Biology Fall Syllabus by liaoqinmei


									                            Biology 331 Course Information – Spring 2011
                        General Microbiology (Writing Intensive, 4 credits)
 This document contains a LOT of information, including a study guide and learning outcomes, and
 everything related to lab (policies, lab notebook rules). Make sure you read and follow it carefully!

Lecture Meeting Times: MW, 10:00-10:50 a.m.
Laboratory: T AND R, 8-10 a.m.
Instructor: Sarah Boomer, Ph.D.
Office/Hours: 219; 8-8209; office hours will be posted on-line and on my door
Website: (has links to course materials)

This writing intensive biology core course is designed to give you a broad knowledge of microbiology
in the context of the planet, humankind, and general science. Course pre-requisites include 200-level
biology (Bi211-3) and chemistry (Bi221-3). Genetics and Cell Biology are strongly recommended and
if you have not taken them, you may need to do additional background reading from the course text.

Text and Required Course Materials: Brock's Biology of Microorganisms (12th Edition). Each
person will maintain a lab notebook using a graph-ruled composition notebook (~$2.50 at bookstore).

Writing: Informal writing is based on lab notebooks and video summaries. Formal writing is based
on reports that accompany several lab assignments, and essay questions on the final.

Exams: 1 lecture exam and 1 lab exam during term, and 1 final. Owing to pre-professional exam
format (MCAT, DAT, GRE), 40% all exams will be multiple-choice. Missed exams cannot be made-
up without a valid excuse (e.g. university-sanctioned trip, note from doctor).

In-Class Videos: Two or three videos will be shown in class, most from a PBS series on global
health issues called Rx for Survival. Each presentation is accompanied by 10 pts. of short answer
questions due in class. So - don't miss class.

Grade Breakdown and Scale                                                       90-100% (A)
Lecture and Lab Exams: 2 X 100 = 200 pts.                                        80-89% (B)
Final: 130 pts.                                                                  70-79% (C)
Lab Assignments and Pop Quizzes: 277 pts.                                        60-69% (D)
Video Summaries: 20 or 30 pts.                                                 59% or less = F
                                   Course Syllabus – Spring 2011
  This is TENTATIVE Because I May Be Called To Do Federal Grant Review For One Week in May
                 Topics/Exams                         Lab (Tuesdays & Thursdays)
3/28         Syllabus and Pre-Test                          Introduction Set-Up
3/30       Introduction and Diversity                      Introduction (FINAL)
4/4        Prokaryotic Cell Biology                             Nitrogen Set-Up
4/6         Unique Chemotrophs                                        TBA
4/11        Phototrophic Bacteria                    Applied - Soil and Antibacterial Set-Up
4/13         Video - Superbugs             Applied - Yogurt & Feces Set-Up - Nitrogen PAPER DUE
4/18     Prokaryotic Central Dogma                            All Projects Follow-Up
4/20         Microbial Control                     All Projects Follow-Up (All Gram Staining!)
4/25   Ecology of You - Normal Flora             Microbial Evolution and All Projects Follow-Up
4/27         Unit One Exam                            Food Set-Up, Evolution Follow-Up
5/2              Immunology                    Food & Evolution (FINAL) - Genome PAPER DUE
5/4     Bacterial Pathogens/Virulence                                TBA
 5/9          Video - Vaccines                      All Projects Follow-Up, Start Plasmid Lab
5/11         Applied Immunology                     Plasmid Isolation - Campy PAPER DUE
5/16        Eukaryotic Pathogens                           Plasmid Fingerprinting
5/18             Virology I                          Immunodiagnostics and Epidemiology
5/23              Virology II                  All Projects Follow-Up - Immunology PAPER DUE
5/25      Virology III, Epidemiology                     No Lab – Academic Showcase
5/30       Memorial Day Holiday                   Lab Exam – Notebooks Due
 6/1              TBA                TBA
                          Final Exam – Monday, June 6 at 10-11:50

                        Study Guide, Learning Outcomes, Final Overview

Guide to Your Text
Your text is a resource for helping you master course materials and answering questions during lab.
Unless stated, exams are only based on information from my lecture notes and labs. These materials
only sometimes follow the structure of the textbook. Therefore, you will be jumping around a lot in the
book to follow my materials; for this reason, you might want to consult with the index.

Here are my top tips for working with the textbook:
(1) Understand that the following chapters cover diversity for specific groups of PROKARYOTES.
Even though I have not included these in the summary below, you will be consulting each
whenever a specific microbe is named, which is OFTEN!

       Chapter 15 = Proteobacteria Phylum              Chapter 16 = All Other Bacterial Phyla
       Chapter 17 = All Archaea

(2) Chapters 34-37 cover infectious pathogens. Even though I have not included these in the
summary below, you will be consulting each whenever a new pathogen is described!

(3) Some chapters contain material that should be review: Chapter 3 (macromolecules), parts of
Chapters 7 & 9 (molecular biology/gene expression), and Chapter 5 (metabolism). Even though I
have not included these in the summary below, you may need to review them.

Study Tip Throughout Term: for every named GENUS, you need to know which DOMAIN, PHYLUM
and/or GROUP it belongs to - in addition to other specific features or processes highlighted in lecture.
          It is therefore wise to develop study note-cards based on each named GENUS.

     Unit One Learning Outcomes = Prokaryotic Diversity - Ecology, Metabolism, Genetics, Control
Lecture            Chapter Key Course-Specific Learning Outcomes - Things to Know, Be Able To Do
Introduction      1, 2      Ways to categorize and describe microbes, examples thereof
                            Microbiology applications and landmarks in microbiology history
Prokaryotic Cell  2, 4      Compare/contrast domain membranes, walls, surface & cytoplasmic structures
Biology                     Environmental bacteria with unique structures and/or lifestyles
Chemotrophy       20-1,     Recognize e- donor and acceptor in prokaryotic reactions
                  23-24     Prokaryotic chemolithotrophic and anaerobic respiration examples
Phototrophy       14, 20,   Compare/contrast domain photosynthesis reactions, pigments, membranes
                  23-24     Earth history landmarks, emphasizing metabolic features
Central Dogma,    8, 11,    Compare/contrast domain structures and processes related to central dogma
Antibacterials     27       Antibacterial drugs - history, source, spectrum, target, resistance
Control            27, 36   Physical and chemical factors that affect microbial growth
Pathogens                   Environmental microbes that evade control, contaminate food
Ecology of You     28, 33   Ecology of normal flora, emphasizing body regions and their control
Nosocomials                 Nosocomial infections, emphasizing overall trends and examples
         Unit Two Learning Outcomes = Medical - Immunology and Pathogens (Prok, Euk, Viral)
Immunology         29       Distinguish nonspecific (1st, 2nd) vs. specific (3rd) defenses, players for each
                            For specific, understand humoral, cell-mediated, mucosal - all players, all Ab
                            Know strategies pathogens use to exploit the defenses - examples
Pathogens,         28       Understand steps of bacterial pathogenesis, virulence factors that facilitate
STD's                       All lecture pathogens (including STD's) that illustrate virulence factors, how
                            Compare/contrast STD agents - all levels (structure, classification, disease…)
Applied            30       Compare/contrast active and passive immunity - natural and artificial
Immunology                  Example vaccines & neutralizing Ab treatments - pathogens/virulence factors
Eukaryotic         18       All major eukaryotic classification groups from lecture
Microbes                    Unique features of fungi and protozoa, example pathogens
Virology I         10, 19   Attributes of viruses - compare/contrast with cells, history/discovery
                            Viral classification, structures and replication cycle features
                            Class I viruses, emphasizing structures, replication, host/diseases
Virology II        10, 19   Class IV-VII viruses, emphasizing structures, replication, host/diseases
                            Compare/contrast viruses in terms of unique evolution, features
                            Compare/contrast viruses in terms of cancer - cis/trans capabilities
Virology III       33       Compare/contrast antivirals - natural and synthetic drugs
Epidemiology                Prions - all levels of understanding (structure, function, disease)
                            Epidemiology vocabulary, strategies, agencies, top 10 global killers
      Lab Learning Outcomes = Culture-Dependent and -Independent Approaches to Microbiology
Basic Techniques 2, 4, 5,   Describe media and septic techniques, including all tools and procedures
                   6, 32    Microbial division and growth curve, counting methods - pros, cons, and math
Nitrogen Cycle,    20-24    Nitrogen cycle chemistry, example genera - their ecology and applications
Enrichments                 N fixation diversity, how different genera handle the oxygen problem
                            Describe enrichment strategies, procedures – advanced methods (paper!)
Applied Micro      21, 25-  Industrial microbiology, example products, all aspects of fermentation
Gram Positives     26, 27   Compare/contrast Gram Positive phylum subgroups, microbes - all levels
                            Soil procedures, microbes and useful products (all antibacterial facts/data)
Evolution          8, 11,   Compare/contrast prokaryotic recombination - transformation methods
                   12       Deino/Thermus applications, genomic biology (paper, review genome lecture!)
Food/Fecal         32, 36   Compare/contrast food/feces-associated Proteobacteria subgroups, microbes
Proteobacteria              Understand medical ID testing, on-line tools for archiving and analyzing DNA
                            Compare/contrast diarrhea agents, toxins, disease/pathogenicity
16S Analysis       12, 26   All molecular tools and procedures - especially plasmid isolation flow chart
Studying/Using              All vector/plasmic features, how they are used in cloning
Plasmids                    Principles of gel electrophoresis, fingerprinting, restriction enzymes
Immunology,        29, 30,  Immunodiagnostic tests – agglutination, ELISA, fluorescence, gel (paper)
Epidemiology       32       Epidemiology vocabulary and example pathogens from lab (including paper)

Final Overview
The final for this course will include 110 points of typical exam questions that will cover lecture
material from the second half of the class, which - in part - emphasizes the top 10 global infectious
disease killers below. Thus, you should use the following "worksheet" to both organize your notes
and research. In addition, you will also be answering long answer essay questions (20 pts, ~2X10 pt.
questions) about research or review papers I provide about global killers ~2 weeks before final.

                               Kind of Microbe          Disease Information
                                                                                Vaccine?         Global
      Agent            If Prokaryotic - Wall, Shape?       Anything From
                                                                                 Kind?        Epidemiology
                            If Virus - Envelope?              Lecture
                      If Eukaryotic - Classification?
  Hepatitis B                   Lecture                    Lecture          Research        Lecture
 N. meningitidis                Lecture                    Lecture          Research        Lecture
     C. tetani                  Lecture                    Lecture          Research        Lecture
  B. pertussis                  Lecture                    Lecture          Research        Lecture
     Measles                 Not In Lecture             Not In Lecture      Research        Lecture
  Plasmodium                    Lecture                    Lecture          Research        Lecture
 M. tuberculosis                Lecture                    Lecture          Research        Lecture
     S. typhi                   Lecture                    Lecture          Research        Lecture
       HIV                      Lecture                    Lecture          Research        Lecture
    Influenza                   Lecture                    Lecture          Research        Lecture

                                               Lab Policy
Lab Attendance
Lab attendance is mandatory and you CANNOT miss the first week because that is when we go over
and practice key safety activities. There are no opportunities to make up labs because each lab
involves significant preparation, including growing fresh materials overnight. For these and other
safety reasons, access to the lab is only during scheduled lab times.

Lab Assignments and POP Quizzes
This is a writing intensive course, with most writing based on lab. Although some lab activities are
done in pairs, assignments are completed and graded individually. There will be SEVEN 10-point pop
quizzes; 40% of these points are extra credit. Note: if you miss a lab with a quiz, you cannot make
up the quiz because of the extra credit component.

            Project                  Turn-In Materials & Notebook              Report Theme
         Introduction                           25 pts.                            None
        Nitrogen Cycle                          25 pts.                  Advanced Research – 20 pts.
            Applied                             25 pts.                            None
           Evolution                            10 pts.                  Genome Research – 20 pts.
         Food/Feces                             25 pts.                  Advanced Detection – 20 pts.
     Plasmid/16S Methods                        25 pts.                            None
   Immunology/Epidemiology                      20 pts.                  Advanced Detection – 20 pts.

Lab Notebook Rules
NOTEBOOKS DO NOT LEAVE THE LAB until the final lab (in preparation for your LAB EXAM). ALL
work on the notebooks MUST OCCUR in the lab and I will collect them at the end of every lab and
grade them at random times throughout the term. At the end of the term, you may keep your
notebook if you sign a “notebook honor promise” statement not to share your materials with others.

The goal of a notebook is to keep a legible, organized, detailed account of EVERYTHING you do,
see, or generate. Before the first day of lab, divide your notebook into 7 sections (reflecting projects
above), leaving 10-15 pages between each and making labeled tabs that identify each section above.
Within each project section, DATED entry(ies) must appear every day you work on a given project.
Within each project section, you need to treat entries as linear-temporal journals (i.e. write down
everything you do each day, in dated time-order within each project section). Throughout each lab
handout, there are BOLD instructions for project-specific things I will be looking for. In addition and
for ALL projects, remember to do the following:
      (1) Record what you label your plates and tubes so you can identify things later
      (2) Record where materials are at end of each day (incubator, refrigerator, discarded, etc.)
      (3) For visual tests, describe what you see (i.e. avoid just saying "test was +").

Lab Reports
For 4/7 lab projects, you will also write formal reports (see lab handouts for specific instructions).
Each is worth 20 points and will require significant homework in the form of careful reading, thinking,
and computer activities. In fact, you might want to read them ASAP because you can start some of
them earlier than a given lab. These assignments must be typed/word processed with 1.5 spacing
and printed out hard-copy; the length of each report should be 3-5 pages.

Comprehensive Lab Exam
At the end of the term, you will take a comprehensive 100-pt. exam covering ALL lab topics, including
lab lectures, procedures, results, on-your-own problems, and some report topics. Pop quizzes and
on-your-own problems (see lab handouts for specific instructions) are good ways to study for this.

Pathogens and Safety Rules in the Lab
During lab, you will handle some known pathogens (e.g. Staphylococcus, Salmonella, Shigella). You
may also encounter unknown pathogens from personal and grocery samples. The following rules will
be applied at all times to prevent contamination and promote safety. Misconduct or failure to abide by
these rules in lab will result in automatic expulsion and course failure.

     1.   Bring lab handouts and your individual lab notebook to every lab, along with writing tools,
          course text, and a calculator. Label materials carefully and keep organized records.
     2.   Store all other items in the shelf beneath lab benches - NOT on the floor or in your work
          area. Absolutely no drinks or food in lab. No gum-chewing, nail-biting, or pen-nibbling.
     3.   Wash desktops with 10% bleach at the beginning and end of lab. Wash hands at the
          beginning and end of lab, and before/after using the restroom.
     4.   Follow appropriate sterile technique when handling ALL materials in lab. Handle materials
          with care and don't waste anything.
     5.   Many items in this lab cannot be replaced if you drop, lose, or squander them. If you spill a
          live culture, there will not be a back-up available. If you misuse or break expensive
          supplies, second copies will not be available and you will lose points.
     6.   If you spill or break contaminated materials, follow these procedures:
             a. If personal injuries occur, stabilize bleeding and clean wound first.
             b. Next, disinfect spill by soaking with bleach for at least five minutes.
             c. Alert your instructor while spill is disinfecting and she will direct further clean-up
     7.   Equipment that can be flame/alcohol sterilized at the bench (e.g. loops, forceps, dally rods)
          is kept in white trays on your bench after you have appropriately decontaminated them.
     8.   All other trash goes in the following designated areas: small items go in waste buckets on
          benches; large items go on front autoclave cart.
     9.   Be careful with Bunsen burners. Double-check that they are off as you leave the lab.

Microscope Rules
Microscopes cost hundreds to repair, thousands to replace; handle and clean microscopes and
prepared slides as directed (if you don’t, you will lose points):

   a. Avoiding moving microscopes; if you have to, use both hands, carrying upright and gently
   b. Clean oil from lenses with lens paper; clean stage with Kimwipe tissues and cleaner
   c. Store microscope covered with lowest power down when finished

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