2005-2006 Graduate Calendar

Jeffrey Atkinson (Chemistry), Robert L.Carlone (Biological Sciences), Alan J. Castle (Biological Sciences), Heather Gordon (Chemistry), Gary Pickering (Biological Sciences), Melanie Pilkington (Chemistry), Art van der Est (Chemistry)

Assistant Professors

Charles Després (Biological Sciences), Travis Dudding (Chemistry), Debra Inglis (Biological Sciences), Costa Metallinos (Chemistry), Adonis Skandalis (Biological Sciences), Gaynor Spencer, (Biological Sciences), Jeffrey Stuart (Biological Sciences)

Adjunct Professors

Lorne Stobbs (Biological Sciences)

Director

Michael J. Bidochka (Biological Sciences)

Administrative Assistant

Caroline Barrow

905-688-5550, extension 3042

Mackenzie Chown F234

http://www.brocku.ca/biotechnology/

At Brock University, the Graduate programs offered by the Centre for Biotechnology encompass the broad fields of chemical and gene biotechnology. These fields are interdisciplinary in nature and collaboration between participating faculty and departments is encouraged.

Admission Requirements - MSc

Students will be admissible to the MSc program on attaining a minimum high B level average grade (78% or above) or the equivalent grade point average in major courses in an undergraduate program in biotechnology, chemistry or the biological sciences (composed of but not limited to biochemistry, biology, genetics, or microbiology) from a recognized university.

Program Requirements - MSc

The program is designed to provide a broad background in the cognate basic disciplines of biotechnology (chemistry and biology). Students with undergraduate degrees in chemistry or the biological sciences will be exposed to the breadth of biotechnology through mandatory participation in the seminar program, and will have the opportunity to focus on selected areas of biotechnology in other graduate courses. Each student will be assigned a supervisory committee composed of three members from at least two of the departments participating in the program. The student will meet with the committee at the start of their program, and on a regular basis, at minimum intervals of six months, for the duration of their program of study. Each meeting will involve the presentation by the student of a report on research objectives and progress, and discussion with the committee on the realization of these goals. In addition, each student will present one research level public seminar during their tenure in the program.

Candidates admitted to the program will require a minimum of one year of full-time study. The program must include BTEC 5F90; two 5(alpha)00 level half credits; two half credits (or one full credit) which may be either at the 4(alpha)00 or 5(alpha)00 level. One of the graduate half credits must be BTEC 5P95; one half credit may be taken from other 5(alpha) level courses offered by the Departments of Biological Sciences, Chemistry or Physics.

Additional credits may be required of candidates with insufficient preparation in their areas of research specialization, at the discretion of the supervisory committee. As part of BTEC 5F90, every MSc candidate must prepare and defend a thesis which demonstrates a capacity for independent work of acceptable scientific calibre.

Admission Requirements - PhD

Students will be admissible to the PhD program on attaining a MSc degree in Biotechnology, Biophysics, Chemistry or the Biological Sciences (composed of but not limited to biochemistry, biology, genetics or microbiology) from a recognized university. Alternatively, students who have successfully completed one year in the biotechnology MSc program may apply to be transferred to the PhD program. In this event, registration in BTEC 5F90 will continue as registration in BTEC 7F99. Candidates admitted to the program will require a minimum of two years of full-time study after completion of the MSc program or transfer from the MSc to the PhD program.

Program Requirements - PhD

Each student will be assigned a supervisory committee composed of three members from at least two of the departments participating in the program. The student will meet with the committee at the start of their program, and on a regular basis, at minimum intervals of six months, for the duration of their program of study. Each meeting will involve the presentation by the student of a report on research objectives and progress, and discussion with the committee on the realization of these goals. In addition, each student will present two research level public seminars during their tenure in the program.

Candidates admitted to the program will require a minimum of two years of full-time study after completion of the MSc program or transfer from the MSc to the PhD program.

The PhD program must include BTEC 7F99; four 5(alpha)00 level half credits; two half credits (or one full credit) which may be either at the 4(alpha)00 or 5(alpha)00 level. One of the graduate half credits must be BTEC 7P96, and one half credit course must be taken from an instructor whose home department is not the one in which the student's research work is located. One half credit may be taken from other 5(alpha)00 level courses offered by the Departments of Biological Sciences, Chemistry or Physics.

Students with an MSc

The PhD program must include BTEC 7F99, as well as four 5(alpha)00 level half credits. Three of these half credits must be chosen from the 5(alpha)00 courses, while the fourth half credit may be chosen from either 4(alpha)00 or 5(alpha)00 level courses being offered. One of the graduate half credits must be BTEC 7P96 and one half course must be taken from an instructor whose home department is not the one in which the student's research work is located. One half credit may be taken from other 5(alpha)00 level courses being offered by the Department of Biological Sciences, Chemistry or Physics.

Additional credits may be required for candidates with insufficient preparation in their areas of research specialization at the discretion of the supervisory committee. As part of BTEC 7F99, every PhD candidate must prepare and defend a thesis which demonstrates a capacity for independent work of acceptable scientific calibre. Continued enrolment in the PhD program requires the successful completion of an oral comprehensive examination at a convenient time within the second or third year of the program. The comprehensive examining committee will be composed of the student's supervisor, two members of the student's supervisory committee, one member from one of the departments involved in the program and one member from a department in the Faculty of Mathematics and Science not participating in the program.

Research Fields

The following research fields are currently represented:

Chemical Biotechnology

Chemical Biotechnology involves the use of the tools and techniques of chemistry to understand and manipulate biological processes. The emphasis in the description of a new field such as Chemical Biotechnology, and its distinction from the existing discipline of biochemistry, lies in the utilization of the core skills and knowledge of chemistry (from synthetic, analytical and physical approaches) to address phenomena of biological interest.

The chemical biotechnologist has the capability to choose a biological problem, the chemical skills to tackle it, and an appreciation that chemistry impacts upon the biology as biology directs the chemistry in an interactive manner. This would, for example, describe an organic chemist who chooses a target molecule for synthesis because it represents a novel structure for a biologically important goal such as enzyme inhibition or receptor binding. The research is then guided by an iterative procedure of bioassay and structure activity relationships, efforts that require knowledge of the biological systems involved, including metabolism, enzyme/protein structure and function, in addition to cellular and molecular biology.

Research areas in the Chemical Biotechnology field include:

1.	Molecular design, synthesis and fermentation technology
	Theoretical, computational, synthetic and applied approaches to the design and biosynthesis of molecules used to investigate and/or modify biological systems.

a)	biocatalysis: the use of whole cells and/or enzymes to effect chemical transformations. Small molecule catalysis: the design of small molecule chiral catalysts with enzyme like activities, synthetic enzymes.
b)	design of key molecules/intermediates for the manipulation of biosynthesis, metabolism or signal transduction. This would include pharmacaphore discovery, drug design and delivery, investigation into molecular modes of action.

2.	Structure and dynamics of macromolecules
	Physical and theoretical approaches to understanding structure and function of macromolecules with biotechnological applications.

structural characterization by mass spectrometry, NMR, EPR, specialized RAMAN, IR and optical spectroscopic techniques.

spectroscopic and theoretical investigations of macromolecular dynamics. Steady state and time resolved NMR, EPR, and optical absorption and emission spectroscopy. Focus on protein and lipid dynamics, protein and lipid interactions, protein conformational changes associated with enzymatic activity, active site dynamics, redox active enzymes and mechanisms of electron transport. Photoactive enzymes and mechanisms of photochemistry. Computer-based molecular modeling techniques applied to biological molecules.

Gene Biotechnology

Gene biotechnology involves the use of DNA technology, bioinformatics and microbiological techniques to study biological phenomena. Molecular biologists, biochemists, chemists and microbiologists increasingly employ such tools to understand the basic concepts in molecular biology. The power of gene biotechnology lies in the ability of a researcher to isolate, manipulate, study, modify and reintroduce genes into organisms. Such modification is deliberate and can answer specific questions that were impossible to address only a few years ago.

Research Areas in the Gene Biotechnology field include:

1.	Regulation of gene expression
	The characterization and manipulation of genes and factors that influence gene expression in prokaryotes and eukaryotes.
2.	Genetic Engineering
	Isolation, analysis, modification and re-introduction of genes into organisms with emphasis on gene expression, protein modification, and protein secretion.

Facilities

The Centre for Biotechnology uses research laboratories in the Departments of Biological Sciences and Chemistry, and the Cool Climate Oenology and Viticulture Institute (Inniskillin Hall). The major equipment holdings include:

In Biological Sciences

Greenhouse, cold rooms, incubators, centrifuges, radiation facilities and all routine equipment necessary for biochemical research and gene manipulation.

In Chemistry

Two high field NMR spectrometers with solid probe facility, electron spin resonance, mass spectrometers with EI, FAB, electrospray, APCI, and CI ionization and GC and LC inlets, ICP analysis equipment, routine UV, IR, GC, HPLC facilities, incubator and sterile environment facilities.

In Cool Climate Oenology and Viticulture Institute

Cold rooms, centrifuges, standard molecular biology equipment for purification, analysis and use of proteins and nucleic acids; and fermentation equipment up to the pilot plant level.

All Brock students are entitled to computer accounts at no charge. These provide for internet and E-mail access, storage space on a central Unix server, and access to the Library, its catalogue and various on-line library services and databases. Students also have access to all campus wide PC and Mac labs, and the software installed on their servers, including word processing, spread sheets, data base, graphics, statistics etc. In addition to the central resources, there are typically one or more networked PCs or Macs in each research lab and in the central instrumentation service labs. Local and networked printers are available. Most major instrumentation is also networked, permitting the movement of experimental data from lab to office. Students may also access a dedicated computer lab that provides powerful molecular modelling/semi-empirical/ab-initio software and other important scientific software.

Course Descriptions

BTEC 5F90

MSc Thesis

The preparation and public defence of a thesis which will demonstrate the candidate's capacity for independent study.

BTEC 5P01

Biocatalysis of Chemical Reactions

The application of biological catalysts in organic chemistry, focussing on the use of isolated enzymes, bacterial and fungal systems for the production of fine chemicals for research and industrial purposes.

BTEC 5P03

Instrumental Analysis for Biotechnology

Analytical chemistry applications in the biotechnology industry emphasizing the fundamentals of gas chromatography, high performance liquid chromatography, atomic spectroscopy, etc. with applied examples drawn from the biotechnology industry. Also included is the application of real-time analytical chemistry to process control in manufacturing aspects of biotechnology. Discussion of research papers on analytical chemistry research in biotechnology will provide a central focus to this course.

BTEC 5P05

Advanced Bio-organic Chemistry

Selected topics from the current literature, such as the understanding of enzyme action through the application of organic reaction mechanisms, enzyme models and host-guest chemistry; catalytic antibodies; the chemical modification of enzymes; and bioconjugate preparation and use.

BTEC 5P06

Bioinformatics

(also offered as BIOL 5P06)

Genone sequencing projects. Gene discovery. Analysis of gene expression. Analysis of DNA/RNA/protein sequence data, including mutagenic processes, molecular evolution and systematics, codon usage, reconstruction of ancient molecules, and prediction of higher level molecular structure.

BTEC 5P09

Advanced Topics in Animal and Plant Signal Transduction Pathways

(also offered as BIOL 5P09)

Perception of stimuli to effects on gene expression. Emphasis on the molecular/biochemical tools used to study these pathways.

BTEC 5P10

Mechanisms in Plant Biochemistry

(also offered as BIOL 5P10)

Molecular and chemical control of plant disease processes and development. Focus on the detailed signaling mechanisms and outcomes of signal transduction to a plant phenotype. Emphasis on case studies that highlight the different phases of this process, including the identification of signals, signal perception, signal transduction and reaction to the signal transduction cascade to produce a phenotype.

BTEC 5P13

Biophysical Photochemistry

(also offered as CHEM 5P13)

The principles of light induced processes such as electron, energy, and signal transfer and their role in biological systems. Marcus theory, Dexter and Foerster mechanisms of energy transfer. The optical and magnetic resonance spectroscopy of excited states.

BTEC 5P14

Computational Chemistry: Applications in Biotechnology

(also offered as CHEM 5P14)

Structure-based drug design; molecular modelling; conformational search techniques; secondary and tertiary protein structure prediction; quantitative structure activity relationships; bioinformatics.

BTEC 5P17

Special Topics in Nuclear Magnetic Resonance (NMR) Spectroscopy

(also offered as CHEM 5P17)

Selected topics in advanced NMR spectroscopy, emphasizing pulse and Fourier transform methods and applications such as multi-dimensional NMR spectroscopy and high-resolution solid-state NMR for the analysis of biological systems.

Prerequisite: CHEM3P40 or equivalent.

BTEC 5P18

Advanced Mass Spectrometry

(also offered as CHEM 5P18)

Application of advanced techniques in mass spectrometry to biological systems, including ESI, MALDI, and FAB MS/MS; use of MS techniques for the analysis of biological molecules, peptide sequencing, whole cell typing, etc.

Prerequisite: CHEM 3P40 or equivalent.

BTEC 5P19

Special Topics in Biophysical Chemistry

Selected topics from the areas of biosensors, membrane chemistry, bioelectrochemistry, at an advanced level.

BTEC 5P22

Special Topics in Chemical Biology

Focuses on the chemical-biology of select biologically active compounds of current interest in the literature. The occurrence, biosynthesis and biological activity, including structure-activity relationships, will be studied. Strategies toward the chemical synthesis of these compounds will also be investigated.

BTEC 5P24

Natural Products Chemistry

(also offered as CHEM 5P24)

Structural features, synthesis and biosynthesis of natural products selected from the acetogenin, alkaloid, steroid and terpene, and other areas.

BTEC 5P25

Medicinal Chemistry

(also offered as CHEM 5P25)

Structure and activity of biologically active organic compounds; introduction to pharmacology, pharmacodynamics, and receptor theory as a background for a more detailed study of chemistry of drugs such as enzyme inhibitors and receptor antagonists; rational drug design, combinatorial libraries, screening and general routes of metabolism.

BTEC 5P27

Enzyme and Co-enzyme Mechanisms

(also offered as CHEM 5P27)

Hydrolytic and other processes catalyzed by enzymes lacking non-protein prosthetic groups; transferase reactions involving biotin, pyridoxal phosphate, thiamine pyrophosphate, folic acid and cobalamin; oxidation mechanisms involving pyridine nucleotides, flavoenzymes, hemeperoxidases, and oxygenases.

Prerequisite: CHEM 3P20 or equivalent.

BTEC 5P40

Advanced Biochemistry

Selected topics from the recent literature covering areas of modern biochemistry.

BTEC 5P50

Advanced Mutagenesis in Disease and Biotechnology

This seminar course will explore the various mechanisms of mutagenesis of the genetic material, how they contribute to disease, and how they can be adapted to produce new biomolecules.

BTEC 5P51

Advanced Molecular Virology

(also offered as BIOL 5P51)

Virus-host interaction, productive cycle, effect of virus on host cell and organism, interferon, DNA and RNA tumor viruses, viral vectors, gene therapy and recombinant viral vaccines.

BTEC 5P52

Advanced Developmental Genetics

(also offered as BIOL 5P52)The role of specific structural and regulatory genes in both vertebrate and invertebrate development; topics include homeotic genes in Drosophila and vertebrate pattern formation, primary induction and peptide growth factor and the use of transgenic mammals and gene targeting to study mammalian embryogenesis.

BTEC 5P53

Advanced Immunology

Humoral and cellular immunity; structure and synthesis of immunoglobulins; origin of antibody diversity; transplantation immunity and the importance of the major histocompatibility complex; autoimmunity and allergic reactions.

Prerequisite: BIOL 4P53 or equivalent.

BTEC 5P54

Advanced Microbiology

Microbial biotechnology, fungal and bacteria biochemistry, molecular and transmission genetics of bacteria and fungi, manipulation and modification of microbial processes for industrial productivity.

BTEC 5P57

Advanced Recombinant DNA Techniques

(also offered as BIOL 5P57)

A survey of recent technical developments in the methodology and application of various recombinant DNA techniques.

BTEC 5P58

Advanced Fungal Genetics

(also offered as BIOL 5P58)

The transmission and molecular genetics of fungi. Recent advances in gene manipulation and the contribution of studies on these organisms to general genetics principles.

BTEC 5P59

Bacterial Genetics

(also offered as BIOL 5P59)

Molecular and transmission genetics of bacteria. Bacterial genetics from early description of transformation and transduction to current developments in molecular practice.

BTEC 5P86

Current Topics in Plant Biology

(also offered as BIOL 5P86)

An investigation of a specific area or group of related topics in contemporary plant biology. Approval of the departmental graduate studies committee is required prior to registration.

BTEC 5P95

Graduate Seminar I

Presentation of one full-length (60 min) research seminar in a public forum and attending at least ten such student seminars (or other seminars designated as appropriate) during the 2 year duration of the student's Master of Science program. Credit in BTEC 5P95 can be converted to credit in BTEC 7P96 by the completion of the additional seminars and course requirements indicated for BTEC 7P96.

BTEC 7F99

PhD Research and Thesis

Preparation, public defence, and examination of a thesis that demonstrates the candidate's ability for independent thought and study at the appropriate level.

BTEC 7P96

Graduate Seminar II

Presentation of two full-length (60 min) research seminars in a public forum and attending at least twenty such student seminars (or other seminars designated as appropriate) during the 4 year duration of the student's PhD program.

Last updated: July 27, 2005 @ 03:17PM