After the deliberation today, I learned a lot about specific ideas of how to prepare, prevent, and stop global warming. For example, one really big issue discussed was the fossil fuels burned by cars, but the general consensus is that buying an electric car is expensive (we all immediately think of Tesla), or we think of electric cars as unappealing, such as the Prius. But Honda and other companies are actually making cars that can run off of hydrogen gas, and would decently affordable. Also the BMW I8, is a sleek sports car that was also recently introduced. Although it doesn’t exactly provide a cheaper option, it does provide a more appealing option for someone looking for a high end sports car, while being planet friendly.

Another topic that was discussed in my group that I thought was really interesting, was the idea of making people change their ways. Some people are more than happy to try to help out the environment and do what they can, but on. the other hand, some people will never want to change their ways, even if there were incentives provided.

• APRIL 24TH 2019
• OBJECTIVE: 
  • Start to work on and create the presentation, and finalize abstract
• PROCEDURE:
  • A Google slides file was hared with all group members, in which information was added to the slides 
  • Comments from the rough draft of the abstract were used to edit. And create a new abstract using google docs 
• RESULT:
  • A google slides presentation was created and edited 
  • A final abstract was created: 
    • Bacteriophage genomic analysis can demonstrate the diversifying effects of mosaicism across phages through the presence of conserved domain gene groups. One mechanism that supports genetic diversity among bacteriophages is Horizontal Gene Transfer, which can allow transmission of localized cassettes. A certain class of cassette involved in DNA replication gene function of the viral genome was identified in NapoleonB. The DNA replication module was noticed to have a specific ordering in common with certain other bacteriophages outside of it’s cluster. The online tool Phamerator was used to visually represent genomes to compare the presence and ordering of genes belonging to a similar module. Genomes of phages that infected multiple different actinobacteria were all found to contain a common gene cassette. A protein folding tool RaptorX was used in tandem with Jmol, a tool for visualizing predicted protein structures, to visualize the function and similarity among these common genes. Clustal Omega and MEGA are sequence alignment tools that were used to make phylogenetic trees. The use of Splitstree allowed for the construction of a phylogenetic network to visualize the parsimony amongst the different bacteriophages studied. The data collected has shown that members of certain clusters can share synteny with members outside of their own cluster. The commonality among the ordering and presence of genes in these clusters provides evidence that allows for the prediction of the function of genes which had no defined predicted function before. Furthermore, if future phages are discovered with this replication cassette, there will be more evidence for making gene function calls using synteny with phages outside of just it’s own cluster.
• CONCLUSION: 
  • Presentation was created 
  • Abstract was edited and finished 
• FUTURE STEPS: 
  • Continue work on presentations 

One of the biggest problems in phage therapy has been in the approval process.   Describe the trouble surrounding FDA approval and recommend some suggestions to improve the process of phage therapy approval.

The trouble surrounding the approval process of the FDA is due to both, the fact that phages tend to have a more negative view in the United States, and the fact that there simply may not be enough research to determine the safety of commercial phage use. Due to the lack of phage use in the Unites States, I feel as if its seen as more of a safety risk because phages haven’t been extensively used, therefore the long term ramifications of commercial phage use have yet to be determined. Also there is also a lot of skepticism surrounding phage use, for example when the FDA responded to Sulakvelidze they had a request that seemed unreasonable: “What Sulakvelidze felt was a less reasonable request was that the FDA also asked him to determine the rate at which each of the six phages in Intralytix’s proposed VRE cocktail would mutate inside an experimental animal” (92). The amount of money and time that would be needed to prove the mutation rate is astronomical and borderline impossible, and it could be agued that it really isn’t even needed. 

Some ways that I feel the phage therapy approval process can be improved is if as a society we can readily adopt the idea of using phages as a from of treatment, and try to diminish the stigma surrounding phage therapy. Secondly, I think if we can approve some form of phage therapy that seems safe and effective, I feel as if that would could help diminish stigma and help us determine the long term ramifications of phages in a real world setting (if there even are any) 

• APRIL 15TH 2019
• OBJECTIVE: 
  • Create a document with all the sequences that need to be run through data bases 
  • Create a background for project 
• PROCEDURE:
  • A document was created and the gene for the terminase of a phage belonging to each of the following clusters was created:
  • AU1 AU2 AU3 AW BI1(bing) BI2 BI3 BI4 CC DJ EL  
  • A background was written for the project
• RESULT:
  • Introduction (Background Information)
  • Horizontal gene transfer (HGT) is the transfer of genes from organism to another in- the gene is being passed along horizontally across a generation 
  • Occurs between bacteria and bacteria, or virus and bacteria 
  • Is a crucial part in antibiotic resistance 
  • Can be used to show ancestry between viruses, to look at genetic similarities 
  • Phamerator is a map of the genomes of phages, and lines are drawn across the gene in order to show synteny, or similarities between phages 
    • https://www.nature.com/articles/445369a
• CONCLUSION: 
  • Document was created 
• FUTURE STEPS: 
  • Finish abstract 

• –APRIL 17TH 2019
• OBJECTIVE: 
  • Write parts of presentation for project (abstract, methods used, results etc.)
• PROCEDURE:
  • A document on google docs was shared with group members 
• RESULT:
  • Title
  • Evidence for Supercluster 46041 and others.
  • Guiding Question
  • Our objective is to compare pham 46041 DNA polymerase and observe the patterns that can be derived from cross-analysis. 
  • Abstract 
  • The Horizontal gene transfer is an evolutionary method that promotes genetic diversity through the passing of genes. A result of the mosaic model within populations of bacteriophage cells is the common appearance of conserved domain groups that are present across different clusters. The smaller size of bacteriophage genome allows the presentation of modules, a group of specialized genes that are localized within the same region. The analysis of a conserved modules in clusters that are associated with the DNA polymerases was conducted in the experiment. Through the tool Phamerator, we observed the phage genome map to determine the range of modules and identify the clusters needed to detect the sequence similarity. We also used RaptorX to observe the protein-protein interaction similarity between the gene modules and constructed phylogenetic trees that visually compares the multiple clusters of actionobacteriophages and demonstrate the shared evolutionary relationship with the DNA Polymerase gene. We have discovered evidence of common modules existing across multiple seemingly dissimilar clusters. This leads us to believe that these clusters all belong to a larger group. 
  • Phage genome have a typically smaller genome that can be analyzed after isolation and characterization through bioinformatic tools such as Phamerator, the construction of a phylogenetic tree based sequence similarity for a specific protein product, and the structure analysis of analogous sequences of the same pham.
  • List of tools used: Tmhmm, raptor X Structure Prediction, Raptor X Deep Align, Jmol,Dendroscope,, HGTree, Phamerator
  • Introduction (Background Information)
  • Horizontal gene transfer (HGT) is the transfer of genes from organism to another in- the gene is being passed along horizontally across a generation 
  • Occurs between bacteria and bacteria, or virus and bacteria 
  • Is a crucial part in antibiotic resistance 
  • Can be used to show ancestry between viruses, to look at genetic similarities 
  • Phamerator is a map of the genomes of phages, and lines are drawn across the gene in order to show synteny, or similarities between phages 
  • https://www.nature.com/articles/445369a
  • Types of Data Collected
  • Protein structure comparison, protein and dna sequences from different clusters, Phylogenetic tree, 
  • Results (to date)
  • Supercluster 46041: AM, AW, AU, BI, CC, DJ, EL
  • Supercluster 45806: AZ, BB, BJ, BL, EB, EH
  • Conclusions (if any have been drawn)
  • For gene 60,  TMHMM results show it is a transmembrane protein. There also shows evidence for synteny in transmembrane call in EL phage. Each transmembrane protein is structurally very different, but is made out of a group of alpha helices then a chain of amino acids then a beta pleated sheets.
  • For gene 61, there also seems to have a G5 domain. Blasted against actinobacteria and resulted in a streptomyces hit with a decent e value. The hit contained 3 conserved domains one of which aligned with the amino acid sequence hit. When comparing visual structures the predicted protein structure matches a typical g5 protein structure.
• CONCLUSION: 
  • Document was created 
• FUTURE STEPS: 
  • Create phylogenetic tree and continue collecting data

• APRIL 8TH 2019
• OBJECTIVE: 
  • Find more primary literature to read in order to deepen our understanding of the project being worked on 
• PROCEDURE: 
  • NCBI was used to search for sources 
  • Annotations were then created for those sources 
• RESULTS: 
  • Sources listed below:
  • https://academic.oup.com/femsre/article/30/3/321/546048
  • Weigel, Christoph, and Harald Seitz. “Bacteriophage Replication Modules.” FEMS Microbiology Reviews 30, no. 3 (May 1, 2006): 321–81. https://doi.org/10.1111/j.1574-6976.2006.00015.x.
  • https://www.sciencedirect.com/science/article/pii/S1084952117306055
  • Hernandez, Alfredo J., and Charles C. Richardson. “Gp2.5, the Multifunctional Bacteriophage T7 Single-Stranded DNA Binding Protein.” Seminars in Cell & Developmental Biology, SI: Human dendritic cells, 86 (February 1, 2019): 92–101. https://doi.org/10.1016/j.semcdb.2018.03.018.
  • https://doi.org/10.1016/S0378-1097(99)00068-3
  • Hamann, Christian, Jörg Hegemann, and Armin Hildebrandt. “Detection of Polycyclic Aromatic Hydrocarbon Degradation Genes in Different Soil Bacteria by Polymerase Chain Reaction and DNA Hybridization.” FEMS Microbiology Letters 173, no. 1 (April 1, 1999): 255–63. https://doi.org/10.1111/j.1574-6968.1999.tb13510.x.
  • https://academic.oup.com/mbe/article/23/9/1688/1014265
  • Filée, Jonathan, Eric Bapteste, Edward Susko, and H. M. Krisch. “A Selective Barrier to Horizontal Gene Transfer in the T4-Type Bacteriophages That Has Preserved a Core Genome with the Viral Replication and Structural Genes.” Molecular Biology and Evolution 23, no. 9 (September 1, 2006): 1688–96. https://doi.org/10.1093/molbev/msl036.
  • https://www.sciencedirect.com/science/article/pii/S0042682218300588?via%3Dihub
  • Jalasvuori, Matti, and Katariina Koskinen. “Extending the Hosts of Tectiviridae into Four Additional Genera of Gram-Positive Bacteria and More Diverse Bacillus Species.” Virology 518 (May 1, 2018): 136–42. https://doi.org/10.1016/j.virol.2018.02.014.
• CONCLSUION: 
  • Articles were read, and annotations were made 
• FUTURE STEPS: 
  • Continue researching gene functions
• –APRIL 10TH 2019
• OBJECTIVE: 
  • Create a document with all the sequences that need to be run through data bases 
• PROCEDURE:
  • A document was created and the gene for the terminase of a phage belonging to each of the following clusters was created:
  • AU1 AU2 AU3 AW BI1(bing) BI2 BI3 BI4 CC DJ EL  
• RESULT:
  • N/A
• CONCLUSION: 
  • Document was created 
• FUTURE STEPS: 
  • Finish adding codes for each terminase protein for a phage of each cluster 

• APRIL 1ST 2019
• OBJECTIVE: 
  • To make sure all are prepared for poster presentations, and can answer questions on the poster
• PROCEDURE: 
  • Students went up to the poster and presented to the class in their groups
  • People asked questions and proper answers were generated 
• RESULTS:
  • N/A
• CONCLUSION: 
  • Students were prepared to present and answer questions on the poster 
• FUTURE STEPS:
  • Formally present the poster at URSA scholars week, and continue working on in depend project

• APRIL 3RD 2019 
• OBJECTIVE:
  • To create a timeline for independent projects 
• PROCEDURE:
  • A google docs was shared where group members added information to create a timeline of project 
  • Phamerator was looked at to determine what specific genes the group wanted to look into 
• RESULTS: 
  • 4/8 : Determine protein structure of gene 62, and see how it interacts with upstream gene 59
  • 4/10: look at synteny and try to come up with a method of representation for synteny of other clusters for gene 62
  • 4/15: Have evidence to show the types of modules in Napoleon/AM cluster. Make setup for presentation, have background rough draft. 
  • 4/17, 19: Start constructing basic outline presentation, look into evidence for gene function in the different types of module. Start on Methods and figures. 
  • 4/22: Organize database of collected evidence for each gene in each module. Began constructing Results. Ensure phylogenetic tree is accurate and well made.  
  • 4/24 Continue collection of evidence for module 1, 2, 
  • 4/29 Finish final touches on presentation, and be able to flawlessly run through the presentation 
  • 5/1- Practice Presentations
    • 59 gene interaction: using raptor x, no correlation 
    • Bing, clustered in BI1: 
    • 60: transmembrane protein matches own cluster, BI 
    • Newly identified, used to calculate it can fit inside the membrane
    • Used synteny phage Camille, and other EL phages that have the same membrane protein.  
• CONCLUSION: 
  • A timeline was made and there will be further investigation into gene 59 of Napoleon B
• FUTURE STEPS: 
  • To analyze proteins made by gene 59 in AM cluster
  • Continue to read primary literature 

• MARCH 25TH, 2019
• OBJECTIVE: 
  • Develop possible independent research question 
• PROCEDURE: 
  • A google docs was created and shared among group members 
  • Phamerator map was used to compare clusters and look and possible synteny 
  • Questions were then typed into a document 
• END RESULT: 
  • The following questions were developed by the group/group members:
    • By observing the conserved genes upstream and downstream of the DNA polymerase commonly identified in several clusters that are members of pham, can we show the point of divergence through a phylogenetic tree? What synteny is conserved is association with the extended DNA polymerase, involving also the helix-turn-helix protein). – Ram
    • Through GC analysis sequence, can we determine the possible source of helix-turn-helix DNA binding protein between phages within the same cluster and demonstrate through a phylogenetic analysis? – Melissa
    • How can attP sites be compared to other phages in the cluster in order to determine if there is a trend in the “aggressiveness” or lysogenic strength of the phages?- Lauren 
    • There are some genes that are unique to only certain phages in the AM cluster, but seem to be common in other clusters. How can we compare the sequences of these genes as well as the synteny of genes in members that contain the gene display differences within the AM cluster as well as similarities between the AM and AU clusters?
• CONCLUSION: 
  • Questions were developed and submitted as a QTM 
• FUTURE STEPS: 
  • Pick one questions and develop a way to use the methods available to answer that question
• MARCH 27TH, 2019 
• OBJECTIVE: 
  • Develop methods to be bale to answer a research question 
• PROCEDURE: 
  • A google doc was created 
  • Phammerator was used to compare he presence of a DNA polymerase between different phages clusters
  • Brain stormed ideas on how to test question
• END RESULT:
  • Research Questions
    • By observing the conserved genes upstream and downstream of the DNA polymerase commonly identified in several clusters that are members of pham, can we show the point of divergence through a phylogenetic tree? What synteny is conserved is association with the extended DNA polymerase, involving also the helix-turn-helix protein). – Ram
    • a look into the cassettes (can determine if its the same gene using promoter sequence even if it doesn’t have function)
    • look sequence promoter  (Can be done using DNA Master “DNA–>Promoter Prediction.” Make sure the settings are for sigma-70 promoters, and then click analyze)
    • compare protein structure through the nucleic acid 
    • Look into function of genes 
    • End goal: be able to create a phylogenetic tree 
    • Why does arthrobacter phage have DNA polymerase?
    • See if arthrobacter itself, has sequence for DNA polymerase….could theoretically be used by phage? Why have they co-evolved? Why don’t phages from other bacteria lack DNA polymerase? 
  • Topic questions: 
    • Question if a high percentage arthrobacter phage has this dna polymerase?
    • What other clusters are have the DNA Polymerase
    • Is there a significant difference with the presence of DNA polymerases in arthrobacter phage? 
    • Actinobacteria
    • Naked DNA? 
    • See if they cluster out?
  • Figure of host and see how those are all related then can see which one of them has DNA polymerases and see if they all branch out in Actinobacteria 
  • In order to get approved you must have a question that is specific and testable.
  • Our objective is to compare pham 19129 DNA polymerase and observe the patterns that can be derived from cross-analysis.
  • Are there some patterns that can be derived from analyzing the differences and similarities among phages that contain the pham 19129? Furthermore, could this insight help us determine the relationship between these phages such as a common ancestor, seeing as they all contain a similar gene despite some infecting different hosts?
  • In addition, you must show your coach that there is enough resources available for you to do your research
  • Protein-protein interaction DNA polymerase and upstream gene, (other biotech sources available on ExpasY) Phages DB, Phamerator, HHPred, and DNA Master. We must also come up with an organized system of data collection. Early evidence. 
  • You must propose a simple method outline for your research project. 
  • Compare host genome using NCBI blasts (must look into tools to compare bacterial genomes)
  • Need to specifically look in differences of DNA polymerases and nucleotide changes within that gene (using Phamerator, DNA master, HHPred)
  • Entire cassetete containing DNA polymerase can be analysed for similarities and differences as well 
  • Need to get rough understand of the DNA polymerase relation in order to find out where to continue further research 
• CONCLUSION: 
  • Possible methods were developed to test research question 
• FUTURE STEPS: 
  • Refine research method and make more specific methods

• MARCH 18TH, 2019
• OBJECTIVE: 
• To work on changes that need to be made on poster 
• PROCEDURE: 
• Adobe spark was used to search for icons that could be used for the headers on the poster 
• The icons were then colored white, then were copied and pasted into GoogleSlide and were sized accordingly (See in image below)
• END RESULT: 
• Icons were added to each header in order to create a more cohesive poster 
• CONCLUSION
• Icons were added to headers
• FUTURE STEPS: 
• Decide on topic for independent project 
• MARCH 20TH, 2019
• OBJECTIVE: 
• Start researching an independent project idea, and fix issues with poster
• PROCEDURE:
• Google Doc was made to answer QTM 
• Icons on poster were edited in size 
• Topics were researched for independent project idea 
• END RESULT:
• QTM was submitted 
• CONCLUSION:
• QTM was submitted, and initial research was started on independent project
• FUTURE STEPS:
• Continue researching and find a topic/question to research 

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. 

 MARCH 4TH, 2019

• OBJECTIVE:
  • Work in large groups, to collaborate and make a combined poster idea 
• PROCEDURE:
  • A powerpoint file was created and shared with all student in the group who then worked on the poster collectively 
• END RESULT 
  • A poster using both teams ideas was created (see image below)
• CONCLUSION:
  • Poster was completed and submitted as a QTM
• FUTURE STEPS:
  • Get critiqued on poster, and continue edits 

MARCH 6, 2019

• OBJECTIVE
  • To pick a poster design that will be used for the class poster
• PROCEDURE:
  • All groups posters were presented using powerpoint, in front of the class 
  • Students then voted on which poster layout they liked the best 
• END RESULT:
  • A poster design was chosen to work with 
• CONCLUSION:
  • A poster deign was chosen, and will continue to be editing combining some elements from other posters 
• FUTURE STEPS:
  • Determine issues with chosen poster and find way to fix those issues 
    

    The group created poster