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.

1. In Russia, phage therapy was used readily rather than antibiotics since it was cheaper to use. The USSR control of the health system caused doctors to seek other methods of treatment. Doctors would look at phage therapy for answers since it was cheaper, and the USSR used its money for weapons for the Cold War rather than medicine for its people and soldiers. Since antibiotics were used more in the western world, Russia placed a negative conation towards antibiotics since they were at “war” with western countries powerhouses. This led Russia to focus on treating diseases via phage therapy and the forgotten cure was born in the west.
2. After the death of Hirszfeld’s daughter, he founded Hirrszfeld Institute after many battles with the Soviet Union. The institute had gone through many events with the Soviet Union, and later Hirszfeld would ultimately give the institute to Milgrom. The institute focuses on phage typing. Other institutes such as Eliava institute and Phage therapy center came to do the same thing and helped in different ways to help cure diseases. Eliava institutes research bacteriophages and their potential use as phage therapy to cure diseases, and the Phage therapy center treat the patients.
3. Merril and his team worked on breeding a phage that could evade the liver and spleen. The team injected phage active against a specific strain of coli into stomachs of mice. They chose a specific phage, called lambda since it was a phage that was studied thoroughly by Delbruck. After seven hours of injection, the team took blood samples from animals, isolated the phages, and serial passaged the phage eight times. The survival rate of these new phages was a thousand times higher than phage lambda, and the team called the phages Argo1 and Argo 2. The team then had to see if the Argo1 and Argo2 could actually save mice infected with E. coli. They took four mice, and all injected with a lethal dose of bacteria. Three of the mice were treated with phage and the last one was used as the control of the experiment. The results showed that untreated mice died in two days, those treated with phage survived, and Argo1 and Argo2 had a milder illness compared to the non-passaged strain of lambda.
4. 1 shows the development and partial characterization of long-circulating bacteriophage. Bacteriophages the could avoid entrapment by the RES were developed by selecting phage strains that could remain in the circulatory system of mice for progressively longer periods. The serial-passage experiment’s goal was to increase the incidence of mutation in phage lambda, so as to enhance the probability that one or more of the phages offspring would have properties that permit evasion of the RES. Both Argo 1 and Argo 2 displayed a similar enhanced capacity to avoid RES entrapment. Fig. 2 shows the comparison of long-circulation Argo phage versus wild-type phage as antibacterial agents in an animal model. All the mice were scored based if they showed signs of illness. Mice treated with W60 showed signs of severe illness before recovering, and both Argo1/Argo2 showed signs of minor signs of illness. Mice that were treated with phage all survived. Fig. 3 shows the ability of the phage to influence bacterial infections is dose-dependent. Animals showed signs of illness with a minimum dose of phage and increases in phage doses showed lower signs of illness. Fig. 4 shows the characterization of Argo 1 and Argo 2. The images compare the lambda phage capsid E protein versus the W60 capsid E protein and show an alkaline shift in the Argo 1 E protein capsid.
5. Many companies discussed inThe Forgotten Cure research on how phage therapy is the alternative to antibiotics. Many companies were discussed in inThe Forgotten Cure such as Phage Therapy, Phage Biotics, GangaGen, Exponential Biotherapies. GangaGen is a company where it has done research to show that phage therapy is the alternative to antibiotics. Since phage therapy was the forgotten cure in the western world, many experiments are needed to be done in order to spread phage therapy in the U.S. Phage therapy must be approved by the Food and Drug Administration (FDA). New methods and therapies would have to go through a series of tests set by the FDA, such as the therapy need to be tested on animals before tested on humans. These advancements will help cure the forgotten cure. Companies are looking to find which treatment via phage therapy is the best to cure many diseases. Companies like the Exponential Biotherapies are working towards phage cocktails, to cure acute kidney injury and irradiation damage from cancer therapies.

Rationale: Present group posters for class opinion

Procedure: The 4 group posters were presented to the class. The class initiated the good and the bad of the posters. The posters were voted on to determine the best poster to represent the class at URSA.

Results: Group 4’s poster and this layout will be used to represent. the class overall poster

Conclusion: Groups said the poster was a great balance of words and images.

Future work: This poster will be fixed until it shows a great presentation of the findings discovered in the class at URSA.

Rationale: 

Finish poster designs in large groups.

Procedure: 

Small groups that created a rough draft of the final poster met to form a larger group. Ideas from both groups were used to form the final poster. The poster was compared, the layout was chosen, and the poster was saved as a powerpoint.

Results: 

The final poster was completed.

Conclusions: 

The poster was finished and submitted. Both groups helped yield the final poster. The groups provided graphs and were consolidated into one poster.

Future plan: 

Fix any error in the poster, choose a poster that will best represent the class at URSA, and to present this final poster to the class so this final poster can be in consideration for the poster that will represent the class.

Rationale: Design and create a poster for Scholars Week

Procedures: Google slide was created so that all group members could have access to the poster as the poster design was set. Lab data from NapoleonB soil metadata were obtained, along with other images of the wet lab results of NapoleonB. Google slides opened and the widths were set at 48in x 36in. Once the poster was done, the poster was saved via. microsoft powerpoint.

Results: Rough draft of the final poster was created. 

Conclusions: The poster was a rough draft that was completed, but the poster was not. Few points are needed in discussions, and the overall design needs to be adjusted to ensure that all boxes are aligned correctly.

Future Work: Poster needs to be finalized and the poster needs to be adjusted. The final poster will be compared with other posters and the class will choose a poster that will best represent the class at Scholars week.

Rationale: Design poster for Scholars Week.

Procedure: Previous SEA-PHAGE posters along with other posters were analyzed to gain insight on how to make a proper poster. The layout of the poster was designed as a sketch in a group of three. Reference posters, paper, and a pencil were used to help design a sketch of the possible poster that could be used to represent the class at URSA poster presentations.

Results: Poster design was done on a blank white sheet of paper. Group decided to leave out the abstract, and a sketch of the whole poster was done. Introduction, methods for both wet lab and in sillico, discussions, conclusions, and references were included.

Conclusion: Poster designs completed, but not filled with any flow charts or any bullet points. Colors of the poster were determined, and the overall ideas of what to add in the poster were established.

Future plans: Finish the poster designs and the layouts. Begin building the poster and to start self-group research questions.

Rationale:

Check over the annotations of NapoleonB as a class in order to identify any mistakes that were made.

Procedure:

1. Using an already auto annotated version of NapoleonB on DNA Master gene 41-44 was confirmed to have the correct annotations.
2. Genemark was pulled and the coding potentials were doubled check for genes 41-44.
3. The rest of the genome was proofed as a class.

Results:

The coding potentials for genes 41, 42, and 44 were covered, but 43 were not. Nothing was changed in annotations, but the annotations were doubled checked. The rest of the genome was moderately corrected in order to fix entry errors.

Conclusions:

It can be confirmed that genes 41-44 was correct in its annotation. It can also be concluded that the annotations for the phage NapoleonB are as of now correct.

Future steps:

The next step will be to conduct an independent research project and to create a poster as a group in order to present at scholars week as a class, along with finalizing a class abstract.

Rationale:

Corrected NapoleonB gene 44 and combined abstracts with other group members for a possible poster abstract.

Procedure:

Opened DNA Master and phage notes. Checked for errors in gene 44 with the help of Genemark, DNA Master, NCBI BLAST, PhageDB, HHpred, and phage notes. The start codon was changed and the product was placed into NCBI BLASTp to check for possible functions.

Results:

Conclusions:

Start codon pulled to 30372 and the product was checked in HHpred, NCBI BLASTp, and PhageDb to see the known function. Few sentences from my abstract were added into Brandon’s abstract, and grammatical errors were fixed as a group. Working in groups can be very beneficial since you will be able to see from multiple points of views, and also helps avoid confirmation bias.

Future Plans:

Start individual projects and designs for conferences.

1. While working with sick locusts, he observed that there was some clearing on his plates, which were called at the time taches vierges. With the discovery of these clearing lead to multiple tests, and at the time he thought he were somehow related to the locusts disease This would later lead to future test performed by d’Herelle and the publishing of his first paper, his results of his findings in these lytic creatures, that are smaller than bacteria. World war one started, and it mission of monitoring disease outbreaks and manufacturing commercial vaccines took on new urgency. This led to the hault of his recent discorvies, but the continuation of how these “clearing” were. Once asked to look into a new outbreak during the war, he performed multiple tests, and saw these taches vierges once again, and lead to many experiments and the publication of his paper.

2. d’Herelle loved sciences as a child and taught himself microbiology/phage biology. As he was returning to Paris from Rio de Janeiro by ship, yellow fever broke out among the passengers and crew. At that moment, he saw something that would lead to him focusing of later to known as phage biology. Following in the footsteps of his hero Louis Pasteur where he would begin his studies studying fermentations. He was very driven by science, and so was Georgi Eliava. The two share many things in common such as they both came from privileged backgrounds. Their fathers were doctors from a well-connected family. Eliava was easily distracted and often carried away with many different ideas, which lead many of his lab experiments remained in his labs for weeks untouched. The two shared a warm friendship and the two published two papers together. Years later. Civil broke out in Spain and Eliava was arrested, which would cut all ties between Tbilisi’s Bacteriophage Institute and the West for more than 50 years.

3. War helped d’Herelle realize that there was a correlation between his last two findings, and it helped him discover an agent that is smaller than bacteria. He performed many tests to prove his hypothesis, and soon he traveled all over the world to help cure diseases around the world. Governments in India changed to allow the use of bacteriophages since phage therapy proved to show success in lab and on humans. With the later wars like WWII and civil wars in the Eastern hemisphere, caused many ties with the western labs. The eastern labs were closed and scientists like Eliava were arrested. Politics and war played a great role with the spread of bacteriophage. If the two scientists were still sharing information during wars, the west might have kept up with bacteriophage. Since the west lost ties, the west found new ways to treating humans (antibodies) while the east kept up with bacteriophage, and they use antibodies as well.

4. One reason that phage therapy failed was due to the fact articles that showed antibiotics were the new thing to cure diseases/illness pushed halted phage therapy in the western hemisphere, whereas phage therapy stopped in the east, but did not completely stop as in the west. Another reason why phage therapy failed in other parts of the country was due to the fact of multiple strains of the same bacteria were in different parts of the country. While d’Herelle helped heal thousands in Bombay, he sent his phage used to cure cholera in Egypt to India, but the phage did not work since the viruses isolated in Indochina didn’t work against the strain of phage bacteria active in Bombay. Without television or radio, word of outbreak of this new phage therapy spread slowly.

5. The two scientists around the same time started bacteriophage research. Delbruck was searching for a way to apply the laws of physics to biology which lead him to bacteriophages. He and two other scientists aimed x-rays at the genes if Drosophila fruit flies and demonstrated that the genes mutated proportionally to given dose of radiation, which proved genes are “the ultimate units of life”. Like Delbruck, Luria began to think of a field that could bride the field of biology along with physics. After reading Delbruck’s paper on the genes, Luria discovered bacteriophages. The two became intrigued with bacteriophages, which lead to meetings that became known as the phage group. Through many talks, the question was if bacteriophages were really genes, like human genes, then it would give a new angle to look at human body genes. The two contributed to phage biology through there similar interests and what they saw in genes and how bacteriophages are the tools for studying genes. The group that was formed by the two introduced chemists, biologists and physicists to change and would be the birth of molecular biology. Phage biology died since scientists were intrigued with a new topic and that topic was how higher organisms reproduce and any role that phages might have once played in curing humans was viewed as a failed effort.

6. Discovery of bacteriophage has come a long way and with the help of multiple scientists, phage have helped cure millions in the early 1900’s to 1950’s. It is amazing to see how much of a role politics plays in our lives. Politics “run” everything and it very important. Wars had a huge effect and how it prevented the spread of this wealth of knowledge. This first few chapters of the book were a really great read and it was very fascinating to see where bacteriophages have come from. We started this class without little to no knowledge about bacteriophage, let alone any of the history, and now we have come to understand a lot about bacteriophages.

Rationale: Finish annotations for NapoleonB genes 41-44. Use knowledge from past few practice annotations to start NapoleonB annotations.

Procedure: NapoleonB FASTa file downloaded from PhageDB, and loaded onto DNA Master. Gene auto-annotated and frames were viewed. NCBI, HHPred, PhageDB, and Phamerator were all pulled up to annotate gene 41. The product of Gene 41 was copied and pasted onto  NCBI, HHPred, PhageDB, and Phamerator. Results were analyzed and annotations were placed into PhageNotes.

Results: 

Gene 42-44 annotation below followed by NCBI, HHPred, GeneMark, and PhageDB:

Gene 42

SSC: 29359 – 30117, CP: The genes covers all coding potential present, SCS: Both, ST:SS, BLAST-Start:Aligns with Circum gp44 NCBI BLAST q1:s1 1 o.00, overlap:2bp gap, LO: NA, RBS: Kibler7 and Karlin Medium 2.404 -3.893 No, F: NFK, SIF-BLAST: NFK, SIF-HHPred: NFK, SIF-Syn: NFK

Gene 43

SSC: 30128 – 30379, CP: No no coding potential near the start, SCS: Both, ST:SS, BLAST-Start:Aligns with KeaneyLin gp42 NCBI BLAST q1:s1 1 2E-43, Gap:12bp gap, LO: NA, RBS: Kibler7 and Karlin Medium 1.687 -5.326 No, F: NFK, SIF-BLAST: NFK, SIF-HHPred: NFK, SIF-Syn: NFK

Gene 44

SSC: 30291 – 30815, CP: No Longest ORF available for this reading frame, SCS: Genemark, ST:NI, BLAST-Start: Aligns with Circum gp46 NCBI BLAST q1:s1 1 6E-106, Aligns with Circum gp46 PhageDB BLAST q1:s1 1 1E-83, Gap: 87bp overlap, LO: Yes, RBS: Kibler7 and Karlin Medium 1.701 -5.296 No, F: NKF, SIF-BLAST:NKF, SIF-HHPred: NKF, SIF-Syn: NKF

Conclusions: Annotation of gene 42,43, and 44 had no known functions.

Future plans: Review genes 41-44.