Difference between revisions of "User:Bklein7"

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*Computer Science
 
*Computer Science
 
**My favorite thing about computer science is the manner in which we program mechanisms that resemble cognition. Such explorations help supplement our understanding of information processes and the human brain.
 
**My favorite thing about computer science is the manner in which we program mechanisms that resemble cognition. Such explorations help supplement our understanding of information processes and the human brain.
 +
 +
==Electronic Lab Notebook==
 +
===Week 1 Individual Journal===
 +
<!--It was not clear to me that the electronic lab notebook was anything more than the summary log kept while working out the assignment until I referenced Kevin Wyllie's user page in doing a final check over my work tonight. Otherwise, I would have completed this while working on the individual assignment on Sunday.-->
 +
 +
*Write out the complementary strand of DNA below the strand shown and be sure to label the 5’ and 3’ ends of the complementary strand.
 +
**In writing the complimentary strand...
 +
***Begin with the 3' and end with the 5' labels, as this strand will run antiparallel to the existing DNA strand.
 +
***Use the rules of complimentary base pairing for DNA (A pairs with T; C pairs with G) to write the complimentary nucleotide sequence.
 +
***The final product can be seen below:
 +
5’-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta-3’
 +
3'-gcatacgattatggtacaaggcgcatattgggtcggcggtcaaggcgaccgccgtaaaat-5'
 +
*Using the [http://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table genetic code], translate all possible reading frames of this DNA sequence.
 +
**In order to translate the DNA sequence, we must first write out the mRNA transcripts of each DNA strand.
 +
***To write these simply copy the DNA sequences, but replace every "T" in the sequence with a "U".
 +
5’-cguaugcuaauaccauguuccgcguauaacccagccgccaguuccgcuggcggcauuuua-3’
 +
3'-gcauacgauuaugguacaaggcgcauauugggucggcggucaaggcgaccgccguaaaau-5'
 +
*There are six possible reading frames that can be used to translate these mRNA strands.
 +
**For the ''+1 reading frame'', take the top strand (which is read 5' to 3' as is) and divide it into trinucleotides-treating the first three nucleotides as the first codon
 +
***'''+1''': 5’-cgu aug cua aua cca ugu ucc gcg uau aac cca gcc gcc agu ucc gcu ggc ggc auu uua-3’
 +
***Next, use the  [http://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table genetic code] to translate each trinucleotide into an amino acid. In writing the polypeptide, begin with the N-terminus and end with the C-terminus. The result is as follows: N-ter-R M L I P C S A Y N P A A S S A G G I L-C-ter
 +
**For the ''+2 reading frame'', ignore the first nucleotide in the sequence, and then divide the remaining sequence into trinucleotides
 +
***'''+2''': 5’-c gua ugc uaa uac cau guu ccg cgu aua acc cag ccg cca guu ccg cug gcg gca uuu ua-3’
 +
***Translate the polypeptide, stopping transcription when a "stop codon" is reached: N-ter-V C (stop)-C-ter
 +
**For the ''+3 reading frame'', ignore the first two nucleotides in the sequence, and then divide the remaining sequence into trinucleotides
 +
***'''+3''': 5’-cg uau gcu aau acc aug uuc cgc gua uaa ccc agc cgc cag uuc cgc ugg cgg cau uuu a-3’
 +
***Translation: N-ter-Y A N T M F R V (stop)-C-ter
 +
**For the ''-1 reading frame'', begin by reversing the bottom mRNA strand so that it reads 5' to 3'. Then divide it into trinucleotides:
 +
***'''-1''': 5'-uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau acg-3'
 +
***Translation: No protein synthesized; first codon within this reading frame is a stop codon
 +
**For the ''-2 reading frame'', redivide the -1 reading frame so that the first nucleotide in the sequence is ignored:
 +
***'''-2''': 5'-u aaa aug ccg cca gcg gaa cug gcg gcu ggg uua uac gcg gaa cau ggu auu agc aua cg-3'
 +
***Translation: N-ter-K M P P A E L A A G L Y A E H G I S I-C-ter
 +
**For the ''-3 reading frame'', redivide the -2 reading frame so that the first two nucleotides in the sequence are ignored:
 +
***'''-3''': 5'-ua aaa ugc cgc cag cgg aac ugg cgg cug ggu uau acg cgg aac aug gua uua gca uac g-3'
 +
***Translation: N-ter-K C R Q R N W R L G Y T R N M V L A Y-C-ter
 +
*Which of the reading frames (if any) of the reading frames you translated is an ''open reading frame'', i.e., does not contain a stop codon?
 +
**The +1, -2, and -3 reading frames did not contain any stop codons. Therefore, these reading frames are considered "open".
  
 
==Links==
 
==Links==

Revision as of 07:52, 15 September 2015

Contact Information

  Brandon J. Klein
  Loyola Marymount University
  1 LMU Drive, MSB #3393
  Los Angeles, CA 90045
  E-mail: bklein7@lion.lmu.edu

Education

Loyola Marymount University, Los Angeles

LMU Seal.png
  • Major: Biology, Minor: Applied Mathematics
  • Expected Graduation Date: May 6, 2018
  • Upper Division Coursework:

Career Interests and Goals

Career Goals

  1. To gain admittance into medical school.
  2. To complete my residency as a specialist-ideally in ophthalmology or neurology.
  3. To apply my skills as a physician to improve the quality of life of those around me and advance medical research.

Research

Current Research Projects

  • Character of Retinal Thickness Measurements and their Relationship to Visual Acuity in Progressing Cases of Dry Macular Degeneration
    • Faulty Mentor: Dr. Lily Khadjavi, Loyola Marymount University
    • We are currently preparing findings for presentation at future conferences and research symposia. A preliminary presentation on this research can be found here.

Research Interests

  1. Age-related macular degeneration: quantifying progression through statistical models and exploring treatment options such as stem cell therapy.
  2. Genomics research, particularly with respect to understanding the mechanisms and outcomes of gene expression.
  3. Abiogenesis and the stepwise creation of artificial life from synthesized organic molecules.

Work Experience

  • Ophthalmic Medical Assistant
    • Southwestern Eye Associates, Las Vegas, Nevada
    • Summer 2015 - Present
    • Responsibilities:
      • Preliminary patient screening-history taking, refraction, and applanation tonometry
      • Performing OCT exams on patients using the CIRRUS Photo 600 by Zeiss©
      • Assisting in minor medical procedures
  • Retinal Photographer
    • Southwestern Eye Associates, Las Vegas, Nevada
    • Fall 2013 - Spring 2015
    • Responsibilities:
      • Performing OCT exams on patients using the CIRRUS Photo 600 by Zeiss©
      • Greeting patients and scheduling exams
      • Cleaning office equipment

Personal Interests and Hobbies

Hobbies

Vinyl Transparent.png
  • Music
    • I have been a percussionist for nearly a decade and occasionally trifle with recording performances.
    • My passion for music often extends to listening to a broad swath of genres, from country to indie rock.
    • My instruments:
      1. Drum Set
      2. Piano
      3. Guitar
  • Travel
    • I enjoy travelling and immersing myself in the various cultures of the world.
    • Unique locations I have visited include Colombia and China.

Academic Passions

  • Biology
    • My favorite thing about biology is its capacity to explain the mechanisms of life-knowledge which can be used to doctor and improve our quality of life.
  • Philosophy
    • My favorite thing about philosophy is its exploration of the subjective aspects of life in endeavoring to determine what is real. Metaphysics and existentialism are fascinating.
  • Computer Science
    • My favorite thing about computer science is the manner in which we program mechanisms that resemble cognition. Such explorations help supplement our understanding of information processes and the human brain.

Electronic Lab Notebook

Week 1 Individual Journal

  • Write out the complementary strand of DNA below the strand shown and be sure to label the 5’ and 3’ ends of the complementary strand.
    • In writing the complimentary strand...
      • Begin with the 3' and end with the 5' labels, as this strand will run antiparallel to the existing DNA strand.
      • Use the rules of complimentary base pairing for DNA (A pairs with T; C pairs with G) to write the complimentary nucleotide sequence.
      • The final product can be seen below:
5’-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta-3’
3'-gcatacgattatggtacaaggcgcatattgggtcggcggtcaaggcgaccgccgtaaaat-5'
  • Using the genetic code, translate all possible reading frames of this DNA sequence.
    • In order to translate the DNA sequence, we must first write out the mRNA transcripts of each DNA strand.
      • To write these simply copy the DNA sequences, but replace every "T" in the sequence with a "U".
5’-cguaugcuaauaccauguuccgcguauaacccagccgccaguuccgcuggcggcauuuua-3’
3'-gcauacgauuaugguacaaggcgcauauugggucggcggucaaggcgaccgccguaaaau-5'
  • There are six possible reading frames that can be used to translate these mRNA strands.
    • For the +1 reading frame, take the top strand (which is read 5' to 3' as is) and divide it into trinucleotides-treating the first three nucleotides as the first codon
      • +1: 5’-cgu aug cua aua cca ugu ucc gcg uau aac cca gcc gcc agu ucc gcu ggc ggc auu uua-3’
      • Next, use the genetic code to translate each trinucleotide into an amino acid. In writing the polypeptide, begin with the N-terminus and end with the C-terminus. The result is as follows: N-ter-R M L I P C S A Y N P A A S S A G G I L-C-ter
    • For the +2 reading frame, ignore the first nucleotide in the sequence, and then divide the remaining sequence into trinucleotides
      • +2: 5’-c gua ugc uaa uac cau guu ccg cgu aua acc cag ccg cca guu ccg cug gcg gca uuu ua-3’
      • Translate the polypeptide, stopping transcription when a "stop codon" is reached: N-ter-V C (stop)-C-ter
    • For the +3 reading frame, ignore the first two nucleotides in the sequence, and then divide the remaining sequence into trinucleotides
      • +3: 5’-cg uau gcu aau acc aug uuc cgc gua uaa ccc agc cgc cag uuc cgc ugg cgg cau uuu a-3’
      • Translation: N-ter-Y A N T M F R V (stop)-C-ter
    • For the -1 reading frame, begin by reversing the bottom mRNA strand so that it reads 5' to 3'. Then divide it into trinucleotides:
      • -1: 5'-uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau acg-3'
      • Translation: No protein synthesized; first codon within this reading frame is a stop codon
    • For the -2 reading frame, redivide the -1 reading frame so that the first nucleotide in the sequence is ignored:
      • -2: 5'-u aaa aug ccg cca gcg gaa cug gcg gcu ggg uua uac gcg gaa cau ggu auu agc aua cg-3'
      • Translation: N-ter-K M P P A E L A A G L Y A E H G I S I-C-ter
    • For the -3 reading frame, redivide the -2 reading frame so that the first two nucleotides in the sequence are ignored:
      • -3: 5'-ua aaa ugc cgc cag cgg aac ugg cgg cug ggu uau acg cgg aac aug gua uua gca uac g-3'
      • Translation: N-ter-K C R Q R N W R L G Y T R N M V L A Y-C-ter
  • Which of the reading frames (if any) of the reading frames you translated is an open reading frame, i.e., does not contain a stop codon?
    • The +1, -2, and -3 reading frames did not contain any stop codons. Therefore, these reading frames are considered "open".

Links

Assignments Pages

Individual Journal Entries

Shared Journal Entries

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