Christopher Chastain

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2018 Spring BCBT461 - Nucleic Acids and Bioinformatics | MW 3:00 - 5:50PM

Course location: Langseth 202 and 208

Pre-requisites: Biol 385 & 385L

 

Co-instructors

E-mail

Office

Research lab

Dr. Chris Chastain

chastain@mnstate.edu

HA407V

LH208

Dr. Sara Anderson

sara.anderson@mnstate.edu

HA407U

HA413

 

Course catalogue description: Advanced theory and practice of techniques for working with DNA and RNA for research and applications. Development of modern bioinformatics skills and applications to genomic research.

 

Expanded description: This course builds on experience from Molecular Biology and will emphasize (i) laboratory methods involving DNA and RNA manipulation and analysis and (ii) use of bioinformatic tools for analyzing genes and genomes. Your time will be budgeted at about 80% lab related activities and 20% lecture. Lectures will cover theory and practice and will usually be held during the first part of the class. Lab will follow directly after lecture and will sometimes begin with a demonstration or brief orientation before you proceed on your own.

 

We plan to address details of working with DNA, then complete a DNA project.  Then we will address details of working with RNA, then complete an RNA project.

 

Lab books - You will be keeping a lab book according to a defined style that will be explained in the first class meeting. The style of lab book will be the hardbound 8.5 x 11 "black-white" speckled kind that you can get at the bookstore.

Lab manual - We do not have a lab manual for this specific course. Instead, you will have an assortment of printed handouts and reference materials provided to you. Insert these in a three ring binder (see below).

3-ring binder - get a simple three ring binder to use for collecting protocols and related printouts we use during the course. I'll have a three-ring punch in the lab. These can be left in the lab between sessions.

D2L site - We will post on D2L a variety of information for use as the course proceeds; check often for materials and announcements.

Computer - The Bioinformatics world involves using computers.  While most of what we will do can be accomplished on the classroom computers, you may find it useful to bring your own laptop if you have one.  Note that many functions will also work on a tablet or phone, but these will be more difficult to work with and some functions will not be possible without a full computer.

 

Student learning outcomes:

  1. Demonstrate proficiency in working with DNA and RNA in a laboratory setting.
  2. Explain the reasoning behind laboratory methods and impacts on results.
  3. Incorporate bioinformatics tools to inform and analyze nucleic acid-based projects.
  4. Accurately and completely record experiments from concept to methods to results and interpretation in a standard scientific notebook.
  5. Explain projects in written and oral formats.


 

Major outline of content areas:

  1. The DNA world
    1. What can we do with DNA?
    2. Isolation methods
    3. Quality control
    4. DNA sequencing
    5. Project
  2. The RNA world
    1. What can we do with RNA?
    2. Isolation methods
    3. Quality control
    4. Expression assays
    5. Project
  3. The digital world
    1. Bioinformatics tied in with our wet lab research
    2. GEP project
    3. Sequence analysis
    4. Genome assembly

 

Grade categories

Notebooks (3 checks)

5

Project report

15

Project presentation

15

GEP

20

DNA unit - assignments

DNA unit - quiz

5

15

RNA unit - assignments

RNA unit - quiz

5

15

TBA

5

  • Note that less than full participation may impact final grade.

 


 

Course policies

Attendance: you are expected to attend all scheduled class periods.  When working with living organisms (e.g., bacteria) it may be necessary to come in outside of regularly scheduled class.  In these cases, we will make arrangements with the entire class ahead of time to ensure the best running of the experiments.

 

Lab safety and protocol policy: you are expected to follow all laboratory protocols accurately and safely to ensure the safety of yourself and others, and to ensure the best possible outcome for experiments.

 

 

MSUM policy statements:

Special Accommodations and Accessibility Resources statement:

"Minnesota State University Moorhead is committed to providing equitable access to learning opportunities for all students. Accessibility Resources (AR) is the campus office that collaborates with students who have disabilities to provide and/or arrange accommodations.

  • If you have, or think you may have, a disability (e.g. mental health, attentional, learning, chronic health, sensory or physical) please contact the AR at (218) 477-4318 (V) or (800)627.3529 (MRS/TTY) to schedule an appointment for an intake.
  • Additional information is available on the AR website: http://www.mnstate.edu/accessibility

If you are registered with the AR and have a current Accommodation Letter, please schedule an appointment to visit with me, during my office hours, to discuss implementation of your accommodations."

 

Sexual Violence Prevention Statement:

●      Acts of sexual violence are intolerable. MSUM expects all members of the campus community to act in a manner that does not infringe on the rights of others. We are committed to eliminating all acts of sexual violence.

●      MSUM faculty and staff are concerned about the well-being and development of our students. We are obligated to share information with the MSUM Title IX Coordinator in certain situations to help ensure that the students’ safety and welfare is being addressed, consistent with the requirements of the law. These disclosures include but are not limited to reports of sexual assault, relationship violence, and stalking.

●      If you have experienced or know someone who has experienced sexual violence, services and resources are available. You may also choose to file a report. For further information, contact Lynn Peterson, Coordinator of Sexual Assault Services at Hendrix Clinic and Counseling Center, 218-477-2211, or Ashley Atteberry, Title IX Coordinator in Owens Hall 208 (218-477-2174; ashley.atteberry@mnstate.edu). Additional information is available at: www.mnstate.edu/titleix