Title: Final Poster Editing

Date: 18 March 2019

Rationale: The purpose of this lab was to make any final edits that were needed to the class poster in order to make it ready for the scholars week presentation.

Tools:

• Microsoft Surface Tablet
• Google Slides

Procedure: 

• Worked to create a figure encompassing wet lab results for NapoleonB
• Worked with rest of the group to ensure the wet lab results were appropriately represented

Results/Observations:

• Below is a picture of the created figure for metadata:
• 

Conclusions/Next Steps:

• Once all sections are edited and revised, the physical construction of the poster can be done and the poster will be ready to present

Title: Making the Scholar’s Week Poster

Date: 27 February 2019

Rationale: Each group will design a poster for NapoleonB and the group will decide which elements belong on the final poster that will be presented.

Tools:

• Microsoft PowerPoint
• PhagesDB Database

Procedure:

• Using PowerPoint and PhagesDB, information was compiled and organized into a PowerPoint slide in order to appropriately design a poster to be submitted.
• The information was divided into an Introduction, Methods, Results, and a Conclusion

Results:

• The poster was not fully completed in the time allotted, but many elements were determined and finalized for the group’s poster
• Below are pictures of some of the elements of the poster:

Conclusions: The poster contains many creative elements that help to explain the methods and results of the experiment, although it does need to be finished. Regardless, it contributes to the group’s effort of compiling a final poster to be presented.

Title: Poster Design

Date: 25 February 2019

Rationale: A rough poster outline will be made in order to formulate a final poster design in preparation for Scholar’s Week

Procedure:

• On a blank sheet of paper, a rough design of the NapoleonB poster was drawn out and planned
• The sheet of paper was saved to be used for reference at a later date

Results: Below is a picture of the designed format for the NapoleonB poster:

Conclusions:

The poster template will be used to help guide the final design of the Scholar’s Week poster at a later date.

Title: Checking NapoleonB’s Genes

Date: 20 February 2019

Rationale: Before the final annotations of NapoleonB are sent in, the genes must be checked for accuracy and any abnormalities double checked and justified.

Tools Used:

• DNA Master
• NCBI BLASTp
• PhagesDB BLAST
• GeneMark

Procedure:

• Genes 47 and 48 were checked to ensure that the chosen start was justified by BLASTing and comparing gene products. Other abnormal calls were also checked by the class and any mistakes fixed as observed.

Results/Observations: The results from NCBI and PhagesDB showed that the starts chosen (not the longest available ORF) were justified (due to q1:s1) as well as a worse blast hit when the reading frame was pulled back. No changes were made to the original calls.

Conclusions/Next Steps: Once a final abstract is selected, poster design will commence as well as possibly another check of the NapoleonB annotations to ensure accuracy. Individual research projects will also start soon.

Title: Abstract Composition and Editing

Date: 18 February 2019

Rationale: The purpose of this lab session was to review and finalize a draft of an abstract to submit for Scholars Day

Procedure: The contents of 4 different abstracts were compiled into one final abstract and submitted for review

Results: A final abstract regarding the discovery, purification, and isolation of NapoleonB along with the characterization of its genes was compiled and finalized. The brainstorming process for a Scholars Day poster was also started.

Conclusions/Next Steps: The other abstracts will be considered and compiled in order to ensure that the best possible abstract is submitted to represent the cohort at Scholars Day.

1. Describe the role that locusts, dysentery, and war had in the discovery of bacteriophage.
   1. D’ Herelle was a scientist that was tasked with working with sickened locusts. By chance, when he was making bacterial assays from the locusts, he noticed that some of the spots had been cleared out on the plate. D’ Herelle named them “taches vierges.” He repeated the same procedure of making plaque assays and kept getting the same, cleared out circles on his plaque assays. He couldn’t replicate it anywhere else and essentially just left it alone until World War I when commercial vaccines started blossoming. French troops came down with a massive case of dysentery, and D’Herelle was assigned to analyzing their stool samples. It was then that he saw the clear spots on the bacterial assays again. He had proof that the clear spots appeared in more than one strain of bacteria, and that the spots only appeared in patients that were getting better from their disease. This led him to the belief that the clear spots were indicative of bacterial death
2.  Discuss the characteristics of d’Herelle that led him to be a successful scientist. How did he compare to Georgi Eliava?  What happened to the Eliava’s?
   1. D’Herelle was a successful scientist due to his perseverance and passion for his newly discovered “taches vierges” and devoted his studies to understanding what could come out of it, rather than becoming frustrated and disregarding the practice completely. D’Herelle also used his discoveries for good, doing his best to make sure the public could benefit from his early form of gene therapy. Like D’Herelle, Eliava carried the same demeanor and attitude regarding phage therapy. They both were in the same headspace, with similar goals for phage therapy development. The Eliava’s were targeted because of their high profile and pre-Revolution education. The family was put into camps and eventually suppressed in order to fulfill the Soviet Socialist agenda of the time.
3. Discuss the influence war and politics had on the spread of phage therapy.
   1. Much like the previous response, a political revolution had broken out in Eastern Europe along with a Civil War in Spain, which thickened the plot for Stalin. Personal affairs and politics got in the way of Eliava’s work during the war and caused the relationship between D’Herelle and Eliava to fade. D’Herelle started getting older and was settling down in Paris, beginning to wean himself off of his advocacy for the spread of phage therapy. The combination of the deteriorating relationship and the end of D’Herelle’s career marked the deterioration of the phage therapy revolution.
4. What are some of the reasons that the spread of phage therapy failed?
   1. Along with politics and war, there were many other reasons why the spread of phage therapy fell short. For example, much of the research done on phages was flawed and conducted in an inconclusive manner, meaning no meaningful conclusions could be drawn. There was also a lot of misunderstanding and ambiguity as to what a bacteriophage was, many people believed it was some sort of enzyme that broke bacteria down. Obviously, this wasn’t the case, but the misunderstanding definitely led to confusion. Lastly, synthetic drugs started to make a rise in the scientific community, leading to a drought in scientific articles regarding phage therapy.
5. How did the physicists Delbruck and Luria end up as part of the Phage Group? What contributions did they make to phage biology?  Why did phage biology die out in the 70’s?
   1. Delbruck, then a physicist, was interested in the way scientists observe organisms, and how technically an organism cannot be observed without modification. He collaborated with another group of scientists interested in genes and radioactive effects enacted on them by x-rays. They were published in an obscure journal but barely discovered by Schrodinger. Their bride between biology in physics took off from there, especially as Delbruck became more interested in biophysics as a result. In Rome, Luria decided his interest in physics was mostly “amateurish” and wished for something more, so he endeavored in biophysics, coming across Delbruck’s paper. He decided to try and test Delbruck’s ideas on genes and discovered bacteriophages. They both decided to devote their studies to bacteriophages and met at a convention. During their meetings, they established a loosely organized group called the Phage Group that was comprised of scientists of many different specialties. Their collaboration helped drive the spirit behind the group that eventually made progress in the bacteriophage world to the point where Luria, Delbruck, and Hershey won a joint Nobel Prize for their efforts and discoveries. Consequently, the Phage Groups discoveries raised doubts that bacteriophages could truly conquer bacteria. Due to this discovery, the research and new discoveries on phages hit a low and started slowing down. The scientists also started shifting their focus to other fields and more complex organisms.

Title: NapoleonB Annotation

Date: 13 February 2019

Rationale: The annotations for NapoleonB will be finished and reviewed for accuracy as well as the starterator (ST) annotation completed

Tools:
– Microsoft Surface Pro 5 Tablet
– DNA Master Software
– NCBI BLASTp tool
– HHPred tool
– GeneMark
– PhagesDB BLAST
– Phamerator

– Starterator (PhagesDB)

Procedure: Using the above tools, gene 95 were annotated completely
and the starterator annotation completed for genes 45, 47, and 48.

For gene 95:
– A start codon call was made based on the Glimmer/GeneMark call
– The product sequence was BLAST’ed to determine any present function
– A function no-call was made

Results/Observations: The following picture contains the results of the
annotation for gene 95:

Conclusions/Next Steps: The starterator annotations were finished, giving insight into what information the other phages in the AM cluster revealed about a specific gene’s start. With the exception of one more final review, the genes in NapoleonB have, for the most part, been completely annotated. They will likely be reviewed and any changes made before the analyzation begins on the genome as a whole.

Title: NapoleonB Annotation

Date: 11 February 2019

Rationale: The annotation for NapoleonB has begun and the genome will be sequenced as thoroughly as possible in order to determine function in relation to other similar phages

Tools: 

• Microsoft Surface Pro 5 Tablet
• DNA Master Software
• NCBI BLASTp tool
• HHPred tool
• GeneMark
• PhagesDB BLAST
• Phamerator

Procedure: Using the above tools, genes 45-48 were annotated completely (with the exception of starterator “ST”). Gene 46 was deleted due to convincing evidence of a bad call. For each gene:

• A start codon call was made based on the Glimmer/GeneMark calls or lack thereof
• The product sequence was BLAST’ed to determine any present function
• A function call was made and any supporting evidence from PhagesDB, Phamerator, and HHPred was logged

Results/Observations: The following picture contains the results of the annotations:

Conclusions/Next Steps: The starterator annotations need to be completed along with gene 95’s complete annotation. All but one gene was labelled as “NKF,” the gene that was able to be identified was an HTH DNA binding domain protein. Once the remaining genes are annotated, NapoleonB will have a completed annotation ready for analyzing.

Title: PhageNotes Entries

Date: 6 February 2019

Tools:

• Microsoft Surface Pro 5 Tablet

Rationale: With the (near) completion of Elesar annotations, the annotations are to be entered into the PhageNotes spreadsheet.

Procedure: 

• The already completed annotations for genes 16 and 17 were copied from DNA Master and entered into PhageNotes corresponding to the category and individual annotation. Genes 23 and 60 were also verified for accuracy.

Results/Observations: 

• Below is a screenshot of the finished product after entering annotations into Elesar PhageNotes:

Conclusions/Next Steps: After learning how to manipulate PhageNotes and appropriately enter annotations, all that is left to learn is Starterator and Synteny in order to have a full repertoire of skills for successfully annotating NapoleonB.