Name: Hope Willenborg

Date: Tuesday, April 18, 2017

Rationale of the work:
The purpose of the lab was to finish the project rough draft.

Tools used and/or Methods:

1. Finish the poster template

Conclusions and next steps:
Today, I designed and perfected the rest of the poster. Will wrote the abstract, and Micah wrote the acknowledgments. For the future, we need to change the title and explain both the introduction and methods more clearly.

Name: Hope Willenborg

Date: Tuesday, April 11, 2017

Rationale of the work:
The purpose of the lab was to continue refining questions to research and finish the project rough draft.

Tools used and/or Methods:

1. Finish the poster template
2. Analyze your research

Conclusions and next steps:
The differences of protein sequences between the phages correlated to the different structures. The phages in the same pham (i.e. small percent difference) look similar, whereas those that are a part of different phams (i.e. bigger percent difference) did not look similar. However, they all only have alpha helix foldings and no beta pleated sheets. This could be a signature of tapemeasure proteins. To further understand how the structure relates to the function for tape measure proteins, the structure of tail proteins could be found in the same phages and compare their structural similarities with their protein similarities.
We gave up on the images on the SwissModel because they were not nearly as good as the RaptorX images. Also, we tried to see if the amino acid sequence length correlated to structure, but we had no evidence. Sonny was 16,399 base pairs. Bennie was 2,567 base pairs. Yank and Moloch were both 1,997 base pairs.

Fig. 1: Bennie

Fig. 2: Moloch

Fig. 3: Yank

Fig. 4: Sonny

Name: Hope Willenborg

Date: Tuesday, March 28, 2017

Rationale of the work:
The purpose of the lab was to continue refining questions to research.

Tools used and/or Methods:

1. Look at previous questions asked to refine your question
2. Look at previous posters to start sketching the template of your poster

Conclusions and next steps:
Our new, refined question is “What is relationship between the different protein sequences of tapemeasure proteins in bacteriophages and their structures?”. The goal of the day was to find new phages to research and figure out how to use SwissModel.
SwissModel’s main data point to look at ended up being the Q Means Score. The scores closest to 1, the better. However, we learned of another structure-predicting program called RaptorX. So we sent in our protein sequence there, and we are hoping to get results back in a couple of days.
We found our genes to use based off of PhagesDB (to ensure we were only using Arthrobacter phages) and Phamerator. We got 3 genes from different phams, and 1 gene from a same pham to act as the control. We are using Yank- Gene 13, pham 6177 (30); Moloch- Gene 13, pham 6177 (30); Sonny- Gene 19, pham 5319 (16); Bennie- Gene 14, pham 962 (33). Their respective similarities are shown below.
For the future, we hope to compare the RaptorX images and start constructing the research poster.

Fig. 1: Sonny and Bennie comparison.

Fig. 2: Yank and Bennie comparison.

Fig. 3: Yank and Sonny comparison.

Fig. 4: Yank and Moloch

Name: Hope Willenborg

Date: Tuesday, March 21, 2017

Rationale of the work:
The purpose of the lab was to continue exploring different questions to research.

Tools used and/or Methods:

1. Look at new databases to search for questions
2. Look at previous posters for inspiration

Conclusions and next steps:
We started to think about Phams and how they relate to one another in terms of size, gaps, or overlaps.
Next, we got on the idea of finding tapemeasure proteins by looking at annotations to see the longest gene, and using the same Pham to find other similar tapemeasure proteins. Then, we would find their percent similarity of the protein sequences and corresponding structure from the SwissModel. Lathan told us GeneBank would eliminate our need to annotate the proteins because it would have the proteins annotated already.
We figured out that proteins with the same Pham, though, have identical sequences. So we revised our experiment to have different proteins from different Phams.
Our overall question of the day was “Will tape measure proteins with different phams, despite their percentage difference within nucleotide sequence, still produce similar structures?” Our method would be Phamerator (to find phages with different Phams)–> GeneBank (to find the protein sequences of the phages)–> BLAST NCBI Alignment (to find the percent similarity between the sequences of the phages)–> SwissModel (to identify the structure of the proteins).
Our next step would be to learn how to use SwissModel because it did not make sense to us. We were using the phages Lore and Timinator to find other phages since they were in different phams. We ended up using Sonny(from Timinator’s Pham) and Yank(from Lore’s Pham). We did not use Timinator nor Yank because their sequences are not available in GeneBank.

Name: Hope Willenborg

Date: Tuesday, March 14, 2017

Rationale of the work:
The purpose of the lab was to start exploring different questions to research.

Tools used and/or Methods:

1. Finish annotating Timinator.
2. Explore these places in phagesdb to get ideas for the project
   1. Glossary
   2. Links
   3. Publications

Conclusions and next steps:
I am in a group with Micah and Will. We were exploring different things we could test with HTH binding protein, holin and lysine, and tapemeasure proteins. We are thinking of doing something with tapemeasure proteins such as: if the phagesdb blast hit is NKF, but the NCBI says tapemeasure protein, can we manipulate the phagesdb hit to figure out if it is also a tapemeasure protein? If we change the length of the tapemeasure protein, will the minor tail protein have any changes? What is the ratio of the tapemeasure protein to the tail proteins of different species?

Name: Hope Willenborg

Date: Tuesday, February 28, 2017

Rationale of the work:
The purpose of the lab was to individually annotate Timinator’s genes.

Tools used and/or Methods:

1. Download Timinator.fasta file
2. Annotate your assigned genes and put your annotations in the google document.

Conclusions and next steps:
I worked on genes 19, 41, 63, 78, and 58. I was able to use auto-annotation on all of them.
Gene 19 was the tapemeasure protein.
Genes 41 and 58 were no known function.
Gene 63 was said to be a DNA binding protein according to NCBI BLAST, but it is not specific enough to give it a function.
Gene 78 was also a no known function while left auto-annotated. However, the gene could be elongated if gene 79 was at a different start site, and this may be prefered because the NCBI BLAST hit was q:1 s:3. Because gene 78 is a reverse gene whereas gene 79 is a forward gene, there needs to be a 50 bp gap for a promoter. When gene 78 is elongated, there is only a 49 bp gap.
The next step is to determine how to read gene 79, so I can properly annotated gene 78.

Gene 19

Gene 41

Gene 63

Gene 78

Gene 58

Name: Hope Willenborg

Date: Tuesday, February 21, 2017

Rationale of the work:
The purpose of the lab was to learn about all the genes from Lore.

Tools used and/or Methods:

1. Finish the powerpoint about the genes you annotated
2. Present your genes

Conclusions and next steps:
We all discussed the genes we annotated and filled out the genes that we had to change and genes that had a specific function. Some important genes to note are genes 3,16,21, and 26. Gene 3 may have a longer start site than originally called for. Gene 16 has q:3 s:2 on NCBI BLAST. Gene 21 has been deleted and will be remade as a reverse gene. Gene 26 was deleted and moved to a different ORF.
The next step is to make a DNAMaster file so we can send our discovery to University of Pittsburg.

Name: Hope Willenborg

Date: Tuesday, February 14, 2017

Rationale of the work:
The purpose of the lab was to learn how to change a start site and annotate on our own.

Tools used and/or Methods:

1. Open DNA Master
2. Open Virtualbox
3. Finish the assigned genes from last week

Change a start?

1. Click on the calculator
2. Click “post”

Delete a gene?

1. Highlight gene
2. Click “delete”

Insert a gene?

1. Click “insert”
2. Fill in the details
3. Click “post”

Conclusions and next steps:
I finished annotating gene 17 of Lore. I also annotated gene 15 and gene 22. They were pretty straightforward. I did not have to change anything about them.
Hopefully next week all the genes of Lore will be completely annotated, so we can work on a new phage.

Name: Hope Willenborg

Date: Tuesday, February 7, 2017

Rationale of the work:
The purpose of the lab was to learn how to use starterator and annotate different genes on our own.

Tools used and/or Methods:

1. Open DNA Master
2. Open Virtualbox
3. Get assigned to a gene
4. Download “Lore” fasta file from phagesdb
5. Annotate the assigned gene in the google drive
   1. Use starterator to find its suggested start site
   2. Enter in the query and subject (q:1 s:1) in the blast hits

Conclusions and next steps:
Starterator is another tool to use to figure out where to start the gene. It is based off other people’s annotated genes, so ultimately our judgement is best. The blue line is the recommended start.
I worked and finished gene 17.
Figuring out the correct function is the hardest part for me in annotating, but after searching through the different functions I am able to make a correct decision. The next step would be to finalize the annotated gene.

Name: Hope Willenborg

Date: Tuesday, January 31, 2017

Rationale of the work:
The purpose of the lab was to understand how to use phamerator in order to figure out the function of genes.

Tools used and/or Methods:

1. Open virtual box
2. Hit start
3. Plug in the password: phamerator
4. Open phamerator (the second drop down)
5. Click phage
6. Search “Link” as well as four other AN Anthrobactors
7. Click map
8. Complete questions that matter

1. Annotate your assigned gene
2. Find the function of the gene using NCBI, NCBI CDD, and Phagesdb

Conclusions and next steps:
Phamerator is different from DNA Master because it compares genomics using multiple sequence alignments. It narrows down databases and allows us to look at drafts.
The next step would be to use our own phage and annotate as well as use the phamerator.