Term 1
Genetics A
No Date Time Lecture Lecturer
1 Tue Aug 12 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 14 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 19 1:15 Complementation - Complementation tests, allelism. Verification by linkage mapping. Genetic interactions of unlinked loci. Allelic series, penetrance, and expressivity. Kelley
4 Tue Aug 26 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 28 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 Zhou
1 Fri Aug 29 5:15 GA-TA1 - General Genetic Principles
6 Tue Sep 02 1:15 Delineating a Pathway - How to identify genes that are functionally related to your favorite gene. Suppression analysis. Synthetic lethal mutants Zhou
7 Thu Sep 04 1:15 Enhancer screens and Pathway Analysis - Enhancer screens. Epistasis grouping and epistasis analysis. Establishing the order of gene functions. Zhou
8 Tue Sep 09 1:15 Bacterial Genetics I - Genetic transmission: haploid and circular genomes, P1-transduction, F-factors, HFRs, conjugation. Rosenberg
2 Tue Sep 09 5:15 GA-TA2 - Bacterial Genetics
9 Thu Sep 11 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 16 1:15 Bacterial Genetics III - Phage lambda in recombination studies. Rosenberg
11 Tue Sep 23 1:15 Bacterial Genetics IV - SOS response. Rosenberg
3 Tue Sep 30 5:15 GA-TA3 - Phenotype, pathway analysis and genetics screens
Wed Oct 01 1:15 Faculty Review -
Thu Oct 02 1:15 Final Exam - 1:15-3:45 -
Method & Logic in Molecular Biology
No Date Time Lecture Lecturer
1 Thu Aug 07 10:00 Method and Logic Meeting - Mardon
2 Tue Aug 12 10:00 Method and Logic Meeting - He
3 Thu Aug 14 10:00 Method and Logic Meeting - Kelley
4 Tue Aug 19 10:00 Method and Logic Meeting - Kuspa
5 Thu Aug 21 10:00 Method and Logic Meeting - Lee
6 Tue Aug 26 10:00 Method and Logic Meeting - Moore
7 Thu Aug 28 10:00 Method and Logic Meeting - Palzkill
8 Tue Sep 02 10:00 Method and Logic Meeting - Pletcher
9 Thu Sep 04 10:00 Method and Logic Meeting - Wilson
10 Tue Sep 09 10:00 Method and Logic Meeting - Zechiedrich
12 Tue Sep 16 10:00 Method and Logic Meeting - Staff
12 Tue Sep 16 10:00 Method and Logic Meeting - Staff
13 Thu Sep 18 10:00 Method and Logic Meeting - Staff
14 Tue Sep 23 10:00 Method and Logic Meeting - Staff
15 Thu Sep 25 10:00 Method and Logic Meeting - Staff
Molecular Methods
No Date Time Lecture Lecturer
1 Mon Aug 04 1:15 Introduction - Objectives of course, integrating methodology into discovery Gilbert
2 Wed Aug 06 1:15 Properties of DNA - DNA structure, melting, Tm, annealing, hybridization, gel electrophoresis, blots (Northern, Southern, colony) Highlander
3 Fri Aug 08 1:15 DNA Analysis - Probes and labeling, polymerases, kinase and reverse transcriptase, restriction enzymes and mapping, cloning, ligation Highlander
4 Mon Aug 11 1:15 DNA manipulation - Sanger DNA sequencing, PCR, quantitative PCR, rtPCR, site directed and random mutagenesis Highlander
1 Tue Aug 12 5:15 MM-TA1 - Lectures 1-4
5 Wed Aug 13 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 15 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
7 Mon Aug 18 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
2 Tue Aug 19 5:15 MM-TA2 - Lectures 5-7
Wed Aug 20 1:15 Midterm Review -
Thu Aug 21 1:15 Midterm Exam -
8 Wed Aug 27 1:15 Isolation/Refolding Strategies - Inclusion bodies, protein refolding strategies to avoid aggregation, disulfide formation and artifical chaperones Gilbert
9 Fri Aug 29 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
10 Wed Sep 03 1:15 Genomics I - 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
11 Fri Sep 05 1:15 Genomics II - annotation of sequences, EST's, specific organism databases Metzker
12 Mon Sep 08 1:15 Molecular Biology Database Use - pattern searches, domains, sequence-function-structure relationships Gilbert
3 Mon Sep 08 5:15 MM-TA3 - Lectures 8-11
13 Wed Sep 10 1:15 Proteomics - mass spectrometry - mass spectometery (MALDI-TOF, electrospray) protein identification Gilbert
14 Fri Sep 12 1:15 Proteomics - protein identification - identification of protein species in large complexes Gilbert
15 Mon Sep 15 1:15 Interaction cloning - systems, false positives and negatives happen, limitations, combinatorial screens, phage display, two-hybrid screen, lambda gt11 screens Feng
4 Tue Sep 16 5:15 MM-TA4 - Lectures 12-14
16 Wed Sep 17 1:15 Protein Localization/Identification - Purification of antigen, polyclonal antibodies, monoclonal antibodies, anti-peptide antibodies, Western blots, GFP fusions, FRAP Feng
17 Fri Sep 19 1:15 High throughput methods - protein arrays, interaction networks Pan
5 Tue Sep 23 5:15 MM-TA5 - Lectures 15-17
Fri Sep 26 1:15 Faculty Review -
Mon Sep 29 1:15 Final Exam - 1:15-3:45 -
Organization of the Cell
No Date Time Lecture Lecturer
1 Mon Aug 04 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 06 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 07 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 08 2:30 Mitochondria, Choloroplasts, Peroxisomes - Structure and biogenesis of mitochondria, chlorplasts, and peroxisomes. Protein import into these organelles Sifers
4 Wed Aug 13 2:30 The Endoplasmic Reticulum - quality control checkpoint and mother of the endomembrane system Sifers
2 Thu Aug 14 5:15 OC-TA2 - Review of protein trafficking
5 Fri Aug 15 2:30 The Golgi Complex - regulated vesicular trafficking in the endomembrane system Sifers
6 Mon Aug 18 2:30 Vesicular Transport in Reverse - the plasma membrane-endosome-lysosome connection Sifers
Fri Aug 22 1:15 Midterm Review -
Mon Aug 25 1:15 Midterm Exam -
7 Wed Aug 27 2:30 Apoptosis - Apoptosis versus necrosis, mechanisms of programmed cell death, regulators of apoptosis. Sifers
3 Thu Aug 28 5:15 OC-TA3 - review of apoptosis
8 Fri Aug 29 2:30 Cytoskeleton I - Actin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility. He
9 Wed Sep 03 2:30 Cytoskeleton II - Actin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility. He
4 Thu Sep 04 5:15 OC-TA4 - review of cytoskeleton
10 Fri Sep 05 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
11 Mon Sep 08 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
12 Wed Sep 10 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
5 Thu Sep 11 5:15 OC-TA5 - review of G-protein signalling, tyrosine kinases, and calcium signalling
13 Fri Sep 12 2:30 Energy Transduction and Bioenergetics - Membrane permeability, mechanisms of transport, bio-energetics, mitochondrial and chloroplast function, chemiosmosis Pedersen
14 Wed Sep 17 2:30 Transport Mechanisms - Active and passive transport, synporters, antiporters, ATPases Pedersen
6 Thu Sep 18 5:15 OC-TA6 - review of bioenergetics, transporters, ion channels
15 Mon Sep 22 2:30 Ion channels - Nernst potential, electrical properties of excitable membranes, action potential Pedersen
Wed Sep 24 1:15 Faculty Review -
Thu Sep 25 1:15 Final Exam - 1:15-3:45 -
Science as a Profession Term 1
No Date Time Lecture Lecturer
1 Tue Aug 05 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 12 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 19 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 26 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 02 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 09 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 16 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 23 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 23 1:15 Graduate Student Symposium - No Class -
1 Fri Nov 21 1:15 Introduction to Cancer Course - Oncogenes - leukemia/lymphoma Plon
2 Mon Nov 24 1:15 Amimal Models in Cancer Research - lung cancer Demayo
3 Wed Nov 26 1:15 Cancer as a Multi-step Process - tumor suppressor genes, colon cancer Plon
Thu Nov 27 1:15 Thanksgiving Holiday - No Class -
Fri Nov 28 1:15 Thanksgiving Holiday - No Class -
4 Mon Dec 01 1:15 Use of familial Cancers to Define Molecular Events - breast cancer Plon
5 Wed Dec 03 1:15 Metastasis - Demayo
Tue Dec 09 1:15 Faculty Review -
Wed Dec 10 1:15 Final Exam - 1:15-3:45 -
Cell Division
No Date Time Lecture Lecturer
1 Mon Oct 13 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 14 5:15 CD-TA1 - Review of cell cycle basics Sazer
2 Wed Oct 15 1:15 Principals of cell cycle regulation - CDKs, cyclins, CKIs, and proteolysis Zhang
3 Mon Oct 20 1:15 Principals of cell cycle regulation - cell cycle transitions, G1/S and G2M Zhang
2 Tue Oct 21 5:15 CD-TA2 - Review of CDK/cyclin/cell cycle transitions Zhang
4 Wed Oct 22 1:15 S phase - Initiation and control of DNA replication at origins of replications Wang
Thu Oct 23 1:15 Graduate Student Symposium - No Class -
5 Fri Oct 24 1:15 DNA Damage - DNA damage and repair Wilson
6 Mon Oct 27 1:15 DNA Repair - Repair of double strand breaks by homologous and non-homologous recombination Wilson
3 Tue Oct 28 5:15 CD-TA3 - Review of DNA replications and recombination Wilson
Wed Oct 29 1:15 Faculty Review Midterm - Lectures 1-6
Thu Oct 30 1:15 Exam I - Lectures 1-6
7 Fri Oct 31 1:15 M phase chromosomes - chromosomes (centromeres, telomeres), chromosome pairing and cohesion, chromosome condensation He
8 Mon Nov 03 1:15 M phase spindle - mechanics of spindle formation and function, kinetochore/spindle attachment He
9 Wed Nov 05 1:15 Cell Cycle Checkpoints - Introduction to cell cycle checkpoints, the DNA damage checkpoint Zhang
4 Wed Nov 05 5:15 CD-TA4 - Review of Mitosis He
10 Fri Nov 07 1:15 Spindle Assembly Checkpoint - the spindle assembly checkpoint Sazer
11 Mon Nov 10 1:15 Exit from mitosis - Exit from mitosis, coordination of exit from mitosis with cytokinesis Sazer
12 Wed Nov 12 1:15 Growth regulation - The cell cycle in growth regulation, development and cancer Westbrook
5 Wed Nov 12 5:15 CD-TA5 - Review of DNA damage and spindle Assembly checkpoints, mitotic exit Zhang
Tue Nov 18 1:15 Faculty Review -
Wed Nov 19 1:15 Exam II - Lectures 7-12
Thu Nov 27 1:15 Thanksgiving Holiday - No Class -
Fri Nov 28 1:15 Thanksgiving Holiday - No Class -
Development
No Date Time Lecture Lecturer
1 Wed Oct 22 2:30 Introduction to Drosophila embryogenesis - A few words on Developmental Biology; Overview of Drosophila oogenesis and embryogenesis Jafar-Nejad
Thu Oct 23 1:15 Graduate Student Symposium - No Class -
2 Fri Oct 24 2:30 Embryonic Patterning in Drosophia I - maternal-effect genes and the establishment of the anteroposterior axes Jafar-Nejad
3 Mon Oct 27 2:30 Embryonic patterning in Drosophila II - maternal-effect genes and the establishment of the dorsoventral axes Jafar-Nejad
4 Fri Oct 31 2:30 Development of Peripheral Nervous System in Drosophila - proneural proteins and Notch signaling Bellen
5 Mon Nov 03 2:30 Development of the Central Nervous System in Drosophila - acquiring neuronal identity Bellen
6 Wed Nov 05 2:30 Early Embryoinc Development in Vertebrates - gametogenesis and pre-implantation development Rodriguez
1 Thu Nov 06 5:15 TA-DE1 -
7 Fri Nov 07 2:30 Gastrulation and Somite Development - Rodriguez
8 Wed Nov 12 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 14 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 14 5:15 TA-DE2 -
10 Mon Nov 17 2:30 Limb Development in Vertebrates - axis specification, outgrowth and patterning. Johnson
11 Fri Nov 21 2:30 Urogenital System Development - Demayo
12 Mon Nov 24 2:30 TGF-beta Signaling and Human Development - pertubation of superfamily signaling and its effects on human organogenesis Brown
3 Tue Nov 25 5:15 TA-DE3 -
Thu Nov 27 1:15 Thanksgiving Holiday - No Class -
Fri Nov 28 1:15 Thanksgiving Holiday - No Class -
4 Wed Dec 03 5:15 TA-DE4 -
Thu Dec 04 1:15 Faculty Review -
Fri Dec 05 1:15 Final Exam - 1:15-3:45 -
Genetics B
No Date Time Lecture Lecturer
1 Tue Oct 14 1:15 Introduction - Comparisons of classical genetics, reverse genetics, and genomics. Strengths and weaknesses of model systems. Nomenclature. Zhou
2 Thu Oct 16 1:15 Yeast I - Basic molecular manipulations in reverse genetics: cloning by complementation, plasmid gap repair, gene disruption/replacement, plasmid shuffle Bertuch
3 Fri Oct 17 1:15 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. Bertuch
4 Tue Oct 21 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 22 5:15 GB-TA1 -
Thu Oct 23 1:15 Graduate Student Symposium - No Class -
5 Tue Oct 28 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 04 1:15 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 in every gene. Mardon
2 Tue Nov 04 5:15 GB-TA2 -
7 Thu Nov 06 1:15 Drosophila II - Genetic tricks: Mosaic analysis, autonomy vs. non-autonomy. Ectopic expression using heat shock, FLP-out and GAL4-UAS. Mardon
8 Tue Nov 11 1:15 Drosophila III - Mardon
9 Thu Nov 13 1:15 Mouse Genetics I - Inbred mice. Microsatellite markers. Mapping genes in mice using crosses. Matzuk
3 Thu Nov 13 5:15 GB-TA3 -
10 Thu Nov 20 1:15 Mouse Genetics II - Insertion of DNA and retrotransposons. Knock-outs and ins. Conditional knock-outs. Matzuk
4 Fri Nov 21 5:15 GB-TA4 -
11 Tue Nov 25 1:15 Human Genetics I - Disease loci and pedigrees. Lupski
12 Wed Nov 26 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 27 1:15 Thanksgiving Holiday - No Class -
Fri Nov 28 1:15 Thanksgiving Holiday - No Class -
13 Mon Dec 01 2:30 Human Genetics III - Effect of imprinting on pedigrees. Models for specific mechanisms of imprinting. Model for evolutionary significance. Lupski
5 Tue Dec 02 5:15 GB-TA5 -
Thu Dec 11 1:15 Faculty Review -
Fri Dec 12 1:15 Final Exam - 1:15-3:45 -
Science as a Profession-Ethics
No Date Time Lecture Lecturer
1 Tue Oct 14 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 21 2:30 NIH Topic 1a (elective) - Scientific Misconduct - Part 2 - Scientific misconduct case studies Gilbert
Thu Oct 23 1:15 Graduate Student Symposium - No Class -
3 Tue Oct 28 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
4 Tue Nov 04 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 Haymond
5 Tue Nov 11 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 13 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
7 Tue Nov 25 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 27 1:15 Thanksgiving Holiday - No Class -
Fri Nov 28 1:15 Thanksgiving Holiday - No Class -
8 Tue Dec 02 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 05 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 07 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 09 1:15 Control of transcription in bacterias - degradation and sequestration of initiation factors, riboswitches, noise in transcription and logic of transcriptional circuits. Herman
4 Mon Jan 12 1:15 Mammalian RNA Polymerase and Co-factors and Promoters - Mammalian RNA Polymerase- Structure- 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). O'Malley
5 Wed Jan 14 1:15 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. O'Malley
1 Wed Jan 14 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 16 1:15 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. O'Malley
Mon Jan 19 1:15 Martin Luther King Day Holiday - No Class -
7 Wed Jan 21 1:15 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. O'Malley
8 Fri Jan 23 1:15 Local Chromatin Changes - histones, nucleosomes, covalent modification of histones, DNAase hypersensitive sites, insulators, locus control regions, polytene chromosomes Wong
9 Wed Jan 28 1:15 Global Chromatin Changes - chromatin subdomains, silencing, position effect variegation, epigenetic inheritance, X-inactivation, imprinting Wong
2 Wed Jan 28 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 30 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 02 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 03 1:15 Midterm Faculty Review -
Wed Feb 04 1:15 MIDTERM EXAM -
12 Thu Feb 05 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 06 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 09 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 11 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 11 5:15 GR TA3 - Splicing and poyadenylation general overview; define mechanisms for alternative splice-site selection, intron vs exon selection
16 Fri Feb 13 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 16 1:15 President's Day Holiday - No Class -
17 Tue Feb 17 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 18 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 19 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 23 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 25 1:15 Regulation of Protein Turnover - Ubiquitin-proteosome mediated degradation., Importance of regulation, protein motifs, PEST sequences, etc. Rosen
4 Tue Mar 03 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 05 1:15 Faculty Review -
Fri Mar 06 1:15 Final Exam - 1:15-3:45 -
Immunology
No Date Time Lecture Lecturer
Mon Jan 19 1:15 Martin Luther King Day Holiday - No Class -
1 Thu Feb 05 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 10 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 12 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 13 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 16 1:15 President's Day Holiday - No Class -
4 Tue Feb 17 2:30 Lymphocyte Activation - B/T cell activation, signal transduction, convergence and integration of signal transduction pathways, anergy, apoptosis Spencer
5 Thu Feb 19 2:30 Integration of an Immune Response - T cell effector functions, transplantation, autoimmunity, tumor immunology Spencer
2 Thu Feb 19 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 26 1:15 Faculty Review -
Fri Feb 27 1:15 Final Exam - 1:15-3:45 -
Molecular Interactions
No Date Time Lecture Lecturer
1 Wed Jan 07 2:30 Course Introduction -Ligand Binding - Definition of Kd. Mass action, basic thermodynamics. Pedersen
2 Fri Jan 09 2:30 Forces in solution and thermodynamics - Enthalpy and entropy, forces in solution, competitive inhibition. Pedersen
3 Wed Jan 14 2:30 Allosterism and protein conformations - Regulation of activity and binding, multiple binding sites and the Hill equation Pedersen
1 Thu Jan 15 5:15 MI-TA Review 1 -
4 Fri Jan 16 2:30 Allosterism and linkage analysis - Heterotropic allosteric interaction and thermodynamic linkage analysis. Pedersen
Mon Jan 19 1:15 Martin Luther King Day Holiday - No Class -
5 Wed Jan 21 2:30 Cooperativity - Koshland-Nemethy-Filmer models. Negative cooperativity Pedersen
2 Thu Jan 22 5:15 MI-TA Review 2 -
6 Fri Jan 23 2:30 Binding kinetics I - reactions and reaction order Pedersen
7 Wed Jan 28 2:30 Binding kinetics II - better kinetics through computation Pedersen
3 Thu Jan 29 5:15 MI-TA Review 3 -
8 Fri Jan 30 2:30 Protein-Ligand Interactions - Molecular basis of specificity, protein ligand interactions - structural basis of H-bonding, salt bridges and other interactions Prasad
9 Mon Feb 02 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
4 Thu Feb 05 5:15 MI-TA Review 4 -
10 Fri Feb 06 2:30 Protein DNA Interactions - Protein-DNA interactions. DNA binding motifs, structural basis of base recognition, backbone interactions Prasad
11 Wed Feb 11 2:30 Enzyme Kinetics and Catalysis - Michaelis-Menten kinetics, Inhibition, kcat and kcat/Km, allosteric enzymes, inhibition, practical features of an assay Gilbert
5 Thu Feb 12 5:15 MI-TA Review 5 -
12 Fri Feb 13 2:30 Mechanisms of Enzyme Catalysis - Acid base catalysis, covalent catalysis, stabilization of transition states, transition state analogs, coenzymes, suicide inhibitors Gilbert
Mon Feb 16 1:15 President's Day Holiday - No Class -
13 Wed Feb 18 2:30 Serine Proteases - Key family members, specificity, catalytic triad/mechanism, inhibition Petrosino
14 Mon Feb 23 2:30 F1/FO ATPases - Macromolecular motors, single molecule kinetics Petrosino
Tue Mar 03 1:15 Faculty Review -
Wed Mar 04 1:15 Final Exam - 1:15-3:45 -
Neuroscience
No Date Time Lecture Lecturer
1 Tue Jan 06 1:15 Information processing in neurons. - The electrical properties of neurons. Ion channel distriution. Coupling electrical signals to neurotransmitter release Pham
2 Thu Jan 08 1:15 Synaptic plasticity - Structure of the synapse. Ligand gated ion channels. Neuortransmitter release. Activity-dependent plasticity Pham
3 Tue Jan 13 1:15 Learning and memory - forms of learning and memory. Molecular coincidence detectors. Perpetuation of biochemical signals. Alterations in gene expression. Structural changes. Pham
4 Thu Jan 15 1:15 Sensory systems - specialized sensory receptors, encoding of information, circuits for information processing, face cells, behavioral control Pham
1 Fri Jan 16 5:15 NE TA Review 1 - Brain anatomy, anatomy of eye and nose, neuron types, action potentials (including review of neurotransmitters)
Mon Jan 19 1:15 Martin Luther King Day Holiday - No Class -
5 Tue Jan 20 1:15 Cognition - Split brain studies, amnesia, PET imaging in cognition, cortical plasticity, diseases of cognition and affect Pham
2 Wed Jan 21 5:15 NE TA Review 2 - Basis of methods used (voltage clamp, imaging of brain); Visual receptors (rods, cones), receptive fields
Mon Jan 26 1:15 Faculty Review -
Tue Jan 27 1:15 Final Exam - 1:15-3:45 -
Mon Feb 16 1:15 President's Day Holiday - No Class -
Term 4
Research Design
No Date Time Lecture Lecturer
1 Tue Mar 17 1:00 Research Design Introduction - Introduction to the design of research projects Gilbert
2 Tue Mar 24 1:00 Research Design Workgroup 2 - Introduction to the design of research projects Schmid
3 Tue Mar 31 1:00 Research Design Workgroup 5 - Introduction to the design of research projects Lichtarge
4 Tue Apr 07 1:00 Research Design Workgroup 6 - Introduction to the design of research projects Prasad
5 Tue Apr 14 1:00 Research Design Workgroup 3 - Staff
6 Tue Apr 21 1:00 Research Design Workgroup 4 - Staff
7 Tue Apr 28 1:00 Research Design Workgroup 7 - Staff
8 Tue May 05 1:00 Research Design Workgroup 8 - Staff
9 Thu May 14 1:00 Research Design Symposium - Staff
Structure of Macromolecules
No Date Time Lecture Lecturer
1 Mon Mar 16 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
2 Wed Mar 18 1:15 Spectroscopic methods for estimating compactness and foldedness of proteins - CD, FTIR, proton exchange Schmid
3 Fri Mar 20 1:15 NMR of proteins and DNA - Basic theory and instrumentation, NOSEY, COSY methods, distance geometry, multi-diminsional NMR, sample requirements Gilbert
4 Mon Mar 23 1:15 Mass spec I - mass spectrometers, ionization methods, the use of MS in protein identification Qin
5 Wed Mar 25 1:15 Mass spec II - use of mass spec in protein interaction, proteomics Qin
6 Mon Mar 30 1:15 Post-translational modification - irreversible, lipid modifications, ubiquitination Weigel
7 Wed Apr 01 1:15 Regulatory post-translational modification - Protein phosphorylation and other reversibale regulatory post-translational modification Weigel
8 Fri Apr 03 1:15 Protein glycosylation and quality control - biosynthetic quality control, additional roles for glycosylation, analysis of glycoproteins Sifers
9 Mon Apr 06 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
10 Wed Apr 08 1:15 DNA Structure and topology II - Methods of analyzing DNA structure, future goals in field of DNA structure/topology, literature project Zechiedrich
1 Wed Apr 08 5:15 TA-1 -
Fri Apr 10 1:15 Good Friday Holiday - No Class -
11 Mon Apr 13 1:15 Protein Taxonomy - Discussion of protein motifs, domains and general structural features. Approaches to function from structure. Tsai
Wed Apr 15 1:15 Mid-term Exam -
12 Fri Apr 17 1:15 Protein Folding - Mechanisms for attaining the correct 3D structure of proteins, experimental approaches to observing protein folding, catalysis of protein folding Gilbert
13 Mon Apr 20 1:15 Fluorescence Methods for Structure analysis - principles of photon absorption and emission, fluorescence energy transfer, anisotropy, lifetime, instrumentation, optics Wensel
14 Wed Apr 22 1:15 Cryoelectron microscopy - a scattering (diffraction)-based structural technique Ludtke
15 Fri Apr 24 1:15 Structure of Lipids and Glycolipids - Major lipids of biomembranes, diversity of composition, relationships between lipid structures and functional properties Ludtke
16 Mon Apr 27 1:15 Membrane Protein Structure - integral and peripheral membrane proteins, protein-lipid interactions, structural features of transmembrane proteins Ludtke
17 Wed Apr 29 1:15 Xray crystallography - a scattering (diffraction)-based structural technique. Crystallization and synmetry. Theory of diffraction Tsai
18 Fri May 01 1:15 Convolution - The diffraction pattern as a Fourier Transform. Some simple examples. Tsai
19 Mon May 04 1:15 The Phase Problem - solving the phase problem, one way or another. EM techniques. Tsai
20 Wed May 06 1:15 Sequence to Structure - primary structure analysis, domain classifications, prediction of secondary and tertiary structure Lichtarge
21 Fri May 08 1:15 Sequence and structure to function - structural genomics and functional site analysis Lichtarge
2 Fri May 08 5:15 TA-2 -
Tue May 12 1:15 Faculty Review -
Wed May 13 1:15 Final Exam - 1:15-3:45 -