BIO226L Syllabus

General Microbiology Laboratory

Spring 2015
General Instructor: Dr. Richard Meyer rmeyer@mail.utexas.edu
Office hours: Mon, Tues 11:30 12:30 NMS 1.124
Lecture: Mon 2-3:00 pm JESA121A
Laboratory Instructor: Dr. Shumaila Hanif Office hrs TBA

1
2

Week of:
Jan 18
Jan 25

Feb 1

Feb 8

Feb 15

Feb 22

Mar 1

Mar 8

9
10

Mar 15
Mar 22

11

Mar 29

12
13
14

Apr 5
Apr 12
Apr 19

15

Apr 26

16

May 3

Laboratories (TWTh):
Lab check-in
I. Streaking out for isolated colonies
and soil sampling
II. Beginning characterization of
isolated soil organism
III. Characterization of soil organism
(continued)
IV. Characterization of 16S RNA;
Streptomyces
Report 1 due (Labs I-III)
V. Agarose gel electrophoresis of PCR
product. DNA sequencing
VI. Mutagenesis of W3110 with UV
Report 2 due (Labs IV-V)
VII. Growth curve and Induction of galactosidase
Spring break
VIII. Assay for -galactosidase

Lecture (M):
None
Prevalence and classification of microorganisms

IX. Bacteriophage
Report 3 due (Labs VI-VIII)
X. Conjugation and transduction
XI. Isolation of plasmid DNA
XII. Analysis of plasmid DNA restriction
fragments and bacterial motility
Report 4 due (Labs IX-XII)
Lab clean-up
No class

Mobile elements

Growth, mutations and

gene regulation

Motility

General information:
1. The objective of this course is to provide, at the introductory level, training in the
manipulation and characterization of microorganisms from the perspective of modern
experimental microbiology. Prerequisites: Credit with a grade of at least C- or registration for
BIO326M or BIO326R (or 226R). BIO326R is recommended.
2. There is a master site for this course on UT Blackboard. The course manual is available for
download on this site. You can download the entire manual, or just sections as you need them.
However, everyone will be expected to have a hard copy of the relevant parts of the manual
during lab periods. From time to time, information for all students in the course may be posted
on the master site, so you should check the site regularly. Section sites on Blackboard will be
reserved for use by each section. Make sure you can access both the general site and the site
for your section (you must be enrolled to do so).
You are not required to purchase supplies for this course. Having your own digital camera or a
cell phone capable of taking pictures, a fine-point felt-tip marker, and a USB flash drive is highly
recommended but not required.
3. Attendance: Attendance at each meeting of your laboratory section and at each weekly
lecture is required. In addition, continuity of group effort from week to week and sharing
results within each section are important in this course. As a result, attending other sections on
a casual basis or switching with other students is not allowed and will count as an absence. An
unexcused absence will result in a loss of 8 points from the final grade.
Occasionally an emergency or another essential activity makes missing a lab, leaving the lab
early, or arriving late, unavoidable. If you foresee one or more absences, send Dr. Richard
Meyer (not the lab instructor or your TA) an e-mail stating (a) your name and the unique
number of your section (b) a clear description of the nature of the conflict and (c) times you are
available during the week of the absence to make up the work. You should do this as soon as
you are aware of the conflict. If the absence is justifiable and an agreed-upon make-up plan is
in place, Dr. Meyer will notify the TAs. In the event of a conflict a lab can be made up only by
attending another section during the same week (TWTH 11-2 and 3-6).
If your absence is due to a sudden, serious emergency, then contact Dr. Meyer as soon as you
know when you will be able to resume your normal activities. You should plan on providing
evidence of the emergency.
As a general guideline, minor illnesses, activities of social clubs, or exams scheduled outside of
normal class time are not justifications for an absence. If an exam in another course is
scheduled during your lab period, the instructor of that course is required to offer you a makeup.

4. Lab Reports. You will be asked to write four reports, summarized in the table below, for this
course. You must turn in (1) a hard copy of your report and (2) the word document containing
the text of the report (illustrations and tables do not need to be included in this document).
The hard copy will be due at the beginning (by 11:05 am or 3:05 pm) of your regular laboratory
class time. The accompanying word document (figures not required as part of this document)
should be sent to the instructor by email no later than one day after the hard copy is submitted.
Reports turned in late, but on the same day they are due, will incur a 3 point penalty. If the
report is turned in the following day, but at or before your regular class time, there will be an
additional 2 pt. penalty. After that time, there will be a 2 pt. penalty for each 24 hr period the
report is late. It is your responsibility to arrange a time with the TA when a late report can be
turned in. Reports will not be considered as submitted until a hard copy is received by the TA
or instructor and a word document of the report has been submitted.
Further information about the reports is in a document uploaded to the class master site.
Report:
Physical and metabolic characterization
of unknown soil organism

Labs:
I,II,III

Date due: lab period, week of:

Feb 15

PartiaI identification of a soil organism by

sequencing 16S RNA and characterization
of a co-isolated species of Streptomyces

IV,V

Mar 1

Isolation and characterization of a Lacmutant of E. coli

Mobile genes: bacteriophage,
transposition and conjugation

VI,VII,VIII

Mar 29

IX,X,XI,XII

Apr 26

5. Lectures. M 2:00 3:00 JESA121A. The lectures will place the experimental work you are
doing in the lab within the broader context of current understanding and knowledge in
microbiology. Visuals will be posted in the Course Documents section of the master site prior
to the lecture, but these are not intended to substitute for your attendance at the lectures. You
will be responsible for mastering all the material covered in the lectures, including information
not shown on the visuals.
6. Final exam. There will be a 90 min exam during the exam period. The exam will test your
understanding of the basic principles, ideas and methodologies covered in the course, as well as
the background information provided in the lectures. The questions in the manual at the end
of each lab section are examples of the kinds of questions that are likely to appear in the exam.
A sample exam, indicating both the format and difficulty of the questions, will be posted on the
Master Site during the semester.

7. Laboratory Quizzes. There will be at least four quizzes in your lab section during the course
of the semester. The quizzes will test whether you have read the Lab Manual and are prepared
for the lab that week. In addition, they will include questions based on the lectures.
8. Performance in class. Students will be evaluated according to whether they come to class
on-time and prepared, participate actively in the lab exercises, contribute information and
results when called upon to do so and show through their performance increased skill and
understanding. Teaching assistants and the instructor observe students and draw conclusions
about the quality of their overall participation and their contributions to the success of the
class. Note that class performance is taken seriously and will make up a significant fraction of
the final grade. Some of the questions that are considered in evaluating student performance
are: (1) Is the student punctual and ready for class (able to answer questions about the weeks
work, has the correct part of the manual in hard copy and is not struggling to determine the
days activities). (2) Is the student a participant or a passive observer during the course of the
laboratory? (3) Does the student post data on time for the class, and carry out the needed
calculations in a timely manner (4) Is the student courteous and helpful to others and able to
keep workspace clean and functional without prompting? (5) For assignments that must be
completed after hours, is the student involved or is a proxy assigned to carry out the necessary
tasks?
If a student is found to be carelessly interfering with the work of others, a grade of 0 points
will be assigned.
You should feel free to discuss your performance at any time with the lab instructor or TA.
The document Lab Safety Rules and Guidelines is available on the master class site on
Blackboard and will also be posted in the laboratories. Students are responsible for adhering to
the procedures outlined in this document. A summary of lab procedures will be given during
the first week.
9. Grading concerns. If you feel that one of the reports was improperly graded, you should
address the issue with the grader (this will be either the TA or the instructor) during the week
after the report was returned. Contact the grader during normal office hours or make an
appointment. If there is no resolution, immediately contact Dr. Meyer, who will discuss the
matter thoroughly with the TA or instructor to reach a final decision. After the one week
period, there will be no reconsideration of report grades.
The TAs will schedule office hours for you to examine your graded exam. If you believe a
question on the exam was improperly graded, you can discuss this with the TA during office
hours. If there is still disagreement, provide to the TA within two days a written explanation of
why the grading was incorrect. The TA and instructor will then review the grading of the
question. Pending a final resolution, exams must remain with the TA. If you take the exam out
of the office then that will be considered as your tacit acceptance of the grade.
4

10. Building and lab availability. Students will occasionally need to return to the lab to
complete work outside of their normal lab hours. This could include Mondays, Fridays and the
weekend. A schedule indicating when the lab will be open and supervised during these times
will be posted. To access the building during the weekend or after 6 pm weekdays, you will
need a UTID prox card. If you are enrolled in the course, the locks will be programmed to allow
you to enter the building.
11. Academic honesty: All students are expected to adhere to the highest standard of
academic honesty. In particular, plagiarized or closely paraphrased writing in reports (including
that of a lab partner or a former student) will result in a severe penalty, including failure in the
course. The Lab Manual is copyrighted and may not be copied or paraphrased in the
preparation of reports. If you have any concerns about the originality of your work, discuss
your paper with the instructor or Dr. Meyer prior to submitting it.
Principles of academic integrity at the University are outlined by the Dean of students at:
http://deanofstudents.utexas.edu/sjs/acint_student.php
12. Disabilities: Students with disabilities may request appropriate academic accommodations
from the Division of Diversity and Community Engagement, Services for Students with
Disabilities, 471-6259, http://www.utexas.edu/diversity/ddce/ssd/ If you have been granted
specific accommodations please notify me in writing by the twelfth class day. Arrangements for
extra time or a non-distracting environment during examinations should be made with the
disabilities office and must coincide as much a possible with the regularly- scheduled time.
13. Religious holidays: UT Austin policy requires that you notify me of your pending absence at
least fourteen days prior to the date of observance of a religious holy day. If you must miss a
class, an examination, a work assignment, or a project in order to observe a religious holy day,
you will be given an opportunity to complete the missed work within a reasonable time after
the absence.

Grading:

A maximum of 100 points can be earned in the course. Points will be assigned as follows:
Reports:

15 pts. for each report (60 pts. total). As a guideline:

14 15:
12 13:
10 11:
8 9:
<8:

A
B
C
D
F

Exam:

Per cent correct x 0.2 = pts. earned (maximum pts. 20)

Quizzes:

12 pts total

In-class
performance: 8 pts
Final grades:
A

93 - 100 pts

A-

89 - < 93

B+

85 - < 89

81 - <85

B-

77 - < 81

C+

73 - <77

69 - < 73

C-

65 - < 69

D+

61 - < 65

57 - < 61

D-

53 - < 57

< 57