Graduate Calendar 2006-2007

Biology

2240 Herzberg Building
Telephone: 520-2600, ext. 8769
Fax: 520-5613
Web site: carleton.ca/biology/ocib/

The Institute

Director of the Institute: V. Trudeau
Associate Director: L. Fahrig

Students pursuing studies in biological sciences at the M.Sc. and Ph.D. levels in the Ottawa area do so in a co-operative program that combines the resources of the Departments of Biology of Carleton University and the University of Ottawa. The two universities have a joint committee supervising the programs, regulations, and student admissions.

Students are admitted for graduate work under the general regulations of the Institute. Additional criteria for admission include academic performance, research experience, and referees' appraisals. The student must also be accepted by a faculty member who will supervise the research project, and the choice of supervisor will determine the primary campus location of the student. The student's advisory committee will normally include faculty members from both universities.

Requests for information and completed applications should be sent to the Director or Associate Director of the Institute. Additional information may also be obtained through the Institute Web site.

Members of the Institute

• S. Aitken, Molecular enzymology
• S. Aris-Brosou, Molecular evolution and bioinformatics
• J.T. Arnason, Biochemical ecology
• B. Blais, Detection technologies for bacterial pathogens
• J.M. Blais, Bio-geochemistry of toxic substances
• G. Blouin-Demers, Reptile conservation and behavioural ecology
• L. Bonen, Molecular biology
• C. Boutin, Agro-ecosystems, plant conservation, wildlife habitat, herbicides, biodiversity
• G. Blouin-Demers, Reptile conservation and behavioral ecology
• S. J. Brooks, Animal biochemistry
• N. Cappuccino, Population and community ecology
• G.R. Carmody, Population genetics
• W. Casley, Genetic complexity in xenobiotic metabolism
• P.M. Catling, Plant biosystematics
• B. Chakravarthy, Molecular signaling and cell adaptation
• N. Chaly, Cell biology
• F. Chapleau, Fish evolution
• C. Charest, Plant physiology
• J.J. Cheetham, Membrane biochemistry
• K. Conlan, Arctic ecology
• D.J. Currie, Macroecology, biogeography
• J. Dawson, Neuroethology and biomechanics of insect flight
• G. Drouin, Molecular genetics
• M. Dumontier, Bioinformatics, drug discovery, cell simulation, genome biology
• M. Ekker, Developmental genetics
• L. Fahrig, Population ecology and ecological modeling
• C.S. Findlay, Evolution
• M.R. Forbes, Evolutionary ecology
• C.M. Francis, Conservation ecology, population biology, modeling, ornithology and mammalogy
• K. Gajewski, Climatology and climatic changes
• A.J. Gaston, Conservation biology
• H. G. Gilchrist, Behavioral ecology, arctic ecology and avian ecology
• K.M. Gilmour, Comparative respiratory physiology
• L. Gillespie, Systematics and evolution of flowering plants
• J.-G. Godin, Behavioural ecology of fishes
• A. Golshani, Proteomics, post-proteomics, molecular biology, microbiology
• C. Hebert, Ecology, isotopes
• S. Hepworth, Plant molecular genetics
• J.G. Houseman, Insect physiology
• D.A. Johnson, Molecular biology
• R. Kassen, Experimental evolution ecology and genetics
• S. W. Kennedy, Environmental toxicology
• J. Kerr, Biodiversity, landscape ecology, geomatics
• I. Lambert, Molecular biology and genetic toxicology
• D.R.S. Lean, Ecotoxicology
• J. Lewis, Neurobiology
• K. Lindsay, Ecology, behaviour and systematics
• B.L.A. Miki, Plant molecular biology
• P. Mineau, Ecotoxicology
• T.W. Moon, Comparative physiology and biochemistry
• A. Morin, Freshwater ecology
• J. Nash, Genomics
• T. Ouellet, Plant molecular pathology, plant molecular biology
• M. Paulin-Levasseur, Cell biology
• S.B. Peck, Arthropod and beetle evolution systematics
• S.F. Perry, Comparative respiratory physiology
• B. Philogène, Ecophysiology of insects, chemical ecology
• F. Pick, Aquatic ecology
• J. Picman, Behavioural ecology
• C. Plowright, Function and mechanisms of choice behaviour, animal cognition and behavioural ecology
• S. Regan, Plan t molecular biology and genomics
• C.B. Renaud, Fish biology
• O. Rowland, Plant molecular biology and biotechnology
• M. Saner, Bioethics
• T. Sherratt, Evolutionary ecology
• A. Simons, Plant life-history evolution
• J. Skevington, Insect systematics
• M. Smith, Fungal molecular genetics
• K.B. Storey, Biochemical adaptations
• V. Trudeau, Comparative endocrinology
• J.P. Vierula, Molecular biology
• J.-M. Weber, Metabolic physiology
• P. White, Environmental toxicology, molecular toxicology, functional genomics
• W.G. Willmore, Biochemistry, biotechnology
• X. Xia, Molecular evolution, bioinformatics
• T. Xing, Plant genomics
• J. E. Yack, Behavioural physiology, entomology
• C. Yauk, Mutations, environmental health

Ottawa-Carleton Specialization inBehavioural Neuroscience

The Departments of Biology and Psychology at Carleton University, and the School of Psychology at the University of Ottawa provide a graduate specialization in behavioural neuroscience at the M.Sc. and Ph.D. level. For further details see the Neuroscience program section of this Calendar.

Ottawa-Carleton Collaborative Program in Chemical and Environmental Toxicology

The Departments of Biology and Chemistry at Carleton University and at the University of Ottawa provide a collaborative program in chemical and environmental toxicology at the M.Sc. level. For further details see the Ottawa-Car leton Collaborative Program in Chemical and Environmental Toxicology's section of this Calendar.

Each campus is well equipped for a wide range of biological research. Some major equipment and facilities include scanning and transmission electron microscopes; confocal laser scanning microscope; digital light microscope and image analysis facilities; conventional and digital darkrooms; animal and plant growth facilities; animal cell culture facilities; electro-physiology equipment; computer systems for genomic studies, modeling of ecological systems, and access to the Internet and the Web; DNA and protein analysis facilities, including electrophoresis and chromatographic equipment, and ultra-centrifuges. Students also benefit from the resources of nearby government laboratories and libraries, including Agriculture Canada, Environment Canada, Health and Welfare Canada, and the National Research Council.

Master of Science

Admission Requirements

An Honours B.Sc. or equivalent degree at a standard acceptable to the two universities is required for admission to the M.Sc. program. Applicants with acceptable standing in a non-honours degree may be admitted to a qualifying-year program which will be determined in each case by the admissions committee.

Applicants must demonstrate a fluent knowledge of English (Carleton), or either English or French (Ottawa).

Program Requirements

The M.Sc. degree will be conferred upon a candidate who has fulfilled the following requirements:

• Completion of the advanced courses specified by the admissions committee and the student's advisory committee; these will range from one to three full (two-term) courses, depending on the background and research program of the student. At least one course at the graduate level must be included, and not more than one course at the fourth-year honours level (completed while registered as a graduate student) may form part of the candidate's co urse requirements. The passing grade for all required courses is 70% or the equivalent, and the student is not allowed a supplemental examination. Directed studies or reading courses may not make up more than half of the required number of courses. The admissions committee or the student's advisory committee may also direct the student to take or to audit additional courses. Knowledge of a second language may be specified as a requirement.
• Completion of at least two terms as a full-time student resident at one of the two universities is normally required. Programs for part-time students may be arranged.
• Presentation of one public seminar on the candidate's thesis research
• Completion of a thesis incorporating the results of original research carried out under the direct supervision of an approved faculty member
• Successful oral defence of the thesis before an examination board of at least three faculty members, normally drawn from both universities.

Guidelines for Completion of Master's Degree

The maximum time limits for the completion of the requirements of the master's program are listed in in the General Regulations, Section 13 of this Calendar. Full-time candidates in the master's program are expected to complete their degree requirements within six terms of first registration for full-time study. Part-time candidates in the master's program, and candidates who elect to complete their program by a combination of full-time and part-time study, are expected to complete their degree requirements within four calendar years or twelve terms from the initial registration in the master's program.

Doctor of Philosophy

Admission Requirements

An M.Sc. from a recognized university is usually required for entry to the Ph.D. program; however, an applicant with a first class B.Sc. and excellent references may be admitted directly to the Ph.D. program. A student already registere d for the M.Sc. may be permitted to transfer to the Ph.D. program following a recommendation by the departmental graduate committee and successful completion of the Qualifying Examination required of Ph.D. candidates.

All applicants must demonstrate a fluent knowledge of English (Carleton), or either English or French (Ottawa).

Program Requirements

The Ph.D. degree will be conferred upon a candidate who has fulfilled the following requirements:

• Completion of the courses at the graduate level specified by the admissions and advisory committees; these will range from one to four full courses (two to six courses if admitted without an M.Sc.), depending on the background and research program of the student. Only graduate courses may form part of the candidate's course requirements. The passing grade for all required courses is 70%, and the student is not allowed a supplemental examination. Directed studies or reading courses may not make up more than half of the required number of courses. The admissions committee or the student's advisory committee may also direct the student to take or to audit additional courses. Knowledge of a second language may be specified as a requirement.
• Scheduling of an oral Qualifying Examination within approximately 12 months of entry into the program and completion normally within 18 months; this examination will cover the candidate's area of research, and related topics. The format of the examination will be established by the departmental graduate committee. The examination committee generally will be composed of faculty members of both universities.
• Presentation of at least one public seminar on the candidate's thesis research.
• A thesis incorporating the results of original research carried out under the direct supervision of an approved faculty member.
• Completion of at least four terms as a full-time student resident at one of the two universities (or six terms if admitted witho ut an M.Sc.) is required. Under exceptional conditions programs may be arranged for part-time students.
• Successful oral defence of the thesis before an examination board of at least five faculty members, with representation from both universities, and including an external examiner from outside the two universities who is an authority on the thesis research area.

Guidelines for Completion of the Doctoral Degree

The maximum time limits for the completion of the program requirements of the doctoral program are listed in the General Regulations, Section 13 of this Calendar. Full-time candidates in the doctoral program are expected to schedule their oral Qualifying Examination within approximately 12 months of entry into the program, and to complete it within 18 months of entry into the program. Part-time candidates in the doctoral program are expected to schedule their oral Qualifying Examination within approximately 18 months after entry into the program. Full-time candidates are expected to complete their degree requirements within 4 calendar years or 12 terms of registered full-time study. Doctoral candidates who have transferred from the master's to the doctoral program without completing the master's program are expected to complete their degree requirements within 4 calendar years or 12 terms of registered full-time study from initial registration in the master's program. Part-time candidates in the doctoral program, and candidates who elect to complete their program by a combination of full- and part-time study, are expected to complete their degree requirements within 6 calendar years or 18 terms after the date of initial registration.

Graduate Courses

Not all of the following courses are offered in a given year. For an up-to-date statement of course offerings for 2006-2007 and to determine the term of offering, consult the Registration Instructions and Class Schedule booklet, published in the summer and available online at: carleton.ca/cu/programs/sched_dates/

University of Ottawa course numbers (in parentheses) follow the current Carleton course number and credit information.

BIOL 5001 [0.5 credit] (BIO 5101)

Topics in Biotechnology

A course concerned with the utilization of biological substances and activities of cells, genes, and enzymes in manufacturing, agricultural, and service industries. A different topic will be selected each year.

Prerequisite: a course in cell physiology or biochemistry, or permission of instructor.

BIOL 5003 [0.5 credit] (BIO 5103)

Comparative Biochemistry

Advanced topics emphasizing biochemical structures, functions, and methodologies in the context of animal (invertebrates and vertebrates) adaptations to environmental stress. The course will be offered in alternate years.

Prerequisite: an undergraduate biochemistry course.

BIOL 5009 [0.5 credit] (BIO 8124)

Ontario Vegetation: Patterns, Processes and Protection

Patterns of vegetation and plant species distributions in Ontario will be investigated with respect to their origin and maintaining processes. Current methods of protection of significant and representative vegetation using zonal concepts will be considered.

BIOL 5100 [0.5 credit] (BIO 5301)

Plant Development

An advanced course dealing with selected topics in the experimental study of plant development.

BIOL 5105 [0.5 credit] (BIO 5302)

Methods in Molecular Genetics

The purpose of this course is to review the fundamental theory and techniques in genetic manipulation of prokaryotes and eukaryotes and to examine some of the innovative new strategies being applied to a variety of problems in molecular biology. Precludes additional credit for BIOL 4106 or BIOL 5107.

Prerequisite: graduate standing and permission of the Department.

BIOL 5106 [0.5 c redit] (BIO 5308)

Laboratory Techniques in Molecular Genetics

This laboratory course, which is complementary to BIOL 5105, is designed to give students practical experience in many of the important techniques in molecular genetics. Precludes additional credit for BIOL 4109 or BIOL 5107.

Prerequisite: graduate standing and permission of the Department.

BIOL 5201 [0.5 credit] (BIO 8301)

Evolutionary Genetics and Computer Analyses

Students will learn the basic concepts in molecular evolution and gain hands-on experience with the computer analysis of DNA sequences.Topics covered will include molecular sequence databases, multiple alignments, amino acid and codon usage, molecular clocks, and phylogenetic trees.

Prerequisites: graduate standing plus basic courses in genetics and evolution; permission of the Department.

BIOL 5202 [0.5 credit] (BIO 8302)

Topics in Evolutionary Genetics

A lecture/seminar course on the genetic mechanisms and forces responsible for variation and evolutionary change in natural populations.Topics to include protein and genome evolution, molecular phylogenies, DNA sequences in population biology, and the evolution of multigene families.

Prerequisites: graduate standing plus basic courses in genetics and evolution; permission of the Department (Alternate years).

BIOL 5203 [0.5 credit] (BIO 8303)

Techniques of Light Microscopy

An advanced laboratory and lecture course on the principles and techniques of light microscopy. Precludes additional credit for BIOL 5200 (BIO 8238) (if taken before 1997-98).

Prerequisite: open to fourth-year and graduate students with consent of the instructor.

BIOL 5204 [0.5 credit] (BIO 8304)

Techniques of Electron Microscopy

An advanced laboratory and lecture course on the principles and techniques of electron microscopy. Precludes additional credit for BIOL 5200 (BIO 8238) (if taken before 1997-98).

Prerequisite: open to Fourth-year and graduate students with permission of the instructor.

BIOL 5205 [1.0 credit] (BIO 5204)

Plant Physiology and Metabolism

An advanced course dealing with selected topics in plant physiology and metabolism.

Prerequisite: graduate standing or permission of the Department.

BIOL 5304 [1.0 credit] (PSY 6201)

Basics of Neuroscience

A comprehensive neuroscience course from cellular levels to neural systems and behaviour. Topics covered include aspects of neuroanatomy, neurophysiology, neuropharmacology and behavioural and cognitive neuroscience. (Also listed as PSYC 5200)

BIOL 5306 [0.5 credit] (BIO 9201)

Photobiology

A course dealing with the interaction between light and living organisms, including an introduction to photochemistry, and a detailed study of photosynthesis, vision, photosensitivity, and photoperiodism.

Prerequisite: an advanced course in animal or plant physiology or biochemistry, or permission of the Department.

BIOL 5307 [0.5 credit] (BIO 8122)

Advanced Insect Physiology

Physiological characteristics of insects.

BIOL 5402 [0.5 credit] (BIO 8162)

Developmental Endocrinology/Topics in Comparative Endocrinology

A lecture and reading course concerned with classical and current topics in the field of comparative endocrinology. Special emphasis on the vertebrates. Offered in alternate years.

Prerequisite: an undergraduate course in endocrinology.

BIOL 5405 [1.0 credit] (BIO 9202)

Project in Applied Ecology

A course in the form of a special research project in which the student identifies an environmental problem and the corporate or go vernmental body that has the power to rectify the problem.

BIOL 5407 [0.5 credit] (BIO 5305)

Quantitative Ecology

A course on analysis of the distribution and abundance of organisms and of related environmental phenomena.

Prerequisites: graduate standing, courses in elementary ecology, elementary statistics and biostatistics, and permission of the Department.

BIOL 5409 [0.5 credit] (BIO 5306)

Mathematical Modeling for Biologists

This course is designed to develop mathematical tools for the modeling of biological processes. The student is taught the necessary mathematics and a computer language, and guidance is given in the choice of simulation of a biological process.

BIOL 5500 [1.0 credit] (BIO 5207)

Selected Topics

Courses in selected aspects of specialized biological subjects not covered by other graduate courses; course details will be available at registration.

BIOL 5501 [0.5 credit] (BIO 8100)

Selected Topics in Biology I

Courses in selected aspects of specialized biological subjects not covered by other graduate courses; course details will be available at registration.

BIOL 5502 [0.5 credit] (BIO 8102)

Selected Topics in Biology II

Courses in selected aspects of specialized biological subjects not covered by other graduate courses; course details will be available at registration.

BIOL 5503 [0.5 credit] (BIO 5901)

Recent Advances in Biology

A course intended for all first-year graduate students to bring them up to date in the various major areas of biology. The course consists of selected readings, lectures, and invited speakers. The course is graded Satisfactory/Unsatisfactory.

BIOL 5506 [0.5 credit] (BIO 5213)

Advanced Insect/Animal Systematics

A lecture and seminar course concerning methods, roles and advances in systematics of insects and other animals. One research project required.

Prerequisite: a 4000-level course in identification or classification of insects or other animals.

BIOL 5508 [0.5 credit] (BIO 8306)

Advanced Topics in Ecology I

Lectures, seminars and discussions on current literature on experimental approaches, concepts, and findings in population and community ecology, ecosystem and landscape ecology, and biostatistics. The content complements BIOL 5509 (BIO 8307).

Precludes additional credit for BIOL 5408 (BIO 9200) (if taken before 1997-98).

BIOL 5509 [0.5 credit] (BIO 8307)

Advanced Topics in Ecology II

Lectures, seminars and discussions on current literature on experimental approaches, concepts and findings in population and community ecology, ecosystem and landscape ecology and biostatistics. The content complements BIOL 5508 (BIO 8306).

Precludes additional credit for Biology 61.548 (BIO 9200) (if taken before 1997-98).

BIOL 5601 [0.5 credit] (BIO 5161)

Advanced Topics in Insect Evolution I

An exploration of major concepts and questions in insect evolution in the areas of systematics, morphology, the fossil record, biology, and behaviour. The content complements BIOL 5602 (BIO 5162).

Precludes additional credit for BIOL 5600 (BIO 5160).

BIOL 5602 [0.5 credit] (BIO 5162)

Advanced Topics in Insect Evolution II

An exploration of major concepts and questions in insect evolution in the areas of systematics, morphology, the fossil record, biology, and behaviour. The content complements BIOL 5601 (BIO 5161).

Precludes additional credit for BIOL 5600 (BIO 5160).

BIOL 5605 [0.5 credit] (BIO 5102)

Field Course

Credit for this 0.5 credit course is based on a total of three weeks of field-course modules, involving one or two we eks of intensive and continuous field work with attendant assignments. For details, see coordinator.

BIOL 5709 [0.5 credit] (BIO 8113)

Chemical Toxicology

An introduction to modeling chemical hazards and exposures at the cellular level. The properties of toxic substances are compared to the responses of enzymatic systems. These interactions are defined as Quantitative Structure-Activity Relationships and used to interpret hazardous materials under regulations such as WHMIS. (Also listed as CHEM 5709/CHM 8157)

Prerequisite: BIOL 6402/CHEM 5708 (BIO 9101/CHM 8156).

BIOL 5801 [0.5 credit] (BIO 5105)

Animal Behaviour

Animal behaviour from an ecological and evolutionary point of view, with additional independent assignments.

Prerequisites: BIOL 3305 and BIOL 3601 or equivalents and registration in a graduate program, or written permission of the Department.

BIOL 5802 [0.5 credit] (BIO 8365)

Advanced Behavioural Ecology I

Recent ideas and research on advanced topics dealing with the evolution of foraging, temporal, spatial, and reproductive strategies are discussed and critically examined. Offered in alternate years.

BIOL 5909

M.Sc. Thesis

BIOL 6001 [0.5 credit] (BIO 8109)

Advanced Molecular Biology I

Recent advances in molecular biology. Topics for discussion may include: DNA structure and function; the organization of the genome; DNA, RNA and protein synthesis; the regulation of gene expression in eukaryotes and prokaryotes. Normally offered in alternate years.

BIOL 6002 [0.5 credit] (BIO 8116)

Advanced Molecular Biology II

Recent advances in molecular biology. Topics for discussion may include: mutagenesis and DNA repair; molecular aspects of gene transfer; recombination and gene arrangement; molecular biology as applied to industrial and medical prob lems. Normally offered in alternate years.

BIOL 6201 [0.5 credit] (BIO 8117)

Advanced Cell Biology I

Recent advances in cell biology. Topics for discussion may include: the composition, biosynthesis, deployment, three-dimensional organization and functions of the cytoskeleton; cell-substrate attachment; cell motility; transport of organelles and axoplasmic transport; cell surface and extracellular matrix. Normally offered in alternate years.

BIOL 6202 [0.5 credit] (BIO 8118)

Advanced Cell Biology II

Topics for discussion may include: the structure, composition and three-dimensional organization of the nucleus, mechanisms and regulation of genome replication, structure organization of transcription. Nuclear reorganization during gamete development, fertilization, viral infection and the mitotic cell cycle. Normally offered in alternate years.

BIOL 6203 [0.5 credit]

Special Topics in Neuroscience

An in-depth study of current topics in neuroscience. Course content varies yearly and has recently included cognitive neuroscience, neuropharmacology, neurodegeneration, and behavioural medicine. (Also listed as PSYC 6300.)

BIOL 6204 [0.5 credit] (ANA 7400)

Neuroscience Techniques

Completion of a research project carried out under the supervision of a neuroscience faculty member. The student will learn a new neuroscience technique and apply it to a research objective. May be repeated for different projects. Students must obtain approval from the Director of the Neuroscience Specialization. (Also listed as PSYC 6204.)

BIOL 6205 [0.5 credit] (BIO 8319)

Advanced Plant Physiology

A lecture and seminar course dealing with selected topics in advanced plant physiology, available only to graduate students.

Prerequisite: BIOL 4209 or equivalent, or permission of the Department.

BIOL 6300 [0.5 credit] (BIO 8320)

Advanc ed Plant Biochemistry

A lecture and seminar course, available only to graduate students, dealing with selected topics in advanced plant biochemistry.

Prerequisites: BIOL 4205 and BIOL 4206/4207, or permission of the Department.

BIOL 6303 [1.0 credit]

Advanced Seminar in Neuroscience

A seminar focusing on the active research areas and interests of faculty, guest lecturers and graduate students, and on trends in diverse areas of neuroscience. (Also listed as PSYC 6200.)

BIOL 6304 [0.5 credit] (BIO 8361)

Advanced Topics in Animal Physiology

In-depth study of areas in animal physiology of current research interest.

BIOL 6401 [0.5 credit] (BIO 8935)

Recent Advances in Plant Biology

Special topics of current interest.

BIOL 6402 [0.5 credit] (BIO 9101)

Principles of Toxicology

This course identifies the basic theorems of toxicology with examples of current research problems. Toxic risk is defined as the product of intensive hazard and extensive exposure. Each factor is assessed in scientific and social contexts and illustrated with many types of experimental material. (Also listed as CHEM 5708/CHM 8156.)

BIOL 6403 [0.5 credit]

Ecotoxicology

Concepts of ecotoxicology, emphasizing whole ecosystem response to hazardous contaminants. The focus is the impacts of chronic and acute exposure of ecosystems to toxicants, the methods of pesticide, herbicide and pollutant residue analysis and the concept of bound residues. (Also listed as CHEM 5705/CHM 9109.)

Prerequisite: BIOL 6402/CHEM 5708 (BIO 9101/CHM 8156.)

BIOL 6404 [0.5 credit] (BIO 8938)

Plant: Animal Interactions

Secondary metabolites of plants and their role as attractants or antifeedants to animals and as allelopathic or antifungal agents. Emphasis is placed on co-evolution of plants and phy tophagous organisms such as insects and mammals, and the ecological and physiological dimensions of this relationship. Offered in alternate years.

BIOL 6405 [0.5 credit] (BIO 9105)

Seminar in Toxicology

This course introduces the seminar format and involves student, faculty and invited seminar speakers. The student will present a seminar and submit a report on a current topic in toxicology. (Also listed as CHEM 5805/CHM 8167.)

BIOL 6505 [0.5 credit] (BIO 8108)

Advanced Topics in Development

Recent advances in developmental biology. Topics may include embryonic induction, regulation of morphogenesis and differentiation, mechanisms of regional specification and pattern formation, and developmental genetics. Offered in alternate years.

BIOL 6909

Ph.D. Thesis