Instructor:   Dr. David Gondek 164 Ctr for Natural Sciences dgondek@ithaca.edu 274-3979 Class material is on Sakai. Lecture Schedule

BIOL-45200  Microbiology (Biology Elective) Spring 2012 Class: MWF, CNS-119  R, CNS115 Lab: WR – CNS107 M,W,F   11-11:50am  /  R 1-4pm

Course Description:

This course examines the structure, physiology, and genetics of microorganisms. An emphasis is placed on understanding microbial growth, ecology, use of microorganisms in research and commerce, how these organisms affect food and water quality, and the human immune response to pathogens. Microbiological laboratory procedures include sterile technique, microscopy, identification, enrichment, isolation, and preservation.  Molecular Biology techniques include genome purification, PCR, cloning, RDP-analysis, and phylogeny construction.

At the conclusion of this course, students will be able to:

• Describe unique microbial structures which confer critical functions/capabilities and are possible targets for antibiotics
• Compare nutrient resources and metabolism of prokaryotic vs eukaryotic organisms
• Contrast the prokaryotic and eukaryotic implementation of the central dogma and gene regulation
• Describe the impact of horizontal transfer, mutation, and asexual reproduction on phylogenetic analysis of microbes
• Appraise pathogenesis as an “arms-race” between virulence and immunity
• Demonstrate advanced scientific thinking and microbiology/molecular biology lab skills
• Construct phylogeny maps and produce a scientific presentation

Grading System: The acceptable grades and corresponding points for GPA calculations are as follows. 

 Grade Points:  A 4.00 (excellent) A- 3.70 B+ 3.30 B 3.00 (good) B- 2.70 C+ 2.30 C 2.00 (satisfactory) C- 1.70 D+ 1.30 D 1.00 D- 0.70 F 0

 Exams
   2 exams 100 pts each
   1 final exam 100 pts
Quizzes/Participation 100 pts (5/per)
 Concept maps 100 pts (10/per)
 Lab final report 100pts
 Lab Questions/skills 100pts
 Total pts awarded = 700

Course details:

Active classroom learning:  The course will employ a variety of active learning techniques which provide the student with an opportunity for self reflection, evaluation, and questioning.

• APQ’s (Application/Practice Questions) – classes will begin with an application based question {similar to a test question}.  Students will pair with their lab teams to discuss the question and then, time permitted, present an answer to the class for further discussion.  Questions will be based on the reading for that days class. 
• Muddy points:  During the last 2 minutes of class, students will provide a one sentence statement about a point which they did not understand or was confusing to them.  Slips of paper will be signed and turned into the instructor before leaving the class.
• Concept maps:  At the beginning of each class a list of vocab/concept words will be provided.  At the end of the section block, students must incorporate those words into a concept map and provide a 1-2page description of the connections in the concept map and why each word was placed in its location.  Items will be uploaded to the assignments tab  on Sakai.
• Journal Papers:  We will discuss 6 papers during the course of the semester.  Instructor will provide the background for the paper and then students will be randomly assigned a figure to discuss from the paper.  It is possible an individual will be selected every time, it is also possible to be never selected {it is random}.  All students should provide input on the discussion of these papers.

Quizzes/Participation: 

Attendance (see below) is expected but not enforced.  However, short quizzes will be announced in class and due the following class period.  Participation grades will be given for in class activities.

Extra Credit:

Students can earn up to 30pts of extra credit throughout the term.  Extra credit can be earned by submitting unique APQ questions generated by the individual.  In addition to the question, the student must provide a typed answer key/explanation for the question.  Extra credit questions should be based on the assigned reading and are due PRIOR to that days lecture.  Each days submission is worth 2pts.  If the question is used as part of an exam, the student earns an additional 3pts.  More than one question can be submitted per day, increasing your chances of being selected for an exam question.

Missed quizzes/participation/concept map assignments:  

The lowest 20% of quiz/participation grades will be dropped.  There are no make-ups.

Missed Exams:  

In accordance with New York State law, students who miss class due to their religious beliefs shall be excused from class or examinations on that day. The faculty member is responsible for providing the student with an equivalent opportunity to make up any examination, study, or work requirement that the student may have missed. It is suggested that students notify their course instructors at least one week before any anticipated absence so that proper arrangements may be made to make up any missed work or examination. Any such work is to be completed within a reasonable time frame, as determined by the faculty member.

Any student, who missed class due to a verifiable family or individual health emergency, or to a required appearance in a court of law, shall be excused. The student or a family member/legal guardian may report the absence to the Office of Student Affairs and Campus Life, (340 Egbert Hall or via email at studentabsence@ithaca.edu or by phone at 607-274-3374) which will notify the student’s dean’s office, as well as residential life if the student lives on campus. The dean’s office will disseminate the information to the appropriate faculty. Follow-up by the student with his or her professors is imperative. Students may need to consider a leave of absence, medical leave of absence, selected course withdrawals, and so on, if they have missed a significant portion of class work.

Laboratory:  The lab is scheduled as a very open ended endeavor.  Three major outcomes must be generated but the conclusion of the semester.

1. A hypothesis selected
2. A minimum of 8 quality DNA samples submitted for sequencing / lab pair
3. A summary report and presentation of the data collected
• ALL DATA including reports will be submitted electronically on sakai
• Notebooks must be turned over at the end of the semester

The lab is not a cook-book lab.  There is no right or wrong answer.  Much like the real world, the outcome of the work is a product formed by a team.  Should something not work and need to be repeated, this may need to happen on the individuals own time.  Lab supplies will be always available for completing additional experiments.  HOWEVER, a budget must be maintained and YOU MAY NOT EXCEED THE BUDGET FOR THE TERM.  Additional details provided in the lab section.

• Notebook:  An accurate and detailed record of your experiments in the laboratory is absolutely essential.  Spiral or glue-bound.  Loose leaf is not acceptable.  The laboratory notebook should include the following:
  

• Table of contents
• Title (daily)
• Date (daily)
• Page numbers
• Your name (daily)
• Written in pen
• Purpose of today’s exp
• A step by step log of WHAT YOU DID (not what you planned to do)
• Time/Temp/Concentration..etc
• Staple/glue annotated data in notebook
• Conclusions or detailed descriptions of data
• Manufacturer/Cat#/Lot# of reagents used
• Budget worksheet (last page)

• Question sets:  Question sets on assigned reading will be due prior to several lab sections.  Typed answers to the questions must be provided in class and/or uploaded to sakai prior to the start of lab.
• Laboratory skills:  While teamwork is key to the success of the lab, an individual must demonstrate proficiency at microbiology skills (spread plates, dilutions, stains, basic microscopy).  Individuals will be assessed throughout the semester on these skills.  Three weeks before the end of the semester, students will be given their skills assessment grade.   Students have the opportunity to accept this final grade or request an OPTIONAL Practical Examination which will take place on 04/26/12 from 1-4pm.
• Lab final presentation:  Group members will individually construct a final lab report on their term-long project.  As a group, the teams will then meet and develop a final presentation 15-30min, describing their final report.  Additional details on laboratory and final presentation will be given at a later date.

Group grading:  

Peer evaluations will be used to determine the level of work put in by the individual as part of the team.  As such you must grade each other’s performance in the group on a 1-4 scale.  You must include yourself in the grading, and a number can only be used once (ie. someone must get a 4, and someone must get a 1).  Grades for the final lab report will be weighted based on these peerevaluations. (You cannot lose more than 1 letter grade, however, you can exceed 100pts for the final project)

Academic honesty:  

Honesty is a cornerstone of the mission of the College. Unless it is otherwise stipulated, students may submit for evaluation only that work that is their own. For more information see Student Handbook 7.1.4 

Attendance: 

Attendance is expected for all classes, and students are responsible for work missed during any absence from class. Students should notify their instructors as soon as possible of any anticipated absences

Online Course Evaluations: 

Student input is highly valued and is important to maintain high quality instruction. Course evaluations are mandatory and must be completed online the last week of classes

Incompletes: 

Incompletes are given only when a student is doing satisfactory work but cannot complete the course for a reason not related to academic performance (i.e., medical, family emergency). Terms for completion will be determined by instructor and are due no later than the end of the following semester. If no complete grade is received by the due date, a grade of F is recorded on the transcript. 

Policy on Grade Disputes: 

Grade disputes will be resolved directly between the course instructor and the student. As a general principle, the authority to change a grade rests with the faculty member.  See Students' Right to Petition 

Accommodations:  

Academic accommodations are available to students with documented disabilities. To access services, students must self-identify and provide appropriate documentation to the Office of Academic Support Services. For further information, please contact the Office of Academic Support Services at 274-1257.

Disclaimer: 

This syllabus is intended to give the student guidance in what may be covered during the semester and will be followed as closely as possible. However, the professor reserves the right to modify, supplement and make changes as the course needs arise.

Lecture Schedule - Subject to change if required 

 FINAL EXAM: Friday  May 11  10:30 am ‐ 1 pm