5/1/19

Rational:

To practice the presetation and receive feedback on the presentation. Also, to listen to two other presentations and give them feedback as well.

Procedure:

• Listened to two groups presentation
• Graded them on the different parts of th presetation such as background info and results
• Presented the presentation
• Listened to feedback from the class
• Received feedback from my group
• Set up a time to meet and finalize the presentation

Observation:

• The other two groups seemed to have more quantitative data than our group which had more qualitative data

Concllusion:

Practiced the presentation and received feedback on what to fix before Friday. Before Friday my group will meet up and make last minute changes on the presentation and re-split up the slides more evenly.

4/29/19

Rational:

To finish the powerpoint presentation and split up the slides between grpup members.

Procedure:

• Edited the unfinished slides
• Using Jmol found the width of NapoleonB’s holin and the width and heighth of it’s endolysin
• Using geometry found the approx. number ofholinstat would be needed to make a hole large enoug to pass the endoysin depending on how it’s oriented
• Added notes to the bottom of the slides
• Split the presentation up between group members

Fig.18 – This figure shows how if endolysin passes through holin longwise it would take about 17 holins to form a pore large enough, if not it would take approx. 11

Conclusion:

We were able to finish the the powerpoint and add some quanitative data as well. Next lab we wil practice present and fix any mistakes found.

4/24/19

Rational:

To create the rough draft of the research presentation and to create the Gly Gly bond to put in the image of NapoleonB’s endolysin’s catalytic site.

Procedure:

• Created the basic outline of all of the slides
• Used a previous presentation to find images to use
• Used Jmol to create the Gly molecule
• Inserted the Gly Gly bridge into the catalytic site of NapoleonB’s endolysin
• Added notes for the background slide

Fig.17 – Shows the background slide explaining the function of both holins and endolysins as well as what clusters are

Conclusion:

We finished the basic outline of the presentation and split up the sections for each member to work on. The Gly molecules were created in Jmol for us to show the Gly Gly bridge in NapoleonB’s endolysin. Next lab we will fix problems in the presentation and start practicing our presntation.

4/17/19

Rational:

To write the abstract for the research porject.

Procedure:

• Found the catalytic region of a lysin A
• Researched the difference between lysin A and endolysin
• Wrote the abstract for the project

Observations:

• Found that proteins called as Lysin A’s have the same catalytic structure as endolysins
• Found that endolysin is probably a general term that includes lysin A

Conclusion:

Looked at the differences between other lysins to see if they had the same catalytic region. Wrote the abstract for the project. Next lab we will polish the abstract and start to create the presentation for the project.

4/15/19

Rational:

To compare the hydropathy plots of possible holin genes in other Arthrobacter phages. To create the outline for the researh presentation.

Procedure:

• Took the amino acid sequences of the predicted holin genes of AM cluster phages and two outside the cluster
• Created hydropathy plots using TMHMM with these sequences
• Added the project title and guiding question to the outline
• Created a basic outline for the abstract

Observations:

• The hydopathy plots of the AM phages were very similar to NapoleonB and at first glance some look almost identical

Fig.15 – NapoleonB’s hydropathy plot (left) looks almost identcal to Arcadia’s (right) another AM cluster phage

• The differences between NapoleonB’s hydropathy plot and phages from other clusters were more obvious than with phages from the AM cluster

Fig.16 – NapoleonB’s hydropathy plot (left) shows more differences with Madamato (right) a BI cluster phage

Conclusion:

Created hydropathy plots for all of the AM phage predicted holins and a few others to compare. Finishd the outline for the research project presentation. Next lab we will write the abstact for our research project.

4/10/19

Rational:

To evaluate the project’s progress as well as my own contributions to the project. Also to create an outline of the presentation for the Symposium on the process behind our research. Comparisons between the different protein stuctures were also done

Procedure:

• Each individual filled out the form for the QTM evaluation
• After the print outs of the different phage’s endolyins and holins were compared to see similarities and differences
• The uses of Jmol were also explored in more detail to be able to use it more efficiently
• The group created a shared presentation and created an outlne for the presenation

Fig.13 – This image shows the original title slide for the presentation

Fig.14 – This image shows the amino acids that are part of the catalyic site of Elesar’s endolysin

Conclusion:

We were able to better understand Jmol so that we can better use it as a tool. We were able to see how similarly or dfferently the structures of other phage’s holin and endolysins were. We were also able to create a outlne for the presentation. Next we will find where the catalytic site is on other phages and finish the presentation for the Symposium on Friday.

4/8/19

Rational:

To find five sources that give background information to the research project. Also, to find the catalytic site for the endolysin.

Procedure:

• Used the folder of sources collected
• Chose five sources that were background information
• Found a tool that could show where certain amino acids are found
• Used Jmol to find the amino acids related to the catlytic site
• Found the possible catalytic site

Fig.12 – This image shows the section (HLH) that is part of the catalytic domain in endolysins

Conclusion:

The five bacground sources that were needed were found. We were also able to find a tool that showed where specific amino acids were found whch was not something that could be done on RaptorX. Next lab we will find the catalytic sites of other phages and figure out how to better use Jmol

4/3/19

Rational:

To finish gathering background material and to create an outline of how the project will proceed.

Procedure:

• Looked for and shared information on the structure of holin and endolysins
• Tried to understand the mechanism of the proteins inrelation to the structure
• Determined the title of the poster
• Refined the research question and added background information
• Added the sources that had been found
• Found three biotechnology tools to use

Observation:

• We were able to find a detailed model of the endolysin structure but not holin

Conclusion:

Our group was able to create a general outline of the project and give a little guidance as to where the project goes. Next lab we will start researching NapoleonB and other phage’s endolysin and holin genes.

4/1/19

Rational:

To practice our poster presentation for when we present during URSA

Procedure:

• Each group of two presented
• The class, the TAs, and Dr. Adair asked questions throughout
• The group had to answer any question to the best of their ability
• The groups and class listened to critiques of the presentation

Observations:

• One critique given was to spend more time on the results and figures than on anything else
• Another thing was to mae sure that all of the terms and procedures on the poster were understood clearly

Conclusion:

We presented watched groups present the poster and lstened to the ways that the presentation could be improved.  When my group presented we used the earlier critiques to improve it and looked for specific ways we needed to improve. Next lab we will contnue working on the indvdual research poster.

3/27/19

Rational:

To create a research question, to start looking at the literature relating to the question, and to look  into how to research the topic chosen.

Procedure:

• BLASTed NapoleonB’s endolysin and holin genes in order to see if they are conserved
• Searched for articles relating to holin proteins, endolysin proteins, and these protens in relation to phages
• Refined the topic on holin and endolysins in phage into a research question

Observations:

• The BLAST showed that both gene have a CDD and are conserved meaning that the genes will likely be similar to other phages
• The final queston was Using bioinformatics can phage’s endolysin and holin structures and functions compare to other Arthrobacter phages?

Conclusion:

By the end of lab we discovered many articles to use in order start our research. We also created the final research question and confirmed that we would be able to with our resources research the topic. Next lab we will prepare for the poster presentation for our class poster.