MBIO4440 Systems Microbiology Syllabus

Transcription

1 MBIO4440 Systems Microbiology Prerequisites MBIO 3030 or MBIO2110 and MBIO/CHEM2370 Lecturer Dr. Silvia T. Cardona 414 A Buller Building cardona@cc.umanitoba.ca Dr. Cardona s Website: Course Description Systems microbiology focuses on complex interactions within the microbial cell looking at the system's behaviors together within the setting of its environment. Genomics, transcriptomics, and proteomics data will be used to create an integrated model of how a microbial cell functions. Course Objectives To integrate knowledge from diverse biological components and data into models of the microbial cell as a whole To create models of microbial cell function using genomic tools Suggested Material (See contents for chapters selection) J.M. Wiley, L. M. Sherwood and C.J. Woolverton Prescott s Microbiology. McGraw- Hill, Eighth edition. J. Zhou, D.K. Thomson, Xu, Y., and Tiedje J.M Microbial Functional Genomics. John Wiley & Sons, Inc. Hoboken, New Jersey. Fraser, C.M. Read, T.D. and Nelson K.E Microbial Genomes. Humana Press, Totowa, New Jersey. Böck, R. Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T. Nyström, J. M. Slauch, C. L. Squires, and D. Ussery (ed.), EcoSal Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington, DC.

2 Course communication tools Lecture notes and other materials will be posted/linked to on an Angel Course Website. (Please, note that you do not own the copyrights to upload these materials to other sites. It is strictly prohibited to use course materials in any activity that does not relate to this course). Assignments will be handled and graded through Angel Course Students are encouraged to bring their I- Clickers to the lectures. You grade will benefit from participation and self- evaluation but there will be no grading points for I- Clicker questions. Course Evaluation Examination schedule: One midterm test 20% Two assignments 10% (5% each) Laboratory 20% Final exam 50% There will be no deferred midterm exams. Students with notes from a counselor, physician, or clergy will write the final exam for 70% of the total grade; students without official notes who did not write the midterm will receive 0% for their midterm mark. Students that fail to hand in their assignments at the established deadline will receive 50% of their earned mark. There will be NO EXCEPTIONS to this rule. 2

3 Course Parts Unit 1) Microbial Genomes Zhou et al. Chapter 1, sections Prescott s Microbiology Chapter 16, sections , and 16.3 The Omics revolution and its Supplementary impact on microbiology Zhou et al. Chapter 3 and Approaches to sequencing 5 Functional microbial genomes Paper Whole- genome Analysis of the Gene prediction/operon random sequencing and Escherichia coli prediction assembly of threonine Haemophilus influenzae From sequencing to functional deaminases. (1995) Fleischman et al. assignments Science 269:5223. Metabolic Pathway Databases Assignment 1: Whole- genome random sequencing and assembly of Haemophilus influenzae Unit 2) Microbial Functional Genomics Prescott s Microbiology Chapter 16, sections 16.4 and 16.5 DNA Microarray and RNA- seq Technology Gene Expression Data analysis Proteomics Midterm: Thursday, February 16th Zhou et al. Chapters 6, 7 and 9 Paper- Microarrays to study environmental stress Environmental Stress in Bacteria 3

4 Unit 3) Genomic analysis of Core Functions: Bacterial Cell Cycle The Division Cycle in E. coli Periods of the division cycle Coupling between division and replication Cell cycle in Caulobacter crescentus Bock et al, Chapter 102. Fraser et al, Chapter 8 Control of Cell Division and D- phase in E. coli. Unit 4) Microbial mutagenesis at the genomic level Transposon mutagenesis. Non- redundant Libraries. Targeted mutagenesis Conditional mutagenesis Zhou et al. Chapter 8 Paper- A transposon mutant library to identify motility genes Motility and Chemotaxis Assignment 2 4

5 Tentative Schedule Content Activity Week Date Unit 1 Lecture1 1 January 10th and 12th Lecture 2 2 January 17 th and 19th Assignment 1 3 January 23rd- 27th Unit 2 Lecture 3 4 January 31 st and February 2nd Lecture 4 5 February 7 th and 9th Midterm 6 February 16th Break 7 February 20 th - 24th Unit 3 Lecture 5 8 February 28 th - March 1st Lecture 6 9 March 6 th and 8th Unit 4 Lecture 7 10 March 13 th and 15th Lecture 8 11 March 20 th and 22th Assignment 2 12 March 26 th to March 30th Note: Changes may be introduced according to course evaluation. Student Responsibilities It is your responsibility to make sure that all eligibility requirements are met to be registered in this class. This means: You have taken the appropriate prerequisites, as noted by the calendar description, or have documented permission from the instructor to waive these prerequisites. You have not previously taken, and are not concurrently registered in this course and another that has been identified as "not to be held with". 5

6 It is your responsibility to make sure you understand the rules regarding cheating and plagiarism at the University of Manitoba. Read the Faculty of Science Statement on Academic Dishonesty (can be found on the last page of this document) Refer to the University of Manitoba General Academic Regulations and Requirements in Section 8 of the Course Calendar: Academic Integrity: ( Read statements on academic dishonesty, including plagiarism, cheating and examination impersonation found on the Faculty of Science webpages: ( ments.html). In cases of cheating during examinations, the test in question will be given a grade of 0% and the student will be reported to the appropriate authorities for disciplinary action. Faculty of Science Statement on Academic Dishonesty The Faculty of Science and The University of Manitoba regard acts of academic dishonesty in quizzes, tests, examinations, laboratory reports or assignments as serious offences and may assess a variety of penalties depending on the nature of the offence. Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another individual, using answers provided by tutors, plagiarism, and examination personation. Note: cell phones, pagers, PDAs, MP3 units or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations. Penalties that may apply, as provided for under the University of Manitoba's Student Discipline By- Law, range from a grade of zero for the assignment or examination, failure in the course, to expulsion from the University. The Student Discipline By- Law may be accessed at: Suggested minimum penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web- page: tml All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department. 6