March 19

Poster Edits 3/18

Rationale: Create figures to represent In-Silico results for the class poster that will be presented at URSA.

Procedure: Groups were created to work on different parts of the poster. Figures and questions were brought up on what figures would best represent the In Silico Results. Work was started to collect data and not all figures were completed.

Results: The figures for the In Silico Results section were started. Questions were brought up on some figures on which figures were needed to best represent the In Silico Results.

Conclusions: Phage notes for NapoleonB were uploaded onto a text file and a program was created to help see the uniqueness of NapoleonB genome compared with all other AM cluster phages.

Future Work: Continue to search through PhageDB and how NapoleonB is a unique AM cluster phage to best represent the In-Silico results for the class poster.

 

Category: Michael Lum | LEAVE A COMMENT
March 18

March 18 2019 Poster Editing

Purpose: The purpose of this lab is to edit the poster for Scholars Week.

Tools/Procedures:

Tools:

  • Poster
  • DNA Master
  • Phage Notes
  • Excel

Procedures:

  1. Groups were created to work on different elements of the poster.
  2. Figures were designed to display the In Silico Results, such as gene function.
  3. Work was started to collect the data for the figures. Not all figures were completed.

Results:
The figures for the In Silico results were started,  but not all of them are finished. Other elements of the posters were also edited by other groups.

Conclusions:
In conclusion, the poster was not finished, but many elements of the poster were edited. The In Silico figures will need to be finished and added to the poster.

Future Work:
Future work will include finalizing all figures for the poster. Also, once all of the elements of the poster are added, the poster will need to be edited to ensure it has the proper layout.

Category: Lucy Potts | LEAVE A COMMENT
March 18

Using Databases to Graph Results 3/18/19

Rationale: In order to collect the  data needed to create a graph to display the comparison between the amount of AM phages that are a member of a pham against non-AM phages that are members I need data from the phamerator and phagesDB databases.

Tools: Excel, DNAMaster, phagesDB, Phamerator, Javascript, Meteor, MySQL, CLion, Purdue Robotics Operating System(PROS)

Procedure:

1. Loaded the phagesDB database into Excel to test to see if I could access the pham data from there. That ended up not working.

2. Went to phamerator and started analyzing  code of the website using Meteor, Javascript, and PROS. Meteor is built on Javascript and is what phamerator is built with.

3. Exported the pham map of NapoleonB as a .svg file then used Atom to change it in to a text file that could be parsed using a C script.

4. Gave the parameters to parse by to Rachel to write a code in CLion to locate the gene number, pham, and total members in the pham.

Results:

N/A

Conclusions and Future Work: There is still much more digging that I need to do to get all the data required. Over the coming days I will analyze more code to find where the database call is in the phamerator code.

 

Category: Sriram Avirneni | LEAVE A COMMENT
March 18

Forgotten Cure pt2 3/18/19

  1. In the 1940s, Winston Churchill, Josef Stalin, and Franklin Delano Roosevelt agreed to introduce antibiotics to the USSR in order to generate more antibiotic production sites during the war. Because this was funded by other countries, it worked temporarily. After the war, however, the USSR had to rely on their own resources to fund antibiotic production and the state funding system was no help to this. The state’s priorities very much played a role in medicine in the following years. The political climate at the time prompted the Russian state to direct their priorities to weapon manufacturing and pushed medicine aside. This resulted in insufficient supplies of antibiotics in hospitals which were in high demand once the population caught word of the new medicine. To cope with this, the state manipulated the population by presenting antibiotics as foreign compared to the traditional natural remedies that were far cheaper. This set the stage perfectly for an increase in bacteriophage use.

 

  1. Ludwik Hirszfeld and his family were some of the many Jewish Poles sent to a ghetto occupied by Russia. There, Ludwik had a medical background which he continued to exercise in the ghetto. He and his family were able to escape and survive with false documents, but his daughter fell ill and died, a tragedy that left Ludwik feeling very distraught about his life work and the political situation he had been forced into where his family could not even go by there real names. Ludwik then moved to Wroclaw and became dean of the medical school. At the time, the Stalin supported idea of Lysenkoism, that genes did not exist and acquired traits were inherited proved to be an obstacle for Ludwik who’s studies were based off genes. He feared for his own persecution until Stalin’s sudden death, which actually enable him to start his own institute. The institute then became a leading center for phage therapy. This is starkly different from the Elavia institute in which Russian politics also played a part. The Eliava institute had been widely successful across the soviet when antibiotics were too expensive and more traditional, cheaper medications were favored by the state. However, when the soviet disbanded, there was not enough cliental to sustain the institute and it fell apart. I think the differences in success exist because Eliava Institute was located in Russia which became very unstable after the war. Hirszfield was located in Poland and was able to receive support from European Union.

 

  1. Merrils early experiments were hampered by the livers and spleens of the mice he was testing. Phages that he introduced into their systems were quickly rendered useless caught inside these organs. He hypothesized that this was the reason phage therapy had historically received poor scientific support. To breed more effective phages that could evade the liver and spleen he tested lamda phage on mice. Lamda phage was chosen because it was the most well known phage and had the most background information available. Lamda was inserted into the mice and then bacteriophages were harvested from the blood stream hours later. These harvested phages were reinjected into mice and the same process was repeated 8 times. In the end, Merril had a wild type phage that could avoid the liver and spleen with a survival rate 1000 times higher than the parent phage. The paper that Merril and his team published showed that over the course of 25 hours, the derived phages named argo1 and argo2 began at a higher concentration in the blood stream and decreased concentration at significantly slower rate. When different groups of mice were injected with the parent strand in comparison to argo1, both phages rid the mouse of disease when the control group resulted in death. The main difference was the effectiveness of the injection. Argo1 was more effective and the mice reached recovery sooner and had symptoms that did not go much past the 1 rating whereas the mice injected with the parent strand showed symptoms up to the 3 rating.

 

  1. GangaGen is a startup company developing ectolysins or highly-specific therapeutic proteins to target bacteria. Their leading ectolysin, p128, is a derived from a phage and can rapidly degrade a bacteria’s cell wall with only making contact with the outside and not having to enter the cell. In order to effectively test p128 by FDA standards, the drug must be administered in three different phases, showing promising results from each one. It must be delivered alongside a control to measure progress, and also used at various concentrations to farther measure effect. It would probably work in GangaGen’s favor to attempt combination trials to see if results could reach an even higher level of effectiveness.
Category: Rachel Melone | LEAVE A COMMENT
March 18

The Forgotten Cure Chapters 5-8

Russia’s state health care was not very good and often the things that doctors and patents needed were not always available. The book mentioned that in Russia they didn’t always have the means to produce all of the antibiotics that were produced in other countries. Often, they would be able to stock a far smaller variety of antibiotics and a smaller quantity of those antibiotics. This meant that the medicine that was need at times was not always available and alternatives needed to be used. Russia itself pushed for the use of herbal medicine to make up for the medicine that they didn’t have. Phage therapy also became more popular and was sometimes used in place of the antibiotics that doctors didn’t always have available.

The outcome of these 2 centers is very different because Eliava Institute was successful in the beginning and its initial struggles were a result of financial collapse. Hirszfelds Institute had different struggles and that was mostly persecution. There is also the perception from the outside world that is different. The Eliava Institute does not focus on bringing this research to people around the world as much as the Hirszfelds Institute does. Also, Eliava Institutes has some stigmatism of Russian medicine attached to it so people may be more wary of it than if it were coming from Hirszfelds Institute.

They first used lambda phage they isolated a sample to help the phage get past the liver and spleen by first tang blood samples from the animals. They then increased the amount of phage present in that sample and reinjected the sample back into the organism. They did this several times before they had a sample of phages that were the most specific to the organism and disease they were combating. Mice were then injected with E. coli and three groups were created one where the original sample of phage was used, another where the new sample was used, and a control group. They then recorded the results of their experiment.

Phage therapy has more of a market now especially since scientists and doctors are becoming increasingly concerned about antibiotic resistance and superbugs. Phage therapy could be used with antibiotics to increase their effectiveness when against a bacteria that is resistant to it. There are also other cases that phage therapy can become more of a use for one example is my grandma who is not able to take antibiotics. My grandma a couple of years ago got sick and while she got better she s unable to take antibiotics anymore. This is because I believe the bacteria is still n her body just in an amount that is not dangerous at the moment but would become dangerous if she were to take antibiotics. I believe that the research that needs to be done on phage therapy could include how effective it is against superbugs as well as researching quicker ways to be able to produce a phage sample specific to the strain of disease a patient has.

Category: Emily Balint | LEAVE A COMMENT
March 18

The Forgotten Cure 2

1. The USSR had a state controlled system of health care. During the cold war, since a lot of money was going into the arms race, there wasn’t anymore ability for the government to supply antibiotics. Therefore, phage therapy became a more popular solution to the issue of bacterial infections. Also, antibiotics were mostly being shipped from the western market, so antibiotics were dissuaded against using propaganda.

2. Stalin was a big proponent of Lysenkoism, which stifled scientific research greatly for Hirszfield. Furthermore, due to the Jewish lineage of Hirszfield and his associates  and the persecution of Jews at the time in Poland the Hirszfield institute was severely stifled in their ability to release any of their research in comparison to the Eliava institute. However, after Stalin died, the Polish government supported the Hirszfield institute. The Eliava institute on the other hand received more support during the war in order to develop therapies for soldiers in war. Later when the Phage Therapy Center opened up they differed in their support as the PTC has access to the research funding pooling effort of the European Union. This contributes to a large portion of research funding of almost all labs in the EU.

3. Merril treated mice with different versions of Lambda phage: the parent strain, Argo1, and Argo2. After the phage had been in the blood stream for some time she took blood samples and isolated the phages from the samples. She grew and propagated the phages then repeated the process for a total of 8 times. The result was  phages that were able to be injected in mice and survive filtration and kill bacteria. They tested the effectiveness on rats infected with E. Coli and Argo1 and Argo2 resulted in a drastic reduction in symptoms.

4. I personally feel like the biggest limiting factor to phage therapy in western medicine is the immense R&D cost preventing initial profit to keep a start-up going. That’s why the current system in place for some of these companies looks extremely promising for getting to the point where we can start producing phage therapy. First R&D needs to go into a more readily understood product such as in the case of EBI production of certain peptides for therapeutic use. The sale of said product can then be used to fund the research into phage therapy. What needs to be researched in my opinion is efficient means of production for phage therapy, as the first issue for any and all new products is development cost. To encourage more research to go into more effective therapy, research into more effective production must occur.

Category: Sriram Avirneni | 1 Comment on The Forgotten Cure 2
March 18

The Forgotten Cure 2

The USSR after WWII had their problems, they were struggling to provide enough antibiotics to the general public. To make up for the lack of mainstream treatment, the government promoted natural treatments such as herbs, since they are from “Here”. Another appeal to the alternative treatment of phage therapy is the low cost, comparing to the manufacture of antibiotics, phage vials were easier and cheaper to produce on a large scale. With the government’s attempt to discredit “Western drugs” such as antibiotics and to promote alternative treatments, phage therapy was used commonly in the Soviet Union.

The major reason that contributed the two different outcomes for the respective research centers is that the political climate of the USSR and its satellite countries, since the collapse of the USSR, the Eliava Institute lost funding and demands for phage therapy. On the other hand the Phage Therapy Center was able to flourish primarily due to the death of Stalin, and later on, Poland joining the EU. However, both institutes contributed greatly to phage research.

In order to find a phage strain that could effectively evade the entrapment of the RES, the team first grew phage on the WT bacterial strain CRM1 and the mutated type CRM2(the strain was used in hopes of inducing the mutations in phage lambda), then they injected the mice with phage and collected blood samples after 7 hrs. The phage collected in the samples were purified and amplified and reinjected into a mice, the experiment was repeated until they the phages injected into the system remained a high concentration after 18 hrs.

The consideration of using phage therapy in most cases is to counter antibiotic-resistant bacterial strains. But these newly founded companies look to develop treatments that utilize phages to potentially cure diseases, not to just be the alternative treatment to bacterial strains with drug resistance. An important concept for phage therapy mentioned in the book is that if you can get the right phage to the right pathogen it’ll work, developments and expansions of phage therapy should look to this as their guild lines, besides finding more phage strains to add to the ever-growing library constructing a way for labs to find the right phage strains faster and amplify them for patients is much more important from my perspective. For more phage therapy treatments to be approved more tests and trials have to be performed, one of the most important experiment is the double-blind test, with a large enough sample size and the right methods(double-blind) the results of phage therapy can be backed up with solid data, even though the book mentioned the villages that excepted treatment and the ones that didn’t have vastly different mortality rate tests with a more rigorous setting is essential. Trials aside proper PR is very important since the discovery of antibiotics phage therapy has faded into the background, hence the name “The Forgotten Cure”, more noise promoting the upsides of phage therapy might help investors to hear about and gain confidence in this resurrected field of treatment.

Category: Yang-En Yu | LEAVE A COMMENT
March 18

3-18-19 — The Forgotten Cure Part 2

1. How did having a state health system influence the treatment of infectious disease in 1940s-50s Russia?  

One of the most important outcomes of the USSR having a state health care system was a focus on alternatives to antibiotics. Given the Russian culture of using natural remedies, the cost of antibiotics, and the association of antibiotics with major western countries, it was easy for the country and its doctors to switch to phage therapy, as it was natural, not costly, and was notably different from the antibiotic route the western countries were taking.

2. The Hirszfeld Institute is also intertwined with Russian history.  A tragic quote is given on page 66 by Hirszfeld about the death of his daughter.  Even so, the outcome of these 2 centers has been very different.  Discuss why you think this is so.
Contrast the Phage Therapy Center in Wroclaw with the Eliava Institute in Tbilisis.

Both the Hirszfeld and Eliava Institutes were medical institutes whose founding shared a place in history with WWII. Although they both focused on phages and both involved being shadowed by regimes, the Hirszfeld Institute was successful while the Eliava Institute was not. This is partially due to their geographical locations. The Eliava Institute in Tbilisis was in a much smaller country with much less funding and control, and thus failed in the end. The Hirszfeld Institute was in Poland, a much larger country with more say in the western world. The location of this institution made it easier for it to receive funding for its specialized pursuits of bacteriophage research and immunology.

3. Research in the USA often differs from other countries because of regulations by the FDA and private investments.  Describe the experimental design that Merril used to determine how to select for phages that were not removed by the liver and spleen. Review the Merril, Carlton, and Adhya PNAS paper, focusing on interpreting their figures.

Merril and his team took lood samples from animals, isolated the phage present, and injected them into mice. This process was repeated a number of times until their survival rate was much higher. These phages were named Argo1 and Argo2. Four mice were taken and injected with a lethal dose of bacteria. The mice that were injected with Argo1 and Argo2 were made slightly sick before recovering, the mouse that was treated with Lambda phage had a slightly more severe illness, and the mouse that went untreated died in two days. This supported his hypothesis of the relative strengths of passaged versus unpassaged phages.

4. The most convincing argument for using phage is tied to the increasing problem of antibiotic resistance.  Even so, many still consider phage therapy an alternative therapy.  Chapter 8 describes several start-up companies: Phage Therapy, Phage Biotics, GangaGen, Exponential Biotherapies.  Research these companies and discuss the potential for phage therapy in modern Western medicine. What experiments need to be done?

Although phage therapies are very promising, one major problem that most of these companies have in common is that they don’t follow the rules and regulations set out by the American government. Since they don’t follow the proper protocols, it’s impossible for them to make much progress in America. Because of this, western doctors are distrusting of the capabilities of phage therapy. A phage therapy institute has recently been opened in California, which shows promise since it would have to operate under American protocols and hopefully gain credibility. Large experiments with control groups following proper American protocol have to be performed in order to gain more support and credibility in the States.

Category: Brandon Reider | 1 Comment on 3-18-19 — The Forgotten Cure Part 2
March 18

Forgotten Cure 2

  1. How did having a state health system influence the treatment of infectious disease in 1940s-50s Russia?
  • After World War II, the funding which the West provided to the East for the increase in the use of antibiotics was stopped which forced the Soviet Union to rely on their own minimal resources. Because of the withdrawal of funding, the Soviet Union government urged the citizens to use homemade remedies rather than the ones created in the West as it made a connection of herbal medicines to loyalty to the country. Also, the drug supply problem came about from the lack of funding by the state. Although it was universal health care, the state did not provide an adequate amount of resources to fulfill the demands of providing a universal health care system. As there has a been an integration of homemade remedies in the culture, it has become an important part of treatment as it serves as a backup for when standard medicine fails to work.

 

  1. The Hirszfeld Institute is also intertwined with Russian history. A tragic quote is given on page 66 by Hirszfeld about the death of his daughter.  Even so, the outcome of these 2 centers has been very different.  Discuss why you think this is so.

 

  • The Hirszfeld Institute, despite the sad history behind the formation of the institute, became known in western Europe for a wide range of research conducted. The history began with L. Hirszfeld, a man born in Warsaw which was then Russian occupied territory. He suffered through the Holocaust and the loss of his daughter in that process. After surviving through the war, Hirszfeld and his wife settled in Wroclaw where he accepted to be the dean of the medical school. During this time, he rebegan his research on blood groups and began mass research and treatment of syphilis. In 1952, he petitioned to open an institute dedicated to immunology within the medical school. The acceptance of the request was slowed by the popularity of the idea of Lysenkoism, a belief that acquired characteristics were inherited. Then, there was a large-scale accusation that Jewish doctors were poisoning Soviet Union officials. This all ended with the death of Stalin, then Hirszfeld’s wish was granted. The institute is now modern and well-staffed, with over 300 employees. The Phage Therapy Center in Wroclaw views phages to be promising in situations where the use of antibiotics has not worked as the treatment. The Eliava Institute in Tbilisi was founded in 1923 by Prof. George Eliava along with the assistance of Felix D’Herelle who first discovered the presence of phages. However, due to Stalin Terror, Eliava was executed in 1937 and D’Herelle never returned. During the reign of the Soviet Union, the Institute prepared and manufactured products that treated almost all major bacterial and viral diseases. The outcomes of both institutes differed due to the possibility that the circumstances both institutes faced regarding the history of the time.

 

  1. Research in the USA often differs from other countries because of regulations by the FDA and private investments. Describe the experimental design that Merril used to determine how to select for phages that were not removed by the liver and spleen.

 

  • To select phages which are not immediately removed by the liver and spleen, Merril and his team injected phage that was active against a strand of E. coli into the stomach of mice. After several hours, Merril and his team took samples of blood and isolated the phage that were still present them reinjected them into the mice. After repeating this task 8 times, Merril and his team managed to isolate several phages which had the ability to survive in the liver and spleen for more than 18 hours. The paper published discussed the overall methods used to test their hypothesis and their results. The figures illustrate the actions of Argo1 and Argo2 with different sets of conditions to determine which experimental set provided the best option.

 

  1. The most convincing argument for using phage is tied to the increasing problem of antibiotic resistance. Even so, many still consider phage therapy an alternative therapy.  Chapter 8 describes several start-up companies:

Phage Therapy, Phage Biotics, GangaGen, Exponential Biotherapies.  Research these companies and discuss the potential for phage therapy in modern Western medicine. What experiments need to be done?

 

All the companies mentioned are focused on developing therapeutic treatments using phages that are found within the environment. These companies may be working on developing a treatment which addresses the widespread of multiple strains of bacteria being resistant to antibiotics. There is potential for phage therapy in that because there is an increasing problem of resistance to antibiotics, phage therapy can prove to be an option of treatment. Some experiments which need to be done are ones that allow scientists to understand which family of phages work as treatment against a specific strain of bacteria.

Category: Sabin Patel | 1 Comment on Forgotten Cure 2
March 18

the forgotten cure 2

  1. Due to having a state health system, which means that all health care services were provided free by the government, it caused citizens to turn more towards alternative medicines, because the USSR was unable to provide adequate and quality antibiotics due to lack of funding. So this made people turn to herbal supplements and phage therapies as a way of curing their ailments. 
  2. The Phage Therapy Center in Wroclaw is a well staffed, a modern building, with many phage samples, and is well funded. They also have proper security for the phage samples. The Elivia Institute on the other hand is lacking funding, and was falling apart…the walls were cracked, and it is a small facility with about 10 individual labs. Some scientists will use the grant money they receive to update the labs conditions, or they themselves will paint and renovate their labs. I believe these 2 institutes have had very different outcomes based on their location and the government they are under. For example the Elivia Institute was thriving before the collapse of the Soviet Union, but now with little funding, they are struggling, and so are the wages of the scientists who work there. While the Phage Therapy center is based in Wroclaw, an area with a booming economy, under Polish rule. Ultimately, this also boils down to the fact that the Phage therapy center gets funding from the West as well, was the Elivia Institute does not.
  3. Merril’s experiment involved injecting lambda phage that kill E.coli into the stomach of mice. After 7 hours he then drew a blood sample and isolated the phages that were still present in the blood, then produced more of them, then re-injected them back into the mice. This is called “serial passage”, and this process was repeated 8 times until a phage that could last 18 hours in the blood stream was achieved. In their research paper, one can see they tested Argo1, Argo2, and a wild type phage. The results showed that argo1 and 2 both last in higher concentrations much longer, than the wild type.
  4. One really large issue plaguing Western medicine right now is “super” bacteria, or bacteria that has developed resistance to all/many antibiotics. Phages would be a great way to combat such bacteria, but some testing would need to be done to determine what happens when that bacteria becomes resistant to the phages being used. Also phages can be used to treat cancer and induce anti-cancer micro environments. This is still being tested and developed though. 
Category: Lauren Foley | 2 Comments on the forgotten cure 2