Fall semester: Masters of Science in Microbiology and Immunology 2015/ P a g e. Program Curriculum. Core courses:

Transcription

1 Fall semester: Core courses: MIIM-7500 Graduate Medical Microbiology (4 credits). This course is designed to introduce graduate students to bacterial, fungal and viral pathogens that are the etiological agents of the most significant infectious diseases worldwide. The course will focus on the basic mechanisms of microbial pathogenesis with emphasis on the host-microbe interactions and the most recent advances on therapeutic and prophylactic treatments to combat these diseases. Important historical discoveries along with current scientific strategies to study the molecular basis of virulence will be discussed, and recent high impact publications will be assigned for reading and discussion. Course director: Lucy Freytag. Book recom-mendation: Sherris Medical Microbiology. 5 th ed. McGraw Hill. Accessible online through Matas Library (via Access Medicine). (Best link to use: MIIM 7600 Medical Immunology (3 credits). This course is designed to provide a basis of terminology relevant to the basic concepts of immunology. It commences with the important components (cell, tissues; antibodies; immunoglobulins) involved in host defense against infectious agents. Introductory lectures serve to describe and differentiate between natural defense (innate) mechanisms and adaptive immunity mediated by functional B and T lymphocytes and their products. Subsequently, cellular interactions, especially the differentiation of helper T cells subsets and the production of relevant cytokines, will be described. This will include the mechanisms of T cell activation and regulation. Finally, clinical immunology will be discussed: autoimmunity and autoimmune diseases; hypersensitivity reactions, including atopic disorders and asthma; mechanisms of transplant rejection; and immunodeficiency disorders. Course director: James McLachlan. Book Recommendation: Nairn, Immunology for Medical Students. 2 nd ed. Elsevier. Accessible through Clinical Key (Matas Library). (Best link to use: MIIM-7550 Microbiology Lab (3 credits). This course is designed to teach students how to perform basic laboratory tests using simple diagnostic tests for infectious diseases techniques. The bulk of the course consists of hands-on laboratory experience conducting laboratory tests with simulated clinical specimens and analyzing prepared teaching specimens. Procedures for organism isolation and identification and rapid diagnostic kits will be covered. Course director: Louise Lawson. MIIM-7010 Seminar in Microbiology (1 credit). The main purpose of the Seminar is to provide students with the opportunity to develop the confidence and skills necessary to make successful scientific presentations, enhance their critical thinking, and engage in thoughtful and productive scientific discussions with their professors and peers. In this course, doctoral graduate students are scheduled to present either a research article or their own work in a 50 min seminar (allowing for 10 min discussion). Masters students are required to attend and participate in the seminars and to write a one-page summary describing the content and significance of each seminar. Course director: Lucy Freytag. 1 P a g e

2 MIIM-7020 Graduate Journal Club (1 credit). This course is a journal club format for discussion of current topics in Microbiology and Immunology. Students will present a seminar to the class on a selected research paper approved by the course instructor. Students will explain the topic background and specific hypothesis being tested, describe in detail the experimental design and results, and discuss the conclusions reached and whether or not they were justified. The student audience is expected to participate in class discussion following the presentation. In addition, each student is required to write a short summary explaining the hypothesis, content and significance of the findings for each presented paper. Course director: Kerstin Honer zu Bentrup. Additional Elective Courses: MIIM-7210 Research Methods (2 credits). This course provides students with an introduction and broad overview to the basic biochemical, molecular and immunological techniques that are commonly used in biomedical research. Topics covered include: cell culture techniques, basic microscopy, recombinant DNA technology and protein analysis methods, amongst others. The theory behind the various techniques, practical applications, and the general procedures for carrying them out will be described. Hands on sessions be included. After taking the course students will have a good fundamental background in molecular methods as they are applied to biomedical research and be familiar with the terminology of molecular biology, thus giving students a better access to the scientific literature. You will gain an understanding of the various methods and their applications and will be better able to evaluate the merits of scientific papers by knowing the strengths and weaknesses of the various techniques used in biomedical research. Students pursuing a career in bench research will be better able to decide which methods to use in which situations and evaluate the strengths and weaknesses of the techniques. For most sessions, students will be responsible for preparing with assigned reading before coming to class. Reading material will be provided to the students at the latest one week before the session. Grading will be on notebook keeping, attendance and participation in class. Course director: Kerstin Honer zu Bentrup. Book Recommendation: At the Bench: A Laboratory Navigator, Updated Edition. Kathy Barker. Cold Spring Harbor Laboratory Press MIIM-7720 Medical Mycology (3 credits). This course consists of a basic introduction to medical mycology and a comprehensive study of the fungi (yeasts and molds) and mycoses (fungal diseases) likely to be encountered in clinical settings by a physician, medical mycologist, or medical technologist. Attention will be distributed as equally as possible between emphasis on the biology of the fungal pathogen and on its disease. Course director: Cindy Morris. Book recommendation: Medical Mycology, A self-instructional Text. 2 nd ed. Blevins & Kern. MIIM-9980 Master s Research (0 credits). Students who would like to take the thesis track will enroll in this course each semester. They also need to register for the MIIM-XXXX Thesis Research Design course in order to receive the 2 credits per semester. NOTE: the Master s Research course carries a $300 fee imposed by the registrar s office. Please talk to Drs Honer zu Bentrup or Freytag before enrolling in this if you are on the thesis track. 2 P a g e

3 Thesis Requirements 1. Writing the thesis involves substantial independent library research and study working under the guidance of a professor from the Department of Microbiology and Immunology. The thesis should demonstrate the student s ability to: o communicate scientific information, o perform analytical literature review, o write a comprehensive summary of the most current state of knowledge in the chosen topic, o acquire scholarly competence and understanding in the field of study The thesis should be formatted according to the BMS guidelines for dissertations (see under thesis requirements, and more specifically: ) and should contain approximately 6000 words including figures and tables, but excluding references. Students can organize the thesis following e.g. Frontiers or Nature reviews examples. 2. A student s Master s thesis committee consists of three faculty members (at least two from the department of Microbiology and Immunology), with the thesis director as the Chair of the committee. 3. The student consults the MS program director (Dr. Honer zu Bentrup) to identify the thesis director. The student consults the thesis director to identify the other 2 thesis committee members. 4. The topic for the thesis must be approved by the thesis director. In the fall semester, the student meets with the thesis director on a monthly basis to define the scope and content of the thesis and becomes familiar with the thesis format. 5. The student submits a preliminary outline of the thesis formatted with subheadings to the thesis director by December The student completes the thesis during the spring semester. The student needs to continue to schedule monthly meetings with the thesis director to assess the student s progress. 7. Deadline for submitting an electronic copy of the thesis to the thesis director is April 3 rd. A final draft of the thesis should be sent to all committee members by April The student will give an oral presentation with a summary of the thesis as a short departmental seminar (30 min). The deadline for oral presentations is April Following the presentation, the thesis committee will have a meeting with the student to evaluate the thesis and oral presentation. This meeting affords the members of the committee the opportunity to make constructive recommendations/suggestions to improve the quality and scientific content of the thesis. 10. Once the student satisfactorily completes the requested changes to the thesis and submits the final copy to the thesis director, the Master s Thesis Form is signed by all members of the committee. 3 P a g e

4 11. The final copy of the thesis is due in the BMS office on May 8 th. MIIM-XXXX Thesis Research Design (2 credits). This course is for students in the Masters Program in Microbiology who have chosen the thesis track for completion of their degree. This course will guide students through the writing process in relation to the field of biomedical science. Topics to be covered include: Defining the scope of the thesis Structuring an outline Collecting, interpreting and critically analyzing literature Scientific writing skills Reference management Document formatting Throughout the semester, students will be required to develop their own thesis research topics, review relevant research and scholarship, and complete their thesis outline with guidance from departmental faculty. Course director: Louise Lawson GBCH-7500 Human Medical Cellular Biochemistry (5 credits). The objectives and content of the Human Medical Cellular Biochemistry course are designed to provide students with a comprehensive understanding of cellular structure and function, and the manner by which cellular processes are normally integrated and regulated. This course stresses both the normal cellular function, and why disease states occur if normal cellular processes are disrupted. Course director: David Franklin. Spring semester Core courses MIIM-7400 Responsible conduct of Biomedical Research (2 credits). This course explores a variety of ethical and policy issues that arise during the conduct of basic, translational, and clinical biomedical scientific research, with special emphasis on research in infectious diseases. Topics addressed include: (1) research misconduct; (2) "every day" ethical issues faced by biomedical scientists; (3) the use of laboratory animals in scientific research; (4) human research participants and scientific research; (5) authorship practices in scientific publications; (6) conflicts of interest arising from scientists acting as policy consultants and experts; (7) data sharing and data secrecy; (8) mentoring; (9) research with stem cells; (10) the dual-use dilemma; (11) select agents and bioterrorism; and (12) scientists as citizens. Course sessions will include lectures, discussion periods, and analyses of case studies. Material will be provided to the students at the latest one week before the session. Course director: John Clements. MIIM-7020 Seminar in Microbiology (1 credit). The main purpose of the Seminar is to provide students with the opportunity to develop the confidence and skills necessary to make successful scientific presentations, enhance their critical thinking, and engage in thoughtful and productive scientific discussions with their professors and peers. In this course, doctoral 4 P a g e

5 graduate students are scheduled to present either a research article or their own work in a 50 min seminar (allowing for 10 min discussion). Masters students are required to attend and participate in the seminars and to write a one-page summary describing the content and significance of each seminar. Course director: Lucy Freytag. MIIM-7030 Topics in Microbiology (1 credit). This course is designed to introduce students to a number of current research fields through studying published research papers, general public resource, and other material. Students will pick a topic of their interest, specifically one that is current. Students will present a summary of their topic to the class and will generate questions for their classmates that will stimulate discussions. Topics can include basic, applied, and clinical research and reviews to canvass the latest developments in the field of Microbiology and/or Immunology. Course director: Kerstin Honer zu Bentrup. MIIM-7320 Lab Research (1 credit (listed as 1-10 cr). Students will work in a laboratory after contacting the PI to learn how different methods are used to carry out research in Microbiology and Immunology. At the end of the semester, students will write a 2 to 3 page summary describing what they learned and the methods they used. Grade will be Pass/Fail. Additional Elective Courses: MIIM-7750 Medical Parasitology (3 credits). The first part of this class will briefly introduce basic concepts and terminology to discuss parasites, vectors, and the (human) host and their relationship to each other. We will then explore a number of important diseases and the diverse set of helminths and protozoa causing them. We will highlight critical aspects of the biology of parasitism and parasitic disease as we go along. The lectures aim to span the entire field ranging from the molecular biology of the parasite to the implementation of control programs in the field. Course director: Cindy Morris. Book recommendation: Medical Parasitology, A self-instructional Text. 6 th ed. Leventhal & Cheadle. MIIM-7250 Vaccine Biology (3 credits). The worldwide eradication of smallpox is the best example of the success of vaccines as the best weapon to combat infectious diseases. This course will discuss vaccines from their historical development to state of the art strategies being currently employed to create new vaccines or improve the ones currently existing. We will focus on antigen discovery, immunological responses required for successful vaccination, and novel adjuvants and immunopotentiation strategies. Specific topics will include methods to link innate and adaptive responses, virulence factors and their role in immunity, strategies used by pathogens to escape the host response, and new delivery systems and biotechnology approaches for the development of vaccines. Course directors: Lucy Freytag/Lisa Morici MIIM-7220 Advanced Research Methods/Data mining (4 credits). This course addresses the process of experimental design and current experimental methodologies in biology. The goal of this course is to introduce graduate students to the principles of current research methods, both in theory and in practice. Additionally, it will introduce methods for data mining, analysis and presentation. The course will be a mixture of lectures, discussion of research papers and hands on 5 P a g e

6 sessions using the instruments discussed during the respective sessions. Most sessions will a l s o involve practical application of computer tools using experimental data sets. Students enrolled in this course will learn basic bioinformatics and data mining techniques using freely available web-based resources tools. Students will also be introduced to the use of advanced features in amongst others - Microsoft Excel, Graphpad Prism, ImageJ and Microsoft Powerpoint in the analysis and graphical presentation of common types of experimental data. Participants will be expected to be reasonably familiar with the basic features of MS Office programs and to have an understanding of first year undergraduate-level statistics. The objective is to not only help students understand the methods they might use in research but to also alert them to alternative research methods that they might not have considered otherwise. For most sessions, students will be responsible for reading a research article that focuses on the particular method, as well as background information on the respective method, before coming to class. Reading material will be provided to the students at the latest one week before the session. Course directors: Debbie Sullivan/Kerstin Honer zu Bentrup. MIIM-7120 Advanced Virology (4 credits). The course includes lecture and discussion of fundamental and advanced topics in medically relevant virology. Topics will be taken from the current literature to allow incorporation of fundamental principles of virology into the current context of the field. Selected Tulane faculty with expertise in the field will lead the discussion. Course directors: Cindy Morris/Debbie Sulivan. Book recommendation: Principles of Virology, 3 rd ed, Flint, Enquist, Racaniello, Skalka. (a copy will be on hand in the departmental library) MIIM-9980 Master s Research (0 credits). See description under Fall semester. MIIM-7320 Lab Research (1 credit (listed as 1-10 cr). Students will work in a laboratory after contacting the PI to learn how different methods are used to carry out research in Microbiology and Immunology. At the end of the semester, students will write a 2 to 3 page summary describing what they learned and the methods they used. Grade will be Pass/Fail. MIIM-XXXX At the Interface - Dynamics of immunologic and microbial interactions (3 credits). Microorganisms living in or on the body of a healthy human adult outnumber human cells by 10 to one. Mucosal surfaces operate through a complex and dynamic interplay between the host and microbiota with the outcomes of these interactions deciding an individual s health or disease status. During the course of this class we will dissect topics focusing on this interface of the immune system and microbiota within mucosal tissue sites. Topics will include creation tolerance and commensal colonization, long-term consequences of acute bacterial infections, and development of chronic inflammatory diseases. By completion of the course, students will have explored immunologic-microbial interfaces through reading and extensive discussion of primary journal articles. Students will also select a relevant topic to prepare a short perspective or review style paper to be edited and refined through a classic peer-review process with fellow students and instructors. Rudimentary knowledge of immunology and microbiology is highly recommended. Course directors Jacob Bitoun and Elizabeth Norton 6 P a g e

7 GBCH-7520 Metabolic Biochemistry of Human Disease (Spring Semester, 5 credits). The objectives and content of the Metabolic Biochemistry of Human Disease course are designed to provide students with a comprehensive understanding of the metabolic pathways involving the four major metabolic compounds: carbohydrates, lipids, amino acids and nucleotides; and the manner by which metabolism is normally integrated and regulated. This course stresses both the normal metabolic function, and why disease states occur if normal metabolic processes are disrupted. Course director: David Franklin. Electives will be selected from graduate courses in Microbiology and Immunology or Biochemistry, as may be offered during the time that the student is in residence. A direct link to a number of the books mentioned above can be found at: 7 P a g e

8 PLEASE NOTE: AS MANDATED BY THE REGISTRAR S OFFICE, A COURSE GRADE OF C (i.e. C+, C, C-) OR BELOW WILL RESULT IN THE LOSS OF THE RESPECTIVE COURSE CREDIT HOURS. SUCCESSFUL GRADUATION FROM THE PROGRAM REQUIRES AT LEAST 30 CREDIT HOURS (TOTAL) AND A FINAL GPA OF 3.0 OR HIGHER. MOST BOOKS ARE AVAILABLE ONLINE THROUGH THE MATAS LIBRARY. THE DEPARTMENT WILL SUPPLY THOSE BOOKS THAT ARE REQUIRED BUT NOT ACCESSIBLE ONLINE TO STUDENTS TAKING THE RESPECTIVE COURSES. Faculty: John D. Clements, Ph.D. Lucy Cardenas-Freytag, Ph.D. David Franklin, Ph.D. (Biochemistry) Robert F. Garry, Jr., Ph.D. Kerstin Honer zu Bentrup, Ph.D (Program director) Laura S. Levy, Ph.D. Louise B. Lawson Ph.D. James McLachlan, Ph.D Lisa Morici, Ph.D Cindy Morris, Ph.D. Elizabeth Norton, Ph.D. Ramesh Prabhu, Ph.D. Deborah E. Sullivan, Ph.D. Adjunct Faculty and Visiting Lecturers: Jane El-Dahr, MD (Peds-Allergy/Immunology) Monica Embers, Ph.D. (TNPRC Bacteriology & Parasitology) Deepak Kaushal, Ph.D. (TNPRC Bacteriology & Parasitology) Susan McLellan, MPH, MD (Medicine/Infectious Diseases) Chad Roy, Ph.D., Ph.D. (TNPRC Bacteriology & Parasitology) Karol Sestak, Ph.D. (TNPRC Bacteriology & Parasitology) A direct link to the pre-health advisor program can be found at: 8 P a g e