Mon, Wed and Fri; 10:30-11:20; Room 107 Anim. Sci. Bldg.

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1 ANSC 2520 (3 CH) Anatomy and Physiology II: Nutrient Utilization Course Outline Course Instructor: Dr. Ehsan Khafipour, PhD Associate Professor of Gastrointestinal Microbiology Department of Animal Science, Faculty of Agricultural and Food Sciences Department of Medical Microbiology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba Research Scientist Children s Hospital Research Institute of Manitoba (CHRIM), Winnipeg, Manitoba Canadian Center for Agri-Food Research in Health and Medicine (CCARM), St. Boniface Hospital Albrechtsen Research Centre Winnipeg, MB, Canada Website: Office: KhafipourMicrobiomeLaboratory.com Room 225 Anim. Sci. Bldg. Contact: Office (204) ; Cell (204) ; Fax (204) Ehsan.Khafipour@umanitoba.ca is the preferred method of communication. Office Hours: Lecture Times & Location TA and Laboratory Coordinator Laboratory Guest Lecturer I II Open door policy; that being said I am supervising a large number of graduate students and technical staff, am involved in several multidisciplinary research projects, and am serving in a number of departmental and university level committees; therefore, to avoid waiting behind my office door, I would suggest sending me an to schedule an appointment. Mon, Wed and Fri; 10:30-11:20; Room 107 Anim. Sci. Bldg. Mrs. Kelsey Fehr, M.Sc., Room 151 Anim. Sci. Bldg. Communication via (fehrk345@myumanitoba.ca) or in-person during the labs. Wed; 2:30 5:25 pm For the details of lab activities please refer to the Lab Outlines/Lab Notes which will be distributed/discussed during the labs. Dissections Room 142 Anim. Sci. Bldg. focus is on the anatomy of the GI tract Microbiology Room 126 Anim. Sci. Bldg. provides an introduction to molecular tools for understanding host-microbial symbiosis in the GI tract Dr. Hooman Derakhshani, DVM, PhD, Room 145e Anim. Sci. Bldg. Communication via (derakhsh@myumanitoba.ca)

2 Course Objectives I Reading Materials II Additional Reading I II Provide a comparative overview of the GI tract anatomy in major domesticated animals and livestock species. Provide a mechanistic overview of the nutri-physio-immuno-ecology of the gut by: a) Discussing how anatomical structures are relevant clinically. b) Understanding the role of microbiome in gut physiology, immunity and nutrient digestion. c) Describing the processes involved in digestion and absorption of nutrients across the GI tract. d) Defining gut health. e) Reviewing how gut health is linked to the development of intestinal and extra-intestinal metabolic disorders and infectious diseases. Course notes; Supplementary materials; Case studies and student presentations The classic veterinary physiology book is Duke s Physiology of Domestic Animals. This book has a few short case based questions at the end of each chapter which can help you better understand the topic. The classic anatomy textbook is Dyce, Sack and Wensing s Textbook of Veterinary Anatomy. The newer editions of this book also contain case studies. III For veterinary anatomy, also you can refer to Pasquini s Anatomy of Domestic Animals. It has some specific examples of how anatomic structures are relevant clinically. IV Additional swine related case studies can be found in Pig Disease Identification and Diagnosis Guide, By Steven McOrist. Evaluation Criteria Assignments Marks Date Labs and quizzes 10% Student presentations 20% Mid-term #1 30% Feb 7, 2018 Mid-term #2 20% Mar 14, 2018 Final exam 20% University exam schedule Total 100% Grading Scale Students earn the grade - my duty as the instructor is to assign the grade! Grades Marks A % A % B % B % C % C % D % F Less than 50% 2

3 Important Dates & Deadlines Course Rules & Expectations Please visit Student Affairs for important dates and deadlines. I If you miss lecture(s), it is your responsibility to obtain information on any announcements. II No make-up exams (or student presentations) will be allowed, except in cases where the absence has been cleared with the instructor. Absences would normally fall into one of the following two categories: a. Medical emergency a written and signed note from a medical doctor is required. b. Schedule clashes a letter from the faculty member in charge of the course or university sanctioned activity. Students who miss an exam (or student presentation) without a valid excuse will receive 0% for the mark associated with that activity. III Students with special learning needs (who for legitimate reasons require extra time to write a test or who require aids or other supports) should speak with Student Accessibility Services so they can inform me at the beginning of semester in order to arrange suitable accommodation. IV You will have one week following the return of any exam to resolve any questions regarding the grading after which all grades are final. V You should retain all graded items until a final course grade is assigned. VI Cheating, Plagiarism and Fraud will result in removal from the course and assignment of an F for the course. All students are required to familiarize themselves with the many forms that plagiarism can take. Plagiarism is a serious offense and is not tolerated at the University of Manitoba. For more information please refer to the Student Affairs website: m_fraud.html VII Use of cell phone to receive or send voice calls and text messages during class is strictly prohibited. If you must answer a call during class, leave the room and answer your phone in the hallway. VIII Students are allowed to use laptops to take notes in this class. Recordings, however, are not permitted except when required to do so by Student Accessibility Services. Even in that case, written authorization from the instructor, guest lecturers, and all students who are giving presentations in the class must be obtained in advance. The recorded material cannot be altered in any way or distributed, and must be deleted as soon as it is no longer required for study purpose, and no later than after a final grade for the course has been received. IX Disruptions due to excessive talking or early departures from the classroom are especially distracting. Please be considerate and respectful of the needs and rights of others in the class. Students should be aware that persistent disruption may result in disbarment from the course. Any student who has a legitimate reason for leaving class early should inform the instructor at the beginning of the class. 3

4 Lectures & Labs Outline Note: Outline is provisional and is subject to change Date Lecture Lab Instructor * / Required Materials Description 03/1/18 X EK Introduction 03/1/18 X EK Introduction to systematic search and review. What is plagiarism and how to avoid it. Systematic search and review Preparation for case studies and class presentations 05/1/18 X Laptop or Tablet 08/1/18 X EK The digestive system overview #1 10/1/18 None EK No Lecture 10/1/18 X KF Introduction to the ANSC 2520 lab + biosafety; team1 12/1/18 X EK The digestive system overview #2 15/1/18 X EK Foregut vs. hindgut 17/1/18 X EK Microbial communities #1 17/1/18 X KF Introduction to the ANSC 2520 lab + biosafety; team2 19/1/18 X EK Microbial communities #2 22/1/18 X EK Microbial communities #3 24/1/18 X EK Microbial communities #4 24/1/18 X KF Lab Kit Digestive systems of livestock: A basic look video + piglet dissection 26/1/18 X HD Case studies #1 29/1/18 X EK Introduction to immunology #1 31/1/18 X EK Introduction to immunology #2 31/1/18 X KF Microbiology lab #1 team1 02/2/18 X EK Case studies #2 05/2/18 X EK Introduction to immunology #3 07/2/18 X EK Introduction to immunology #4 07/2/18 None KF Mid-term #1 09/2/18 X EK Digestive tract a closer look at the structure and function #1 12/2/18 X EK Digestive tract a closer look at the structure and function #2 14/2/18 X EK Case studies #3 14/2/18 X KF Microbiology lab #1 team2 16/2/18 X EK Case studies # /2/18 None None Louis Riel day & mid-term break no classes 26/2/18 X EK Ruminant digestive system #1 28/2/18 X EK Ruminant digestive system #2 28/2/18 X KF Lab Kit Ruminant digestive systems: Closer look video + rumen dissection 02/3/18 X EK Ruminant digestive system #3 05/3/18 X KF Case studies #5 07/3/18 X KF Case studies #6 07/3/18 X KF Microbiology lab #2 team1 09/3/18 X EK Ruminant digestive system #4 12/3/18 X HD Microbial communities of udder and mastitis 14/3/18 X HD Case studies #7 14/3/18 None KF Mid-term #2 16/3/18 X EK Small and large intestines#1 19/3/18 X EK Small and large intestines#2 21/3/18 X HD Case studies #8 21/3/18 X KF Microbiology lab #2 team2 23/3/18 X HD Immune system within the intestines 4

5 26/3/18 X EK Accessory digestive organs 28/3/18 X EK Case studies #9 28/3/18 X KF Lab Kit Piglet dissection 30/3/18 X EK Case studies#10 02/4/18 X EK Avian digestive system 04/4/18 X EK Case studies#11 04/4/18 X KF Lab Kit Poultry dissection 06/4/18 X EK Overview of course materials TBD Final exam *Abbreviations: EK: Dr. Ehsan Khafipour HD: Dr. Hooman Derakhshani KF: Mrs Kelsey Fehr Case Studies Two-page Summary Format I General Guidelines: - Provide enough information for the readers so that they can grasp the topic in a clear and concise fashion. - Minimum of 3 key referenced papers to be used for discussion. - Target audience are your peers so avoid overuse of unfamiliar acronyms and define where appropriate. II Formatting Guidelines: - A two-page summary including references. - Font: Times New Roman, Size Single space. Margins: 2.54 cm. - Include your name in the header area. Include page number. - General formatting (headings, units, abbreviations, etc) as per Canadian Journal of Animal Science format. - Acceptable references include: journal articles, books, conference proceedings, theses. The value of each reference type was discussed in the class. Wikipedia is not a permitted reference source. - References should be cited in the body of the paper using the same format as that adopted by the Canadian Journal of Animal Science. - A complete reference list should be provided at the end of the summary (Canadian Journal of Animal Science format). An example of a review paper has been included (Kebreab, E., K. Clarke, C. Wagner-Riddle, and J. France Methane and nitrous oxide emissions from Canadian animal agriculture a review. Can. J. Anim. Sci. 86: Presentation Guideline I Length: 12 min of presentation + 5 to 8 min of questions and discussion. II Format: a. Introduction - Hypothesis development. i.e. what is the current issue you are going to deal with/what are you trying to accomplish? 5

6 - Describe the implications. b. Body - Provide information about the topic/issue using existing information. - Use graphs, figures, images from a number of sources to illustrate key points. - Interpretation of this information is critical part of the presentation. - Avoid overuse of unfamiliar acronyms and define where appropriate. c. Summary and Conclusions - Provide a brief summary of the information which you have just presented and interpreted. - Reinforce practical application(s). Submissions and Deadlines Submit your 2-page summary in.docx format to the instructor. Submit your slides in.ppt format to the instructor. Instructor will share both documents with the class. Deadline for submission is the day of your presentation before class starts. A 10% penalty will be considered for each hour late submission. Case Study Topics January 26, 2018; Case studies #1 Probiotics in animal production systems what are probiotics? What are their modes of action? What is an ideal probiotic? Which probiotics? Potential use and their associated challenges! Antibiotics in animal production systems what are antibiotics? What are their modes of action? What is an ideal antibiotic? Which antibiotics? Their use in animal production system and their associated challenges! February 2, 2018; Case studies #2 Prebiotics in animal production systems what are prebiotics? What are their modes of action? What is an ideal prebiotic? Which prebiotics? Potential use and their associated challenges! Alternative to antibiotics in animal production systems what are those alternatives? Pick 3 of them and discuss their modes of action? Are they ideal? Their use in animal production system and their associated challenges! February 14, 2018; Case studies #3 6

7 Helicobacter pylori How is the microbial community of gastric stomach? Who are the main members of this community? Do they have a major role in digestion? Or they are more important in health and disease? If so, what are the consequences of the presence or the absence of these members in the gastric stomach? In particular, discuss the role of Helicobacter pylori when reviewing the above items. What is survival strategy of this bacterium in the stomach and discuss the mechanism of its pathogenicity. Bacterial lipopolysaccharide Gut contains many immunogenic compounds that if translocate into blood circulation can activate the immune response. One such compound is bacterial lipopolysaccharide (LPS) or Endotoxin. What is LPS? When it is released in the gut? How it is causing trouble? Give an example of feeding strategy in dairy or beef cows that result in increased LPS in the rumen or hindgut. Discuss the consequences. What are the prevention strategies? February 16, 2018; Case studies #4 Peptic ulcer disease (PUD) what is a peptic ulcer? How the natural defense of the gastric stomach can breakdown? What are the major causes of peptic ulcers? Is PUD more common in men or women and why? What are idiopathic peptic ulcers (IPU)? What causes them? How peptic ulcers can be treated? Structure of rumen epithelium and its role in absorption of VFA Describe the structure of rumen epithelium? Does the functional capacity of rumen epithelium varies from animal to animal? How that is possible? What impacts the absorption capacity of epithelium? How genetic and epigenetic could play a role? How such difference in the functional capacity of epithelium may affect animal health and production efficiency? March 05, 2018; Case studies #5 Ruminants and methane production What is a Greenhouse gas (GHS)? What are major GHGs? How much is the contribution of agriculture sector and more importantly ruminant production systems in global GHSs? How and why methane is produced? Can we stop methane production in the rumen? What are some of the strategies toward reduction of methane production in ruminants? How is their efficiency? And why is that? Bloat and ruminants What is bloat? What are different types of bloat? What causes each? What is the role of rumen microbes in 7

8 development of bloat? What are the current recommendations for prevention of bloat in beef cattle? What treatment options exist? March 07, 2018; Case studies #6 The spectrum of inflammatory bowel disease (IBD) What is IBD? What are the major causes of IBD (discuss the role of genetics, environment, nutrition, and microbiome). How is the epidemiology of IBD in Canada compared to the world? Is IBD under control or its spreading more and more around the world? Why is that the case? The spectrum of insulin resistance (from insulin resistance to diabetes, obesity and cardiovascular disease) Who discovered the insulin? What is insulin resistance? How it is related to diabetes? How insulin resistance and diabetes are related to obesity and cardiovascular disease? How gut microbiome plays a role in all these issues? How insulin resistance can be controlled? March 14, 2018; Case studies #7 Microbiome engineering using fecal transplant What it is and under what conditions it is recommended? How its done? Current concerns about Fecal Microbiota Transplantation (FMT)? Ethic issues? Alternatives? Nutritional diarrhea at weaning Pigs are typically weaned at around 3 weeks of age. However, in the natural state pigs will be weaned at about 8 weeks of age. This early weaning causes several problems, one of which is the proliferation of nutritional diarrhea. What causes this problem? Discuss prevention strategies? How and why each strategy works? March 21, 2018; Case studies #8 Johne s Disease What is JD? How JD and IBD are different? What is the causative agent of JD and how is the mechanism of its pathogenicity? Is it possible that microbiome plays a role in development of JD? How is the epidemiology of JD in Canada? How JD can be controlled? Ketosis in ruminants What is ketosis? How physiology of dairy cows at early lactation may result in ketosis? Different treatment strategies such as Dextrose, Glucocorticoids, Insulin, or Propylene glycol administration have been recommended for treatment of ketosis. What is the mode of action of each of these items? Refer to 8

9 systematic reviews or meta-analyses and see what is the best treatment strategy and why? March 28, 2018; Case studies #9 Acidosis What are acute and sub-acute ruminal acidosis? What is hindgut acidosis? How prevalent they are in dairy production system? At what stage of production they are more prevalent and why? Do calves get acidosis as well? What about beef cattle? What are the clinical signs and symptom? What is the role of rumen and hindgut microbes in development of acidosis? What are the treatment and prevention strategies? Horses and laminitis What is laminitis? How the diet of race horses can play a role in development of laminitis? How quick that can happen? How the structure of horse gastrointestinal (GI) tract plays a role in development of laminitis? What is the role of microbe in development of laminitis? What are the prevention and treatment strategies? March 30, 2018; Case studies #10 Irritable bowel syndrome (IBS) What is IBS? How IBS and IBD are different? What is the causative agent of IBS? Is it possible that microbiome plays a role in development of IBS? How is the epidemiology of IBS in Canada? How IBS can be treated? Primary vs. secondary bile salts and Clostridium difficile infection What are primary and secondary bile salts? How they are produced, what are their functions? How Clostridium difficile (recently reclassified as Clostridioides difficile) infection is associated with bile salts composition? How C. diff can be treated? April 4, 2018; Case studies #11 Role of microbiome in Type 1 diabetes What is the Type 1 diabetes and how it is different from Type 2? What causes Type 1 diabetes? In the past couple of years, we have understood that microbiome plays a major role in development of Type 1 diabetes. Mechanistically describe how that works? Is this information can open new opportunities for prevention/treatment of Type 1 diabetes? If so, how? 9