| Term 1 |
|
| Genetics A |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Tue Aug 11 |
1:15 |
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. |
Kelley |
| 2 |
Thu Aug 13 |
1:15 |
Genetic Linkage - Building a genetic map based on recombination frequency. Ordering genes by three factor crosses. Ordering genes by deletion mapping. |
Kelley |
| 3 |
Tue Aug 18 |
1:15 |
Complementation - Complementation tests, allelism. Verification by linkage mapping. Genetic interactions of unlinked loci. Allelic series, penetrance, and expressivity. |
Kelley |
| 4 |
Tue Aug 25 |
1:15 |
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. |
Kelley |
| 5 |
Thu Aug 27 |
1:15 |
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 |
Bates |
| 1 |
Fri Aug 28 |
5:15 |
GA-TA1 - General Genetic Principles |
|
| 6 |
Tue Sep 01 |
1:15 |
Delineating a Pathway - How to identify genes that are functionally related to your favorite gene. Suppression analysis. Synthetic lethal mutants |
Bates |
| 7 |
Thu Sep 03 |
1:15 |
Enhancer screens and Pathway Analysis - Enhancer screens. Epistasis grouping and epistasis analysis. Establishing the order of gene functions. |
Bates |
| 8 |
Tue Sep 08 |
1:15 |
Bacterial Genetics I - Genetic transmission: haploid and circular genomes, P1-transduction, F-factors, HFRs, conjugation. |
Rosenberg |
| 2 |
Tue Sep 08 |
5:15 |
GA-TA2 - Bacterial Genetics |
|
| 9 |
Thu Sep 10 |
1:15 |
Bacterial Genetics II - Phage lambda: lysis versus lysogeny, Campbell model of integration, site specific recombination, establishing repression, host factors, specialized transduction, induction. |
Rosenberg |
| 10 |
Tue Sep 15 |
1:15 |
Bacterial Genetics III - Phage lambda in recombination studies. |
Rosenberg |
| 11 |
Tue Sep 22 |
1:15 |
Bacterial Genetics IV - SOS response. |
Rosenberg |
| 3 |
Tue Sep 29 |
5:15 |
GA-TA3 - Phenotype, pathway analysis and genetics screens |
|
| |
Wed Sep 30 |
1:15 |
Faculty Review - |
|
| |
Thu Oct 01 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Method & Logic in Molecular Biology |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Thu Aug 06 |
10:00 |
Method and Logic Meeting - |
Lumpkin |
| 2 |
Tue Aug 11 |
10:00 |
Method and Logic Meeting - |
Kelley |
| 3 |
Thu Aug 13 |
10:00 |
Method and Logic Meeting - |
Bonnen |
| 4 |
Tue Aug 18 |
10:00 |
Method and Logic Meeting - |
Bertuch |
| 5 |
Thu Aug 20 |
10:00 |
Method and Logic Meeting - |
Lee |
| 6 |
Tue Aug 25 |
10:00 |
Method and Logic Meeting - |
Chen |
| 7 |
Thu Aug 27 |
10:00 |
Method and Logic Meeting - |
Deneen |
| 8 |
Tue Sep 01 |
10:00 |
Method and Logic Meeting - |
Herman |
| 9 |
Thu Sep 03 |
10:00 |
Method and Logic Meeting - |
Zechiedrich |
| 10 |
Tue Sep 08 |
10:00 |
Method and Logic Meeting - |
Mardon |
| 12 |
Tue Sep 15 |
10:00 |
Method and Logic Meeting - |
Wang |
| 12 |
Tue Sep 15 |
10:00 |
Method and Logic Meeting - |
Shaulsky |
| 13 |
Thu Sep 17 |
10:00 |
Method and Logic Meeting - |
Staff |
| 14 |
Tue Sep 22 |
10:00 |
Method and Logic Meeting - |
Staff |
| 15 |
Thu Sep 24 |
10:00 |
Method and Logic Meeting - |
Staff |
| Molecular Methods |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Mon Aug 03 |
1:15 |
Introduction - Objectives of course, integrating methodology into discovery |
Gilbert |
| 2 |
Wed Aug 05 |
1:15 |
Properties of DNA - DNA structure, melting, Tm, annealing, hybridization, gel electrophoresis, blots (Northern, Southern, colony) |
Highlander |
| 3 |
Fri Aug 07 |
1:15 |
DNA Analysis - Probes and labeling, polymerases, kinase and reverse transcriptase, restriction enzymes and mapping, cloning, ligation |
Highlander |
| 4 |
Mon Aug 10 |
1:15 |
DNA manipulation - Sanger DNA sequencing, PCR, quantitative PCR, rtPCR, site directed and random mutagenesis |
Highlander |
| 1 |
Tue Aug 11 |
5:15 |
MM-TA1 - Lectures 1-4 |
|
| 5 |
Wed Aug 12 |
1:15 |
Vectors&Hosts - Plasmids (properties, purification); transformation and selection in E. coli; ColE1-based vectors, TOPO vectors; recombinant cloning vectors. BACs.' M13 (life cycle, vectors, phagemids). Lambda vectors (biology, recombinant construction, in vitro packaging and cosmids). PACs and YACs |
Highlander |
| 6 |
Fri Aug 14 |
1:15 |
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) |
Metzker |
| 7 |
Mon Aug 17 |
1:15 |
Next Generation Sequencing - mapping strategies (FISH mapping, RH mapping), genome sequencing strategies (BAC-by-BAC, library construction, STS or FP, contig assembly, minimum tiling paths, whole genome shotgun), HTP instrumentation (96 capillary machines), data analysis (bsecalling, |
Metzker |
| 2 |
Tue Aug 18 |
5:15 |
MM-TA2 - Lectures 5-7 |
|
| |
Wed Aug 19 |
1:15 |
Midterm Review - |
|
| |
Thu Aug 20 |
1:15 |
Midterm Exam - |
|
| 8 |
Wed Aug 26 |
1:15 |
Protein Expression - Expression in E. coli; transcription and translation signals, production of native proteins,fusion proteins, baculovirus expression systems, in vitro translation |
Gilbert |
| 9 |
Fri Aug 28 |
1:15 |
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 |
Gilbert |
| 10 |
Mon Aug 31 |
1:15 |
Isolation/Refolding Strategies - Inclusion bodies, protein refolding strategies to avoid aggregation, disulfide formation and artifical chaperones |
Gilbert |
| 11 |
Wed Sep 02 |
1:15 |
Sanger Sequencing and Applications - annotation of sequences, EST's, specific organism databases |
Metzker |
| 12 |
Fri Sep 04 |
1:15 |
Molecular Biology Database Use - pattern searches, domains, sequence-function-structure relationships |
Feng |
| 13 |
Wed Sep 09 |
1:15 |
Interaction cloning - systems, false positives and negatives happen, limitations, combinatorial screens, phage display, two-hybrid screen, lambda gt11 screens |
Feng |
| 3 |
Wed Sep 09 |
5:15 |
MM-TA3 - Lectures 8-11 |
|
| 14 |
Fri Sep 11 |
1:15 |
Protein Localization/Identification - Purification of antigen, polyclonal antibodies, monoclonal antibodies, anti-peptide antibodies, Western blots, GFP fusions, FRAP |
Feng |
| 15 |
Mon Sep 14 |
1:15 |
High throughput methods - protein arrays, interaction networks |
Pan |
| 4 |
Tue Sep 15 |
5:15 |
MM-TA4 - Lectures 12-14 |
|
| 16 |
Wed Sep 16 |
1:15 |
Proteomics - mass spectrometry - mass spectometery (MALDI-TOF, electrospray) protein identification |
Gilbert |
| 17 |
Fri Sep 18 |
1:15 |
Proteomics - protein identification - identification of protein species in large complexes |
Gilbert |
| 5 |
Tue Sep 22 |
5:15 |
MM-TA5 - Lectures 15-17 |
|
| |
Fri Sep 25 |
1:15 |
Faculty Review - |
|
| |
Mon Sep 28 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Organization of the Cell |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Mon Aug 03 |
2:30 |
Overview and the Secretory Pathway - Course organization, outline etc. General protein expression and maturation. The secretory pathway and nature of various organelles. |
Sifers |
| 2 |
Wed Aug 05 |
2:30 |
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 |
Sifers |
| 1 |
Thu Aug 06 |
5:15 |
OC-TA1 - Review general cell structures, their function and generation. Concepts of vesicular transport and protein import and export for the organelles |
|
| 3 |
Fri Aug 07 |
2:30 |
Mitochondria, Choloroplasts, Peroxisomes - Structure and biogenesis of mitochondria, chlorplasts, and peroxisomes. Protein import into these organelles |
Sifers |
| 4 |
Wed Aug 12 |
2:30 |
The Endoplasmic Reticulum - quality control checkpoint and mother of the endomembrane system |
Sifers |
| 2 |
Thu Aug 13 |
5:15 |
OC-TA2 - Review of protein trafficking |
|
| 5 |
Fri Aug 14 |
2:30 |
The Golgi Complex - regulated vesicular trafficking in the endomembrane system |
Sifers |
| 6 |
Mon Aug 17 |
2:30 |
Vesicular Transport in Reverse - the plasma membrane-endosome-lysosome connection |
Sifers |
| |
Fri Aug 21 |
1:15 |
Midterm Review - |
|
| |
Mon Aug 24 |
1:15 |
Midterm Exam - |
|
| 7 |
Wed Aug 26 |
2:30 |
Apoptosis - Apoptosis versus necrosis, mechanisms of programmed cell death, regulators of apoptosis. |
Sifers |
| 3 |
Thu Aug 27 |
5:15 |
OC-TA3 - review of apoptosis |
|
| 8 |
Fri Aug 28 |
2:30 |
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 |
Wensel |
| 9 |
Mon Aug 31 |
2:30 |
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 |
Wensel |
| 10 |
Wed Sep 02 |
2:30 |
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 |
Wensel |
| 4 |
Thu Sep 03 |
5:15 |
OC-TA4 - Review of G-protein signaling and tyrosine kinase signaling |
|
| 11 |
Fri Sep 04 |
2:30 |
Cytoskeleton I - Actin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility. |
He |
| 12 |
Wed Sep 09 |
2:30 |
Cytoskeleton II - Actin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility. |
He |
| 5 |
Thu Sep 10 |
5:15 |
OC-TA5 - Review of cytoskeleton and calcium signaling |
|
| 13 |
Fri Sep 11 |
2:30 |
Energy Transduction and Bioenergetics - Membrane permeability, mechanisms of transport, bio-energetics, mitochondrial and chloroplast function, chemiosmosis |
Pedersen |
| 14 |
Wed Sep 16 |
2:30 |
Transport Mechanisms - Active and passive transport, synporters, antiporters, ATPases |
Pedersen |
| 6 |
Thu Sep 17 |
5:15 |
OC-TA6 - review of bioenergetics, transporters, ion channels |
|
| 15 |
Mon Sep 21 |
2:30 |
Ion channels - Nernst potential, electrical properties of excitable membranes, action potential |
Pedersen |
| |
Wed Sep 23 |
1:15 |
Faculty Review - |
|
| |
Thu Sep 24 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Science as a Profession Term 1 |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Tue Aug 04 |
2:30 |
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 |
Basinger |
| 2 |
Tue Aug 11 |
2:30 |
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 |
Slaughter |
| 3 |
Tue Aug 18 |
2:30 |
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 |
Slaughter |
| 4 |
Tue Aug 25 |
2:30 |
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 |
Gilbert |
| 5 |
Tue Sep 01 |
2:30 |
Coping with challenges/Grevience Procedures - Social/Emotional adjustment to grad school, coping with stress, dealing with your peers, dealing with faculty, where to go for help, grievences procedures |
Basinger |
| 6 |
Tue Sep 08 |
2:30 |
The funding structure of science - Government organizations, private funding sources, applying for fellowships, structure of a grant, grant review system |
Brinkley |
| 7 |
Tue Sep 15 |
2:30 |
Scientific Societies/Public Policy - advantages of membership, participation in committee activity, science advocacy ( what you can do), how Congress manages its scientific effort |
Brinkley |
| 8 |
Tue Sep 22 |
2:30 |
Keeping on track toward your degree - judging your progress, what are reasonable expectations, , how to get your mentor and committee to help. How do you know you're done? |
Sazer |
| Term 2 |
| Cancer |
| No |
Date |
Time |
Lecture |
Lecturer |
| |
Thu Oct 22 |
1:15 |
Graduate Student Symposium - No Class - |
|
| 1 |
Fri Nov 20 |
1:15 |
Introduction to Cancer Course - Oncogenes - leukemia/lymphoma |
Plon |
| 2 |
Mon Nov 23 |
1:15 |
Amimal Models in Cancer Research - lung cancer |
Demayo |
| 3 |
Wed Nov 25 |
1:15 |
Cancer as a Multi-step Process - tumor suppressor genes, colon cancer |
Plon |
| |
Thu Nov 26 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| |
Fri Nov 27 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| 4 |
Mon Nov 30 |
1:15 |
Use of familial Cancers to Define Molecular Events - breast cancer |
Plon |
| 5 |
Wed Dec 02 |
1:15 |
Metastasis - |
Demayo |
| |
Tue Dec 08 |
1:15 |
Faculty Review - |
|
| |
Wed Dec 09 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Cell Division |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Mon Oct 12 |
1:15 |
Course Introduction/Cell Cycle Overview - Discovery of cell cycle regulation--Cell cycle stages, mitosis and meiosis, discovery of CDK/cyclin/MPF |
Sazer |
| 1 |
Tue Oct 13 |
5:15 |
CD-TA1 - Review of cell cycle basics |
Sazer |
| 2 |
Wed Oct 14 |
1:15 |
Principals of cell cycle regulation - CDKs, cyclins, CKIs, and proteolysis |
Zhang |
| 3 |
Mon Oct 19 |
1:15 |
Principals of cell cycle regulation - cell cycle transitions, G1/S and G2M |
Zhang |
| 2 |
Tue Oct 20 |
5:15 |
CD-TA2 - Review of CDK/cyclin/cell cycle transitions |
Zhang |
| 4 |
Wed Oct 21 |
1:15 |
S phase - Initiation and control of DNA replication at origins of replications |
Wang |
| |
Thu Oct 22 |
1:15 |
Graduate Student Symposium - No Class - |
|
| 5 |
Fri Oct 23 |
1:15 |
DNA Damage - DNA damage and repair |
Wilson |
| 6 |
Mon Oct 26 |
1:15 |
DNA Repair - Repair of double strand breaks by homologous and non-homologous recombination |
Wilson |
| 3 |
Tue Oct 27 |
5:15 |
CD-TA3 - Review of DNA replications and recombination |
Wilson |
| |
Wed Oct 28 |
1:15 |
Faculty Review Midterm - Lectures 1-6 |
|
| |
Thu Oct 29 |
1:15 |
Exam I - Lectures 1-6 |
|
| 7 |
Fri Oct 30 |
1:15 |
TBA - |
|
| 8 |
Mon Nov 02 |
1:15 |
M phase chromosomes - chromosomes (centromeres, telomeres), chromosome pairing and chromosomes (centromeres, telomeres), chromosome pairing and cohesion, chromosome condensation |
He |
| 9 |
Wed Nov 04 |
1:15 |
M phase spindle - mechanics of spindle formation and function, kinetochore/spindle attachment |
He |
| 4 |
Wed Nov 04 |
5:15 |
CD-TA4 - Review of Mitosis |
He |
| 10 |
Fri Nov 06 |
1:15 |
Cell Cycle Checkpoints - Introduction to cell cycle checkpoints, the DNA damage checkpoint |
Sazer |
| 11 |
Mon Nov 09 |
1:15 |
Spindle Assembly Checkpoint - the spindle assembly checkpoint, Exit from mitosis, coordination of exit from mitosis with cytokinesis |
Sazer |
| 12 |
Wed Nov 11 |
1:15 |
Cytokenesis - cytokenesis mechanisms |
Sokac |
| 5 |
Wed Nov 11 |
5:15 |
CD-TA5 - Review of DNA damage and spindle Assembly checkpoints, mitotic exit |
Wilson |
| 13 |
Fri Nov 13 |
1:15 |
Growth regulation - The cell cycle in growth regulation, development and cancer |
Westbrook |
| |
Tue Nov 17 |
1:15 |
Faculty Review - |
|
| |
Wed Nov 18 |
1:15 |
Exam II - Lectures 7-12 |
|
| |
Thu Nov 26 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| |
Fri Nov 27 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| Development |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Wed Oct 21 |
2:30 |
Introduction to Drosophila embryogenesis - A few words on Developmental Biology; Overview of Drosophila oogenesis and embryogenesis |
Jafar-Nejad |
| |
Thu Oct 22 |
1:15 |
Graduate Student Symposium - No Class - |
|
| 2 |
Fri Oct 23 |
2:30 |
Embryonic Patterning in Drosophia I - maternal-effect genes and the establishment of the anteroposterior axes |
Jafar-Nejad |
| 3 |
Mon Oct 26 |
2:30 |
Embryonic patterning in Drosophila II - maternal-effect genes and the establishment of the dorsoventral axes |
Jafar-Nejad |
| 4 |
Fri Oct 30 |
2:30 |
Early Embryoinc Development in Vertebrates I - gametogenesis and pre-implantation development |
Behringer |
| 5 |
Mon Nov 02 |
2:30 |
Early Embryoinc Development in Vetebrates II - gametogenesis and pre-implantation development |
Behringer |
| 6 |
Wed Nov 04 |
2:30 |
Heart and Vessel Developmehnt in Vetebrates I - acquiring neuronal identity |
Dickinson |
| 1 |
Thu Nov 05 |
5:15 |
TA-DE1 - |
|
| 7 |
Fri Nov 06 |
2:30 |
Heart and Vessel Developmehnt in Vetebrates II - |
Dickinson |
| 8 |
Wed Nov 11 |
2:30 |
Neural Development in Vertebrates - developmental anatomy of the nervous system. Molecular aspects of neural induction, formation of the neural plate and neurogenesis |
Lee |
| 9 |
Fri Nov 13 |
2:30 |
Regionalization of the Vertebrate Nervous System - Molecular mechanisms of dorsal-ventral and anterior-posterior patterning. Combinatorial and antagonistic signaling involved in dorsoventral patterning of the neural tube |
Lee |
| 2 |
Fri Nov 13 |
5:15 |
TA-DE2 - |
|
| 10 |
Mon Nov 16 |
1:15 |
Limb Development in Vertebrates - axis specification, outgrowth and patterning. |
Johnson |
| 11 |
Fri Nov 20 |
2:30 |
Urogenital System Development - |
Demayo |
| 12 |
Mon Nov 23 |
2:30 |
TGF-beta Signaling and Human Development - pertubation of superfamily signaling and its effects on human organogenesis |
Brown |
| 3 |
Tue Nov 24 |
5:15 |
TA-DE3 - |
|
| |
Thu Nov 26 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| |
Fri Nov 27 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| |
Thu Dec 03 |
1:15 |
Faculty Review - |
|
| |
Fri Dec 04 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Genetics B |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Tue Oct 13 |
1:15 |
Introduction - Comparisons of classical genetics, reverse genetics, and genomics. Strengths and weaknesses of model systems. Nomenclature. |
Zhou |
| 2 |
Wed Oct 14 |
2:30 |
Yeast I - Basic molecular manipulations in reverse genetics: cloning by complementation, plasmid gap repair, gene disruption/replacement, plasmid shuffle |
Ira |
| 3 |
Mon Oct 19 |
2:30 |
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. |
Ira |
| 4 |
Tue Oct 20 |
1:15 |
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. |
Zhou |
| 1 |
Wed Oct 21 |
5:15 |
GB-TA1 - |
|
| |
Thu Oct 22 |
1:15 |
Graduate Student Symposium - No Class - |
|
| 5 |
Tue Oct 27 |
1:15 |
C. elegans II - C. elegans transformation. Positional cloning and complementation. Impact of the C. elegans genome project. Reverse genetics using RNA interference. |
Zhou |
| 6 |
Tue Nov 03 |
1:15 |
Drosophila I - Introduction. Nomenclature and markers; chromosome cytology (polytene chromosomes) and chromosome rearrangements; using balancer chromosomes to follow segregation and to isolate mutations; P-elements and transformation; site-specific integration using the PhiC31 system. |
Mardon |
| 2 |
Tue Nov 03 |
5:15 |
GB-TA2 - |
|
| 7 |
Thu Nov 05 |
1:15 |
Drosophila II - Genetic screens. Mutagens: ems, x-rays and P-elements; classic genetic screens to identify mutations in Drosophila: F1, F2, F3 screens; modifier (suppressor and enhancer) screens; isolating mutations, mapping lethal mutations; deficiency mapping; high-throughput sequencing. |
Mardon |
| 8 |
Thu Nov 05 |
2:30 |
Drosophila III - Gene function. Mosaic analysis; autonomy versus non-autonomy; mitotic recombination using the FLP/FRT system, methods of marking clones; ectopic expression using heat shock, GAL4-UAS, and flp-out; MARCM analysis. |
Mardon |
| 9 |
Thu Nov 12 |
1:15 |
Mouse Genetics I - Inbred mice. Microsatellite markers. Mapping genes in mice using crosses. |
Matzuk |
| 3 |
Thu Nov 12 |
5:15 |
GB-TA3 - |
|
| 10 |
Thu Nov 19 |
1:15 |
Mouse Genetics II - Insertion of DNA and retrotransposons. Knock-outs and ins. Conditional knock-outs. |
Matzuk |
| 4 |
Fri Nov 20 |
5:15 |
GB-TA4 - |
|
| 11 |
Tue Nov 24 |
1:15 |
Human Genetics I - Disease loci and pedigrees. |
Lupski |
| 12 |
Wed Nov 25 |
2:30 |
Human Genetics II - Mapping with DNA markers. Sources of polymorphisms. Simple vs. complex traits. Genome scans for quantitative trait loci. |
Lupski |
| |
Thu Nov 26 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| |
Fri Nov 27 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| 13 |
Tue Dec 01 |
1:15 |
Human Genetics III - Effect of imprinting on pedigrees. Models for specific mechanisms of imprinting. Model for evolutionary significance. |
Lupski |
| 5 |
Wed Dec 02 |
5:15 |
GB-TA5 - |
|
| |
Thu Dec 10 |
1:15 |
Faculty Review - |
|
| |
Fri Dec 11 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Science as a Profession-Ethics |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Tue Oct 13 |
2:30 |
NIH Topic 1 (req'd) - Scientific Misconduct- Part 1 - Definitions - Falsification, fabrication, plagiarism - allegations, investigations, penalties. College policy and mechanisms for handling misconduct allegations |
Gilbert |
| 2 |
Tue Oct 20 |
2:30 |
NIH Topic 1a (elective) - Scientific Misconduct - Part 2 - Scientific misconduct case studies |
Gilbert |
| |
Thu Oct 22 |
1:15 |
Graduate Student Symposium - No Class - |
|
| 3 |
Tue Oct 27 |
2:30 |
NIH Topic 1b (elective) - 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 |
Gilbert |
| 4 |
Tue Nov 03 |
2:30 |
NIH Topic 8 (req'd) - 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 |
Berg |
| 5 |
Tue Nov 10 |
2:30 |
NIH Topics 3 & 5 (req'd) 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 |
Brinkley |
| 6 |
Thu Nov 12 |
2:30 |
NIH Topic 4 (req'd) - Data Management/Ownership - Keeping a laboratory notebook, maintaining other records/computer files, ownership of scientific materials/data, sharing results and reagents |
Slaughter |
| 7 |
Tue Nov 24 |
2:30 |
NIH Topic 7 (req'd) - 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 |
Michael |
| |
Thu Nov 26 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| |
Fri Nov 27 |
1:15 |
Thanksgiving Holiday - No Class - |
|
| 8 |
Tue Dec 01 |
2:30 |
NIH Topics 2 & 6 (req'd) - 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 |
Slaughter |
| Term 3 |
| Gene Regulation |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Mon Jan 04 |
1:15 |
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, |
Cooper |
| 2 |
Wed Jan 06 |
1:15 |
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. |
Herman |
| 3 |
Fri Jan 08 |
1:15 |
Control of transcription in bacteria - degradation and sequestration of initiation factors, riboswitches, noise in transcription and logic of transcriptional circuits. |
Herman |
| 4 |
Mon Jan 11 |
1:15 |
Eukaryotic RNA polymerase and transcriptional initiation - Structures and activities of the 3 eukaryotic RNA polymerases. Pathways for transcription initiation by RNA pol II holoenzyme plus general transcription factors |
Moore |
| 5 |
Wed Jan 13 |
1:15 |
Modes of DNA binding and basic transcription factors - Structures of DNA binding domains and the molecular basis for DNA sequence recognition. How do transcription factors find their sites? Genome wide networks of transcriptional regulation. |
Moore |
| 1 |
Wed Jan 13 |
5:15 |
GRTA1 - Overview of regulation of transcription and translation including review of overall process of transcription and translation, introduce reporter genes (rationale) |
|
| 6 |
Fri Jan 15 |
1:15 |
Coactivators and corepressors - Identification of transcriptional coregulators and evolution of understanding of transcriptional activation. Enymatic activities of coactivators and corepressors. Post-transcriptional modulation of coregulator function. Why are there so many coregulators? |
Moore |
| |
Mon Jan 18 |
1:15 |
Martin Luther King Day Holiday - No Class - |
|
| 7 |
Wed Jan 20 |
1:15 |
Chromatin 1 - Local - Histones, nucleosomes, covalent modification of histones, DNA accessibility, insulators, locus control regions, polytene/lapbrush chromosomes |
Lonard |
| 8 |
Fri Jan 22 |
1:15 |
Chromatin 2 - Global - Chromatin sub domains, gene silencing, position effect variegation, epigenetic inheritance, X-inactivation, gene imprinting |
Lonard |
| 9 |
Wed Jan 27 |
1:15 |
Chromatin - Relationship between DNA sequence genes, transcription and Chromatin - Emerging pictures of genes and chromosomes - Enabling technologies for global chromatin and transcriptome analysis, evolving understanding of gene structure, promoters, enhancers, relationship between primary DNA sequence, chromatin and transcription |
Lonard |
| 2 |
Wed Jan 27 |
5:15 |
GR TA2 - Review of assembly of transcription complex including order and identity of factor loading Identify major transcriptional activator families and mechanisms |
|
| 10 |
Fri Jan 29 |
1:15 |
Regulation of RNA Polymerase II Elongation - Transcriptional elongation - an important regulatory step; Negative factors that limit elongation (NELF, DSIF); Positive factor that activates elongation (P-TEFb); HIV system (Tat, TAR RNA, P-TEFb); Drosophila heat shock genes and elongation; Current questions in this area |
Rice |
| 11 |
Mon Feb 01 |
1:15 |
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. |
Rice |
| |
Tue Feb 02 |
1:15 |
Midterm Faculty Review - |
|
| |
Wed Feb 03 |
1:15 |
MIDTERM EXAM - |
|
| 12 |
Thu Feb 04 |
1:15 |
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 |
Cooper |
| 13 |
Fri Feb 05 |
1:15 |
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), Trans-splicing, |
Cooper |
| 14 |
Mon Feb 08 |
1:15 |
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 |
Cooper |
| 15 |
Wed Feb 10 |
1:15 |
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) |
Cooper |
| 3 |
Wed Feb 10 |
5:15 |
GR TA3 - Splicing and poyadenylation general overview; define mechanisms for alternative splice-site selection, intron vs exon selection |
|
| 16 |
Thu Feb 11 |
1:15 |
Editing - RNA editing, Insertional/deletion editing (Mitochondrial mRNA editing, contrast with trans-esterifiction, editsome complex, spliceosome), Substitutional or modification editing in the nucleus (Apoliprotein B and cytidine deaminase, AMPA receptor and adenosine deaminase. |
Rosen |
| |
Mon Feb 15 |
1:15 |
President's Day Holiday - No Class - |
|
| 17 |
Tue Feb 16 |
1:15 |
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 |
Rosen |
| 18 |
Wed Feb 17 |
1:15 |
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 |
Rosen |
| 19 |
Thu Feb 18 |
1:15 |
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. |
Lloyd |
| 20 |
Mon Feb 22 |
1:15 |
Translational Regulation II Mechanisms - mRNA-specific 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. |
Lloyd |
| 21 |
Wed Feb 24 |
1:15 |
Regulation of Protein Turnover - Ubiquitin-proteosome mediated degradation., Importance of regulation, protein motifs, PEST sequences, etc. |
Rosen |
| 4 |
Tue Mar 02 |
5:15 |
GR-TA4 - RNA self-splicing overview, concept of regulating synthesis and degradation of mRNA, review of ribosome assembly and initiation and termination of translation |
|
| |
Thu Mar 04 |
1:15 |
Faculty Review - |
|
| |
Fri Mar 05 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Immunology |
| No |
Date |
Time |
Lecture |
Lecturer |
| |
Mon Jan 18 |
1:15 |
Martin Luther King Day Holiday - No Class - |
|
| 1 |
Thu Feb 04 |
2:30 |
Principles of Specific Immunity - innate vs. specific immunity, cells of the immune system, clonal selection principle, strategies for self-nonself discrimination |
Spencer |
| 2 |
Tue Feb 09 |
2:30 |
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 |
Zheng |
| 3 |
Thu Feb 11 |
2:30 |
Cellular Differentiation and Selection in the Immune system - B/T cell development and selection. Self vs. nonself selection, Tolerance |
Zheng |
| 1 |
Fri Feb 12 |
5:15 |
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 |
|
| |
Mon Feb 15 |
1:15 |
President's Day Holiday - No Class - |
|
| 4 |
Tue Feb 16 |
2:30 |
Lymphocyte Activation - B/T cell activation, signal transduction, convergence and integration of signal transduction pathways, anergy, apoptosis |
Spencer |
| 5 |
Thu Feb 18 |
2:30 |
Integration of an Immune Response - T cell effector functions, transplantation, autoimmunity, tumor immunology |
Spencer |
| 2 |
Thu Feb 18 |
5:15 |
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 |
|
| |
Thu Feb 25 |
1:15 |
Faculty Review - |
|
| |
Mon Mar 01 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Molecular Interactions |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Wed Jan 06 |
2:30 |
Course Introduction -Ligand Binding - Definition of Kd. Mass action, basic thermodynamics. |
Pedersen |
| 2 |
Fri Jan 08 |
2:30 |
Forces in solution and thermodynamics - Enthalpy and entropy, forces in solution, competitive inhibition. |
Pedersen |
| 3 |
Wed Jan 13 |
2:30 |
Allosterism and protein conformations - Regulation of activity and binding, multiple binding sites and the Hill equation |
Pedersen |
| 1 |
Thu Jan 14 |
5:15 |
MI-TA Review 1 - |
|
| 4 |
Fri Jan 15 |
2:30 |
Allosterism and linkage analysis - Heterotropic allosteric interaction and thermodynamic linkage analysis. |
Pedersen |
| |
Mon Jan 18 |
1:15 |
Martin Luther King Day Holiday - No Class - |
|
| 5 |
Wed Jan 20 |
2:30 |
Cooperativity - Koshland-Nemethy-Filmer models. Negative cooperativity |
Pedersen |
| 2 |
Thu Jan 21 |
5:15 |
MI-TA Review 2 - |
|
| 6 |
Fri Jan 22 |
2:30 |
Binding kinetics I - reactions and reaction order |
Pedersen |
| 7 |
Wed Jan 27 |
2:30 |
Binding kinetics II - better kinetics through computation |
Pedersen |
| 8 |
Fri Jan 29 |
2:30 |
Enzyme Kinetics and Catalysis - Michaelis-Menten kinetics, Inhibition, kcat and kcat/Km, allosteric enzymes, inhibition, practical features of an assay |
Gilbert |
| 3 |
Fri Jan 29 |
5:15 |
MI-TA Review 3 - |
|
| 9 |
Mon Feb 01 |
2:30 |
Mechanisms of Enzyme Catalysis - Acid base catalysis, covalent catalysis, stabilization of transition states, transition state analogs, coenzymes, suicide inhibitors |
Gilbert |
| 4 |
Thu Feb 04 |
5:15 |
MI-TA Review 4 - |
|
| 10 |
Fri Feb 05 |
2:30 |
F1/FO ATPases - Macromolecular motors, single molecule kinetics |
Pedersen |
| 11 |
Wed Feb 10 |
2:30 |
Serine Proteases - Key family members, specificity, catalytic triad/mechanism, inhibition |
Pedersen |
| 5 |
Thu Feb 11 |
5:15 |
MI-TA Review 5 - |
|
| |
Mon Feb 15 |
1:15 |
President's Day Holiday - No Class - |
|
| 12 |
Wed Feb 17 |
2:30 |
Protein-Ligand Interactions - Molecular basis of specificity, protein ligand interactions - structural basis of H-bonding, salt bridges and other interactions |
Prasad |
| 13 |
Mon Feb 22 |
2:30 |
Protein-Protein Interactions - Protein-protein interactions. Structural motifs that serve as protein-protein interaction domains, structural basis of surface complementarity, engineering tight binding |
Prasad |
| 14 |
Wed Feb 24 |
2:30 |
Protein DNA Interactions - Protein-DNA interactions. DNA binding motifs, structural basis of base recognition, backbone interactions |
Prasad |
| |
Tue Mar 02 |
1:15 |
Faculty Review - |
|
| |
Wed Mar 03 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Neuroscience |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Thu Jan 07 |
2:30 |
Fast and dirty into the Brain - chemicals, channels, cells, and structures |
Jankowsky |
| 2 |
Tue Jan 12 |
2:30 |
Experienced-induced plasticity - Environmental enrichment, adult neuorgenesis |
Jankowsky |
| 3 |
Thu Jan 14 |
2:30 |
Neuronal silencing - knockouts for neuroscience |
Jankowsky |
| 4 |
Tue Jan 19 |
2:30 |
Hair cell regeneration in the inner ear - If birds can do it why can't we? |
Groves |
| 5 |
Thu Jan 21 |
2:30 |
Molecular and Cellular Biology and Neuroscience - The role of sleep in learning and memory |
Ji |
| |
Tue Jan 26 |
1:15 |
Faculty Review - |
|
| |
Thu Jan 28 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| Term 4 |
| Research Design |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Tue Mar 16 |
1:00 |
Research Design Introduction - Introduction to the design of research projects |
Gilbert |
| 2 |
Tue Mar 23 |
1:00 |
Research Design Workgroup 2 - Introduction to the design of research projects |
Schmid |
| 3 |
Tue Mar 30 |
1:00 |
Research Design Workgroup 3 - Introduction to the design of research projects |
Gilbert |
| 4 |
Tue Apr 06 |
1:00 |
Research Design Workgroup 6 - Introduction to the design of research projects |
Prasad |
| 5 |
Tue Apr 13 |
1:00 |
Research Design Workgroup 3 - |
Staff |
| 6 |
Tue Apr 20 |
1:00 |
Research Design Workgroup 4 - |
Staff |
| 7 |
Tue Apr 27 |
1:00 |
Research Design Workgroup 7 - |
Staff |
| 8 |
Tue May 04 |
1:00 |
Research Design Workgroup 8 - |
Staff |
| 9 |
Thu May 13 |
1:00 |
Research Design Symposium - |
Staff |
| Structure of Macromolecules |
| No |
Date |
Time |
Lecture |
Lecturer |
| 1 |
Mon Mar 15 |
1:15 |
Protein Taxonomy - Discussion of protein motifs, domains and general structural features. Approaches to function from structure. |
Tsai |
| 2 |
Wed Mar 17 |
1:15 |
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 |
Schmid |
| 3 |
Fri Mar 19 |
1:15 |
Spectroscopic methods for estimating compactness and foldedness of proteins - CD, FTIR, proton exchange |
Schmid |
| 4 |
Mon Mar 22 |
1:15 |
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 |
Zechiedrich |
| 5 |
Wed Mar 24 |
1:15 |
DNA Structure and topology II - Methods of analyzing DNA structure, future goals in field of DNA structure/topology, literature project |
Zechiedrich |
| 6 |
Mon Mar 29 |
1:15 |
Protein Folding - Mechanisms for attaining the correct 3D structure of proteins, experimental approaches to observing protein folding, catalysis of protein folding |
Gilbert |
| 7 |
Wed Mar 31 |
1:15 |
NMR of proteins - Basic theory and instrumentation, NOSEY, COSY methods, distance geometry, multi-diminsional NMR, sample requirements |
Gilbert |
| |
Fri Apr 02 |
1:15 |
Good Friday Holiday - No Class - |
|
| 8 |
Mon Apr 05 |
1:15 |
Fluorescence Methods for Structure analysis - principles of photon absorption and emission, fluorescence energy transfer, anisotropy, lifetime, instrumentation, optics |
Wensel |
| 9 |
Wed Apr 07 |
1:15 |
Xray crystallography - a scattering (diffraction)-based structural technique. Crystallization and synmetry. Theory of diffraction |
Tsai |
| 10 |
Fri Apr 09 |
1:15 |
Convolution - The diffraction pattern as a Fourier Transform. Some simple examples. |
Tsai |
| 11 |
Mon Apr 12 |
1:15 |
The Phase Problem - solving the phase problem, one way or another. EM techniques. |
Tsai |
| 12 |
Wed Apr 14 |
1:15 |
Cryoelectron microscopy - a scattering (diffraction)-based structural technique |
Ludtke |
| 1 |
Wed Apr 14 |
5:15 |
TA-1 - |
|
| |
Thu Apr 15 |
1:15 |
Mid-Term Faculty Review - |
|
| |
Fri Apr 16 |
1:15 |
Mid-term Exam - |
|
| 13 |
Mon Apr 19 |
1:15 |
Structure of Lipids and Glycolipids - Major lipids of biomembranes, diversity of composition, relationships between lipid structures and functional properties |
Ludtke |
| 14 |
Wed Apr 21 |
1:15 |
Membrane Protein Structure - integral and peripheral membrane proteins, protein-lipid interactions, structural features of transmembrane proteins |
Ludtke |
| 15 |
Fri Apr 23 |
1:15 |
Sequence to Structure - primary structure analysis, domain classifications, prediction of secondary and tertiary structure |
Lichtarge |
| 16 |
Mon Apr 26 |
1:15 |
Sequence and structure to function - structural genomics and functional site analysis |
Lichtarge |
| 17 |
Wed Apr 28 |
1:15 |
Mass spec I - mass spectrometers, ionization methods, the use of MS in protein identification |
Malovannaya |
| 18 |
Fri Apr 30 |
1:15 |
Mass spec II - use of mass spec in protein interaction, proteomics |
Malovannaya |
| 19 |
Mon May 03 |
1:15 |
Post-translational modification - irreversible, lipid modifications, ubiquitination |
Weigel |
| 20 |
Wed May 05 |
1:15 |
Regulatory post-translational modification - Protein phosphorylation and other reversibale regulatory post-translational modification |
Weigel |
| 21 |
Fri May 07 |
1:15 |
Protein glycosylation and quality control - biosynthetic quality control, additional roles for glycosylation, analysis of glycoproteins |
Sifers |
| 2 |
Fri May 07 |
5:15 |
TA-2 - |
|
| |
Tue May 11 |
1:15 |
Faculty Review - |
|
| |
Wed May 12 |
1:15 |
Final Exam - 1:15-3:45 - |
|
| |