BIOLOGY 590: ION CHANNELS

http://nanobiologynotes.blogspot.com/2006/02/ion-channels-gates-in-cell-wall.html

Spring 2009
CRN 29755 2 cr

Bio 590 (Section 01)

ION CHANNELS

Instructor:
E. E. Serrano

January 15-May 9

1:30-3:30 pm
O’Donnell 241

updated 04/04/09 ees

COURSE GOALS AND OUTCOMES

CLASS SCHEDULE

RESOURCE LINKS

ASSIGNMENTS & GRADING

POLICIES AND PROCEDURES

http://www.ipmc.cnrs.fr/~duprat/neurophysiology/patch.htm

Instructor	Dr. Elba Serrano Ph. D. Stanford University Regents Professor of Biology, NMSU Research Interests: Neuroscience, Biophysics, Sensory Systems
Office	Foster Hall 459
Office hours:	MW 11-12:30; Tues 2-3 pm and by appointment
Telephone	646-5217
email	serrano@nmsu.edu
Appointments	Sign up on sheet outside FH 459 OR make appointment for other times via email or phone
Required Textbooks:	None
Recommended Textbooks:	Ion Channels and Disease, Ashcroft Publisher: Academic Press; 1st edition (January 15, 2000) ISBN-10: 0120653109; ISBN-13: 978-0120653102 Ion Channels: Methods and Protocols (Methods in Molecular Biology) Stockand / Shapiro Humana Press; 1 edition (April 17, 2006) ISBN-10: 1588295761; ISBN-13: 978-1588295767
Textbook Vendors	Textbooks can be obtained at the bookstore or online from vendors such as Amazon and ecampus or Best Book Buys.
GOALS & OUTCOMES	This course is for students who are interested in · the origins of diseases and research that aims to develop treatments to improve human health. · industry careers in drug discovery and chemical biology · how the brain, muscle, and senses accomplish designated tasks. · modern methods in biophysics and molecular biology such as: crystallography, protein prediction algorithms, bioelectronics, heterologous expression systems, fluorescence detection of molecular targets, patch clamp. The class format integrates lectures, case studies, primary literature, historical perspectives, and interactive in-class activities. Students who complete the course will increase their ability to: 1. analyze, critique, and present original research papers 2. solve quantitative problems in membrane biophysics 3. investigate ion channel gene expression using in silico simulations 4. apply knowledge gained in the class by identifying a research question 5. prepare a fellowship application using the NIH F31/32 format.

CLASS SCHEDULE

DATE

THEME

PRESENTER/READING/ACTIVITY

Jan 15

Course Organization

Assessment of student skills

Jan 22

Ion Channel Basics:

Genetics and Structure

Classic Contributions

Nobel Laureates

1- Browse All Resource Links

2- For each assigned article, identify FIVE major concepts, ten KEY words and three QUESTIONS that arise from the readings

· Neuroscience Core Concepts

http://www.sfn.org/skins/main/pdf/core_concepts/core_concepts.pdf

· Chapter 13 Physics in Biology and Medicine in binder outside Foster 450

· Chapter 5.4-5.6 Cellular and Molecular Neurobiology in binder outside Foster 450

· Hodgkin Ionic Basis of Nervous Conduction

http://nobelprize.org/nobel_prizes/medicine/laureates/1963/hodgkin-lecture.pdf

· Chapter 1: Axon Guide for Electrophysiology & Biophysics http://www.moleculardevices.com/pages/instruments/axon_guide.html

Jan 29

Classic Contributions

Nobel Laureates

Literature Reviews

Nobel Speeches: For each assigned article, identify FIVE major concepts, ten KEY words and three QUESTIONS that arise from the readings

· Huxley The Quantitative Analysis of Excitation and Conduction in Nerve http://nobelprize.org/nobel_prizes/medicine/laureates/1963/huxley-lecture.pdf

· Neher Ion Channels for Communication Between and Within Cells http://nobelprize.org/nobel_prizes/medicine/laureates/1991/neher-lecture.pdf

· MacKinnon Potassium Channels and the Atomic Basis of Selective Ion Conduction http://nobelprize.org/nobel_prizes/chemistry/laureates/2003/mackinnon-lecture.pdf (also in video format at Nobel site)

· Select one from:

http://www.nature.com/nature/journal/v423/n6935/pdf/423021a.pdf

http://www.nature.com/nature/journal/v419/n6902/pdf/nature00978.pdf

http://www.nature.com/nature/journal/v456/n7224/pdf/nature07620.pdf

Feb 5

Classic Contributions

Nobel Laureates

Methods to study channels

Continue discussion of classic contributions papers (Jan 29)

Recordings from Membranes: Passive/Active

· Axon Guide for Electrophysiology & Biophysics http://www.moleculardevices.com/pages/instruments/axon_guide.html

Feb 12

Ion Channel Structure and Nomenclature

· IUPHAR DATABASE OF RECEPTORS AND ION CHANNELS- http://www.iuphar-db.org/index.jsp

· Ion channel database http://www.ionchannels.org/database.php

Feb 19

Problems 1 due

Ion Channel Genetics

· Microarray analysis> Dr. Tushun Powers

· Software/In silico experimentation

Feb 26

Neurotransmitters

Individual presentations

· Alicia/ACh peripheral

· Regina/ACH central

· Eddie/glutamate

· Andrea/glycine

· Lauren/dopamine

· Daniel/serotonin

· Chelsea/Substance P

· Noha/ GABA

· Selene/ATP

Mar 5

Journal due

250 pts

Channelopathies 1

Voltage-Gated Ion Channels and Hereditary Disease, Frank Lehmann-Horn and Karin Jurkat-Rott, Physiological Reviews, Vol. 79, No. 4, October 1999, pp. 1317-1372

Mar 12

Mid Term Review

· Summary Lecture

· Genes and Diseases - browse this website :

· http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=gnd.TOC&depth=2 Electrophysiology - come prepared to answer questions about these articles (Quiz!) .

http://www.nature.com/nature/journal/v423/n6935/pdf/423021a.pdf

http://www.nature.com/nature/journal/v419/n6902/pdf/nature00978.pdf

http://www.nature.com/nature/journal/v456/n7224/pdf/nature07620.pdf

Mar 19

Methods to study channels

· Imaging

· Exogenous Expression

· Channel Regulation bring your laptops to explore this site

http://elm.eu.org/links.html

· Reference http://www2.montana.edu/cftr/IonChannelPrimers/methods_to_study_ion_channels.htm

Mar 26

Spring Break

No Class

Apr 2

Proposal draft due

100 pts

DOWNLOAD HERE

Methods to study channels

Modeling Channel Structure: Protein Prediction

BioImaging

Apr 9

Methods to study channels

Modeling Channel Structure: Protein Prediction

Confocal Imaging

Proposal Draft Critiques

Apr 16

Channelopathies 1

Individual Presentations (15 slides)

· Alicia

· Regina

· Eddie

· Andrea

Apr 23

Channelopathies 2

Individual Presentations (15 slides)

· Lauren

· Daniel

· Chelsea

· Selene

Apr 30

Final Proposal due

200 pts

DOWNLOAD HERE

Toxins, Drugs, & Channels

Lecture

Tuesday

May 5

Final Class

1:00-3:00 pm

Proposal Argument (10 minute slide blitz)

Student Concept Presentations for Lay Public /K-12 dissemination (OPTIONAL)

RESOURCE LINKS

Disease and Relevance to Human Health

· Channelopathies http://www.kcnq.org/health/diseases.php

· Hereditary Hearing Loss Homepage: http://webh01.ua.ac.be/hhh/

Electrophysiology

· Axon Guide for Electrophysiology & Biophysics http://www.moleculardevices.com/pages/instruments/axon_guide.html

History

· Nobel Laureates http://nobelprize.org/

· NeuroTree http://neurotree.org/neurotree/

Literature

· Core concepts http://www.sfn.org/skins/main/pdf/core_concepts/core_concepts.pdf

· Brain Briefings http://www.sfn.org/index.cfm?pagename=brainBriefings_main

· Brain Facts http://www.sfn.org/index.cfm?pagename=brainfacts

Methods

· Patch & Voltage Clamping http://www.adinstruments.com/applications/research/Patch-&-Voltage-Clamping/

· Multiple Methods http://www2.montana.edu/cftr/IonChannelPrimers/methods_to_study_ion_channels.htm

Genetics/Informatics

· NCBI Databases http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?itool=toolbar

· Guide to Receptors and Channels (GRAC), 3rd edition Alexander, S.P.H., Mathie, A. & Peters, J.A. (2008). Br. J. Pharmacol., 153 (Suppl. 2), S1–S209.

· UBC Bioinformatics Links http://www.bioinformatics.ca/links_directory/

· Nottingham Bioinformatics Links http://evol.nott.ac.uk/cmelun/links.html

· UCSC-genome browser- http://genome.ucsc.edu/

· OMIM - Online Mendelian Inheritance in Man- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

· UniGene database- http://www.ncbi.nlm.nih.gov/unigene

· NCBI Entre Gene database- http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene

· UniProt- http://www.uniprot.org/

· HGNC search- http://www.genenames.org/cgi-bin/hgnc_search.pl

· NetAffx from Affymetrix (need to login to use NetAffx)- http://www.affymetrix.com/analysis/netaffx/index.affx

· Xenbase- http://www.xenbase.org

· Biomart to mine Ensembl- http://www.ensembl.org/biomart/martview/cfc7687927376ef2e849c6730ba6eff5

· JGI X. tropicalis v4.1 Home (click on downloads to get to sequences)- http://genome.jgi-psf.org/Xentr4/Xentr4.home.html

ASSIGNMENTS & GRADING

Earning your grade (1000 points):

In class participation: (150 pts) Based on your contribution to class discussion, and activities as presenter, 15 pts per class

Presentations. each week , students will make presentations or discuss assigned readings.

Readings and Questions The class discussion is stimulated if the reading is completed prior to the class, and if questions are asked during the session. Come prepared to participate

Journal (250 pts) The journal will compile structure and function information that will be used to develop the research questions and background for your proposal.

Problems/Quizzes/Talks (300 pts) Problem Sets. Take home assignments to build problem solving skills; can be completed individually or in teams of 2-3. Talks to build oral communication skills

Research Proposal (300 pts) Students will prepare a 5-8 page single spaced research proposal using the NIH F31/F32 guidelines. Detailed instructions to follow LINK HERE

Lay Public/ K-12 Dissemination (100 pts-OPTIONAL) Student swill prepare a presentation or demonstration that can be used to explain a conceptabout ion channel structure function to the lay public.

Grade scale

A 90-100 %
B 80-89 %
C 70-79 %
D 60-69 %
F < 60 %
S (Satisfactory) requires at least a C
Note: The grade scale may be curved at the end of the semester at the discretion of the instructor.

Late assignments. 10% of the total points will be deducted for each week the assignment is late. Assignments will not be accepted if handed in more than 2 weeks after the due date.

Attendance: Debate and discussion are essential components of this class, therefore, students are expected to attend all classes except for a documented university business, medical emergency etc. Documentation must be submitted if you are absent and it is best to inform the instructor in advance if possible if you will need to miss class. 15 points will be deducted from your overall points for each unexcused absence.

S/U Option: Students must meet all requirements of the course. A grade of C is required to earn an S.

Withdrawals: It is your responsibility to withdraw from the course. The instructor will not automatically drop you from the course for failure to attend class or to complete exams or assignments.

Incompletes, academic misconduct, and make-up work: Incompletes will be given only if a student has passed the first half of the course and is precluded from completing the course by a documented illness or family crisis. Make-ups of assignments for excused absences must be discussed with the instructor within one week of the due date of the assignment. There are no provisions for extra credit work. The penalty for plagiarism or other forms of academic misconduct (as defined in the Student Code of Conduct) is failure of the course: no exceptions.

Important dates:

Feb 19 Problems 1 due

Mar 5 Journal due

Apr 2 Proposal draft due

Apr 30 Final Proposal due

May 5 Lay public/K-12 dissemination (optional)

POLICIES AND PROCEDURES

SYLLABUS MODIFICATION: The instructor reserves the right to modify this syllabus during the semester as considered necessary to enhance the quality of the instruction, to meet the needs of students in the class and to achieve course objectives. Any changes to the syllabus [or to the course schedule] will be announced in class and you are responsible for being aware of them.

XEROX and/or BACKUP all assignments before submitting them to the instructor.

SAVE xeroxes of all graded assignments and exams from this course at least until you have received your final grade.

PLAGIARISM: Students found guilty of plagiarism have engaged in academic misconduct and shall be subject to disciplinary action. The library maintains a website with important information: http://lib.nmsu.edu/plagiarism/. The penalty for plagiarism or other forms of academic misconduct (as defined in the Student Code of Conduct) is failure of the course: no exceptions. The current University definition of plagiarism can be found at http://www.nmsu.edu/%7Evpsa/SCOC/misconduct.html . It reads as follows:

“Plagiarism is using another person’s work without acknowledgment, making it appear to be one’s own. Any ideas, words, pictures, or other intellectual content taken from another source must be acknowledged in a citation that gives credit to the source. This is irrespective of the origin of the material, including the Internet, other students’ work, unpublished materials, or oral sources. Intentional and unintentional instances of plagiarism are considered instances of academic misconduct. It is the responsibility of the student submitting the work in question to know, understand, and comply with this policy.If no citation is given, then borrowing any of the following would be an example of plagiarism.:

·          an idea or opinion, even when put into one’s own words (paraphrase)

·          a few well-said words, if these are a unique insight

·          many words, even if one changes most of them

·          materials assembled by others, for instance quotes or a bibliography

·          an argument

·          a pattern of ideas

·          graphs, pictures, or other illustrations

·          facts

·          all or part of an existing paper or other resource

* This list is not meant to include all possible examples of plagiarism.

Even with a citation, failure to put quotation marks around direct quotations also constitutes plagiarism, because it implies that the writing is your own.   Material should either be paraphrased or clearly designated as a quotation.   Note that replacing words with synonyms, changing verb tense or other minor alterations do not qualify as paraphrasing. ”

STUDENTS WITH DISABILITIES:   Additional information is available at http://www.nmsu.edu/~ssd/

·          If you have or believe you have a disability and would benefit from any accommodations, you may wish to self-identify by contacting the Services for Students with Disabilities (SSD) Office located at Corbett Center (phone: 646-6840).

·          If you have already registered, please make sure that your instructor receives a copy of the accommodation memorandum from SSD within the first two weeks of classes. It is your responsibility to inform either your instructor or SSD representative in a timely manner if services/accommodations provided are not meeting your needs.

·          If you have a condition which may affect your ability to exit safely from the premises in an emergency or which may cause an emergency during class, you are encouraged to discuss any concerns with the instructor and/or the SSD Coordinator.

EQUITY: Feel free to call Jerry Nevarez, Director of Institutional Equity, at 505-646-3635 with any questions you may have about NMSU's Non-Discrimination Policy and complaints of discrimination, including sexual harassment.

ADA:   Feel free to call Michael Armendariz, Coordinator of Services for Students with Disabilities, at 505-646-6840 with any questions you may have on student issues related to the Americans with Disabilities Act (ADA) and/or Section 504 of the Rehabilitation Act of 1973. All medical information will be treated confidentially.

BIOLOGY DEPARTMENT :     The Department Chair is Dr. Marvin Bernstein. The Department office is in Foster 275, 646-3611

GUIDELINES FOR CLASS DISCUSSION: During the semester, opinions will be voiced in the class. You may strongly disagree with some of these, or you may find them amusing. Outbursts can be misinterpreted or counterproductive to meaningful and thoughtful debate. Therefore, it is important that you exercise self-discipline and self-control, and treat all members of the class with the courtesy that you are entitled to receive in turn. The key words are: respect and courtesy. Please turn off cell phones and beepers while in class.       Thank you!