previous work =<br />
<br />
== Existing DIY cyclers ==<br />
<br />
*[http://openpcr.org/ openpcr]<br />
*[http://russelldurrett.com/lightbulbpcr.html lightbulb pcr]<br />
*[http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS Arduino PCR]<br />
*griessen pcr<br />
*[http://pimm.wordpress.com/2009/10/31/lavaamp-cheapest-pocket-pcr-thermocycler-dreamed-for-diy-biologists/ lava-amp]<br />
<br />
*[http://diyhpl.us/~bryan/papers2/microfluidics/2010-01-20/Petri%20dish%20PCR%20-%20laser-heated%20reactions%20in%20nanoliter%20droplet%20arrays.pdf laser-heated petri dish PCR]<br />
*[http://144.206.159.178/ft/943/73743/1264824.pdf A portable battery-operated chip thermocycler based on induction heating]<br />
<br />
== Useful links ==<br />
<br />
* [http://hackteria.org/wiki/index.php/Jugaad_PCR_Thermocyclers Hackteria PCR notes]<br />
* [http://openwetware.org/wiki/DIYbio:Notebook/Open_Thermal_Cycler DIYbio:Notebook/Open Thermal Cycler]<br />
* [http://russelldurrett.com/lightbulbpcr.html The Light Bulb PCR Machine]<br />
* [http://groups.google.com/d/topic/diybio/XqIJ3l-IHZ8/discussion $10 buck thermocycler design work]<br />
* [http://groups.google.com/d/msg/diybio/r7opEnSApkU/arffsaDtv_oJ Re: inexpensive PCR designs UnBlockedâ„¢]<br />
* [http://groups.google.com/d/topic/diybio/ZzMZohMpgB8/discussion The open-source Pacer PCR]<br />
* [http://groups.google.com/d/topic/diybio/tlPUBoCTf-Q/discussion Cheaper OpenPCR]<br />
<br />
= Documentation =<br />
<br />
== Peltier ==<br />
Note: Comments moved to different section of this page: Temperature control -> Cooling.<br />
<br />
== MOSFETs ==<br />
<br />
*[http://bildr.org/2012/03/rfp30n06le-arduino/ bildr tutorial]<br />
*[http://www.sparkfun.com/news/819 20 min video about MOSFETs]<br />
<br />
= Protocols =<br />
<br />
== DNA extraction ==<br />
<br />
http://www.scq.ubc.ca/the-macgyver-project-genomic-dna-extraction-and-gel-electrophoresis-experiments-using-everyday-materials/<br />
<br />
== Transformation ==<br />
<br />
[http://hackteria.org/wiki/index.php/GFP_Protocol_Jugaad GFP]<br />
<br />
== Electrophoresis ==<br />
<br />
[http://learn.genetics.utah.edu/content/labs/gel/electrophoresis/ University of utah's guide]<br />
[http://www.instructables.com/id/How-to-Prepare-an-Electrophoresis-Argarose-Gel/step3/Cast-the-Gel/ How to prepare a gel]</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=CORE_I_RSVP&diff=2494CORE I RSVP2013-02-15T03:26:03Z<p>208.87.217.74: </p>
<hr />
<div>The CORE I course will be offered at Sudo Room on Thursday, Feb. 21st from 6:30-9:30pm. <br />
<br />
The CORE I class teaches students how to prepare a family disaster plan, reduce common household hazards, create emergency supply kits, and respond to a number of possible emergencies, including earthquakes and fires.<br />
<br />
This is the first in a series of three classes. In the CORE II class, folks learn how to organize a neighborhood command post and create emergency response teams, (i.e. communications, damage assessment, hazard reduction/utilities, search and rescue, disaster first aid, shelter and special needs).<br />
<br />
==RSVP List==<br />
We need 15 confirmed attendees in order to proceed!<br />
<br />
(Please use the Signature icon above to register for this course, or send an email to jenny [at] thepyre [dot] org!)<br />
:1. --[[User:Tunabananas|Tunabananas]] ([[User talk:Tunabananas|talk]]) 03:56, 12 January 2013 (CET)<br />
:2. --[[User:Juul|Juul]]<br />
:3. Jehan<br />
:4. Tracy<br />
:5. Felicia<br />
:6. Andrew<br />
:7. Dora<br />
:8. Brandon Y<br />
:9. [[User:garrettr|garrettr]]<br />
:10. Noni A--[[Special:Contributions/98.248.211.211|98.248.211.211]] 09:08, 2 February 2013 (UTC)<br />
:11. Christine<br />
:12. --[[User:Rch|Rch]] ([[User talk:Rch|talk]]) 16:00, 9 February 2013 (UTC)<br />
:13. Eno<br />
:14. <br />
:15.</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Mesh&diff=2277Mesh2013-02-02T21:01:12Z<p>208.87.217.74: /* Projects */</p>
<hr />
<div><br />
==Meetup Info==<br />
*Join the [http://lists.sudoroom.org/listinfo/mesh Mailing List!]<br />
*We meet weekly on Thursdays, 8:30-10pm at [[Getting_there|Sudo Room]]<br />
<br />
==Meeting Minutes==<br />
*[http://lists.sudoroom.org/pipermail/mesh/2013-January/000000.html 2013-01-31]<br />
<br />
==Projects==<br />
*[http://510pen.org 510pen] - East Bay community wireless mesh network spawned in 2009 by [[User:mfb|Mark Burdett]]<br />
*[http://wiki.tidepools.com Tidepools] - [[User:tunabananas|Jenny Ryan]] is designing local use cases for a community mobile mapping application built to run on mesh networks.</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2076Phage therapy2013-01-23T21:34:05Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: This project was established to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseia gonorrhoeae'' with the hope of developing prophylactics and therapies to stop the emergence of non-treatable gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases around the globe<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2075Phage therapy2013-01-23T21:31:07Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: This project was established to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, ''Neisseia gonorrhoeae'' with the hope of developing prophylactics and therapies to stop the emergence of non-treatable gonorrhea.<br />
<br />
: This project is in its early stages. We are working to accomplish the following tasks:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact the Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases around the globe<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2074Phage therapy2013-01-23T21:21:16Z<p>208.87.217.74: </p>
<hr />
<div>== Introduction ==<br />
: This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread of STDs.<br />
<br />
: This project is in its early stages. We are working to accomplish the following:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact the Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
== What is Phage Therapy ==<br />
: Phage therapy is a biological therapy that uses bacteriophages (bacterial viruses) to infect and lyse bacterial pathogens.<ref>[http://www.landesbioscience.com/journals/bacteriophage/AbedonBP1-2.pdf] Phage Treatment of Human Infections. Abedon, et al. 2011.</ref> <br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases around the globe<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2065Phage therapy2013-01-23T20:39:28Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread of STDs.<br />
<br />
: This project is in its early stages. We are working to accomplish the following:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact the Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases around the globe<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2059Phage therapy2013-01-23T19:33:49Z<p>208.87.217.74: </p>
<hr />
<div>== Introduction ==<br />
: This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread of STDs.<br />
<br />
: The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
: This project is in its early stages. We are working to accomplish the following:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact the Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> of which about 50% are estimated to be reported ( for a total of 700,000 estimated new cases in 2011). The World Health Organization reports that there are between 65-105 million new cases around the globe<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2058Phage therapy2013-01-23T19:23:14Z<p>208.87.217.74: </p>
<hr />
<div>== Introduction ==<br />
: This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread of STDs.<br />
<br />
: The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
: This project is in its early stages. We are working to accomplish the following:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact the Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] Detailed STD Facts </ref> (50% of which were reported ~349,000)<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
== References ==<br />
<references /></div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2057Phage therapy2013-01-23T19:20:19Z<p>208.87.217.74: /* Sexually Transmitted Bacterial Infections */</p>
<hr />
<div>== Introduction ==<br />
: This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread of STDs.<br />
<br />
: The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
: This project is in its early stages. We are working to accomplish the following:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact the Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
: This project will begin by studying ''Neisseria gonorrhoeae'' the causative agent of gonorrhea. <br />
: Neisseria gonorrhoeae is a facultative intracellular pathogen that is able to infect the eye, pharynx, anus/rectum, urogenital tract, and may be disseminated throughout the body in more complex cases. The Center for Disease Control reports that in 2011 there were an 321,849 new cases of gonorrhea reported in the U.S.<ref>[http://www.cdc.gov/std/gonorrhea/STDFact-gonorrhea-detailed.htm] </ref> (50% of which were reported ~349,000)<br />
<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2056Phage therapy2013-01-23T18:44:02Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread of STDs.<br />
<br />
: The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
: This project is in its early stages. We are working to accomplish the following:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: <br />
: If you would like to help with any of these short term project goals, please contact the Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
:<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2055Phage therapy2013-01-23T18:43:03Z<p>208.87.217.74: </p>
<hr />
<div>== Introduction ==<br />
: This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread of STDs.<br />
<br />
: The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
: This project is in its early stages. We are working to accomplish the following:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: If you can help with any of these steps, please contact the Craig (moleculararts [at] riseup [dot] net).<br />
<br /><br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
:<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2054Phage therapy2013-01-23T18:42:14Z<p>208.87.217.74: /* Introduction */</p>
<hr />
<div>== Introduction ==<br />
: This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread of STDs.<br />
<br />
: The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
: This project is in its early stages. We are working to accomplish the following:<br />
# Perform a comprehensive literature review;<br />
# Update this wiki with background research so all participating citizen scientists can begin in the laboratory with the same rudimentary knowledge;<br />
# Find a space that has the equipment (or acquire/build equipment) we need in which we can conduct our research.<br />
: If you can help with any of these steps, please contact the Craig at MolecularArts<br />
<br /><br />
<br />
== Sexually Transmitted Bacterial Infections ==<br />
:<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2053Phage therapy2013-01-23T18:35:07Z<p>208.87.217.74: </p>
<hr />
<div>== Introduction ==<br />
This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread of STDs.<br />
<br />
The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
<br /><br />
== Sexually Transmitted Bacterial Infections ==<br />
:<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
: http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
: http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
: http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
: http://www.youtube.com/watch?v=3VjE1zddXWk<br />
: http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
: http://www.youtube.com/watch?v=egY-Br_oTHE<br />
: http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
: http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
: http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
:<br />
== '''Meeting Announcements and Contact Information''' ==<br />
<br />
'''''Next Call: 1/27/13 8:00pm PST/10:00pm CST'''''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2052Phage therapy2013-01-23T18:32:30Z<p>208.87.217.74: </p>
<hr />
<div>== Introduction ==<br />
This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread in STDs.<br />
<br />
The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
<br /><br />
== Sexually Transmitted Bacterial Infections ==<br />
:<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
<br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''. Our social quest is the pursuit of knowledge. We are not approaching this project with the hope of making money. We want to collectively answer questions and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
<br />
http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
http://www.youtube.com/watch?v=3VjE1zddXWk<br />
http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
http://www.youtube.com/watch?v=egY-Br_oTHE<br />
http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
<br />
<br />
== Meeting Announcements and Contact Information ==<br />
<br />
''Next Call: 1/27/13 8:00pm PST/10:00pm CST''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2051Phage therapy2013-01-23T18:31:08Z<p>208.87.217.74: </p>
<hr />
<div>== Introduction ==<br />
This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread in STDs.<br />
<br />
The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
<br /><br />
== Sexually Transmitted Bacterial Infections ==<br />
:<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
<br />
== Questions ==<br />
:<br />
== Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
<br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: '''Science is a ''quest''ion'''Our social goal is the pursuit of medical knowledge. We are not approaching this project with the hope of making money. We want to answer questions - collectively- and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
<br />
http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
http://www.youtube.com/watch?v=3VjE1zddXWk<br />
http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
http://www.youtube.com/watch?v=egY-Br_oTHE<br />
http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
<br />
<br />
== Meeting Announcements and Contact Information ==<br />
<br />
''Next Call: 1/27/13 8:00pm PST/10:00pm CST''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2050Phage therapy2013-01-23T18:28:03Z<p>208.87.217.74: </p>
<hr />
<div>== Introduction ==<br />
This project was established with the desire to better understand and characterize bacteriophages from antibiotic-resistant, sexually-transmitted, bacterial pathogens with the hope of developing prophylactics and therapies to stop the spread in STDs.<br />
<br />
The development of bacteriophage therapies for antibiotic-resistant, sexually-transmitted infections is becoming increasingly important with the rise in bacterial resistance to 3rd-generation antibiotics.<br />
<br />
<br /><br />
== Sexually Transmitted Bacterial Infections ==<br />
:<br />
== Antibiotic Resistance ==<br />
:<br />
== Bacteriophages ==<br />
:<br />
<br />
== Design of Experiments ==<br />
:<br />
== Laboratory Needs ==<br />
:<br />
== Social Project Goals and Community Agreements == <br />
<br />
:Throughout the course of this project, participants will co-create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community and scientific creativity.<br />
<br /><br />
<br /><br />
:Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender, race, age, accreditation, education, class, or access to resources. We stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of '''mutual respect''', '''compassion''' and '''safety'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments, data interpretation, and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: Our social goal is the pursuit of medical knowledge. We are not approaching this project with the hope of making money. We want to answer questions - collectively- and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free''' and '''accessible'''!<br />
<br />
<br />
== Relevance ==<br />
<br />
http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
<br />
== Resources ==<br />
'''Here are some videos to review'''<br />
<br />
http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
http://www.youtube.com/watch?v=3VjE1zddXWk<br />
http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
http://www.youtube.com/watch?v=egY-Br_oTHE<br />
http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen<br />
<br />
<br />
== Meeting Announcements and Contact Information ==<br />
<br />
''Next Call: 1/27/13 8:00pm PST/10:00pm CST''<br />
<br /><br />
<br />
: if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2048Phage therapy2013-01-23T18:12:51Z<p>208.87.217.74: </p>
<hr />
<div>== Introduction ==<br />
<br /><br />
<br />
<br />
== Meeting Announcements and Contact Information ==<br />
<br />
''Next Call: 1/27/13 8:00pm PST/10:00pm CST''<br />
<br /><br />
<br />
== Social Project Goals and Community Agreements == <br />
<br />
<big>Throughout the course of this project, participants will help create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community scientific creativity.</big><br />
<br /><br />
<br /><br />
Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender; race; age; accreditation; education; class; or access to resources. We will stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of mutual '''respect''', '''safety and understanding'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: Our social goal is the pursuit of medical knowledge. We are not approaching this project with the hope of making money. We want to answer questions - collectively- and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free and accessible'''!<br />
<br />
<br />
== Relevance ==<br />
<br />
http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
------------------<br />
<br />
<br />
'''Here are some videos to review'''<br />
<br />
http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
<br />
http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
<br />
<br />
http://www.youtube.com/watch?v=3VjE1zddXWk<br />
<br />
http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
<br />
<br />
http://www.youtube.com/watch?v=egY-Br_oTHE<br />
<br />
http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
<br />
http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
<br />
http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=2047Phage therapy2013-01-23T18:12:19Z<p>208.87.217.74: </p>
<hr />
<div>== The isolation, characterization and pre-clinical screening of novel bacteriophages as therapies for antibiotic resistant, sexually-transmitted bacterial infections. ==<br />
<br /><br />
<br />
<br />
== Meeting Announcements and Contact Information ==<br />
<br />
''Next Call: 1/27/13 8:00pm PST/10:00pm CST''<br />
<br /><br />
<br />
== Social Project Goals and Community Agreements == <br />
<br />
<big>Throughout the course of this project, participants will help create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community scientific creativity.</big><br />
<br /><br />
<br /><br />
Those participating in this project adhere to the following statements:<br />
: <br />
''We are Non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender; race; age; accreditation; education; class; or access to resources. We will stand in solidarity against oppression and hierarchy.<br />
<br />
''We believe in open access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of mutual '''respect''', '''safety and understanding'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''We believe in full Consensus'': <br />
: We believe scientists should be open to discussion around research experiments and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''We believe in asking (and answering) questions'': <br />
: Our social goal is the pursuit of medical knowledge. We are not approaching this project with the hope of making money. We want to answer questions - collectively- and serve our communities. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free and accessible'''!<br />
<br />
<br />
== Relevance ==<br />
<br />
http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
------------------<br />
<br />
<br />
'''Here are some videos to review'''<br />
<br />
http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
<br />
http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
<br />
<br />
http://www.youtube.com/watch?v=3VjE1zddXWk<br />
<br />
http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
<br />
<br />
http://www.youtube.com/watch?v=egY-Br_oTHE<br />
<br />
http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
<br />
http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
<br />
http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=1963Phage therapy2013-01-21T20:30:28Z<p>208.87.217.74: </p>
<hr />
<div>== The isolation, characterization and pre-clinical screening of novel bacteriophages as therapies for antibiotic resistant, sexually-transmitted bacterial infections. ==<br />
<br /><br />
<br />
''Next Call: 1/27/13 8:00pm PST/10:00pm CST''<br />
<br /><br />
<br />
== Social Project Goals and Community Agreements == <br />
<br />
<big>Throughout the course of this project, participants will help create and foster an open access citizen science project that accomplishes specific scientific goals while educating and nurturing community scientific creativity.</big><br />
<br /><br />
<br /><br />
Everyone participating in this project agrees to the following:<br />
: <br />
''We are non-hierarchical'': <br />
: We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, denies access to science, and holds back global scientific development. As a collective of citizen scientists working toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and gender; race; age; accreditation; education; class; or access to resources. We will stand in solidarity against oppression and hierarchy.<br />
<br />
''Open Access and transparency'': <br />
: Everyone is invited to participate in and learn from this project. We will always make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to a value system of mutual '''respect''', '''safety and understanding'''; while accepting that these values will be '''enforced via community-based decision making'''.<br />
<br />
''Decision-making'': <br />
:'''Consensus'''; we believe scientists should be open to discussion around research experiments and project directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''Answering Questions'': <br />
: Our social goal is the pursuit of medical knowledge, we are not approaching this project with the hope of making money; we want to answer questions - collectively- and serve humanity. We will stand in solidarity against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free and accessible'''!<br />
<br />
<br />
<br />
<br />
if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
------------------<br />
'''Relevance'''<br />
<br />
http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
------------------<br />
<br />
<br />
'''Here are some videos to review'''<br />
<br />
http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
<br />
http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
<br />
<br />
http://www.youtube.com/watch?v=3VjE1zddXWk<br />
<br />
http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
<br />
<br />
http://www.youtube.com/watch?v=egY-Br_oTHE<br />
<br />
http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
<br />
http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
<br />
http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen</div>208.87.217.74https://newweb.sudoroom.org/mediawiki/index.php?title=Phage_therapy&diff=1960Phage therapy2013-01-21T19:57:07Z<p>208.87.217.74: </p>
<hr />
<div>'''<big>The isolation, characterization and pre-clinical screening of novel bacteriophages as therapies for antibiotic resistant, sexually-transmitted bacterial infections</big>'''.<br />
<br /><br />
<br />
''Next Call: 1/27/13 8:00pm PST/10:00pm CST''<br />
<br /><br />
<br />
'''<big>Social Project Goals</big>''': <br />
<br />
*Create and foster an open access citizen science project that accomplishes specific project goals while educating and nurturing community scientific creativity.<br />
<br />
*'''Community Agreements:'''<br />
<br />
''We are non-hierarchical'': We recognize the outcomes of hierarchy. Hierarchy represses creative thought in science, <br />
denies access to science, and holds back global scientific development. As a community of citizen scientists working <br />
toward a more complete understanding of molecular medicine, we commit ourselves to nurturing creative, positive voices <br />
within our community. We commit ourselves to hearing everyone and refuse to acknowledge hierarchy based on: sex and <br />
gender; race; age; accreditation; education; class; or access to resources. We will stand in solidarity against <br />
oppression and hierarchy.<br />
<br />
''Open Access and transparency'': Everyone is invited to participate in and learn from this project. We will always <br />
make time for conversation and teaching opportunities. Online meetings, communications regarding this project, and <br />
all findings will be publicized on this fully-editable wiki with the stipulation that those participating adhere to <br />
a value system of mutual '''respect''', '''safety and understanding'''; while accepting that these values will be <br />
'''enforced via community-based decision making'''.<br />
<br />
''Decision-making'': '''Consensus'''; we believe scientists should be open to discussion around research experiments,<br />
and directions. To foster a spirit of openness and understanding, no decision will be made without 100% consensus. <br />
<br />
''Answering Questions'': Our social goal is the pursuit of medical knowledge, we are not approaching this project with<br />
the hope of making money; we want to answer questions - collectively- and serve humanity. We will stand in solidarity <br />
against anyone who chooses to co-opt or privatize any portion of this project. All knowledge must be '''free and accessible'''!<br />
<br />
<br />
<br />
<br />
if you'd like to attend the conference call, please contact: Craig (moleculararts [at] riseup [dot] net)<br />
<br />
------------------<br />
'''Relevance'''<br />
<br />
http://www.smithsonianmag.com/science-nature/phenom_oct00.html?c=y&page=1<br />
------------------<br />
<br />
<br />
'''Here are some videos to review'''<br />
<br />
http://www.youtube.com/watch?v=LiPZq2K_Tos&NR=1&feature=endscreen<br />
<br />
http://www.youtube.com/watch?v=ehbZpo8oXSs<br />
<br />
<br />
http://www.youtube.com/watch?v=3VjE1zddXWk<br />
<br />
http://www.youtube.com/watch?v=ZENpYdQg-z4<br />
<br />
<br />
http://www.youtube.com/watch?v=egY-Br_oTHE<br />
<br />
http://www.youtube.com/watch?v=Oms5SA_4-kE<br />
<br />
http://www.youtube.com/watch?v=3eQhNyX7DRQ<br />
<br />
http://www.youtube.com/watch?v=lUcMGktSc7c&NR=1&feature=endscreen</div>208.87.217.74