Core Curriculum Syllabus

 

 

Term 1

 

 

Ethics - Year 1

No

Date

Time

Lecture

Lecturer

1

Thu Sep 03

2:30

(1M) 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

Johnson

2

Thu Sep 10

2:30

(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

Nelson

3

Thu Sep 17

2:30

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

Faculty

4

Thu Sep 24

2:30

(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

 

Mon Sep 07

 

Labor Day Holiday - No Class -

 

 

 

 

 

 

 

Genetics A

No

Date

Time

Lecture

Lecturer

1

Tue Aug 04

1:15

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

Dierick

2

Thu Aug 06

1:15

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

Dierick

3

Tue Aug 11

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 13

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 18

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 19

5:15

GA-TA1 - General Genetic Principles

 

6

Thu Aug 20

1:15

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

Bates

7

Tue Aug 25

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 27

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

 

Thu Aug 27

2:30

Faculty Review -

 

2

Fri Aug 28

5:15

GA-TA2 - Phenotype, pathway analysis and genetics screens

 

 

Mon Aug 31

1:00

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

 

9

Thu Sep 03

1:15

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

Herman

10

Tue Sep 08

1:15

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

Rosenberg

11

Thu Sep 10

1:15

Bacterial Genetics II - Recombination.

Rosenberg

12

Tue Sep 15

1:15

Bacterial Genetics III - SOS response, transposition

Rosenberg

13

Thu Sep 17

1:15

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

Venken

3

Fri Sep 18

5:15

GA-TA3 - Bacterial Genetics

 

14

Tue Sep 22

1:15

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

Venken

 

Thu Sep 24

1:15

Faculty Review -

 

4

Thu Sep 24

5:15

GA-TA4 - Genetic Engineering

 

 

Fri Oct 02

1:00

GA Final Exam - 1:00-4:00

 

 

Mon Sep 07

 

Labor Day Holiday - No Class -

 

 

 

 

 

 

 

Molecular Methods

No

Date

Time

Lecture

Lecturer

1

Mon Aug 03

1:15

Introduction - Overview of course contents and schedule

Weigel

2

Wed Aug 05

1:15

DNA Manipulation, Amplification and Detection - Enzymes 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

3

Fri Aug 07

1:15

DNA Cloning I - Applications of cloning, vectors, transformation methods, plasmid purification systems, traditional cloning methods, cloning diagnosis.

Venken

4

Mon Aug 10

1:15

DNA Cloning II - Applications of advanced cloning and mutagenesis; Gateway, sequence and ligation independent cloning, Gibson cloning, Type II's cloning; mutagenesis, recombineering cloning

Venken

1

Tue Aug 11

5:15

MM-TA1 - Lectures 1-4

 

5

Wed Aug 12

1:15

cDNA and Genomic Libraries - Construction and handling of cDNA libraries; whole genome libraries, targeted strategies such as exome and regional capture, circulating cell-free genomic libraries

Metzker

6

Fri Aug 14

1:15

First-Generation Sequencing and Genotyping - Introduction to Maxam-Gilbert, Sanger and automated Sanger sequencing; microarrays, high-throughput genotyping assays

Metzker

7

Mon Aug 17

1:15

Next Generation Sequencing - Technology 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

2

Tue Aug 18

5:15

MM-TA2 - Lectures 5-7

 

8

Wed Aug 19

1:15

Genomic Profiling - Functional assays using NGS: RNA sequencing (RNA-Seq) and data analysis, single cell analyses, other functional sequencing assays

Zong

9

Mon Aug 24

1:15

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

Sederstrom

3

Tue Aug 25

5:15

MM-TA3 - Lectures 8-9

 

10

Wed Aug 26

1:15

CRISPR/Cas9 - Guide selection, Cas9 nickase, reagent production for in vitro and in vivo applications. Nonhomologous end joining, homology directed repair and homologus recombination. On target and off target screening; emerging applications.

Heaney

 

Fri Aug 28

1:15

Midterm Review -

 

 

Tue Sep 01

1:00

MM Midterm Exam -

 

12

Fri Sep 04

1:15

Detection of Protein-Protein Interactions - Principles of: Western immunoblotting, Westerns coupled to co-immunoprecipitation; in vitro (GST) pull-down assays; yeast two-hybrid system; bimolecular fluorescence complementation (BiFC).

Lydon

11

Tue Sep 08

2:30

Antibody Production, Characterization and Research Applications - Monoclonal 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

13

Wed Sep 09

1:15

Visualizing Proteins - Immunohistochemical detection methods; lacZ reporters; green fluorescence protein (GFP) reporters; luciferase reporters; fluorescence resonance energy transfer (FRET); bimolecular fluorescence complementation (BiFC); fluorescence recovery after photobleaching (FRAP); the fluorescent timer

Lydon

4

Wed Sep 09

5:15

MM-TA4 - Lectures 10-13

 

14

Fri Sep 11

1:15

High Throughput Methods - Chromatin 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

15

Mon Sep 14

1:15

Protein Expression - Which proteins and what for; which expression systems (E. coli, yeast, insect and mammalian cells), which fusion tags to use (6x His, GST, MBP, intein);

Kim

16

Wed Sep 16

1:15

Protein Purification - How pure and how much. Native or denatrued; basic principles of purification (centrifugation, ammonium sulfate precipitant, affinity, ion exchange, hydrophobic, size exclusion). Evaluating function, purity and concentration (SDS-PAGE, Bradford and extinction coefficients and biological assays).

Kim

17

Mon Sep 21

1:15

Proteomics Mass Spectrometry - Basic Principles - Mass spectometer instruments and analytical methods; principles of identification for peptides and post-translational modifications (PTMs); data processing

Malovannaya

5

Tue Sep 22

5:15

MM-TA5 - Lectures 14-16

 

18

Wed Sep 23

1:15

Proteomics Mass Spectrometry - Applications in Biology - MS-based quantification, global proteome profiling, PTM profiling, protein-protein interaction networks from IP/MS

Malovannaya

19

Fri Sep 25

1:15

RNA Interference and genetic screens - RNA interference (RNAi) mechanisms, RNAi tools, genetic screening methods, technical considerations in using RNAi

Westbrook

6

Fri Sep 25

5:15

MM-TA6 - Lectures 17-19

 

 

Mon Sep 28

1:15

Faculty Review -

 

 

Wed Sep 30

1:00

MM Final Exam - 1:00-4:00

 

 

Mon Sep 07

 

Labor Day Holiday - No Class -

 

 

 

 

 

 

 

Organization of the Cell

No

Date

Time

Lecture

Lecturer

1

Mon Aug 03

2:30

Overview and the Secretory Pathway - Course organization, outline etc. General protein expression and maturation. The secretory pathway and nature of various organelles.

Sifers

2

Wed Aug 05

2:30

Nuclear Transport - Overall structure of the nucleus and nuclear pore complexes. Transport of proteins and RNAs into and out of the nucleus. Nuclear transport and the control of gene expression

Sifers

1

Thu Aug 06

5:15

OC-TA1 - Review general cell structures, their function and generation. Concepts of vesicular transport and protein import and export for the organelles

 

3

Fri Aug 07

2:30

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

Sifers

4

Mon Aug 10

2:30

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

Sifers

5

Wed Aug 12

2:30

The Golgi Complex - Regulated vesicular trafficking in the endomembrane system

Sifers

2

Thu Aug 13

5:15

OC-TA2 - Review of additional protein trafficking schemes

 

6

Fri Aug 14

2:30

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

Sifers

7

Mon Aug 17

2:30

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

Sifers

 

Wed Aug 19

2:30

Midterm Review -

 

3

Thu Aug 20

5:15

OC-TA3 - Review of cytoskeleton

 

 

Fri Aug 21

1:00

OC Midterm Exam -

 

8

Mon Aug 24

2:30

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

Sokac

9

Wed Aug 26

2:30

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

Sokac

10

Fri Aug 28

2:30

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

Wensel

11

Wed Sep 02

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

4

Thu Sep 03

5:15

OC-TA4 - Review of endocytosis, apoptosis and G-protein signaling

 

12

Fri Sep 04

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

13

Wed Sep 09

2:30

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

Pedersen

5

Thu Sep 10

5:15

OC-TA5 - Review of tyrosine kinase signaling, energy transduction and calcium signaling

 

14

Fri Sep 11

2:30

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

Pedersen

15

Mon Sep 14

2:30

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

Pedersen

 

Wed Sep 16

2:30

Faculty Review -

 

6

Thu Sep 17

5:15

OC-TA6 - Review of bioenergetics, transporters and ion channels

 

 

Fri Sep 18

1:00

OC Final Exam - 1:00-4:00

 

 

Mon Sep 07

 

Labor Day Holiday - No Class -

 

 

 

 

 

 

 

Science as a Profession

No

Date

Time

Lecture

Lecturer

1

Tue Aug 04

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 11

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

Shaulsky

3

Tue Aug 18

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

Kuspa

4

Tue Aug 25

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

Smith

 

 

 

 

 

 

Term 2

 

 

ABC-Applications to Biology of Computation

No

Date

Time

Lecture

Lecturer

1

Tue Oct 13

9:00

Introduction to ABC course and 'Omic' biology - Epigenomics and genome biology. Classes will be held in N315.

Milosavljevic

1

Wed Oct 14

5:15

TA Session 1 - Hardware and Contemporary Computing Infrastructure.

 

2

Thu Oct 15

9:00

Network 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

2

Fri Oct 16

5:15

TA Session 2 - A Beginner’s guide to UNIX / Linux and qsub commands.

 

3

Tue Oct 20

9:00

A Primer in Network Biology I - Elements in transcription networks, network motif and graph theory.

Liu

4

Thu Oct 22

9:00

A Primer in Network Biology II - Network inference from genomics data.

Liu

5

Tue Oct 27

9:00

Computational Analysis of Networks and Pathways I - Introduction to computational methods to analyze biological information from networks.

Liu

6

Fri Oct 30

9:00

Computational Analysis of Networks and Pathways II - Computational methods to decode and to analyze biological information from networks - advanced topics.

Liu

7

Tue Nov 03

9:00

Genome Structure - Variation, evolution and cancer.

Milosavljevic

8

Thu Nov 05

9:00

Recent Developments in Gene Mapping - Focused on gene mapping approach and challenges in functional annotation, interpretation and prioritization. Review of 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

9

Tue Nov 10

9:00

NGS Variation Analysis - Focused on SNP calling algorithms in NGS datasets, for both personal genome (when N=1) and population genomic studies (when N=many). Introduce and review the most popular SNP callers applied to NGS data analysis, including Samtools, GATK, and my own software (Atlas2 and SNPTools).

Yu

10

Thu Nov 12

9:00

Cancer Genomics - Application 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

11

Tue Nov 17

9:00

Cancer Genomic Medicine - - Practical challenges on implementing NGS-based tests in a cancer clinics. Why is it important (some case examples)? Progress made so far. What are the missing pieces? Opportunities for biomedical computational science.

Chen

12

Thu Nov 19

9:00

From Sequence to Structure - A 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

13

Mon Nov 23

9:00

Macromolecular Structure - This 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

14

Tue Nov 24

9:00

Sequence-Structure-Function I - This lecture will be an overview of common tools utilized in evolutionary analysis: BLAST, alignments, substitution matrices, and phylogenetic trees.

Wilkins

15

Tue Dec 01

9:00

Sequence-Structure-Function II - This lecture will focus on tools that take advantage of evolutionary information in order identify function and functional sites.

Wilkins

16

Thu Dec 03

9:00

Evolutionary Analysis - A formal approach to the genotype-phenotype relationship with molecular, clinical and population genetics applications.

Lichtarge

 

Thu Dec 10

9:00

ABC - Final Exam - Final Exam will be held in N315.

 

 

Thu Oct 29

 

Graduate Student Symposium - No Class -

 

 

Thu Nov 26

 

Thanksgiving Day - No Class -

 

 

Fri Nov 27

 

Thanksgiving Holiday - No Class -

 

 

 

 

 

 

 

Cancer

No

Date

Time

Lecture

Lecturer

1

Mon Nov 16

1:15

Introduction - Cancer and mouse models of cancer

Pangas

2

Fri Nov 20

1:15

Basic Concepts I - Oncogenes

Pangas

3

Mon Nov 23

2:30

Basic Concepts II - Tumor Supressor Genes

Pangas

4

Mon Nov 30

2:30

Tumor Microenvironment - The microenvironment and cancer stress response

Chen

5

Wed Dec 02

2:30

Tumor Metastasis -

Zhang

6

Fri Dec 04

2:30

Cancer Stem Cells -

Chan

 

Mon Dec 07

1:15

Faculty Review -

 

 

Tue Dec 08

1:00

CA Final Exam - 1:00-4:00

 

 

Thu Nov 26

 

Thanksgiving Day - No Class -

 

 

Fri Nov 27

 

Thanksgiving Holiday - No Class -

 

 

 

 

 

 

 

Cell Division

No

Date

Time

Lecture

Lecturer

1

Mon Oct 12

1:15

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

Zhang

2

Wed Oct 14

1:15

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

Zhang

3

Fri Oct 16

1:15

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

Zhang

4

Mon Oct 19

1:15

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

Ira

1

Tue Oct 20

5:15

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

 

5

Wed Oct 21

1:15

DNA Damage - DNA damage and repair

Ira

6

Fri Oct 23

1:15

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

Ira

7

Mon Oct 26

1:15

DNA Damage, Cell Cycle Checkpoints and Cancer - Cell cycle checkpoints, the DNA damage checkpoint and implications for cancer

Donehower

 

Mon Oct 26

2:30

Faculty Review Midterm - Lectures 1-7

 

2

Tue Oct 27

5:15

CD-TA2 - Review of DNA recombination and repair

 

 

Wed Oct 28

1:00

CD Midterm Exam - Lectures 1-7

 

8

Fri Oct 30

1:15

Chromosomes - Chromatin duplication and M phase chromosomes organization

Dang

9

Mon Nov 02

1:15

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

Bertuch

10

Fri Nov 06

1:15

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

Chang

11

Mon Nov 09

1:15

Cytokinesis - Cytokinesis mechanisms

Sokac

3

Tue Nov 10

5:15

CD-TA3 - Review of chromosome/chromatin/telomeres

 

12

Wed Nov 11

1:15

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

Westbrook

 

Tue Nov 17

2:30

Faculty Review - Lecture 8-12

 

4

Tue Nov 17

5:15

CD-TA4 - Review of cytokinesis, spindle & kinetochore assembly and growth regulation

 

 

Wed Nov 18

1:00

CD Final Exam - Lectures 8-12. (1:00-4:00 PM)

 

 

Thu Oct 29

 

Graduate Student Symposium - No Class -

 

 

 

 

 

 

 

Development

No

Date

Time

Lecture

Lecturer

1

Mon Oct 12

2:30

Core Concepts in Developmental Biology -

Groves

2

Wed Oct 14

2:30

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

Groves

3

Fri Oct 16

2:30

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

Groves

4

Mon Oct 19

2:30

Patterning the embryo from head to tail -

Groves

5

Wed Oct 21

2:30

ES cells, pluripotency and reprogramming / iPS -

Groves

1

Thu Oct 22

5:15

TA-DE1 -

 

6

Fri Oct 23

2:30

Stem cells in the adult -

Nguyen

2

Thu Oct 29

5:15

TA-DE2 -

 

 

Mon Nov 02

2:30

Mid-Term Faculty Review -

 

 

Wed Nov 04

1:00

DE Midterm Exam - 1:00-4:00

 

7

Fri Nov 06

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

Mon Nov 09

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

Wed Nov 11

2:30

Limb Development - A model system to illustrate developmental concepts

Groves

3

Thu Nov 12

5:15

TA-DE3 -

 

10

Fri Nov 13

2:30

Introduction to Drosophila embryogenesis - Overview of Drosophila oogenesis and embryogenesis

Jafar-Nejad

11

Mon Nov 16

2:30

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

Jafar-Nejad

12

Thu Nov 19

2:30

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

Jafar-Nejad

4

Thu Nov 19

5:15

TA-DE4 -

 

 

Fri Nov 20

2:30

Faculty Review -

 

 

Tue Nov 24

1:00

DE Final Exam - 1:00-4:00

 

 

Thu Oct 29

 

Graduate Student Symposium - No Class -

 

 

 

 

 

 

 

Ethics - Year 2

No

Date

Time

Lecture

Lecturer

1

Mon Oct 12

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

Nelson

2

Mon Oct 19

10:00

(2M) 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

Smith

3

Mon Oct 26

10:00

(2L2) Ethics of Biomedical Studies 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

4

Mon Nov 02

10:00

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

Faculty

 

Thu Oct 29

 

Graduate Student Symposium - No Class -

 

 

 

 

 

 

 

Genetics B

No

Date

Time

Lecture

Lecturer

1

Tue Oct 13

1:15

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

Zhou

2

Thu Oct 15

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 20

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 21

5:15

GB-TA1 - Held in N315

 

4

Thu Oct 22

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

5

Thu Oct 22

2:30

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

6

Tue Oct 27

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

2

Wed Oct 28

5:15

GB-TA2 - Held in N315

 

7

Tue Nov 03

1:15

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

Zhou

8

Thu Nov 05

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

3

Fri Nov 06

5:15

GB-TA3 - Held in N315

 

 

Tue Nov 10

2:30

Faculty Review -

 

 

Thu Nov 12

1:00

GB Midterm Exam - 1:00-4:00

 

9

Tue Nov 17

1:15

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

Matzuk

10

Thu Nov 19

1:15

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

Matzuk

4

Fri Nov 20

5:15

GB-TA4 - Held in N315

 

11

Mon Nov 23

1:15

Human Genetics I - Disease loci and pedigrees.

Lupski

12

Thu Dec 03

1:15

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

Lupski

13

Fri Dec 04

1:15

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

Lupski

5

Fri Dec 04

5:15

GB-TA5 - Held in N315

 

 

Wed Dec 09

1:15

Faculty Review -

 

 

Fri Dec 11

1:00

GB Final Exam - 1:00-4:00

 

 

Thu Oct 29

 

Graduate Student Symposium - No Class -

 

 

Thu Nov 26

 

Thanksgiving Day - No Class -

 

 

Fri Nov 27

 

Thanksgiving Holiday - No Class -

 

 

 

 

 

 

 

Method and Logic in Molecular Biology

No

Date

Time

Lecture

Lecturer

1

Tue Oct 13

10:00

Method and Logic Meeting - Attendance 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.

Mardon

2

Tue Oct 20

10:00

Method and Logic Meeting - Classes will be held in N302, N304, N310, N317 and M303 from this class onwards. Classes begin at 10 AM and end at noon.

Wilson

3

Thu Oct 22

10:00

Method and Logic Meeting -

Deneen

4

Tue Oct 27

10:00

Method and Logic Meeting -

Suter

5

Fri Oct 30

10:00

Method and Logic Meeting -

Scott

6

Tue Nov 03

10:00

Method and Logic Meeting -

Frankfort

7

Thu Nov 05

10:00

Method and Logic Meeting -

Wang

8

Tue Nov 10

10:00

Method and Logic Meeting -

Herman

9

Thu Nov 12

10:00

Method and Logic Meeting -

Chen

10

Tue Nov 17

10:00

Method and Logic Meeting -

Catanese

11

Thu Nov 19

10:00

Method and Logic Meeting -

Groves

12

Tue Dec 01

10:00

Method and Logic Meeting -

Jafar-Nejad

13

Thu Dec 03

10:00

Method and Logic Meeting -

Bertuch

 

Thu Oct 29

 

Graduate Student Symposium - No Class -

 

 

Thu Nov 26

 

Thanksgiving Day - No Class -

 

 

Fri Nov 27

 

Thanksgiving Holiday - No Class -

 

 

 

 

 

 

 

Term 3

 

 

Ethics - Year 3

No

Date

Time

Lecture

Lecturer

1

Thu Jan 07

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 14

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

3

Thu Jan 21

9:00

(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

Johnson

4

Thu Jan 28

9:00

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

Faculty

 

Mon Jan 18

 

Martin Luther King Day Holiday - No Class -

 

 

 

 

 

 

 

Ethics - Year 4

No

Date

Time

Lecture

Lecturer

1

Thu Feb 04

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

2

Thu Feb 11

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

3

Thu Feb 18

9:00

(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

4

Tue Feb 23

9:00

(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. This Class (only) will be held in M112.

Johnson

 

Mon Feb 15

 

President's Day Holiday - No Class -

 

 

 

 

 

 

 

Gene Regulation

No

Date

Time

Lecture

Lecturer

1

Mon Jan 04

1:15

Introduction to Gene Regulation - Sites of Gene Regulation: transcription initiation, termination, alternative RNA splicing, 3' end processing, nuclear export, cytoplasmic mRNA stability, translational regulation, protein degradation. Analysis of gene expression.

Cooper

2

Wed Jan 06

1:15

RNA Polymerase - the bacterial enzyme summarizing the kinetics and thermodynamics of the protein and its interactions with DNA, subunit function of the bacterial enzyme compared with the subunit structure of the eukaryotic enzyme. Regulatory functions of the polymerase.

Herman

3

Fri Jan 08

1:15

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

Herman

4

Mon Jan 11

1:15

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

Foulds

5

Wed Jan 13

1:15

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

Foulds

1

Wed Jan 13

5:15

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

 

6

Fri Jan 15

1:15

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

Foulds

7

Wed Jan 20

1:15

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

Lonard

8

Fri Jan 22

1:15

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

Lonard

9

Mon Jan 25

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

10

Wed Jan 27

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

2

Wed Jan 27

5:15

GR TA2 - Review of assembly of transcription complex including order and identity of factor loading Identify major transcriptional activator families and mechanisms

 

11

Fri Jan 29

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

12

Tue Feb 02

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

 

Wed Feb 03

1:15

Midterm Faculty Review -

 

 

Thu Feb 04

1:00

GR Midterm Exam -

 

13

Mon Feb 08

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

Wed Feb 10

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

Fri Feb 12

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

16

Tue Feb 16

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

17

Wed Feb 17

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

3

Wed Feb 17

5:15

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

 

18

Fri Feb 19

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

Mon Feb 22

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

20

Wed Feb 24

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

21

Fri Feb 26

1:15

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

Lloyd

4

Fri Feb 26

5:15

GR-TA4 - RNA self-splicing overview, concept of regulating synthesis and degradation of mRNA, review of ribosome assembly and initiation and termination of translation

 

 

Thu Mar 03

1:15

Faculty Review -

 

 

Fri Mar 04

1:00

GR Final Exam - 1:00-4:00

 

 

Mon Jan 18

 

Martin Luther King Day Holiday - No Class -

 

 

Mon Feb 15

 

President's Day Holiday - No Class -

 

 

 

 

 

 

 

Immunology

No

Date

Time

Lecture

Lecturer

1

Tue Feb 02

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

Tue Feb 09

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

3

Thu 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

1

Fri Feb 12

5:15

IM TA Review 1 - Overview of response to pathogen: Anatomy and function of organs of lymphatic system: general overview of B and T cell development and function

 

4

Tue Feb 16

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

5

Thu 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

2

Fri Feb 19

5:15

IM TA Review 2 - MHC I and MHC II - functions, derivation; B cells - antibody structure - subtypes, receptors and surface molecules, VDJ recombination; T cells - receptor and surface molecules, maturation, subtypes/function; T and B cell interactions

 

6

Tue Feb 23

2:30

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

Levitt

 

Thu Feb 25

2:30

Faculty Review -

 

 

Mon Feb 29

1:00

IM Final Exam - 1:00-4:00

 

 

Mon Feb 15

 

President's Day Holiday - No Class -

 

 

 

 

 

 

 

Macromolecules: Structure and Interactions

No

Date

Time

Lecture

Lecturer

1

Mon Jan 04

2:30

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

Tsai

2

Wed Jan 06

2:30

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

Weigel

1

Thu Jan 07

5:15

MSI-TA Review 1 -

 

3

Fri Jan 08

2:30

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

Tsai

4

Mon Jan 11

2:30

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

Tsai

5

Wed Jan 13

2:30

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

Tsai

2

Thu Jan 14

5:15

MSI-TA Review 2 -

 

6

Fri Jan 15

2:30

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

Schmid

7

Wed Jan 20

2:30

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

Schmid

3

Thu Jan 21

5:15

MSI-TA Review 3 -

 

8

Fri Jan 22

2:30

NMR - Basic theory and instrumentation, NOESY, COSY methods, distance geometry, multi-dimensional NMR, sample requirements.

Schmid

9

Mon Jan 25

2:30

Fluorescence/optical spectroscopy - Principles of photon absorption and emission, fluorescence energy transfer, anisotropy, lifetime instrumentation, optics. CD/IR

Schmid

10

Wed Jan 27

2:30

Ligand Binding & Forces in Solution/Thermodynamics - General 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

4

Thu Jan 28

5:15

MSI-TA Review 4 -

 

 

Fri Jan 29

2:30

Midterm Faculty Review -

 

 

Mon Feb 01

1:00

MS Midterm Exam - 1:00-4:00

 

11

Wed Feb 03

2:30

Allostery 1 - Ligand binding and how it alters protein structure and dynamics; allostery and how it mediates and regulates protein function.

Pedersen

5

Thu Feb 04

5:15

MSI-TA Review 5 -

 

12

Fri Feb 05

2:30

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

Pedersen

13

Mon Feb 08

2:30

Binding Kinetics - Basic kinetics of unimolecular and bimolecular reactions. Introduction to enzyme kinetics.

Pedersen

14

Wed Feb 10

2:30

Enzyme Kinetics/Catalysis - Michaelis-Menten kinetics, Inhibition, kcat and kcat/Km, allosteric enzymes. Computational kinetics.

Pedersen

6

Thu Feb 11

5:15

MSI-TA Review 6 -

 

15

Fri Feb 12

2:30

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

Pedersen

16

Wed Feb 17

2:30

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

Pedersen

7

Thu Feb 18

5:15

MSI-TA Review 7 -

 

17

Fri Feb 19

2:30

Protein – Small Molecule Interactions - Molecular basis of specificity, protein ligand interactions - structural basis of H-bonding, salt bridges and other interactions

Prasad

18

Mon Feb 22

2:30

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

Prasad

19

Wed Feb 24

2:30

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

Prasad

20

Fri Feb 26

2:30

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

Pedersen

 

Tue Mar 01

1:15

Faculty Review -

 

 

Wed Mar 02

1:00

MS Final Exam - 1:00-4:00

 

 

Mon Jan 18

 

Martin Luther King Day Holiday - No Class -

 

 

Mon Feb 15

 

President's Day Holiday - No Class -

 

 

 

 

 

 

 

Neuroscience

No

Date

Time

Lecture

Lecturer

1

Tue Jan 05

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 07

2:30

Neuronal Biophysics - Structure and function of the major membrane proteins responsible for establishing ionic gradients in neurons and how they are used to transmit electrical information.

Jankowsky

3

Tue Jan 12

2:30

Synaptic Physiology - Specialized structures and proteins that allow electrical signals to be converted to chemical messengers and then back again to facilitate cell-cell communication

Jankowsky

4

Thu Jan 14

2:30

Systems Neuroscience - General principles of how neuronal networks are wired to process sensory signals and inform an animal's behavior.

Jankowsky

5

Tue Jan 19

2:30

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

Jankowsky

 

Thu Jan 21

2:30

Faculty Review -

 

 

Tue Jan 26

1:00

NE Final Exam - 1:00-4:00

 

 

Mon Jan 18

 

Martin Luther King Day Holiday - No Class -

 

 

 

 

 

 

 

Term 4

 

 

Introduction to Biostatistics

No

Date

Time

Lecture

Lecturer

1

Tue Mar 15

1:15

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

Frolov

2

Thu Mar 17

1:15

Summarizing Data -

Guffey

3

Tue Mar 22

1:15

Differences between groups -

Minard

4

Thu Mar 24

1:15

Special cases of two groups -

Minard

5

Tue Mar 29

1:15

Rates and proportions -

Minard

6

Thu Mar 31

1:15

Measures of association -

Sangi-Haghpeykar

7

Tue Apr 05

1:15

Power and sample size -

Minard

8

Thu Apr 07

1:15

Confidence intervals -

Liu

 

Tue Apr 12

1:00

BS Midterm Exam - 1:00-4:00

 

9

Thu Apr 14

1:15

Multiple factors and interaction -

Minard

10

Tue Apr 19

1:15

Linear regression and correlation -

Minard

11

Thu Apr 21

1:15

Multiple regression -

Minard

12

Tue Apr 26

1:15

Repeated measures -

Minard

13

Thu Apr 28

1:15

Nonparametric methods -

Liu

14

Tue May 03

1:15

Survival analysis -

Hilsenbeck

15

Thu May 05

1:15

Experimental design -

Minard

 

Thu May 12

1:00

BS Final Exam - 1:00-4:00

 

 

Fri Mar 25

 

Easter Holiday - No Class -

 

 

 

 

 

 

 

Introduction to Intellectual Property

No

Date

Time

Lecture

Lecturer

1

Tue Mar 22

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: Classes will be held in N311.

Turley

2

Thu Mar 24

9:00

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

Turley

3

Tue Mar 29

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 31

9:00

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

Turley

5

Tue Apr 05

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 07

9:00

Copyrights - Copyright law, particularly with regard to course content and articles and other faculty publications.

Turley

7

Tue Apr 12

9:00

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

Turley

8

Thu Apr 14

9:00

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

Turley

 

Fri Mar 25

 

Easter Holiday - No Class -

 

 

 

 

 

 

 

Introduction to Scientific Writing

No

Date

Time

Lecture

Lecturer

1

Mon Mar 14

2:30

Getting Prepared to Write - Class meets in N311

Marriott

2

Thu Mar 17

2:30

Parts of a Scientific Manuscript - I -

Marriott

3

Mon Mar 21

2:30

Parts of a Scientific Manuscript - II -

Marriott

4

Thu Mar 24

2:30

Writing the First Draft -

Marriott

5

Mon Mar 28

2:30

Striving for Clarity -

Marriott

6

Thu Mar 31

2:30

Achieving Brevity through Revision -

Marriott

7

Mon Apr 04

2:30

Grammar for Scientists -

Marriott

8

Thu Apr 07

2:30

Submitting, Revising and Responding to Reviews -

Marriott

 

Fri Mar 25

 

Easter Holiday - No Class -

 

 

 

 

 

 

 

Research Design

No

Date

Time

Lecture

Lecturer

1

Wed Mar 16

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 23

1:00

Working Groups 1 - Project selection and design. Room assignments will be provided in the March 18 Introduction session.

Peters

3

Wed Mar 30

1:00

Working Groups 2 - Project selection and design

Prasad

4

Wed Apr 06

1:00

Working Groups 3 - Project selection and design

Zhou

5

Wed Apr 13

1:00

Working Groups 4 - Project selection and design

Staff

6

Wed Apr 20

1:00

Working Groups 5 - Project selection and design

 

7

Wed Apr 27

1:00

Working Groups 6 -

 

8

Wed May 04

1:00

Working Groups 7 -

Staff

9

Wed May 11

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 Mar 25

 

Easter Holiday - No Class -