Alex Munoz

26 April 2017

Objective of the day: Practice Independent project presentation before Friday!

Tools: Our presentation

My group and I presented in front of two other groups and Ashley, whom gave us very helpful feedback and criticism.

Results: Ashley said she would double-check with Adair if cartoon graphics were allowed in the presentations and if we were allowed to open external links to show results. Also, she suggested we put less text and become more familiar with the background of the biotech software that we used.

Next Class: We will be presenting our Independent Projects!

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.

A phage therapeutic company, Intralytix, had jumped through many hurdles and gone through many trials in order to receive approval from the FDA. The FDA is the Food and Drug Administration that regulates public health by ensuring that all new drugs and treatment are safe and reliable. In order to make a new treatment, it is extremely costly and time consuming to not only just put in an application, but to also correct all details the FDA wants to make sure are regulated. As a result, this has slowed the progress of bacteriophage treatments in modern medicine today.

The owner of Intralytix, Sulakvelidze, had heard of the rumors when applying to have a new treatment approved by the FDA. The FDA only allowed as few as 18% of medicines that make it to Phase I clinical trials reach the market. The process of drug development and approval costs an average of $800 million and takes 10 years. Therefore, Sulakvelidze had taken many precautions to gain approval before applying, such as: assembling an impressive team, hired an outside consulting company that specialized in steering biotech startups through the FDA’s regulatory maze and had an ally named Marissa Miller, a program officer for the NIH’s National Institute for Allergies and Infectious Diseases, who assisted in writing grants and coached Intralytix through their application to the FDA. However, when they put in their application and discussed regulating phage therapy with the FDA, they had several concerns.

The FDA wanted to be sure that solely lytic phages would be included in the treatment and that more sickly animal models should be used in the treatment trials to represent “the sickest of the sick”. However, one question the FDA wanted answered was what was the rate at which of each of the six phages in Intralytix’s proposed phage cocktail would mutate inside an experimental animal and how these mutations would affect the composition of the animal’s gut flora. Following up on all of the FDA’s points would take Intralytix about 2 years and close to $1 million to complete. Since the company didn’t have this money, they decided to focus on meat, poultry and agriculture and come back to phage therapy in humans at a later time.

In order to make phage therapy a more viable options for people, it is important that the FDA make their application less expensive and shorten the process. I believe that it is important to regulate; however, these regulations must be reasonable and must all be examined at once so that applications can be submitted a max of two times. If the FDA analyzes all details at once, they can either reject or approve it and the researchers are either able to apply again knowing they will gain approval once they fix the details or move on to more readily available and less controversial ways of treatment, such as Intralytix did with agriculture instead of people. Also, the government and FDA must allocate more money specifically for research.

Day 20: 4/24/17

Alex Munoz

24 April 2017

Objective of the day: Have our abstract looked over by Dr. Adair; work on final powerpoint project presentation

Tools: Powerpoint Online

Emily, Navya and I were able to have the abstract looked over by Dr. Adair who suggested that we change our wording on some of the sentences and also gave us some insight/suggestions on further research that we can add in our final presentation. After editing these minor changes, we began working on our final presentation. During our lab time, we were able to complete the majority of our presentation.

Results: A complete first draft of the abstract and a complete first draft of the powerpoint presentation!

Next Class: We will have Dr. Adair look over our presentation and begin practicing for Friday.

Day 19: 4/19/17

Alex Munoz

19 April 2017

Objective of the day: gather evidence for conclusions on research; begin working on abstract for research

Tools: SWISS-MODEL, TM-Align, NCBI

Dr. Adair instructed us not to use Phamerator, so Navya needed a new assignment. Thus, Adair suggested we work on the SWISS-MODEL software. While our group got familiar with the SWISS-MODEL software and used the TM-Align software, I gathered further information on HNH endonucleases and uploaded the primary articles into our box folder.

Results: The TM-Align provided moving images of two protein structures superimposed on one another and how similar their structures are. It also provided 3D-like rotating images of what each protein structure looks like. I found a primary article on NCBI that described the basic function and structure of a homing endonuclease. We also began working on the abstract that is due Wednesday.

Next Class: Over the weekend, my group and I will meet to finish writing the abstract, so that next class we are able to ask Dr. Adair her thoughts on it and begin making our presentation for Friday.

Day 18: 4/12/17

Alex Munoz

12 April 2017

Objective of the day: Present Independent Project Planning, Start gathering research and evidence for research

Tools: NCBI Global Align, NCBI Multiple Alignment, DNA Master

My group and I downloaded all of the fasta files onto DNA Master and began collecting evidence using the amino acid products from each gene that had an HNH endonuclease protein. I used NCBI Global Align, NCBI Multiple Alignment and began taking screenshots of all of my data.

Results: My group and I completed our tasks and gathered evidence/data on the similarities of structure of the protein and the similarities/identities of the amino acid sequences.

Next Class: We will collect all of our data and see the results.

Day 17: 4/10/17

Alex Munoz

10 April 2017

Objective of the day: Completing Independent Project Planning

Tools: Web of Science, Scopus, NCBI, Word

My group and I were able to divide tasks. Emily would work with MUSCLE Alignment and Clustal programs, such as ClustalW2 and Clustal Omega, Navya would work with Phamerator and compare GC content from PhagesDB and I would work with all NCBI programs, such as Global Align and Multiple Alignment. Once we divided the tasks, we typed all of our assignment up including the primary articles, roles/tasks assigned and methods.

Results: Completed Independent Project Planning assignment

Next Class: My group and I will begin gathering evidence to conclude data for our project.

Lab Day 16: 4/5/17

Alex Munoz

5 April 2017

Objective of the day: Continue the search for an independent project, start Independent Project Planning assignment

Tools: MUSCLE Alignment, NCBI Blast,

Emily, Navya and I found that HNH endonuclease proteins were in all three genomes. Therefore, we chose this protein and decided to start our Independent Project Planning assignment by finding primary articles that could give us insight on the significance of HNH endonucleases. Then, we decided to look into different biotechnology programs that could analyze two or more amino acid products for each genome.

Results: We were all able to find primary research articles on present day research concerning HNH endonucleases and were able to find multiple programs such as: MUSCLE, NCBI Blast, Global Align and Multiple Alignment.

Next Class: My group and I will complete the Independent Project Planning assignment and turn it in.

Day 15: 4/3/17

Alex Munoz

3 April 2017

Objective of the day:Find groups for independent project; Start exploring different ideas for an independent project

Tools: Past years’ independent projects

Emily, Navya and I had originally thought it would be interesting to tie factors such as location found, ancestral lineage and phylogeny to relate the bacteriophage clusters AU, AK and AL. However, when we discussed this idea with Dr. Adair she believed that it would be too broad and the data would most definitely be inconclusive since bacteriophages are abundant all over the world. She did suggest however, that we could find a specific function or protein that Caterpillar, Nubia and Shrooms had in common and relate those back to their clusters.

Results: Our original idea was a good starting point; however, it was too broad. Dr. Adair pointed us in a more specific and concise direction.

Next Class: Navya, Emily and I will analyze all three genomes in order to find a similar function/protein they have in common.

Alex Munoz

Day 10: 3/15/17

Objective of the day: Upload DNA Master Complete Work; Work on URSA Scholars Week poster with group

Tools: Baylor Box, Canvas, Powerpoint, Google Docs

Christina compiled a box folder with all of the final documents needed to upload our complete product for Nubia’s annotated genome. So I sent her my completed DNA Master version and then uploaded it onto the assignment on Canvas. Cori, Niru, Noah and I all contributed our ideas for the poster and split up tasks to accomplish over the weekend.

Results: Nubia has finally been annotated and my poster presentation group and I have begun brainstorming for what’s to come.

Next Class: My poster group and I will see what has been accomplished over the weekend and work from there for our poster.

Day 11: 3/20/17

Objective of the day: Work on poster for presentations on March 22

Tools: Powerpoint, Google Docs

The group gathered and discussed what they thought needed to be changed and what should stay on our poster. We fixed those details and finished the final product.

Results: A finished poster!

Next Class: Present out poster to the class and we will pick the best two to be displayed at URSA Scholars Week.

Day 12: 3/22/17

Objective of the day: Scholars Day Poster Presentations

Tools: Ourselves 🙂

Each group presented

Results: Two groups were chosen to have their poster displayed at URSA Scholars Week and our poster was selected to be one of the two! yay!

Next Class: practice with the chosen posters for URSA Scholars Week

Day 13: 3/27/17

Objective of the day:Practice presentations with the top two posters chosen for URSA Scholars Week poster presentation on 3/29

Tools: Our presentation skills

Ashley, Jennifer and Dr. Adair gave us feedback as we used the selected posters to present as we would on the actual presentation day.

Results: Each group was given feedback, which was helpful for the day we presented.

Next Class: We present!

Day 14: 3/29/17

Objective of the day: Presented posters at URSA Scholars week

Tools: Ourselves

We all took shifts during our lab time period and presented to different judges our research the we have accomplished over the past two semesters.

Results: A great experience!

Next Class: Begin working on Independent Projects

Alex Munoz

Lab Day 5: 2/20/17 through Lab Day 8: 3/1/17

Objectives of those lab days: Revising genes 33-48

Tools: DNA Master, Glimmer, GeneMark, NCBI BLAST, PhagesDB BLAST, Starterator, Phamerator

Pranav and I peer reviewed genes 33-48, which were annotated by Christina and Navya. Pranav reviewed the even numbers and I reviewed the odd numbers. Genes 46 and 48 were deleted and all of the entries were put in correctly as far as we could tell. There were a couple of typos in the Master Excel Sheet, but as we reviewed we corrected them.

Results: There were no major corrections that I needed to make, only a few typos.

Next Class: Prepare the Final DNA Master Upload to be revised by Lathan and Dr. Adair.

Lab Day 9: 3/13/17

Objective of the day:Preparing Final DNA Master Upload with all new changes/revisions included; get in groups to work on URSA poster

Tools: DNA Master, Glimmer, GeneMark, NCBI BLAST, PhagesDB BLAST, Starterator, Phamerator

I began preparing the Final DNA Master Upload with all of the deletions, insertions, and revisions included. I followed a procedure given by PhagesDB step-by-step and was able to complete the final annotation of Nubia. Dr. Adair also assigned a poster “competition” in which we got into groups of four and create posters to be selected for URSA. I decided to be in a group with Cori, Niru and Noah.

Results: Completed final annotation of Nubia including all revisions and chose a group for my poster.

Next Class: Begin working on poster for URSA