Syllabus


Instructor

 

Dr. Brown

James W. Brown

4524B Thomas Hall <-- Note new office location!
james_brown@ncsu.edu (this is the best way to contact me)
919/515-8803 (Office - calling this number is futile - use email)
919/749-3172 (Cell - it'd better be urgent)
www.microbiology.ncsu.edu/JWB/JWB.html
Office hours by appointment: go to: http://www.mbio.ncsu.edu/JWB/schedule.html


Time & Place

 

The traditional ("face-to-face") section (001) meets M, W and F at 11:45AM-12:35PM in Fox 140
The online/DE section (601) is online at: http://www.mbio.ncsu.edu/MB451/


Course Description

 

Molecular, biochemical and evolutionary diversity of the microbial world, including Bacteria, Archaea, and Eukaryotes. Evolutionary perspective on microbial relationships, molecular methods of study and classical and modern biotechnological methods utilizing this genetic diversity to explore the microbial world and use the resulting insight to meet the needs of our own species.
The course is required for Microbiology majors, and is taught every spring semester.


Learning Outcomes

 

After taking this course, students should be able to ...

  1. demonstrate an in-depth familiarization with the evolutionary perspective on microbial relationships, and how these relationships are determined,
  2. generate a phylogenetic tree from sequence data
  3. describe a wide range of microbial groups in terms of their morphology, ecology, metabolism, and evolutionary diversity,
  4. read, interpret, and summarize scientific articles in microbiology and related fields, and
  5. apply this knowledge and perspective to microbiological problems in the form of experimental design.

Course Structure

 

Lecture Sessions

The format of the Monday and Wednesday lectures are traditional. The lecture series can be divided into three very different sections:

Part 1 - Molecular Phylogenetics
The first section begins with some preliminaries; defining the scope of the course, defining the perspective, providing a historical context, &c. The main part of this section is a practical guide to molecular phylogenetic analysis, focusing on how to create and interpret phylogenetic trees, and a overview of “the Tree of Life”.

Part 2 - Microbial Survey
The second section is a tour through each of the major phylogenetic groups of Bacteria and Archaea (microbial eukaryotes and viruses are also covered briefly), discussing the general properties of the organisms in each group, and describing in more detail some specific representatives. One or two general topics raised by these organisms will be discussed in each lecture.

Part 3 - Microbial Ecology & Complexity
The third section is more conceptual and experimentally defined, making heavy use of the primary research literature. This section discusses how molecular phylogenetic analysis is used by microbiologists, from identification of unknown and potentially uncultivable organisms, to molecular surveys of populations, and linking processes with specific organisms. This leads to a discussion of various conceptual aspects of microbial complexity, from genomics and cell biology.

Students present in class will be presented with these lectures in the traditional fashion. DE students or students absent from the lecture will work from the on-line course material. Both resources are available to all students: any enrolled student has the on-line material available to them, and any enrolled student free to participate in the lectures on days they can do so.

Discussion Sessions

The discussion sessions will be online discussions, mostly about papers reviewed on the Discussion Session wiki. DE students can work in groups or individually on the Discussion assignment. The assignments for each week, details, and due dates/times are listed on the Discussion page.


Prerequisites & Restrictions

 

MB 411 (Medical Microbiology) and either GN 311 (General Genetics) or BCH 351/451 (General Biochemistry)

I will generally also allow students with any advanced Microbiology class and molecular biology background of some kind to enroll.


On-line Resources

 

The course web site is located at http://www.mbio.ncsu.edu/MB451/

This web site contains a wide variety of information that will be critical for all students throughout the semester.

The course web site contains student exam grades posted by self-assigned PIN.

This course may involve electronic sharing or posting of personally identifiable student work or other information with persons not taking or administering the course. Students will be asked to sign a consent allowing disclosure of their personally identifiable work. No student is required to sign the consent as a condition of taking the course. If a student does not want to sign the consent, he or she has the right to ask the instructor for an alternative, private means of completing the coursework.


Attendance Policy

 

Physical attendance is obviously not expected of DE students, but it is critical that these students work consistently on the course material if they are to succeed.


Academic Integrity

 

Academic Integrity

Students are required to comply with the university policy on academic integrity found in the Code of Student Conduct found at http://www.ncsu.edu/policies/student_services/student_discipline/POL11.35.1.php

Academic Honesty

See http://www.ncsu.edu/policies/student_services/student_discipline/POL11.35.1.php for a detailed explanation of academic honesty.

Honor Pledge

Your signature on any test or assignment indicates "I have neither given nor received unauthorized aid on this test or assignment."


Student Evaluations

 

Schedule: Online class evaluations will be available for students to complete during the last 2 weeks of spring term.

Students will receive an email message directing them to a website where they can login using their Unity ID and complete evaluations. All evaluations are confidential; instructors will never know how any one student responded to any question, and students will never know the ratings for any particular instructors.

Evaluation website: https://classeval.ncsu.edu/
Student help desk: classeval@ncsu.edu
More information about ClassEval: http://www.ncsu.edu/UPA/classeval/


Textbooks, Expenses & Materials

 

The textbook for this course is:

Principles of Microbial Diversity, by James W. Brown, ASM Press, 2014
ISBN-13: 978-1555814427 or ISBN-10: 1555814425

This book is available in the NCSU bookstore, the usual online bookstores, or directly from the ASM Press.

This courses otherwise requires only the usual materials for taking notes in class. Routine access to a computer with a modern web browser, word processor, email, and printer is required.

There are no extra fees or expenses for this course.


Transportation

 

This course will not require students to provide their own transportation. Non-scheduled class time for field trips or out-of- class activities is NOT required for this class.


GEP Information

 

This course does not fulfill a General Education Program category or co-requisite.


Safety & Risk Assumptions

 

None


Accommodations for Disabilities

 

Reasonable accommodations will be made for students with verifiable disabilities. In order to take advantage of available accommodations, student must register with the Disability Services Office (http://www.ncsu.edu/dso) located at 1900 Student Health Center, Campus Box 7509, 515-7653. For more information on NC State's policy on working with students with disabilities, please see the Academic Accommodations for Students with Disabilities Regulation at http://www.ncsu.edu/policies/academic_affairs/courses_undergrad/REG02.20.1.php.


Non–discrimination Policy

 

NC State University provides equality of opportunity in education and employment for all students and employees. Accordingly, NC State affirms its commitment to maintain a work environment for all employees and an academic environment for all students that is free from all forms of discrimination. Discrimination based on race, color, religion, creed, sex, national origin, age, disability, veteran status, or sexual orientation is a violation of state and federal law and/or NC State University policy and will not be tolerated. Harassment of any person (either in the form of quid pro quo or creation of a hostile environment) based on race, color, religion, creed, sex, national origin, age, disability, veteran status, or sexual orientation also is a violation of state and federal law and/or NC State University policy and will not be tolerated. Retaliation against any person who complains about discrimination is also prohibited. NC State's policies and regulations covering discrimination, harassment, and retaliation may be accessed at http://www.ncsu.edu/policies/campus_environ or http://www.ncsu.edu/equal_op. Any person who feels that he or she has been the subject of prohibited discrimination, harassment, or retaliation should contact the Office for Equal Opportunity (OEO) at 515-3148.