Fall	Winter
TMM40121	TMM40122
TMM4950	6 credits of optional courses in TMM
3 credits of optional courses in TMM	3 credits of courses in either humanities or social sciences
1.5 credits in advanced methods laboratory courses	1.5 credits in advanced methods laboratory courses

For the list of optional 4000-level TMM courses and advanced methods laboratory courses, please consult the program catalogue. 

TMM4012: Honours Research Project

Synopsis

This course aims to develop research, communication and technical skills through the completion of a research project under the supervision of a TMM faculty member and the submission of an honours thesis. The course emphasises the design of a scientifically sound project that analyzes a complex problem or addresses a significant research question with insight and imagination, the production of an original thesis that utilizes evidence in a convincing manner, and the presentation of results that are well organized, effectively delivered, knowledgeable, and appropriate for a multi-disciplinary audience.

Key objectives and core competencies

By the end of this course, the student will be able to:

• Apply existing knowledge to solve technical problems and explain issues, demonstrating complex intellectual and creative skills. 
• Demonstrate knowledge of relevant scientific literature and be able to identify gaps in understanding.
• Formulate a testable hypothesis and design appropriate experiments to test it, including controls based on sound rationale
• Understand and critically analyze a variety of scientific texts and data, whether spoken, written, or graphic.
• Demonstrate an intellectual grasp of the scientific method
• Demonstrate the scientific and technical skills necessary to do independent research on defined problems
• Communicate research findings to faculty and peers and support a claim in a significant piece of formal writing (thesis).
• Make connections between existing scientific literature and their own research findings

Evaluations

• Poster Presentation 15%
• Oral Presentation 20%
• Written Thesis in JBC Format 35%
• Mid-year Progress Review 10%
• Year-end Review 20%

TMM4950: Science Communication

Synopsis

This course provides a foundation for the mastery of scientific communication and toolbox to bring scientific discoveries to the world, including the structure and delivery of oral presentations and posters, the design and writing of papers for scientific and general audiences, and the communication of science in the digital world. The course also facilitates the development of professional and advocacy skills, including networking, elevator pitches and the use of social media, and emphasizes the importance of delivering research discoveries in the right way, to the right audience at right time.

Core competencies

By the end of this course, the learner should :

• Identify target audiences and adapt scientific content accordingly.
• Understand and apply the basics of writing a scientific paper to tell a strong science story.
• Create and present scientific posters that will stand out from the crowd. 
• Develop and deliver scientific presentations that will engage the audience and sell their research.
• Write a science article for the public that will make complex scientific concepts not only simple to grasp but exciting.
• Build and maintain professional networks and establish a strong LinkedIn profile
• Create an effective elevator pitch

Breakdown of the marks

• Network Development 5%
• Lay Abstract & Intro Assignment 20%
• Scientific Presentation 20%
• Elevator Pitch 10%
• Poster Presentations 20%
• Scientific Narrative 25%

TMM4102: Regenerative Medicine

Synopsis

This course builds a comprehensive perspective of topics in regenerative medicine by introducing concepts and knowledge relating to current frontiers and biomedical and medical applications. The course covers embryonic stem cells, adult stem cells, reprogramming of mature adult cells into pluripotent stem cells, and cancer stem cells, and outlines applications of stem cells for the treatment of 50+ diseases, including bone marrow transplantation and stem cell-based gene therapy. It emphases the evaluation and debate of research literature and the integration and application acquired knowledge to synthesize cancer research proposals and design experiments.

Key objectives and core competencies

By the end of this course, the student will be able to:

• Gain the basic knowledge of stem cells
• Apply important concepts in the field of regenerative medicine
• Recognize the current frontiers and controversial questions in the field of regenerative medicine
• Develop a deeper understanding and ability to evaluate the regenerative medicine primary literature.
• Synthesize and apply knowledge through writing a grant application-abstract in regenerative medicine

Evaluations

• Assignment 1 20%
• Assignment 2 10%
• Assignment 3 15%
• Assignment 4 15%
• Module II 30%
• Class participation 10%

TMM4103: Metabolomics and Integrative Research Methods in Metabolic Diseases

Synopsis

This course offers a comprehensive exploration of metabolic disease processes and methods used in metabolic disease research studies. The course focuses on obesity as an instigator of metabolic dysfunction leading to diseases like diabetes and fatty liver disease, and experimental methods to study metabolic dysfunctions, including approaches for the analysis of large ‘-omics’ data sets (e.g., from lipidomics, metabolomics).

TMM4104: Probability and Statistics for Molecular Medicine and Genomics

Synopsis

This course provides a knowledge foundation for the application of modern statistical methods used to analyze data related to molecular medicine and genomics, including preprocessed gene expression data, protein and metabolite abundance data, and genome-wide association study data. The course introduces false discovery rates of various kinds and Bayesian posterior probabilities as alternatives to p values, emphasizing the application of modern approaches to address shortcomings of conventional data analysis methods.

TMM4105: Neurological Disease (not offered in 2019/2020)

Synopsis

This course provides an introduction to neurological and neuromuscular disorders with emphasis on molecular-level pathogenic mechanisms and therapeutic strategies. The course covers clinical presentations as well as genetic and environmental factors contributing to the development or progression of representative diseases and syndromes, including epilepsy, dementias, sclerosis and muscular dystrophy.

TMM4106: Model Systems of Diseases

Synopsis

This course provides a foundation for the study of causal mechanisms of human disease using single cell organisms such as yeast to more complex animals such as nematodes, fruit fly and the mouse. The course covers commonly-used model organisms and experimental approaches, including gene-editing, induced pluripotent stem cells, and patient-derived xenografts, and emphasises how the knowledge gained from model organisms provides an essential step towards diagnosis and/or therapy for many human disorders.

TMM4107: Viral Pathogenesis

Synopsis

This course introduces basic principles of molecular virology, including the molecular processes involved in viral entry, replication, assembly, exit and maturation, that are essential for understanding viral pathogenesis, immunity, vaccines, antiviral drug development, and virus evolution and emergence. The course emphasises the integration and application of knowledge to problems such as those related to the development and progression of viral diseases, outbreaks and drug resistance.

Key objectives and core competencies

By the end of this course, the student will be able to:

• Obtain a general understanding of the field of virology, along with a broad knowledge of virus diversity and classification methods.
• Understand the various stages of the viral life cycle.
• Understand the molecular mechanisms involved in virus infection and replication.
• Understand the basics of immune defenses against viruses and vaccine-induced immunity.

Evaluations

• Participation in active learning sessions: 5%
• Case study with an oral presentation: 15%
• Midterm exam: 40%
• Final exam: 40%

TMM4108: Bacterial Diseases

Synopsis

The course aims to develop a knowledge foundation to understand molecular mechanisms of bacterial pathogenesis and the treatment of associated disease. The course provides an introduction to the bacterial cell and medically relevant topics, such as biofilm formation, antibiotic resistance, and the regulation of virulence factor expression and secretion, with emphasis on the integration and application of acquired knowledge in pathogen-specific research

Key objectives and core competencies

By the end of this course, the student will be able to:

• Understand the principles of microbial growth.
• Understand the importance of the microbiome.
• Understand the molecular mechanisms involved in microbial pathogenesis and persistence including expression of virulence factors, secretion of effectors, development of antibiotic resistance and biofilm formation.
• Present a research plan to identify a pathogen-specific antibiotic.

Evaluations

• Midterms 2 x 30%
• Active Learning Activities 40%

TMM4300A: Selected Topics in Biomedical Research – Biology of Aging

Synopsis

This course provides exposure to deep foundational knowledge of the aging process, including genetic components of longevity, and the conservation of aging in mammalian populations. The course emphasises the causes of cellular aging by examining genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis and mitochondrial dysfunction.  Special emphasis will be given to current research in age-related disease and decline including cancer, cardiology, endocrinology, metabolism, immunology, and neuroscience.

TMM4300B: Selected Topics in Biomedical Research - Molecular Imaging and Radiochemistry

Synopsis

This course provides an introduction to contemporary methods in molecular imaging with an emphasis on fundamental principles of nuclear medicine modalities, such as positron emission tomography and single-photon emission computed tomography, and the interdisciplinary nature of molecular imaging research and practice. The course covers the biophysics of radiation and tracer imaging, image quantification, radioisotopes and associated chemistry, as well as applications of molecular imaging in clinical diagnosis and pharmaceutical development.

Key objectives and core competencies

By the end of this course, the student will be able to:

• Understand nuclear reactions that are relevant to molecular imaging and the principles of radiation detectors;
• Analyze ligand receptor interactions given example data from autoradiography or in vivo imaging;
• Evaluate a radiotracer candidate based on pharmacokinetic properties;
• Recall the most important radiochemical reactions with important isotopes and apply these to designing synthetic routes;
• Describe clinical applications of radiopharmaceuticals in brain, heart, skeletal, and cancer imaging;
• Evaluate the strengths, limitations, and complementarity of various biomedical imaging modalities;
• Knowledgably participate in discussions about molecular imaging with researchers and practitioners.

Evaluations

• 20% problem sets
• 20% presentations
• 30% mid-term exam
• 30% final exam

TMM 4300C: Nanomedicine and Tissue Engineering

Synopsis

This course provides an overview of the emerging disciplines of nanomedicine and tissue engineering, with a focus on nanotechnology applications in medicine. This is a rapidly expanding interdisciplinary field that seeks to develop new and improved techniques for the screening, diagnosis, treatment, and prevention of diseases. This course covers basic concepts related to bio-nanomaterials, their unique physicochemical properties at the nanoscale, their interactions with biological structures at the molecular level, and their applications in diagnostics, therapy and tissue engineering.

Key objectives and core competencies

By the end of this course, the student will:

• Have gained basic knowledge in nano-biomaterials development and their characterization
• Understand the fundamental aspects of nano-bio interactions
• Understand the concepts behind nanotechnology applications in medicine.
• Have been exposed to new frontiers in nano-based clinical technologies, including diagnostics, imaging modalities, therapies and tissue engineering.
• Understand the basic concepts/steps related to bench to bedside translation of nanomedicines. This includes, technology development in the lab settings, intellectual properties, scale-up, start-up and entrepreneurship.

Evaluations

• Class participation 20%
• Active learning: Development of new nanotechnology-based, therapy in a business case format 40%
• Written report on the idea in the format of a scientific article 20%

TMM4300D: Hormonal Regulation of Metabolism

Synopsis

This course covers a wide range of topics regarding hormones and hormonal regulation of signalling and energy metabolism. In addition to both cellular and integrative whole body physiology, the course will also cover diseases associated with dysregulation of hormone-regulated metabolic pathways and unconventional disease mechanisms.

Key objectives and core competencies

By the end of this course, the student will be able to:

• Understand the fundamental mechanisms by which hormones can regulate cellular metabolic processes
• Describe the synthesis and regulation of well-characterized hormones, their receptors, activated signaling pathways, and metabolic outcomes
• Describe the classic endocrine organs as well as those whose primary function is not endocrine but display significant endocrine function in health and disease
• Explain how hormone signaling in various tissues is integrated to regulate whole body metabolism 
• Apply the knowledge of basic metabolic pathways to the complexity of metabolic and chronic diseases

Evaluations

• Quiz 1 (Lectures 1-4) - 16%
• Presentation 1  - 28%
• Quiz 2 (Lectures 5-7 ) - 12%
• Presentation 2  - 28%
• Quiz 3 (Lectures 8-11) – 16%

TMM4301: Special Topics in Biochemistry - Genome Stability and Chromosome Dynamics

Synopsis

This course introduces the basic mechanisms that maintain the integrity and transmission of the eukaryotic genome, including chromosome segregation and condensation, DNA replication and fork stability, the DNA damage response, p53 function, and telomere dynamics. The course also provides insight into how defects in these chromosomal processes can contribute to human diseases, such as immune system disorders, developmental syndromes, and cancer.

TMM4302: Special Topics in Epidemiology (not offered in 2019/2020)

No information is available.

TMM4303: Special Topics in Neuroscience

Synopsis

This provides opportunity to explore what leading research topics are being pursued in international and national neuroscience laboratories. The course emphasizes current ground-breaking research discoveries and contributions through reviews of scientific publications by leading neurosciencients as well as interactions and discussions with these expert scientists during a weekly seminar attended by professors and trainees in neuroscience and related disciplines.

Key objectives and core competencies

By the end of this course, the student will be able to:

• Know about the latest new breakthroughs in basic and clinical Neuroscience
• Know about the ongoing challenges in basic and clinical Neuroscience and ongoing clinical trials.
• Have acquired the skills to quickly grasp the key points from any professional scientific presentation
• Have acquired the skills to critically evaluate the scientific data and identify the ongoing challenges in basic and clinical research
• Have acquired the skill to formulate questions that strike the heart of a seminar’s topic and inspire productive discussion

Evaluations

• 50%: written assignment
• 25%: oral presentation
• 25%: seminar participation evaluation

TMM 4304: Special Topics in Infectious Diseases

Synopsis

The course expands on basic understanding of immunology to build a comprehensive understanding of current topics and methods through independent exploration and analysis, in-class presentations and peer-discussion of contemporary research literature in the areas of cancer immunology, microbiome and host interaction, and chronic infection and inflammation.

TMM4910C: Advanced Methods in Biomedical Research – Genome Editing

Synopsis

This course aims to develop expertise in the application of recently developed CRISPR/Cas9-based reagents that facilitate the manipulation and editing of specific areas of mammalian genomes. The course emphasises hands-on practice through the completion of training exercises as well as the independent work in which students create their own knockout mammalian cell line and estimate their targeting efficiency.

TMM4911: Advanced Methods in Biomedical Research – Cell Biology and Microscopy

Synopsis

This course introduces key aspects of biological imaging, from the principles of image formation to the application of imaging-based assays, to explore biological questions at the level of individual cells. The course covers a range of techniques ranging from immunofluorescence for standard and super-resolution imaging through live cell imaging and cell-based assays, and emphasizes the development of practical skills for acquiring, analyzing, interpreting and critiquing imaging data.

Key objectives and core competencies

By the end of this course, the student will be able to:

• Understand the principles of image formation and the relative contributions of magnification, resolution and contrast to the end result
• Evaluate an experiment in order to determine the type of microscope system (and settings) required and the necessary controls
• Appreciate the difference between qualitative and quantitative imaging data and the stringency required for each
• Analyze and interpret various types of imaging data
• Understand the ethical considerations inherent in imaging approaches

Evaluations

• Class participation : 40%
• Written Assignment : 30%
• Final Take-home exam : 30%

TMM4912: Advanced Methods in Biomedical Research – Biochemistry and Biophysics

Synopsis

This course provides practical training in the biochemical and biophysical principles and methods used to determine the structure and function of protein. The course covers advanced experimental methods to gather data on the biophysical properties of proteins, including circular dichroism, differential scanning and isothermal titration calorimetry, as well as methods to understand protein folding and complex enzyme kinetics. It emphasizes laboratory training and the development of data analysis expertise, including the creation of protein crystals, the interpretation of X-ray diffraction patterns and protein engineering.

Key objectives and core competencies

By the end of this course, the student will be able to:

• Understand how to measure Circular dichroism spectra and interpret its results
• Understand how to measure differential scanning calorimetry spectra and interpret its results
• Understand how to measure isothermal titration calorimetry spectra and interpret its results
• Understand how to obtain protein crystals, interpret an X-ray diffraction pattern and solve its crystal structure It is expected that the student will learn how to use Coot and refinement programs such as Refmac.

Evaluation

• 25% laboratory participation
• 25% laboratory preparation
• 50% laboratory report.

TMM4913: Advanced Methods in Biomedical Research – Nucleic Acids

Synopsis

This course focuses on the development of competency to perform microbiome profiling. The course provides a general introduction to high-throughput sequencing of 16S rRNA genes as well as experimental approaches to microbiome analysis, including the extraction of bacterial DNA and the construction of amplicon libraries. It also provides training in the use of bioinformatic tools to analyse sequencing datasets, and the integration of knowledge from multiple sources to discuss the implications and potential clinical applications.

Key objectives and core competencies

By the end of this course, the student will be able to:

• Understand high-throughput sequencing technologies and multiplexing
• Appreciate the role of the microbiome in human health and research
• Become familiar with bioinformatic analyses of high-throughput sequencing data
• Perform microbiome profiling of selected samples using bioinformatics approaches
• Integrate knowledge from multiple sources to discuss microbiome populations

Evaluations

• Ability to perform DNA extraction 15%
• Ability to make the library 15%
• Ability to perform computer-based microbiome analysis 30%
• Laboratory report 40%

TMM4914: Advanced Methods in Biomedical Research – Flow Cytometry

Synopsis

This course aims to provide expertise in the design of experiments for flow cytometry analysis as well as hands-on training in instrument operation and maintenance. The course introduces basic flow cytometry concepts but has a strong emphasis on practical applications, including techniques for sample preparation, troubleshooting and advanced analysis.

Key objectives

• Understand the basic theoretical concepts of flow cytometry
• Learn how to operate a flow cytometer
• Learn how to prepare samples for flow cytometry analysis
• Learn flow cytometry techniques to:
  • Study the cell cycle
  • Titrate antibodies
  • Immunophenotype cells with a multi-color antibody panel

Breakdown of marks

Lab sessions (4x 10% each): 40%*

Final exam (written): 30%

Final practical exam: 30%

* Attendance to the labs is mandatory.

TMM4915: Advanced Methods in Biomedical Research – Epigenetics and Genomics

No information is available.

TMM4916: Advanced Methods in Biomedical Research – Electrophysiology

Synopsis

This course provide practical training in the measurements of resting and action potentials in skeletal muscle fibers and covers methods to measure ion channel activity via membrane conductance measurement, including the cable theory and patch clamp techniques. The course also discusses how microelectrode characteristics can explain certain measurement artifacts and as well as mitigating and corrective strategies.

TMM4917: Advanced Methods in Biomedical Research – Microbiology (not offered in 2019/2020)

No information is available.

TMM4918: Advanced Methods in Biomedical Research – Proteomics

Synopsis

This course provides an introduction to proteomic methodologies and approaches and covers protein identification, quantitation and post-translational analysis by high-throughput mass spectrometry. The course emphasizes the development of expertise in the practical skills related to proteomics, including laboratory and bioinformatics methods for data generation, analysis and interpretation.