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Course Curriculum Syllabus

2017-2018


  
Term 1
  
  Course: GS-GS-501: Organization of the Cell
Course Director(s): Bissig, Karl-Dimiter \ Sifers, Richard N
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Jul 312:30 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 022:30 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 035:15 PMN315TA #1Review of general cell structures, their function and generation. Concepts of vesicular transport and protein import and export for the organelles.
  Fri Aug 042:30 PMN315Mitochondria and PeroxisomesStructure and biogenesis of mitochondria and peroxisomes. Protein import into these organelles.Sifers, Richard N
  Mon Aug 072:30 PMN315The Endoplasmic ReticulumQuality control checkpoint and mother of the endomembrane system.Sifers, Richard N
  Wed Aug 092:30 PMN315The Golgi ComplexRegulated vesicular trafficking in the endomembrane system.Sifers, Richard N
  Thu Aug 105:15 PMN315TA #2Review of additional protein trafficking schemes.
  Fri Aug 112:30 PMN315Vesicular Transport in ReverseThe plasma membrane-endosome-lysosome connection.Sifers, Richard N
  Mon Aug 142:30 PMN315Apoptosis - Programmed Cell DeathApoptosis versus necrosis, mechanisms of programmed cell death, regulators of apoptosis.Sifers, Richard N
  Wed Aug 162:30 PMN315Midterm Review
  Thu Aug 175:15 PMN315TA #3
  Fri Aug 181:15 PMN315Midterm Exam
  Mon Aug 212:30 PMN315Diseases of Altered Proteostasis IGeneral aspects of proteostasis, diseases of proteostasis Bissig, Karl-Dimiter
  Wed Aug 232:30 PMN315Alterations of Proteostasis IIGenome engineering and macromolecular therapies for altering proteostasis Bissig, Karl-Dimiter
  Thu Aug 245:15 PMN315TA #4
  Fri Aug 252:30 PMN315Cytoskeleton IActin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility.Sokac, Anna Marie
  Wed Sep 062:30 PMN315Cytoskeleton IIActin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility.Sokac, Anna Marie
  Thu Sep 075:15 PMN315TA #5
  Fri Sep 082:30 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
  Mon Sep 111:15 PMN315Growth Factors/Tyrosine Kinase SignalingLecture runs 1:30-2:30 pm. 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, Theodore G
  Wed Sep 132:30 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
  Thu Sep 145:15 PMN315TA #6
  Fri Sep 152:30 PMN315Faculty Exam Review
  Mon Sep 181:15 PMN315Final Exam1:00 - 4:00 PM
  
  Course: GS-GS-502: Molecular Methods
Course Director(s): Weigel, Nancy L
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Jul 311:15 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.
  Wed Aug 021:15 PMN315DNA Cloning IApplications of cloning, vectors, transformation methods, plasmid purification systems, traditional cloning methods, cloning diagnosis.Venken, Koen J. T.
  Fri Aug 041:15 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.
  Mon Aug 071:15 PMN315Flow CytometryIntroduction to the technique of flow cytometry and cell sorting, detecting fluorescent cells through expressed antigens and endogenous fluorescent molecules.Sederstrom, Joel
  Tue Aug 085:15 PMN315TA #1Lectures 1-3.
  Wed Aug 091:15 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
  Fri Aug 111:15 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 141:15 PMN315First-Generation Sequencing and GenotypingIntroduction to Maxam-Gilbert, Sanger and automated Sanger sequencing; microarrays, high-throughput genotyping assays.Metzker, Michael Lee
  Wed Aug 161:15 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 detectionMetzker, Michael Lee
  Wed Aug 165:15 PMN315TA #2Lectures 6-8.
  Mon Aug 211:15 PMN315CRISPR/Cas9Guide selection; Cas9 nickase; reagent production for in vitro and in vivo applications; nonhomologous end joining, homology directed repair, and homologous recombination; on target and off target screening; emerging applications.Heaney, Jason D
  Wed Aug 231:15 PMN315Single cell genomics: method and applicationsSingle cell DNA and RNA-Seq: platforms and applicationsChen, Rui
  Wed Aug 235:15 PMN315TA #3Lectures 4, 5, 9.
  Fri Aug 251:15 PMN315Midterm Review
  Tue Sep 052:30 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 061:15 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 065:15 PMN315TA #4Chen, Lydon first lecture (Sharpe TA).
  Fri Sep 081:15 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
  Sat Sep 099:00 AMN315Midterm Exam9 am - 12 pm
  Mon Sep 112:30 PMN315Protein PurificationLecture time 2:45-3:45 Cell 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
  Tue Sep 125:15 PMN315TA #5York first and second lectures (Burger TA).
  Wed Sep 131:15 PMN315RNA Interference and Genetic screensRNA interference (RNAi) mechanisms, RNAi tools, genetic screening methods, technical considerations in using RNAi.Westbrook, Thomas
  Fri Sep 151:15 PMN315Proteomics Mass Spectrometry - Basic PrinciplesMass spectrometer instruments and analytical methods; principles of identification for peptides and post-translational modifications (PTMs); data processing.Malovannaya, Anna
  Wed Sep 201:15 PMN315Proteomics Mass Spectrometry - Applications in BiologyMS-based quantification, global proteome profiling, PTM profiling, protein-protein interaction networks from IP/MS.Malovannaya, Anna
  Wed Sep 205:15 PMN315TA #6Westbrook and Malovannaya (Bowling TA).
  Fri Sep 221:15 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
  Fri Sep 225:15 PMN315TA #7Lydon second and third lectures (Sharpe TA).
  Wed Sep 271:15 PMN315Faculty Review
  Fri Sep 291:15 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
  Wed Aug 029:00 AMN315(1M) The Mentor/Mentee RelationshipSelecting a lab and developing a group of mentors, what to look for in the mentor/mentee relationship, keeping on track toward your degree.Bertuch, Alison Ann
  Wed Aug 099:00 AMN315(1L8) Setting Goals for Your Scientific Development and Coping with Academic 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, where to get help and information, thinking now about the next step.Smith, Carolyn L
  Wed Aug 169:00 AMN315(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
  Wed Aug 239:00 AMN315(1L2) Responsible Authorship and PublicationGiving credit when credit is due, when to cite or not, how to use direct quotes, paraphrasing, plagiarism, copyright and copyright permission.Smith, Carolyn L
  Wed Sep 209:00 AMN315(1L9) Conflict ResolutionPotential causes of conflict during graduate training, approaches to conflict resolutionHyle, Laurel
  
  Course: GS-GS-503: Genetics A
Course Director(s): Herman, Christophe \ Dierick, Herman A.
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Aug 011:15 PMN315Mendelian GeneticsGene nomenclature: gene/allele/genotype/phenotype. Dominant v. recessive mutations. Mendel's laws. Penetrance v. expressivity.Dierick, Herman A.
  Thu Aug 031:15 PMN315Cellular Mechanisms of Mendelian Genetics and LinkageMeiosis v. mitosis. Linkage. Two-point and three-point mapping. Complementation.Dierick, Herman A.
  Tue Aug 081:15 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 101:15 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 145:15 PMN315TA #1General Genetic Principles
  Tue Aug 151:15 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 171:15 PMN315Selecting and Identifying MutantsIdentifying mutated genes. Selection and screening strategies, reporter genes and secondary screens.Bates, David B.
  Tue Aug 221:15 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 241:15 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 242:30 PMN315Midterm Review
  Fri Aug 255:15 PMN315TA #2Phenotype, pathway analysis and genetics screens.
  Tue Sep 051:15 PMN315Bacterial Genetics IGenetic transmission: haploid and circular genomes, P1-transduction, F-factors, HFRs, conjugation.Rosenberg, Susan M
  Thu Sep 071:15 PMN315Bacterial Genetics IIRecombination.Rosenberg, Susan M
  Fri Sep 089:00 AMN315Midterm Exam1:00 PM - 4:00 PM
  Tue Sep 121:15 PMN315Bacterial Genetics IIISOS response, transpositionRosenberg, Susan M
  Wed Sep 139:00 AMN315Viral/Phage GeneticsVirus cycle, complementation group.Herman, Christophe
  Thu Sep 141:15 PMN315Genetic Engineering IArtificial chromosomes, recombineering in bacteria, homing endonucleases (I-SceI), seamless versus remnant engineering.Venken, Koen J. T.
  Mon Sep 185:15 PMN315TA #3Bacterial Genetics.
  Tue Sep 191:15 PMN315Genetic Engineering IIIntegrases, Zn finger technology, TALE technology, Crispr/Cas technology.Venken, Koen J. T.
  Thu Sep 211:15 PMN315Faculty Review
  Thu Sep 215:15 PMN315TA #4Genetic Engineering.
  Mon Sep 251:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  
Term 2
  
  Course: GS-GS-504: Genetics B
Course Director(s): Zhou, Zheng
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Oct 101:15 PMN315IntroductionForward and reverse genetics. Strengths of model systems. Nomenclature. The concept of maternal effect.Zhou, Zheng
  Thu Oct 121:15 PMN315C. elegans IAdvantages and special considerations of hermaphrodite genetics. How to construct strains, strategies of genetic screens, cloning genes, balancers.Zhou, Zheng
  Tue Oct 171:15 PMN315C. elegans IIC. elegans transformation. Impact of the C. elegans genome project. Reverse genetics using RNA interference and gene deletions. CRISPR gene editing.Zhou, Zheng
  Wed Oct 185:15 PMN315TA #1
  Thu Oct 191:15 PMN315Yeast IBasic molecular manipulations in reverse genetics: cloning by complementation, plasmid gap repair, gene disruption/replacement, plasmid shuffle.Ira, Grzegorz
  Tue Oct 241:15 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
  Wed Oct 255:15 PMN315TA #2
  Tue Oct 311:15 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
  Thu Nov 021:15 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 022:30 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 035:15 PMN315TA #3
  Mon Nov 065:00 PMN315Midterm Faculty Review
  Tue Nov 071:15 PMN315Midterm Exam1:00 PM - 4:00 PM
  Thu Nov 091:15 PMN315Mouse Genetics IInbred mice. Microsatellite markers. Mapping genes in mice using crosses.Matzuk, Martin Matthew
  Thu Nov 161:15 PMN315Mouse Genetics IIInsertion of DNA and retrotransposons. Knock-outs and ins. Conditional knock-outs.Matzuk, Martin Matthew
  Mon Nov 201:15 PMN315Human Genetics IDisease loci and pedigrees.Lupski, James R
  Mon Nov 205:15 PMN315TA #4
  Tue Nov 281:15 PMN315Human Genetics IIMapping with DNA markers. Sources of polymorphisms. Simple vs. complex traits. Genome scans for quantitative trait loci.Lupski, James R
  Thu Nov 301:15 PMN315Human Genetics IIIEffect of imprinting on pedigrees. Models for specific mechanisms of imprinting. Model for evolutionary significance.Lupski, James R
  Fri Dec 015:15 PMN315TA #5
  Wed Dec 061:15 PMN315Faculty Review
  Fri Dec 081:15 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 091:15 PMN315Course Introduction/Cell Cycle OverviewDiscovery of cell cycle regulation--Cell cycle stages, mitosis and meiosis, discovery of CDK/cyclin/MPF.Dang, Weiwei
  Wed Oct 111:15 PMN315Principles of Cell Cycle Regulation ICDKs, cyclins, CKIs, and proteolysis.Dang, Weiwei
  Fri Oct 131:15 PMN315Principles of Cell Cycle Regulation IICell cycle transitions, G1/S and G2M.Dang, Weiwei
  Mon Oct 161:15 PMN315S Phase: DNA ReplicationMechanism and cell cycle regulation of DNA replication.Ira, Grzegorz
  Tue Oct 175:15 PMN315TA #1Review of cell cycle basics and S phase.
  Wed Oct 181:15 PMN315DNA Damage and RepairOverview of DNA damage and repair. Base excision repair, nucleotide excision repair, mismatch repair, damage tolerance pathway.Ira, Grzegorz
  Fri Oct 201:15 PMN315Repair of DNA BreaksMechanism and cell cycle regulation of DNA breaks repair.Ira, Grzegorz
  Mon Oct 231:15 PMN315Cell Cycle CheckpointsIntroduction to cell cycle checkpoints, the DNA damage checkpoint.Lin, Weei-Chin
  Mon Oct 235:15 PMN315TA #2Review of DNA recombination and repair.
  Tue Oct 242:30 PMN315Faculty Review MidtermLectures 1-7.
  Wed Oct 251:15 PMN315Midterm ExamLectures 1-7. N315 1:00 - 4:00 pm.
  Fri Oct 271:15 PMN315Chromosome Nuclear Organization3D chromosome organization and folding.Lin, Charles
  Mon Oct 301:15 PMN315Chromosome DuplicationChromatin duplication and M phase chromosomes organization.Lin, Charles
  Tue Oct 315:15 PMN315TA #3Review of chromosome organization and duplication.
  Fri Nov 031:15 PMN315TelomeresStructure and synthesis. Telomere dysfunction-induced DNA damage checkpoint response. Crisis and survival in the absence of telomerase.Bertuch, Alison Ann
  Mon Nov 061:15 PMN315M Phase SpindleMechanisms of spindle formation and function, kinetochore/spindle attachment.Chang, Eric C
  Tue Nov 075:15 PMN315TA #4Review of telomeres and spindle.
  Wed Nov 081:15 PMN315CytokinesisCytokinesis mechanisms.Sokac, Anna Marie
  Fri Nov 101:15 PMN315Cell Cycle and Gene ExpressionRNA regulation in the cell cycle.Cheng, Chonghui
  Tue Nov 142:30 PMN315Faculty ReviewLecture 8-13.
  Tue Nov 145:15 PMN315TA #5Review of cytokinesis, cell cycle and gene expression.
  Wed Nov 151:15 PMN315Final ExamLectures 8-13. 1:00 PM - 4:00 PM
  
  Course: GS-GS-508: Cancer
Course Director(s): Pangas, Stephanie A
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Nov 131:15 PMN315IntroductionCourse introduction to cancerPangas, Stephanie A
  Fri Nov 171:15 PMN315MetastasisCurrent concepts in cancer metastasisZhang, Xiang
  Mon Nov 202:30 PMN315Oncogenes and Tumor SuppressorsBasic concepts of oncogenes and tumor suppressor genesPangas, Stephanie A
  Mon Nov 271:15 PMN315Tumor Cell - Stromal InteractionsInteraction of stromal cells with tumor cells in cancer progressionChen, Xi
  Wed Nov 291:15 PMN315Mouse Models of CancerIntroduction to methods for generation and analysis of mouse genetic modelsHeaney, Jason D
  Fri Dec 011:15 PMN315Cancer Stem CellsDefinition and function of cancer stem cells in cancer biologyChan, Keith
  Mon Dec 041:15 PMN315Faculty Review
  Tue Dec 051:15 PMN315CA Final Exam1:00-4:00
  
  Course: GS-GS-523: Method and Logic in Molecular Biology
Course Director(s): Mardon, Graeme \ Shroyer, Noah Freeman
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Oct 099:00 AM201AMethod 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 9:00 and ends promptly at 10:00.
  Tue Oct 1710:00 AMmultipleMethod 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.
  Thu Oct 1910:00 AMmultipleMethod and Logic Meeting
  Tue Oct 2410:00 AMmultipleMethod and Logic Meeting
  Fri Oct 273:30 PMmultipleMethod and Logic Meeting
  Tue Oct 3110:00 AMmultipleMethod and Logic Meeting
  Thu Nov 0210:00 AMmultipleMethod and Logic Meeting
  Tue Nov 0710:00 AMmultipleMethod and Logic Meeting
  Thu Nov 0910:00 AMmultipleMethod and Logic Meeting
  Tue Nov 1410:00 AMmultipleMethod and Logic Meeting
  Thu Nov 1610:00 AMmultipleMethod and Logic Meeting
  Tue Nov 2810:00 AMmultipleMethod and Logic Meeting
  Thu Nov 3010:00 AMmultipleMethod and Logic Meeting
  
  Course: GS-GS-506: Development
Course Director(s): Groves, Andrew Kelton
  DateStart TimeRoomLectureDescriptionLecturer
  Mon Oct 092:30 PMN315Core Concepts in Developmental BiologyIntroduction to class.Groves, Andrew Kelton
  Wed Oct 112:30 PMN315Setting up the vertebrate body plan IAxis determination and gastrulation.Groves, Andrew Kelton
  Mon Oct 162:30 PMN315Setting up the vertebrate body plan IIMammalian development and embryonic stem cells.Groves, Andrew Kelton
  Tue Oct 172:30 PMN315Setting up the vertebrate body plan IIIPatterning the embryo from head to tail.Groves, Andrew Kelton
  Wed Oct 182:30 PMN315ES cells, pluripotency and reprogramming / iPSBiology and epigenetics of embryonic stem cells.Groves, Andrew Kelton
  Fri Oct 202:30 PMN315Introduction to Drosophila embryogenesisOverview of Drosophila oogenesis and embryogenesis.Jafar-Nejad, Hamed
  Fri Oct 205:15 PMN315TA #1Review of Lectures 1-5.
  Mon Oct 232:30 PMN315Embryonic patterning in Drosophila - IMaternal-effect genes and the establishment of the anteroposterior axis (1).Jafar-Nejad, Hamed
  Fri Oct 272:30 PMN315Embryonic patterning in Drosophila IIMaternal-effect genes and the establishment of the anteroposterior axis (2).Jafar-Nejad, Hamed
  Fri Oct 275:15 PMN315TA #2Review of Lectures 6-8.
  Mon Oct 302:30 PMN315Faculty Midterm Review
  Wed Nov 011:15 PMN315Midterm Exam1:00 PM - 4:00 PM
  Fri Nov 032:30 PMN315Evolutionary Conservation of Developmental Principles Parchem, Ronald J.
  Mon Nov 062:30 PMN315Vertebrate neural development IDevelopmental anatomy of the nervous system. Molecular aspects of neural induction, formation of the neural plate and neurogenesis.Deneen, Benjamin
  Wed Nov 082:30 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
  Fri Nov 102:30 PMN315Limb developmentA model system to illustrate developmental concepts.Groves, Andrew Kelton
  Fri Nov 105:15 PMN315TA #3Review of Lectures 9-12.
  Mon Nov 132:30 PMN315Stem cells in the adultOverview of the biology of stem cells in adult mammals.Nakada, Daisuke
  Thu Nov 162:30 PMN315Development and diseaseParchem, Ronald J.
  Thu Nov 165:15 PMN315TA #4Review of Lectures 13-14.
  Fri Nov 172:30 PMN315Faculty Final Exam Review
  Tue Nov 211:15 PMN315 Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-527: ABC-Applications to Biology of Computation
Course Director(s): Lichtarge, Olivier \ Wilkins, Angela Dawn
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Oct 109:00 AMN315Deep Learning and NeuroscienceIntroduction to the ABC course and deep learning in neuroscience.Tolias, Andreas Savas
  Wed Oct 115:15 PMN315TA #1A Beginner’s guide to UNIX / Linux and qsub commands.
  Thu Oct 129:00 AMN315A Primer in Network Biology IElements in transcription networks, network motif and graph theory.Liu, Zhandong
  Tue Oct 179:00 AMN315A Primer in Network Biology INetwork inference from genomics data.Liu, Zhandong
  Thu Oct 199:00 AMN315Computational Analysis of Networks and Pathways Introduction to computational methods to analyze biological information from networks.Liu, Zhandong
  Tue Oct 249:00 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
  Fri Oct 279:00 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
  Tue Oct 319:00 AMN315Principles of Genome Organization and Gene Regulation This lecture will delve into organizing principles of the human genome. Where are the genes? Are there variations in gene length, GC content, and density? How do non-coding repetitive elements help shape patterns of gene regulation?Lin, Charles
  Thu Nov 029:00 AMN315RNA Structure and FunctionRNA is commonly thought of as simply the “messenger” from gene to protein. Here we will explore RNA structure and function as a nucleic acid. We will explore computational approaches to map secondary structure and learn how evolutionary conservation of structure can give insights into RNA function.Lin, Charles
  Tue Nov 079:00 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
  Thu Nov 099:00 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
  Tue Nov 149:00 AMN315Big Data GeneticsIntroduction to “Omic” biology - Epigenomics and genome biology.Milosavljevic, Aleksandar
  Thu Nov 169:00 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 209:00 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 219:00 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 289:00 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 Nov 309:00 AMN315Evolutionary AnalysisA formal approach to the genotype-phenotype relationship with molecular, clinical and population genetics applications.Lichtarge, Olivier
  Thu Dec 079:00 AMN315Final Exam9:00 AM - 12:00 PM
  
  Course: GS-GS-529: Responsible Conduct of Research - Year 2
Course Director(s): Bertuch, Alison Ann
  DateStart TimeRoomLectureDescriptionLecturer
  Wed Oct 119:00 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 LaboratoryNelson, David L
  Wed Oct 189:00 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.Pereira, Frederick A
  Wed Oct 259:00 AMN315(2C) Case Studies - Scientific Misconduct/AnimalsScientific misconduct and experiments with animals (small group discussion format with faculty facilitator).
  Wed Nov 019:00 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 resourceBertuch, Alison Ann
  Wed Nov 089:00 AMN315(2L3) Conflict ResolutionHyle, Laurel
  
  
Term 3
  
  Course: GS-GS-517: Ethics - Year 4
Course Director(s): Bertuch, Alison Ann
  DateStart TimeRoomLectureDescriptionLecturer
  Thu Jan 259:00 AMN315(4L2 The scientist as a responsible member of society.Contemporary ethical issues in biomedical research and the environmental and societal impacts of scientific research
  Thu Feb 019:00 AMN315(4L1) Research with Human SubjectsDefinition of research with human subjects, experiments with human material, confidentiality of medical data, experiments involving humans, informed consent.
  Thu Feb 089:00 AMN315(4L5) Rigor and ReproducibilityThe scientific method, blinding and randomization, technical vs. biological replicates, authentication of key biological and/or chemical resources, transparency.
  Wed Feb 149:00 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
  Thu Feb 229:00 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.
  
  Course: GS-GS-509: Gene Regulation
Course Director(s): Cooper, Thomas
  DateStart TimeRoomLectureDescriptionLecturer
  Wed Jan 031:15 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 051:15 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 081:15 PMN315Control of Transcription in BacteriaDegradation and sequestration of initiation factors, riboswitches, noise in transcription and logic of transcriptional circuits.Herman, Christophe
  Wed Jan 101:15 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
  Fri Jan 121:15 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 171:15 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
  Wed Jan 175:15 PMN315TA #1Overview of regulation of transcription and translation including review of the overall process of transcription and translation. Introduce reporter genes (rationale).
  Fri Jan 191:15 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.Foulds, Charles E
  Mon Jan 221:15 PMN315Chromatin 1 - LocalHistones, nucleosomes, covalent modification of histones, DNA accessibility, insulators, locus control regions, polytene/lapbrush chromosomes.Lonard, David
  Wed Jan 241:15 PMN315Chromatin 2 - GlobalChromatin subdomains, gene silencing, position effect variegation, epigenetic inheritance, X-inactivation, gene imprinting.Lonard, David
  Fri Jan 261:15 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
  Fri Jan 265:15 PMN315TA #2Review of the assembly of transcription complex including order and identity of factor loading. Identify major transcriptional activator families and mechanisms.
  Tue Jan 301:15 PMN315Midterm Faculty Review
  Wed Jan 311:15 PMN315Midterm Exam
  Thu Feb 011:15 PMN315Splicing of Pre-mRNA (I)Overview of RNA chemistry (basis for lability and reactivity) and RNA structure. Comparisons of intron/exon architecture, Autocatalytic RNA. The spliceosome. U12-dependent introns. Domain structure of RNA binding proteins.Cooper, Thomas
  Fri Feb 021:15 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
  Mon Feb 051:15 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 071:15 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
  Fri Feb 091:15 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.Neilson, Joel
  Mon Feb 121:15 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
  Mon Feb 125:15 PMN315TA #3Splicing and poyadenylation general overview; define mechanisms for alternative splice-site selection, intron vs exon selection.
  Wed Feb 141:15 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
  Fri Feb 161:15 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 201:15 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.Costa-Mattioli, Mauro
  Wed Feb 211:15 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.Costa-Mattioli, Mauro
  Fri Feb 231:15 PMN315Regulation of Protein TurnoverUbiquitin-proteosome mediated degradation. Importance of regulation, protein motifs, PEST sequences, etc.Costa-Mattioli, Mauro
  Fri Feb 235:15 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 011:15 PMN315Faculty Review
  Fri Mar 021:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-511: Neuroscience
Course Director(s): Ray, Russell Scott
  DateStart TimeRoomLectureDescriptionLecturer
  Tue Jan 022:30 PMN315Cellular and Structural NeuroanatomyMajor subdivisions of the mammalian brain, their general organization and the specialized cells required for function.
  Thu Jan 042:30 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.
  Tue Jan 092:30 PMN315Learning and MemoryMolecular and cellular requirements for storing new information and recalling it later.
  Thu Jan 112:30 PMN315Synaptic PhysiologySpecialized structures and proteins that allow electrical signals to be converted to chemical messengers and then back again to facilitate cell-cell communication.
  Tue Jan 162:30 PMN315Learning and MemoryMolecular and cellular requirements for storing new information and recalling it later.
  Thu Jan 182:30 PMN315Faculty Review
  Tue Jan 231:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-518: Macromolecules: Structure and Interactions
Course Director(s): Prasad, B V Venkatar \ Zhou, Ming
  DateStart TimeRoomLectureDescriptionLecturer
  Wed Jan 032:30 PMN315IntroductionRelationship of known structural principles; structural determination; principles of interaction; thermodynamics; and signal transduction based on binding and dynamics.
  Fri Jan 052:30 PMN315Protein Structure and FoldingProtein structure elements: from building blocks to quaternary structure; protein topology; "form follows function"; and protein taxonomy. Protein folding (Anfinsen theorem); energy landscapes; molecular chaperones; and protein misfolding diseases. Zhou, Ming
  Fri Jan 055:15 PMN315TA #1
  Mon Jan 082:30 PMN315Lipid/Membrane StructureLipid classification; micelles and bilayers; membrane structures; membrane proteins.Zhou, Ming
  Wed Jan 102:30 PMN315DNA StructureA-, B- and Z- DNA structure; building blocks; DNA topology; from DNA to RNA.Zhou, Ming
  Thu Jan 115:15 PMN315TA #2
  Fri Jan 122:30 PMN315X-ray - 1Scattering, (diffraction)-based technique, diffraction theory. Reading and interpreting X-ray structure papers.Zhou, Ming
  Wed Jan 172:30 PMN3153D-Cryo EMCryo-electron microscopy: single particle analysis, reconstruction, and tomography.
  Thu Jan 185:15 PMN315TA #3
  Fri Jan 192:30 PMN315NMRMeasurement of interactions with NMR. Basic theory and instrumentation, NOESY, COSY methods, distance geometry, multi-dimensional NMR, sample requirements.
  Mon Jan 222:30 PMN315Fluorescence SpectroscopyPrinciples of photon absorption and emission, fluorescence energy transfer, anisotropy, lifetime instrumentation, optics.
  Wed Jan 242:30 PMN315Protein – Post-translational ModificationsCommon reversible and irreversible post-translational modifications: regulation and roles in protein function.Weigel, Nancy L
  Thu Jan 255:15 PMN315TA #4
  Fri Jan 262:30 PMN315Midterm Faculty Review
  Mon Jan 291:15 PMN315Midterm Exam1:00 PM - 4:00 PM
  Tue Jan 302:30 PMN315Ligand Binding and Forces in Solution/ThermodynamicsGeneral Principles of ligand binding: formalism, mass action, and basic energetics. Methods for measuring binding. Basic forces in solution; what holds structures together?
  Fri Feb 022:30 PMN315Allostery 1Ligand binding and how it alters protein structure and dynamics; allostery and how it mediates and regulates protein function.
  Fri Feb 025:15 PMN315TA #5
  Mon Feb 052:30 PMN315Allostery and CooperativityHow protein structural changes mediate cooperative effects in enzymes and binding proteins.
  Wed Feb 072:30 PMN315Binding KineticsBasic kinetics of unimolecular and bimolecular reactions. Introduction to enzyme kinetics.
  Wed Feb 075:15 PMN315TA #6
  Fri Feb 092:30 PMN315Enzyme Kinetics/CatalysisMichaelis-Menten kinetics, Inhibition, kcat and kcat/Km, allosteric enzymes. Computational kinetics.
  Mon Feb 122:30 PMN315Mechanisms of CatalysisAcid base catalysis, covalent catalysis, stabilization of transition states, transition state analogs, coenzymes, suicide inhibitors.
  Wed Feb 142:30 PMN315Single Molecule MethodsMacromolecular motors, single molecule kinetics, examples.
  Thu Feb 155:15 PMN315TA #7
  Fri Feb 162:30 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 202:30 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 212:30 PMN315Protein – DNA InteractionsDNA binding motifs, structural basis of base recognition, backbone interactions.Prasad, B V Venkatar
  Thu Feb 225:15 PMN315TA #8
  Fri Feb 232:30 PMN315Systems BiologySome principles and examples from systems biology approaches to understanding signaling in regulatory networks.
  Tue Feb 271:15 PMN315Faculty Review
  Wed Feb 281:15 PMN315Final Exam1:00 PM - 4:00 PM
  
  Course: GS-GS-512: Immunology
Course Director(s): Levitt, Jonathan Michael
  DateStart TimeRoomLectureDescriptionLecturer
  Thu Jan 252:30 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.
  Thu Feb 012:30 PMN315Innate ImmunityThe gateway to defense against the world around us: pattern recognition receptors, PAMPs/DAMPs, phagocytes and chemical mediators of immunity.
  Thu Feb 015:15 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 062:30 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.
  Thu Feb 082:30 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.
  Thu Feb 085:15 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 132:30 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.
  Thu Feb 152:30 PMN315T Cell Development and Signaling: Consequences for Transplantation and TumorsT cell effector functions, transplantation, autoimmunity, vaccines, tumor immunology.
  Thu Feb 222:30 PMN315Faculty Review
  Mon Feb 261:15 PMN315Final Exam1:00 PM - 4:00 PM

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