Download current curriculum schedule

Lecturers
Term 1
Genetics A
FullName
*Susan Rosenberg
*Zheng Zhou
Richard Kelley
Phone
713-798-6924
713-798-6489
713-798-4526
Room
S809
322B
T728
Email
[email protected]
[email protected]
[email protected]
Phone
713-798-8731
713-798-8278
713-798-3313
713-798-5126
713-798-8082
713-798-5760
713-798-4526
713-798-5194
713-798-5524
713-798-5609
713-798-2093
Room
T222
S338A
N61006
220A
S430
T342
T728
N1519
N803
223A
T926
Email
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Phone
713-798-5880
713-798-6311
713-798-1507
713-798-7565
713-798-4756
Room
371A1
219A
T303
N1409
137D
Email
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Room
T228
T428
N430
T926
322B
Email
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Room
371A1
N204
204GA
N204D
Email
[email protected]
[email protected]
[email protected]
[email protected]
Method & Logic in Molecular Biology
FullName
*Graeme Mardon
Adam Kuspa
David Moore
E. Zechiedrich
Gad Shaulsky
John Wilson
Richard Kelley
Rui Chen
Scott Pletcher
Timothy Palzkill
Xiangwei He
Molecular Methods
FullName
*Hiram Gilbert
*Sarah Highlander
Jun Qin
Michael Metzker
Xin-Hua Feng
Organization of the Cell
FullName
*Richard Sifers
*Steen Pedersen
Theodore Wensel
Xiangwei He
Zheng Zhou
Phone
713-798-3169
713-798-3888
713-798-6994
713-798-2093
713-798-6489
Science as a Profession Term 1
FullName
*Hiram Gilbert
Barbara Slaughter
Bill Brinkley
Scott Basinger
Phone
713-798-5880
713-798-6644
713-798-5263
713-798-4100
Term 2
Cancer
FullName
*Sharon Plon
Francesco Demayo
Phone
832-824-4251
713-798-6241
Room
120020
M725A
Email
[email protected]
[email protected]
Phone
713-798-4531
713-798-5760
713-798-1866
713-798-2093
Room
375A
T342
T411
T926
Email
[email protected]
[email protected]
[email protected]
[email protected]
Phone
713-798-6865
713-798-5550
713-798-6421
713-798-3454
Room
S803
M804
N620.0
T903
Email
[email protected]
[email protected]
[email protected]
[email protected]
Phone
713-798-8731
713-798-4683
832-824-4579
713-798-4795
713-798-5440
Room
T222
N604.0
124008
T619
S413A
Email
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Phone
713-798-5880
713-798-6644
713-798-5263
713-798-6825
713-798-6776
Room
371A1
N204
204GA
N104
7062
Email
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Phone
713-798-6210
713-798-5774
713-798-6205
713-798-2126
713-798-6294
713-798-8993
713-798-3141
Room
M638A
824DB
M613
S909
M732
860E
268B
Email
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Cell Division
FullName
*Shelley Sazer
John Wilson
Pumin Zhang
Xiangwei He
Development
FullName
*Armin Schumacher
Kathleen Mahon
Paul Overbeek
Ramiro Ramirez-Solis
Genetics B
FullName
*Graeme Mardon
*Tae-Ho Shin
Alison Bertuch
Arthur Beaudet
Monica Justice
Science as a Profession-Ethics
FullName
*Hiram Gilbert
Barbara Slaughter
Bill Brinkley
Lloyd Michael
Morey Haymond
Term 3
Gene Regulation
FullName
*Jeffrey Rosen
Andrew Rice
Bert O'Malley
Christophe Herman
Jiemin Wong
Richard Lloyd
Thomas Cooper
Immunology
FullName
*Biao Zheng
David Spencer
Phone
713-798-8796
713-798-6475
Room
N90305
N903.0
Email
[email protected]
[email protected]
Phone
713-798-5686
713-798-4007
713-798-3888
Room
N410
112C
T428
Email
[email protected]
[email protected]
[email protected]
Phone
713-798-9174
Room
M822A
Email
[email protected]
Phone
713-798-5880
713-798-5734
713-798-5686
713-798-5126
713-798-4007
713-798-5646
Room
371A1
N420
N410
220A
112C
T921
Email
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Room
N420
M515
220A
315BA
371A1
T303
T921
T228
N420
N430
Email
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Molecular Interactions
FullName
*B Prasad
*Joseph Bryan
Steen Pedersen
Neuroscience
FullName
*Tony Pham
Term 4
Research Design
FullName
*Hiram Gilbert
*Michael Schmid
B Prasad
E. Zechiedrich
Joseph Bryan
Olivier Lichtarge
Structure of Macromolecules
FullName
*Michael Schmid
*Nancy Weigel
E. Zechiedrich
Francis Tsai
Hiram Gilbert
Jun Qin
Olivier Lichtarge
Richard Sifers
Steven Ludtke
Theodore Wensel
Phone
713-798-5734
713-798-6234
713-798-5126
713-798-8668
713-798-5880
713-798-1507
713-798-5646
713-798-3169
713-798-9020
713-798-6994
Lecture Calendar
Term 1
Date
Mon Jul 30
Tue Jul 31
Wed Aug 01
Thu Aug 02
Fri Aug 03
Mon Aug 06
Tue Aug 07
Wed Aug 08
Thu Aug 09
Fri Aug 10
Mon Aug 13
10:0012:00
1:15-2:15
2:30-3:30
MM1
OC1
1SP1
OC2
MM2
1:00-4:00
ML1
ML2
ML3
Tue Aug 14
Wed Aug 15
Thu Aug 16
Fri Aug 17
Mon Aug 20
Tue Aug 21
Wed Aug 22
Thu Aug 23
Fri Aug 24
Mon Aug 27
Tue Aug 28
Wed Aug 29
Thu Aug 30
Fri Aug 31
Mon Sep 03
Tue Sep 04
Wed Sep 05
Thu Sep 06
Fri Sep 07
Mon Sep 10
ML4
Tue Sep 11
Wed Sep 12
Thu Sep 13
Fri Sep 14
Mon Sep 17
ML12
ML5
ML6
ML7
ML8
ML9
ML10
ML11
MM3
MM4
GA1
MM5
GA2
MM6
MM7
OC3
OC4
1SP2
OC5
OC6
Traber
2:30-5:30
GA3
1SP3
OC - Midterm Review 1:15-3:00
OC - Midterm Exam 1:15-3:45
MM - Midterm Review 1:15-3:00
MM - Midterm Exam 1:15-3:45
GA4
1SP4
MM8
OC7
GA5
MM9
OC8
MM10
OC9
GA6
1SP5
MM11
OC10
GA7
MM12
OC11
Labor Day
GA8
1SP6
MM13
OC12
GA9
MM14
OC13
MM15
Traber
2:30-5:30
GA10
1SP7
MM16
OC14
ML13
MM17
OC15
5:15-6:30
MMTA1
OCTA1
OCTA2
MMTA2
GATA1
OCTA3
MMTA3
OCTA4
GATA2
OCTA5
MMTA4
Tue Sep 18
Wed Sep 19
Thu Sep 20
Fri Sep 21
Mon Sep 24
Tue Sep 25
Wed Sep 26
Thu Sep 27
Fri Sep 28
ML14
ML15
GA11
1SP8
OC ER
OC - Final Exam 1:15-3:45
MM - Evaluation/Review 1:15-3:00
MM - Final Exam 1:15-3:45
MMTA5
GATA3
GA - Evaluation/Review 1:15-3:00
GA - Final Exam 1:15-3:45
Term 2
Date
10:0012:00
1:15-2:15
2:30-3:30
1:00-4:00
Mon Oct 08
Tue Oct 09
Wed Oct 10
Thu Oct 11
Fri Oct 12
Mon Oct 15
CD1
GB1
CD2
GB2
CD3
CD4
Tue Oct 16
Wed Oct 17
Thu Oct 18
Fri Oct 19
Mon Oct 22
Tue Oct 23
Wed Oct 24
Thu Oct 25
Fri Oct 26
Mon Oct 29
Tue Oct 30
Wed Oct 31
Thu Nov 01
Fri Nov 02
Mon Nov 05
Tue Nov 06
Wed Nov 07
Thu Nov 08
Fri Nov 09
Mon Nov 12
GB3
CD5
GB4
CD6
GB5
DE1
GB6
2SP3
CD - Midterm Review 1:15-3:00
CD - Midterm Exam 1:15-3:45
CD7
DE2
CD8
DE3
GB7
2SP4
CD9
DE4
GB8
CD10
DE5
CD11
DE6
GB9
2SP5
CD12
DE7
GB10
2SP6
GB11
DE8
Traber
CD Evaluatio 2:30-5:30
n/Review
1:15-3:00
CD - Final Exam 1:15-3:45
CA1
DE9
GrdSymp
Tue Nov 13
Wed Nov 14
Thu Nov 15
5:15-6:30
2SP1
Traber
2:30-5:30
2SP2
CDTA1
CDTA2
GBTA1
GBTA2
DETA1
GBTA3
CDTA3
DETA2
GBTA4
Fri Nov 16
Mon Nov 19
Tue Nov 20
Wed Nov 21
Thu Nov 22
CA2
DE10
CA3
DE11
GB12
2SP7
CA4
DE12
Thanksgivi
ng
Thanksgivi
ng
CA5
GB13
2SP8
DE - Evaluation/Review 1:15-3:00
DE - Final Exam 1:15-3:45
Fri Nov 23
Mon Nov 26
Tue Nov 27
Wed Nov 28
Thu Nov 29
Fri Nov 30
Mon Dec 03
Tue Dec 04
Wed Dec 05
Thu Dec 06
Fri Dec 07
DETA3
DETA4
GBTA5
CA - Evaluation/Review 1:15-3:00
CA - Final Exam 1:15-3:45
GB - Evaluation/Review 1:15-3:00
GB - Final Exam 1:15-3:45
Term 3
Date
10:0012:00
1:15-2:15
2:30-3:30
1:00-4:00
5:15-6:30
Mon Dec 31
Tue Jan 01
Wed Jan 02
Thu Jan 03
Fri Jan 04
Mon Jan 07
NewYears
NE1
GR1
NE2
GR2
GR3
MI2
MI3
Traber
2:30-5:30
NETA1
Tue Jan 08
Wed Jan 09
Thu Jan 10
Fri Jan 11
Mon Jan 14
Tue Jan 15
Wed Jan 16
Thu Jan 17
Fri Jan 18
Mon Jan 21
Tue Jan 22
Wed Jan 23
Thu Jan 24
Fri Jan 25
Mon Jan 28
Tue Jan 29
NE3
GR4
MI4
NE4
MI5
GR5
MI6
MLKDay
NE5
GR6
MI7
GR7
MI8
GR8
MI9
NE - Evaluation/Review 1:15-3:00
NE - Final Exam 1:15-3:45
GR9
MI10
GR10
GR11
MI11
GRTA1
GR - Midterm Review 1:15-3:00
MITA2
MI1
MITA1
NETA2
NETA3
GRTA2
Wed Jan 30
Thu Jan 31
Fri Feb 01
Mon Feb 04
Tue Feb 05
Wed Feb 06
Thu Feb 07
Fri Feb 08
Mon Feb 11
GR - Midterm Exam 1:15-3:45
GR12
MI12
GR13
GR14
MI13
MITA3
GR15
GR16
GR17
GR18
MI14
IM4
MI15
Traber
2:30-5:30
IM5
MI - Evaluation/Review 1:15-3:00
MI - Final Exam 1:15-3:45
GR19
PresDay
IM - Evaluation/Review 1:15-3:00
IM - Final Exam 1:15-3:45
GR20
DB
Retreat
GR21
Tue Feb 12
Wed Feb 13
Thu Feb 14
Fri Feb 15
Mon Feb 18
Tue Feb 19
Wed Feb 20
Thu Feb 21
Fri Feb 22
Mon Feb 25
Tue Feb 26
Wed Feb 27
Thu Feb 28
Fri Feb 29
GRTA3
IMTA1
MITA4
IMTA2
GRTA4
GR - Evaluation/Review 1:15-3:00
GR - Final Exam 1:15-3:45
Term 4
Date
Mon Mar 10
Tue Mar 11
Wed Mar 12
Thu Mar 13
Fri Mar 14
Mon Mar 17
Tue Mar 18
Wed Mar 19
Thu Mar 20
Fri Mar 21
Mon Mar 24
Tue Mar 25
Wed Mar 26
Thu Mar 27
Fri Mar 28
10:0012:00
1:15-2:15
2:30-3:30
SM1
Traber
2:30-5:30
1:00-4:00
5:15-6:30
RD1
SM2
SM3
SM4
RD2
SM5
CareerDay
SM6
SM7
RD3
SM8
SM9
SMTA1
Mon Mar 31
Tue Apr 01
Wed Apr 02
Thu Apr 03
Fri Apr 04
Mon Apr 07
SM10
RD4
SMTA2
RD5
SMTA3
SM11
GoodFri
SM12
Tue Apr 08
Wed Apr 09
Thu Apr 10
Fri Apr 11
Mon Apr 14
Tue Apr 15
Wed Apr 16
Thu Apr 17
Fri Apr 18
Mon Apr 21
Tue Apr 22
Wed Apr 23
Thu Apr 24
Fri Apr 25
Mon Apr 28
Tue Apr 29
Wed Apr 30
Thu May 01
Fri May 02
Traber
2:30-5:30
SM13
SM14
SM15
RD6
SM16
SM17
SM18
RD7
SM19
SM20
RD8
SMTA4
SM - Evaluation/Review 1:15-3:00
SM - Final Exam 1:15-3:45
Term 5
Date
10:0012:00
1:15-2:15
Mon May 12
Tue May 13
Wed May 14
Thu May 15
Fri May 16
Mon May 19
Tue May 20
Wed May 21
Thu May 22
Fri May 23
Mon May 26
Tue May 27
Wed May 28
Thu May 29
2:30-3:30
Traber
2:30-5:30
MemDay
1:00-4:00
5:15-6:30
Fri May 30
Mon Jun 02
Tue Jun 03
Wed Jun 04
Thu Jun 05
Fri Jun 06
Mon Jun 09
Tue Jun 10
Wed Jun 11
Thu Jun 12
Fri Jun 13
Mon Jun 16
Tue Jun 17
Wed Jun 18
Thu Jun 19
Fri Jun 20
Mon Jun 23
Tue Jun 24
Wed Jun 25
Thu Jun 26
Fri Jun 27
Mon Jun 30
Tue Jul 01
Wed Jul 02
Thu Jul 03
Fri Jul 04
Mon Jul 07
Tue Jul 08
Wed Jul 09
Thu Jul 10
Fri Jul 11
Mon Jul 14
Tue Jul 15
Wed Jul 16
Thu Jul 17
Fri Jul 18
Traber
2:30-5:30
IndDay
Traber
2:30-5:30
Lecture Schedule
Term 1
Genetics A
No
1
Date
Tue Aug 07
Time
1:15
2
Thu Aug 09
1:15
3
Tue Aug 14
1:15
4
Tue Aug 21
1:15
1
5
Tue Aug 21
Thu Aug 23
5:15
1:15
6
Tue Aug 28
1:15
7
8
Thu Aug 30
Tue Sep 04
1:15
1:15
2
9
Tue Sep 04
Thu Sep 06
5:15
1:15
10
Tue Sep 11
1:15
11
Tue Sep 18
1:15
Lecture
Principles, Model Systems and Nomenclature Mendel's laws. The chromosomal basis of inheritance,
definitions of genes, alleles, mutants. Sex linkage.
Life cycles and nomenclature of key model systems.
Haploid vs. diploid genetics, tetrad analysis in yeast.
Genetic Linkage - Building a genetic map based on
recombination frequency. Ordering genes by three
factor crosses. Ordering genes by deletion mapping.
Complementation - Complementation tests, allelism.
Verification by linkage mapping. Genetic interactions
of unlinked loci. Allelic series, penetrance, and
expressivity.
Bacterial Genetics I - Genetic transmission: haploid
and circular genomes, P1-transduction, F-factors,
HFRs, conjugation.
GA-TA1 - General Genetic Principles
Bacterial Genetics II - Phage lambda: lysis versus
lysogeny, Campbell model of integration, site specific
recombination, establishing repression, host factors,
specialized transduction, induction.
Bacterial Genetics III - Phage lambda in
recombination studies.
Bacterial Genetics IV - SOS response.
Genetic Screens Molecular Basis of the Phenotype
- Conception and design of genetic screens.
Verification and evaluation of results. Modern genetic
philosophy and practice. Classes of mutations.
GA-TA2 - Bacterial Genetics
Classes of mutations - Genetics as a study of how
proteins interact, fold, and function. Nonsense
suppression of null alleles. Partial loss of function
alleles. Conditional alleles
Delineating a Pathway - How to identify genes that
are functionally related to your favorite gene.
Suppression analysis. Synthetic lethal mutants
Enhancer screens and Pathway Analysis - Enhancer
screens. Epistasis grouping and epistasis analysis.
Lecturer
Kelley
Kelley
Kelley
Rosenberg
Rosenberg
Rosenberg
Rosenberg
Zhou
Zhou
Zhou
Zhou
3
Tue Sep 25
5:15
Wed Sep 26
Thu Sep 27
1:15
1:15
Establishing the order of gene functions.
GA-TA3 - Phenotype, pathway analysis and genetics
screens
Faculty Review Final Exam - 1:15-3:45 -
Method & Logic in Molecular Biology
No
1
2
3
5
6
7
8
9
10
11
12
13
14
15
Date
Thu Aug 02
Tue Aug 07
Thu Aug 09
Thu Aug 16
Tue Aug 21
Thu Aug 23
Tue Aug 28
Thu Aug 30
Tue Sep 04
Thu Sep 06
Tue Sep 11
Thu Sep 13
Tue Sep 18
Thu Sep 20
Time
10:00
10:00
10:00
10:00
10:00
10:00
10:00
10:00
10:00
10:00
10:00
10:00
10:00
10:00
Lecture
Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting Method and Logic Meeting -
Lecturer
Mardon
Chen
Shaulsky
Kelley
Moore
Zechiedrich
Kuspa
He
Palzkill
Pletcher
Wilson
Staff
Staff
Staff
Lecture
Introduction - Objectives of course, expectations,
problem sets
Properties of DNA - DNA structure, melting,
annealing, hybridization, blots (Northern, Southern),
probes and labeling
MM-TA1 - Intro - cover 5'-3' ends, intron/exon
boundaries, 5' and 3' overhangs from restriction
enzymes, plasmid, screen vs selection,
oligonucleotides, labeling (why it's done rather than
how), vector/host, library, clone/cloning (various
definitions), exonucleas
DNA Analysis - Gels for DNA Analysis, restriction
mapping, cloning, ligation
DNA manipulation - PCR, quantitative PCR, rtPCR,
DNA sequencing (small scale), site directed and
random mutagenesis
Vectors&Hosts - Plasmids (properties, purification);
preparation of insert DNA (restriction fragments,
PCR, cDNA); transformation and selection in E. coli
and yeast; M13 (life cycle; derived vectors).
Phagemids, vector switching; lambda (biology,
vectors, recombinant construction, in vitro
packaging); cosmids and fosmids; BACs and PACs
Lecturer
Gilbert
Molecular Methods
No
1
Date
Mon Jul 30
Time
1:15
2
Wed Aug 01
1:15
1
Wed Aug 01
5:15
3
Fri Aug 03
1:15
4
Mon Aug 06
1:15
5
Wed Aug 08
1:15
Highlander
Highlander
Highlander
Highlander
6
Fri Aug 10
1:15
7
Mon Aug 13
1:15
2
Tue Aug 14
5:15
8
Fri Aug 17
Mon Aug 20
Wed Aug 22
1:15
1:15
1:15
9
Fri Aug 24
1:15
10
Mon Aug 27
1:15
3
Tue Aug 28
5:15
11
Wed Aug 29
1:15
12
Fri Aug 31
1:15
13
Wed Sep 05
1:15
(bkgrd; vectors); YACs (vectors, construction); EBVbased human articial chromosome vectors,
recombination cloning
Protein Expression - Expression in E. coli;
transcription and translation signals, production of
native proteins,fusion proteins, baculovirus expression
systems, in vitro translation
Protein Purification - Opening the cell, inhibition of
proteolysis, precipitants, chromatography (gel
filtration, ion exchange, hydrophobic interaction,
affinity, HPLC, reversed phase), ultracentrifugation,
isoelectric focusing and electrophoresissucrose
density gradient,deterg
MM-TA2 - go over general scheme by which you
would detect a gene (hybridization/blots including end
labeling), map its restriction sites, PCR it from cDNA,
and insert it into a vector), define BACs, PACs, YAC
and describe preparation of cDNA library including
conc
Midterm Review Midterm Exam Isolation/Refolding Strategies - Affinity tags,
inclusion bodies, refolding, disulfide formation
Libraries and screening - Construction and handling
of libraries with different vectors; cDNA libraries
(statistics, subtracted libraries, normalized libraries,
reference libraries such as IMAGE); immunological
and hybridization screening; genomic libraries (sizes,
PCR- and hybridization methods for analyzing)
Genomics I - mapping strategies (FISH mapping, RH
mapping), genome sequencing strategies (BAC-byBAC, library construction, STS or FP, contig
assembly, minimum tiling paths, whole genome
shotgun), HTP instrumentation (96 capillary
machines), data analysis (bsecalling,
MM-TA3 - Go over purpose of large-scale physical
mapping, contig assembly, FISH in locating the
position/sequence of a gene of interest, approaches to
large scale sequencing, genebank, BLASTA and
internet tools for searching sequence.
Genomics II - annotation of sequences, EST's,
specific organism databases
Proteomics II - mass spectometery (MALDI-TOF,
electrospray) protein identification
Proteomics III - identification of protein species in
large complexes
Gilbert
Gilbert
Gilbert
Metzker
Metzker
Metzker
Qin
Qin
14
15
Fri Sep 07
Mon Sep 10
1:15
1:15
16
Wed Sep 12
1:15
4
Wed Sep 12
5:15
17
Fri Sep 14
1:15
5
Thu Sep 20
5:15
Fri Sep 21
Mon Sep 24
1:15
1:15
Proteomics I - protein arrays, interaction networks
Molecular Biology Database Use - pattern searches,
domains, paralogs and orthologs, sequence-function
relationships
Interaction cloning - systems, false positives and
negatives happen, limitations, combinatorial screens,
phage display, two-hybrid screen, lambda gt11
screens
MM-TA4 - review BLAST/FASTA searches
(purpose/output), mutagenesis (deletion, insertion,
random, directed), protein expression in coli (fusion
and non-fusion proteins), induction of expression,
baculovirus
Protein Localization/Identification - Purification of
antigen, polyclonal antibodies, monoclonal antibodies,
anti-peptide antibodies, Western blots, GFP fusions,
FRAP
MM-TA5 - review protein purification,
chromatography, protein quantitation, refolding of
inclusion bodies, phage display /two-hybrid screens,
antibody production and characterization, proteomics.
Faculty Review Final Exam - 1:15-3:45 -
Feng
Feng
Lecture
Overview and the Secretory Pathway - Course
organization, outline etc. General protein expression
and maturation. The secretory pathway and nature of
various organelles.
Nuclear Transport - Overall structure of the nucleus
and nuclear pore complexes. Transport of proteins
and RNAs into and out of the nucleus. Nuclear
transport and the control of gene expression
OC-TA1 - Review general cell structures, their
function and generation. Concepts of vesicular
transport and protein import and export for the
organelles
Mitochondria, Choloroplasts, Peroxisomes Structure and biogenesis of mitochondria, chlorplasts,
and peroxisomes. Protein import into these organelles
The Endoplasmic Reticulum - quality control
checkpoint and mother of the endomembrane system
The Golgi Complex - regulated vesicular trafficking
in the endomembrane system
OC-TA2 - Review of protein trafficking
Vesicular Transport in Reverse - the plasma
Lecturer
Sifers
Feng
Feng
Organization of the Cell
No
1
Date
Mon Jul 30
Time
2:30
2
Wed Aug 01
2:30
1
Thu Aug 02
5:15
3
Fri Aug 03
2:30
4
Mon Aug 06
2:30
5
Wed Aug 08
2:30
2
6
Wed Aug 08
Fri Aug 10
5:15
2:30
Sifers
Sifers
Sifers
Sifers
Sifers
7
Wed Aug 15
Thu Aug 16
Wed Aug 22
1:15
1:15
2:30
3
Thu Aug 23
5:15
8
Fri Aug 24
2:30
9
Mon Aug 27
2:30
10
Wed Aug 29
2:30
4
Wed Aug 29
5:15
11
Fri Aug 31
2:30
12
Wed Sep 05
2:30
5
Wed Sep 05
5:15
13
Fri Sep 07
2:30
14
Wed Sep 12
2:30
15
Fri Sep 14
2:30
membrane-endoxome-lysosome connection
Midterm Review Midterm Exam Energy Transduction and Bioenergetics Membrane permeability, mechanisms of transport,
bio-energetics, mitochondrial and chloroplast
function, chemiosmosis
OC-TA3 - Review of Lipid synthesis and transport.
Energy transduction and bioenergetics, membrane
transport and ion channel
Transport Mechanisms - Active and passive
transport, synporters, antiporters, ATPases
Ion channels - Nernst potential, electrical properties
of excitable membranes, action potential
G Proteins - Signalling mechanisms, ligand
recognition and conformation changes by receptors,
GDP release kinetics, G protein structure and
function, effectors, signal processing, inactivation and
desensitization, receptor kinases and arrestins,
putative roles for PKC
OC-TA4 - Review of G-proteins, growth factors, Tyrkinase signalling and ion channel
Growth Factors/Tyrosine Kinase Signaling Ligands and signals, structure of families of
membrane receptors with intrinsic tyrosine kinase
activity and introduction to cascades activated by
binding to phosphotyrosines, SH2 and SH3 domains,
tyrosine kinases associated with membrane bound
receptors
Calcium and phospholipase signaling - Calcium and
its protein complexes Phosphoinositides,
phospholipase C, protein kinase C, IP3 receptors,
proteins regulated by Ca, calmodulin, Ca-regulated
channels, annexins, overview of methods for
monitoring intracellular Ca and phosphoplipase
activity
OC-TA5 - Review of calcium and phospholipase
signaling, cytoskeleton
Cytoskeleton I - Actin, microtubules, intermediate
filaments, junctional complexes and cellular
architecture, cell motility.
Cytoskeleton II - Actin, microtubules, intermediate
filaments, junctional complexes and cellular
architecture, cell motility.
Apoptosis - Apoptosis versus necrosis, mechanisms
of programmed cell death, regulators of apoptosis.
Pedersen
Pedersen
Pedersen
Wensel
Wensel
Wensel
He
He
Zhou
Thu Sep 20
1:15
Final Exam - 1:15-3:45 -
Science as a Profession Term 1
No
1
Date
Tue Jul 31
Time
2:30
2
Tue Aug 07
2:30
3
Tue Aug 14
2:30
4
Tue Aug 21
2:30
5
Tue Aug 28
2:30
6
Tue Sep 04
2:30
7
Tue Sep 11
2:30
8
Tue Sep 18
2:30
Term 2
Lecture
Setting goals for your scientific development Career paths for the professional scientist, career
decisions (how and when to make them), what to do
in your first year to ensure your success, developing
curiosity, coursework(what to expect in gradschool),
lifelong learning, the scientific literature, finding a
lab/rotation, selecting a mentor, where to get help and
information, thinking now about the next step
Organization of the literature - Organization and
purpose of a paper, how to read the current literature,
what is contained in the various sections of a paper,
computer searching vs browsing, parts of a scientific
paper and what you can learn from each
The Scientific Method - thinking like a scientist The scientific method (hypothesis vs results-driven
science), elements of experimental design (developing
models/hypotheses), designing experimental tests of
your hypotheses, fishing expeditions, controls ,
replication of experiments and data selection - ethical
considerations, Interpreting your results
The Mentor/Student relationship - What you
should expect from your mentor, getting along with
your mentor, your advisory committee, accumulating
references for your next step
Coping with challenges - Social/Emotional
adjustment to grad school, coping with stress, dealing
with your peers, dealing with faculty, where to go for
help
The funding structure of science - Government
organizations, private funding sources, applying for
fellowships, structure of a grant, grant review system
Scientific Societies/Public Policy - advantages of
membership, participation in committee activity,
science advocacy ( what you can do), how Congress
manages its scientific effort
Grievance procedures - When you have problems
with: courses/exams, program administration,
graduate school administration, other students or lab
personnel, mentor, thesis committee, health/safety
concerns, when your research isn't progressing
Lecturer
Basinger
Slaughter
Gilbert
Slaughter
Basinger
Brinkley
Brinkley
Basinger
Cancer
No
1
Date
Wed Nov 14
Time
1:15
2
Thu Nov 15
Fri Nov 16
2:30
1:15
3
4
Mon Nov 19
Wed Nov 21
1:15
1:15
5
Thu Nov 22
Fri Nov 23
Mon Nov 26
1:15
1:15
1:15
Tue Dec 04
Wed Dec 05
1:15
1:15
Lecture
Introduction to Cancer Vocabulary - epidemiology
and carcinogenesis - lung cancer
Graduate Student Symposium - No Class Cancer as a Multi-step process - tumor suppressor
genes - colon cancer
Activation of Oncogenes - leukemia/lymphoma
Animal Models in Cancer Research - prostate
cancer
Thanksgiving Holiday - No Class Thanksgiving Holiday - No Class Use of familial cancers to define molecular events breast cancer, course summary
Faculty Review Final Exam - 1:15-3:45 -
Lecturer
Plon
Lecture
Course Introduction/Cell Cycle Overview Discovery of cell cycle regulation--Cell cycle stages,
mitosis and meiosis, discovery of CDK/cyclin/MPF
G1/S - G1 phase and the G1 to S phase transition,
CDK regulation by phosphorylation and protein
degradation, CDK regulation of initiation of DNA
replication
S phase - Initiation and control of DNA replication at
origins of replications
DNA Damage - DNA damage and repair
CD-TA1 - Review of DNA replication
DNA Repair - Repair of double strand breaks by
homologous and non-homologous recombination
G2/M - G2 phase and the G2 to M phase transition
CD-TA2 - Review of recombination
Faculty Review Midterm - Lectures 1-6
Exam I - Lectures 1-6
Cell Cycle Checkpoints - Introduction to cell cycle
checkpoints, the DNA damage checkpoint
M phase chromosomes - chromosomes (centromeres,
telomeres), chromosome pairing and cohesion,
chromosome condensation
M phase spindle - mechanics of spindle formation
and function, kinetochore/spindle attachment
Spindle Assembly Checkpoint - the spindle
assembly checkpoint
Exit from mitosis - Exit from mitosis, coordination of
exit from mitosis with cytokinesis
Lecturer
Sazer
Demayo
Plon
Demayo
Plon
Cell Division
No
1
Date
Mon Oct 08
Time
1:15
2
Wed Oct 10
1:15
3
Fri Oct 12
1:15
4
1
5
Mon Oct 15
Tue Oct 16
Wed Oct 17
1:15
5:15
1:15
6
2
7
Fri Oct 19
Mon Oct 22
Wed Oct 24
Thu Oct 25
Fri Oct 26
1:15
5:15
1:15
1:15
1:15
8
Mon Oct 29
1:15
9
Wed Oct 31
1:15
10
Fri Nov 02
1:15
11
Mon Nov 05
1:15
Zhang
Wilson
Wilson
Wilson
Wilson
Zhang
Wilson
Zhang
He
He
Sazer
Sazer
12
Wed Nov 07
1:15
3
Wed Nov 07
5:15
Mon Nov 12
Tue Nov 13
Thu Nov 15
Thu Nov 22
Fri Nov 23
1:15
1:15
2:30
1:15
1:15
Growth regulation - The cell cycle in growth
regulation, development and cancer
CD-TA3 - Review of cell cycle regulation, mitosis,
mitotic entry and exit, cytokinesis
Faculty Review Exam II - Lectures 7-12
Graduate Student Symposium - No Class Thanksgiving Holiday - No Class Thanksgiving Holiday - No Class -
Zhang
Lecture
Introduction - Overview and objectives of the course.
Introduction to major animal models used in
developmental studies and relative advantages of
each. Brief description of Drosophila oogenesis and
embryogenesis
Embryonic patterning in Drosophila I Introduction to the genetic hierarchy that subdivides
the embryo into progressively smaller units. The
concept of gradients and asymmetric distribution of
morphogenetic determinants in organizing the
Drosophila embryo. Maternal-effect genes and the
establishment of the anteroposterior axes.
Embryonic patterning in Drosophila II - Maternaleffect genes and the establishment of the dorsoventral
axes.
Embryonic patterning in Drosophila III - The role
of the wingless and hedgehog signaling pathways in
the formation of embryonic segments and
compartments. The concept of segments as
developmental compartments.
TA-DE1 Embryonic patterning in Drosophilia IV Homeotic selector (HOM) genes and their role in
defining positional identity in each of the segments of
the fly embryo along the A-P axis
Early embryonic development in vertebrates Mammalian germline development. Fertilization and
pre-implantation mammalian development
Formation of the vertebrate body plan I Gastrulation. Somitogenesis and somite differentiation
Formation of the vertebrate body plan II Development of the cardiovascular and urogenital
system
TA-DE2 Establishment of left-right asymmetry in
Lecturer
Schumacher
Zhang,
Sazer, He
Development
No
1
Date
Mon Oct 22
Time
2:30
2
Fri Oct 26
2:30
3
Mon Oct 29
2:30
4
Wed Oct 31
2:30
1
5
Thu Nov 01
Fri Nov 02
5:15
2:30
6
Mon Nov 05
2:30
7
Wed Nov 07
2:30
8
Fri Nov 09
2:30
2
9
Fri Nov 09
Wed Nov 14
5:15
2:30
Schumacher
Schumacher
Schumacher
Schumacher
RamirezSolis
RamirezSolis
RamirezSolis
Overbeek
10
Thu Nov 15
Fri Nov 16
2:30
2:30
11
Mon Nov 19
2:30
3
12
Tue Nov 20
Wed Nov 21
5:15
2:30
Thu Nov 22
Fri Nov 23
Wed Nov 28
Thu Nov 29
1:15
1:15
1:15
1:15
vertebrates - Regulatory and signaling pathways
involved in establishing left-right asymmetry in the
vertebrate embryo. The relationship between heart
looping and asymmetric positioning of other organs.
Graduate Student Symposium - No Class Introduction to neural development in vertebrates Mahon
- Developmental anatomy of the nervous system.
Molecular aspects of neural induction, formation of
the neural plate and neurogenesis
Regionalization of the vertebrate nervous system - Mahon
Molecular mechanisms of dorsal-ventral and anteriorposterior patterning. Combinatorial and antagonistic
signaling involved in dorsoventral patterning of the
neural tube. The role of Hox genes in regional
specification along the anterior-posterior axis.
TA-DE3 Development of the vertebrate brain - Integration of Mahon
conserved genetic networks and signaling centers in
the formation and specification of the forebrain,
midbrain and hindbrain.
Thanksgiving Holiday - No Class Thanksgiving Holiday - No Class Faculty Review Final Exam - 1:15-3:45 -
Genetics B
No
1
Date
Tue Oct 09
Time
1:15
2
Thu Oct 11
1:15
3
Tue Oct 16
1:15
4
Thu Oct 18
1:15
5
Mon Oct 22
1:15
6
Tue Oct 23
1:15
Lecture
Introduction - Comparisons of classical genetics,
reverse genetics, and genomics. Strengths and
weaknesses of model systems. Nomenclature.
Yeast I - Basic molecular manipulations in reverse
genetics: cloning by complementation, plasmid gap
repair, gene disruption/replacement, plasmid shuffle
Yeast II - Genome analysis and functional genomics.
The impact of the yeast genome project. Systematic
manipulation of entire gene sets to monitor mRNA
expression and protein localization in vivo.
Mouse Genetics I - Inbred mice. Microsatellite
markers. Mapping genes in mice using crosses.
Mouse Genetics II - Insertion of DNA and
retrotransposons. Knock-outs and ins. Conditional
knock-outs.
Drosophila I - Isolation of lethal mutations that affect
pattern formation. Modifier (enhancer and
suppressor) screens. P-elements as mutagens.
Positional cloning, P-element transformation. Aim of
the Drosophila genome project: a P-element insertion
Lecturer
Shin
Bertuch
Bertuch
Justice
Justice
Mardon
1
2
7
Tue Oct 23
Mon Oct 29
Tue Oct 30
5:15
5:15
1:15
8
9
Thu Nov 01
Tue Nov 06
1:15
1:15
3
10
Tue Nov 06
Thu Nov 08
5:15
1:15
11
4
12
Fri Nov 09
Tue Nov 13
Thu Nov 15
Tue Nov 20
1:15
5:15
2:30
1:15
13
Thu Nov 22
Fri Nov 23
Tue Nov 27
1:15
1:15
1:15
Tue Nov 27
Thu Dec 06
Fri Dec 07
5:15
1:15
1:15
5
in every gene.
GB-TA1 GB-TA2 Drosophila II - Genetic tricks: Mosaic analysis,
autonomy vs. non-autonomy. Ectopic expression
using heat shock, FLP-out and GAL4-UAS.
Drosophila III C. elegans I- - Advantages and special considerations
of hermaphrodite genetics. Significance of having the
detailed fate map of the organism. Developmental
genetics at the single cell level.
GB-TA3 C. elegans II - C. elegans transformation. Positional
cloning and complementation. Impact of the C.
elegans genome project. Reverse genetics using RNA
interference.
Human Genetics I - Disease loci and pedigrees.
GB-TA4 Graduate Student Symposium - No Class Human Genetics II - Mapping with DNA markers.
Sources of polymorphisms. Simple vs. complex traits.
Genome scans for quantitative trait loci.
Thanksgiving Holiday - No Class Thanksgiving Holiday - No Class Human Genetics III - Effect of imprinting on
pedigrees. Models for specific mechanisms of
imprinting. Model for evolutionary significance.
GB-TA5 Faculty Review Final Exam - 1:15-3:45 -
Mardon
Mardon
Shin
Shin
Beaudet
Beaudet
Beaudet
Science as a Profession-Ethics
No
1
Date
Tue Oct 09
Time
2:30
2
Tue Oct 16
2:30
3
Tue Oct 23
2:30
4
Tue Oct 30
2:30
Lecture
Data Management/Ownership - Keeping a
laboratory notebook, maintaining other
records/computer files, ownership of scientific
materials/data, sharing results and reagents
Scientific Misconduct- Part 1 - Definitions Falsification, fabrication, plagiarism (case studies)
Research with Human Subjects - definition of
research with human subjects, experiments with
human material, confidentiality of medical data,
experiments involving humans, informed consent, the
role of the IRB
Scientific Misconduct - Part 2 - Policies of the
college –allegations, inquiries, investigations,
penalties (case studies)
Lecturer
Slaughter
Gilbert
Haymond
Gilbert
5
Tue Nov 06
2:30
6
Thu Nov 08
2:30
7
Thu Nov 15
Tue Nov 20
2:30
2:30
8
Thu Nov 22
Fri Nov 23
Tue Nov 27
1:15
1:15
2:30
Publishing your Work - Authorship/Peer Review Organizing your paper, preparing manuscripts, who
should be an author?, responsibilities of an author,
manuscript review systems, responsibilities of a
reviewer, dealing with criticism
Experimental error and honesty - Experimental
measurements and error, replication of experiments,
influence of statistics on experimental design, how
errors affect your conclusions, statistical significance,
correlations, when is it ethical to ignore some
experiments
Graduate Student Symposium - No Class Ethics of Experiments with Animals - when can
animals be used ethically in research, avoiding
unnecessary pain/suffering and euthanasia,
appropriate selection of numbers/types of animals in
research, animal use approval
Thanksgiving Holiday - No Class Thanksgiving Holiday - No Class Plagiarism/Conflicts of Interest - Plagiarism
(definition and examples), attributing credit to others,
financial conflicts of interest, conflicts of interest in
peer review, plagiarasm and computers, copyright,
acceptable use policies of the College
Brinkley
Lecture
Introduction to Gene Regulation - Sites of Gene
Regulation: transcription initiation, termination,
alternative RNA splicing, 3' end processing, nuclear
export, cytoplasmic mRNA stability, translational
regulation, protein degradation, Methods of Assessing
Levels of Regulation,
RNA Polymerase - the bacterial enzyme
summarizing the kinetics and thermodynamics of the
protein and its interactions with DNA., subunit
function of the bacterial enzyme compared with the
subunit structure of the eukaryotic enzyme,
Regulatory functions of the polymerase pol.
Control of transcription in bacterias - degradation
and sequestration of initiation factors, riboswitches,
noise in transcription and logic of transcriptional
circuits.
GRTA1 - Overview of regulation of transcription and
Lecturer
Rosen
Gilbert
Michael
Slaughter
Term 3
Gene Regulation
No
1
Date
Wed Jan 02
Time
1:15
2
Fri Jan 04
1:15
3
Mon Jan 07
1:15
1
Tue Jan 08
5:15
Herman
Herman
4
Wed Jan 09
1:15
5
Fri Jan 11
1:15
6
Mon Jan 14
Wed Jan 16
1:15
1:15
7
Thu Jan 17
1:15
8
Fri Jan 18
1:15
9
Wed Jan 23
1:15
translation including review of overall process of
transcription and translation, introduce reporter genes
(rationale)
Mammalian RNA Polymerase and Co-factors and
Promoters - Mammalian RNA PolymeraseStructure- function complexity of mammalian RNA
pol II. Chromatin is a tough substrate for Pol II to
transcribe, and many proteins and much energy is
required. The Cis- and Trans- regulation of
transcription at the TATA box. The chemistry and
biology of General Transcription Factors (GTFs).
Transcription factors: Upstream Activation
Sequences and Enhancers - Enhancer regulatory
proteins and their structure-function relationships.
Introduction to integrator coregulators, such as
CBP/p300.Structure-function characteristics of
coactivators. Description of the SRC family of
coactivators. Coactivators as enzymes.
Martin Luther King Day Holiday - No Class Mechanisms of action of coactivators and
corepressors - Coactivators function in high
molecular weight complexes. The kinetics of
coactivator complex interactions with target gene
promoter regions; association and dissociation of the
complex. The functional diversity of coactivators.
Regulation of substeps of transcription by
coactivators. Coactivators have evolved to regulate
genes that function together. Regulation of coactivator
levels by the proteasome and activities by
phosphorylation cascades.
Biology and Pathologies of Coactivators and
Corepressors - Structure-function relationships of
corepressors. Signaling to coregulators from the
environment. Coordinate steps in transcription factor
(e.g., NR) and coactivator (egg SRC-3) function in
signaling pathways. The role of secondary
coactivators. Tissue specificity and transcription
factor specificity of coregulators. The role of
coregulators in pharmaceutical drugs. The role of
coactivators in pathologies such as cancer, genetic
disease, CVS disease.
Local Chromatin Changes - histones, nucleosomes,
covalent modification of histones, DNAase
hypersensitive sites, insulators, locus control regions,
polytene chromosomes
Global Chromatin Changes - chromatin
O’Malley
O’Malley
O’Malley
O’Malley
Wong
Wong
10
Thu Jan 24
1:15
2
Thu Jan 24
5:15
11
Fri Jan 25
1:15
12
Tue Jan 29
Wed Jan 30
Thu Jan 31
1:15
1:15
1:15
13
Fri Feb 01
1:15
14
Mon Feb 04
1:15
15
Wed Feb 06
1:15
subdomains, silencing, position effect variegation,
epigenetic inheritance, X-inactivation, imprinting
Regulation of RNA Polymerase II Elongation Transcriptional elongation – an important regulatory
step; Negative factors that limit elongation (NELF,
DSIF); Positive factor that activates elongation (PTEFb); HIV system (Tat, TAR RNA, P-TEFb);
Drosophila heat shock genes and elongation; Current
questions in this area
GR TA2 - Review of assembly of transcription
complex including order and identity of factor loading
Identify major transcriptional activator families and
mechanisms
Nuclear export of RNA - Nuclear pores – structure
and dynamics; Retroviral systems: Retroviral life
cycle, HIV system (Rev, RRE RNA, CRM1,
RAN/GTP), Mason-Pfizer Monkey Virus (MMPV;
CTE, TAP); Experimental methods to study RNA
export; Export pathways of different classes of
cellular RNAs; Current questions in this area.
Midterm Faculty Review MIDTERM EXAM Splicing of Pre-mRNA (I) - Overview of RNA
chemistry (basis for lability and reactivity), overview
of RNA structure, comparisons of intron/exon
architecture, Autocatalytic RNA: Group I & II
autocatalytic introns and hammerheads, The
spliceosome; U12-dependent introns, domain
structure of RNA binding proteins
Splicing of Pre-mRNA (II) - How the spliceosome
finds vertebrate exons, intron definition vs exon
definition, splicing enhancers and silencers, SR
proteins, Exon junction complex (EJC), Transsplicing,
3’ end formation / Polyadenylation - 3' end
formation of pol II genes, transcription termination;
cotranscriptional 3’ end formation; relationship
between 3' end formation and splicing, histone 3' end
formation; spatial relationship between splicing and
transcription within nucleus
Alternative splicing - Drosophila paradigms, yeast
and vertebrate systems; splicing microarrays; effects
on coding potential; regulatory factors and
mechanisms of regulation; signaling pathways;
splicing and human disease (direct cause and as
genetic modifier)
Rice
Rice
Cooper
Cooper
Cooper
Cooper
16
Thu Feb 07
1:15
3
Thu Feb 07
5:15
17
Fri Feb 08
1:15
18
Mon Feb 11
1:15
19
Fri Feb 15
1:15
20
Mon Feb 18
Thu Feb 21
1:15
1:15
21
Mon Feb 25
1:15
4
Tue Feb 26
5:15
Wed Feb 27
Thu Feb 28
1:15
1:15
Immunology
Editing - RNA editing, Insertional/deletion editing
(Mitochondrial mRNA editing, contrast with transesterifiction, editsome complex, spliceosome),
Substitutional or modification editing in the nucleus
(Apoliprotein B and cytidine deaminase, AMPA
receptor and adenosine deaminase.
GR TA3 - Splicing and poyadenylation general
overview; define mechanisms for alternative splicesite selection, intron vs exon selection
Posttranscriptional Regulation - Short RNAs, RNAi
and miRNAs. History, Biogenesis of RNAi and
miRNAs, miRNAs in development and cancer. RNAi
and heterochromatin silencing. RNAi reagents,
forward genetic screens and shRNA libraries
Posttranscriptional Regulation - mRNA Turnover I
& II- Multilevel regulation: e.g. histone gene
expression during the cell cycle. Translation Coupled
mRNA Degradation. Poly A shortening and 5' -> 3'
degradation, P-bodies and mRNA decay. Non-polyA
shortening mechanisms. Nonsense-mediated mRNA
decay. mRNA stability in prokaryotes -genetics and
biochemistry, Role of 3'UTR sequences in mRNA
localization.
Translational Regulation I - Review of protein
synthesis and initiation steps, Cap-dependent and cap
independent translation. 5'-3' interactions and
recycling. Global regulation mechanisms; eIF2 kinase
mechanisms, eIF4E inhibitors, viral mechanisms,
mTOR, TOP mRNAs.
President's Day Holiday - No Class Translational Regulation II Mechanisms - mRNAspecific regulation; scanning blockers, (uORFs, IRE,
autoregulatory systems), cellular IRESs, shunt
mechanisms, 3' UTR-based regulation (CPEB in
oocytes and neurons) - stress mechanisms (stress
granules and P bodies), Frameshifting.
Regulation of Protein Turnover - Ubiquitinproteosome mediated degradation., Importance of
regulation, protein motifs, PEST sequences, etc.
GR-TA4 - RNA self-splicing overview, concept of
regulating synthesis and degradation of mRNA,
review of ribosome assembly and initiation and
termination of translation
Faculty Review Final Exam - 1:15-3:45 -
Rosen
Rosen
Rosen
Lloyd
Lloyd
Rosen
No
1
Date
Mon Jan 14
Thu Jan 24
Time
1:15
3:30
2
Thu Jan 31
3:30
3
Tue Feb 05
3:30
4
Thu Feb 07
2:30
1
Fri Feb 08
5:15
5
Tue Feb 12
2:30
2
Mon Feb 18
Tue Feb 19
Wed Feb 20
Thu Feb 21
1:15
1:15
1:15
5:15
Lecture
Martin Luther King Day Holiday - No Class Principles of Specific Immunity - innate vs. specific
immunity, cells of the immune system, clonal
selection principle, strategies for self-nonself
discrimination
Antigen-Recognition - Antigens for B and T cells,
Antigen-binding molecules, Antibody/T Cell receptor
structure and genetics, Generation of diversity: Gene
rearrangements, MHC Complex Genes, Antigen
presentation
Cellular Differentiation and Selection in the
Immune system - B/T cell development and
selection. Self vs. nonself selection, Tolerance
Lymphocyte Activation - B/T cell activation, signal
transduction, convergence and integration of signal
transduction pathways, anergy, apoptosis
IM TA Review 1 - Overview of response to
pathogen: Anatomy and function of organs of
lymphatic system: general overview of B and T cell
development and function
Integration of an Immune Response - T cell effector
functions, transplantation, autoimmunity, tumor
immunology
President's Day Holiday - No Class Faculty Review Final Exam - 1:15-3:45 IM TA Review 2 - MHC I and MHC II - functions,
derivation; B cells - antibody structure - subtypes,
receptors and surface molecules, VDJ recombination;
T cells - receptor and surface molecules, maturation,
subtypes/function; T and B cell interactions
Lecturer
Lecture
Course Introduction -Ligand Binding - Definition
of Kd. Mass action, basic thermodynamics.
Forces in solution and thermodynamics - Enthalpy
and entropy, forces in solution, competitive inhibition.
Allosterism and protein conformations - Regulation
of activity and binding, multiple binding sites and the
Hill equation
Allosterism and linkage analysis - Heterotropic
allosteric interaction and thermodynamic linkage
analysis.
Cooperativity - Koshland-Nemethy-Filmer models.
Negative cooperativity
Lecturer
Pedersen
Spencer
Zheng
Zheng
Spencer
Spencer
Molecular Interactions
No
1
Date
Tue Jan 01
Time
2:30
2
Thu Jan 03
2:30
3
Fri Jan 04
2:30
4
Wed Jan 09
2:30
5
Thu Jan 10
2:30
Pedersen
Pedersen
Pedersen
Pedersen
1
6
7
Thu Jan 10
Fri Jan 11
Mon Jan 14
Wed Jan 16
5:15
2:30
1:15
2:30
8
Thu Jan 17
2:30
9
Fri Jan 18
2:30
10
Wed Jan 23
2:30
11
Fri Jan 25
2:30
2
12
Tue Jan 29
Thu Jan 31
5:15
2:30
13
Mon Feb 04
2:30
3
14
Tue Feb 05
Wed Feb 06
Wed Feb 13
Thu Feb 14
Mon Feb 18
5:15
2:30
1:15
1:15
1:15
MI-TA Review 1 Binding kinetics I - reactions and reaction order
Martin Luther King Day Holiday - No Class Binding kinetics II - better kinetics through
computation
Protein-Ligand Interactions - Molecular basis of
specificity, protein ligand interactions - structural
basis of H-bonding, salt bridges and other interactions
Protein-Protein Interactions - Protein-protein
interactions. Structural motifs that serve as proteinprotein interaction domains, structural basis of surface
complementarity, engineering tight binding
Protein DNA Interactions - Protein-DNA
interactions. DNA binding motifs, structural basis of
base recognition, backbone interactions
Enzyme Kinetics and Catalysis - Michaelis-Menten
kinetics, Inhibition, kcat and kcat/Km, allosteric
enzymes, inhibition, practical features of an assay
MI-TA Review 2 Mechanisms of Enzyme Catalysis - Acid base
catalysis, covalent catalysis, stabilization of transition
states, transition state analogs, coenzymes, suicide
inhibitors
Protein Machines I - Stable and Dynamic
Assemblies. Oligomers and Polymers. ATP synthases
MI-TA Review 3+G133 Protein Machines II - Actin-myosin motors
Faculty Review Final Exam - 1:15-3:45 President's Day Holiday - No Class -
Pedersen
Pedersen
Prasad
Prasad
Prasad
Bryan
Bryan
Bryan
Bryan
Neuroscience
No
1
Date
Tue Jan 01
Time
1:15
2
Thu Jan 03
1:15
1
Thu Jan 03
5:15
3
Tue Jan 08
1:15
4
Thu Jan 10
1:15
Lecture
Information processing in neurons. - The electrical
properties of neurons. Ion channel distriution.
Coupling electrical signals to neurotransmitter release
Synaptic plasticity - Structure of the synapse.
Ligand gated ion channels. Neuortransmitter release.
Activity-dependent plasticity
NE TA Review 1 - Brain anatomy, anatomy of eye
and nose, neuron types, action potentials (including
review of neurotransmitters)
Learning and memory - forms of learning and
memory. Molecular coincidence detectors.
Perpetuation of biochemical signals. Alterations in
gene expression. Structural changes.
Sensory systems - specialized sensory receptors,
Lecturer
Pham
Pham
Pham
Pham
5
Mon Jan 14
Tue Jan 15
1:15
1:15
2
Tue Jan 15
5:15
Mon Jan 21
Tue Jan 22
Mon Feb 18
1:15
1:15
1:15
encoding of information, circuits for information
processing, face cells, behavioral control
Martin Luther King Day Holiday - No Class Cognition - Split brain studies, amnesia, PET imaging Pham
in cognition, cortical plasticity, diseases of cognition
and affect
NE TA Review 2 - Basis of methods used (voltage
clamp, imaging of brain); Visual receptors (rods,
cones), receptive fields
Faculty Review Final Exam - 1:15-3:45 President's Day Holiday - No Class -
Term 4
Research Design
No
1
Date
Tue Mar 11
Time
1:00
2
3
4
5
6
7
8
Tue Mar 18
Tue Mar 25
Tue Apr 01
Tue Apr 08
Tue Apr 15
Tue Apr 22
Tue Apr 29
1:00
1:00
1:00
1:00
1:00
1:00
1:00
Lecture
Research Design Introduction - Introduction to the
design of research projects
Research Design Workgroup 2 Research Design Workgroup 3 Research Design Workgroup 4 Research Design Workgroup 5 Research Design Workgroup 6 Research Design Workgroup 7 Research Design Workgroup 8 -
Lecturer
Gilbert
Schmid
Zechiedrich
Bryan
Lichtarge
Prasad
Staff
Staff
Structure of Macromolecules
No
1
Date
Mon Mar 10
Time
1:15
2
Wed Mar 12
1:15
3
Fri Mar 14
1:15
4
Mon Mar 17
1:15
Lecture
Hydrodynamic methods - methods for estimating
size, shape compactness and oligomeric state of
proteins (and interactions among them)--analytical
ultracentrifugation, native gels, size exclusions
chromatorraphy, dynamical light scattering, small
angle x-ray scattering
Spectroscopic methods for estimating compactness
and foldedness of proteins - CD, FTIR, proton
exchange
NMR of proteins and DNA - Basic theory and
instrumentation, NOSEY, COSY methods, distance
geometry, multi-diminsional NMR, sample
requirements
DNA Structure and topology I - Structure of B, Z
and A DNA, topology, structural effects on
electrophoretic properties of DNA, R-loops, D-loops,
Literature project on DNA structure/function
Lecturer
Schmid
Schmid
Gilbert
Zechiedrich
1
5
Tue Mar 18
Wed Mar 19
5:15
1:15
6
Thu Mar 20
Fri Mar 21
1:15
1:15
7
Mon Mar 24
1:15
8
Wed Mar 26
1:15
9
Fri Mar 28
1:15
10
Mon Mar 31
1:15
2
11
Tue Apr 01
Wed Apr 02
5:15
1:15
12
Fri Apr 04
Mon Apr 07
1:15
1:15
3
13
Tue Apr 08
Wed Apr 09
5:15
1:15
14
Fri Apr 11
1:15
15
Mon Apr 14
1:15
16
Wed Apr 16
1:15
17
Fri Apr 18
1:15
18
Mon Apr 21
1:15
19
Wed Apr 23
1:15
TA-1 DNA Structure and topology II - Methods of
analyzing DNA structure, future goals in field of
DNA structure/topology, literature project
Career Day - No Class Protein Taxonomy - Discussion of protein motifs,
domains and general structural features. Approaches
to function from structure.
Protein Folding - Mechanisms for attaining the
correct 3D structure of proteins, experimental
approaches to observing protein folding, catalysis of
protein folding
Cryoelectron microscopy - a scattering (diffraction)based structural technique
Xray crystallography - a scattering (diffraction)based structural technique. Crystallization and
synmetry. Theory of diffraction
Convolution - The diffraction pattern as a Fourier
Transform. Some simple examples.
TA-2 The Phase Problem - solving the phase problem, one
way or another. EM techniques.
Good Friday Holiday - No Class Mass spec I - mass spectrometers, ionization
methods, the use of MS in protein identification
TA3 Mass spec II - use of mass spec in protein interaction,
proteomics
Regulatory post-translational modification Protein phosphorylation and other reversibale
regulatory post-translational modification
Post-translational modification - irreversible, lipid
modifications, ubiquitination
Protein glycosylation and quality control biosynthetic quality control, additional roles for
glycosylation, analysis of glycoproteins
Fluorescence Methods for Structure analysis principles of photon absorption and emission,
fluorescence energy transfer, anisotropy, lifetime,
instrumentation, optics
Structure of Lipids and Glycolipids - Major lipids
of biomembranes, diversity of composition,
relationships between lipid structures and functional
properties
Membrane Protein Structure - integral and
peripheral membrane proteins, protein-lipid
Zechiedrich
Tsai
Gilbert
Ludtke
Tsai
Schmid
Schmid
Qin
Qin
Weigel
Weigel
Sifers
Wensel
Ludtke
Ludtke
20
Fri Apr 25
1:15
Thu May 01
Fri May 02
1:15
1:15
interactions, structural features of transmembrane
proteins
Sequence to Structure - primary structure analysis,
domain classifications, prediction of secondary and
tertiary structure
Faculty Review Final Exam - 1:15-3:45 -
Lichtarge