Madison Powell

4/26/17

Rationale of today’s work: On our final lab day, we will present our presentation for suggestions.

Results: Josh, Haley, and I presented our project to Ashley. We had a few minor fixes, which we fixed, and then we practiced our presentation together.

Conclusion: Today we edited and submitted our final presentation. On Friday, we will present at the CURES in BIO seminar.

Madison Powell

4/24/17

Rationale of today’s work: Today Josh, Haley, and I will finish our presentation.

Results: We finished putting all of our data together, found our conclusion, and put together our presentation. Our presentation can be see here.

Conclusion: Our presentation is finished. Next lab we will present our in hopes for improvement suggestions.

Madison Powell

4/19/17

Rationale of today’s work: Today Josh, Haley, and I will enter all of our data into excel, and find the consensus sequences.

Tools: Google sheets

Results: We inserted all of the data into a google sheet. Then I went onto find the consensus sequences. Josh worked with the terminator prediction software. Haley did the intro and conclusion. We wrote our abstract and started to put our presentation together.

Our consensus sequences can be seen below:

Conclusion: I was able to compute all of the consensus sequences and we found that the consensus for AQ is similar to that of the sigma 70 for E. coli.  Next lab, we will finish putting our presentation together.

Madison Powell

4/17/17

Rationale of today’s work: Today Josh, Haley, and I started to collect the data for the promoter sequences for our independent projects.

Tools: Phamerator, PhagesDB, and DNA master (Promoter prediction).

Results: First we started by downloading the DNAMaster files for the phages we were to study. Also, we decided to look in both gaps between genes 10 and 11, and genes 83 and 84.

Conclusion: Today we collected our data, and found on average 9 or 10 different promoter sequences for each phage between the two locations. Next lab, we will put this data into google sheets and let it average the sequences.

On page 94, it is mentioned that lytic phages must be used for phage therapy rather than lysogenic phages. Throughout this chapter, many examples are given to show that some of the most deadly bacteria have come from lysogenic phages. This is most likely attributed to the fact that they incorporate their DNA into the host and then lie dormant for an extended period of time. This allows for many mutations to arise. Also, if a lysogenic phage is used, and it carries a toxin gene, that gene has the chance to start a chain reaction which will lead to cell death. So, if I had to decide what to do before approving phage therapy, I would come up with some type of software that could screen the phages that will be used for the therapy. In the screening, I would make sure that all phages being used were in fact lytic phages. I would also have it screen the DNA for toxin genes, just in case there was a mistake where a lysogenic phage was used. I would also try to engineering the lytic phages so that after replication, they would not lyse the host cell. The book mentions a possibility of the cell lysing and releasing toxins into the surrounding area. This has a very slim chance of hurting us if the host cell is in us, but the chance is still there. These are the two many things that I would focus on as a scientist that is trying to get phage therapy into clinical practice.

The current system of phage therapy has some risks to it. One of these is represented by the possibility of pushing the bacteria host to become even more resistant. Also, phage therapy struggles with the problem of a narrow host range for each phage; thus, the wrong phage will not work and may even cause a negative effect. A risk also lies in the immunogenicity of the phages, and the pharmacokinetic behaviors that follow along. Although, even with these possible risks, phage therapy has great pros to offer. This is why I believe phage therapy should be researched more so that it can be used in clinical practice, but first, screening for lytic phages only should be done; specifically those that do not lyse the cell after replication.

Madison Powell

4/12/17

Rationale of today’s work: Today Josh, Haley, and I presented our idea to the class, and then began research.

Results: We found research articles that pertained to the background of our study. Also, we began to work towards finding the promoter sequences.

Conclusion: Today we collected our background information. Next lab we will start the process to find the promoter sequences.

Madison Powell

4/10/17

Rationale of today’s work: Today Josh, Haley, and I started to work on our independent project. We will decide on our question.

Results: We originally thought that we wanted to research how phages was put into clusters, but after LeTourneau, we were inspired towards promoter sequences. After looking at phamerator maps, we decided to look specifically at AQ phages.

Conclusion: Today we came up with our topic of promoter sequences and our question of what promoter exist in the AQ genome? Next lab we will look more into background information, and begin to find the promoter sequences that exist.

Madison Powell

4/5/17

Rationale of Today’s Work: Today Cori, Niru, and presented our poster to the class for practice.

Results: We decided who would speak on each section of the poster. It was decided that I continue to present the methods sections. We had the same poster B from URSA for LeTourneau.

Conclusion: We had more practice with our poster and we fixed anything needed. That weekend, we presented at LeTourneau. Next lab, we will start our independent projects.

Madison Powell

4/3/17

Rationale of today’s work: Today Niru, Cori, and I worked with Ashley to edit our Abstract to be submitted for LeTourneau.

Results: Today we edited the original abstract to fit the poster more. Then this was submitted to LeTourneau. Our abstract is seen below:

Genomic Analysis of Arthrobacteriophage Shrooms, Caterpillar, and Nubia

Nirupama T Ancha, Catherine Corinne N Hughes, Madison C Powell

Over  bacteriophage exist within our biosphere but little is understood about them. This experiment was formulated with the intention of increasing the understanding of phage genomics and to help unlock future discoveries within the field of bacteriophage research. A series of isolation, purification, and amplification procedures were performed with the intention of isolating phage from a soil sample using the host bacterium, Arthrobacter sp. ATCC 21022. Twenty-four soil samples were analyzed and 17 phages were isolated. Four phages were sequenced using Illumina sequencing and three were annotated using bioinformatic tools. The three genomes annotated demonstrated high levels of diversity with various genome lengths and genes of known function. All three genomes were found to have at least one gap that exceeded 400 base pairs, an uncommon occurrence for most phage genomes. Final annotations will be submitted to a phage database. By characterizing additional phage genomes and learning more about how they function and interact with their host, advances can be made in phage applications such as bioremediation and phage therapy.

Conclusion: Niru, Cori, and I edited the original abstract to fit this poster more. This was submitted when we register for the meeting. Next lab, we will present our posters to the class for practice for LeTourneau.

Madison Powell

3/27/17

Rationale of today’s work: Today the class had the opportunity to present with one of the class posters. We used this to gain more knowledge of the information, and to ask any questions we had.

Results: I was assigned to the methods section of poster B (the blue one). I determined what was important to talk about while presenting, and practiced a lot.

Conclusion: Today our groups practiced with the posters in preparation for URSA. Next lab, we will present the posters at URSA.