Undergraduate Programs in Microbiology and Immunology (MICI) Dalhousie University

1 Undergraduate Programs in Microbiology and Immunology (MICI) Dalhousie University Draft March 25 2015 Students should check with the Department to ensure that the draft they have is the most recent one Department of Microbiology and Immunology Sir Charles Tupper Medical Building Dalhousie University Halifax, Nova Scotia B3H 4R2

2 Microbiology and Immunology (MICI) 2100 Introductory Microbiology and Immunology (F) (W online) 2115 Human Organs and Tissues (W) 2400 Laboratory Methods in Microbiology and Immunology (W) 3024 Microscopy (F) (may not be offered every year) 3114 Virology (F) 3115 Immunology (F) 3119 Physiology of the Prokaryotic Cell (F) 3620 Experiential Learning in Microbiology and Immunology (only by permission) 4027 Molecular Mechanisms of Cancer (W) (may not be offered every year) 4033 Advanced Microbial Genetics (W) 4100 Processes and Mediators of Inflammation (W) 4114 Advanced Topics in Molecular and Medical Virology (W) 4115 Immunology of Host Resistance (W) 4116 Current Topics in Mucosal Immunology (F) 4118 Molecular Bacterial Pathogenesis (F) (may not be offered every year) 4218 Clinical Microbiology (W) 4302 Molecular Immunology (F) 4700 Directed Research Project (F and W) (not for Honours students) 4701/4702 Advanced Topics in Microbiology and Immunology (F or W) (only by permission) 4900 Honours Research and Thesis (F and W) MICI approved courses in Biology (BIOL) 2004 Diversity of Life II (W) 3101 Microbial Ecology (W) 3102 Microbial Eukaryotes (F) 3322 Parasitology (F) MICI approved course in Psychology and Neuroscience (PSYO/NESC) 3180 Psychoneuroimmunology/Ecoimmunology (F) MICI approved courses in Biochemistry & Molecular Biology (BIOC) 4010 Bioinformatics (W) 4403 Genes and Genomes (W) 4404 Gene Expression (F) 4501 Medical Biotechnology I (F) 4835 Human Genetics (W) MICI approved courses in Food Science & Technology FOSC 3080 Food Microbiology (F) F = fall term W = winter term

3 HONOURS DEGREE IN MICROBIOLOGY and IMMUNOLOGY General University Requirements 1) Total credits required for degree: 20 (40 half-year courses) 2) a) one credit in a math b) one credit in one or more language/humanities subjects c) one credit in one or more social science subjects d) one writing course 3) Minimum of 9 credits (18 half-year courses) maximum of 11 credits (22 half-year courses) beyond the 1000-level in the Honours subject grade must be C or better to count. 4) Total credits required above the 1000 level 12 (24 half-year courses.) Required GPA for graduation: 3.00 (Honours subject courses only are used for the calculation) Graduation with first class honours: GPA 3.70 Suggested program: YEAR 1: BIOL 1010 and 1011 or 1020 and 1021 CHEM 1011 and 1012 MATH 1000 or MATH 1215 MATH 1010 or STAT 1060 One credit in one or more language/humanities subjects One credit in one or more social science subjects One writing course: may use SCIE1111 for this requirement YEAR 2: MICI 2100, Introductory Microbiology and Immunology (F), MICI 2400, Laboratory Methods in Microbiology and Immunology (W) BIOL 2020, Cell Biology (F or W), BIOL 2030, Genetics and Molecular Biology (F or W), BIOC 2300 and 2610, Introduction to Biochemistry (Lecture and Lab courses) (W) CHEM 2401 and 2402, Organic Chemistry I and II 1.0 elective credits (2 half-year courses) YEAR 3: BIOC 3400, Nucleic Acid Biochemistry and Molecular Biology (F) MICI 3114, Virology (F) MICI 3115, Immunology (F), MICI 3119, Physiology of the Prokaryotic Cell (F) 3.0 elective credits (6 half-year courses). We suggest you include a 0.5 credit (1 half-year course) in a MICI or MICI-approved course here. The courses that count towards a degree in MICI are listed on page 2.

4 YEAR 4: MICI 4900, Honours Research and Thesis (F and W) 0.5 credit (1 half-year course) in a 4 th year MICI course and 0.5 credit (1 half-year course) in a MICI or MICIapproved course Enough credits in MICI or MICI-approved courses to complete the 9-credit requirement for a MICI degree Enough elective credits to complete the 20-credit requirement for a B.Sc. degree Required courses for an Honours Degree in Microbiology and Immunology: MICI 2100, 2400, 3114, 3115, 3119, 4900, 1 half-year course in MICI 4XXX, 1 half-year course in MICI 4XXX or MICI -approved 4th year level course BIOL 2020 and 2030, BIOC 2300, 2610 and 3400, CHEM 2401 and 2402 Departmental minimum grade requirements 1. For entry into MICI 2100, a grade of B- in first year Biology and Chemistry is required. For students in DISP, a final overall grade equal to or greater than the median is required. 2. MICI 2100, 2400, 3114, 3115, 3119, 4900 You must obtain a grade of B or greater in 5 of the 6 following courses MICI 2100, 2400, 3114, 3115, 3119, 4900X/Y and a grade of B or greater in the sixth course. 3. BIOL 2020 and 2030, BIOC 2300, 2610 and 3400, CHEM 2401 and 2402. You must obtain a grade of C or greater. Note that for entry into third and fourth year courses there are additional minimum grade requirements see the Calendar for details. For entry into the Honours program you must obtain approval from an academic advisor of Microbiology and Immunology. We suggest you contact one of them, at the latest, during the second year of your program. ADVISORS: C. Barnes (494-2123; Chris.Barnes@dal.ca) L. Murray (494-6933; Lois.Murray@Dal.Ca) D. Stoltz (494-2590; dstoltz@dal.ca)

5 COMBINED HONOURS DEGREE in MICI and BIOC The Department of Microbiology and Immunology (MICI) offers a combined Honours degree with either Biology (BIOL) (see the Calendar) or Biochemistry & Molecular Biology (BIOC). If you wish to pursue a combined Honours degree with a different department you must contact an academic advisor of Microbiology and Immunology. This is a 4-year program. General University Requirements 1) Total credits required for degree: 20 (40 half-year courses) 2) a) one credit in math b) one credit in one or more language/humanities subjects c) one credit in one or more social science subjects d) one writing course 3) Minimum of 11 credits (22 half-year courses) maximum of 14 credits (28 half-year courses) beyond the 1000-level in the two subjects, not more than 9 credits (18 half-year courses) nor fewer than 5 credits (10 halfyear courses) being in either of them. Grade must be C or better to count. 4) Total credits required above the 1000 level 12 (24 half-year courses.) Required GPA for graduation: 3.00 (Honours subject courses are only used for the calculation) Graduation with first class Honours: GPA 3.70 Departmental Requirements 1000 level BIOL 1010 and 1011 or 1020 and 1021 CHEM 1011 and 1012 MATH 1000 or MATH 1215 MATH 1010 or STAT 1060 2000 level MICI 2100 and 2400 BIOL 2020 and 2030 BIOC 2300 and 2610 CHEM 2401 and 2402 3000 level BIOC 3300 and 3400 and 3700 MICI 3114 and 3115 and 3119

6 4000 level 1.0 credit from any of: BIOC 40XX, 43XX, 44XX, 45XX, or 47XX 0.5 credit from MICI 4XXX Either MICI 4900X/Y or BIOC 4604/05 Additional requirements are 1.5 credits (3 half-year courses) from either MICI or BIOC approved courses. Departmental minimum grade requirements 1. For entry into MICI 2100, a grade of B- in first year Biology and Chemistry is required. For students in DISP, a final overall grade equal to or greater than the median is required. 2. MICI 2100, 2400, 3114, 3115, 3119, 4900 You must obtain a grade of B or greater in 5 of the 6 following courses MICI 2100, 2400, 3114, 3115, 3119, 4900X/Y and a grade of B or greater in the sixth course. 3. BIOL 2020 and 2030, BIOC 2300, 2610 and 3400, CHEM 2401 and 2402. You must obtain a grade of C or greater. Note that for entry into third and fourth year courses there are additional minimum grade requirements see the Calendar for details.

7 CO-OP DEGREE IN MICROBIOLOGY and IMMUNOLOGY The Department of Microbiology and Immunology offers a Co-op Science experience to qualified students enrolled in Honours, Combined Honours, or Major degree programs. Note that national regulations presently require that at least one academic term be replaced by a work term; thus, co-op programs take an extra semester to complete. Work placements, beginning in the summer following completion of either second or third year studies, are in university or government research laboratories, diagnostic laboratories, or industry. These environments provide an excellent opportunity for students to learn cutting edge technologies, and to interact with working professionals; in so doing, coop students may be better prepared for post-graduation employment in fields that are relevant to their educational training. Application: Interested students will normally apply to enroll in a co-op program after their first year of study. Acceptance requires a GPA of 3.30 (B + ) or better; the same level of academic achievement will be required for continuance in the program; in addition, a grade of B+ is required in both MICI 2100 and MICI 2400. Format: Co-op students participate in a required, non-credit series of focused workshops, which are designed to prepare them for the first work-term period; these are scheduled in the evening in the A term only. A one-time fee of $300 is assessed for this course. Each of the three required work terms will be the subject of a written report, a grade for which becomes part of the academic transcript. Work terms are arranged according to the schedule shown below. Note that graduation with the Co-op designation requires that at least three work terms be completed successfully. Year September/December January/April May/August 1 Academic Academic Free 2 Academic Academic Work term 1 3 Academic Academic Work term 2 4 Work term 3 Academic 5 Academic (Alternatively, the 1 st work term could occur in the summer of year 3; the 3 rd work term would then take place in either the spring or summer of year 5; other possibilities exist!) N.B. Students cannot do an honours research project and a co-op work term concurrently. Disadvantages: Your degree program will take 4.5 years to complete. Accordingly, co-op may not be the best path for students with a focused interest in medicine/dentistry, as entry into those programs will be delayed by a year. One or more of your work terms is likely not to be in the Maritimes. Co-op students must attend a series of non-credit workshops (SCI 2800) Advantages: While work term jobs are not guaranteed, both the Co-op Office and the Dept. nonetheless feel obligated to do their best to assist you in this; the success rate has been consistently high. Jobs in government labs are often easier to access in the case of co-op students; as you might expect, jobs in government labs tend to pay better! Contact: D.B. Stoltz, Dept. of Microbiology and Immunology (dstoltz@dal.ca; 494-2590). Theresa Myra, Director, Fac. of Science Co-op (Theresa.myra@dal.ca; 494-6448); Lisa Galway, Coordinator, (lisa.galway@dal.ca; 494-1768).

8 MAJOR DEGREE IN MICROBIOLOGY and IMMUNOLOGY General University Requirements 1) Total credits required for degree: 20 (40 half-year courses) 2) Total credits required above 1000 level: 12 (24 half-year courses) 3) Minimum of 5 (10 half-year courses), maximum of 10 credits (20 half-year courses) in the major subject beyond the 1000 level, including 3 credits (6 half-year courses) above the 2000 level. 4) a) one credit in math b) one credit in one or more language/humanities subjects c) one credit in one or more social science subjects d) one writing course Required GPA for graduation: 2.00 Graduation with distinction: GPA 3.70 Departmental Requirements: Note that the departmental requirements require 3.5 credits (7 courses) above the 2000 level in the major subject First-year required courses: BIOL 1010/1011 or BIOL1020/1021 CHEM 1011/1012 MATH 1000 or MATH 1215 MATH 1010 or STAT 1060 Note: We suggest that you fulfill the math, social sciences, language/humanities, and writing requirements in the first year. Second-year required courses: MICI 2100, 2400 BIOL 2020, 2030 BIOC 2300, 2610 CHEM 2401, 2402 Note: For these courses to count towards a Major degree, you must obtain a grade of C or better. In some cases, you will need a grade of B or a B as a prerequisite for entry into 3000-level courses (see Calendar). We suggest that you take the above courses in your second year, so that: a) you have the prerequisites to enter the more advanced 3000-4000 level courses; b) there are fewer conflicts in your timetable. Third and fourth-year required courses: BIOC 3400 MICI 3114, 3115, 3119 Plus 1.0 credits (2 half-year courses) at or above the 3000 level in MICI-approved courses (see page 2) Plus 0.5 credit from MICI 4XXX Note: For these courses to count towards a Major degree you must obtain a grade of C or better. We suggest that you take BIOC 3400, MICI 3114, MICI 3115, and MICI 3119 in your third year, which gives you the prerequisites to enter advanced follow-up courses in your fourth year.

9 DOUBLE MAJORS DEGREE General University Requirements 1) Total credits required for degree - 20 (40 half-year courses) 2) Total credits required above 1000 level 12 (24 half-year courses) 3) Minimum of 10 (20 half-year courses) and a maximum of 14 credits (28 half-year courses) in the major subjects beyond the 1000 level are to be in the two subjects, with no more than 9 (18 half-year courses) and no fewer than 5 (10 half-year courses) in either, including at least 2 credits (4 half-year courses) beyond the 2000 level in each of the two major subjects. 4) a) one credit in math b) one credit in one or more language/humanities subjects c) one credit in one or more social science subjects d) one writing course Required GPA for graduation 2.00 Graduation with distinction - GPA of 3.70 MICI Departmental Requirements: First-year required courses: BIOL 1010/1011 or BIOL1020/1021 CHEM 1011/1012 Note: we suggest that you fulfill the math, social sciences, language/humanities, and writing requirements. Second-year required courses: MICI 2100, 2400 BIOL 2020, 2030 BIOC 2300, 2610 CHEM 2401, 2402 Note: For these courses to count towards a Major degree you must obtain a grade of C or better. We suggest that you take them in your second year to obtain the prerequisites for the more advanced courses. In some cases you will need a grade of B or a B as a prerequisite for entry into 3000-level courses (see Calendar). Third and Fourth-year required courses: BIOC 3400 MICI 3114, 3115, 3119, plus 0.5 credit from MICI 4XXX Note: For these courses to count towards a Major degree you must obtain a grade of C or better. We suggest that you take BIOC 3400, MICI 3114, 3115 and MICI 3119 in your third year so that you have the prerequisites to enter more advanced courses in fourth year.

10 BACTERIOLOGY/GENETICS The importance of bacterial infections as a threat to human health is immense. Infectious diseases as a whole (including those caused by bacteria) are still the number one cause of death in the world; therefore, the study of infectious disease is of great importance for human health and well being. Bacteriology Research Interests The infectious process that bacterial pathogens follow to cause disease consists of several defined steps of: 1) Initial host-pathogen interaction 2) Colonization of the host 3) Evasion of host-defense mechanisms 4) Damage to the host The study of the above steps constitutes the basis for teaching and research in the area of bacterial pathogenesis, with two main objectives: to understand the underlying mechanisms of infectious diseases and to find new ways to prevent or cure them. Faculty members within our department who teach different aspects of bacterial pathogenesis (from either a clinical or basic science perspective) carry out active research covering all the steps of the infectious process listed above. In fact, our department has had, and continues to have, notable contributions to this field of research: from 1) confirming that listeriosis is a food-borne disease, 2) elucidating the molecular basis of resistance of the ulcer-causing bacterium to the antibiotic metronidazole and 3) discovering a new toxin in the bacterium that causes antibiotic-associated diarrhea, to 4) developing new vectors for effective and safe vaccines. The Microbiology and Immunology department has strong links with the university-affiliated hospitals (QEII and IWK-Grace Health Research Centers). In addition, the Dalhousie Infectious Diseases Research Alliance (DIDRA) provides an environment in which researchers involved in the study of infectious diseases can share ideas, resources and expertise. Bacteriology Course Selections Are you interested in this area of Microbiology? You may want to consider the following courses offered by our Department: MICI 3119 (Physiology of the Prokaryotic Cell), MICI 4033 (Advanced Microbial Genetics), MICI 4218 (Clinical Microbiology), MICI 4118 (Molecular Bacterial Pathogenesis). At the Honours level, students are required to conduct a novel research thesis topic under the supervision of a faculty member (MICI 4900) (Honours Research and Thesis). Faculty involved in bacterial pathogenesis (Drs. Davidson, Douglas, Halperin, S. Lee, Y-H. Li, Thomas and Rohde) would be pleased to provide you with details of their own research interests and potential research projects. Genetics Research Interests Classical genetics is the study of how traits (genes) are transmitted from one generation to another. With the development of recombinant DNA technologies the field of genetics has expanded to encompass every aspect of biology. Modern genetics (or molecular genetics) has evolved into an experimental approach that provides the researcher with the capacity to isolate and modify genes, determine the underlying function of gene products and manipulate the genetic material of cells to not only understand fundamental issues of biology but

11 also to create tools that can be used to improve human health. Although the application of molecular genetics now underpins essentially all aspects of biological research, a number of labs within the Department of Microbiology and Immunology have focused on the use of a combination of classical and molecular genetics to explore fundamental issues of gene expression, development, cell behaviour and host/pathogen interactions. For some of these molecular genetics labs, an experimental system of choice is the budding yeast, Saccharomyces cerevisiae, a unicellular eukaryote. One of the most exciting findings of the past few years has been the appreciation that essentially all cells (from yeast to humans) display a remarkable conservation of function so that the molecular and genetic facility of yeast can be exploited to investigate basic cellular activities of all eukaryotic cells. Thus, labs with within the Department use yeast to explore issues such as control of cell proliferation, development and morphogenesis, and the regulation of gene expression. Genetics Course Selections The microbial genetics curriculum in the Department is a gradually staged exposure to concepts in genetics, of increasing sophistication and conceptualization with the more advanced courses. An undergraduate s first exposure to genetics is usually in second year through the Biology department with BIOL 2020, and BIOL 2030, and the Microbiology and Immunology department with MICI 2100 (Introductory Microbiology and Immunology). Third year students then take BIOC 3400 (Nucleic Acid Biochemistry and Molecular Biology) and MICI 3119 (Physiology of the Prokaryotic Cell). Advanced courses such as MICI 4033 (Advanced Microbial Genetics), MICI 4027 (Molecular Mechanisms of Cancer), BIOC 4404 (Gene Expression), BIOC 4501 (Medical Biotechnology I) round out the offerings. At the Honours level, students are required to conduct a novel research thesis topic under the supervision of a faculty member (MICI 4900) (Honours Research and Thesis). Faculty involved in microbial and/or molecular genetics (Drs. Berman, Murray, Rohde, and Thomas) would be pleased to provide you with details of their own research interests and potential research projects.

12 IMMUNOLOGY Immunology research, teaching, and interest have mushroomed in the Department over the past decade. Main areas of interest of the faculty include 1) studying the mechanisms of inflammation, 2) cancer research, 3) transplantation, and 4) host defense to infectious diseases. The common interests among faculty members have led to the establishment of the Cancer Immunotherapy Research Group and the Dalhousie Inflammation Group. Many immunologists also participate in the Dalhousie Infectious Diseases Research Alliance. Some faculty hold appointments in clinical departments and the links to the clinical setting are readily established. Research Interests Faculty specifically study transplant rejection, immunomodulation by herbal medicines, gastrointestinal inflammation, lymphocyte immunity to cancer, mast cell regulation of inflammation, mechanisms of leukocyte infiltration into sites of (lung and arthritis) inflammation, aspects of host defense to viral and bacterial pathogens, and vaccine development. All the faculty support student trainees, who may do research in the lab as Honours students or Major students. Research experience in the laboratory and the current contents of the Immunology course offerings prepare students for jobs in the biomedical/pharmaceutical sciences, or for further study at the graduate levels of M.Sc. and Ph.D. Immunology Course Selections The Immunology curriculum in the department is a gradually staged exposure to concepts in Immunology that increases in sophistication and conceptualization with the more advanced courses. An undergraduate s first exposure to Immunology is in MICI 2100 (Introductory Microbiology and Immunology), involving a series of introductory lectures. Following MICI 2100, interested students may register in MICI 2115 (Human Organs and Tissues: Infection and Immunity) in the same year, then take MICI 3115 (Immunology) in the following year. Following MICI 3115, students are recommended to take MICI 4115 (Immunology of Host Resistance), which is their first introduction to immunological experimentation as represented in publications. This course consists of lectures based on recent research publications chosen by the course coordinator. MICI 4115 prepares students for the remaining senior level undergraduate courses: MICI 4100 (Processes and Mediators of Inflammation), MICI 4302, (Molecular Immunology), and MICI 4116 (Topics in Mucosal Immunology), all of which require student presentations of current literature. Interested students are encouraged to consider taking PSYO/NESC 3180 (Psychoneuroimmunology/Ecoimmunology). At the Honours level, students are required to conduct a novel research thesis topic under the supervision of a faculty member (MICI 4900) (Honours Research and Thesis). Faculty involved in immunology (Drs. Halperin, Hoskin, B. Johnston, P. Lee, T. Lee, Legare, Lehmann, Liwski, Marshall, Stadnyk, Stanford, Wang, West and Zhou) would be pleased to provide you with details of their own research interests and potential research projects.

13 VIROLOGY Virology has had a long and distinguished history at this University; in fact, Dalhousie s first Ph.D. degree was earned, in 1959, by a virology student. In more recent years, virologists associated with this Department have, among other things: made a significant contribution to the province s decision to ban aerial spraying of chemical pesticides (this resulted from crucially important research into the cause of Reye s Syndrome); described and named an entirely new, and very large, family of viruses; discovered new cell-fusing polypeptides with potential application in the field of gene therapy; and developed sophisticated molecular tools for the diagnosis of important human pathogens. Research Interests Virology constitutes a major focus on teaching and research within the Department; in fact, ours represents the only such focus east of Montreal. Current areas of research include: the reoviruses (Drs. Duncan, P. Lee), which constitute one of the largest and certainly the most diverse group of viruses known; the polydnaviruses (Dr. Stoltz), the only group of viruses known to have entered into obligatory mutualistic relationships with their hosts; and dengue virus (Dr. Anderson), an important human pathogen in the tropics (but likely to move north as a consequence of global warming); influenza virus surveillance, diagnosis and pathogenesis (Drs. Hatchette, McCormick); and Kaposi s sarcoma-associated herpesvirus, an important human tumour virus (Dr. McCormick). Dalhousie virologists collaborate extensively with biochemists and immunologists (both here and at other institutions), the Canadian Forestry Service, and the National Microbiology Laboratory (Health Canada, Winnipeg), among others. Virology Course Selections Teaching in virology begins with MICI 2100 (Introductory Microbiology and Immunology), followed by MICI 3114 (Virology) and MICI 4114 (Advanced Topics in Molecular and Medical Virology). Students having a particular interest in virology will profit from exposure to required and elective courses in cell biology, immunology and biochemistry, emerging upon graduation with a solid foundation in the discipline. Advice regarding academic programs in general, and academic virology in particular, (including the Co-op Program) can be obtained from Dr. Stoltz. At the Honours level, students carry out a research project under the supervision of a faculty member (MICI 4900: Honours Research and Thesis). Faculty involved in virology (Drs. Anderson, Corcoran, Duncan, P. Lee, McCormick, Richardson, and Stoltz) would be pleased to provide you with details of their own research interests and potential research projects.

14 Dalhousie University policy on intellectual honesty and plagiarism (Excerpts taken directly from the Dalhousie Undergraduate Calendar Website) Intellectual Honesty A University should epitomize the quest for intellectual honesty. Failure to measure up to the quest for such a standard can result in an academic offence. The seniority of the student concerned, the presence of a dishonest intent, and other circumstances may all be relevant to the seriousness with which the matter is viewed. Plagiarism or Self-Plagiarism Dalhousie University defines plagiarism as the presentation of the work of another author in such a way as to give one's reader reason to think it to be one's own. Plagiarism is a form of academic fraud. Plagiarism is considered a serious academic offence which may lead to loss of credit, suspension or expulsion from the University, or even the revocation of a degree. In its grossest form plagiarism includes the use of a paper purchased from a commercial research corporation, or prepared by any person other than the individual claiming to be the author. Self-plagiarism is the submission of work by a person which is the same or substantially the same as work for which he or she has already received academic credit. The University attaches great importance to the contribution of original thought to scholarship. It attaches equal importance to the correct attribution of authorities from which facts and opinions have been derived. The proper use of footnotes and other methods of attribution varies from discipline to discipline. Failure to abide by the attribution standards of the discipline concerned in the preparation of essays, term papers and dissertations or theses may, in some cases, constitute plagiarism. Students who are in any doubt about the proper forms of citation and attribution of authorities and sources should discuss the matter in advance with the faculty members for whom they are preparing assignments. In many academic departments, written statements on matters of this kind are made available as a matter of routine or can be obtained on request.