January 17

1/16/2019 Phage Therapy and DNA Master

Rationale: 

The purpose of today’s lab was to present the phage therapy powerpoint and configure DNA Master and its preferences to begin annotation. FASTA file of phage “Elesar” was loaded and auto-annotated as well.

Tools Used:

  • Computer/Laptop
  • DNA Master Program

Procedure:

The lab began with presentations which covered an array of topics all focused on the area of phage therapy and the experiments associated with the practice. Once presentations were completed, the classroom discussed various methods to increase our ability to present things scientifically, and how to improve on being a public speaker overall. Once this exercise was complete, the lab was walked through the DNA Master installation process, and the FASTA file for phage Elesar was uploaded and auto annotated.

Observations:

  • Several phage therapies, such as phage pVp-1 therapy with Vibrio parahaemolyticus, were successfully tested against animal patients and host to treat human illnesses.
  • Enclosing phage used for treatment in liposomes allows the phage to survive longer in the patient’s body, providing a solution to the issue of the immune system of the patient attacking the foreign phage particles.
  • The auto annotated results of phage Elesar yielded 66 genes with one RNA and 66 ORFs.

Conclusions:

It can be concluded that the lab has a general knowledge of phage therapy, and what our research means in relation to that. Also, with DNA master installed, it now yields the opportunity to begin to annotate phage NapoleonB, to discover which genes code for which proteins, and the functions behind each of those coded proteins.

Next Steps:

The next steps for this research are to begin manually annotating the genome of Arthrobacterphage NapoleonB to discover the proteins coded by the genes and what the function of those proteins are.

Category: Gabriel Andino | LEAVE A COMMENT
January 16

DNA Master and Phage therapy 1/16

Purpose: Present phage therapy presentations to peers and learn the basic functions of DNA Master.

Procedure: Presented phage therapy presentations in front of the class, and showed how Vibro parahaemolyticus can help with multiple-antibiotic-resistant O3: K6 cure mice. DNA Master was downloaded and created a guide on how to set up DNA Master. The Fasta file for Elesar was obtained from PhageDB and imported to DNA Master. Auto-annotation was performed on Elesar, and saved onto a computer.

Observations: With presentations, look over the material and practice the presentation before class so when presenting in front of an audience, it should be easy. DNA Master is a great platform for gene annotation and with the help of DNA Master, the annotation of Napoleon can start.

Conclusions: With the start of the semester with presentations, it gave the class as to where we are right now at the start of the semester since the class will have to present multiple times throughout the semester. Prepare for a presentation before the actual presentation. DNA Master was successfully installed, and the next step will be to learn how to annotate.

Category: Michael Lum, Uncategorized | LEAVE A COMMENT
January 16

January 16 2019 Introduction to DNA Master and Annotation

Purpose: The purpose of this lab was to become familiar with and understand how to use DNA Master, as well as learn how to auto annotate.

Tools/Procedures:

  • Tools
    • DNA Master
    • Elesar
    • PhagesDB
  1. DNA Master was successfully updated and installed.
  2. The Fasta file for Elesar was obtained from PhagesDB and imported to DNA Master. The file was exported and a sequence entry was made.
  3. Auto-annotation was performed on Elesar.
  4. The auto-annotations were examined and saved.

Results:

  • No annotations were started today.
  • DNA Master was successfully opened and used.

Conclusions:
DNA Master was successfully installed and the process of learning how to operate the software was begun. The installation and proper set-up took time, and the software had to be reinstalled. After reinstallation and troubleshooting, the program is successfully running.

Future Work:
For future work, the next step will be to learn how to annotate and begin the process.

Category: Lucy Potts | LEAVE A COMMENT
January 16

Setting up software 1/16/18

Rationale: In order to aide in performing annotations this year, the software “DNA Master” was installed onto my laptop. The FASTA file of the phage Elesar was used to test whether the program was installed properly.

Tools:

1. WINE was used in order to help install the Windows version of the software on my mac, as it seemed to be more stable than the mac version.

2. PhagesDB was used to download the executable installer and the FASTA file for Elesar.

Procedure:
1. The executable installer was downloaded from the PhagesDB website as well as WINE.

2. WINE was installed and the executable was run through WINE to install DNA Master.

3. The FASTA file for Elesar was downloaded from PhagesDB and loaded into DNA Master.

4. An auto-annotation was run on the Elesar genome.

Results: The program successfully auto-annotated the genome of Elesar from the FASTA file provided.

Conclusion: DNA Master was successfully installed properly onto my laptop.

Future Work: Next I will practice annotation on the genome of Elesar using the help of the newly installed program. Once I have sufficiently practiced, I will start annotating the genome of NapoleonB.

Category: Sriram Avirneni | LEAVE A COMMENT