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College of Graduate Studies

CGS 701/702 Unit Syllabi

Quicklist

Chemistry of Life Processes

Dr. Craig Beeson
QF 309C, 876-5091
beesonc@musc.edu

DateLecturesFlexInstructor

Wed Aug 20

1. Molecular Structure

Tinker Toys

Beeson

Thu Aug 21

1. Chemical Reactivity Assignment #1 Handout

Structure & Reactivity Questions

Beeson

Fri Aug 22

1. Solvation and Electrostatics

 Beeson

Mon Aug 25

1. Biological thermodynamics & kinetics
2. Overview of bioenergetics & redox

 

Beeson

Tue Aug 26

1.Lipids, bilayers & membranes
2.Transporters & channels

Assignment 1 Due

Beeson

Wed Aug 27

1. Mechanisms in Glycolysis
2. Stuctural Aspects of Regulation Assignment #2 Handout

 Beeson

Thu Aug 28

1. Electron transport chain
2. Chemiosmotic energy transduction & Oxidative Phosphorylation
 Lemasters
Fri Aug 291. Beta oxidation & citric acid cycle
2. Mitochondrial physiology
Assignment 2 DueLemasters
Mon Sep 1NO CLASS (Labor Day)  
Tue Sep 21. Regulation of catabolism versus anabolism
2. Signaling in regulation of metabolism
 Beeson
Wed Sep 3Mitochondrial Dysfunction in Disease Chan
Thu Sep 4Probing Metabolism in vitro and in vivoReviewBeeson

Fri Sep 5

UNIT EXAM  

Faculty

Craig Beeson, Ph.D., Drug Discovery and Biomedical Sciences
Sherine Chan, Ph.D., Drug Discovery and Biomedical Sciences
John J. Lemasters, MD, Ph.D., Drug Discovery and Biomedical Sciences, Biochemistry and Molecular Biology

General Reading

 Lehninger (5th ed)Stryer
(7th ed)
Intro to Metabolism
14
14
Bioenergetics
13
 
Lipids, membranes
10
12
Ion channels
11
13
Glycolysis
14, 15
16
TCA
16
17
Oxidative-Phosph
19
18
Fatty Acid Oxidation
17
22
Pentose Phosphate
15
20
Pathway (HMP-shunt)
Gluconeogenesis
14-15
16
Glycogen Synthesis
15
21
Glycogen Catabolism
15
21
Fatty Acid Synthesis
17
22

Useful Websites:

http://www.bmb.leeds.ac.uk/illingworth/oxphos/
http://www.esf.edu/efb/course/EFB325/default.htm
http://www.aw-bc.com/mathews/
http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/MB1index.html

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Macromolecules: Proteins

Dr. Scott Eblen
BSB 313F; 792-8367
eblen@musc.edu

DateLecturesFlexInstructor

Mon Oct 20

Protein Properties and Expression

Paper discussionEblen

Tues Oct 21

Protein Modifications

Paper discussion

Eblen

Wed Oct 22

Protein Folding and StabilityChan & Dill PaperBeeson/Isaacs

Mon Oct 27

Protein-Protein Interactions

Paper discussion

Hsu

Tues Oct 28

Purification

Flex ActivityHsi

Wed Oct 29

Enzyme KineticsKinetics questionsBeeson

Mon Nov 3

Principles of X-ray CrystallographyFlex Activity

Olsen

Tues Nov 4

Enzymes and Catalysis

Flex activity

Olsen

Wed Nov 5

Protein Purification/ProteomicsFlex activityBall

Fri Nov 7

Unit Exam  

Faculty

Scott Eblen, Ph.D., Cell and Molecular Pharmacology & Experimental Therapeutics
Craig Beeson, Ph.D., Drug Discovery and Biomedical Sciences
Jennifer Isaacs, Ph.D., Cell and Molecular Pharmacology & Experimental Therapeutics
Yi-Te Hsu, Ph.D., Biochemistry and Molecular Biology
Shaun Olsen, Ph.D., Biochemistry and Molecular Biology
Lauren Ball, Ph.D., Cell and Molecular Pharmacology & Experimental Therapeutics

General reading Prerequisite readings for this Unit are Chapters 2, 3, 6, 10.3, 10.4, 23.2, and 23.3
in Stryer 6th Ed; or Chapters 2,3,8,9,10,23.1,23.2, 30.4 and 30.5 in Stryer 7th Ed.

All assignments are due by 10:00 am on the assigned date: bring completed assignments to class. Read Assigned papers before class and be prepared to discuss them.

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Receptors & Signaling

Dr. Steven A. Rosenzweig
BSB 313G; 792-5841
rosenzsa@@musc.edu

DateLecturesFlexInstructor

Mon Nov 10

Overview of receptors & signaling

Methods in cell signaling

Rosenzweig

Tues Nov 11

Receptor tyrosine kinases in Cancer

Paper discussion (1)

Rosenzweig

Wed Nov 12

G protein coupled receptors

Paper discussion (2)

Blumer

Thurs Nov 13

G proteins and their regulatory proteins

Paper discussion (3)

Blumer

Mon Nov 17

Photoreceptors

Paper discussion (4)

Koutalos

Tues Nov 18

Protein: protein interactions in signal transduction

Methods for identifying/studying protein interactions

Ball

Wed Nov 19

The Pl3 Kinase signaling pathway in diseasePaper discussion (5)Muise-Helmericks
Thurs Nov 20Protein kinases: MAP kinasesPaper discussion (6)Eblen
 
Fri Nov 21Cell signaling in response to hypoxiaPaper discussion (7)Isaacs
 

Mon Nov 24

Unit Exam  

Faculty

Steven Rosenzweig, Ph.D., Cell and Molecular Pharmacology
Joe Blumer, Ph.D., Cell and Molecular Pharmacology
Yiannis Koutalos, Ph.D., Ophthalmology
Lauren Ball, Ph.D., Cell and Molecular Pharmacology
Robin Muise-Helmericks, Ph.D., Regenerative Medicine and Cell Biology
Scott Eblen, Ph.D., Cell and Molecular Pharmacology
Jennifer Isaacs, Ph.D., Cell and Molecular Pharmacology

General reading

Prerequisite: Chapters 15, 17 & 20 of Molecular Biology of the Cell, 5th Ed, Alberts et al.

Specific Reading

Papers will be posted on Moodlerooms as required

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Macromolecules: Nucleic Acids

Dr. Tilman Heise
BSB 507; 792-6979
heise@musc.edu

DateLecturesFlexInstructor

Mon Sept 8

Introduction to Unit

History
Nucleic Acid Structure I

Preparation time for upcoming lectures

Heise

Hennig

Tues Sept 9

Nucleic Acid Structure II
Catalytic RNA
Transfer and messenger RNA structure and functionHennig

Wed Sept 10

Biosensor and Long Non-coding RNA'sPaper discussion and in-Unit assignmentHeise

Mon Sept 15

Prokaryotic DNA replication
Eukaryotic DNA replication
Techniques in DNA replicationMohanty

Tues Sept 16

DNA Damage and Checkpoints
DNA Repair and Recombination
In-Unit assignment: QuizMohanty

Wed Sept 17

In vitro mutagenesis
Genome editing

 David Kurtz

Mon Sept 22

Genomics and information resources
Next Generation Sequencing
Paper discussionJeremy Barth

Tues Sept 23

RNA VirusesPaper discussionSommer

Wed Sept 24

DNA Viruses

Paper discussion

Heise

Fri Sept 26

Unit Exam  

Faculty

Jeremy Barth, Ph.D., Regenerative Medicine and Cell Biology
Tilman Heise, Ph.D., Biochemistry and Molecular Biology
Mirko Hennig, Ph.D., Biochemistry and Molecular Biology
David Kurtz, Ph.D., Pharmacology and Experimental Therapeutics
Bidyut Mohanty, Ph.D., Biochemistry and Molecular Biology
Gunhild Sommer, Ph.D., Biochemistry and Molecular Biology

General reading

Chapters 4-7 of Molecular Biology of the Cell, 5th Ed, Alberts et al.
Also useful are Chapters 4, 5, 28, 29 & 30 in Stryer, 6th ed.

Specific Reading

Dr. Hennig’s lectures:
Principles of Nucleic Acid Structure (W Saenger, 1984, Springer, NY)
Biophysical Chemistry; Part I The Conformation of Biological Macromolecules, (Cantor and Schimmel, 1980, Freeman, NY)
See folder T. Heise for reviews on long non-coding RNAs (Sept 10)

Dr. Mohanty’s lectures:
See folder B. Mohanty for reviews on replication (Sept 15)

Dr. Barth’s lectures:
1. Genomes. 2nd edition; Chapter 2: Genome Anatomies; Section 2.2 The Anatomy of the  Eukaryotic Genome
http://www.ncbi.nlm.nih.gov/books/NBK21120/
2. Genomes. 2nd edition; Chapter 6: Sequencing Genomes; Section 6.2 Assembly of a Contiguous DNA Sequence
http://www.ncbi.nlm.nih.gov/books/NBK21117/

Flextimes:
October 30 (Dr. Heise):
Identification of a long non-coding RNA-associated RNP complex regulating metastasis at the translational step. Gumireddy K, et al. EMBO J. 2013 Oct 16;32(20):2672-84.
doi: 10.1038/emboj.2013.188. Epub 2013 Aug 23

November 11 (Dr. Barth):
“A genomic view of mosaicism and human disease.” Biesecker LG, Spinner NB. Nat Rev Genet. 2013 May;14(5):307-20. doi: 10.1038/nrg3424. Review. PMID: 23594909

In class assignments: One homework and one quiz.

Grading: 25% of the Unit grade will derive from in-class assignments, and 75% will derive from the Unit exam (closed-book, in-class).

 

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Regulation of Gene Expression

Dr. David T. Kurtz
BSB 319F; 792-5844
kurtzdt@@musc.edu

DateLecturesFlexInstructor

Mon Sept 29

Prokaryotic transcriptional regulation

Discussion of student presentations
Molecular Biological Techniques I

Zhang

Tues Sept 30

Eukaryotic Transcription/Regulation of Gene ExpressionTechniques IIKurtz

Wed Oct 1

Integrating Transcriptional Regulation Signaling Events

Epigenetic Regulation of Gene Expression

Transgenic miceKurt

 Mon Oct 6

HDAC's and HAT's Role in Gene Expression I and II

 Menick

Tues Oct 7

Micro RNAs I and II

 Menick

Wed Oct 8

Regulation of mRNA Processing and Localization I and II

Practice talks

Heise

Thurs Oct 9

Regulation of mRNA Stability and Translation
Regulation of Translation and Degradation
Practice talks Heise

Mon Oct 13

Student presentations of research papers  
Tues Oct 14Student presentations of research papers  
Wed Oct 15Student presentations of research papers
Overview of Exam
 
Fri Oct 17Unit Exam  

Faculty

David Kurtz, Ph.D., Cell and Molecular Pharmacology and Experimental Therapeutics
Donald Menick, Ph.D., Medicine
Tilman Heise Ph.D., Biochemistry & Molecular Biology
Yong-Mei Zhang, Ph.D., Biochemistry & Molecular Biology.

General Reading

Prerequisite: Chapters 7, 8 and section 6.6 of Lodish et al, 6th ed. Additional reading from recent reviews may be assigned by each lecturer.

Flex-Time
Primary research papers will be presented and discussed. Each student will select a current paper on gene expression. Selected papers will be submitted for Unit leader approval by Monday, October 6, 2014. The Unit Leader will give guidelines for the presentation and grading criteria during flex time. The students will have a practice session with a TA on October 8 or 9, 2014. This will be done with 3 students and the TA will critique each presentation. In these practice sessions the students will have the opportunity to ask questions and get very good input on their presentation. Students will give their formal presentation to the entire class on October 13, 14 and 15, 2014.

Grading
25% of the Unit grade will derive from in-Unit research paper presentation, and 75% will derive from the Unit exam (closed-book, in-class).

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Immunology

Dr. Carl Atkinson
BSB 214B, 843-792-1716
atkinsoc@musc.edu

DATELecturesFlexInstructor
Mon Dec 1IIntroduction to Immune system – Structure Function.

Methods: Immunopathology
(Atkinson)

Atkinson
Tue Dec 2Innate Immunity Atkinson
Wed Dec 3TLR/InflammasomesPOPs learning assignment
(Atkinson, Assignment 1)
Guo/Atkinson
Mon Dec 8The recognition of antigen/The generation of lymphocyte AG Receptors.Methods: Flow Cytometry
(Soloff)
Paulos
Tues Dec 9Ag Presentation to lymphocytes/signal transductionPaper ReviewsHaque/Atkinson
Wed Dec 10Development and survival of lymphocytesMethods: T cell Assays
(Rubinstein)
Rubinstein
Thurs Dec 11B cell activation and Ig isotype distribution and functionAntibody Assignment
(Kasman, Assignment 2)
Sutkowski/Kasman
Mon Dec 15B cell toleranceReview Study SessionAtkinson
Tues Dec 16Immunology and DiseaseReview Study SessionLi
Thurs Dec 18Unit Exam  

Faculty

Carl Atkinson, Ph.D., Microbiology and Immunology
Beicho Guo, Ph.D., Microbiology and Immunology
Chrystal Paulos, Ph.D., Microbiology and Immunology
Adam Soloff, Ph.D., Microbiology and Immunology
Laura Kasman, Ph.D., Microbiology and Immunology
Natalie Sutkowski, Ph.D., Microbiology and Immunology
Mark Rubinstein, Ph.D., Surgery/Microbiology and Immunology
Aziz Haque, Ph.D., Microbiology and Immunology
Zihai Li, Ph.D., Microbiology and Immunology

General Reading and Resources

Immunobiology    7th  ed (2008) Charles A. Janeway et al.
Cellular and Molecular Immunology  7th ed (2011) Abul K. Abbas et al.
The Immune System    3rd ed (2009) Peter Parham

On-line Resource:
Dr. Harris Goldstein Immunology Lecture Mini-Course
Albert Einstein College of Medicine
http://www.einstein.yu.edu/video/?SCID=23&ts=conferences#top

Specific Reading

Papers will be posted on Moodlerooms as required.

Flex-Time

Will focus on presentation and discussion of immunological techniques to build upon the foundations discussed in formal lectures. The aim of these sessions is to explore methodologies in an interactive informal tutorial setting.

Grading

25% of the Unit grade will be derived from two in-Unit assignments carried out in a designated Flex-time session, and 75% will be derived from a closed-book, in-class exam.

Learning Objective:

The course aims are to guide the student through the immune system in all its aspects - from anatomy, first engagement of innate immunity, to the generation of the adaptive immune response and its clinical/disease consequences. The course will encompass topics such as the complement system, Toll-like receptors, mucosal immunity, T cell tolerance, B cell function and immune diseases.

Specifically students will learn:

• Differences between innate and adaptive immunity
• Structure, function and cellular constituents of immune system
• Immune programing
• Normal function of immune system
• Immune system and disease
• Introduction to key methods in Immunology
 

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Cellular Functions

Dr. Robert Gemmill
HCC 712B; 792-4643
gemmill@@musc.edu

DateLecturesFlexInstructor

Mon Jan 5

1. Overview of Unit structure (brief) with introduction to Cell Biology
2. Two background lectures, Team 1
Sign-up for 1 of 4 presentation topics:
Literature databases
All Faculty
Gemmill & Findlay
50 min each

Tues Jan 6

Integration of growth signals (2h)
MicroRNAs & metastomiRs (2h)
Literature databases

Gemmill-(Section I)
Findlay-(Section II)

Wed Jan 7

Integration of growth signals (2h)
MicroRNAs & metastomiRs (2h)
Finalize four groups
Search for papers
Prepare for next two topics
Gemmill-(Section 1I)
Findlay-(Section I)

Thur Jan 8

Two background lectures, Team 2
Cell: Extracellular Matrix Interactions
Cell Motility

Techniques discussion
Work on presentations

Bradshaw & Nasarre
50 min each

Mon Jan 12

Cell:  Extracellular Matrix Interactions (2h)
Cell Motility (2h)
Techniques discussion
Work on presentations

Bradshaw-(Section I)
Nasarre-(Section II)

Tues Jan 13

Cell: Extracellular Matrix Interactions (2h)
Cell Motility (2h)
 Techniques disc Or work on presentationsBradshaw-(Section II)
Nasarre-(Section I)

Wed Jan 14

In Class review of materials, experiments, papers Quizzes (all four) due by midnight Friday Jan 18Faculty and Students
All Faculty present
Mon Jan 19MLK Day - no class  

Tues Jan 20

Student Presentations from first two groups

 

Students
All Faculty present

Wed Jan 21

Student Presentations from last two groups Students
All Faculty present

Fri Jan 23

Unit Exam

  

Faculty

Amy Bradshaw, PhD (bradshad@musc.edu) Regenerative Medicine and Cell Biology
Victoria Findlay, PhD (findlay@musc.edu) Department of Pathology and  Laboratory Medicine
Robert Gemmill, PhD (gemmill@musc.edu) Department of Medicine
Patrick Nasarre, PhD (nasarre@musc.edu) Department of Medicine
 

General Reading
Chapters 13, 14, 17-20, 22 and 25 Molecular Cell Biology, 6th edition, Lodish

Specific Reading
Papers will be posted on Moodlerooms before the relevant lecture.  Students are to read and complete the Journal Article Worksheet and bring two copies to class.

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Cell Injury and Response

Dr. Julie Woolworth Hirschorn
Children's Hospital, EH 222B, 792-1181
woolworj@@musc.edu

DateLecturesFlexInstructor

Mon Jan 26

Introduction

Cell Injury Part 1: causes, mechanisms, and morphology

Flex-Time #1: Solutions

Woolworth

Tues Jan 27

Cell Injury Part II: adaptations and deathReceive in-Unit assignment #1Woolworth

Wed Jan 28

Inflammation Part 1: mechanismsIn-Unit assignment #1 due.  Receive reading and in-Unit assignment #2Woolworth

Mon Feb 2

Immune System I

In-class activity #3

Kasman

Tues Feb 3

chronic inflammation and immune Atkinson

Wed Feb 4

Techniques Rotation Day

Techniques Rotation

 

Mon Feb 9

Prepare paper discussion with group members

Article discussion #4

Woolworth

Tues Feb 10

Hypersensitivity

Immunopathology organ transplant rejection

In-Unit Assignment

Review

Self

Woolworth

Wed Feb 11

Technique papers due 9:00am

All Day - Techniques
Presentations from Groups
  

Fri Feb 13

Unit Exam

 

 

Faculty

Julie Woolworth Hirschhorn, Ph.D., Pathology & Laboratory Medicine
Laura Kasman, Ph.D., Microbiology & Immunology
Sally Self, MD, Pathology and Laboratory Medicine
Carl Atkinson, Ph.D., Microbiology and Immunology
 

Learning Objectives will be provided at the start of the Unit

General reading

Robbins Basic Pathology, 7th edition (on reserve); the following chapters will supplement lecture notes:

Chapter 1, Cellular Injury and response, Aging, Apoptosis
Chapter 2, Inflammation
Chapter 5, Diseases of Immunity
Chapter 6, Neoplasia

Kumar, Robbins and Cotran Pathologic Basis of Disease, Professional Edition, 9th Ed. Available from the MUSC Library home page, Physician Assistant Library Resources, Pathology and Laboratory Medicine.
http://www.library.musc.edu/page.php?id=1900&SASB=4   or http://www.mdconsult.com/books/page.do?eid=4-u1.0-B978-1-4557-2613-4..C2011-0-05573-4&isbn=978-1-4557-2613-4&uniqId=453037193-2#4-u1.0-B978-1-4557-2613-4..C2011-0-05573-4--TOP

Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury, and Death

Chapter 3: Inflammation and Repair

Kuby’s Immunology, 6th ed. (Kuby et al, 2006,) Chapters 1-10 contain basic information that supplements lecture notes.

To study normal versus pathologic situations in tissue, a good resource can be found at the MUSC Library home page, Physician Assistant Library Resources, AccessMedicine, Textbooks, Lange Educational Library, Histology Image Review.  http://www.accessmedicine.com/resourceTOC.aspx?resourceID=24

Relevant Unit questions are available at the Brainscape website at https://www.brainscape.com/study?pack_id=814223 (also available with the Brainscape or Flashcards+ app for iPad and iPhone). These apps are currently not available for Android or Blackberry)

Specific Reading will be posted on Moodlerooms before the relevant lecture and/or assignment.

 

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Human Physiology

Dr. Perry Halushka
BE 311; 876-2405
halushpv@@musc.edu

DateLecturesFlexInstructor (email)

Mon Feb 16

Introduction to the Unit
The Heart and Arterial Pressure Control Mechanisms
 Halushka

Tues Feb 17

Renal Physiology Bell

Wed Feb 18

The autonomic nervous system Kurtz

Mon Feb 23

Cardiovascular Diseases/Hypertension

 Lackland

Tues Feb 24

Presentation of Classic Papers TBA

Wed Feb 25

Gastrointestinal Physiology Smolka

Mon Mar 2

Endocrinology Luttrell

Tues Mar 3

Pulmonary Physiology
 
 Koutalos

Wed Mar 4

Pulmonary
Pathophysiology/COPD/Asthma
 Atkinson

Fri Mar 6

Unit Exam  

Faculty

Perry Halushka, Ph.D., M.D., Medicine/Cell and Molecular Pharmacology
P. Darwin Bell, Ph.D., Medicine
David Kurtz, Ph.D., Cell and Molecular Pharmacology
Dan Lackland, DRPH, Neuroscience
Adam Smolka, Ph.D., Medicine
L. Luttrell, M.D., Ph.D., Medicine
Ioannis Koutalos, Ph.D., Ophthalmology
Carl Atkinson, Ph.D., Microbiology and Immunology

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