Rationale:

FInalizations for the poster were discussed then corrected.  Then, each group was assigned to a team leader and work on the independent project began.

Tools:

• Personal Computational Device

Results:

• After the discussion of the small things that needed to be fixed on the poster was done, each group found out their team leader and then gathered in their groups to begin the independent project.
• First, the group discussed potential questions that can be tested with the provided databases. A page was provided to act as a guide for the formation of the question.
• Each individual of the group decided to pick their favorite topic then to do more research on their possible question.

Conclusion

After the poster discussion, groups were assigned to team leaders and then gathered to think of possible questions.

Future

To come to an agreement with the group on which question would be best

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.

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.

• 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.

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.

• 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.

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?

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.

Rationale: The posters were presented to the class and a vote was made to decide which poster was the best for the overall template and certain parts from other posters were taken to be put into the most voted one.

Tools:

• Posters

Results:

• After presentations were given, the groups gathered together and discussed which poster had the best layout along with which had better figures, introduction, discussion, etc.
• The class voted on poster 4 to be the overall template.
• As a class, aspects from other posters were pulled to be added to poster 4.

The Most Voted Poster

Other Posters

Conclusion:

Presentations were given and a vote was made on which poster should be the final layout. After the vote, parts from other posters were pulled to be added into the voted poster.

Future:

Work will be done to finalize the poster.

Rationale:

The posters were finalized with the ideas of the assigned groups and that of another group. Together, the poster was completed and submitted.

Tools:

• Computational Device
• Rough Draft of Poster
• Google Slides

Results:

• With the template of one group and the figures of another, the components of both posters were put together.
• The discussions and introduction were made shorter in order to fulfill the guideline of a minimum of 28 font size.
• The figures were retouched in order to make them more clear and easy to view.

Conclusion:

The posters were finalized with the ideas from two groups: one with the template, introduction, references, and acknowledgments, and the other group provided the figures and discussions. Upon the addition of the other group’s ideas, the text boxes and other small details were finalized then submitted.

Future:

The two groups will present the poster to the class.

Rationale:

From the templates made last class, a rough draft was made with a computational device along with the addition of the text for the introduction, discussions, and texts besides the figures.

Tools:

• Computational Device
• Template
• Google Slides

Results:

• A rough draft of the scientific poster was made in google slides.
• The introduction, discussions, and texts were all completed.

Conclusion:

With the template, the rough draft of the poster was made with Google slides.

Future:

The best poster will be chosen.

Rationale: Groups were made for the individual research group and rough drafts of the scientific posters were made.

Tools:

• Examples from previous years
• Paper and Pencil

Results:

• Groups were assigned then a template was made for the scientific poster.
• The main focus of the template was for it to be symmetrical along with a good color scheme.
• The results of each lab were divided into the “wet lab” and the “in silico lab.”
• The abstract was left out as it took up too much space.

Conclusion:

Because it was decided that the best template provided symmetry and color scheme, the template was based on that idea.

Future:

With the template, a rough draft of the poster will be made with the usage of a computational device.

Rationale:

The genome was looked over to make sure that every gap was accounted for in order to make sure each function was found. To check, databases such as NCBI, PhagesDB, GeneMark, and Phamerator were used to recheck the annotation for the genes. Also, an introduction to research posters was made.

Results:

• FIrst, the entire genome was looked over as a class to check and make sure that each gene reached it’s longest open reading frame.
• While the class skimmed over the genes, several genes had massive gaps between them and the previous genes which led to the genes being checked with the help of the databases to make sure that it was the best open reading frame.
• After the genome was checked and corrected, an introduction to posters was made which discussed the importance of small, certain aspects on the overall presentation.
• The class divided into the groups and discussed which aspect of the posters was the most important and what final preparations needed to be made before the posters were made.

Conclusion:

As a class, the genome was looked over to make sure that gaps were covered and some discussion occurred as to why some gaps could not be covered. Along with that, the small details of symmetry and figures in posters were discussed in class. Groups from previous class rejoined to discuss the importance of certain aspects of the poster.

Future:

The class may be divided into groups for individual research projects.

Rationale:

Groups were made and assigned to correct and go over the assigned gene to make sure that there were no mistakes in the annotation. Also, the groups were assigned to finalize an abstract through the addition of each group members abstract into the final abstract.

Tools:

• Personal Computational Device
• DNA Master
• NCBI
• PhagesDB
• Phamerator

Results:

• The group was assigned gene 96 and to elongate the gene was much as possible to obtain a better reading for the function.
• Different frames were tried out to determine if the function changed based on the results from the coding potential on GeneMark.
• One coding potential was the best within the frame; however, it overlapped with the next gene.
• After it was decided that no other gene was able to fill the whole coding potential, the original gene was kept.
• The original gene was kept and the abstracts were finalized by the incorporation of every group members part of their abstract into the final one.

Conclusion:

Groups were created to correct the genes which were assigned. The group was told to look over the large gap between gene 95 and 96 and to determine if the gap can be coded with the addition of new genes. New genes were created in the forward and the reverse in order to achieve the best coding potential, but it was later decided that the original gene had the best coding potential. Also, abstracts were revised to create a final abstract with the abstracts of all the group members.

Future:

Questions for the individual projects will be decided along with the structure of the poster.

Towards the beginning of the century, little to no knowledge was recorded of the presence of bacteriophage within the vast biosphere of our world. The exciting world of bacteriophages was brought about when Felix d’Herelle. D’Herelle developed a love for microbiology at a young age, but his decision to delve into field work when he noticed that he remained calm when he witnessed multiple people dying from yellow fever. He never received higher education in the sciences but he was self-taught. Due to his lack of education, he went straight into fieldwork. While working at the Pasteur Institute, he discovered bacteriophages on accident. He was observing locusts when he noticed clear spots on the cloudy background. His curiosity led him to have a desire to further study the strange event but he was unable to begin. His understanding of the strange spots began when he was ordered to analyze samples from the troops to detect any new form of the virulent infection. It was during this time that he observed that the strange spots appeared again; therefore, he was unable to claim these results were insignificant. One patient that entered the hospital in the Pasteur Institute was monitored for their progress through her illness and also through her recovery to locate the clear spots from her stool. Using different methods such as filtration and plates, he observed that the plate contained only dysentery bacteria after several days. After this observation, he was definite that a particle smaller than bacteria existed. After publishing his first paper, he faced a lot of controversy such as numerous explanations to reason that no such thing exists. The controversies behind phages continued into the early 1940s, but that did not prevent d’Herelle from visioning the potential behind bacteriophages against diseases in living organisms. Through numerous experiments on those who are sick, he received successful results from the insertion of bacteriophages within those who were infected with virulent diseases. After several years of moving around to promote the usage of bacteriophages as a weapon against virulent diseases, d’Herelle received an invitation from Georgi Eliava to establish a center in Tbilisi. Eliava entered d’Herelle’s life at a low point in his life. They both shared many things in common such as their passion for phages. However, they also had some differences. Eliava was relaxed and charming while d’Herelle was sharp and businesslike. The differences did not prevent them from becoming lifelong friends. As they were getting ready to open the bacteriophage institute in Tbilisi, Stalin gained control over the government which hindered their development of the center. Because of the growing fear in the Soviet Union, the Eliavas, after having been arrested two time times, were executed. Due to his death, the ties between the bacteriophage institute in the east and those of the west were cut. After d’Herelle’s death, the idea of bacteriophage was still not clearly defined. However, this problem did not leave to the decline in usage of bacteriophage; new medical discoveries were being brought about to prove to be more effective and cheaper such as the company Bayer making a new drug known as sulfanilamide. With increasing medical discoveries, more institutions began to lean towards these new discoveries which eventually led to the field of phage therapy to be forgotten. When the medical field abandoned the usage of bacteriophage, uses were found within other disciplines of science. Two men, Luria and Delbruck, who both found a passion for the integration of biology and physics, discovered the concept of using bacteriophage as a tool for studying genes which gave birth to the field of molecular biology.  With the history of the coming up of bacteriophages, it is really interesting how a man with no higher education was able to test for the presence of particles that make up a vast portion of the biosphere. It was also interesting how scientists have integrated the use of bacteriophages within many disciplines of science.

Rationale:

Upon the completion of the annotation of gene 33, genes 34-36 were annotated with the usage of a variety of programs and databases.

Tools:

• Personal Computational Device
• DNA Master
• NCBI
• PhagesDB
• GeneMark

Results:

• After the annotation of gene 33 was checked, the annotation of gene 34 began after the gene was viewed on DNA Master to determine if it had any gaps or overlaps.
• Because there was a gap, a better reading frame to minimize the gap was attempted to be found but the original was the largest open reading frame.
• From the databases, evidence was gathered to prove the function which showed to have no known function.
• The annotation of gene 34 was shown to be

• After the completion of 34, gene 35 was viewed on DNA Master and it was seen that the best open reading frame was not chosen
• To change the frame, the 5′ base pair was changed to obtain the best frame.
• After the change, the coding potential was viewed which showed that there was no coding potential regardless if the best or original reading frame was chosen.
• The annotation of gene 35 was shown to be

• Gene 36 was then annotated with the same process that was used to determine the annotation of gene 34.

Conclusion:

For this lab, genes 34-36 were annotated and gene 33 was checked. The 5′ end of gene 35 had to be changed to fit the best open reading frame and then the coding potential was viewed on GeneMark. Other than this difference, all the genes required evidence to prove that the function was what it was which was no known function for all the genes.

Future:

Because the annotation for all the genes have been completed and checked, individual research questions will be thought of for the individual projects.