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Course Curriculum Syllabus

2016-2017


  
Term 1
  
  Course: GS-GS-501: Organization of the Cell
Course Director(s): Pedersen, Steen E \ Sifers, Richard N
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Aug 012:30 PMN315Overview and the Secretory PathwayCourse organization, outline etc. General protein expression and maturation. The secretory pathway and nature of various organelles.Sifers, Richard N
  Wed Aug 032:30 PMN315Nuclear TransportOverall 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, Richard N
  Thu Aug 045:15 PMN315TA #1Review of general cell structures, their function and generation. Concepts of vesicular transport and protein import and export for the organelles.
  Fri Aug 052:30 PMN315Mitochondria and PeroxisomesStructure and biogenesis of mitochondria and peroxisomes. Protein import into these organelles.Sifers, Richard N
  Mon Aug 082:30 PMN315The Endoplasmic ReticulumQuality control checkpoint and mother of the endomembrane system.Sifers, Richard N
  Wed Aug 102:30 PMN315The Golgi ComplexRegulated vesicular trafficking in the endomembrane system.Sifers, Richard N
  Thu Aug 115:15 PMN315TA #2Review of additional protein trafficking schemes.
  Fri Aug 122:30 PMN315Cytoskeleton IActin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility.Sokac, Anna Marie
  Mon Aug 152:30 PMN315Cytoskeleton IIActin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility.Sokac, Anna Marie
  Wed Aug 172:30 PMN315Midterm Review
  Thu Aug 185:15 PMN315TA #3Review of cytoskeleton.
  Fri Aug 191:15 PMN315Midterm Exam
  Mon Aug 222:30 PMN315Vesicular Transport in ReverseThe plasma membrane-endosome-lysosome connection.Sifers, Richard N
  Wed Aug 242:30 PMN315ApoptosisApoptosis versus necrosis, mechanisms of programmed cell death, regulators of apoptosis.Sifers, Richard N
  Thu Aug 255:15 PMN315TA #4Review of endocytosis, lysosomes, and apoptosis.
  Fri Aug 262:30 PMN315G ProteinsSignaling 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, Theodore G
  Tue Aug 302:30 PMN315Growth Factors/Tyrosine Kinase SignalingLigands 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, Theodore G
  Thu Sep 015:15 PMN315TA #5Review of G-protein signaling and tyrosine kinase signaling.
  Fri Sep 022:30 PMN315Calcium and phospholipase signalingCalcium 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, Theodore G
  Wed Sep 072:30 PMN315Energy Transduction and BioenergeticsMembrane permeability, mechanisms of transport, bio-energetics, mitochondrial and chloroplast function, chemiosmosis.Pedersen, Steen E
  Thu Sep 085:15 PMN315TA #6Review of calcium signaling and bio-energetics.
  Fri Sep 092:30 PMN315Transport MechanismsActive and passive transport, symporters, antiporters, ATPases.Pedersen, Steen E
  Mon Sep 122:30 PMN315Ion channelsNernst potential, electrical properties of excitable membranes, action potential and energy transduction.Pedersen, Steen E
  Wed Sep 142:30 PMN315Faculty Review
  Thu Sep 155:15 PMN315TA #7Review of transporters and ion channels.
  Fri Sep 161:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-502: Molecular Methods
Course Director(s): Weigel, Nancy L
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Aug 011:15 PMN315IntroductionOverview of course contents and schedule.Weigel, Nancy L
  Wed Aug 031:15 PMN315DNA Manipulation, Amplification and DetectionEnzymes to modify, label amplify or quantify nucleic acids; Polymerase chain reaction (PCR) and derivatives such as hybrid PCR, quantitative PCR, real time PCR, droplet PCR.Venken, Koen J. T.
  Fri Aug 051:15 PMN315DNA Cloning IApplications of cloning, vectors, transformation methods, plasmid purification systems, traditional cloning methods, cloning diagnosis.Venken, Koen J. T.
  Mon Aug 081:15 PMN315DNA Cloning IIApplications of advanced cloning and mutagenesis; Gateway, sequence and ligation independent cloning, Gibson cloning, Type II's cloning; mutagenesis.Venken, Koen J. T.
  Tue Aug 095:15 PMN315TA #1Lectures 1-4.
  Wed Aug 101:15 PMN315Flow CytometryIntroduction to the technique of flow cytometry and cell sorting, detecting fluorescent cells through expressed antigens and endogenous fluorescent molecules.Sederstrom, Joel
  Fri Aug 121:15 PMN315cDNA and Genomic LibrariesConstruction and handling of cDNA libraries; whole genome libraries, targeted strategies such as exome and regional capture, circulating cell-free genomic libraries.Metzker, Michael Lee
  Mon Aug 151:15 PMN315First-Generation Sequencing and GenotypingIntroduction to Maxam-Gilbert, Sanger and automated Sanger sequencing; microarrays, high-throughput genotyping assays.Metzker, Michael Lee
  Wed Aug 171:15 PMN315Next Generation SequencingTechnology approaches and advances of current NGS platforms focusing on both clonally-amplified and single molecule strategies, alignment for variant detection; haplotype phasing and structural variant detection.Metzker, Michael Lee
  Wed Aug 175:15 PMN315TA #2Lectures 5-7.
  Mon Aug 221:15 PMN315Genomic ProfilingFunctional assays using NGS: RNA sequencing (RNA-Seq) and data analysis, single cell analyses, other functional sequencing assays.Zong, Chenghang
  Wed Aug 241:15 PMN315Antibody Production, Characterization and Research ApplicationsMonoclonal antibodies(mAbs) - mouse and rabbit hybridomas, B cell IgG cloning and recombinant single domain mAbs; polyclonal antibodies; antibodies to protein post-translational modifications and peptides, characterization and validation of antibodies.Edwards, Dean
  Wed Aug 245:15 PMN315TA #3Lectures 8-9.
  Fri Aug 261:15 PMN315Midterm Review
  Wed Aug 311:15 PMN315Midterm Exam
  Fri Sep 021:15 PMN315CRISPR/Cas9Purification of epitope tagged proteins; inclusion bodies; protein refolding strategies; disulfide formation and artificial chaperones.Heaney, Jason D
  Tue Sep 062:30 PMN315Detection of Protein-Protein InteractionsPrinciples of: Western immunoblotting, Westerns coupled to co-immunoprecipitation; in vitro (GST) pull-down assays; yeast two-hybrid system; bimolecular fluorescence complementation(BiFC) and phage display.Lydon, John P
  Wed Sep 071:15 PMN315Visualizing ProteinsImmunohistochemical detection methods; lacZ reporters; green fluorescence protein (GFP) reporters; luciferase reporters; fluorescence resonance energy transfer (FRET); bimolecular fluorescence complementation (BiFC); fluorescence recovery after photobleaching.Lydon, John P
  Wed Sep 075:15 PMN315TA #4Lectures 10-13.
  Fri Sep 091:15 PMN315High Throughput MethodsChromatin immunoprecipitation (ChIP) on ChIP (ChIP-Chip); ChIP and high throughput DNA sequencing (ChIP-Seq); protein microarrays (i.e. reverse and forward phase protein microarrays); tissue microarrays.Lydon, John P
  Mon Sep 121:15 PMN315Protein ExpressionExpression systems (E. coli, yeast, insect and mammalian cells), fusion tags (6x His, GST, MBP, intein); co-expression for protein complexes and in vitro translation.York, Robert Brian
  Wed Sep 141:15 PMN315Protein PurificationCell disruption methods; centrifugation, ammonium sulfate precipitation, liquid chromatography (affinity, ion exchange, hydrophobic, size exclusion); SDS-PAGE; evaluating protein concentration (Bradford and extinction coefficients) and biological assays.York, Robert Brian
  Mon Sep 191:15 PMN315Proteomics Mass Spectrometry - Basic PrinciplesMass spectometer instruments and analytical methods; principles of identification for peptides and post-translational modifications (PTMs); data processing.Malovannaya, Anna
  Tue Sep 205:15 PMN315TA #5Lectures 14-16.
  Wed Sep 211:15 PMN315Proteomics Mass Spectrometry - Applications in BiologyMS-based quantification, global proteome profiling, PTM profiling, protein-protein interaction networks from IP/MS.Malovannaya, Anna
  Fri Sep 231:15 PMN315RNA Interference and genetic screensRNA interference(RNAi) mechanisms, RNAi tools, genetic screening methods, technical considerations in using RNAi.Westbrook, Thomas
  Fri Sep 235:15 PMN315TA #6Lectures 17-19.
  Wed Sep 281:15 PMN315Faculty Review
  Fri Sep 301:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-503: Genetics A
Course Director(s): Herman, Christophe \ Dierick, Herman A.
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Aug 021:15 PMN315Mendelian GeneticsGene nomenclature: gene/allele/genotype/phenotype. Dominant v. recessive mutations. Mendel's laws. Penetrance v. expressivity.Dierick, Herman A.
  Thu Aug 041:15 PMN315Cellular Mechanisms of Mendelian Genetics and LinkageMeiosis v. mitosis. Linkage. Two-point and three-point mapping. Complementation.Dierick, Herman A.
  Tue Aug 091:15 PMN315Statistical Methods in Genetics.Basics of pedigrees. Binomial statistics: identifying probabilities of alternative choices. Bayesian statistics: altering a priori probability. X square tests: testing data against a model.Dierick, Herman A.
  Thu Aug 111:15 PMN315Population GeneticsMultifactorial traits: continuous, dichotomous and meristic traits. Polygeneticity and heritability. Allele frequencies, genotype frequencies and Hardy Weinberg. Inbreeding and inbreeding coefficients. Selection and balanced polymorphisms.Dierick, Herman A.
  Mon Aug 155:15 PMN315TA #1General Genetic Principles.
  Tue Aug 161:15 PMN315Genetic ScreensMutant building: discovering genes involved in a biological process through screens. Mutagens and screen saturation. Yeast genetics and tetrad analysis.Bates, David B.
  Thu Aug 181:15 PMN315Selecting and Identifying MutantsIdentifying mutated genes. Selection and screening strategies, reporter genes and secondary screens.Bates, David B.
  Tue Aug 231:15 PMN315Genetic SuppressionGenetics as a study of how proteins interact, fold and function. Mechanisms of genetic suppression. Genetic enhancement and synthetic lethality.Bates, David B.
  Thu Aug 251:15 PMN315Epistasis and Pathway AnalysisDetermining the order of action of proteins in a pathway by epistasis analysis. Ordering genes in metabolic and regulatory pathways.Bates, David B.
  Thu Aug 252:30 PMN315Midterm Review
  Fri Aug 265:15 PMN315TA #2Phenotype, pathway analysis and genetics screens.
  Mon Aug 291:15 PMN315Midterm Exam1:00 PM - 4:00 PM
  Thu Sep 011:15 PMN315Viral/Phage Genetics.Virus cycle, complementation group.Herman, Christophe
  Tue Sep 061:15 PMN315Bacterial Genetics IGenetic transmission: haploid and circular genomes, P1-transduction, F-factors, HFRs, conjugation.Rosenberg, Susan M
  Thu Sep 081:15 PMN315Bacterial Genetics IIRecombination.Rosenberg, Susan M
  Tue Sep 131:15 PMN315Bacterial Genetics IIISOS response, transposition.Rosenberg, Susan M
  Thu Sep 151:15 PMN315Genetic Engineering IArtificial chromosomes, recombineering in bacteria, homing endonucleases (I-SceI), seamless versus remnant engineering.Venken, Koen J. T.
  Mon Sep 195:15 PMN315TA #3Bacterial Genetics.
  Tue Sep 201:15 PMN315Genetic Engineering IIIntegrases, Zn finger technology, TALE technology, Crispr/Cas technology.Venken, Koen J. T.
  Thu Sep 221:15 PMN315Faculty Review
  Thu Sep 225:15 PMN315TA #4Genetic Engineering.
  Mon Sep 261:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-528: Responsible Conduct of Research - Year 1
Course Director(s): Bertuch, Alison Ann
  DateStart TimeRoomLectureDescriptionLecturer
  Thu Aug 042:30 PMN315(1L6) Accessing the Scientific Literature and Other Resources Accessing the scientific literature (e.g., Pubmed, Scopus, Google Scholar). Navigating the plethora of journals and papers. Resources in the TMC Library.
  Thu Aug 112:30 PMN315(1L5) Rigor and Reproducibility The scientific method, blinding and randomization, technical vs. biological replicates, authentication of key biological and/or chemical resources, transparency.Bertuch, Alison Ann
  Thu Aug 182:30 PMN315(1L7) Professionalism in Science Government organizations, private funding sources, applying for fellowships, structure of a grant, grant review system, consequences of fraud in grant applications, science advocacy. Kuspa, Adam
  Tue Aug 232:30 PMN315(1L8) Setting Goals for Your Scientific Development and Coping with Challenges 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 grad school), lifelong learning, selecting rotations, where to get help and information, thinking now about the next step.Smith, Carolyn L
  Thu Sep 012:30 PMN315(1L1) Data Acquisition and Record Keeping Responsibilities Responsibilities for record keeping, challenges in keeping accurate and understandable notebooks, ownership of research materials, reagent/data sharing.Nelson, David L
  Thu Sep 082:30 PMN315(1L2) Responsible Authorship and Publication Giving credit when credit is due, when to cite or not, how to use direct quotes, paraphrasing, plagiarism, copyright and copyright permission. Smith, Carolyn L
  Thu Sep 152:30 PMN315(1C) Case Studies Data Management/PlagiarismRecord keeping, ownership of research materials, responsible citation, and plagiarism.
  Thu Sep 222:30 PMN315(1M) Progress to Degree – Year 1 Selecting a lab and developing a group of mentors, what to look for in the mentor/mentee relationship, keeping on track toward your degree. Building resilience.Bertuch, Alison Ann
  
  
Term 2
  
  Course: GS-GS-504: Genetics B
Course Director(s): Zhou, Zheng
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Oct 111:15 PMN315IntroductionForward and reverse genetics. Strengths of model systems. Nomenclature. The concept of maternal effect.Zhou, Zheng
  Thu Oct 131:15 PMN315C.elegans IAdvantages and special considerations of hermaphrodite genetics. How to construct strains, strategies of genetic screens, cloning genes, balancers.Zhou, Zheng
  Tue Oct 181:15 PMN315C.elegans IIC.elegans transformation. Impact of the C.elegans genome project. Reverse genetics using RNA interference and gene deletions. Studies of gene interaction.Zhou, Zheng
  Wed Oct 195:15 PMN315TA #1
  Tue Oct 251:15 PMN315Yeast IBasic molecular manipulations in reverse genetics: cloning by complementation, plasmid gap repair, gene disruption/replacement, plasmid shuffle.Ira, Grzegorz
  Thu Oct 271:15 PMN315Yeast IIGenome 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, Grzegorz
  Mon Oct 315:15 PMN315TA #2
  Tue Nov 011:15 PMN315Mouse Genetics IInbred mice. Microsatellite markers. Mapping genes in mice using crosses.Matzuk, Martin Matthew
  Thu Nov 032:30 PMN315Mouse Genetics IIInsertion of DNA and retrotransposons. Knock-outs and ins. Conditional knock-outs.Matzuk, Martin Matthew
  Fri Nov 045:15 PMN315TA #3
  Tue Nov 081:15 PMN315Drosophila IIntroduction. 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, Graeme
  Tue Nov 082:30 PMN315Midterm Review
  Thu Nov 101:15 PMN315Midterm Exam1:00 PM - 4:00 PM
  Tue Nov 151:15 PMN315Drosophila IIGenetic 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, Graeme
  Thu Nov 171:15 PMN315Drosophila IIIGene 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, Graeme
  Fri Nov 185:15 PMN315TA #4
  Mon Nov 281:15 PMN315Human Genetics IDisease loci and pedigrees.Lupski, James R
  Tue Nov 291:15 PMN315Human Genetics IIMapping with DNA markers. Sources of polymorphisms. Simple vs. complex traits. Genome scans for quantitative trait loci.Lupski, James R
  Thu Dec 011:15 PMN315Human Genetics IIIEffect of imprinting on pedigrees. Models for specific mechanisms of imprinting. Model for evolutionary significance.Lupski, James R
  Fri Dec 025:15 PMN315TA #5
  Wed Dec 071:15 PMN315Faculty Review
  Fri Dec 091:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-505: Cell Division
Course Director(s): Ira, Grzegorz \ Chang, Eric C
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Oct 101:15 PMN315Course Introduction/Cell Cycle OverviewDiscovery of cell cycle regulation--Cell cycle stages, mitosis and meiosis, discovery of CDK/cyclin/MPF.Zhang, Pumin
  Wed Oct 121:15 PMN315Principles of cell cycle regulation ICDKs, cyclins, CKIs, and proteolysis.Dang, Weiwei
  Fri Oct 141:15 PMN315Principles of cell cycle regulation IICell cycle transitions, G1/S and G2M.Dang, Weiwei
  Mon Oct 171:15 PMN315S phaseInitiation and control of DNA replication at origins of replications.Ira, Grzegorz
  Tue Oct 185:15 PMN315TA #1Review of cell cycle basics, S phase.
  Wed Oct 191:15 PMN315DNA DamageDNA damage and repair.Ira, Grzegorz
  Fri Oct 211:15 PMN315DNA RepairRepair of double strand breaks by homologous and non-homologous recombination.Ira, Grzegorz
  Mon Oct 241:15 PMN315Cell Cycle CheckpointsIntroduction to cell cycle checkpoints, the DNA damage checkpoint.Lin, Weei-Chin
  Mon Oct 242:30 PMN315Midterm ReviewLectures 1-7.
  Tue Oct 255:15 PMN315TA #2Review of DNA recombination and repair.
  Wed Oct 261:15 PMN315Midterm ExamLectures 1-7.
  Fri Oct 281:15 PMN315Chromosome nuclear organization3D chromosome organization and folding.Lieberman, Erez S
  Mon Oct 311:15 PMN315ChromosomesChromatin duplication and M phase chromosomes organization.Dang, Weiwei
  Fri Nov 041:15 PMN315TelomeresStructure and synthesis. Telomere dysfunction-induced DNA damage checkpoint response. Crisis and survival in the absence of telomerase.Bertuch, Alison Ann
  Mon Nov 071:15 PMN315M phase spindleMechanisms of spindle formation and function, kinetochore/spindle attachment.Chang, Eric C
  Tue Nov 085:15 PMN315TA #3Review of chromosome/chromatin/telomeres.
  Wed Nov 091:15 PMN315CytokinesisCytokinesis mechanisms.Sokac, Anna Marie
  Fri Nov 111:15 PMN315Growth regulationThe cell cycle in growth regulation, development and cancer.Westbrook, Thomas
  Tue Nov 152:30 PMN315Faculty ReviewLecture 8-12
  Tue Nov 155:15 PMN315TA #4Review of cytokinesis, spindle & kinetochore assembly and growth regulation.
  Wed Nov 161:15 PMN315Final ExamLectures 8-12. 1:00 PM - 4:00 PM
  
  Course: GS-GS-506: Development
Course Director(s): Groves, Andrew Kelton
  DateStart TimeRoomLectureDescriptionLecturer
  Wed Oct 122:30 PMN315Core Concepts in Developmental BiologyIntroduction to class.Groves, Andrew Kelton
  Fri Oct 142:30 PMN315Setting up the vertebrate body plan IAxis determination and gastrulation.Groves, Andrew Kelton
  Mon Oct 172:30 PMN315Setting up the vertebrate body plan IIMammalian development and embryonic stem cells.Groves, Andrew Kelton
  Wed Oct 192:30 PMN315Setting up the vertebrate body plan IIIPatterning the embryo from head to tail.Groves, Andrew Kelton
  Fri Oct 212:30 PMN315ES cells, pluripotency and reprogramming / iPSGroves, Andrew Kelton
  Fri Oct 215:15 PMN315TA #1Review of Lectures 1-4.
  Fri Oct 282:30 PMN315Stem cells in the adultNguyen, Hoang
  Fri Oct 285:15 PMN315TA #2Review of Lectures 5-6.
  Mon Oct 312:30 PMN315Midterm Review
  Wed Nov 021:15 PMN315Midterm Exam1:00 PM - 4:00 PM
  Thu Nov 031:15 PMN315Introduction to Drosophila embryogenesisOverview of Drosophila oogenesis and embryogenesis.Jafar-Nejad, Hamed
  Fri Nov 042:30 PMN315Embryonic patterning in Drosophila - IMaternal-effect genes and the establishment of the anteroposterior axes.Jafar-Nejad, Hamed
  Mon Nov 072:30 PMN315Embryonic patterning in Drosophila IIMaternal-effect genes and the establishment of the dorsoventral axes.Jafar-Nejad, Hamed
  Wed Nov 092:30 PMN315Vertebrate neural development IDevelopmental anatomy of the nervous system. Molecular aspects of neural induction, formation of the neural plate and neurogenesis.Deneen, Benjamin
  Thu Nov 105:15 PMN315TA #3Review of Lectures 7-9.
  Fri Nov 112:30 PMN315Vertebrate neural development IIMolecular mechanisms of dorsal-ventral and anterior-posterior patterning. Combinatorial and antagonistic signaling involved in dorsoventral patterning of the neural tube.Deneen, Benjamin
  Thu Nov 172:30 PMN315Limb DevelopmentA model system to illustrate developmental concepts.Groves, Andrew Kelton
  Thu Nov 175:15 PMN315TA #4Review of Lectures 10-12.
  Fri Nov 182:30 PMN315Faculty Review
  Tue Nov 221:15 PMN315 Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-508: Cancer
Course Director(s): Pangas, Stephanie A
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Nov 141:15 PMN315Introduction, OncogenesCourse introduction; Basic concepts I: Oncogenes.Pangas, Stephanie A
  Fri Nov 181:15 PMN315Mouse modelsMouse models to study cancer.Heaney, Jason D
  Mon Nov 212:30 PMN315Tumor suppressor genesBasic concepts II: Tumor suppressors.Pangas, Stephanie A
  Mon Nov 282:30 PMN315Tumor cell - stromal interactionsTumor cell - stromal interactions.Chen, Xi
  Wed Nov 302:30 PMN315MetastasisMetastasis.Zhang, Xiang
  Fri Dec 022:30 PMN315Cancer stem cellsCancer stem cells.Chan, Keith
  Mon Dec 051:15 PMN315Faculty Review
  Tue Dec 061:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-515: Ethics - Year 2
Course Director(s): Bertuch, Alison Ann
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Oct 1010:00 AMN315(2L1) Research misconduct - (NIH b3) Safe Practices in the LaboratoryDefinitions - Falsification, fabrication, plagiarism – whistleblowers, allegations, investigations, penalties. College policy and mechanisms for handling misconduct allegations, federal policies and procedures. (NIH b3) Safe Practices in the Laboratory.Nelson, David L
  Mon Oct 1710:00 AMN315(2M) MentorshipMeeting with 2nd year students and their mentors, matching expectations between mentor student, developing communication channels, picking an appropriate thesis topic, the thesis committee as a resource.Bertuch, Alison Ann
  Mon Oct 2410:00 AMN315(2L2) Ethics of Biomedical Studies with AnimalsWhen 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.Buckmaster, Cindy A
  Mon Oct 3110:00 AMN315(2C) Case Studies - Scientific Misconduct/AnimalsScientific misconduct and experiments with animals (small group discussion format with faculty facilitator).
  Mon Nov 0710:00 AMN315(2L5) Rigor and ReproducibilityThe scientific method, blinding and randomization, technical vs. biological replicates, authentication of key biological and/or chemical resources, transparency.Bertuch, Alison Ann
  
  Course: GS-GS-523: Method and Logic in Molecular Biology
Course Director(s): Mardon, Graeme
  DateStart TimeRoomLectureDescriptionLecturer
  Thu Oct 1310:00 AMN315Method and Logic MeetingAttendance at this class (to be held in N315) is mandatory for all students who intend to take this course. This organizational meeting begins at 10:15 and runs until 11:45 AM.
  Tue Oct 1810:00 AMN315Method and Logic MeetingClasses will be held in N302, N304, N310, N317 and M303 from this class onwards. Classes begin at 10 AM and end at noon.
  Fri Oct 2110:00 AMN315Method and Logic Meeting
  Tue Oct 2510:00 AMN315Method and Logic Meeting
  Thu Oct 2710:00 AMN315Method and Logic Meeting
  Tue Nov 0110:00 AMN315Method and Logic Meeting
  Thu Nov 0310:00 AMN315Method and Logic Meeting
  Tue Nov 0810:00 AMN315Method and Logic Meeting
  Thu Nov 1010:00 AMN315Method and Logic Meeting
  Tue Nov 1510:00 AMN315Method and Logic Meeting
  Thu Nov 1710:00 AMN315Method and Logic Meeting
  Tue Nov 2910:00 AMN315Method and Logic Meeting
  Thu Dec 0110:00 AMN315Method and Logic Meeting
  
  Course: GS-GS-527: ABC-Applications to Biology of Computation
Course Director(s): Lichtarge, Olivier \ Milosavljevic, Aleksandar
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Oct 119:00 AMN315Big Data GeneticsIntroduction to the ABC course and “Omic” biology - Epigenomics and genome biology.Milosavljevic, Aleksandar
  Wed Oct 125:15 PMN315TA #1Hardware and Contemporary Computing Infrastructure.
  Thu Oct 139:00 AMN315Network BiologyNetwork Biology - Inference and knowledge representation. This lecture will focus on (1) inference of pathways, networks, and network modules; (2) Interpretation of Big Data experiments using networks, pathways, and modules as background knowledge; (3) Computational representation of network and pathway knowledge.Milosavljevic, Aleksandar
  Fri Oct 145:15 PMN315TA #2A Beginner’s guide to UNIX / Linux and qsub commands.
  Tue Oct 189:00 AMN315Genome StructureVariation, evolution and cancer.Milosavljevic, Aleksandar
  Fri Oct 219:00 AMN315A Primer in Network Biology IElements in transcription networks, network motif and graph theory.Liu, Zhandong
  Tue Oct 259:00 AMN315A Primer in Network Biology IINetwork inference from genomics data.Liu, Zhandong
  Thu Oct 279:00 AMN315Computational Analysis of Networks and Pathways IIntroduction to computational methods to analyze biological information from networks.Liu, Zhandong
  Tue Nov 019:00 AMN315Computational Analysis of Networks and Pathways IIComputational methods to decode and to analyze biological information from networks - advanced topics.Liu, Zhandong
  Thu Nov 039:00 AMN315Recent Developments in Gene MappingFocused on gene mapping approach and current approach and challenges in functional annotation, interpretation and prioritization. It will review the basic disease models (common vs rare) and gene mapping frameworks (GWAS, Exome, CVAS vs RVAS). Guiding principles in functional prioritization and challenges going forward.Yu, Fuli
  Tue Nov 089:00 AMN315NGS Variation AnalysisFocused on the SNP calling algorithms in NGS datasets, for both personal genome (when N = 1) and population genomic studies (when N = many). It will serve as an introduction lecture and review the most popular SNP callers applied the NGS data analysis, including Samtools, GATK, and my own software (Atlas2 and SNPTools).Yu, Fuli
  Thu Nov 109:00 AMN315Cancer GenomicsApplication of NGS variation analysis onto tumor samples. How do tumor genomes differentiate from normal genomes? What have we learned from large- scale cancer genome sequencing such as TCGA, etc.?Chen, Ken
  Tue Nov 159:00 AMN315Cancer Genomic MedicinePractical challenges on implementing NGS-based tests in a cancer clinics. Why is it important(some case examples)? Progresses made so far. What are the missing pieces? Opportunities for biomedical computational science.Chen, Edward S
  Thu Nov 179:00 AMN315Sequence-Structure-Function IThis lecture will be an overview of common tools utilized in evolutionary analysis: BLAST, alignments, substitution matrices, and phylogenetic trees.Wilkins, Angela Dawn
  Mon Nov 219:00 AMN315Sequence-Structure-Function IIThis lecture will focus on tools that take advantage of evolutionary information in order identify function and functional sites.Wilkins, Angela Dawn
  Tue Nov 229:00 AMN315From Sequence to StructureA brief overview of the sequence-based tools and algorithms used to interpret protein structure and function. This lecture will also highlight current approaches in homology and template-free modeling.Baker, Matthew L
  Tue Nov 299:00 AMN315Macromolecular StructureThis lecture focuses on methods for interpreting and modeling macromolecular structure and function, as well as validation methods commonly used with these techniques. A particular emphasis will be on integrative or hybrid methods that combine multiple types of structure/functional data.Baker, Matthew L
  Thu Dec 019:00 AMN315Evolutionary AnalysisA formal approach to the genotype-phenotype relationship with molecular, clinical and population genetics applications.Lichtarge, Olivier
  Thu Dec 089:00 AMN315Final Exam9:00 AM - 12:00 PM
  
  
Term 3
  
  Course: GS-GS-509: Gene Regulation
Course Director(s): Cooper, Thomas
  DateStart TimeRoomLectureDescriptionLecturer
  Wed Jan 041:15 PMN315Introduction to Gene RegulationSites of Gene Regulation: transcription initiation, termination, alternative RNA splicing, 3' end processing, nuclear export, cytoplasmic mRNA stability, translational regulation, protein degradation. Analysis of gene expression.Cooper, Thomas
  Fri Jan 061:15 PMN315RNA PolymeraseThe 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.Herman, Christophe
  Mon Jan 091:15 PMN315Control of transcription in bacteriaDegradation and sequestration of initiation factors, riboswitches, noise in transcription and logic of transcriptional circuits.Herman, Christophe
  Wed Jan 111:15 PMN315Eukaryotic RNA polymerase and transcriptional initiationStructures and activities of the 3 eukaryotic RNA polymerases. Pathways for transcription initiation by RNA pol II holoenzyme plus general transcription factors.Foulds, Charles E
  Wed Jan 115:15 PMN315TA #1Overview of regulation of transcription and translation including review of overall process of transcription and translation, introduce reporter genes (rationale).
  Fri Jan 131:15 PMN315Modes of DNA binding and basic transcription factorsStructures 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.Foulds, Charles E
  Wed Jan 181:15 PMN315Coactivators and corepressorsIdentification of transcriptional coregulators and evolution of understanding of transcriptional activation. Enzymatic activities of coactivators and corepressors. Post-transcriptional modulation of coregulator function. Why are there so many coregulators?Foulds, Charles E
  Fri Jan 201:15 PMN315Chromatin 1 - LocalHistones, nucleosomes, covalent modification of histones, DNA accessibility, insulators, locus control regions, polytene/lapbrush chromosomes.Lonard, David
  Mon Jan 231:15 PMN315Chromatin 2 - GlobalChromatin subdomains, gene silencing, position effect variegation, epigenetic inheritance, X-inactivation, gene imprinting.Lonard, David
  Wed Jan 251:15 PMN315Chromatin - Relationship between DNA sequence genes, transcription and ChromatinEmerging 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, David
  Wed Jan 255:15 PMN315TA #2Review of assembly of transcription complex including order and identity of factor loading Identify major transcriptional activator families and mechanisms.
  Fri Jan 271:15 PMN315Regulation of RNA Polymerase II ElongationTranscriptional elongation. 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, Andrew Patrick
  Tue Jan 311:15 PMN315Nuclear export of RNANuclear 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 cell.Rice, Andrew Patrick
  Wed Feb 011:15 PMN315Splicing of Pre-mRNA(I)Overview of RNA chemistry (basis for lability and reactivity), overview of RNA structure, comparisons of intron/exon architecture, Autocatalytic RNA: The spliceosome; U12-dependent introns, domain structure of RNA binding proteins.Cooper, Thomas
  Thu Feb 021:15 PMN315Midterm Review
  Fri Feb 031:15 PMN315Midterm Exam
  Mon Feb 061:15 PMN315Splicing 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, Thomas
  Wed Feb 081:15 PMN3153’ end formation / Polyadenylation3' end formation of pol II genes, transcription termination; cotranscriptional 3’ end formation; relationship between 3' end formation and splicing, histone 3' end formation.Cooper, Thomas
  Wed Feb 085:15 PMN315TA #3Splicing and poyadenylation general overview; define mechanisms for alternative splice-site selection, intron vs exon selection.
  Fri Feb 101:15 PMN315Alternative splicingDrosophila 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, Thomas
  Mon Feb 131:15 PMN315Translational Regulation IReview 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, Richard E.
  Wed Feb 151:15 PMN315Translational Regulation II MechanismsmRNA-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, Richard E.
  Fri Feb 171:15 PMN315RNA(and DNA) EditingRNA editing, insertional/deletion editing (mitochondrial mRNA editing, contrast with trans-esterifiction, editsome complex, spliceosome), tRNA editing and codon recognition, ADAR activity and function, interplay with the microRNA pathway, AMPA receptor, cytosine deaminases.Neilson, Joel
  Tue Feb 211:15 PMN315Noncoding RNA FunctionBiogenesis and function of microRNAs. MicroRNA target prediction. RNAi. Modes of effecting RNAi in eukaryotic systems and forward genetic screens with shRNA libraries. LincRNAs and chromatin.Neilson, Joel
  Wed Feb 221:15 PMN315Posttranscriptional mRNA RegulationThe impact of turnover on steady state RNA levels e.g. histone gene expression during the cell cycle. Modes and mechanisms of RNA decay. Poly A shortening and 5' -> 3' degradation, P-bodies and mRNA decay. Non-polyA shortening mechanisms. Translation coupled mRNA degradation. Nonsense-mediated mRNA decay. Role of 3'UTR sequences in mRNA localization.Neilson, Joel
  Fri Feb 241:15 PMN315Regulation of Protein TurnoverUbiquitin-proteosome mediated degradation. Importance of regulation, protein motifs, PEST sequences, etc.Lloyd, Richard E.
  Fri Feb 245:15 PMN315TA #4RNA self-splicing overview, concept of regulating synthesis and degradation of mRNA, review of ribosome assembly and initiation and termination of translation.
  Thu Mar 021:15 PMN315Faculty Review
  Fri Mar 031:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-511: Neuroscience
Course Director(s): Jankowsky, Joanna Louisa
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Jan 032:30 PMN315Cellular and Structural NeuroanatomyMajor subdivisions of the mammalian brain, their general organization and the specialized cells required for function.Al-Ramahi, Ismael
  Thu Jan 052:30 PMN315Neuronal BiophysicsStructure and function of the major membrane proteins responsible for establishing ionic gradients in neurons and how they are used to transmit electrical information.Al-Ramahi, Ismael
  Thu Jan 055:15 PMN315TA #1
  Tue Jan 102:30 PMN315Synaptic PhysiologySpecialized structures and proteins that allow electrical signals to be converted to chemical messengers and then back again to facilitate cell-cell communicationAl-Ramahi, Ismael
  Thu Jan 122:30 PMN315Learning and MemoryMolecular and cellular requirements for storing new information and recalling it later.Al-Ramahi, Ismael
  Tue Jan 172:30 PMN315Neurobiology of DiseaseWhat happens when things go wrong in the brain.Al-Ramahi, Ismael
  Thu Jan 192:30 PMN315Faculty Review
  Tue Jan 241:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-512: Immunology
Course Director(s): Levitt, Jonathan Michael
  DateStart TimeRoomLectureDescriptionLecturer
  Thu Jan 262:30 PMN315Principles of immunityOverview of the immune system: innate vs. acquired immunity, cells of the immune system, clonal selection principle, strategies for “self-nonself/danger” discrimination.Levitt, Jonathan Michael
  Thu Feb 022:30 PMN315Innate ImmunityThe gateway to defense against the world around us: pattern recognition receptors, PAMPs/DAMPs, phagocytes and chemical mediators of immunity.Levitt, Jonathan Michael
  Fri Feb 035:15 PMN315TA #1Overview of response to pathogen: Anatomy and function of organs of lymphatic system: general overview of B and T cell development and function.
  Tue Feb 072:30 PMN315Antibody structure, antigen receptor diversity and B-cell developmentAntigens for B cells, Antibody receptor structure and genetics, Generation of diversity, Gene rearrangements and class switching.Decker, William K
  Thu Feb 092:30 PMN315B-cell activation, MHC and antigen presentationB cell development and selection. Self-nonself recognition, Tolerance, T cell antigen recognition, MHC structure and function. MHC antigen presentation and processing.Decker, William K
  Fri Feb 105:15 PMN315TA #2MHC 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.
  Tue Feb 142:30 PMN315Role and development of T lymphocytesTypes of T cells, T cell selection and central tolerance, education at thymic university, T cell activation and peripheral tolerance, signaling in T cells, anergy in T cells, apoptosis.Levitt, Jonathan Michael
  Thu Feb 162:30 PMN315T cell development and signaling: consequences for transplantation and tumorsT cell effector functions, transplantation, autoimmunity, vaccines, tumor immunology.Levitt, Jonathan Michael
  Thu Feb 232:30 PMN315Faculty Review
  Mon Feb 271:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-516: Ethics - Year 3
Course Director(s): Bertuch, Alison Ann
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Jan 039:00 AMN315(3L1) Authorship/Peer Review - NIH a) Other Conflicts of InterestOrganizing your paper, preparing manuscripts, who should be an author, responsibilities of an author, manuscript review systems, responsibilities of a reviewer, dealing with criticism - (NIH a) Other Conflicts of Interest - conflicts of interest in the peer review process, financial and professional conflicts and their management.Smith, Carolyn L
  Tue Jan 109:00 AMN315(3L2) Collaborative research including collaborations with industryThe values/responsibilities of collaboration, establishing collaborative relationships, grants, contracts, intellectual property considerations, impact of industry collaborations on publication, thesis submission.Zechiedrich, E. Lynn
  Tue Jan 179:00 AMN315(3M) MentorshipMeeting with 3rd year students and their mentors, matching expectations between mentor student, developing communication channels, assessing your progress, risky experiments and backup projects, the thesis committee as a resource.Bertuch, Alison Ann
  Tue Jan 249:00 AMN315(3C) Case Studies Peer Review/CollaborationPeer review of grants and papers, conflicts of interest, collaboration (small group discussion format with faculty facilitator).
  Tue Jan 319:00 AMN315(3L5) Rigor and ReproducibilityThe scientific method, blinding and randomization, technical vs. biological replicates, authentication of key biological and/or chemical resources, transparency.Bertuch, Alison Ann
  
  Course: GS-GS-517: Ethics - Year 4
Course Director(s): Bertuch, Alison Ann
  DateStart TimeRoomLectureDescriptionLecturer
  Thu Jan 269:00 AMN315(4M) MentorshipMeeting with 4nd year students and their mentors, matching expectations between mentor student, maintaining communication channels, timeline for graduation, backup projects, the thesis committee as a resource, career decisions, the next step.Bertuch, Alison Ann
  Thu Feb 029:00 AMN315(4L1) Research with Human SubjectsDefinition of research with human subjects, experiments with human material, confidentiality of medical data, experiments involving humans, informed consent.Berg, Stacey L
  Thu Feb 099:00 AMN315(4L5) Rigor and ReproducibilityThe scientific method, blinding and randomization, technical vs. biological replicates, authentication of key biological and/or chemical resources, transparency.Bertuch, Alison Ann
  Thu Feb 169:00 AMN315(4L2) The scientist as a responsible member of societyContemporary ethical issues in biomedical research and the environmental and societal impacts of scientific research.Mcguire, Amy Lynn
  Thu Feb 239:00 AMN315(4C) Case Studies Human Research/Science and SocietyResearch with human subjects, societal impact of research (genetics/genomics, stem cells, neuroethics) (small group discussion format with faculty facilitator.
  
  Course: GS-GS-518: Macromolecules: Structure and Interactions
Course Director(s): Pedersen, Steen E \ Prasad, B V Venkatar
  DateStart TimeRoomLectureDescriptionLecturer
  Wed Jan 042:30 PMN315IntroductionRelationship of known structural principles, structural determination, principles of interaction, thermodynamics, dynamics, and signal transduction based on binding and dynamics.Pedersen, Steen E
  Fri Jan 062:30 PMN315Protein Structure and FoldingProtein structure elements: from building blocks to quaternary structure; protein topology; "Form follows function; protein taxonomy. Protein folding (Anfinsen theorem); energy landscapes; molecular chaperones; and protein misfolding diseases. Zhou, Ming
  Fri Jan 065:15 PMN315TA #1
  Mon Jan 092:30 PMN315Lipid/Membrane StructureLipid classification; micelles and bilayers; membrane structures; membrane proteins; mitochondria.Zhou, Ming
  Wed Jan 112:30 PMN315DNA StructureA-, B- and Z- DNA structure; building blocks; DNA topology; from DNA to RNA.Zhou, Ming
  Thu Jan 125:15 PMN315TA #2
  Fri Jan 132:30 PMN315X-ray - 1Scattering, (diffraction)-based technique, diffraction theory. Reading and interpreting X-ray structure papers.Zhou, Ming
  Wed Jan 182:30 PMN315Cryo EMCryo-electron tomography.Schmid, Michael F
  Thu Jan 195:15 PMN315TA #3
  Fri Jan 202:30 PMN315NMRBasic theory and instrumentation, NOESY, COSY methods, distance geometry, multi-dimensional NMR, sample requirements.
  Mon Jan 232:30 PMN315Fluorescence/optical spectroscopyPrinciples of photon absorption and emission, fluorescence energy transfer, anisotropy, lifetime instrumentation, optics. CD/IR.Schmid, Michael F
  Wed Jan 252:30 PMN315Protein – post-translational modificationsCommon reversible and irreversible post-translational modifications: regulation and roles in protein function.Weigel, Nancy L
  Thu Jan 265:15 PMN315TA #4
  Fri Jan 272:30 PMN315Midterm Review
  Mon Jan 301:15 PMN315Midterm Exam1:00 PM - 4:00 PM
  Tue Jan 312:30 PMN315Ligand Binding & Forces in Solution/ThermodynamicsGeneral Principles of ligand binding formalism, mass action, and basic energetics. Basic forces in solution. What holds structures together? Thermodynamics of binding and how this relates to basic forces.Pedersen, Steen E
  Wed Feb 012:30 PMN315Allostery 1Ligand binding and how it alters protein structure and dynamics; allostery and how it mediates and regulates protein function.Pedersen, Steen E
  Thu Feb 025:15 PMN315TA #5
  Mon Feb 062:30 PMN315Allostery and CooperativityHow protein structural changes mediate cooperative effects in enzymes and binding proteins.Pedersen, Steen E
  Wed Feb 082:30 PMN315Binding KineticsBasic kinetics of unimolecular and bimolecular reactions. Introduction to enzyme kinetics.Pedersen, Steen E
  Thu Feb 095:15 PMN315TA #6
  Fri Feb 102:30 PMN315Enzyme Kinetics/CatalysisMichaelis-Menten kinetics, Inhibition, kcat and kcat/Km, allosteric enzymes. Computational kinetics.Pedersen, Steen E
  Mon Feb 132:30 PMN315Mechanisms of CatalysisAcid base catalysis, covalent catalysis, stabilization of transition states, transition state analogs, coenzymes, suicide inhibitors.Pedersen, Steen E
  Wed Feb 152:30 PMN315Single Molecule MethodsMacromolecular motors, single molecule kinetics, examples.Pedersen, Steen E
  Thu Feb 165:15 PMN315TA #7
  Fri Feb 172:30 PMN315Protein – Small Molecule InteractionsMolecular basis of specificity, protein ligand interactions - structural basis of H-bonding, salt bridges and other interactions.Prasad, B V Venkatar
  Tue Feb 212:30 PMN315Protein – Protein InteractionsStructural motifs that serve as protein-protein interaction domains, structural basis of surface complementarity, engineering tight binding.Prasad, B V Venkatar
  Wed Feb 222:30 PMN315Protein/DNA InteractionsDNA binding motifs, structural basis of base recognition, backbone interactions.Prasad, B V Venkatar
  Thu Feb 235:15 PMN315TA #8
  Fri Feb 242:30 PMN315Systems BiologySome principles and examples from systems biology approaches to understanding signaling in regulatory networks.Pedersen, Steen E
  Tue Feb 281:15 PMN315Faculty Review
  Wed Mar 011:15 PMN315Final Exam1:00 PM - 4:00 PM

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