April 30

DNA Day 25

1 May 2019 ✷ Independent Research Presentation Practice

Rationale: The presentation was rehearsed in order to prepare for CURES on Friday.

Procedure

  • The class was broken up into 3 chunks consisting of 2-3 research groups
  • The chunks went to different classrooms and practiced their presentations
  • The group that wasn’t presenting critiqued the presenting group and then the roles reversed
  • Presentations were adjusted according to the feedback
    • Fonts were increased
    • images were made larger
    • all of the AM-specific genes were re-BLASTed to see how many hit with high GC bacteria or only AM phages
    • charts/tables were updated with this new information

Results

image of the rubric

Conclusion

We need to be more specific in parts of the presentation that we understand really well but others won’t; better and more concise explanation will make the presentation flow smoother.

Future plans

Finalize and present!

Category: Lily Goodman | LEAVE A COMMENT
April 29

Polishing CURES in BIO Presentation (4/29/19)

Rationale:

Performed a final check on the presentation for CURES in BIO Symposium.

Procedures:

  1. Corrected abstract for CURES in BIO.
  2. Calculated approximately the number of holins required to oligomerization.
  3. Finished presentation.

Results:

Final abstract submitted for CURES in BIO is shown below.

The following images shown were used as measurements when calculating the number of holins required to oligomerization.

The following calculations were made to find the number of holins required for oligomerization.

The following image shows the slides of the CURES in BIO presentation.

The following is the video in the CURES in BIO presentation.

Conclusion:

Depending on the orientation the endolysin exits the cell, it would take approximately 11 holins (if endolysin was oriented vertically) or 17 holins (if endolysin was oriented horizontally). This is an estimate. The estimated number would have more accuracy if calculations used calculus and/or physics-based algorithms and if factors such as spacing between holins were taken into account. Due to limited time, research was not conducted into these variables and methods.

Future Work:

Practice giving presentation in front of class.

Category: Kathryn Adkins | LEAVE A COMMENT
April 29

April 29 2019 Independent Research Presentation

Purpose: The purpose of this lab is to complete the final project presentation.

Tools/Procedures:

Tools:

  • Google Slides
  • Excel
  • DNA Master

Procedures:

  1. An outline for the final presentation was created.
  2. Tables and graphs were made for the data section of the presentation.
  3. Work was done on each section of the presentation, editing the slides and adding visuals to each slide.
  4. Transitions were added to the slides.
  5. The presentation was looked over one last time and then completed.

Results:
The results of this lab included finalizing the final presentation and creating figures and visuals to make the presentation more visually appealing.

Picture of a slide from the presentation.

 

Conclusions: 
In conclusion, the presentation was finished and is ready to present on Wednesday.

Future Work:
Future work will include practicing the presentation for the final presentation on May 3rd. Also, after the practice presentation on Wednesday, final edits will need to be made to the presentation.

Category: Lucy Potts | LEAVE A COMMENT
April 29

4.29.19 Finishing PowerPoint

4.29.19 Finishing PowerPoint

Rationale: Since the presentation is Friday and today was designed in the schedule to finish and revise our PowerPoint to make sure it would be ready to rehearse on Wednesday.

Procedure:

  • Review progress on PowerPoint from previous weeks
  • Determined needs
  • Assigned parts to each group member
  • Researched and completed parts, including conclusion slides, graphics, and citations
  • Reviewed and submitted PowerPoint

Results:

  • Presentation that is ready to rehearse and assign roles to is ready for Friday’s CURES in Bio Symposium

Conclusions:

  • Today marks the final work day on the independent research projects. The information found will now be what we draw our conclusions for and we will only be making minor adjustments with fine tweaks before Friday’s official presentation for our final project grade.

Next Steps:

  • Practice presentation and find any potential holes before Friday’s presentation.
Category: Henry Burns, Uncategorized | LEAVE A COMMENT
April 26

Final Abstract Writing and Research Wrap Up 4/24/19

Final Abstract Writing and Research Wrap Up 4/24/19

Rationale

The rationale behind today in lab was to create a final abstract in preparation for our final presentation. In addition, when we were done with our abstract, we continued working on sequencing and protein folding in order to collect the necessary data.

Tools/Procedure

  1. Final abstract was submitted
  2. MEME Motif was used to find repeating motifs in the TMPs of selected proteins from each usable cluster
  3. The phylogenetic tree generated by ClustalOmega was used to examine if motifs appeared to be related

Results

The results above were generated using the MEME software to find motifs. The logo above represents a motif that was found in almost all 43 selected TMPs suggesting an area of conservation. In addition, when searching for other common motifs several appeared with much less frequency but much more similarity, which will require further research. This motif shows that there is less similarity in the actual amino acid sequences, but the color coding suggests that structure is more likely to be conserved as many of the amino acids at a location are color-coded the same, suggesting that the amino acids will behave very similarly. In addition, while analysis of the phylogenetic tree is incomplete, it appears that there are definite examples of motifs being related to each other.

***I made a mistake when I previously reported that the motifs were found in all 43 sequences, while some are, the biggest one I found was not and I now need to examine the implications of this***

Conclusion

The motifs I’ve found suggest that there areas of conserved amino acids, but maybe not one unifying motif that I wanted to find.

Future Plans

In the future, we will continue to look for similarities and difference in the amino acid while continuing our folding of proteins to try to figure out what to make of the conserved regions we’ve found in TMPs. We will also complete our final research presentation.

Category: Lucy FIsher | LEAVE A COMMENT
April 26

4-22-19 — Final Abstract

Final Abstract

Date: 4-24-19

  • Rationale
    • The rational for this lab is to rewrite the abstract for the project based on constructive criticism.
  • Procedure
    1. Each group member individually edited a version of the previous abstract.
    2. The group compared individual versions and chose the aspects and sections that were the best from each to form a final abstract.
  • Results

    • Final abstract

    • A short summary of results found
  • Future Plans
    • The next step is to continue to create a powerpoint presentation to present data.
Category: Brandon Reider | LEAVE A COMMENT
April 26

APRIL 24TH- LABS

  • APRIL 24TH 2019
  • OBJECTIVE: 
    • Start to work on and create the presentation, and finalize abstract
  • PROCEDURE:
    • A Google slides file was hared with all group members, in which information was added to the slides 
    • Comments from the rough draft of the abstract were used to edit. And create a new abstract using google docs 
  • RESULT:
    • A google slides presentation was created and edited 
    • A final abstract was created: 
      • Bacteriophage genomic analysis can demonstrate the diversifying effects of mosaicism across phages through the presence of conserved domain gene groups. One mechanism that supports genetic diversity among bacteriophages is Horizontal Gene Transfer, which can allow transmission of localized cassettes. A certain class of cassette involved in DNA replication gene function of the viral genome was identified in NapoleonB. The DNA replication module was noticed to have a specific ordering in common with certain other bacteriophages outside of it’s cluster. The online tool Phamerator was used to visually represent genomes to compare the presence and ordering of genes belonging to a similar module. Genomes of phages that infected multiple different actinobacteria were all found to contain a common gene cassette. A protein folding tool RaptorX was used in tandem with Jmol, a tool for visualizing predicted protein structures, to visualize the function and similarity among these common genes. Clustal Omega and MEGA are sequence alignment tools that were used to make phylogenetic trees. The use of Splitstree allowed for the construction of a phylogenetic network to visualize the parsimony amongst the different bacteriophages studied. The data collected has shown that members of certain clusters can share synteny with members outside of their own cluster. The commonality among the ordering and presence of genes in these clusters provides evidence that allows for the prediction of the function of genes which had no defined predicted function before. Furthermore, if future phages are discovered with this replication cassette, there will be more evidence for making gene function calls using synteny with phages outside of just it’s own cluster.
  • CONCLUSION: 
    • Presentation was created 
    • Abstract was edited and finished 
  • FUTURE STEPS: 
    • Continue work on presentations 
Category: Lauren Foley | LEAVE A COMMENT
April 26

Individual Project 4/24/19

Rationale: Complete final version of abstract and continue to accumulate data

Process:

  • Lathan had commented that the RMSD (root mean square deviation) values for comparing tertiary protein structures were not very meaningful so I looked into another way to mathematically analyze the differences between the tape measure proteins (TMP)
  • All of the structures had been folded by RaptorX so I started aligning them all in comparison to the NapoleonB TMP

Results:

  • I found a paper that said that the TM-score is the best way to compare protein structures because it is independent of protein length. The tape measure proteins vary greatly in size so this is necessary to reduce error.
  • TM-align also gives a TM-score with its results (it is actually the main poi for the software) so it was an easy switch over.
  • Began to organize results in a tabular manner:
phage name residues residues in common RMSD of common residues TM-score notes image
Anansi 1432 1356 78.945 0.1524 random structural similarity
Andrew 787 787 40.957 0.1597 random structural similarity
Atraxa 616 616 29.188 0.1309 random structural similarity
BeautusComedenti 1029 1029 28.36 0.2266
BossLady 876 876 48.243 0.1695
Cheesy 1492 1492 49.672 0.2379
Chubster 1180 1180 41.169 0.2402
Constance 1298 1298 56.792 0.1247 random structural similarity
Corgi 555 555 34.341 0.0913 random structural similarity
DrManhattan 744 744 31.479 0.1715
EdgarPoe 1113 1113 27.514 0.2428
ElephantMan 1463 1427 24.285 0.368
Elesar 1607 1493 47.103 0.1432 random structural similarity
Faja 1348 1348 48.361 0.1552
Galaxy 793 793 32.454 0.1618
Gorgeous 1432 1356 79.112 0.1528
Hestia 1325 1325 43.792 0.153
Joann 853 853 29.797 0.1764
KellEzio 1029 1029 44.416 0.1805
KitKat 1029 1029 28.965 0.2266
Laila 665 665 34.138 0.1063
Laroye 946 946 25.419 0.2367

Next Steps:

Continue aligning stuctures and then use the data to create a figure.

Category: Rachel Melone | LEAVE A COMMENT
April 26

Research Presentation

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.

Category: Emily Balint | LEAVE A COMMENT
April 26

Independent Research Project and Final Abstract 4/24/19

Rationale

Today we will finish data collection and complete our final abstract for the independent research project.

Procedure

  • Each AM specific gene in NapoleonB’s genome was BLASTed on NCBI
  • Results were recorded if it hit was of low %GC content
  • Our abstract was edited and revised to account for the comments made previously. The results presented in the abstract were updated to match the data collection conducted today.
  • Slides for the final presentation were created.

Results

Abstract: Arthrobacter is a gram-positive soil bacteria that has a guanine and cytosine nucleotide composition (%GC) of 63.41% in its genome. NapoleonB and other Arthrobacter AM phages have a comparatively lower %GC of 45.3% and 45.2%, respectively. This is interesting because phages tend to have similar %GC compositions relative to their host bacteria. This project tests the hypothesis that lateral gene transfer is responsible for this discrepancy in %GC. %GC3 analyzes the GC content of the third codon, which is significant in the analysis of codon usage. In order to test this hypothesis, phams were used to separate NapoleonB’s genes into AM specific genes and genes shared with phages outside of the AM cluster. The percent GC and GC3 were analyzed for each gene and compared using Student’s T-test. AM specific genes were compared using NCBI BLAST, to search for matches from host or viruses with low %GC. The %GC of AM-specific genes was significantly lower than non-AM specific genes (P= 0.0029). However, no significant difference was seen between the GC3 values. 51 AM specific genes were checked for BLAST hits with low %GC species, and 12 genes had matches. The evidence indicates that lateral gene transfer from low percent GC bacteria is a potential cause of low %GC content in AM cluster phages, compared to their host. Future analysis of other sequenced genomes could help to strengthen this hypothesis.

An example of results for a single AM-specific gene is shown below:

  • Gene 6
    • Clostridium
      • Hypothetical Protein
      • E value: 3 x 10^-7
      • Identity: 34.34
    • Candidatus Moranbacteria bacterium
      • Hypothetical Protein
      • E value 3 x 10^-14
      • Identity: 42.70

Conclusion/Next Steps

It was concluded that lateral gene transfer could be a probable cause for the exceptionally low %GC content in AM cluster phages and genes. Next, we will continue working on our final presentation.

Category: Emily Gaw | LEAVE A COMMENT