Faculty of Arts & Science 2011-2012 Calendar

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Cell and Systems Biology

Faculty

† Cross-appointed

The study of life, biology, has been transformed in recent decades by powerful new ways of asking fundamental questions about how living organisms work. In particular, molecular approaches are revealing both the incredible complexity of organization at the cellular level, and the underlying principles drawn from chemistry, physics and information science that will eventually enable us to understand that complexity.

The Department of Cell and Systems Biology brings together biologists who study life at the level of molecules to functioning individual organisms. Our undergraduate programs reflect this diversity and research strength.  Cell Biology is a vibrant and broad discipline that seeks to understand the underlying molecular processes that control cell behaviour in a developmental and physiological context. In this broad sense, cell biology comprises molecular biology (Cell and Molecular Biology Specialist and Major), developmental biology (Developmental Biology Specialist), genetics and physiology (Animal Physiology Major) and their sub-disciplines. Systems biology is an exciting new discipline that studies dynamic networks in biological systems through the integration of large datasets arising from the genomics revolution. Computer modeling and bioinformatics are integrated with the study of detailed information about genomes (genomics), the temporal and spatial distribution of all gene transcripts (transcriptomics), cellular proteins and their physical interactions (proteomics), and small molecules that cells assimilate or synthesise (metabolomics) (Genome Biology Major). 

Student Counseling and Enquiries:

Associate Chair (Undergraduate): Professor S. Varmuza (416-978-2759).

Contact the Undergraduate Office, Room 424 in the Ramsay Wright Laboratories (416-978-3477) and consult the departmental web site, www.csb.utoronto.ca.

Cell and Systems Biology Programs

Animal Physiology Major (Science program)

Enrolment in this program requires the completion of 4.0 courses.

(8 full courses or their equivalent)

Students who have taken BIO150Y1, do not take BIO120H1 and BIO220H1 in this program. Students who have taken BIO240H1 and BIO241H1, do not take BIO130H1 and BIO230H1 in this program.

First Year: BIO120H1, BIO130H1; (CHM138H1, CHM139H1)/CHM151Y1; JMB170Y1/ (MAT135H1, MAT136H1)/MAT135Y1/MAT137Y1/MAT157Y1/(PHY131H1, PHY132H1)/(PHY151H1, PHY152H1)
Higher Years:
1.    (BIO220H1, BIO230H1/BIO255H1)/BIO255Y1
2.    BIO270H1, BIO271H1
3.    CSB325H1
4.    0.5 FCEs from: CSB332H1, CSB343H1, CSB346H1
5.    1.5 FCEs (at least 0.5 FCE must be at the 300+level) from: BCH210H1; BIO260H1/HMB265H1; CSB299Y1, CSB327H1, CSB330H1, CSB331H1, CSB332H1, CSB343H1, CSB345H1, CSB346H1, CSB347H1, CSB352H1; EEB263Y1; PSY397H1; STA220H1
6.    0.5 FCE at the 400-level from CSB425H1, CSB430H1, CSB445H1, CSB497H1, CSB498Y1, CSB499Y1; HMB430H1, HMB472H1, HMB499Y1; PSL432H1, PSL443H1, PSL452H1

Biology: see Biology

Bioinformatics and Computational Biology: see Biochemistry

Cell & Molecular Biology Specialist (Science program)

This is a limited enrolment program that can only accommodate a limited number of students.  Admission will be determined with a minimum grade of 70% in BIO130H1.  If the student does not achieve 70% in BIO130H1, admission can be determined with a minimum grade of 70% in BIO230H1.  Achieving these marks does not necessarily guarantee admission to the program in any given year.  Enrolment also requires the completion of four courses, including BIO120H1, BIO130H1; (CHM138H1, CHM139H1)/CHM151Y1; JMB170Y1/(MAT135H1, MAT136H1)/MAT135Y1/MAT137Y1/MAT157Y1.

(12.5 full courses or their equivalent, including at least one 400-series course)

Students who have taken BIO150Y1, do not take BIO120H1 and BIO220H1 in this program.  Students who have taken BIO240H1 and BIO241H1, do not take BIO130H1 and BIO230H1 in this program.

First Year:
BIO120H1, BIO130H1; (CHM138H1, CHM139H1)/CHM151Y1; JMB170Y1/(MAT135H1, MAT136H1)/MAT135Y1/MAT137Y1/MAT157Y1.
Higher Years:
1.     (PHY131H1, PHY132H1)/(PHY151H1, PHY152H1)
2.    (BIO220H1, BIO230H1/BIO255H1)/BIO255Y1, (BIO270H1, BIO271H1), BIO260H1/HMB265H1; BCH210H1
3.    CSB330H1/CSB350H1, CSB331H1, CSB349H1, CSB428H1
4.    0.5 FCE from the following:  BCH422H1, BCH426H1, BCH445H1, CSB327H1, CSB347H1
5.    3.0 FCEs from the following (at least 0.5 FCE must be at the 400-level):  BCH440H1, BCH441H1, BCH444H1, CSB299Y1, CSB327H1, CSB328H1, CSB332H1, CSB340H1, CSB351Y1, CSB352H1, CSB353H1, CSB429H1, CSB430H1, CSB435H1, CSB450H1, CSB452H1, CSB458H1, CSB459H1, CSB460H1, CSB472H1, CSB473H1, CSB474H1, CSB475H1, CSB490H1, CSB491H1, CSB497H1, CSB498Y1, CSB499Y1, HMB499Y1, MGY480Y1

Enrolment in this program requires the completion of 4.0 courses.

(8 full courses or their equivalent)

Students who have taken BIO150Y1, do not take BIO120H1 and BIO220H1 in this program.  Students who have taken BIO240H1 and BIO241H1, do not take BIO130H1 and BIO230H1 in this program.

First Year: BIO120H1, BIO130H1; (CHM138H1, CHM139H1)/CHM151Y1; JMB170Y1/(MAT135H1, MAT136H1)/MAT135Y1/MAT137Y1/MAT157Y1/(PHY131H1, PHY132H1)/(PHY151H1, PHY152H1)
Higher Years:
1.   (BIO220H1,  BIO230H1/BIO255H1)/ BIO255Y1
2.    BIO260H1/HMB265H1; BCH210H1
3.    CSB349H1
4.    1.0 FCE from: CSB327H1, CSB328H1, CSB331H1, CSB340H1, CSB351Y1
5.    1.5 FCE (at least 0.5 FCE must be at the 300+level and 0.5 FCE at the 400-level) from: BCH422H1, BCH426H1, BCH444H1, BCH445H1, CSB299Y1, CSB327H1, CSB328H1, CSB330H1, CSB331H1, CSB332H1, CSB340H1, CSB347H1, CSB350H1, CSB351Y1, CSB352H1, CSB353H1, CSB428H1, CSB429H1, CSB430H1, CSB435H1, CSB450H1, CSB452H1, CSB458H1, CSB459H1, CSB460H1, CSB472H1, CSB473H1, CSB474H1, CSB475H1, CSB490H1, CSB491H1, CSB497H1, CSB498Y1, CSB499Y1, HMB499Y1, MGY480Y1. No more than 0.5 FCE in BCH can be used towards this requirement.

This is a limited enrolment program that can only accommodate a limited number of students. Admission will be determined with a minimum grade of 70% in BIO130H1.  If the student does not achieve 70% in BIO130H1, admission can be determined with a minimum grade of 70% in BIO230H1.   Achieving these marks does not necessarily guarantee admission to the program in any given year.  Enrolment also requires the completion of four courses, including BIO120H1, BIO130H1; (CHM138H1, CHM139H1)/CHM151Y1; JMB170Y1/(MAT135H1, MAT136H1)/MAT135Y1/MAT137Y1/MAT157Y1.

(12.5 full courses or their equivalent, including at least one 400-series course)

Students who have taken BIO150Y1, do not take BIO120H1 and BIO220H1 in this program.  Students who have taken BIO240H1 and BIO241H1, do not take BIO130H1 and BIO230H1 in this program.

First Year:
BIO120H1, BIO130H1; (CHM138H1, CHM139H1)/CHM151Y1; JMB170Y1/(MAT135H1, MAT136H1)/MAT135Y1/MAT137Y1/MAT157Y1
Higher Years:
1.    BCH210H1; (BIO220H1, BIO230H1/BIO255H1)/BIO255Y1, BIO260H1; CHM220H1/CHM247H1/CHM249H1
2.     1.0 FCE from BIO251H1, BIO270H1, BIO271H1
3.    CSB349H1
4.    CSB328H1, CSB340H1
5.    2.5 (or 3.5*) courses from: ANA300Y1, ANA301H1; BCH340H1, BCH370H1, BCH425H1, BCH426H1; CSB327H1, CSB330H1, CSB331H1, CSB350H1, CSB352H1, CSB425H1, CSB435H1, CSB450H1, CSB459H1 CSB460H1, CSB472H1, CSB473H1, CSB475H1; EEB340H1, EEB460H1; IMM334Y1, IMM428H1; IMM429H1; MGY425H1, MGY428H1, MGY451H1, MGY452H1, MGY470H1; PSL303Y1, PSL420H1
6.    1.0 (or 2.0*) courses from CSB428H1, CSB429H1, CSB430H1, CSB431H1, CSB458H1, CSB483H1, CSB484H1, CSB497H1, CSB498Y1, CSB499Y1; HMB499Y1; MGY480Y1

* Requirements 5. and 6. must include a total of at least 4.5 full courses

Genome Biology: see Biology

Neuroscience: see Human Biology

Cell and Systems Biology Courses

The 199Y1 and 199H1 seminars are designed to provide the opportunity to work closely with an instructor in a class of no more than twenty-four students. These interactive seminars are intended to stimulate the students’ curiosity and provide an opportunity to get to know a member of the professorial staff in a seminar environment during the first year of study. Details here.

One of the goals of modern biology is to understand how the basic building blocks of life give rise to biological form and function. This course provides students with a common lexicon to understand the key principles and concepts in molecular and cell biology, with a focus on how the building blocks of life lead to functioning cells.

The genome is the book of life, providing instructions to construct an organism. This course introduces genome biology and explores how the building blocks of life are networked into functioning organisms. We will investigate how cells perceive internal and external cues, how gene expression is shaped by this perception, and how these events give rise to the myriad of life around us.

An introduction to the structure and function of cells at the molecular level: key cellular macromolecules; transfer of genetic information; cell structure and function; cellular movement and division. The Enhanced Laboratory provides the opportunity for greater laboratory skill development in modern investigative techniques and is intended for students interested in conducting their own laboratory research.

This is a problem based course which discusses classical, molecular, developmental, and population genetics and genomics with emphasis on model organisms for genetic analysis.

The main ideas of physiology and the contribution of experimentation to our understanding of life processes. Uses examples from throughout the animal kingdom, and includes the physiology of homeostasis and the endocrine system. Accompanying laboratories reinforce the concepts introduced in lecture and teach relevant techniques.

The main ideas of physiology and the contribution of experimentation to our understanding of life processes. Uses examples from throughout the animal kingdom, and includes the physiology of the nervous and cardiorespiratory systems. Accompanying laboratories reinforce the concepts introduced in lecture and teach relevant techniques.

This course is intended to provide non-science students with an understanding of basic concepts in molecular biology to allow them to explore, and analyze current scientific issues and controversies covered in the media and relevant to society at large.

Credit course for supervised participation in faculty research project. Details here.

The regulation of physiological processes by hormones and other signalling molecules in non-human chordates. An integrated genes-to-environment approach is used to examine aspects of hormonal evolution, physiological information flow, behaviour and neuroendocrinology, and xenobiotic endocrine disruptors.  Students will have the opportunity to research areas of their own interest via group interaction in a series of tutorial sessions.

Examines expression, structure and function of the four major classes of ECM macromolecules: collagen, proteoglycans, non-collagenous structural proteins and glycoproteins. In addition to forming elaborate networks that give tissues and organs their unique architectural design and biophysical properties, ECM molecules act as potent regulators of all cellular activities. Emphasis is placed on the morphoregulatory contribution(s) of ECM molecules to normal and pathological development.

Basic concepts in developmental biology. Early development of invertebrates and vertebrates will be discussed with emphasis on experimental and molecular analysis of developmental mechanisms. Tutorials demonstrate examples of descriptive and experimental embryology and discuss primary literature of selected topics in developmental biology.

Laboratory course on molecular and cell biology research techniques used to study genes and proteins.  Topics include plasmid cloning, PCR, bioinformatics, gene expression analyses, protein-protein interactions, and protein subcellular localization.

The development of multicellular organisms is dependent on a broad variety of different cell-cell and cell-matrix adhesive mechanisms. The course examines the molecules and mechanisms involved and how they act in concert to regulate distinct developmental and physiological events. Emphasis is placed on the experimental approaches and technology used to study the molecular interactions and dynamics and alter structure-function relationships in cells and organisms.

Examination of all aspects of the synapse in both the peripheral and central nervous systems of invertebrates and vertebrates. Topics include: synapse formation, synaptic transmission, synaptic plasticity, learning and memory, and neurological disorders.

Plant developmental genetics at the molecular, cellular and organismal level, generation and use of genomic resourses in plant model organisms. Questions address the genetic dissection of plant embryo and meristem development, plant stem cell specification and tissue patterning. Genomic approaches applicable to plant biotechnology are also covered.

Animal structure and function, at all levels from molecule to whole animal, are dependent on energy. This course describes how the supply, consumption, transformation, exchange and storage of energy can facilitate, constrain and limit animal function. Emphasis is placed on systems level physiological function and whole animal performance.

An introduction to the regulation of sleep-wake states and the functions of sleep - why and how animals sleep. Integrates all levels of biological organization, including molecular biology, cell biology, systems physiology, control theory, behaviour and evolution, with comparisons across phyla. (Offered in alternate years.)

Integrated control of cardio-respiratory physiology and metabolism in mammals. Topics include exercise, diving, sleep and hibernation.

In-depth survey of unique cellular adaptations of different tissues and organisms to overcome environmental stresses such as hypoxia. Emphasis is placed on cellular strategies, particularly second messenger responses, although systematic and whole organism responses will be investigated. Broad-ranging common strategies among diverse organisms are examined.

Genome structure and the regulation of gene expression in eukaryotic cells. Topics include gene duplication, repetitive DNA, transcription, RNA interference and expression profiling. Tutorials emphasize problem based learning exercises that relate to recent advances in the broad field of eukaryotic gene expression.

Laboratory methods used in plant molecular biology research. Topics include vector construction, plant transformations, PCR, DNA blots, high-throughput screens, genetic mapping, and bioinformatic analyses.

An introduction to basic and medical virology. Attendance in tutorials is optional.

Use of available programs for analyzing biological data. This is an introductory course with a strong emphasis on hands-on methods meant for Biology and Human Biology/GGB specialists/majors. Some theory is introduced, but the main focus is on using extant bioinformatics tools to analyze data and generate biological hypotheses.

Plants have co-evolved with microbes ever since their first appearance on land, resulting in sophisticated strategies of pathogenicity, symbiosis, commensalisms and mutualism. This course presents an overview of these strategies with examples of bacteria, fungi, oomycetes and viruses that have evolved intimate associations with plants, and discusses plant immune systems.

An instructor-supervised group project in an off-campus setting. Details here.

An instructor-supervised group project in an off-campus setting. Details here.

The student will investigate the endocrine and paracrine signalling mechanisms that act to coordinate the reorganization of tissues in animals in special situations. The topics covered will include metamorphosis in agnathans and amphibians, sex change in teleost fishes, limb and regeneration in reptiles and amphibians, and neural regeneration in birds and mammals. (Offered in alternate years.)

This advanced course covers cell polarity and cytoskeletal dynamics emphasizing current literature. For each topic, the course examines (1) the proteins involved, (2) their interactions and regulation, and (3) how they organize specific cellular structures. The coordination of these complexes required for orchestrating complex cellular processes are addressed.

This course will discuss the genetic and cell biological aspects of the development of gametes, gonads, and sex related traits in animals, including invertebrates and vertebrates. In the accompanying seminar, primary literature is used to discuss selected topics in germ cell biology.

An examination of the molecular and cellular basis of neurogenesis in developing an adult nervous system. Experimental evidence from recent studies in selected invertebrate and vertebrate model systems will be discussed. Topics include neural stem cells, regional specialization of neurogenesis, neuronal and glial differentiation, extrinsic regulation of neurogenesis, adult neurogenesis, and the evolution of neurogenesis. Students are expected to have a basic knowledge of molecular genetics, developmental biology and/or neuroanatomy. Lectures will be complemented by student directed seminars that focus on specialized research studies published in leading scientific journals.

This course begins with a comparison of embryonic development in the major animal taxa. The evolution of developmental mechanisms is then considered with emphasis on the molecular and genetic basis of these mechanisms. Subsequent discussion examines the impact of developmental processes on the evolution of animal diversity. Tutorials feature the study of embryos representing diverse animal taxa.

This course will expose students to several of the best-understood regulatory networks in molecular biology, as well as recent technological and methodological developments. Emphasis is on the mechanistic basis for these systems, methods and models for quantitative analysis of regulatory networks and the biological logic they encode.

Covers theories on the biological function of sleep-wake states why and how animals sleep. Integrates all levels of organization, including molecular biology, homeostasis, bioenergetics, neurophysiology, endocrinology, behaviour and evolution, with comparisons across phyla. This course emphasizes student participation in seminar discussion and debates. (Offered in alternate years.)

A discussion on current proteomic approaches to understand biological processes.  The role of  mass spectrometry,  gel electrophoresis, protein-protein interaction and structural biology in understanding how proteins function in pathways and interaction networks will be discussed.

This course explores the molecular strategies that microbes and plants have evolved to live with each other. The variety of strategies will be summarized with emphasis on the molecular mechanisms of pathogenic relationships.

A seminar course exploring non-Mendelian phenomena in plants, fungi and animals that reveal aspects of genome organization and regulation that may provide insight into genome function and evolution.

This course introduces students to major features of gene expression and signal transduction in plants. Topics include strategies for generating transgenic plants and regulating gene expression, as well as the importance of signal transduction in plant growth and survival. How plants sense and respond at the molecular level to environmental stresses such as drought, salinity, cold and disease will be discussed. The application of this basic scientific information in biotechnological strategies for improving agronomic traits will also be addressed.

Plant development, ecological adaptation and crop plant productivity depend on the sophisticated potential of plants to sense and compute signals to regulate their responses. An arsenal of genetic and genomic tools is employed to elucidate these plant signal transduction pathways. Examples from the original literature will be used to introduce general concepts of plant signal transduction, molecular biology and genomics and their application in understanding and influencing plant growth and development.

Computational analyses of DNA and RNA expression data. Understanding biological databases, sequence alignment, sequence annotation, gene prediction, computational analysis of function, motif analysis, phylogenetic analysis, and microarray analysis. Applied, theoretical and statistical issues will be addressed.

This course surveys the field of Chemical Genomics, focusing on the analysis of biological problems using chemical approaches. Topics covered include chemical genetics, combinatorial chemistry and combinatorial strategies in molecular biology. Examines both the underlying biological and chemical concepts; however, the focus is primarily biological.

This is a hands-on, laboratory based course offered through the Centre for the Analysis of Genome Evolution and Function (CAGEF).  It will teach students how to produce and analyze data that are central to the fields of genomics and proteomics. Techniques taught include DNA and RNA extraction, PCR, DNA sequencing, quantitative PCR, transcript profiling using microarrays, 2D-gel proteome analysis, and associated bioinformatics analyses.

This course introduces students to major features of plant metabolism. The content covers plant physiology, natural product chemistry, genetics, molecular biology, and genomics. Topics also include strategies for designing how we modulate metabolic pathways and how we utilize plants for biotechnology through metabolic engineering.

Seminars analyzing the major problems in developmental biology from cellular, genetic and molecular perspectives.

Students will choose a major issue in contemporary Developmental Biology and critically analyze present and future prospects in that field.

A team-based learning course with emphasis on questions in the fields of protein biochemistry, enzymology, structural biology, metabolic engineering and protein-protein interaction.  Lectures and seminars will focus on current research topics within these fields and will provide the background knowledge for students to work in teams to explore the primary research literature, and for each team to develop a formal research proposal.

CSB491H1 will build on the team-based learning approaches learned in CSB490H1 to develop the laboratory and team-work skills needed to succeed in the workplace, particularly the multi-disciplinary environment that characterizes modern biological research. CSB491H1 is a team-based research course with emphasis on questions in the fields of protein biochemistry, enzymology, structural biology, metabolic engineering and protein-protein interaction. Students will form semester-long laboratory research teams to evaluate hypotheses that were developed into a research proposal in CSB490H1.

An original research project (a literature review alone is not sufficient) requiring the prior consent of a member of the Department to supervise the project. The topic is to be one mutually agreed on by the student and supervisor. They must arrange the time, place, and provision of any materials and submit to the Undergraduate Office a signed form of agreement outlining details prior to being enrolled. This course is normally open only to Fourth Year students with adequate background in Cell and Systems Biology. All students are required to make written and, perhaps, oral presentations of the results of their projects and participate in a poster session. A copy of a written report must be submitted to the Undergraduate Office.

An original research project (a literature review alone is not sufficient) requiring the prior consent of a member of the Department to supervise the project. The topic is to be one mutually agreed on by the student and supervisor. They must arrange the time, place, and provision of any materials and submit to the Undergraduate Office a signed form of agreement outlining details prior to being enrolled. This course is normally open only to Fourth Year students with adequate background in Cell and Systems Biology. All students are required to make written and, perhaps, oral presentations of the results of their projects and participate in a poster session. A copy of a written report must be submitted to the Undergraduate Office.

Allows students to do a second independent project, supervision of which must be different from CSB497H1/CSB498Y1. Operates in the same manner as CSB497H1/CSB498Y1.