4/26 Emily Johnson

Purpose: The purpose of today’s lab was to practice our presentation and get suggestions on how to improve

Methods: We split it up so Navya is doing the introduction and further research part, Alex is explaining our methods and part of our results and I am explaining the other half of our results and our conclusion

Ashley gave us some really good tips to help clean up our slides and make the presentation flow smoother. She recommended that we add our own chart into the presentation to have more results and that we move some images around to make it more organized. We also planned on using a hyperlink to show a rotating 3D model, but she warned us that would not work and that we should just use screenshots. Finally she hinted that we research the software we used further in case anyone asks questions about it because it is different software than most other groups would be using and people might have questions about it.

Next lab will be Friday when we will be presenting our project:)

4/24 Emily Johnson

Purpose: The purpose of lab today was to create our powerpoint presentation for Friday

Materials:

Microsoft Powerpoint

Methods:

We utilized microsoft powerpoint online and were able to make all of our presentation today  because we had met up over the weekend to write our abstract. We decided to put at least one image on every slide to make it more visually appealing and took screenshots of our data to insert as results since a lot of it depended on pictures.

Next lab we will practice presenting in front of two other groups so we can get some feedback and suggestions on how to improve.

4/12 Emily Johnson

Purpose: The goal for today was to use bioinformatics tools to compare our HNH Endonuclease sequences

Materials:

PhagesDB

Phamerator

NCBI Multiple Align

NCBI Global Align

EBI Clustal-Omega

EBI MUSCLE Alignment

Methods:

We divided up the work today: Navya was in charge of using PhagesDB and Phamerator to gather data about our gene, such as GC content, pham numbers, etc. Alex used NCBI Multiple Align, and Global Align to run comparisons on the genes, and I used EBI (the European NCBI) Clustal-Omega, and MUSCLE Alignment to compare two genes at once and three genes at once.

First, I used DNA Master to copy the nucleotide and amino acid sequences from each gene so I could run them through the databases.

Then, I used Clustal-Omega to compare the nucleotide sequences of: Caterpillar v Nubia, Caterpillar v Shrooms, and Nubia v Shrooms

I then used Clustal-Omega again to compare the amino acid sequences of: Caterpillar v Nubia, Caterpillar v Shrooms, and Nubia v Shrooms

After I did that, I realized that I could use MUSCLE Align on EBI to compare all three genomes, so I then did that where Sequence 1=Caterpillar, Sequence 2= Nubia and Sequence 3= Shrooms and obtained a percent identity matrix.

Results:

Nucleotide Similarity:

Caterpillar vs Nubia Nucleotide Similarity; Sequence 1=Caterpillar, 2=Nubia

Caterpillar vs Shrooms Nucleotide Similarity ;Sequence 1=Caterpillar, 2=Nubia

Nubia vs Shrooms Nucleotide Similarity; Sequence 1= Nubia, 2=Shrooms

Amino Acid Similarity:

Caterpillar vs Shrooms Amino Acid Similarity; Sequence 1=Caterpillar, 2=Shrooms

Nubia vs Shrooms Amino Acid Similarity;Sequence 1=Nubia, 2=Shrooms

Identity Matrix:

Sequence 1=Caterpillar, 2=Nubia, 3=Shrooms

Discussion:

So, from this we learned that the percent similarity of the nucleotide sequences is much higher because it can only be made of 4 options: A,G,T, or C while there are 20 options for each amino acid. Also, as we can see here, Caterpillar and Nubia have the highest percent amino acid similarity of 27%. Event though this is the highest similarity, it is not a significant percent similarity.

Next lab, I will hopefully be able to compare the structures of the proteins, not just the sequences. Because the sequences of Caterpillar and Nubia are the most similar, I would expect that the structures of the two are also the most similar.

4/10 Emily Johnson

Purpose: The purpose of today’s lab was to decide on a research question and fill out our project planning sheet (which was due at 4pm)

Methods:

We came back to our idea of comparing one gene from each of our genomes. We searched through the functions list on the google spreadsheet of each gene and wrote down the proteins that all three genomes had in common. This ended up being only two proteins: HNH Endonucleases and Tape Measure Proteins. We decided to use HNH Endonuclease because it seemed more interesting than the Tape Measure Proteins. Interestingly, each genome had only one HNH Endonuclease so we thought that it may be more conserved, and we had no worries that there would be multiple types of HNH Endonuclease in a single genome.

We decided our research question would be: how does the he HNH Endonuclease protein compare across the three clusters AL, AK and AU?

On Shrooms, the HNH Endonuclease was gene 90

On Caterpillar, the HNH Endonuclease was gene 3

On Nubia, the HNH Endonuclease was gene 63

Next lab, we will start gathering data to answer our question.

4/5 Emily Johnson

Purpose: The purpose of today was to set a research question

Originally, we wanted to compare the three genomes Nubia, Shrooms and Caterpillar to see how location of discovery, ancestral lineage and phylogeny factor in to how the genomes are clustered. However, we found that location has already been studied and that there was no correlation. We tried to think of ways to compare ancestral lineage and phylogeny by using bioinformatics tools such as NCBI Blast and Multiple Align, however we were unable to figure out how to compare the full genome, because before we had only used a single gene at a time. After spending a good chunk of class time on the computer trying to figure out how to make this work, we decided that we couldn’t and we should choose a different topic.

We knew that we wanted to compare our three genomes, because they are all in different clusters and we wanted to see what that means on a molecular level. We decided that even though we could not compare three whole genomes, we could compare three different genes. Then we ran out of class time, so we decide to revisit this idea next lab.

Next lab, we hope to finally decide on our research topic and turn in our project planning sheet.

4/3 Emily Johnson

Purpose: Today in lab we were assigned our independent project

Methods:

We spent a lot of class time talking about our requirements and discussing the assignment. In the end of class we broke into groups- my group is Navya Katragadda, Alex Munoz and me. We began discussing topics, but we did not have a lot of time so we have not settled on anything yet.

Next lab we hope to decide on a topic and set our question.

3/29 Emily Johnson

Purpose: Today was finally the day to present our posters at URSA Scholars Day

Methods: We met in the atrium of the BSB and had each signed up for certain time slots to present our posters. Josh, Navya, Thomas and I were signed up for a later time slot so we spent the first hour or so walking around the atrium and viewing other posters. It was a really great experience and was very fascinating to see all the other research that has been going on at Baylor. I even knew a couple of people who were presenting their research projects which made it even more interesting to here what they have been doing all year. I even had enough time to see the posters from the internship that I’ll have next year!

When it was my turn to present, I was a bit nervous, but we only had one person come by and he had some questions but not too many and we were able to answer all of them. It was a great experience to present the research that we had been working on all year and getting to share our knowledge. I especially enjoyed that we all got a turn to present our project because while I do not enjoy public speaking, I felt proud that I was able to explain my work (aka my baby) to someone else and watch them understand.

Purpose: The purpose of today’s lab is to perfect our presentations on the poster so we are fully prepared for Wednesday’s URSA presentation

Methods:

My group- Josh, Thomas, and Navya- were assigned poster 2 to practice. We each took turns standing up and presenting the poster for half of the class, and then answering questions that we might be asked and being critiqued. Our practice went well, we knew the answers to the questions and our critique was talking too fast, saying um, and our transitions were not smooth.

We also signed up for time slots to present Wednesday, and next lab that is what we’ll be doing.

Purpose: The purpose of today’s lab is to present our posters and then vote on which two we want to present at URSA Scholar’s week.

Today, Josh and I had to scramble at the beginning of lab because Thomas did not do his one job of making the poster. So Josh, Navya and I threw one together really quick, which was a bit disappointing because it did not let us put as much time on it as we wanted to.

We presented our poster and then voted for the top two. The class decided on Stu’s groups poster and Niru’s groups poster. Tomorrow, the class will divide into two groups to practice presenting the posters for next Monday (3/29).