Difference between revisions of "User:Bklein7"

Revision as of 17:49, 16 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

Major: Biology, Minor: Applied Mathematics
Expected Graduation Date: May 6, 2018
Upper Division Coursework:
- MATH 360- Intro to Probability and Statistics
- BIOL/CMSI 367- Biological Databases

Career Interests and Goals

Career Goals

To gain admittance into medical school.
To complete my residency as a specialist-ideally in ophthalmology or neurology.
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

Age-related macular degeneration: quantifying progression through statistical models and exploring treatment options such as stem cell therapy.
Genomics research, particularly with respect to understanding the mechanisms and outcomes of gene expression.
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

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 2

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...
  1. Begin with the 3' and end with the 5' labels, as this strand will run antiparallel to the existing DNA strand.
  2. Use the rules of complimentary base pairing for DNA (A pairs with T; C pairs with G) to write the complimentary nucleotide sequence.
  3. 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:
  1. Simply copy the DNA sequences, but replace every "T" in the sequence with a "U".
  2. The final product can be seen below:

5’-cguaugcuaauaccauguuccgcguauaacccagccgccaguuccgcuggcggcauuuua-3’
3'-gcauacgauuaugguacaaggcgcauauugggucggcggucaaggcgaccgccguaaaau-5'

There are six possible reading frames that can be used to translate these mRNA strands.
1. 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
2. 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
3. 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
4. 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
5. 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
6. 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".

Week 3

Complement of a Strand

Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand.

Begin with a cat command to view a text file with a DNA sequence
After the pipe character, link together a sed command that invokes a letter by letter replacement of A, T, C, and G with their complementary bases (T, A, G, and C in that order).

cat sequence_file | sed "y/atcg/tagc/"

Reading Frames

Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence.

To tackle this problem, start by crafting the simplest sequence of commands that will carry out the central dogma by translating DNA sequences to amino acid sequences. This command sequence will serve as the "backbone" from which all 6 reading frame sequences are built. Incidentally, this code will also align with that necessary to transcribe the +1 reading frame.
1. Begin with a cat command to view a text file with a DNA sequence
  - cat sequence_file
2. Add a sed command representing the transcription of DNA to RNA, replacing "T" nucleotides with "U" nucleotides
  - cat sequence_file | sed "s/t/u/g"
3. Add a sed command representing the (+1) reading frame for the codons, inserting a space after every three characters
  - cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g"
4. Add a sed command to translate each codon to its associated amino acid. For this exercise, the simplest way to do this is to read from the rules file ~dondi/xmlpipedb/data/genetic-code.sed
  - cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
5. Add a sed command to remove lingering nucleotides at the beginning and/or end of the output that were not translated due to not being present in a triplet in the present reading frame. This will prevent confusing these untranslated nucleotides with amino acids
  - cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "[atcg]//g"
6. Finally, remove spaces from in between the separate amino acid designations to condense the output (has both aesthetic and practical purposes). This will yield the final command sequence:
  - cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"

+1 Reading Frame
- The command sequence above already processes the genetic code within the +1 reading frame:

cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"

+2 Reading Frame
- Simply alter the +1 reading frame code to include a sed command for the deletion of the first character of the text file (i.e. nucleotide) prior to division into triplets:

cat sequence_file | sed "s/t/u/g" | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"

+3 Reading Frame
- Alter the +1 reading frame code to include a sed command for the deletion of the first two characters of the text file (i.e. nucleotides) prior to division into triplets:

cat sequence_file | sed "s/t/u/g" | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"

-1 Reading Frame
- The "backbone" command sequence from above will have to be slightly altered for the negative reading frames to account for the reading of a complimentary, antiparallel strand of DNA
  1. Begin with the code from the +1 reading frame
    - cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"
  2. Add the sed command from the "Compliment of a Strand" section above at the beginning of this sequence. This will yield the DNA sequence complimentary to that which we were originally working with
    - cat sequence_file | sed "y/atcg/tagc/" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"
  3. Add a rev command after the code has been transcribed to the complimentary mRNA. This accounts for the fact that the genetic code is read in the 5' to 3' direction. With this final change, the command sequence will now translate the DNA sequence within the -1 reading frame:

cat sequence_file | sed "y/atcg/tagc/" | sed "s/t/u/g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" |
sed "s/ //g"

-2 Reading Frame
- As in the positive reading frames, alter the -1 reading frame code to include a sed command for the deletion of the first character of the text file (i.e. nucleotide) prior to division into triplets:

cat sequence_file | sed "y/atcg/tagc/" | sed "s/t/u/g" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed |
sed "s/[atcg]//g" | sed "s/ //g"

-3 Reading Frame
- Alter the -1 reading frame code to include a sed command for the deletion of the first two characters of the text file (i.e. nucleotides) prior to division into triplets:

cat sequence_file | sed "y/atcg/tagc/" | sed "s/t/u/g" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed |
sed "s/[atcg]//g" | sed "s/ //g"

Check Your Work

Fortunately, online tools are available for checking your work; we recommend the ExPASy Translate Tool, sponsored by the same people who run SwissProt. You’re free to use this tool to see if your text processing commands produce the same results.

Links

User Page: Brandon Klein
Team Page: The Class Whoopers

Assignments Pages

Individual Journal Entries

Shared Journal Entries

@@ Line 120: / Line 120: @@
 Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand.
 #Begin with a cat command to view a text file with a DNA sequence
-#After a vertical bar, link together a sed command that invokes a letter by letter replacement of A, T, C, and G with their complementary bases (T, A, G, and C in that order).
+#After the pipe character, link together a sed command that invokes a letter by letter replacement of A, T, C, and G with their complementary bases (T, A, G, and C in that order).
   cat ''sequence_file'' | sed "y/atcg/tagc/"