April 5

Poster Presentations 4/1/19

Rationale

Today we will practice presenting our posters for URSA Scholars Day.

Procedure

  • Each pair that signed up to present for Scholar’s day presented in front of the class.
  • Questions and critiques were made to each group that presented.
  • Helpful tips for presentations were given.

Results

Each group was able to create an outline for their presentation the following days. We all gained a better understanding of what a poster presentation consisted of.

Conclusions/Next Steps

Next, we will present our poster at URSA Scholar’s Day and then begin to work on our independent research projects.

Category: Emily Gaw | LEAVE A COMMENT
April 5

04/03/19 Independent Project Research

Rationale:

The purpose of today’s lab was to continue researching our independent project topics to gather more information of the mechanisms behind phage holin and endolysin proteins.

Tools:

  • PUBMED
  • HHMI
  • TMHMM

Procedure:

  • Began by discussing previously discovered information and narrowing down a project title and worked on the QTM.
  • Searched for articles discussing the peptidoglycan bridges in bacterial cell walls to find any information that suggests Arthrobacter has the same bridges as Staph. aureus.
  • Discussed possible holin mechanisms given the presence of acidic residues placed outside the membrane.

Results:

  • Noted a sequence of amino acids “PEPEK” that lies outside of the bacterial membrane called the periplasmic loop for the holin protein.
  • No significant research could justify that Arthrobacter cell walls contain bridges similar to Staph. aureus.

Conclusions:

It can be hypothesized that this region of amino acids is a key characteristic of phage holin and could possibly be used to determine function to phages with unknown holin genes. It is still unclear as to what mechanism stops the proton motive force, and very well could be caused by just the physical damage the holin protein inflicts on the bacterial plasma membrane.

Next Steps:

The next steps for this experiment is to finalize any research information on holins and endolysins and begin folding these proteins to determine any key characteristics that could help determine gene function in other phages.

Category: Gabriel Andino | LEAVE A COMMENT
April 5

4.3.19 Next Steps of Independent Research Project

4.3.19 Next Steps of Independent Research Project

Rationale: After the brief intermission to practice presentations, the class returned to our independent research projects. Therefore, my group spent time furthering our understanding of repeats and making an outline to organize our group project.

Tools/Procedure: Gepard, DNA Master, Clustal Omega, Phamerator, NCBI BLAST

I focused my attention on browsing through literature, Gepard, and DNA Master to find repeats that could potentially be of significance. I took sequences from different genes, converted them to FASTA files, and used Gepard to visualize a dot plot that would reveal any potential repeated sequences that could have been of interest.

Results: One long repeat of 51 base pairs was found to be intriguing and effort and time was spent to find the significance. We have concluded that it is conserved across members of the AM cluster and it is close to tail proteins, but more investigating needs to be done to fully determine the purpose of this long repeat.

Conclusions: The problem of finding repeats has proved to be mostly solvable, so our topic for the project appears to be intact. More investigation will be needed to figure out whether this conjecture is true or false.

Next Steps: Members of the group will be investigating the repeat independently to gain knowledge and to investigate potential reasoning for why it is there before the next lab period.

Category: Uncategorized | LEAVE A COMMENT
April 5

4.1.19 Practicing Presentations

4.1.19 Practicing Presentations

Rationale: It was found to be necessary to pause the independent research projects to practice our URSA presentations as a class. Therefore, the time was dedicated to reviewing important information about our poster and highlighting key parts of the presentations that should and should not be emphasized.

Tools/Procedure: Each duo of presenters went up to either give a full or abbreviated presentation, with feedback and live situations simulated by the entire class.

Results: As the presentations were practiced and refined, they were found to get better and be more cohesive. The feedback from our presentation guided me in my practicing for my time slot during URSA week.

Conclusions: Group practicing of presentations was very helpful, as some interesting and potentially problematic situations were encountered and worked through. As I was hearing others present the sections I was going to present, I was able to learn different phrases and techniques for presenting the topics that were more cohesive or easier to comprehend for someone without full experience in bacteriophages. Therefore, this additional time to practice and prepare as a class was helpful and I believe that it will drastically improve the quality of presentations given by those at the research poster at a given moment.

Next Steps: Each pair will go to their assigned 15 minute time slot and present the rehearsed and polished information!

Category: Henry Burns | LEAVE A COMMENT
April 5

Independent Research Projects 4.3.19

Rationale:

To understand more about phage, the class was divided into several small groups to generate research questions that utilize bioinformatic tools to learn more about questions about NapoleonB and/or related phages.

Materials:
  • Laptop
  • Canvas Bio-Lab info page
  • Gepard dot plot software
  • DNA Master
Procedure & Results:
  1. Scientific literature that relates to the topic were found and treated as reference.
  2. More repeats within the NapoleonB genome were found.
  3. A new method for a more efficient way to scan for repeats may be needed.

QTM for lab was written:

Presentation Title (Can be changed): Discovery of repeats in Arthrobacter phages and examination of potential functions.

Two research articles discussing your area of research

Guiding Research Question (include any background information relevant to the question)

Is it possible to use repeats in coding or noncoding regions of the genomes within the AM phage cluster to predict the functions of genes with no known functions?

Three bioinformatic tools you plan to use in your research

  • DNA Master Scan
  • Gepard
  • Phamerator
  • Clustal Omega

You will be presenting your findings at the CURES in Biology Symposium on Friday, May 3. You will do a ‘practice presentation’ on May 1st to your coaches. There are 7 lab days before the May 3rd presentation. While most of your research can be completed during class, presentation practice and presentation design will need to be worked on outside of class. With this in mind, formulate a schedule with ‘check points’ for your group to make sure you stay on track during this busy time of the year. Dates of lab meetings have been provided, but if you plan to meet outside of class as well feel free to include those times.

4/8 – Look for repeats and deepen understanding of prospective repeats that are being investigated

4/10 – Select most promising repeats to focus on and find more information and research to give meaning to the sequences found

4/15 – Apply findings to other AM Cluster phages and begin to finalize data and observations

4/17 – (by the end of lab) Have concrete findings (positive/or negative) that can serve as an answer to the question

4/22 – Compile data and results & create graphics to display findings

4/24 – Organize findings and research into presentation form

4/29 – Finish and revise presentation

5/1- Practice Presentations

5/3- CURES in Biology Presentations 2-5 pm

The Next Step:

The next lab would be to look for repeats and deepen understanding of prospective repeats that are being investigated.

Category: Yang-En Yu | LEAVE A COMMENT
April 5

URSA Presentation Preparation 4.1.19

Rationale:

To prepare for the coming URSA poster presentation, the pairs doing the presentation together present the poster in lab as practice, and the whole lab can provide feedback to improve the overall presentation.

Materials:
  • Poster
Procedure & Results:

Two of the students in lab that signed up in the same time slot presented the poster together in lab. (preferably in 5 minutes) Then the listeners ask questions or provide feedback to the presenters.

The Next Step:

In the next lab, the independent research project will be resumed.

Category: Yang-En Yu | LEAVE A COMMENT
April 5

Independent Research Project 4/3

Rationale: Continue to find data and articles for the proposed question set for independent research

Procedures: Met with groups and started gathering data for starts of Tail protein found in Arthrobacter phages. Used PhagesDB to download FASTA file to determine starts and which genes where tail proteins. Two research articles were found to help support the significance of start sites in bacteriophage.

Results: 

:

Conclusions/Future work: continue to list all sequenced Arthrobacter phage and obtain FASTA files to check the start sites. Then manipulate the starts of the protein sequence and see if a change in structure had occurred.

Category: Michael Lum | LEAVE A COMMENT
April 5

Collecting Data for Independent Group Project (4/3/19)

Rationale:  

Plan for the rest of the semester was discussed about and data was collected on start codons.  

Tools: 

  • PhagesDB 
  • DNA Master  
  • Excel 

Procedure: 

  1. A plan for the remainder of the semester was talked about, and decisions on goals to reach each day were discussed.  
  2. Research articles on topics were found, and title ideas were discussed about.  
  3. Ideas were formulated on how to strategically obtain all the data.  
  4. A FastA file was downloaded from PhagesDB, and start codon was noted on an Excel sheet for AM cluster phages.  

Results: 

Start Codons for Phages were collected, and below is an example of start codons collected for Phage Arcadia

Conclusion: 

Some similar observations were noted of the start codon of AM Cluster Phages that have been collected.  

Future Work: 

Start Codons of other phages including different cluster and different hosts will be collected and used to possibly create a phylogenetic tree.  

Category: Sona Subramanian | LEAVE A COMMENT
April 5

URSA Poster Presentation (4/1/19)

Rationale:  

Presentation for URSA Scholars Week Poster was practiced.  

Tools: 

  • Poster 

Procedure: 

  1. Each group for URSA Scholars Week presented.  
  2. Critiques and improvements were provided.  
  3. Possible Questions and suggestions were asked. 
  4. Clarifications on figures and background images were provided.   

Results: 

Presentations were perfected and practiced with critiques from others. The poster was presented on Tuesday and Wednesday.  

Conclusion:  

More about poster presentations were reviewed, including topics that should be focused on, and a better understanding of the figures were attained.  

Future Work:  

Poster will be presented this week. Work for Independent Group Projects will be continued, and more research will be conducted regarding it.  

 

Category: Sona Subramanian | LEAVE A COMMENT
April 4

Lab Day 20-21: Presentation and Independent Research

Rationale

Practice presentations for URSA and make sure as a class, we know every detail about NapoleonB. Also to start researching and working on project outlines for the independent research project

Procedure

  1. practiced presentations in front of class and helped critiqued classmates
  2. created a project outline for independent research
  3. performed multiple sequence alignment with 20 sequences (6 from AM cluster and 14 from non AM cluster)
  4. recorded results in the same doc.

Conclusions/Next Steps

URSA presentation went well and was able to be prepared for questions. Results from multiple sequence alignment are shown in pic below. Next lab day, my group and I will use RaptorX to see the protein model of the nicotinamide mononucleotide transporter

Category: Soo-Un Jeong | LEAVE A COMMENT