2015 Course Summary (pdf) - Laboratory Medicine and Pathobiology

This course explores
the
powerful
intersection
of
Physics, Biological
science, and Imaging
technologies. Basic
principles of optics
such as the nature
of light, diffraction,
refraction,
the
nature of lenses, and the design of the light microscope will be covered in this course. We will discuss
phase contrast, dark field, interference contrast, and modulation contrast, as well as polarization and
fluorescence microscopy. Different types of microscopes and imaging technologies and their use in
biological sciences including dissecting, compound, scanning and transmission electron microscopes,
positron emission tomography, single photon emission computed tomography, nuclear magnetic
resonance imaging, ultrasound, optical imaging, stereology and 3D imaging, optical microscopy,
nanoscopy, live cell and whole animal imaging techniques, cytogenetics, X-ray crystallography and
imaging in forensic science and their use in diagnostic pathology will be discussed. Some of the lectures
will be complemented by laboratory sessions demonstrating these systems. As a result, students will
have the opportunity for hands-on experience with state-of-the-art optical, electronic, and digital
imaging equipment guided by an experienced staff from the University, hospitals, research facilities,
government agencies as well as the industry. This course will
focus on the theory, application and implementation of
different imaging techniques, and more importantly, on
application of biological experimentation relevant to modern
biological research or clinical biochemical studies and the common real-life research goal in the industry,
hospitals and research laboratories.
Objective: At the end of this course participants
Schedule: Tuesdays from January 13 to March
are expected to have acquired knowledge about
31, 2015. See program schedule for full details.
different types of microscopes and imaging
technologies, their functionality and use in
Curriculum: Each lecture consists of theory
biological sciences. The course will provide
and/or
hands
on
microscopy/imaging
students with the knowledge and expertise to
instrument, research facility or laboratory tour,
implement cutting edge microscopic and
or instrument demonstration.
imaging methods within their own laboratories.
Prerequisite: No specific courses are required;
however, students should have successfully
completed advanced courses in molecular
biology, cell biology and/or biochemistry.
Priority will be given to more senior PhD
students.
Evaluation: Four methods of evaluation will be
used. (1) 10% Participation in Lectures and
Laboratory Sessions (2) 25% Midterm Test (3)
35% Written Grant Proposal (4) 30% Oral
Presentation.
Coordinator: Dr. Sima Salahshor
Department of Laboratory Medicine and Pathobiology (LMP), Faculty of Medicine, University of Toronto
E: [email protected] || T: (+1) 416-841-7959
LMP1006H - 2015
Last updated Jan 2015
Jan 13, 2015
10 AM- 12 Noon
Dr. Sima Salahshor
Department of Laboratory of Medicine and Pathobiology (LMP)
Faculty of Medicine, University of Toronto & ScienceHA, Inc.
E: [email protected]
Title: Course overview
Synopsis: Course content and grant proposal format will be discussed
Dr. Sergio Grinstein
The Hospital for Sick Children, Department of Biochemistry, U of T
E: [email protected]
Title: An overview of the fundamentals of fluorescence microscopy
Synopsis: This lecture will cover the basic principles and will describe the equipment necessary to
visualize fluorescently labeled specimens (both live and fixed). The topics featured will include the
fundamentals of fluorophore absorption/excitation/emission, and microscope and camera optics. The
goal is to familiarize students with the theoretical and practical aspects behind fluorescence microscopy,
with a focus on cellular imaging.
Paul Paroutis and Michael Woodside
The Hospital for Sick Children, Imaging Facility, McMaster North Annex and TMDT
E: [email protected] || [email protected]
Title: Basic and advanced live cell imaging: principles and applications
Synopsis: This lecture will focus on four specialized fluorescence microscopy techniques pertaining to
live cell imaging. More specifically, techniques such as total internal reflection microscopy (TIR-FM),
fluorescence lifetime imaging (FLIM), fluorescence recovery after photobleaching (FRAP) and Forster
resonance energy transfer (FRET) will be described, with a view to establishing quantitative
measurements of protein mobility, protein-protein interactions and vesicle fusion.
Jan 20, 2015
10 AM- 12 Noon
Dr. Shiva Amiri
Ontario Brain Institute
E: [email protected]
Title: Imaging as Big Data - The Opportunities and Challenges
Synopsis: As imaging technologies improve and their numbers and types increase as a tool for diagnosis,
we are faced with a big data challenge and an array of opportunities to make the most of this data. Not
only is the size, volume, variety, and potential privacy issues of this data present some unique challenges
but our ability to efficiently standardize, collect, manage, and process this data ultimately determines
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it's utility and the efficacy of the resulting analysis. It is an exciting time for big data approaches for
imaging which holds promise for improved and faster diagnosis and discovery!
Dr. Isabelle Aubert
Sunnybrook Health Sciences Centre, Imaging Research, Sunnybrook Research Institute
E: [email protected]
Title: It’s your data: Make it count, Make it shine. Introduction to unbiased stereology and virtual slices
Synopsis: This lecture will provide an introduction to a set of methods designed to rigorously quantify
and present imaging data. Stereology is used to quantify the size, length, volume and number of objects
(i.e. cells). Two-dimensional (2D) and three-dimensional (3D) virtual slide acquisition, analysis and
presentation will also be discussed.
Jan 27, 2015
10 AM- 12 Noon
Dr. Jeff Lee
Department of Laboratory Medicine and Pathobiology, University of Toronto
E: [email protected]
Title: X-ray crystallography: principles and applications
Synopsis: X-ray crystallography has become the most common method to obtain three-dimensional
structures of proteins and protein–protein complexes. This lecture will briefly describe the fundamentals
of X-ray crystallography and its applications in medical research. Topics to be covered include
background to structural biology and the techniques involved in structure determination. In addition,
students will learn to critically examine crystal structures deposited in the Protein Data Bank. Finally, the
importance of protein structures to drug development and biomedical research will be illustrated with
real life examples.
Feb 3, 2015
10 AM- 12 Noon
Douglas Holmyard and Dr. Rita Kandel
Advanced Bioimaging Centre
The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital
Department of Pathology and Laboratory Medicine, U of T
E: [email protected] | E: [email protected]
Title: Principle of Scanning (SEM) and Transmission Electron Microscopy (TEM)
Synopsis: General principles underlying electron microscope and differences between
scanning and transmission microscopes will be discussed.
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Feb 10, 2015
10 AM- 12 Noon
Dr. Sima Salahshor
Department of Laboratory of Medicine and Pathobiology
Faculty of Medicine, University of Toronto & ScienceHA, Inc.
Mid-term Exam: Multiple choice exam from 10 AM to 10:45 AM
Proposal Q & A: Grant Proposal Application Review
Feb 17, 2015
10 AM- 12 Noon
Dr. Susan Newbigging
Mount Sinai Hospital, Toronto Centre for Phenogenomics
E: [email protected]
Title: Microscopic analysis and interpretation in veterinary pathology
Richard Steele
Olympus Canada Inc.
E: [email protected]
Title: Principles of Light Microscopy in Biomedical Research
Synopsis: Light microscopy is vital to experimental pathology. Appropriate tissue handling, fixation and
orientation are features of the sample that impact interpretation of the tissue under the microscope.
These features will determine the type of architectural and cellular features that are visible and
quantifiable at different magnifications. Understanding human vision, optics and tissue preparation are
all key to coming up with a valuable and well-guided interpretation of tissue architecture. Using
examples from various lab animal species, review of the principles of optics in light microscopy such as
illumination, lenses, magnification, numerical aperture and optical aberrations, in order to interpret
meaningful histological and histopathology data will be discussed. Aspects of experimental design will
be reviewed as well ie. when to use histology slides for analysis, what objectives to analyze certain
lesions at, why do histopathology; what to quantify, how to quantify; when you need a pathologist;
advantages and disadvantage of brightfield versus fluorescence imaging for pathology analysis.
Feb 24, 2015
10 AM- 12 Noon
Dr. Kenichi Okamoto and Dr. John Georgiou
Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute
E: [email protected] || E: [email protected]
Title: Application of 2-Photon Microscopy for Cellular Imaging and Photoactivation
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Synopsis: Synopsis: 2-photon microscopy is suitable for deep tissue imaging using infra-red light pulses,
allowing photo-activation within a small volume. This lecture will outline the principles of 2-photon
microscopy and demonstrate applications of live photoactivation techniques combined with imaging of
fluorescent probesin living brain sections. We will discuss molecular and cellular imaging, 2-photon
photoactivation of protein activity and imaging at the synapse level.
March 3, 2015
10 AM- 12 Noon
Dr. Mina Lakshman & STTARR Team
VisualSonics, Inc & STTARR Innovation Centre
E: [email protected]
Title: High-frequency ultrasound and photoacoustic imaging for preclinical research
Synopsis: The lecture will focus on the research applications of high-frequency ultrasound and
photoacoustic imaging for preclinical research. Participants will learn and see how these technologies
work in a laboratory setting and understand the basics of the workflow and software quantification
tools. Specific examples will be presented in the fields of cancer and cardiovascular research.
March 10, 2015
10 AM – 12 Noon
Dr. Kevin Conway
Nikon Canada Inc.
E: [email protected]
Title: Latest Advances in Imaging Technologies
Dr. Roya Navab
Princess Margaret Cancer Centre, Ontario Cancer Institute, University of Toronto
E: [email protected]
Title: Molecular imaging of tumor stroma alterations in cancer
Synopsis: Tumor stromal biomarkers have been recognized to play a critical role in the development and
metastasis of several epithelial carcinomas, including non-small cell lung cancer (NSCLC). Expression of
these stromal genes appears to be associated with structural alterations of fibrillar collagen matrices,
such as collagen cross-linking and collagen stiffness. These alterations can be readily visualized and
quantified using second harmonic generation (SHG) microscopy.
Diagnosis is a vital step in cancer management and typically involves histological imaging of biopsied or
resected tissue sections. The focus of the lecture is SHG imaging as a powerful method of illuminating
fibrillar collagens in clinical diagnosis of cancer. It is a label-free imaging technique that enables
surgeons to perform live biopsies during endoscopic procedures. Molecular imaging of tumor stroma
using SHG allows for early detection and treatment of cancer.
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March 17, 2015*
11 AM - 1 PM
Dr. Mary Ann George and Raymond Wong
Cytogenomics Laboratory, Department of Paediatric Lab Medicine, and Cytogenomics & Genome
Resources Facility, The Centre for Applied Genomics, The Hospital for sick Children
E: [email protected] || E: [email protected]
Title: Cytogenomic technologies to investigate genomic organization and structural alterations.
Synopsis: This lecture will briefly introduce the field of cytogenetics and molecular cytogenetics and
then outline the current major technologies that are used to detect both intra and interchromosomal
rearrangements. These include methods used for bright field microscopy such as G-banding, C-banding
as well as those used for fluorescence microscopy. There will be a focus on Fluorescence in situ
Hybridization (FISH) applications including interphase and metaphase FISH, Spectral Karyotyping (SKY)
and whole chromosome painting. The most appropriate choice of technology for validation, detection or
characterization of specific chromosomal alterations will be discussed. Illustrative cases or projects from
research and clinical settings will be presented.
March 24, 2015
10 AM- 12 Noon
Dr. Mojgan Hodaie
Department of Surgery, Faculty of Medicine, University of Toronto
Neurosurgery, Joey and Toby Tanenbaum Gamma Knife Radiosurgery Centre, University Health
Network, Toronto Western Hospital
E: [email protected]
Title: Multimodality Imaging in Stereotactic & Functional Neurosurgery
Synopsis: This lecture will cover the application of structural magnetic resonance imaging (MRI) in
patients undergoing functional neurosurgery. Students will be introduced to imaging techniques that
assay cortical and subcortical grey matter in such patients, e.g. cortical thickness analysis and voxelbased morphometry methods. There will also be a particular focus on diffusion-weighted imaging (DWI),
a type of imaging that measures the in vivo movements of water molecules, and how white matter
tracts in individual patients can be visualized from this imaging. With such nerve characterization,
microstructure can then be subsequently analyzed and possibly linked to pathophysiological
mechanisms in these patients. The lab demonstration will highlight how white matter tracts can be
generated from DWI scans and what information can be gleaned for neurosurgical purposes.
March 31, 2015*
9 AM - 1 PM
Dr. Sima Salahshor
Department of Laboratory of Medicine and Pathobiology (LMP), Faculty of Medicine, U of T
E: [email protected]
Final Exam: Grant Proposal Presentation
Grant Proposal Submission and Oral Presentation
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