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

Johnson

3

Tue Aug 18

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

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