MCB3023 section 3556 syllabus

MCB 3023: Principles of Microbiology, Section 3556-Spring 2012 (3 credits)

MCB3023 is an upper division course on Microbial Biology. This course will cover eukaryotic and prokaryotic microbes and viruses, but will emphasize on Bacteria. This course will provide a conceptual background in microbiology sufficient to enable students to take more advanced courses in related fields. Student Learning Outcomes After successful completion of this course, students will be able to:

1) Compare and contrast basic groups of microbes, including Eukaryotic microbes, Archaea, Bacteria
and viruses. 2) Compare and contrast major pathways of anabolism and list the key products of each pathway. 3) Compare and contrast major pathways of catabolism, specify the relative energy yield from each pathway, and list the key products of each pathway. 4) Specify the role of microbes in global C, N, S and P cycles and list examples of microbes that contribute to key metabolic aspects of these cycles. 5) Draw typical microbial growth and killing curves, explain the rationale for the shape of the curve and predict the effect of different environmental conditions on the curve. 6) Describe mechanisms of regulation of gene expression in bacterial cells. 7) Compare and contrast the acquisition of novel genetic information in microbes via mutations and genetic exchange. 8) Compare and contrast prokaryotic and eukaryotic cell division and development. 9) Describe how microbes can adapt to their environment. 10) List different types of symbiotic interactions between microbes and other organisms, including commensalism, mutualism, and parasitism, and provide examples of each. 11) Summarize common features of microbial pathogens, with emphasis on bacterial and viral pathogens. 12) Compare and contrast examples of beneficial and pathogenic microbe-plant and microbe-animal interactions. 13) Compare and contrast beneficial and harmful use of organisms, including applications in biotechnology and bioterrorism. Lectures: Instructors:

LAR0310
Dr. Claudio F Gonzalez Dr. Graciela L Lorca

M, W, F 1:55-2:45 PM Period 7 Office: Genetics Institute, Room 306 Office: Genetics Institute, Room 307

Teaching Assistant: Rafael Rodrigues de Oliveira (rafaeloliveira@ufl.edu) online Discussion board WebPage: Sakai (http://lss.at.ufl.edu/). Please select MCB 3023 (section 3556). REQUIREMENT: STUDENTS ARE REQUIRED TO BRING A LAPTOP FOR THE TESTS!!! Prerequisite: "C" grade or better in Core Biology (BSC2010, 2010L, 2011, 2011L) or equivalent General Chemistry (CHM2045, CHM2045L, CHM2046, CHM2046L) or equivalent Organic Chemistry (CHM2210 or CHM2200) or equivalent. MCB and MCY majors must take CHM2210. Communication: for questions regarding class and textbook content use the Discussion Board, for issues on Home Work Assignments, class organization check first the syllabus, the announcements and calendar on SAKAI, then post your questions on the discussion board. For all other issues contact Claudio Gonzalez or Graciela Lorca.

MCB3023 section 3556 syllabus

Contact Information: Use INSTRUCTOR ROLE is your emails through Sakai Dr. Claudio F Gonzalez: Email (the most efficient): Use the Sakai e-mail in priority (If you do not have access to the e-learning platform and need to contact us for an emergency, use cfgonzalez@ufl.edu) Phone: 273 8088 (please leave a message). Office hours: Wednesdays and Fridays 3:15 to 4:15 PM at Genetics Institute, Room 306. By appointment: (only if you cannot make it to office hours) send an e-mail with three suggested times and I will choose one for us to meet. Dr. Graciela L Lorca: Email (the most efficient): Use the Sakai e-mail in priority. (If you do not have access to the e-learning platform and need to contact us for an emergency, use glorca@ufl.edu) Office hours: Wednesdays and Fridays 3:15 to 4:15 PM at Genetics Institute, Room 307. By appointment: (only if you cannot make it to office hours) send an e-mail with three suggested times and I will choose one for us to meet. - Discussion Board: A discussion board is available in Sakai. It is very useful, please post and answer your questions on class content and organization there. Postings and answers are monitored by the instructors to make sure no mistakes get propagated. There are several discussion themes. Please post your questions in the adequate section. The discussion board is also used for certain graded assignments to prepare for lecture and for the group monograph assignment. Material - Textbook: The required textbook for this course is: Prescotts Principles of Microbiology, Willey-Sherwood-Woolverton. McGraw-Hill, NY.

Attendance is expected and encouraged. Reading the assigned chapter pages (or additional chapters provided in Sakai) before coming to lecture is required.

Evaluation of learning Assignment (120 points): Group monograph (120 points). Students will analyze a specific area of microbiology in an essay format. Titles of proposed areas will be provided. This assignment will assess their research abilities, application of what is learned in class, use of the information available in the web, ability to synthesize complex information and work in groups. (See guidelines in a separate file in elearning and Example) DEADLINE FOR SUBMISION: (through assignment tool) MARCH 26TH 2012. Groups of 3-4 students will be designated at random. The monographs should be 5 pages-long (not including references). Should be written in Arial font 12 point, with 1 inch margins, single spaced. One person in the group will be designated for submission through sakai. Online Quizzes (200 points): The quizzes are MANDATORY and count towards the final grade. The quizzes will be delivered online on the date marked in the calendar (see at the end of the syllabus). Exams (680 points): Exams will assess your knowledge of the concepts covered in this class and your ability to apply them by solving problems that you will not have been previously exposed to. Students must be on time and bring their GATOR ID cards or will not be able to take the exam. The assessment will be performed in Four Mandatory Mid-term exams. The student will be given the option to take a final cumulative exam to improve the grade obtained through the mid-term exams.

MCB3023 section 3556 syllabus

- Mid-terms (680 points): There will be four 50 minutes proctored mid-term exams (170 points each) with multiple choice questions, true/false, fill in the blanks questions and short answers questions. All exams are mandatory and will count towards the final grade. Exams will test learning and understanding of material presented in the textbook, in lectures and in assignments as well as integration and application skills. - Final (optional-680 points). The final exam is optional. It will be held during finals week. Questions will assess basic microbiology concepts and advanced comprehension. The final cannot be taken if the student missed any of the mid-term exams. Make-Up policy: No make-up exams. If one exam is missed, it will result in a score of 0 for the test (see below for Excused absences). Excused absences: Documentation MUST be provided for absences caused by serious illness, accident, jury duty, or death in the immediate family. You must contact the instructor IN ADVANCE of the missed exam and I will arrange an alternative time for the exam. Exams extra support - Optional Online selftesting quizzes (Non Graded). The quizzes are not mandatory and are designed to allow student self-assessment prior to exams. Questions will be similar to those to be used in the tests. We strongly encourage to our students to take the quizzes and participate in the review section prior to the test to maximize their possibilities on mandatory evaluations. After the exam: The grades will be available on sakai three days after the exam, unless notified by an announcement. Test questions will not be made available, a few will be discussed in class in debriefing sessions and students can review their exams individually during office hours. Extra-credit opportunities (50 points maximum) - Tell me about yourself during the first two weeks of class (5 pts). Submit through the assignment tool on elearning. Students will write a paragraph or two. Deadline January 23rd, 2012 - Watching the seminars online recorded from the Microbiology and Cell Science Department (Mondays at 4 pm) (10 pts each/20 max). You are not required to physically attend. After the seminars the students are required to write a summary (max 1 page) and submit it through sakai (within the assignment tool) within a week of the seminar. Late summaries will not be accepted. - Special Topics Podcasts (25 points). Students in groups of 3 or 4 can choose to make a podcast in which they will explain different topics. The podcast will cover a topic that will be assigned by the instructor. To take advantage of this possibility the students will have to send an e-mail (through e-learning) to the instructor and a topic will be assigned. DEADLINE for sign-up is February 10th, 2012. Deadline for submission is April 9th, 2012. Grading: Straight scale See Scale in PDF document Grading Scale A 900 or above A860-899 B+ 830-859 B 790-829 B750-789 C+ 720-749 C 690-719 C660-689 D+ 630-659

MCB3023 section 3556 syllabus

D DE

600-629 570-599 560 or below

The grading scale may be adjusted slightly, based on class performance.

Punctuality and class etiquette: The class will begin at 1:55 pm. Please be on time and in place. If you are late coming to class, please use the rear doors. If you need to leave the class early, please notify me at the beginning of the class and sit in the back. Please do not forget to shut cell phones down. Recommendation letters: Many of you need recommendation letters. Students who both achieve an A AND show active participation in and outside the class can request letters. Students requesting letters need to attend the last lecture of the semester with a folder containing a picture, resume and GPA, then contact the instructor by e-mail (cfgonzalez@ufl.edu, or glorca@ufl.edu) during the 2012 fall semester to schedule an interview. Academic Honesty: As a result of completing the registration form at the University of Florida, every student has signed the following statement: "I understand that the University of Florida expects its students to be honest in all their academic work. I agree to adhere to this commitment to academic honesty and understand that my failure to comply with this commitment may result in disciplinary action up to and including expulsion from the University. Software Use: All faculty, staff and students of the University are required and expected to obey the laws and legal agreements governing software use. Failure to do so can lead to monetary damages and/or criminal penalties for the individual violator. Because such violations are also against University policies and rules, disciplinary action will be taken as appropriate. Accommodations for Students with Disabilities: Students requesting classroom accommodation must first register with the Dean of Students Office. This office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation. UF Counseling Services: available on-campus for students having personal problems or lacking clear career and academic goals include: University Counseling Center, 301 Peabody Hall, 392-1575, personal and career counseling Student Mental Health, Student Health Care Center, 392-1171, personal counseling. Sexual Assault Recovery Services (SARS), Student Health Care Center, 392-1161, sexual assault counseling Career Resource Center, Reitz Union, 392-1601, career development assistance and counseling

MCB3023 section 3556 syllabus

MCB 3023 Date 01/09/12 01/11/12 01/13/12

Section 3556 Spring 2012 Calendar Period 7 1h55-2h45 PM LAR RM 0310 Lecture Instructor Microbe Description In classroom Gonzalez/Lorca Syllabus- Introduction to the Microbe World P1 C.F. Gonzalez Chapter 1&2 History and Methods to Study Microbiology P2 / In classroom C.F. Gonzalez Chapter 3 Prokaryotic Cell Structure/ Review with C. F. Gonzalez 01/16/12 No Class 01/18/12 P3 C.F. Gonzalez Chapter 3 Prokaryotic Cell Structure 01/20/12 P5 / In classroom C.F. Gonzalez Chapter 5 Viruses and other Acellular Agents/ Review with C. F. Gonzalez 01/23/12 P4+ myself EC C.F. Gonzalez Chapter 4 Eukaryotic Cell Structure 01/25/12 P6 C.F. Gonzalez Chapter 6 Microbial nutrition 01/27/12 P7 / In classroom C.F. Gonzalez Chapter 7&8 Growth of Microbial Populations/Control of Microorganisms / Review with C. F. Gonzalez 01/30/12 P8 C.F. Gonzalez Chapter 9 Introduction to Metabolism 02/01/12 P9 C.F. Gonzalez Chapter 10 Catabolism: Energy Release and Conservation 02/06/12 In classroom Discussion / Review with C. F. Gonzalez On line Optional Quiz 02/08/12 In class - Test 1 (P1 to P9) BRING LAPTOP!!!!!! 02/10/12 P10 G.L. Lorca Chapter 11 Anabolism The use of Energy in Biosynthesis 02/13/12 P11 G.L. Lorca Chapter 12 Genes Structure, Replication and Expression 02/15/12 P12 G.L. Lorca Chapter 12 Genes Structure, Replication and Expression 02/17/12 In classroom Discussion / Review G.L. Lorca 02/20/12 P13 G.L. Lorca Chapter 12 Genes Structure, Replication and Expression 02/22/12 P14 G.L. Lorca Chapter 13 Regulation of the Gene Expression 02/24/12 In classroom Discussion / Review G.L. Lorca 02/27/12 P15 G.L. Lorca Chapter 13 Regulation of the Gene Expression 02/29/12 P16 G.L. Lorca Chapter 14 Mechanisms of Genetic variation On line Optional Quiz 03/02/12 In class - Test 2 (P10 to P16) BRING LAPTOP!!!!!! 03/05-09/12 SPRING BREAK!! 03/12/12 P17 G.L. Lorca Chapter 15 Microbial Genomics & Bioinformatics 03/14/12 P18 G.L. Lorca Chapter 16 Biotechnology and Industrial Microbiology 03/16/12 In classroom Discussion / Review C.F. Gonzalez 03/19/12 P19 C.F. Gonzalez Chapter 17 Origin of life 03/21/12 P19 C.F. Gonzalez Chapter 17 Microbial Evolution, Taxonomy and Diversity 03/23/12 In classroom Discussion / Review C.F. Gonzalez 03/26/12 P20+ GM C.F. Gonzalez Chapters 19-22 Bacterial Classification 03/28/12 P21 C.F. Gonzalez Chapter 18 and Archaea-Characteristics of Fungal Divisions 23 03/30/12 P22 C.F. Gonzalez Chapter 24 Viral Diversity 03/30/12 In classroom Discussion / Review C.F. Gonzalez On line Optional Quiz 04/02/12 In Class Test 3 (P17 to P22) BRING LAPTOP!!!!!! 04/04/12 P23 G.L. Lorca Chapter 25 Biogeochemical Cycling/Microbial Ecology 04/06/12 P24/ G.L. Lorca Chapter 27 Microbial Interactions classroom 04/09/12 P25+ STP G.L. Lorca Chapter 30-33 Pathogenicity of Microorganisms, Epidemiology 04/11/12 P26 G.L. Lorca Chapter 31 Antimicrobial Chemotherapy 04/13/12 In classroom Discussion / Review G.L. Lorca 04/16/12 P27 + SS G.L. Lorca Chapter 34 Food Microbiology 04/18/12 P28 C.F. Gonzalez Chapter 35 Applied and Environmental Microbiology 04/20/12 In classroom Discussion / Review Gonzalez/Lorca On line Optional Quiz 04/23/12 In Class Test 4 (P23 to P28) 05/05/12 Cumulative Final (optional) Friday 12,30-2,30 PM in classroom BRING LAPTOP!!!!!!
GM= group monograph (required) STP= Special topics podcast (optional) SS= Seminars summary (optional) In red box: Mandatory online quizzes. myself EC (optional)

MCB3023 section 3556 syllabus

Date 01/11/12 01/18/12 01/25/12 02/01/12 02/15/12 02/22/12 02/29/12 03/14/12 03/21/12 03/28/12 04/04/12 04/11/12 04/18/12

Podcasts included MANDATORY quizzes P1 P2 and P3 P4, P5, and P6 P7, P8, and P9 P10, P11 and P12 P13, P14 P15 and P16 P17 and P18 P19 P20 and P21 P23 P24 and P25 P26, P27 and P28

in

online

List of seminars You will ONLY receive credits for the seminars listed below. Seminars will be recorded and streamlined (the web site will be posted in the announcement tab as they become available). January 30, 2012 Charles Turnbough. University of Alabama Regulation of pyrimidine gene expression in bacteria: repression without repressors February 13, 2012 M.J. Rosovitz. Battelle National Biodefense Institute Microbial Forensics Using Genomics February 27, 2012 Nemat Keyhani. University of Florida From fungal virulence to insect olfaction March 19, 2012 William Self. University of Central Florida Narrow spectrum antimicrobials: targeting selenium metabolism in pathogenic microbes March 26, 2012 Alexei Savchenko. University of Toronto Structural insight into the function of bacterial pathogenic factors involved in host interactions and antibiotic resistance April 9, 2012 Mansour Mahamadzadeh. University of Florida Novel targeted oral vaccine for cancer and pathogens