April 26

Final Abstract

04/25/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

  1. The individual research was worked on.
  2. group members used jmol and raptor x to start structure analysis
  3. the final abstract for the presentation was submitted
  4. The group worked until the end of lab.

Results

based on the analysis of protein structures, there is a significant difference in the structure when the start codon is changed for the tape measure protein of phage cheesy, elsa and napoleon b.

example, AUG, GUG and UUG in order for phage Elsa

final abstract:

AUG, UUG and GUG are the three start codons that initiate gene translation in all bacteria. Different start codons produce different amino acids, which interact differently with other amino acids to form different structure. Genes in arthrobacter phage genomes were used to explore whether changing the start codon of the gene causes a significant difference in the structure of the product protein which could explain why the original start codon was preferred..The start codons for tape measure proteins, major tail proteins, and minor tail proteins in the annotated genome of known, sequenced arthrobacter phage were collected using the Phages DB Database and DNA Master. The gene length, genome length, cluster ,%GC, and direction of the genes were also recorded to determine possible factors that make one start codon preferable to another in the phage genome. Raptor X and Jmol were used to determine the most probable structure of the product protein based on the amino acid sequence and compare the structures. The protein structures were drastically different even though the gene length, pham, and preferred start codon were the same. Overall, many factors that were noted in the quantitative data for the AM Tape Measure were the same or very similar, while the qualitative data produced varying protein structures. Knowledge of how certain start codon may result in a more preferable protein structure may help future research for designing  phages to be more effective by simply changing the start codon.

Conclusion:

currently, from our qualitative data, all we can conclude is that the protein structure changes. quantitative data is still currently being analyzed.

Future steps

Look into primary literature and find information to understand the difference in structures.

Category: Aman Patel, Dr. Adair | LEAVE A COMMENT
April 26

Compiling a Presentation 4/24/19

Title: Compiling a Presentation

Date: 24 April 2019

Rationale: With the present results, a presentation will be compiled that will be presented at the CURE in Bio symposium.

Procedure: A powerpoint presentation was compiled that summarized the introduction, methods, and results of the research done in the lab this semester. The presentation still needs to be refined with additional figures and background information, as well as practiced thoroughly to ensure smoothness.

Results/Observations: As a final result, our group decided that the sequence is most likely a regulator or promoter sequence, this is reflected in the elimination of many other functions in our presentation.

Conclusions/Next Steps: The presentation needs work and practice, and will be worked on in the next few days. Otherwise, this will conclude lab work for this semester.

Category: Cooper Johnson | LEAVE A COMMENT
April 26

04/24/19 Final Abstract and Presentation

Rationale:

The purpose of today’s lab was to rewrite the final abstract as well as begin the final presentation. Also Jmol was used to try and represent endolysin complex with Glycine-Glycine bridges

Tools:

  • Jmol
  • Microsoft Word
  • Microsoft Powerpoint

Procedure:

  • Final abstract was rewritten using the notes left on the previous abstract submission.
  • A general outline of the final presentation was made, with general ideas for slides put out onto each slide.
  • Used Jmol to visually represent Glycine-Glycine fitting into the catalytic region of our M23 peptidase endolysin.

Results: 

Copy of the Final Abstract

Visual Representation of Glycine-Glycine bridges fitting in active site.

Conclusions:

With the final abstract written, we are able to continue with creating the presentation for the CURES Symposium. Also, the ability to represent Glycine bridges fitting into NapoleonB’s endolysin catalytic region gives us another method of comparison between M23 Peptidase and PGRP endolysins.

Next Steps:

Our next steps for this project are to finish the final presentation for the symposium as well as finalize the PGRP catalytic region.

Category: Gabriel Andino | LEAVE A COMMENT
April 26

4/24 ~ Final Abstract

Rationale: Work on the final abstract for the independent research project and continue searching for data

 

Materials:

  • Google Drive
  • DNA Master
  • Laptop

 

Procedure:

  • Worked together in the research groups to refine the rough draft of the abstract
  • Submitted the final abstract draft as the QTM

 

Observations:

  • The final abstract

     

    Conclusion/Next Steps: Will continue to work on gathering data for one more workday and then will work on drawing conclusions and discussion.

Category: Justin Yu | LEAVE A COMMENT
April 25

4.24.19 IRP

Rationale:

To fix the abstract and to continue working on the presentation.

Procedures:

  1. Looked at the abstract comments and revised the current abstract.
  2. Continued working on the presentation.

Conclusions/Next-Steps:

We fixed the abstract according to the recommended fixes and we will continue working on the presentation in order to present the findings of our project.

Category: Nathan Newton | LEAVE A COMMENT
April 25

Lab Day 26: Final Abstract and Presentation Slides

Rationale

Fixed abstract from comments made by coach. Continued working on the presentation slides and also fix other parts of the research

Procedure

  1. took comments from coach and applied them to the final abstract
  2. fixed background and conclusion on presentation slides

Conclusion/Next Steps

We fixed our conclusion/discussion for our research and since my group and I have finished faster than our schedule we made, all we have to do next time in lab is to go over the powerpoint and practice presenting

Category: Soo-Un Jeong | LEAVE A COMMENT
April 25

Abstract for Independent Group Project (4/24/19) 

Rationale:

Abstract was worked on and perfected for the independent group project. 

Tools: 

  • Excel  
  • Google Doc 

Procedure: 

  1. Previous abstract was used, and corrections were viewed.  
  2. Individually corrections were made.  
  3. Group decided upon the best abstract and created the final abstract  
  4. Results were noted on a google doc about observations obtained from the data collected

Results: 

Some of the results that were found in the study: 

Abstract:

Inserting image...

Conclusion: 

The results did not provide enough certainty to sub-cluster the phages based off start codons, but other interesting common features were found within each phage of the cluster.  

Future Work:  

Power point will be made and presentations will be practiced for our independent group project.  

Category: Sona Subramanian | LEAVE A COMMENT
April 25

Independent Project (4/24/19)

Rationale:

  • In lab, the abstract was corrected and more information such as results and future plans were added. Along with abstract correction, comparisons were made with the qualitative data to the quantitative data to find significant results.

 

Tools:

  • Personal Computational Device
  • JMol
  • Raptor X
  • Google Excel Sheet
  • Phamerator
  • PhagesDB
  • NCBI

 

Above, the protein structures of Elsa and Nason are compared. The top row are the protein structures of Elsa with AUG (preferred start codon), GUG as the changed start codon, then UUG as the other changed start codon. What we found interesting is that both tape measure proteins from phages that are within the same cluster, same preferred start codon, and from the same pham, so we wondered why there is a drastic protein structure change.

 

Results:

  • First, the data was checked with Phamerator to make sure that no updates have been made with the gene that is to be studied.
  • Protein structures were made based on similarities that were found in the quantitative data.
  • With the differences in the protein structures, primary literature was used to understand the reason for the drastic differences in protein structures.
  • For the abstract, corrections were made based on the comments posted.
  • Additionally, a results portion was added as the group found more significant correlations and a conclusion was also added.

 

Conclusion:

  • Corrections were made to the abstract as was submitted as the final abstract. Also, significant results were found and assumptions were made. To rule out which reasoning was unimportant for the change in protein structure, primary literature was used.

 

Future Plans:

  • For the last work day in lab, most of the results will be organized and the powerpoint will be completed.
Category: Sabin Patel | LEAVE A COMMENT
April 25

DNA Day 24

24 April 2019 ✷ Independent Research

Rationale: The trends in the percent GC of the genes were analyzed and justification was sought out.

Procedure

  • Every AM-specific gene was run through NCBI’s BLASTp in order to search for low-GC bacteria it shares genes with
    • this is evidence of horizontal gene transfer
  • The abstract was edited and finalized
  • the presentation was created and work was started for it

Results

Genes 6, 22, 40, 43, 45, 47, 48, 49, 51, 60, 85, and 96 had hits with low-GC bacteria.

the abstract:

Conclusion

Many of the AM-specific genes hit with viruses or bacteria with low %GC. This could be indicative of lateral gene transfer, which could explain why the AM phages have a much lower GC content than the other Arthrobacter phages and Arthrobacter host.

Future plans

Work on presentation

Category: Lily Goodman | LEAVE A COMMENT
April 25

Wednesday 4/24

Purpose: Finish our Abstract and conclude the research.

Procedure:

  • Reviewed Lathan’s Comments on Abstract draft
  • Corrected issues sequentially
  • Reviewed new abstract
  • Worked on our powerpoint project
  • Figured out sources from various bioinformatic tools
  • Reviewed other slides until the end of class

Results:
Finished the abstract, and have found all of our sources.

Future Plans: Finish the power point and begin practicing our presentation for next Friday.

Category: Uncategorized | LEAVE A COMMENT