Difference between revisions of "User:Kwyllie"

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Kevin Wyllie - User Bio

Contact

kwyllie@lion.lmu.edu

1 LMU Dr. 90045, MSB 7967

Education

• Major: Biochemistry
• Expected year of graduation: 2016
• Relevant coursework:
  1. General chemistry, with lab
  2. Organic chemistry, with lab
  3. Biochemistry, with lab
  4. General biology
  5. Cell function
  6. Genetics
  7. Pathophysiology
  8. Microbiology, with lab
  9. Biological databases (See the course's Main Page)

Career

• After completing my B.S. in biochemistry, I plan to participate in post-grad service. Following one or two years of service, I hope to attend medical school.
• Research Experience:
  • Howard Hughes Medical Institute's Bacteriophage Lab (Fall 2012 through Spring 2013)
    • Mentors: Dr. Carl Urbinati, Dr. Yiwen Fang
    • Extraction and sequencing of a bacteriophage genome, using both micriobiological and bioinformatic methods.
    • Publication

Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science; Phage Hunters Integrating Research and Education; Mycobacterial Genetics Course. April, 2015. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife.

• • Dahlquist Lab (2014 to present)
    • Mentor: Dr. Kam D. Dahlquist
    • Investigating transcription factors involved in the cold stress response in Saccharomyces cerevisiae via DNA microarray analysis and growth experiments.(See my electronic lab notebook for microarray data normalization)
• See my full curriculum vitae

Work Experience

• Paralegal's assistant, Omikron IP Law (Summer 2011 through Summer 2012)
  • Managed transmittance of patent information between paralegal and clients
• Front desk assistant, LMU Library (Summer 2014)
  • Managed check-out and check-in of books and media
  • Carried and some clerical, customer information and financial duties

Personal Interests

• Service and social justice - particularly restorative justice
• Running
• Experimental/progressive/multi-genre music

More Information

• My favorite thing about biology is that it forces us to see ourselves as being just as embedded in nature as the life forms we study. As a species that sees itself as being highly complex and sophisticated, we often fall victim to human exceptionalism. Biology reminds us that we, as organisms, are at the mercy of the same fundamental principles as the most primordial prokaryote.
• I have very little background in computer science, but what I most appreciate about the field is its contribution to the well-being of humanity.

Wiki Syntax Help

To help me complete this assignment, I used this page.

Journal Assignments

• Class Journal Week 1

• Kevin Wyllie Week 2 (See the original assignment.)
• Kevin Wyllie Week 3
• Kevin Wyllie Week 4
• Kevin Wyllie Week 5
• Kevin Wyllie Week 6
• Kevin Wyllie Week 7
• Kevin Wyllie Week 8
• Kevin Wyllie Week 9
• Kevin Wyllie Week 10
• Kevin Wyllie Week 11
• Kevin Wyllie Week 12
• Kevin Wyllie Week 14
• Kevin Wyllie Week 15

Template:JournalLinks

Electronic Lab Notebook

Week 2 Individual Journal Assignment

1. First, using the given DNA strand, write out the sequence for the complementary strand. A's pair with T's, while C's pair with G's.
   • Remember that although you may have written the new strand from left to right, due to DNA's antiparallel characteristic, it will be read in the reverse direction, assuming you designated that this new strand was the "bottom strand." To remind yourself of this, add the 5' and 3' notation as done for the original strand, although remember that the sides for either will be reversed.
2. To avoid errors when using the amino acids translation chart (discussed below), you should write out the mRNA transcript for all six of the frames.
   1. Start by copy/pasting the original (or top) strand and grouping the nucleotides into groups of three (retaining their order, of course). This allows you to more easily visualize each codon. This first sequence is your "+1" frame.
   2. Again, copy/paste the top strand, and group into threes, but this time start by deleting the very first nucleotide in the sequence. You'll notice that you have two nucleotides left over at the end. These can also be deleted. This is your "+2" frame.
   3. For the "+3" frame, start by deleting the first two nucleotides and continue as normal.
   4. For the "-1" frame, you should start by re-writing the strand in the 5' to 3' direction (remember that it is currently in the 3' to 5' direction). This may be tedious, but it can get very confusing to read the strand in reverse. After that, as before, group the nucleotides into groups of three.
   5. Once the bottom strand has been re-written appropriately, repeat the steps used for the "+" frames to get your "-2" and "-3" frames.
3. Finally, translate each frame.
   • Use the amino acid translator chart to convert each codon into an amino acid. Here's an amino acids chart from ManyLabs.org
   • If a "stop codon" is reached, the amino acid chain is terminated. No need to write "STOP." Instead, indicate the beginning and end of the chain with the "Nter" and "Cter" notation.
     • "Nter," short for "N-terminus" denotes the beginning of the chain, while "C-ter" denotes the end.
   • If a frame does not contain a STOP codon, then it referred to as an "open reading frame."