April 11

4.8.2019 Furthering Investigation of Repeats

4.8.2019 Furthering Investigation of Repeats

Rationale: At the end of the previous lab, we focused on one particular repeat of interest. Today, it would be beneficial to gain more knowledge and information about that repeat to determine whether or not there are interesting findings to be had.

Procedure: Today, DNA Master and NCBI BLAST were used to analyze this particular repeat along with Phamerator. We examined sequences in DNA Master and used Phamerator and NCBI BLAST to contextualize our results.

Results: The repeat in NapoleonB along with the other members of the AM bacteriophage cluster had an inverted repeat of TAAA and AAAT, leading us to the hypothesis that this sequence may be a transposon.

Conclusions: Since there was an inverted repeat that was present in a conserved sequence, we hypothesized that this could be a transposon, as it has all of the basic qualities of that phenomenon. However, more investigation to confirm this idea is needed before any direct and influential data can be compiled and had conclusions drawn from it.

Next Steps: On Wednesday, we will take a more detailed look at trying to determine the classification of this sequence.

April 11

Continue Individual Research

03/27/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

  1. The individual research has now begun
  2. the group members have started finding the start codons for their assigned proteins using phages db for the fasta file and dna master for the sequence
  3. The grouped worked until the end of lab.

Results

so far. no real results. a lot of  the data collection has been performed.

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. enough data can be collected for the research in the given time.

Future steps

do more research, look into primary literature and find more tools that can be used.

April 11

Work On Individual Research

03/27/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

  1. The individual research has now begun
  2. the group members have started finding the start codons for their assigned proteins using phages db for the fasta file and dna master for the sequence
  3. there are approximately 230 arthrobacter phages that can be used.
  4. The grouped worked until the end of lab.

Results

so far. no real results. a lot of  the data collection has been performed.

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. enough data can be collected for the research in the given time.

Future steps

do more research, look into primary literature and find more tools that can be used.

April 10

April 10 2019 Independent Research Continued

Purpose: The purpose of this lab is to continue work on the final project, collecting and analyzing data.

Tools/Procedures:

Tools:

  • DNA Master
  • PhagesDB
  • PhageNotes

Procedures:

  1. The genes of NapoleonB were analyzed to determine which genes were specific to the AM cluster, and which were not.
  2. Statistical analyses were performed on the data found in the last lab.
  3. It was found that the AM-specific genes had a statistically significant lower %GC than the non-AM genes.
  4. No significant difference was found for the %GC3 of the AM and non-AM cluster genes.
  5. It was also determined that the arthrobacter AM cluster phages have a significantly lower %GC than all non-AM arthrobacter phages.

Results: 
The analyses of the data collected show that AM cluster phages have %GC that are lower than the average arthrobacter phage %GC. While all of the genes in NapoleonB have a lower average %GC, the AM-specific genes have an even lower average than the non-AM specific genes.

%GC Difference Sample Diff. Std. Err. DF T-Stat P-value
μ1 – μ2 1.89 0.66921299 95.842177 2.824213 0.0029

Conclusions:
In conclusion, it was found that AM cluster genes have lower %GC than most other arthrobacter phage clusters.

Future Work:
Future work will include gathering more data about AM cluster genes, and trying to determine why they have a lower %GC than other genes. This could include looking at genes not found in AM phage, as well as looking at what makes AM phages different from the other arthrobacter clusters.

April 10

Lab Day 22-23: Independent Research Project

Rationale

Find resources through primary literature, form and revise guiding question, and start making results and analyze them.

Procedure

  1. found 5 sources and revised question
  2. NCBI blasted NapoleonB’s gene 93 sequence
  3. Found 6 bacteria and 6 non AM (3 AU and 3 EG) clusters that HHPred called as NMT
  4. multiple sequence alignment with all 18 sequences, 6 AM, 6 non AM, 6 bacteria, 3 AU, and 3 EG.
  5. Saved pdf filed for all 6 multiple sequence alignment results

Conclusion/Next Steps

We found that when we blasted NapoleonB, we found that it had some hits from bacteria. So that raised a hypothesis that NMT from NapoleonB might have come from or evolved from bacteria. From the MSA results from all 18 sequences, we found that bacteria and AM/AU cluster had more similarity and the EG cluster was pretty different compared to everything else. At one point, we found that there might have been a mistake in the pham results that some were called as a nicotinamide riboside transporter/transferase. The next day, our phage were put into a different pham from that other clusters. We doubled checked through raptorx and TMHMM that our phage’s sequence is indeed a NMT. In the next time, my group and I will make a phylogenetic tree and a figure to show which part of the sequences were similar from which cluster/bacteria

April 10

Analyzing Patterns in Trans-membrane Proteins 4/10/19

Rationale: My partners are working on putting together the phylogenetic tree and looking more in to the  differences between the  members  of each cluster in the supergroup. So, I am going to look more in to  the  different transmembrane  proteins to  try to find a pattern.

Tools: Jmol,  RaptorX

Procedure:

1. After running a member of  each cluster’s transmembrane  protein through raptorX I viewed each protein in Jmol.

2. Noticed a pattern of alpha helix cluster and beta pleated sheet section.

3. Noted my findings  and  tried to find correlation with clusters outside of the group of clusters we are currently looking at.

Results:

Conclusions and Future Work: I will be working more on trying to correlate the  findings with out  groups  to provide a comparison against which to make my claim that there is some kind of relationship among all these clusters.

April 9

The Forgotten Cure 3

Prompt: 

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 FDA approval process is long and daunting for any new drug or therapy treatment. Only about 18% of medicines make it to Phase I of clinical trials, according to the Forgotten Cure. Because of the rigorous tests the drugs must pass, it is hard for them to advance past this phase. Another problem is the cost and time of development and FDA approval. On average, it costs $800 million for development and approval of new treatments. This makes the large pharmaceutical companies not want to invest in this research themselves, leaving it for others to do.

The researchers who want to conduct an FDA trial must first submit an application for their trial to be approved. In the case represented in the Forgotten Cure, the researchers submitted an application and then had to undergo a series of questions relating to the trial, to show they were serious and to help prove that their trial would be beneficial, and would not cause further problems. In phage therapy, some of the concerns for FDA trials were lytic phages and the scientist’s ability to identify different phages. The FDA was concerned that temperate phages, that undergo the lysogenic cycle, could exchange genes with other organisms and cause problems during and after testing.

Because phage therapy is to be used on humans, it is much more regulated by the FDA than other animals, and therefore harder to gain approval. The FDA was worried about transduction and that it would cause harm to humans who used the therapy if toxins were to be released. The companies described in the Forgotten Cure had more success in using phage therapy for animals such as chickens. Starting with cows and chickens, however, is one way to help gain public approval.

There are many ways that scientists can help improve the process of phage therapy approval. The work done by Ramachandran in the Forgotten Cure is an example of ways scientists can try to make phage therapy safer for humans. Ramachandran was able to inactivate endolysin, which allows phage to escape from the bacterial cell by weakening the cell wall. In his tests, all of the mice treated with this engineered vaccine survived, while 80% of those untreated did not (Forgotten Cure). Designing methods and techniques like Ramachandran will help the FDA to be more comfortable with giving bacteriophage to humans and will help speed and improve the approval process for scientists and doctors interested in the subject.

Scientific researchers are not the only ones needed for clinical trials. Physicians will need to be involved and collaborate with the researchers to have a successful phage research trial. If physicians do not think that phage therapy will work, or that it is not safe, it will be hard to conduct clinical trials. Helping to educate physicians on phage therapy will improve the approval process.

Another way to help improve phage therapy approval is to increase the understanding of phages general population and convince them of their safety and effectiveness. While gaining FDA approval can be hard, another step is getting patients to accept phage therapy as an acceptable treatment. This can be done by teaching individuals about bacteriophage, and then about phage therapy, making it seem like a common treatment, as it was for the Georgians, who even had vials of phage in first aid kits in the war. Another way to increase the public’s feelings of safety with bacteriophages is to continue to discover more about them, researching phage not only for their potential therapeutic uses but also to learn more about them so that scientists and others can better understand what they are researching and using.

 

April 8

April 8 2019 Independent Project Research

Purpose: The purpose of this lab is to collect sources for the independent project, and to continue researching the project question.

Tools/Procedures:

Tools

  • DNA Master
  • PhagesDB
  • Google Sheets

Procedures:

  1. Sources were found for the project and citations were made for each of them.
  2. %GC for all arthrobacter phage were compared and the average was found.
  3. %GC and GC3 were found for all of NapoleonB’s genes., an AM cluster phage.
  4. %GC and GC3 were found for all of Sonali’s genes, an FG cluster phage.
  5. Averages and standard deviations were found for the above information.
  6. %GC was compared for all AM specific genes to the %GC of non-AM specific genes.
  7. Research was saved.

Results:
In this lab, data was collected for the %GC of genes in an AM cluster phage, the arthrobacter cluster with the lowest %GC, and for an FG cluster phage, the arthrobacter cluster with the highest %GC. The data will be analyzed in a future lab.
It was found that Arthrobacter phage have an average %GC of 59.7%, while AM phage have an average 0f 45.2%.
For NapoleonB, it was found that the phage had an average %GC for its genes of 44.9%, and GC3 of 43.97%
For Sonali, it was found that the phage had an average %GC for its genes of 67.7%, and GC of 89.6%

Conclusions: 
In conclusion, this lab was used to begin data collection on %GC and GC3 of different clusters and different Arthrobacter phage. Overall, it was found that the %GC in Arthrobacter clusters has a high standard deviation, meaning it has a wide range. However, the standard deviation for AM compared to other Arthrobacter clusters, had an even higher standard deviation. It was also found that the GC3 of Sonali’s genes differed sigificantly from the %GC of the genes, and from the average %GC.

Future Work:
Future work will include collecting more data for AM and non AM cluster phages, concerning their %GC. Also, in the future, the data collected will be analyzed, to see if there is a significant difference, and why.

April 8

Analyzing Conserved domains of Gene 61 4/8/19

Rationale: Since I was not able to find a relationship between gene 61 and 62 using protein-protein interaction I decided to go back to looking through NCBI and CDD to find evidence for a function for this gene.

Tools: BLASTp, Jmol, RaptorX, CDD

Procedure:

1. Blasted the gene 61 of NapoleonB against actinobacteria.

2. Resulted in  a hit against streptomyces which I looked more into the gene it hit to.

3. Located 3 conserved domains within the streptomyces  gene.

4. Lined up the conserved domain location to  the location that the NapoleonB  gene  matched with the streptomyces gene.

5. Found that the conserved domain G5 lined up  with the gene from NapoleonB.

6. Analyzed the structure of a G5 domain and compared to the predicted structure of  gene  61 and  found that  they are extremely similar.

Results:

Conclusions  and Future  Work: This  most likely  means  that this gene was  just  picked up at the same time as the  DNA polymerase. Now we are going to  work on  putting together a phylogenetic tree mapping the members of this group of  clusters. Also I  will start looking for other instances of groupings of clusters.

April 5

Final Project Outline

4/3/19

Rational:

To finish gathering background material and to create an outline of how the project will proceed.

Procedure:

  • Looked for and shared information on the structure of holin and endolysins
  • Tried to understand the mechanism of the proteins inrelation to the structure
  • Determined the title of the poster
  • Refined the research question and added background information
  • Added the sources that had been found
  • Found three biotechnology tools to use

Observation:

  • We were able to find a detailed model of the endolysin structure but not holin

Conclusion:

Our group was able to create a general outline of the project and give a little guidance as to where the project goes. Next lab we will start researching NapoleonB and other phage’s endolysin and holin genes.