April 26

4/26/2017: Lab Day 20- Practice Presentation

Navya Katragadda

4/26/2017

Rationale: Finish up any last touches for our PowerPoint and practice our presentation

Today, we finished the last bit of the PowerPoint, decided who is going to present what part, and then practiced our presentation. Alex will be presenting the methods and the sequence results. Emily will be presenting the structural results and conclusion. I will be presenting the Introduction, the questions we are asking, and the Discussion/ Future Research. After we practiced our presentation, Ashley gave us some tips on how to make the presentation even better. Then, we used her suggestions and improved our PowerPoint and the presentation. We are presenting second at the CURES Symposium on Friday.

Next Step: On Friday, we will be presenting our independent project at the CURES Symposium.

April 26

The Forgotten Cure #3

Navya Katragadda

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.

Though phage therapy has had its up and downs in the science world, it has recently become a popular field of research for many scientists who are looking for an alternative way to treat patients. FDA stands for the Food and Drug Association. The FDA’s main goal is to promote and ensure public safety by testing and approving food, drugs, treatment plans, and much more before they are distributed to people. Through the FDA is working towards ensuring the safety of the public, the process to get a drug or treatment approved by the FDA takes a long time and it costs a lot of money. The FDA gives a lot more money to pharmaceutical companies instead of researchers, which slows down the process for a treatment to get approved. No medicine or treatment can be used on patients until it gets approved by the FDA. There are four main steps in the FDA approval process. The first step is that the drug company needs to get the drug tested. The second step is send the CDER results from the test to make that the results show that the test is safe for use and distribution. The third step is that a team of CDER professionals that consists of doctors, statiscians, pharmacologists, and others will go to the company and see the data the company had collected and how they are planning to label the drug. The final step is that if the benefits of the drug outweighs the cost, then the drug will get approved for distribution and for use on patients.

Two companies, Intralytix and GangaGen, worked very hard to get their respective phage therapy ideas to get passed by the FDA. Intralytix was founded in 1998 by Sulakvelidze and is based in Baltimore, Maryland. Intralytix is a company that focuses on selling bacteriophage-based products that could combat bacterial pathogens in the environment, in medical settings, in food, and in much more. Intralytix was actually the first company to get approved by the FDA for the use of bacteriophage-based products in food. GangaGen was founded in 2003 by Dr. Ramachandran in India and was trying to find ways to fight antibiotic resistant bacteria using phages. GangaGen figured out that a bacteriophage-based protein called ectolysin that would bind to the antiobiotic resistant bacteria and eventually kill them. However, he ran into a problem when he was trying to get this treatment approved because he knew that the FDA would not approve anything that could potentially lead to toxins entering the patient’s body. So, he had to figure out a way to ensure that the phages used in the treatment would not lyse their host cell and enter the human body.

In my opinion, there are two ways that could speed up the FDA approval process for not only phage therapy but for new medication as well. The first way comes from the researcher’s side. If the researcher thinks of all the possible side effects and negative consequences of the drug or treatment and work to reduce those negative effects, then the FDA will more likely approve of the treatment or drug since it will not pose any serious consequences for the patient’s that take this. Researchers could do this by letting other scientists review their work and give their input. This would help tremendously because sometimes a fresh set of eyes can help to figure out if there are any issues. The second way would be if the FDA could allot more money to research because then the researchers will be able to consider multiple results of the treatment or drug, and then work to eliminate the negative effects and to ensure the success of the drug. It is very difficult to come up with a successful treatment or drug if the researchers do not have enough money to carry out the study to the best of their ability. It is important for researchers to put their best foot forward when conducting these studies because the treatments and drugs that come out of the study will eventually be used on patients and if the studies for the treatments and drugs are not thorough, it could be very detrimental to the patients that consume the drugs or take part in the treatments.

April 24

4/24/2017: Lab Day 19- Work on PowerPoint for Presentation

Navya Katragadda

4/24/2017

Rationale: Make sure that our abstract is logical and work on the PowerPoint for our presentation

Today, Dr. Adair approved our abstract. We also worked on our PowerPoint and included the introduction, our question, methods, results, conclusion, discussion, and works cited. We made sure to include pictures and figures that we acquired from our data.

Next Step: We are going to practice our presentation since we are presenting on Friday.

April 19

4/19/2017: Lab Day 18- Finished Gathering Data

Navya Katragadda

4/19/2017

Rationale: Finish gathering data and analyze the results

Tools Used: NCBI, SWISS-MODEL, TM-align

Today, we were able to finish gathering our data. Since we could not use Phamerator for the structural figures, Emily and I worked on creating the structural figures through the SWISS-MODEL. We found out that the SWISS-MODEL can create a rotating model for each individual HNH endonuclease and it could superimpose two of the proteins so we could see what parts of the proteins are similar and what parts are unique to that specific HNH endonuclease from its respective genome. So, we first created individual rotating models for the HNH endonucleases from each of the three genomes. Then, we superimposed Nubia and Shrooms, Shrooms and Caterpillar, and Caterpillar and Nubia. While Emily and I were working on the SWISS-MODEL, Alex was doing research on what exactly a HNH endonuclease is and what does it do. She used NCBI to find and article that we can later use for our abstract and our presentation.

Results: Apart from getting really interesting structural figures, we realized that Nubia and Shrooms were the most similar structurally while Caterpillar and Nubia had the highest sequence similarity value. We thought this was very interesting and we are going to look into that.

Individual Protein Figures:

Shrooms:

Nubia:

Caterpillar:

Superimposed Figures:

Caterpillar and Nubia:

Caterpillar and Shrooms:

Nubia and Shrooms:

Next Step: During the next lab session, we will finish up working on our abstract, and then we will work on the PowerPoint for the Presentation.

April 12

4/12/2017: Lab Day 17- Gathered Data

Navya Katragadda

4/12/2017

Rationale: Start gathering data for the independent project

Tools Used: NCBI Global Assign, NCBI Multiple Alignment, DNA Master, Phamerator, Clustal-Omega, and MUSCLE Align

Today, we finally started gathering the data for our independent project. We first downloaded the Fasta files for Caterpillar, Shrooms, and Nubia so that we can get the nucleotide and protein sequences for each of the HNH endonucleases that we were working with from the different phage genomes. We all used different tools to see if there were any similarities between the HNH endonucleases in each of the genomes. Alex used NCBI Global Assign and NCBI Multiple Alignment to gather her data. Emily used Clustal-Omega and MUSCLE Align on EBI to gather her data. I used Phamerator to see if I can find the structure of each individual HNH endonuclease. Dr. Adair told me that Phamerator did not have the ability to make create structural figures and she suggested that I use SWISS-MODEL. Overall, we got a sufficient amount of data from the tests that we ran today.

Results: 

From NCBI Multiple Alignment and NCBI Global Assign:

From Clustal-Omega and MUSCLE Align on EBI:

Caterpillar vs. Nubia: Caterpillar vs Nubia DNA Similarity-2l7isbi

Caterpillar vs. Shrooms: Caterpillar vs Shrooms DNA Similarity-1770jso

Nubia vs. Shrooms: Nubia vs Shrooms DNA Similarity-1icowdb

Next Step: We will finish running some more tests, including the SWISS-MODEL and then analyze our results if we have time.

April 10

4/10/2017: Lab Day 16- Created our Project Plan

Navya Katragadda

4/10/2017

Rationale: Make a plan on how to successfully carry out our research plan

Today, we created a step by step plan for how we wanted to conduct this research project. We also found three scientific articles that we could use for some background knowledge. Then, we divided up the work and listed out what each of us are going to do. Lastly, we came up with the final question that we wanted to research: How HTH endonucleases relate to each other based on clusters AK, AU, and AL?

Next Step: We will start gathering our data during the next lab session.

April 5

4/5/2017: Lab Day 15- Thinking of Ideas Independent Project

Navya Katragadda

4/5/2017

Rationale: Finalize our topic for the independent project

Today, we got the chance to talk to Dr. Adair to ask her about our topic and she said that it was too broad. So, we decided to refocus and blast the genomes of the different phages in order to see how similar the phages are. This topic was approved by Dr. Adair.

Next Step: Make a plan on how we are going to execute this project and gather all the data that we need to get to a proper conclusion.

April 3

4/3/2017: Lab Day 14- Independent Project Instructions

Navya Katragadda

4/3/2017

Rationale: Finish any remaining annotations for the AN phage and then start thinking about the independent projects

Today, I formed my group for the independent project. My group consists of Alex, Emily, and me. We decided to look into different ideas that we could possibly research since none of us were going to LeTourneau. We came up with a few ideas such as figuring out if the GC content of the phage genomes changes with location both around the world and around the United States and creating a phylogenetic tree to compare the different genomes.

Next Step: Talk to Dr. Adair to see if our topic can be used for our independent project.

March 29

3/29/2017: Lab Day 13- URSA Scholar’s Week Poster Presentation

Navya Katragadda

3/29/2017

Rationale: Present our posters at URSA Scholar’s Week

Today, we got the opportunity to present the posters that we chose at URSA Scholar’s Week to different judges and students. Our presentation was successful and we even won first place for our research-inquiry based presentations.

Our Posters:

 

Our Award:

Next Step: Those who were going to LeTourneau will work on their posters while everyone else will be wrap up any annotations that have not been completed and start working on the Independent Project.

 

March 27

3/27/2017: Lab Day 12- Present Poster to the Class

Navya Katragadda

3/27/2017

Rationale: Present our posters and pick the top 2

Today, each of the six groups presented their respective posters. We were able to talk about the positive and negative aspects of each of the posters. There were a few aspects of different posters that we though would be better if they were combined. At the end of the day, we each voted on the two posters that we liked the best.

Our Poster:

Next Step: We will be presenting the two posters that we chose at URSA Scholar’s Week.