Gary Kuleck

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Current Courses

Current course descriptions for BIOL 439 and BIOL 398 are available.

Annotation Resources

  1. General Annotation Protocol - Non-coding exons
  2. Annotating individual variant UTR regions
  3. Efficient Annotation of Genes with multiple variants
  4. Example of Multiple Variant Annotation
  5. Summary Table of All Exons for Multiple Variants
  6. Annotation Documentation Sample
  7. Student Annotation Progress Tracker
  8. Sample Syllabi for Embedded Bioinformatics Section
  9. Sample Syllabi  for Stand Alone/Independent Study
  10. Student poster on Synteny analysis D. mojavensis


Teaching and Undergraduate Research

  1. Combining Teaching and Undergraduate Research using Genome Annotation
  2. Undergraduate Research Annotation Poster


GEP Summer Alliance

  1. Goals of the GEP Summer Alliance
  2. Teaching Genomics in Beijing, China


Overview

  • Dr. Gary Kuleck
  • Office Hours: Thursday 10:45 AM-12:30 PM, Fri 9:30 AM-11 AM


Books

  1. Principles of Genetic 4th eds- Snustad et. al. (text-lecture, required)
  2. Laboratory DNA Science- Bloom, Freyer, Micklos (text-laboratory)


Resources

  1. I will host a web page on the ERES system. Most of the material which I pass out will be found on Eres ( http://eres.lmu.edu) password: XXXX
  2. Internet and Web resources - I will provide and post web sites of interest and for your assignments throughout the semester.


Grading and Course requirements

Since all students are taking both the lecture and the laboratory courses, the grades are combined. Please carefully examine the points scheduled for each and the appropriate breakdown.


Lecture

Reading

It is essential that you read the text/materials before class. If I perceive that students are not being attentive to this duty, I will at my discretion, create a pop-quiz which all will take.


Participation

This class is designed to be a dialogue between the teacher and student. My style is to involve students throughout the course in the learning process. This has two purposes: active learning works best in this course and retention is enhanced if you are participating. To stimulate your involvement, I have assigned 50 discretionary pts. to the class grading system.


Attendance

It should be obvious that in order to participate, you need to attend class. Failure to attend regularly will be reflected in the discretionary point total.


Quizzes

Generally biweekly (given in laboratory period) (25 pts each, lowest two worth 60, 40 respectively) 100 pts

Quizzes will cover material from either the laboratory or lecture of recent vintage. Topics to be covered will be announced in advance.

Please note: You must do homework assignments and not copy other's work. Some of the questions on the quizzes will resemble homework problems.


Exams

  • One Midterms - One hour - Will be scheduled before Fall break = 100 pts each
  • Final - as scheduled in the Fall 2008 Schedule of Classes = 100pts


Homework

  • Assignments of problems- Assignments will vary but will total 100 pts Mastery of molecular biology requires a conceptual understanding which can only be achieved by problem solving. Problems will range from the mundane to challenging. Your turned-in work must be typed and legible.

While partial credit is possible, it is best that I can understand what you have done.

Homeworks are due on the date announced. Homework turned in a day late will suffer a 20% reduction in grade per day and will not be accepted if more than three days late. Please note that some of the homework may involve a unique problem for you. = 100 pts


Seminars

Attendance at 2 departmental or equivalent is required. You will be given a format to write-up your seminar experience. Of course, you are encouraged to get into the habit of attending seminars.

IMPORTANT: The work that you submit must be you own. Avoid plagiarism. While I will not discourage you from working together, you must submit you own work. .Homework or other assignments which are turned in essentially the same as another student or copied will suffer substantial reduction in grade or will not be accepted.

Total points possible: 1030 pts.


Summary of Lecture grading

Summary of Lecture grading Points
Reading/participation/attendance/etc. 50
Quizzes (5 quizzes drop one) 100 pts
Mid-term Exam 100 pts
Final Exam 100 pts
Homework 100 pts
Attendance at two seminars and write-up 30 pts
Total 480 pts


Laboratory

In this laboratory, you will not only learn molecular techniques, but take part in ongoing research using molecular biology. This will require you to be dedicated, consistent in your participation and willing to complete your work to achieve success. You will be exposed, perhaps for the first time, to the process of science rather that simply content. Here, you will learn to think like a scientist in approaching a problem in biology. The entire laboratory component of the course is devoted to encouraging you and to measuring how you are doing in experiencing the process. Enjoy the ride!

Laboratory Part I. Examining Microbial Diversity using Molecular Biology

Introduction

Molecular biology has allowed us to define and refine tools to use DNA sequences to identify organisms. This is especially useful in working with microbes since identification by classical means, e.g. staining, colony morphology is a slow, often erroneous process. In addition, these techniques require culturing of bacteria to get enough to complete the study. Finally, they also required individuals to become 'experts' in the particular staining techniques which often leads to misidentification.

In this course, you will develop the molecular biology tools required to 'fingerprint' and identify bacteria isolated from the Ballona Wetlands. This is part of ongoing research projects in the Ballona Wetlands. The following techniques are part of the process;

  1. gel electrophoresis- agarose and polyacrylamide
  2. DNA isolation
  3. Subcloning
  4. PCR amplification
  5. Restriction enzyme digestion
  6. DNA sequencing
  7. BLAST annotation

Another major goal of this course is to assess how well your journey in experiencing the process of science is going. The major aspect will be the creation of an online team project notebook in which you will record your data and analysis on an ongoing basis. Here are the components required:

  1. pre-test and post-test surveys- objective and subjective components
  2. mini-research proposal with annotated bibliography (given to you at the beginning of course)
  3. ongoing, online team research notebook--> peer-reviewed
  4. peer reviews of other team's work
  5. Biweekly project review meeting- team and class
  6. Periodic quizzes,practicum to review grasp of equipment use
  7. Offline individual notebook
  8. Final presentation

Details will be provided as course continues.


Summary of Laboratory grading

Topic Points
1) Survey submissions - pre-, post test
Warning! Must be completed in a timely fashion or no grade will be assigned.
25 pts. (individual)
2) Ongoing notebook 100 pts (Group)
3) Offline individual notebook 50 pts (Individual)
4) Peer reviews (required for grade) 25 pts (Group)
5) Attendance/participation in group meetings 40 pts (individual)
6) Quizzes, practicums Warning!
Failure to complete practicum may delay participation in research project.
40 pts (individual)
7) Final presentation (Power Point) 50 pts (group)
8) Reflective piece submission (required for grade) 20 pts (individual)
350 pts


Laboratory Part II. Gene Discovery and Genome Annotation

Introduction

  1. Pre-, post-test genomics
  2. Completion of introductory exercises
    1. gene discovery exercise
    2. genomics walkthrough
  3. Final presentation- identifying genes in a fosmid

Grading

1) pre-, post test genomics, reflective piece 25 pts (Individual)
2) Exercises (must be submitted for grade) 40 pts (group)
3) Final presentation- fosmid 100 pts (group)
SUBTOTAL 165pts
Lab participation evaluation 35 pts
200 pts
TOTAL 550 pts


Tentative schedule

(Every effort will be made to follow this schedule. However, the actual scheduling of events and material covered may vary from this list).

Topic Readings*
A. Defining a Gene: Classical vs. Molecular-synthesis Chap 1,15, paper
From nucleotides to chromosomes
  (central dogma review-regulation)
Chap 9, Chap 16
---
B. Analyzing DNA I. Chap 15
A Primer on DNA synthesis
  -PCR technology
  -Uses of PCR technology
---
C. Ananlyzing DNA II
  1. DNA isolation/fragmentation (restriction digests)
  2. Southern blotting & probing
  3. DNA sequencing
---
D. Manipulating DNA
  a. Cloning DNA
  b. vector systems
  c. library creation
  d. Gene mapping-human examples
---
EXAM I- sections I., II.
---
IV. The Genome
Genomic sequence analysis Chap 21
Bioinformatics Chap 21, pp 531-535, Handout
Gene Annotation
---
V. Detecting and measuring gene expression
  a. the nature of mRNA Chap 12(review)
  b. in vitro analysis- Northerns, run-off, PCR Handout
  c. in vivo analysis- in situ hybridization
---
Eukaryotic gene regulation Chap 24
1. protein structure and translation
2. measuring protein levels in vitro- Westerns, antibody technology
3. Analyzing protein content in vivo
Chap 13(review)
Chap 20(497-502)
---
EXAM II - Sections III., IV.
---
VI. Manipulating gene expression and biotechnology
1. Gene construction at the bench
  a. modular nature of gene structure
  b. mapping regulatory regions and manipulation, cDNA and reporter genes
  c. analyzing the role of a gene product- creating under/over expressors
    1. antisense RNA
    2. dbs i RNA
TBA
2. Getting gene construct into a cell
  a. transient gene expression
  b. permanent gene expression
    1. creating transgenic plants
      -Agrobacterium transformation
      -shotgun transformation
    2. creating transgenic animals
      -stem cell transformation
Chap 22, pp. 561-568
---
VII. Interesting Case Studies in Molecular Biology
  a. Human disease- causes, diagnosis, treatment Chap 22, pp. 547-561
  b. our evolution history Handout
  c. jumping genes and evolution Chap 18, pp. 446- 458
---
FINAL
  • Occasionally papers will be assigned to supplement the text.


Organization of course

  1. Introduction of structure of gene - classical vs. molecular comparison
  2. Physical structure of chromosome
  3. Central dogma- gene structure and regulation
    1. Emphasis on overall review
    2. Role of chromosome in gene expression regulation
  4. Analyzing DNA
    1. DNA isolation/fragmentation
    2. Southern blotting
      1. Method and versatility
      2. Gene regulation
        1. nuclease sensitivity assay
    3. DNA synthesis and technology
      1. i. Primer on DNA synthesis
      2. PCR - tool to amplify DNA
      3. DNA sequencing
  5. Manipulating DNA
    1. DNA cloning
      1. Individual genes
        1. traditional
        2. PCR
      2. Libraries and vectors
        1. Creation
          1. Genomic
          2. Expression
            1. cDNA
            2. protein expression
          3. Screening
            1. mol probes
            2. antibodies
  6. Detecting and measuring gene expression
    1. mRNA
      1. Nature of mRNA
      2. RNA isolation-total vs polyA+
      3. In vitro analysis- Northerns, run-off, RT-PCR, polysomal RNA
      4. In vivo analysis- in situ hybridization
    2. proteins
      1. Nature of proteins
      2. Isolation and handling
        1. HPLC
      3. in vitro analysis- SDS-PAGE, Western blotting
      4. in vivo analysis- immunoblotting
    3. Examples of complex gene regulation
      1. Lac operon- prokaryotes
      2. Eukaryotic gene expression- levels TBA
  7. Genome Analysis
    1. Nature of genomes
      1. Prokaryotes
      2. Eukaryotes
    2. Computer-based- Bioinformatics
    3. Wet lab- microarrays(genome-wide gene expression analysis)
      1. History
      2. Basic principles
  8. Manipulating gene expression and biotechnology
    1. Gene construction at the bench
      1. Modular nature of gene structure
      2. Mapping regulatory regions and manipulation
        1. cDNA and reporter genes
      3. analyzing the role of a gene product- creating over/under expressors
        1. antisense RNA
        2. dbs i RNA
    2. Changing the genetics of a cell
      1. Transient gene expression
        1. electroporation
      2. permanent gene expression
        1. creating transgenic plants
          1. Agro transformation
          2. Shotgun transformation
        2. creating transgenic animals
          1. technology TBA
  9. Human molecular biology
    1. disease-causes, diagnosis, treatment
    2. our evolutionary history


Additional Course Materials

  1. Biol 439 - Molecular Biology Applications Laboratory Syllabus - Fall 2008
  2. General Comments on Beginning Annotation in Teaching Laboratory