Updated: December 10, 2014
2015 MEDI 502 SYLLABUS
MEDI 502 is an interdivisional laboratory research course that is required of all new graduate students in the Experimental Medicine Program. The format of this course creates a unique opportunity for graduate students to become acquainted with research topics and techniques outside the scope of their own laboratory or of the Division within which the students are enrolled. This benefits not only the students, but fosters interactions between faculty and students in all Divisions of the Department of Medicine.
This is also a course in which the student must take most of the responsibility for arranging the laboratory rotations and deciding on a grant proposal topic. The format allows a great deal of flexibility, as well as responsibility, on the part of the student. The two main goals are to be able to present a research seminar, and to prepare a research proposal, both of which are essential for any future careers in biomedical research.
Laboratory rotations: Period 1:January 8 to February 13, 2015
Period 2:February 16 to March 13, 2015
For each period, students must arrange research rotations in the laboratories of faculty members in the Experimental Medicine Program, in two divisions that are distinct from the division in which the student is working. At least one of the rotations should be outside of the site at which the student is working. The time allotted to each research rotation has generally been at least 4 full workdays over each period, but any arrangement can be made between the individual student and faculty. In no case should the amount of time be less than four days, but the upper limit will depend on the student and supervisor's interests and time availability. During this time, the student will be exposed to the theory and techniques being used in one or more projects of the host laboratory. It is expected that the student will interact with multiple members of the host laboratory, and wherever possible, participate in experimental procedures.
Introductory Meeting: There will be an introductory meeting of the class on Tuesday, January 8, 2015, 3:00 – 5:00 pm, at the Eye Care Centre Auditorium, 2550 Willow Street. The Course Coordinatorswill discuss course objectives and deadlines and present two lectures covering the elements of a good scientific presentation, and how to write a grant proposal.
Research Validation: Dr. Robert Kay will present this lecture on Tuesday, January 20th at 3:00-5:00 pm at the Eye Care Centre Auditorium.
Seminar presentations: Seminar presentations by students based on either or both laboratory rotations. These presentations will be limited to 20 minutes, typically 15 minutes for the formal presentation and 5 minutes for a spirited question and answer session.
Date / Time / LocationThursday, January 8 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Tuesday, January 20 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Tuesday, February 17 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Thursday, February 19 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Tuesday, February 24 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Thursday, February 26 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Tuesday, March 3 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Thursday, March 5 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Tuesday, March 10 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Thursday, March 12 / 3:00 – 5:00 pm / Eye Care Centre Auditorium
Thursday, March 26 / 3:00 – 5:00 pm / Diamond Healthcare Centre
10th floor -10206 (PIZZA)
Grant proposal: A formal, CIHR-style grant proposal will form a major part of the mark. The student will complete this using CIHR’s forms for research and budget modules and Common CV for CV module. Design of this proposal should be done in consultation with faculty members from the host labs, and should incorporate elements of the work that the student was exposed to during the laboratory rotations, but can also incorporate some of the student's own research interests. A technical abstract will be due midnight March 6, 2015. This will be reviewed by the Course Coordinators to help direct development of the proposal. Electronic submission of proposals will be due midnight Wed. April 29, 2015 (last day of exam week). On the last meeting day (Mar 26) another presentation describing the design and preparation of the grant proposals will be given by the course coordinator and the floor will be open to discussion.
Assessment of the student's performance:
a)Evaluations by the principle investigators in both host laboratories (20%).
b) Evaluation of the seminar presentation (25%), by the class and course co-ordinators.
c) Grant proposal (45%).
d)Attendance (10%) ≤1 absence=10%, 2 absences=7%, 3 absences=4%, >3 absences=0)
e)BONUS discussion points (maximum of 3%).
MEDI 502 LABORATORY RESEARCH ROTATION SLOTS
2015
CARDIOLOGY
Cardiac Imaging
Principal Investigator: Dr. G.B. John Mancini
Contact: Eunice Yeoh, VGH Research Pavillion
Phone: 604-875-5477
E-mail:
The Cardiac Imaging Research Laboratory is dedicated to determining the structure and function of arterial beds for the purpose of evaluating effectiveness of therapies designed to promote vascular health. The laboratory is a pioneer in the application of digital imaging methods to coronary arteriograms and cardiac ventriculograms. The laboratory has also expanded to facilitate quantitation of carotid atherosclerosis and endothelial function using brachial ultrasound techniques and is currently involved in mult-centre trials using cardiac computed tomography. The largest ongoing projects are world-wide clinical trials requiring our laboratory to undertake computerized image analyses. These trials are investigating the optimal initial approach for management of coronary disease (i.e. percutaneous coronary intervention versus drug treatment) and whether prognosis can be improved by stenting previously occluded coronary arteries. These trials are funded by the NIH, MRC and the VA Clinical Trials Program.
Critical Care
Principal Investigator: Dr. Keith R. Walley, M.D. (University of Manitoba, 1981)
Phone:604-806-8136
Fax: 604-806-8351
E-mail:
The focus of this laboratory is to:
- Investigate the mechanism of decreased cardiac function during severe infections.
- Investigate the mechanism of impaired oxygen consumption during severe infections.
- Understand the mechanisms that lead to organ dysfunction (lung and gut) during severe infections.
- Techniques in use include isolation and culture of cardiac myocytes and leukocytes, ELISA, RT-PCR, caspase activity assays, EMSA, morphometric analysis of tissue samples, and 3D deconvolution microscopy.
CARDIOVASCULAR PHYSIOLOGY
Principal Investigator: Dr. Darren E. R. Warburton
Phone: 604-822-1337
Email:
Internet address:
The Cardiovascular Physiology and Rehabilitation Laboratory evaluates the effects of improvements in cardiovascular function on the health status and Quality of Life of children, adolescents, adults, the elderly and patients with chronic disease and/or disability (including individuals with heart disease, organ transplantation, and spinal cord injury). We also specialize in the evaluation and training of high performance able-bodied and disabled athletes.
Our facility houses a mass spectrometer (Amis 2000), an applanation tonometer, a transcranial Doppler system, a stand-alone 2-D Doppler cardiac ultrasound (Sonos 2500 Hewlett-Parkard), two impedance cardiography systems, a beat-by-beat blood pressure monitor (Finapres, Ohmeda), a near-infrared spectrophotometer (Niro 300, Hammamatsu), two cardiac stress testing systems (including two 12 lead ECG and treadmill systems), two metabolic carts (including a portable metabolic cart), a telemetric electrocardiography (3-lead) system, several pulse oximeters, heart rate variability analysis equipment, eight interactive video game training systems (GameBikeTM, Cateye), ten Monark rehabilitation cycle ergometers, three electronically braked cycle (arm and leg) ergometers, and an automated defibrillator. This equipment allows for the complete evaluation of left ventricular function, diffusion capacity, oxygen kinetics, endothelial function, heart rate variability, and cerebral and skeletal muscle oxygenation and blood flow during resting and/or exercise conditions.
Nutritional Epigenomics and Cardiometabolic Disease
Principal Investigator: Dr Angela M Devlin, PhD
Division of Endocrinology, Department of Paediatrics, Child & Family Research Institute
Phone:604.875.2000 x 5378
Fax: 604.875.3597
E-mail:
My laboratory is focused on investigating:
- the interactions of dietary factors with epigenetic processes and development of cardiometabolic risk factors (eg obesity)
- the molecular mechanisms contributing to vascular dysfunction associated with obesity, hyperhomocysteinemia
- metabolic programming and risk for cardiovascular disease
Techniques include: genotyping, gene expression, immunoblots, DNA methylation analysis (Pyrosequencing), chromatin immunoprecipitation, cell culture.
DERMATOLOGY
Molecular Markers of Skin Cancer and Skin Inflammation
Principal Investigator:Youwen Zhou, MD, Ph D, Assistant Professor
MD. 1995, University of Toronto, Ph.D. 1990, State University of New York
Molecular Medicine Lab (MML) & Chieng Genomics Centre
Department of Dermatology and Skin Science
Phone: 604-875-4747
Fax: 604-873-9919
Email:
The MML Lab aims to translate the latest advances in biomarker research into clinical applications. The experimental approaches used include expression genomics, next generation sequencing, molecular genetics techniques, and retroviral mediated gene transfer.
Current projects include:
(1). Pathogenic significance and therapeutic targeting of extracellular matrix molecules in metastatic melanoma
(2). Novel diagnostic and prognostic markers for cutaneous T cell lymphoma
(3). Mutation identification of hereditary primary hyperhidrosis
(4). Novel anti-inflammatory agents for chronic inflammatory skin diseases
Skin appendages in health and disease
Principal Investigator: Dr. Kevin McElwee, Ph.D. (University of Dundee, 1996)
Phone: 604 875-4111 ext. 63908
Fax: 604 875-4376
E-mail:
Webpage:
The following projects are the main focus of this laboratory:
- The mechanisms of hair loss involved in alopecia areata and scarring alopecias (suspected autoimmune alopecias).
- Immune privilege in hair follicles and its functional role.
- The relationship of skin cancer to hair follicle biology.
- The role of chemokines in the development and growth of basal cell carcinomas.
IMMUNOLOGY - Cellular Immunology/Gene Expression Profiling Laboratory
Principal Investigator: Dr. Cheryl D. Helgason, Ph.D.
Cancer Endocrinology Dept., B.C. Cancer Research Center
Phone: 604-877-6098 ext. 3007 Fax: 604-877-6011E-mail:
The primary research area in this laboratory involves examining the role of dendritic cells (DC) and regulatory T (Tr) cells in initiation and control of cellular immune responses. We utilize both transgenic and knock-out mouse models of disease to understand what role these two cell types play in the initiation and progression of autoimmunity and prostate cancer. Techniques utilized in these studies include isolation of lymphoid tissues, magnetic purification of sub-populations of immune cells, flow cytometry, cell culture, and various types of functional analyses (i.e. T cell proliferation assays). A second area of investigation involves the use of serial analysis of gene expression (SAGE) and Affymetrix array analysis to determine gene expression profiles during mouse embryonic development and during the in vitro differentiation of murine embryonic stem (ES) cells respectively. The first project involves the dissection of selected tissues from mouse embryos at critical stages during organ/tissue development. The second involves the culture and differentiation of ES cells. Data analysis requires the use of a number of bioinformatic tools (i.e. GeneSpring; DiscoverySpace) to generate lists of candidate genes that may be involved in the biological processes of interest (i.e. pancreas organogenesis). Validation studies involve techniques such as quantititative RT-PCR, in situ hybridization, and ultimately inhibition and/or over-expression studies.
Innate Immunity
Principal Investigator: Dr. Ted Steiner (M.D. Duke Univ., 1992)
Phone: 604-875-4111 x 68492Fax:604-875-4013 E-mail:
Areas of active research include basic mechanisms of flagellin regulation by Toll-like receptor 5 and downstream signaling pathways; Role of anti-flagellin immune responses in colitis; Effects of stress signals on TLR responses in intestinal epithelial cells.
Innate Immunity
Principal Investigator: ZakariaHmama, PhD
UBC-Division of Infectious Diseases
D458, Heather Pavilion East, 2733 Heather St. Email:
Research in this lab is concerned with molecular and subcellular mechanisms of Tuberculosis pathogenesis with a particular focus on intracellular persistence of M. tuberculosis in the macrophage and down-modulation of antigen presentation.
Methodologies & Techniques: Cloning, Transformation, Transfection, Protein Expression and Purification, SDS-PAGE/WB, FACS, Confocal, ELISA.
Neonatal Immunology
Principal Investigator: Pascal Lavoie, MD PhD FRCPC
Child & Family Research Institute
Phone: 604-875-2000 x7318 (office) 604-875-2000 x6705 (lab) Fax: 604-875-3106
E-mail:
This laboratory studies on innate and adaptive immune defenses in neonates, particularly those born early in gestation. One main project focuses on understanding why newborns are highly susceptible to infections. This is achieved specifically by investigating mechanisms for inflammatory Toll-like receptor-mediated hypo-responses in babies born prematurely, using cell immunology, flow cytometry and molecular biology techniques (Q-PCR gene expression, western blots). Toll-like receptors are family of molecules playing a critical role in first-line innate immune defenses, particularly in neonates.
A second main project focuses on neonatal invariant Natural Killer T cells and their unique phenotype expressed in neonatal life. T lymphocytes play a central role in adaptive immune defenses by "orchestrating" the activity of other cells such as the antibody-producing B lymphocytes, or by killing virally-infected cells directly. NKT cells are of main interest because of their potential in regulating excessive inflammatory responses from other innate (i.e. first line) immune cell types. At the moment, our efforts in this area are focused on understanding how NKT cells emerge in neonates, with particular emphasis on receptor regulating proliferation and maintenance of this highly specialized immunological compartment.
Clinical Immunology Laboratory
Principal Investigator: Dr. Paul Keown
Phone: 604-875-5555 ext. 62042
Fax: 604-875-4709
E-mail:
The clinical immunology laboratory is located at the Vancouver General Hospital and serves as a central laboratory for the number of UBC programs, including bone marrow transplantation, solid organ transplantation, autoimmunity and genetic disorders. It comprises four principal divisions:
1)Histocompatibility and immunogenetics (HLA typing, donor-recipient cross-matching, paternity testing, gene polymorphism using robotics DNA extraction, PCR, automated gene sequencing, fragment analysis, liquid bead-based reverse SSOP (Sequence Specific Oligonucleotide Probe)
2)Immunologic monitoring (T-cells, B-cells and antibody monitoring using Flow cytometry and solid-phase Luminex assay)
3)Immunotherapeutics (clinical trial-oriented research that involves study of pharmacokinetics and pharmacodynamics of immunosuppressive drugs)
4)Autoimmunity (auto-antibody detection using ELISA technique)
Cellular regulation of peripheral tolerance
Principal Investigator: Dr. Megan Levings
Phone: 604-875-4111 ext 66742
Fax:604-875-4497
E-mail:
Research in my laboratory is focused on a novel subset of CD4+ T cells, termed T regulatory (Tr) cells, which control immune homeostasis. Current work is focused on determining how Tr cells differ from normal CD4+ T cells at both the biochemical and molecular phenotype, and elucidating their role in transplantation tolerance, cancer and infectious diseases. An immediate goal is to identify novel Tr-specific molecules which may reveal their mechanism of action and/or be used as a tool to isolate and track Tr cells more efficiently. A long term goal is to a) develop methods to generate Tr cells in vitro for use as a cellular therapy to replace standard immunosuppression in the context of organ transplantation; and b) identify ways to deplete Tr cells in order to increase the immune response to cancer and chronic infectious diseases.
Signal Transduction in Cell Adhesion and Migration
Principal Investigator: Dr C. James Lim, PhD
Assistant Professor, UBC Department of Pediatrics
Scientist, Child and Family Research Institute
Email:
Phone: 604 875 2000 ext. 4795
Research Interest:
Integrins in cell adhesion and migration, protein-protein interactions, protein phosphorylation and kinase signaling.
My lab research is aimed at understanding the molecular mechanisms governing cell adhesion and motility, in particular those involving white blood cell function in normal as well as in pathologic outcomes, including cancer and autoimmunity. Circulating white blood cells represent the immune system’s frontline defence against infection. The successful and accurate targeting of white blood cells to inflamed tissues is facilitated by cell adhesion receptor proteins expressed on the surface of these cells. However, aberrant function of these receptor proteins and the cellular signals that regulate them can lead to diseases of the immune system, including leukemia, lymphoma and autoimmunity. Ongoing research is focused on understanding the differences in cellular signalling between healthy and diseased cells in order to explore and evaluate novel signalling targets for therapeutic intervention in blood diseases. My laboratory employs a multi-disciplinary approach that encompasses cell biology, protein biochemistry, molecular biology and immunology.
Signal Transduction
Principal Investigator: Dr. Alice Mui
Phone: 604-875-5555 ext 62242 Fax:604-875-4497
E-mail:
The cytokine interleukin-10 (IL-10) is a key regulator of both innate and acquired immunity with activities ranging from co-stimulation of thymocytes, mast cells and B-cells to inhibition of macrophage, NK, dendritic and T-cell function. Produced by activated B-cells, keratinocytes, monocytes and macrophages, IL-10 was initially detected as a Th2 cell product that inhibited the proliferation, development and function of Th1 cells. The molecular cloning of IL-10 and subsequent studies utilizing recombinant cytokine revealed that although IL-10 exerted direct effects on T-cells, its major site of action was the activated macrophage. Research interests in my lab focus on the IL-10 regulation of macrophage and T cell activation, IL-10 induced gene expression, and the role of STAT transcription factors in signal transduction.
INFECTIOUS DISEASES DIVISION - Bioinformatics Studies of Bacterial Genomes.
Principal Investigator: Dr. Artem Cherkasov
Phone: 604-875-4111 x 68541 Fax: 604-875-4013
E-mail:
My group's research is focused on bioinformatics and molecular modeling methods and techniques for studying genomes and proteomes of pathogenic organisms.
Studies are currently underway on:
- Development of new bioinformatics methods for identification of pathogenic virulence factor proteins.
- 'In silico' development of new antimicrobial drugs.
- Development of reliability analysis approach for the area of structural genomics.
Innate Immunity
Principal Investigator: Dr. Neil E. Reiner A.B. (Oberlin College, 1970), M.D. (Case-Western Reserve University, 1974)
Phone: 604-875-4011
Fax:604-875-4013
E-mail:
Areas of active research include the regulation of macrophage activation, monocyte gene expression, and the role of protein kinases and phosphoproteins in signal transduction for monocyte activation, phagosome biogenesis.