March 29

Research Question Discussion 3.25.19

Rationale:

To understand more about phage, the class was divided into several small groups to generate research questions that utilize bioinformatic tools to learn more about questions about NapoleonB and/or related phages.

Materials:
  • Laptop
  • Canvas Bio-Lab info page
Procedure & Results:

Different aspects of possible research directions were explored and four questions were generated. The Gepard dot plot software was used to find repeats in the NapoleonB genome. The leading question for the group is:

Is it possible to use repeats in coding or noncoding regions of the genomes within the AM phage cluster to predict the functions of genes with no known functions?

The Next Step:

The next step would be trying to refine the question and have a clear and specific objective.

March 22

Poster Final Check 3.20.19

Rationale:

To present the research, the lab members were divided into groups to discuss and design a poster, two groups were combined to produce the best parts of the two poster designs.

Materials:
  • Laptop
  • Google Slides
Procedure:

The advisors for the research projects were announced.

The potential gene 96-B was annotated and added to the in-silico results.

Results:

The poster design (without the in-silico results).

The Next Step:

The next step would be working on individual research projects with the assigned group.

March 22

Poster Layout Design 3.18.19

Rationale:

To present the research, the lab members were divided into groups to discuss and design a poster, two groups were combined to produce the best parts of the two poster designs.

Materials:
  • Laptop
  • Google Slides
Procedure:
  1. Work assignments were distributed among the class.
  2. Worked on the overall layout and design of the poster.
Results:

The Logos were swapped with versions with better resolutions, the font was changed to aerial and the text were aligned at the middle for most text boxes.

The Next Step:

The next lab would be the final poster design and the introduction to the individual research projects,

March 18

The Forgotten Cure 2

The USSR after WWII had their problems, they were struggling to provide enough antibiotics to the general public. To make up for the lack of mainstream treatment, the government promoted natural treatments such as herbs, since they are from “Here”. Another appeal to the alternative treatment of phage therapy is the low cost, comparing to the manufacture of antibiotics, phage vials were easier and cheaper to produce on a large scale. With the government’s attempt to discredit “Western drugs” such as antibiotics and to promote alternative treatments, phage therapy was used commonly in the Soviet Union.

The major reason that contributed the two different outcomes for the respective research centers is that the political climate of the USSR and its satellite countries, since the collapse of the USSR, the Eliava Institute lost funding and demands for phage therapy. On the other hand the Phage Therapy Center was able to flourish primarily due to the death of Stalin, and later on, Poland joining the EU. However, both institutes contributed greatly to phage research.

In order to find a phage strain that could effectively evade the entrapment of the RES, the team first grew phage on the WT bacterial strain CRM1 and the mutated type CRM2(the strain was used in hopes of inducing the mutations in phage lambda), then they injected the mice with phage and collected blood samples after 7 hrs. The phage collected in the samples were purified and amplified and reinjected into a mice, the experiment was repeated until they the phages injected into the system remained a high concentration after 18 hrs.

The consideration of using phage therapy in most cases is to counter antibiotic-resistant bacterial strains. But these newly founded companies look to develop treatments that utilize phages to potentially cure diseases, not to just be the alternative treatment to bacterial strains with drug resistance. An important concept for phage therapy mentioned in the book is that if you can get the right phage to the right pathogen it’ll work, developments and expansions of phage therapy should look to this as their guild lines, besides finding more phage strains to add to the ever-growing library constructing a way for labs to find the right phage strains faster and amplify them for patients is much more important from my perspective. For more phage therapy treatments to be approved more tests and trials have to be performed, one of the most important experiment is the double-blind test, with a large enough sample size and the right methods(double-blind) the results of phage therapy can be backed up with solid data, even though the book mentioned the villages that excepted treatment and the ones that didn’t have vastly different mortality rate tests with a more rigorous setting is essential. Trials aside proper PR is very important since the discovery of antibiotics phage therapy has faded into the background, hence the name “The Forgotten Cure”, more noise promoting the upsides of phage therapy might help investors to hear about and gain confidence in this resurrected field of treatment.

March 7

Final Lab Poster Design Presentation & Selection 3.6.19

Rationale:

To present the research, the lab members were divided into groups to discuss and design a poster, two groups were combined to produce the best parts of the two poster designs.

Materials:
  • Laptop
  • PowerPoint
Procedure:
  1. The poster made by the groups were presented in the lab, with the pros and cons of the different posters discussed.
  2. The most appealing poster was then picked out by the class and corrections on the poster were proposed.
Results:

The poster selected for the lab

The Next Step:

The next lab would be making adjustments based on some of the propositions made in the lab.

March 7

Final Group Poster Submission 3.4.19

Rationale:

To present the research, the lab members were divided into groups to discuss and design a poster, two groups were combined to produce the best parts of the two poster designs.

Materials:
  • Laptop
  • PowerPoint
Procedure:
  1. The best elements of the two posters were discussed and combined to produce a final poster that was submitted to Canvas.
Results:

The Next Step:

The poster would be presented by the combined group in the next lab and the most appealing design would be picked out as the final poster format.

March 1

Poster Design 2.17.19

Rationale:

To present the research, the lab members were divided into groups to discuss and design a poster.

Materials:
  • Sketching paper
  • Stationary
  • Laptop
  • Google Slides
Procedure:
  1. Design the poster based on the sketch made in the last lab
  2. Submit the results to Canvas
Results:

The Next Step:

The posters would continue to be revised and critiqued until it is complete.

 

March 1

Poster Layout Design 2.15.19

Rationale:

To present the research, the lab members were divided into groups to discuss and design a poster.

Materials:
  • Sketching paper
  • Stationary
  • Laptop
Procedure:
  1. A discussion on the pros and cons of previous posters design
  2. Decide within the group which of the components can be used on the new poster
  3. Sketch the design on the paper and turn in the result
Results:

The Next Step:

In the next lab, the small group will work on making the poster.

 

 

February 22

Annotation Check for NapoleonB & Abstract Draft Continue 2.20.19

Rationale:

To begin the genome analysis of phage NapoleonB, DNA Master has been chosen to be the software to annotate the genetic sequence. PhageNotes is also introduced as a convenient way to annotate genes and revising them. Abstract for the presentation was discussed, since an abstract should concisely inform readers or poster viewers the important points of the research.

Materials:
  • Laptop
  • DNA Mastering Program
  • Gene sequence of phage NapoleonB
Procedure:
  1. The whole annotation result was reviewed as a class and few adjustments were made, mostly data input error.
  2. The important points that should show up in an abstract and a poster was discussed.
Results/Next Steps:

There are a couple large gaps in the NapoleonB genome that is conserved but showed no coding potential and protein blast hits, and a reverse blast hit was found in the forward gene region.

In the next lab abstracts and posters would be the main focus.

February 22

Annotation Check for NapoleonB & Abstract Draft 2.18.19

Rationale:

To begin the genome analysis of phage NapoleonB, DNA Master has been chosen to be the software to annotate the genetic sequence. PhageNotes is also introduced as a convenient way to annotate genes and revising them. Abstract for the presentation was discussed, since an abstract should concisely inform readers or poster viewers the important points of the research.

Materials:
  • Laptop
  • DNA Mastering Program
  • Gene sequence of phage NapoleonB
Procedure:
  1. Some of the red flags on gene annotations were reviewed, gene 78 was examined since it has a 35 bp overlap with the previous gene.
  2. Abstract draft was discussed and written in a small group and submitted at the end of the lab.
Results/Next Steps:

Abstract Draft:

Arthrobacter is a bacteria genus commonly found in soil and sewage that can be utilized in bioremediation and degradation of pesticides. The HHMI SEA-PHAGE initiative at Baylor University (BEARS in the SEA) used Arthrobacter sp. ATCC 21022 as a host to isolate Arthrobacter phage found around the Baylor campus. From over 60 soil samples collected, 8 were positive for Arthrobacter phage, six were submitted to PhagesDB, and novel Arthrobacter phage NapoleonB was sequenced. The genome of the bacteriophage was annotated using bioinformatic tools. Of the 100 predicted genes of Bacteriophage NapoleonB, 72 of the genes had no clear functionality. The predicted genes have been put into a database and used to cross-reference with other phages. Further research could be conducted in order to determine the functions of the unknown proteins.

The gene 78 call wasn’t changed in order to cover the coding potential in the overlapped region.

In the next lab, final gene annotations and abstract draft would still be the main objective.