Core Curriculum Syllabus

 

 

Term 1

 

 

Ethics - Year 1

No

Date

Time

Lecture

Lecturer

1

Thu Aug 29

10:00

(1L1) Data aquisition and record keeping responsibilities - responsibilities for record keeping, challenges in keeping accurate and understandable notebooks, ownership of research materials, reagent/data sharing

Slaughter

2

Thu Sep 05

10:00

(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

3

Thu Sep 12

10:00

(1C) Case Studies Data Management/Plagiarism - record keeping, ownership of research materials, responsible citation, and plagiarism

Faculty

4

Thu Sep 19

10:00

(1L3) The Mentor/Student relationship - Selecting a lab and developing a group of mentors, what to look for in rotations, keeping on track toward your degree

Sazer

 

Mon Sep 02

 

Labor Day Holiday - No Class -

 

 

 

 

 

 

 

Genetics A

No

Date

Time

Lecture

Lecturer

1

Tue Jul 30

1:15

Mendelian Genetics - Gene nomenclature: gene/allele/genotype/phenotype. Dominant v. recessive mutations. Mendel's laws. Penetrance v. expressivity.

Dierick

2

Thu Aug 01

1:15

Cellular Mechanisms of Mendelian Genetics and Linkage - Meiosis v. mitosis. Linkage. Two-point and three-point mapping. Complementation.

Dierick

3

Tue Aug 06

1:15

Statistical 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

4

Thu Aug 08

1:15

Population Genetics - Multifactorial 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

5

Tue Aug 13

1:15

Genetic Screens - Mutant building: discovering genes involved in a biological process through screens. Mutagens and screen saturation. Yeast genetics and tetrad analysis.

Bates

1

Wed Aug 14

5:15

GA-TA1 - General Genetic Principles

 

6

Thu Aug 15

1:15

Selecting and Identifying Mutants - Identifying mutated genes. Selection and screening strategies, reporter genes and secondary screens.

Bates

7

Tue Aug 20

1:15

Genetic Suppression - Genetics as a study of how proteins interact, fold and function. Mechanisms of genetic suppression. Genetic enhancement and synthetic lethality.

Bates

8

Thu Aug 22

1:15

Epistasis and Pathway Analysis - Determining the order of action of proteins in a pathway by epistatis analysis. Ordering genes in metabolic and regulatory pathways.

Bates

2

Fri Aug 23

5:15

GA-TA2 - Phenotype, pathway analysis and genetics screens

 

 

Tue Aug 27

1:15

Faculty Review -

 

 

Thu Aug 29

1:00

GA Mid-term Exam - 1:00-4:00

 

9

Tue Sep 03

1:15

Viral/Phage Genetics. - Virus cycle, complementation group.

Herman

10

Thu Sep 05

1:15

Bacterial Genetics I - Genetic transmission: haploid and circular genomes, P1-transduction, F-factors, HFRs, conjugation.

Rosenberg

11

Tue Sep 10

1:15

Bacterial Genetics II - Recombination.

Rosenberg

12

Thu Sep 12

1:15

Bacterial Genetics III - SOS response, transposition

Rosenberg

3

Fri Sep 13

5:15

GA-TA3 - Bacterial Genetics

 

13

Tue Sep 17

1:15

Genetic Engineering I - Artificial chromosomes, recombineering in bacteria, homing endonucleases (I-SceI), seamless versus remnant engineering

Venken

14

Thu Sep 19

1:15

Genetic Engineering II - Integrases, Zn finger technology, TALE technology, Crispr/Cas technology

Venken

4

Fri Sep 20

5:15

GA-TA4 - Genetic Engineering

 

 

Tue Sep 24

1:15

Faculty Review -

 

 

Thu Sep 26

1:00

GA Final Exam - 1:00-4:00

 

 

Mon Sep 02

 

Labor Day Holiday - No Class -

 

 

 

 

 

 

 

Molecular Methods

No

Date

Time

Lecture

Lecturer

1

Mon Jul 29

1:15

Introduction - Objectives of course, integrating methodology into discovery

Smith

2

Wed Jul 31

1:15

DNA Structure and Properties - Structural components, melting/denaturation, Tm, annealing/hybridization, Cot, gel electrophoresis, nucleic acid hybridization and stringency

Highlander

3

Fri Aug 02

1:15

DNA Manipulation 1 - Traditional cloning methods, restriction endonucleases, ligases, transformation, plasmid purification, restriction mapping

Highlander

4

Mon Aug 05

1:15

DNA manipulation 2 - Enzymes to modify, label, amplify or quantify nucleic acids. DNA polymerases, labels, polymerase chain reaction (PCR), quantitative PCR, Real Time-PCR

Highlander

1

Tue Aug 06

5:15

MM-TA1 - Lectures 1-4

 

5

Wed Aug 07

1:15

Vectors & Mutagenesis - Simple vectors and commercial vector systems, BACs, M13 single-stranded phage for mutagenesis and phage display, PCR-directed mutagenesis

Highlander

6

Fri Aug 09

1:15

Libraries and screening - Construction and handling of libraries; cDNA libraries; immunological and hybridization screening; genomic libraries and their analysis.

Metzker

7

Mon Aug 12

1:15

Sanger Sequencing and Applications - annotation of sequences, EST's, specific organism databases

Metzker

2

Tue Aug 13

5:15

MM-TA2 - Lectures 5-7

 

 

Wed Aug 14

2:30

Midterm Review -

 

 

Fri Aug 16

1:00

MM Midterm Exam -

 

8

Mon Aug 19

1:15

Next Generation Sequencing - mapping strategies, genome sequencing strategies, HTP instrumentation, data analysis.

Metzker

9

Fri Aug 23

1:15

Flow Cytometry - Introduction to the technique of flow cytometry and cell sorting, detecting fluorescent cells through expressed antigens and endogeneous fluorescent moledules

Sederstron

10

Mon Aug 26

1:15

Proteomics - mass spectrometry - Mass spectometery (MALDI-TOF, electrospray) protein identification

Qin

11

Wed Aug 28

1:15

Proteomics - protein identification - Identification of protein species in large complexes

Qin

12

Fri Aug 30

1:15

Interaction cloning - Systems, false positives and negatives happen, limitations, combinatorial screens, phage display, two-hybrid screen, lambda gt11 screens

Lydon

13

Wed Sep 04

1:15

Protein Localization/Identification - Purification of antigen, polyclonal antibodies, monoclonal antibodies, anti-peptide antibodies, Western blots, GFP fusions, FRAP

Lydon

3

Wed Sep 04

5:15

MM-TA3 - Lectures 8-11

 

14

Fri Sep 06

1:15

High throughput methods - protein arrays, interaction networks

Lydon

15

Mon Sep 09

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

4

Tue Sep 10

5:15

MM-TA4 - Lectures 12-14

 

16

Wed Sep 11

1:15

Protein Purification - sources of protein to purify, opening the cell, precipitants, chromatography, ultracentrifugation, sucrose density gradient, assays, and quantitation of purity and yield.

Gilbert

17

Fri Sep 13

1:15

Isolation/Refolding Strategies - Inclusion bodies, protein refolding strategies to avoid aggregation, disulfide formation and artificial chaperones

Gilbert

5

Tue Sep 17

5:15

MM-TA5 - Lectures 15-17

 

 

Fri Sep 20

1:15

Faculty Review -

 

 

Mon Sep 23

1:00

MM Final Exam - 1:00-4:00

 

 

Mon Sep 02

 

Labor Day Holiday - No Class -

 

 

 

 

 

 

 

Organization of the Cell

No

Date

Time

Lecture

Lecturer

1

Mon Jul 29

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 Jul 31

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 01

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 02

2:30

Mitochondria, Choloroplasts, Peroxisomes - Structure and biogenesis of mitochondria, chlorplasts, and peroxisomes. Protein import into these organelles

Sifers

4

Wed Aug 07

2:30

The Endoplasmic Reticulum - quality control checkpoint and mother of the endomembrane system

Sifers

2

Thu Aug 08

5:15

OC-TA2 - Review of protein trafficking

 

5

Fri Aug 09

2:30

The Golgi Complex - regulated vesicular trafficking in the endomembrane system

Sifers

6

Mon Aug 12

2:30

Vesicular Transport in Reverse - the plasma membrane-endosome-lysosome connection

Sifers

7

Wed Aug 14

1:15

Apoptosis - Apoptosis versus necrosis, mechanisms of programmed cell death, regulators of apoptosis.

Sifers

3

Thu Aug 15

5:15

OC-TA3 - Review of Golgi, reversed trafficking and apoptosis

 

 

Mon Aug 19

2:30

Midterm Review -

 

 

Wed Aug 21

1:00

OC Midterm Exam -

 

8

Fri Aug 23

2:30

G Proteins - Signalling mechanisms, ligand recognition and conformation changes by receptors, GDP release kinetics, G protein structure and function, effectors, signal processing, inactivation and desensitization, receptor kinases and arrestins, putative roles for PKC

Wensel

9

Mon Aug 26

2:30

Growth Factors/Tyrosine Kinase Signaling - Ligands and signals, structure of families of membrane receptors with intrinsic tyrosine kinase activity and introduction to cascades activated by binding to phosphotyrosines, SH2 and SH3 domains, tyrosine kinases associated with membrane bound receptors

Wensel

10

Wed Aug 28

2:30

Calcium and phospholipase signaling - Calcium and its protein complexes Phosphoinositides, phospholipase C, protein kinase C, IP3 receptors, proteins regulated by Ca, calmodulin, Ca-regulated channels, annexins, overview of methods for monitoring intracellular Ca and phosphoplipase activity

Wensel

4

Thu Aug 29

5:15

OC-TA4 - Review of G-protein signaling and tyrosine kinase signaling

 

11

Fri Aug 30

2:30

Cytoskeleton I - Actin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility.

Pedersen

12

Wed Sep 04

2:30

Cytoskeleton II - Actin, microtubules, intermediate filaments, junctional complexes and cellular architecture, cell motility.

Pedersen

5

Thu Sep 05

5:15

OC-TA5 - Review of cytoskeleton and calcium signaling

 

13

Fri Sep 06

2:30

Energy Transduction and Bioenergetics - Membrane permeability, mechanisms of transport, bio-energetics, mitochondrial and chloroplast function, chemiosmosis

Pedersen

14

Wed Sep 11

2:30

Transport Mechanisms - Active and passive transport, synporters, antiporters, ATPases

Pedersen

6

Thu Sep 12

5:15

OC-TA6 - review of bioenergetics, transporters, ion channels

 

15

Fri Sep 13

2:30

Ion channels - Nernst potential, electrical properties of excitable membranes, action potential

Pedersen

 

Mon Sep 16

1:15

Faculty Review -

 

 

Wed Sep 18

1:00

OC Final Exam - 1:00-4:00

 

 

Mon Sep 02

 

Labor Day Holiday - No Class -

 

 

 

 

 

 

 

Science as a Profession

No

Date

Time

Lecture

Lecturer

1

Tue Jul 30

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

2

Tue Aug 06

2:30

The funding structure of science and public policy - Government organizations, private funding sources, applying for fellowships, structure of a grant, grant review system, science advocacy

Slaughter

3

Tue Aug 13

2:30

The Scientific Method - thinking and talking 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

4

Tue Aug 20

2:30

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 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

Sazer

 

 

 

 

 

 

Term 2

 

 

ABC-Applications to Biology of Computation

No

Date

Time

Lecture

Lecturer

1

Tue Oct 08

9:00

Genomics I - Genome Assembly - Overview of the task of genome assembly that builds the references used for all genomic analyses from the first reference human genome through the many comparative genomes of other species to the current human medical and cancer genomics. Basic information about the nature of genome sequence data and the limitations of a reference genome.

Worley

2

Thu Oct 10

9:00

Genomics II - Genomic Databases - Accessing and using genomic data

Ritter

3

Tue Oct 15

9:00

Genomics III - Annotating genomic features and idenfying the functional genome

Ritter

4

Wed Oct 16

9:00

Epigenomics I - Epigenomic profiles of healthy and diseased cells

Li

5

Tue Oct 22

9:00

Transcriptomics I - Expressed sequences and annotating the genome

Qin

6

Thu Oct 24

9:00

Transcriptomics II - Expression levels in RNA-Seq and ChIP-Seq. Introduction of analysis principles and software tools for analyzing expression datasets.

Mo

7

Tue Oct 29

9:00

Genomics IV - Human resequencing and applications to medicine and biology.

Worley

8

Thu Oct 31

9:00

Epigenomics II - Discovering patterns in genomes and epigenomes

Milosavljevic

9

Tue Nov 05

9:00

Genomics V - Human resequencing and applications to medicine and biology

Wheeler

10

Thu Nov 07

9:00

Optical Imaging I -

Larina

11

Tue Nov 12

9:00

Systems Biology I - Networks and pathways

Lisewski

12

Thu Nov 14

9:00

Systems Biology II - Networks and pathways

Lisewski

13

Tue Nov 19

9:00

Systems Biology III - Discovering network patterns

Milosavljevic

14

Thu Nov 21

9:00

Optical Imaging II -

Larina

15

Mon Nov 25

9:00

Evolution I - Theoretical introduction to using evolutionary data to study biology

Lichtarge

16

Tue Nov 26

9:00

Evolution II - Practical tools developed to study evolutionary processes

Wilkins

 

Thu Dec 05

9:00

ABC - Final Exam - 8:30 to 11:30

 

 

Thu Oct 17

 

Graduate Student Symposium - No Class -

 

 

Thu Nov 28

 

Thanksgiving Day - No Class -

 

 

Fri Nov 29

 

Thanksgiving Holiday - No Class -

 

 

 

 

 

 

 

Cancer

No

Date

Time

Lecture

Lecturer

1

Tue Nov 12

1:15

Introduction to Cancer Course - Mouse models of cancer using lung cancer as an example

Demayo

2

Fri Nov 15

1:15

Oncogenes -

Pangas

3

Mon Nov 18

1:15

Cancer as a Multi-Step Process -

Pangas

4

Wed Nov 20

1:15

Tumor Cell - Stromal Interactions -

Pangas

5

Fri Nov 22

1:15

Metastasis -

Demayo

6

Mon Nov 25

1:15

Cancer Stem Cells -

Chan

 

Tue Dec 03

1:15

Faculty Review -

 

 

Wed Dec 04

1:00

CA Final Exam - 1:00-4:00

 

 

Thu Nov 28

 

Thanksgiving Day - No Class -

 

 

Fri Nov 29

 

Thanksgiving Holiday - No Class -

 

 

 

 

 

 

 

Cell Division

No

Date

Time

Lecture

Lecturer

1

Mon Oct 07

1:15

Course Introduction/Cell Cycle Overview - Discovery of cell cycle regulation--Cell cycle stages, mitosis and meiosis, discovery of CDK/cyclin/MPF

Zhang

2

Wed Oct 09

1:15

S phase - Initiation and control of DNA replication at origins of replications

Ira

3

Fri Oct 11

1:15

Principles of cell cycle regulation I - CDKs, cyclins, CKIs, and proteolysis

Zhang

4

Mon Oct 14

1:15

Principles of cell cycle regulation II - Cell cycle transitions, G1/S and G2M

Zhang

5

Wed Oct 16

1:15

Cell Cycle Checkpoints - Introduction to cell cycle checkpoints, the DNA damage checkpoint

Zhang

1

Thu Oct 17

5:15

CD-TA1 - Review of cell cycle basics, S phase

 

6

Fri Oct 18

1:15

DNA Damage - DNA damage and repair

Ira

7

Mon Oct 21

1:15

DNA Repair - Repair of double strand breaks by homologous and non-homologous recombination

Ira

2

Tue Oct 22

5:15

CD-TA2 - Review of cell cycle regulation

 

 

Wed Oct 23

1:15

Faculty Review Midterm - Lectures 1-6

 

 

Fri Oct 25

1:00

CD Midterm Exam - Lectures 1-6

 

8

Mon Oct 28

1:15

Chromosomes - Chromatin duplication and M phase chromosomes organization

Dang

9

Wed Oct 30

1:15

Telomeres - Structure and synthesis. Telomere dysfunction-induced DNA damage checkpoint response. Crisis and survival in the absence of telomerase.

Bertuch

3

Wed Oct 30

5:15

CD-TA3 - Review of DNA recombination and repair

 

10

Mon Nov 04

1:15

M phase spindle - Mechanisms of spindle formation and function, kinetochore/spindle attachment

Chang

11

Wed Nov 06

1:15

Cytokinesis - Cytokinesis mechanisms

Sokac

12

Fri Nov 08

1:15

Growth regulation - The cell cycle in growth regulation, development and cancer

Westbrook

 

Tue Nov 12

2:30

Faculty Review - Lecture 7-12

 

4

Tue Nov 12

5:15

CD-TA4 - Review of CDK/cyclin cell cycle transitions

 

 

Wed Nov 13

1:00

CD Final Exam - 1:00-4:00

 

 

Thu Oct 17

 

Graduate Student Symposium - No Class -

 

 

 

 

 

 

 

Development

No

Date

Time

Lecture

Lecturer

1

Mon Oct 07

2:30

Core Concepts in Developmental Biology -

Groves

2

Wed Oct 09

2:30

Setting up the vertebrate body plan I - Axis determination and gastrulation

Groves

3

Mon Oct 14

2:30

Setting up the vertebrate body plan II - Mammalian development and embryonic stem cells

Groves

4

Tue Oct 15

2:30

Patterning the embryo from head to tail -

Groves

1

Tue Oct 15

5:15

TA-DE1 - Please note: This session will be held at 4:00-5:15 in N311 so that 1st year graduate students can attend the Lab Coat ceremony.

 

5

Mon Oct 21

2:30

ES cells, pluripotency and reprogramming / iPS -

Groves

6

Mon Oct 28

2:30

Stem cells in the adult -

Nguyen

2

Tue Oct 29

5:15

TA-DE2 -

 

 

Wed Oct 30

2:30

Mid-Term Faculty Review -

 

 

Fri Nov 01

1:00

DE Midterm Exam - 1:00-4:00

 

7

Mon Nov 04

2:30

Vertebrate neural development I - Developmental anatomy of the nervous system. Molecular aspects of neural induction, formation of the neural plate and neurogenesis

Deneen

8

Wed Nov 06

2:30

Vertebrate neural development II - Molecular mechanisms of dorsal-ventral and anterior-posterior patterning. Combinatorial and antagonistic signaling involved in dorsoventral patterning of the neural tube

Deneen

9

Fri Nov 08

2:30

Limb Development - A model system to illustrate developmental concepts

Groves

3

Fri Nov 08

5:15

TA-DE3 -

 

10

Mon Nov 11

2:30

Introduction to Drosophila embryogenesis - Overview of Drosophila oogenesis and embryogenesis

Jafar-Nejad

11

Thu Nov 14

2:30

Embryonic patterning in Drosophila - I - Maternal-effect genes and the establishment of the anteroposterior axes

Jafar-Nejad

12

Fri Nov 15

2:30

Embryonic patterning in Drosophila II - Maternal-effect genes and the establishment of the dorsoventral axes

Jafar-Nejad

4

Tue Nov 19

5:15

TA-DE4 -

 

 

Wed Nov 20

2:30

Faculty Review -

 

 

Thu Nov 21

1:00

DE Final Exam - 1:00-4:00

 

 

Thu Oct 17

 

Graduate Student Symposium - No Class -

 

 

 

 

 

 

 

Ethics - Year 2

No

Date

Time

Lecture

Lecturer

1

Mon Oct 14

10:00

(2L2) 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

Buckmaster

2

Mon Oct 21

10:00

(2L1) Research misconduct - (NIH b3) Safe Practices in the Laboratory - Definitions - 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 – refresher of material covered at orientation regarding laboratory safety

Slaughter

3

Mon Oct 28

10:00

(2C) Case Studies - Scientific Misconduct/Animals - scientific misconduct and experiments with animals (small group discussion format with faculty facilitator)

Faculty

4

Mon Nov 04

10:00

(2L3) Mentorship - Meeting 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

Sazer

 

Thu Oct 17

 

Graduate Student Symposium - No Class -

 

 

 

 

 

 

 

Genetics B

No

Date

Time

Lecture

Lecturer

1

Tue Oct 08

1:15

Introduction - Forward and reverse genetics. Strengths of model systems. Nomenclature. The concept of maternal effect.

Zhou

2

Thu Oct 10

1:15

Yeast I - Basic molecular manipulations in reverse genetics: cloning by complementation, plasmid gap repair, gene disruption/replacement, plasmid shuffle

Ira

3

Tue Oct 15

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.

Ira

1

Wed Oct 16

5:15

GB-TA1 -

 

4

Fri Oct 18

2:30

C. elegans I - Advantages and special considerations of hermaphrodite genetics. How to construct strains, strategies of genetic screens, cloning genes, balancers.

Zhou

5

Tue Oct 22

1:15

C. elegans II - C. elegans transformation. Impact of the C. elegans genome project. Reverse genetics using RNA interference and gene deletions. Studies of gene interaction.

Zhou

2

Wed Oct 23

5:15

GB-TA2 -

 

6

Thu Oct 24

1:15

Drosophila I - Introduction. Nomenclature and markers; chromosome cytology (polytene chromosomes) and chromosome rearrangements; using balancer chromosomes to follow segregation and to isolate mutations; P-elements and transformation; site-specific integration using the PhiC31 system.

Mardon

7

Tue Oct 29

1:15

Drosophila II - Genetic screens. Mutagens: ems, x-rays and P-elements; classic genetic screens to identify mutations in Drosophila: F1, F2, F3 screens; modifier (suppressor and enhancer) screens; isolating mutations, mapping lethal mutations; deficiency mapping; high-throughput sequencing.

Mardon

8

Thu Oct 31

1:15

Drosophila III - Gene function. Mosaic analysis; autonomy versus non-autonomy; mitotic recombination using the FLP/FRT system, methods of marking clones; ectopic expression using heat shock, GAL4-UAS, and flp-out; MARCM analysis.

Mardon

 

Thu Oct 31

2:30

Faculty Review -

 

3

Fri Nov 01

5:15

GB-TA3 -

 

 

Tue Nov 05

1:00

GB Midterm Exam - 1:00-4:00

 

9

Mon Nov 11

1:15

Mouse Genetics I - Inbred mice. Microsatellite markers. Mapping genes in mice using crosses.

Matzuk

10

Thu Nov 14

1:15

Mouse Genetics II - Insertion of DNA and retrotransposons. Knock-outs and ins. Conditional knock-outs.

Matzuk

4

Fri Nov 15

5:15

GB-TA4 -

 

11

Tue Nov 19

1:15

Human Genetics I - Disease loci and pedigrees.

Lupski

12

Mon Nov 25

2:30

Human Genetics II - Mapping with DNA markers. Sources of polymorphisms. Simple vs. complex traits. Genome scans for quantitative trait loci.

Lupski

13

Tue Nov 26

1:15

Human Genetics III - Effect of imprinting on pedigrees. Models for specific mechanisms of imprinting. Model for evolutionary significance.

Lupski

5

Wed Nov 27

1:15

GB-TA5 -

 

 

Thu Dec 05

1:15

Faculty Review -

 

 

Fri Dec 06

1:00

GB Final Exam - 1:00-4:00

 

 

Thu Oct 17

 

Graduate Student Symposium - No Class -

 

 

Thu Nov 28

 

Thanksgiving Day - No Class -

 

 

Fri Nov 29

 

Thanksgiving Holiday - No Class -

 

 

 

 

 

 

 

Method and Logic in Molecular Biology

No

Date

Time

Lecture

Lecturer

1

Thu Oct 10

10:00

Method and Logic Meeting - Attendance at this class (to be held in 187A) is mandatory for all students who intend to take this course. This organizational meeting begins at 10:30 AM.

Mardon

2

Tue Oct 15

10:00

Method and Logic Meeting - Classes will be held in M319.01, M319.06, M319.08, N304 and N310 from this class onwards. Classes begin at 10 AM and end at noon.

Samaco

3

Fri Oct 18

10:00

Method and Logic Meeting -

Deneen

4

Tue Oct 22

10:00

Method and Logic Meeting -

Suter

5

Thu Oct 24

10:00

Method and Logic Meeting -

Scott

6

Tue Oct 29

10:00

Method and Logic Meeting -

Moore

7

Thu Oct 31

10:00

Method and Logic Meeting -

Shaulsky

8

Tue Nov 05

10:00

Method and Logic Meeting -

Herman

9

Thu Nov 07

10:00

Method and Logic Meeting -

Chen

10

Tue Nov 12

10:00

Method and Logic Meeting -

Catanese

11

Thu Nov 14

10:00

Method and Logic Meeting -

Groves

12

Tue Nov 19

10:00

Method and Logic Meeting -

Mardon

13

Thu Nov 21

10:00

Method and Logic Meeting -

Bertuch

 

Thu Oct 17

 

Graduate Student Symposium - No Class -

 

 

 

 

 

 

 

Term 3

 

 

Ethics - Year 3

No

Date

Time

Lecture

Lecturer

1

Thu Jan 09

9:00

(3L1) Authorship/Peer Review - NIH a) Other Conflicts of Interest - Organizing 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

2

Thu Jan 09

10:00

(3M) Mentorship - Meeting 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

Sazer

3

Thu Jan 16

9:00

(3L2) Collaborative research including collaborations with industry - The values/responsibilities of collaboration, establishing collaborative relationships, grants, contracts, intellectual property considerations, impact of industry collaborations on publication, thesis submission

Zechiedrich

4

Thu Jan 16

10:00

(3C) Case Studies Peer Review/Collaboration - peer review of grants and papers, conflicts of interest, collaboration (small group discussion format with faculty facilitator)

Faculty

 

 

 

 

 

 

Ethics - Year 4

No

Date

Time

Lecture

Lecturer

1

Thu Jan 23

9:00

(4L2 The scientist as a responsible member of society. - Contemporary ethical issues in biomedical research and the environmental and societal impacts of scientific research

Mcguire

2

Thu Jan 23

10:00

(4M) Mentorship - Meeting 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

Johnson

3

Thu Jan 30

9:00

(4L1) Research with Human Subjects - definition of research with human subjects, experiments with human material, confidentiality of medical data, experiments involving humans, informed consent

Berg

4

Thu Jan 30

10:00

(4C)Case Studies Human Research/Science and Society - research with human subjects, societal impact of research (genetics/genomics, stem cells, neuroethics) (small group discussion format with faculty facilitator

Faculty

 

 

 

 

 

 

Gene Regulation

No

Date

Time

Lecture

Lecturer

1

Thu Jan 02

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. Analysis of gene expression.

Cooper

2

Fri Jan 03

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.

Herman

3

Mon Jan 06

1:15

Control of transcription in bacteria - degradation and sequestration of initiation factors, riboswitches, noise in transcription and logic of transcriptional circuits.

Herman

4

Wed Jan 08

1:15

Eukaryotic RNA polymerase and transcriptional initiation - Structures and activities of the 3 eukaryotic RNA polymerases. Pathways for transcription initiation by RNA pol II holoenzyme plus general transcription factors.

Foulds

1

Wed Jan 08

5:15

GRTA1 - Overview of regulation of transcription and translation including review of overall process of transcription and translation, introduce reporter genes (rationale)

 

5

Fri Jan 10

1:15

Modes of DNA binding and basic transcription factors - Structures of DNA binding domains and the molecular basis for DNA sequence recognition. How do transcription factors find their sites? Genome wide networks of transcriptional regulation.

Foulds

6

Mon Jan 13

1:15

Coactivators and corepressors - Identification of transcriptional coregulators and evolution of understanding of transcriptional activation. Enymatic activities of coactivators and corepressors. Post-transcriptional modulation of coregulator function. Why are there so many coregulators?

Foulds

7

Wed Jan 15

1:15

Chromatin 1 - Local - Histones, nucleosomes, covalent modification of histones, DNA accessibility, insulators, locus control regions, polytene/lapbrush chromosomes.

Lonard

8

Fri Jan 17

1:15

Chromatin 2 - Global - Chromatin subdomains, gene silencing, position effect variegation, epigenetic inheritance, X-inactivation, gene imprinting.

Lonard

9

Tue Jan 21

1:15

Chromatin - Relationship between DNA sequence genes, transcription and Chromatin - Emerging pictures of genes and chromosomes. Enabling technologies for global chromatin and transcriptome analysis, evolving understanding of gene structure, promoters, enhancers, relationship between primary DNA sequence, chromatin and transcription.

Lonard

2

Wed Jan 22

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

Thu Jan 23

1:15

Regulation of RNA Polymerase II Elongation - Transcriptional 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

11

Fri Jan 24

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

 

Mon Jan 27

1:15

Midterm Faculty Review -

 

 

Wed Jan 29

1:00

GR Midterm Exam -

 

12

Thu Jan 30

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: The spliceosome; U12-dependent introns, domain structure of RNA binding proteins.

Cooper

13

Fri Jan 31

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 03

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.

Cooper

15

Wed Feb 05

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 05

5:15

GR TA3 - Splicing and poyadenylation general overview; define mechanisms for alternative splice-site selection, intron vs exon selection

 

16

Fri Feb 07

1:15

RNA (and DNA) Editing - RNA 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

17

Mon Feb 10

1:15

Noncoding RNA Function - Biogenesis 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

18

Wed Feb 12

1:15

Posttranscriptional mRNA Regulation - The 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

19

Fri Feb 14

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

4

Tue Feb 18

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

 

20

Wed Feb 19

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

Fri Feb 21

1:15

Regulation of Protein Turnover - Ubiquitin-proteosome mediated degradation. Importance of regulation, protein motifs, PEST sequences, etc.

Lloyd

5

Tue Feb 25

5:15

GR-TA5 -

 

 

Thu Feb 27

1:15

Faculty Review -

 

 

Fri Feb 28

1:00

GR Final Exam - 1:00-4:00

 

 

Mon Jan 20

 

Martin Luther King Day Holiday - No Class -

 

 

Mon Feb 17

 

President's Day Holiday - No Class -

 

 

 

 

 

 

 

Immunology

No

Date

Time

Lecture

Lecturer

1

Tue Feb 04

2:30

Principles of immunity - Overview of the immune system: innate vs. acquired immunity, cells of the immune system, clonal selection principle, strategies for “self-nonself/danger” discrimination

Levitt

2

Thu Feb 06

2:30

Innate Immunity - The gateway to defense against the world around us: pattern recognition receptors, PAMPs/DAMPs, phagocytes and chemical mediators of immunity

Levitt

1

Fri Feb 07

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

 

3

Tue Feb 11

2:30

Antibody structure, antigen receptor diversity and B-cell development - Antigens for B cells, Antibody receptor structure and genetics, Generation of diversity, Gene rearrangements and class switching

Decker

4

Thu Feb 13

2:30

B-cell activation, MHC and antigen presentation - B cell development and selection. Self-nonself recognition, Tolerance, T cell antigen recognition, MHC structure and function. MHC antigen presentation and processing.

Decker

2

Fri Feb 14

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

 

5

Tue Feb 18

2:30

Role and development of T lymphocytes - Types 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

6

Thu Feb 20

1:15

T cell development and signaling: consequences for transplantation and tumors - T cell effector functions, transplantation, autoimmunity, vaccines, tumor immunology

Levitt

 

Thu Feb 20

2:30

Faculty Review -

 

 

Mon Feb 24

1:00

IM Final Exam - 1:00-4:00

 

 

Mon Feb 17

 

President's Day Holiday - No Class -

 

 

 

 

 

 

 

Macromolecules: Structure and Interactions

No

Date

Time

Lecture

Lecturer

1

Thu Jan 02

2:30

DNA Structure - A-, B- and Z- DNA structure; building blocks; DNA topology; from DNA to RNA

Tsai

2

Fri Jan 03

2:30

Protein Structure - Protein structure elements: from building blocks to quaternary structure; protein topology; "Form follows function"; protein taxonomy.

Tsai

3

Mon Jan 06

2:30

Protein Folding - Protein folding (Anfinsen theorem); energy landscapes; molecular chaperones; and protein misfolding diseases.

Tsai

4

Wed Jan 08

2:30

Protein – post-translational modifications - Common reversible and irreversible post-translational modifications: regulation and roles in protein function

Weigel

1

Thu Jan 09

5:15

MSI-TA Review 1 -

 

5

Fri Jan 10

2:30

Lipid/Membrane Structure - Lipid classification; micelles and bilayers; membrane structures; membrane proteins; mitochondria.

Tsai

6

Mon Jan 13

2:30

X-ray/Cryo EM - 1 - Scattering, (diffraction)-based technique, diffraction theory. Reading and interpreting X-ray structure papers.

Schmid

7

Tue Jan 14

1:15

X-ray/Cryo EM - 2 - EM single particle methods, averaging helical and crystallographic reconstructions. Cryo-electron tomography.

Schmid

8

Wed Jan 15

2:30

NMR & Fluorescence/optical spectroscopy - Basic theory and instrumentation, NOESY, COSY methods, distance geometry, multi-dimensional NMR, sample requirements. Principles of photon absorption and emission, fluorescence energy transfer, anisotropy, lifetime instrumentation, optics.

Schmid

2

Thu Jan 16

5:15

MSI-TA Review 2 -

 

 

Fri Jan 17

2:30

Midterm Faculty Review -

 

 

Wed Jan 22

1:00

MS Midterm Exam - 1:00-4:00

 

3

Thu Jan 23

5:15

MSI-TA Review 3 -

 

9

Fri Jan 24

2:30

Ligand Binding - General Principles of ligand binding formalism, mass action, and basic energetics. Techniques for doing binding analysis.

Pedersen

10

Mon Jan 27

2:30

Forces in Solution/Thermodynamics - Basic forces in solution. What holds structures together? Thermodynamics of binding and how the relate to basic forces.

Pedersen

11

Thu Jan 30

2:30

Allostery 1 - Protein dynamics and structural allostery and how it mediates and regulates protein function.

Pedersen

4

Thu Jan 30

5:15

MSI-TA Review 4 -

 

12

Fri Jan 31

2:30

Allostery and Cooperativity - How protein structural changes mediate cooperative effects in enzymes and binding proteins

Pedersen

13

Mon Feb 03

2:30

Binding Kinetics - Basic kinetics of unimolecular and bimolecular reactions.

Pedersen

14

Wed Feb 05

2:30

Enzyme Kinetics/Catalysis - Michaelis-Menten kinetics, Inhibition, kcat and kcat/Km, allosteric enzymes, inhibition, practical features of an assay

Pedersen

5

Thu Feb 06

5:15

MSI-TA Review 5 -

 

15

Fri Feb 07

2:30

Mechanisms of Catalysis - Acid base catalysis, covalent catalysis, stabilization of transition states, transition state analogs, coenzymes, suicide inhibitors

Pedersen

16

Mon Feb 10

2:30

Single Molecule methods - Macromolecular motors, single molecule kinetics, examples

Pedersen

17

Wed Feb 12

2:30

Protein – small molecule interactions - Molecular basis of specificity, protein ligand interactions - structural basis of H-bonding, salt bridges and other interactions

Prasad

6

Thu Feb 13

5:15

MSI-TA Review 6 -

 

18

Fri Feb 14

2:30

Protein – Protein interactions - Protein-protein interactions. Structural motifs that serve as protein-protein interaction domains, structural basis of surface complimentarity, engineering tight binding.

Prasad

19

Wed Feb 19

2:30

Protein/DNA interactions - Protein-DNA interactions. DNA binding motifs, structural basis of base recognition, backbone interactions

Prasad

20

Fri Feb 21

2:30

Systems Biology - Some principles and examples from systems biology approaches to understanding signaling in regulatory networks

Pedersen

 

Tue Feb 25

1:15

Faculty Review -

 

 

Wed Feb 26

1:00

MS Final Exam - 1:00-4:00

 

 

Mon Jan 20

 

Martin Luther King Day Holiday - No Class -

 

 

Mon Feb 17

 

President's Day Holiday - No Class -

 

 

 

 

 

 

 

Neuroscience

No

Date

Time

Lecture

Lecturer

1

Tue Jan 07

2:30

Cellular and Structural Neuroanatomy - Major subdivions of the mammalian brain, their general organization and the specialized cells required for function.

Jankowsky

2

Thu Jan 09

2:30

Ion Channels and Action Potentials - Structure and function of membrane proteins responsible for establishing ionic gradients in neurons and how they use ionic imbalances to transmit electrical information.

Jankowsky

3

Tue Jan 14

2:30

Synapses and Postsynpatic Receptors - Specialized structures and proteins that allow electrical signals to be converted to chemical messengers and then back again

Jankowsky

4

Thu Jan 16

2:30

Learning and Memory - Molecular and cellular requirements for storing new information and recalling it later

Jankowsky

5

Tue Jan 21

2:30

Neurobiology of Disease - What happens when things go wrong in the brain.

Jankowsky

 

Thu Jan 23

2:30

Faculty Review -

 

 

Tue Jan 28

1:00

NE Final Exam - 1:00-4:00

 

 

Mon Jan 20

 

Martin Luther King Day Holiday - No Class -

 

 

 

 

 

 

 

Term 4

 

 

Intro to Intellectual Property

No

Date

Time

Lecture

Lecturer

1

Tue Mar 18

9:00

Introduction & Overview - Brief introduction to law, including discussion of statutes, regulations, guidelines, and judicial interpretation (case law). Also included will be a brief discussion of the US Courts and how case law is made. Note: Class will be held in N311 except April 3.

Turley

2

Thu Mar 20

9:00

Patent Overview - What patents are and how to obtain a patent.

Turley

3

Tue Mar 25

9:00

Patents in Depth - What can be patented, how to read and understand a patent. Discussion of cases involving patentablility of life forms and genes.

Turley

4

Thu Mar 27

9:00

Patent Infringement and International Patenting - What constitutes infringement. How to obtain patents outside of the USA.

Turley

5

Tue Apr 01

9:00

Trademarks, Trade Secrets and Agreements - Overview of trademarks and trade secrets and how these differ from patents. Overview of the different types of intellectual property agreements you may encounter as an inventor.

Turley

6

Thu Apr 03

9:00

Copyrights - Copyright law, particularly with regard to course content and articles and other faculty publications. The April 3 class will be held in N317.

Turley

7

Tue Apr 08

9:00

Exam Review - Review of key concepts learned in class as applied to real-world situations.

Turley

8

Thu Apr 10

9:00

"Now What?" - Now that you have learned about intellectual property, what can you do with this information?

Turley

 

 

 

 

 

 

Introduction to Biostatistics

No

Date

Time

Lecture

Lecturer

1

Tue Mar 11

1:15

Summarizing data - Please consult Blackboard for required text book and reading assignment prior to first class.

Minard

2

Thu Mar 13

1:15

Measures of association -

Minard

3

Tue Mar 18

1:15

Differences between groups -

Minard

4

Thu Mar 20

1:15

Differences between two groups -

Minard

5

Tue Mar 25

1:15

Rates and proportions -

Minard

6

Thu Mar 27

1:15

Confidence intervals -

Liu

7

Tue Apr 01

1:15

Linear regression and correlation -

Minard

 

Tue Apr 01

2:30

Midterm faculty review -

 

 

Thu Apr 03

1:00

BS Midterm Exam - 1:00-4:00

 

8

Tue Apr 08

1:15

Nonparametric methods -

Liu

9

Thu Apr 10

1:15

Measures of association -

Sangi-Haghpeykar

10

Tue Apr 15

1:15

Multiple factors and interaction -

Minard

11

Thu Apr 17

1:15

Multiple regression -

Minard

12

Tue Apr 22

1:15

Multiple measures per subject -

Minard

13

Thu Apr 24

1:15

Power and sample size -

Ahern

14

Tue Apr 29

1:15

Survival analysis -

Hilsenbeck

15

Thu May 01

1:15

Putting it all together -

Minard

 

Thu May 01

2:30

Final Exam Review -

 

 

Thu May 08

1:00

BS Final Exam - 1:00-4:00

 

 

Fri Apr 18

 

Easter Holiday - No Class -

 

 

 

 

 

 

 

Introduction to Scientific Writing

No

Date

Time

Lecture

Lecturer

1

Mon Mar 17

1:15

Getting Prepared to Write - Class meets in N311

Marriott

2

Wed Mar 19

1:15

Parts of a Scientific Manuscript - I -

Marriott

3

Mon Mar 24

1:15

Parts of a Scientific Manuscript - II -

Marriott

4

Wed Mar 26

1:15

Writing the First Draft -

Marriott

5

Mon Mar 31

1:15

Striving for Clarity -

Marriott

6

Wed Apr 02

1:15

Achieving Brevity through Revision -

Marriott

7

Mon Apr 07

1:15

Grammar for Scientists -

Marriott

8

Wed Apr 09

1:15

Submitting, Revising and Responding to Reviews -

Marriott

 

 

 

 

 

 

Research Design

No

Date

Time

Lecture

Lecturer

1

Wed Mar 12

1:00

Research Design Introduction - The application of the scientific method in proposing and designing research projects. The thought processes and methods used in grant applications and qualifying examinations. This class will meet in N311 at 1 PM.

Schmid

2

Wed Mar 19

1:00

Working Groups 1 - Project selection and design.

Room assignments will be provided in the March 12 Introduction session.

Peters

3

Wed Mar 26

1:00

Working Groups 2 - Project selection and design

Prasad

4

Wed Apr 02

1:00

Working Groups 3 - Project selection and design

Zhou

5

Wed Apr 09

1:00

Working Groups 4 - Project selection and design

Staff

6

Wed Apr 16

1:00

Working Groups 5 - Project selection and design

 

7

Wed Apr 23

1:00

Working Groups 6 -

 

8

Wed Apr 30

1:00

Working Groups 7 -

Staff

9

Wed May 07

1:00

Research Design Symposium - A competitive, judged, symposium in which each of the student groups presents the design of their research project and answers questions about it.

Staff

 

Fri Apr 18

 

Easter Holiday - No Class -