Micro 509 Laboratory Schedule for Winter, 2005
based on Nester et al., 2004, 4th edition and Leboffe & Pierce, 2002, lab manual
This schedule was last updated on Friday, December 31, 2004
|
To view
lectures (PowerPoint presentations) see: www.mansfield.ohio-state.edu/~sabedon/lectures/index.html#microbiology or www.phage.org/lectures/index.html#microbiology Your syllabus can be found at www.phage.org/school_syllabus.htm For
first day of lectures we will be covering chapters 1, 2, and 3 (through “Morphology of Prokaryotic Cells” on p. 49). The following is an approximate lecture schedule
for the quarter:
The above
schedule is to give you heads up on reading your text for the first and
subsequent days of lecture. Don’t be ignorant: take the time to read your text as assigned, and read it well! |
|
Micro 509 Grading Scheme Midterm #1: 250 points Midterm #2: 250 points Midterm #3: 250 points Lab exam #1: 60 points Lab exam #2: 90 points Lab participation and attitude: 30 points Lab quizzes: 30 points Lab cleanup: 20 points Lab unknown: 20 points Total: 1000
points |
1. This isn’t high school. Uncertainty and ambiguity are two painful aspects of biology, science, and medicine. In microbiology things will not always work. Get used to it. We will be working day in and day out with living things that don’t always cooperate, and we will be learning challenging techniques that won’t always be immediately pleasureful. Furthermore, though I’ve seen plenty of people try to prove otherwise, it is next to impossible to do well in microbiology lecture or lab without making an effort to read your texts and supporting documents (such as this document). If you don’t want to be challenged—or are not equipped in terms of time or ability to do the necessary reading and other preparations for lectures and for labs—then don’t take microbiology.
2. Difficulty is no excuse for apathy. Your success in this lab and this course can be affected by your attitude. If you are fighting microbiology, convinced that taking microbiology is an unreasonable expectation imposed upon you, then you will not excel in this course. A key component to learning microbiology is becoming aware of how to do microbiology in the laboratory. If you are not paying attention—if you don’t care—you only end up creating trouble both for yourself and for those who are counting upon you.
3. Refer to this document (i.e., read the appropriate sections as indicated below) to have a clue as to what you need to be doing and how you need to be doing it in lab. You will be lost if you do not. In other words, follow all directions, instructions, and tips from your lab text unless those are contradicted by instructions found in this document. By all means seek help from your lab instructor if you are confused, but make sure that you have at the very least first looked for the information in your lab text and in this document.
4. Your lab grade is in part based on your lab participation and attitude. Remember, you need to be coming to lab, doing your share of the work, using proper (and appropriate) laboratory techniques, making meaningful observations of experimental results, taking sufficiently detailed notes so that you have some sense, come exam time of what you have done; and conduct yourself in a professional, courteous, civil, and approachable manner.
5.
Your lab grade
will also be based, in part, on learning your binomials. Starting the second lab (and then as indicted) you will be quizzed at
the start of labs. Quizzes will consist, at least in part, of the equivalent of
matching genus to species. You will be held responsible only for those
organisms indicated as actually being used for a given lab (i.e., if we
indicate that one organisms is replacing another, then learn the organism we
are using, not that which is being replaced). The purpose of this exercise is
to familiarize you with the organisms you will be working with, and binomial
nomenclature in general.
6. Your lab grade will also be based, in part, on understanding what you will be doing for a given lab. In conjunction with the your binomial quizzes you will also be quizzed on your appreciation of just what it is you will be doing in lab on a given day. Yes, we do have an expectation that you will read your labs (and this document) prior to coming to lab, but note that the primary concern of these quizzes will be what you will be doing in the lab the day the quiz is given. That is, you should not beat yourself up over memorizing the interpretation of procedures (e.g., what it means when colonies are red) unless you are instructed to start and complete a procedure that day (interpretation, however, will be an important component of lab exams). Our hope, instead, is to motivate you to learn the material necessary to safely and efficiently perform the laboratory that you will be doing that day.
7. Your lab grade is also based, in part, on how thoroughly you clean up and otherwise keeps carts, counters, and drawers neat. See below for a discussion of proper cleanup procedures. This aspect of your grade will come from both your overall section’s cleanliness and observations that are made of individual lapses on your part. Please contact your instructor if you observe any problems that you are unsure how to deal with.
8. Your lab grade is also based, in part, on your identification of your bacterial unknown. To ID your unknown you will need to attend lab on a regular basis, record data, and have some clue as to what you are doing in lab, but otherwise you should avoid being kept up at night worrying about this procedure.
9.
Your lab grade will also include two, open-lab-text exams. To do well in the lab
portion of this course you should conscientiously complete the assigned
laboratory exercises; record results, answer all questions (unless directed not
to); and review your lab text (well) prior to taking the lab exam. In the exam
you will be tested on lab results as well as your ability to perform specific
techniques, but in particular you will be
tested on what results mean.
Lab exams are open-book and include questions assigned in advance. This style
of lab exam keeps the focus on learning rather than on memorizing. Just imagine
the alternative: a lab practical for which you have to memorize all of the
material!!!
10. Read your lab text prior to coming to lab. You will understand what is going on better if you familiarize yourself with what you will be doing. Remember that your goal is to more easily do and understand the labs once you get to lab. Try to get a sense of what needs to be done, what materials you will need, etc. You may be quizzed, at the beginning of labs on how well you have prepared.
11. Labs
will not begin early.
Laboratory periods are set to begin at 12:30 or 2:45. Please show up on time to
labs to take the lab quizzes. However, please refrain from entering or
attempting to enter labs until the official start time for your laboratory
section. Whatever you do, do not ask your lab instructor or anybody else found
in association with the microbiology prep lab to let you into the teaching
laboratory early. Getting caught asking
will result in 5 points being deducted from your grade (on a 1000-point
scale)!!! If you want to finish labs on time you should work diligently
while in lab, choose partners who will also work diligently, and, above all,
have a very good sense of what you will be doing in lab prior to starting. At
the appropriate start of laboratory periods take the initiative to get yourself
started by collecting reagents, setting up, and, to the extent that you can do
so without instructor demonstration, performing procedures.
12. Place only a minimal amount of personal materials on your lab bench. Lab benches are places where contamination of belongings could occur. Please keep backpacks, extra clothing, extra books, and other unused materials away from your lab bench. Getting caught placing these materials on your lab bench will be deducted from your grade (1 point per incident on 1000-point scale).
13. Work safely I. In addition to the safety instructions listed in your lab text, remember: (i) Be prepared and work with care. (ii) Do not knowingly harm yourself. (iii) Do not knowingly ingest any substance in the laboratory or cause others to do so, even this is something that you have brought into the laboratory. (iii) Do not knowingly harm others. Violations of these rule (i) will result in deduction of points from your lab grade. Violation of rule (ii) may very well result in your being reported to the administration. Violation of rule (iii) will result in deduction of 5 points per incident from your grade (on 1000-point scale). If you violate rule (iv) you will be reported to the administration, and perhaps also the police!
14. Work safely II. (iv) Avoid touching your face with your hands. (iv) Wear disposable gloves when handling stains (i.e., as used for observing bacteria under a microscope; note that this is not an instruction to wear gloves at all times for all procedures though you certainly are welcome to do so should you feel compelled). (v) Please keep burners burning only (approximately) as they are actually being used.
15. Do not return unused cultures and media to where you got them from unless you receive permission from your laboratory instructor to do so. Doing so could spoil procedures for other students. Getting caught doing so will result in 5 points being deducted from your grade (on a 1000-point scale).
16. Do your labs in the orders indicated in Table 1. If you would prefer to deviate from suggested orders then please first discuss this with your instructor. There may very well be a reason for the order suggested, but not always.
17.
Your lab text has
blue pages in the back. These are questions
associated with individual lab exercises. There will be an indication of which
questions need to be answered. You are
responsible for these questions unless otherwise instructed. However, you do
not need to hand in these questions. They instead may be found as part of your
laboratory exam. Think of them as take-home exam questions (that is exactly
what they are).
18.
If you have an
idea about how a lab may be run better then please inform your instructor. We are doing our best to design labs so that diligent
students can finish them in the allotted time. Please come to lab prepared to
work quickly, efficiently, and safely, but let us know how we can improve
procedures.
19.
Make up labs will be extremely
difficult or impossible to accomplish due to our use
throughout these labs of living microorganisms. Therefore, please try hard to
attend labs.
20.
Label all media and cultures, using marker on glass. These reagents will not be labeled for you
and you will not be able to distinguish cultures without labels.
21.
Use black, felt-tipped pens for most labeling. Save red Gram-stain
permanent pens only when you will be destaining slides using organic solvents,
e.g., when Gram staining. Note that the red ink is meant to be difficult to
wash off and this makes it next to impossible to remove writing from tubes
marked with Gram-stain pens. Do not remove labels from batches
containing otherwise unlabeled individual materials.
22. Take care of your microscope. Only the 100x objective lens can be brought into contact with oil. Do not get oil on the 40x, 10x, and 4x objective lenses. Use alcohol and cotton swabs for most microscope cleaning. Use only lens paper—never kimwipes or paper towels—to clean the optics on your microscope. Do not even think of using paper towels to clean your microscope optics!!!!
23. These
are various ways that media can be prepared. A deep is a
regular tube filled with 10 ml (or in some cases, as specified, 25 ml) of agar
media (use melted, not solidified; if used solidified this is stab). A
pour tube is a large tube filled with 25 ml agar media (used melted). A shake
tube also is a large tube filled with 25 ml agar media (also used melted).
24. Incubators. We typically will be using either a 25ºC or a 37ºC incubator. Some procedures will not work given a 37ºC incubation, so please keep track of what incubator you should be placing your cultures into. In many cases you will be asked to place your cultures on one or more trays which in turn will be placed in incubators for you. When incubations need to be completed before the next lab period, your cultures (if properly placed in the appropriate location) will be removed to a refrigerator. Where your text says 35ºC incubation we will be employing the incubator labeled “37ºC”.
25.
Make sure you both stow your cultures in incubators properly
and then clean up properly: See Appendix 1 for tips on how to how to clean up the lab
and otherwise successfully complete your lab procedures.
TABLE
1: Summary of Labs[1]
|
#.wk.day[2] |
day |
unit-lab-page[3] |
action |
approximate
lab name[4] |
temp |
length |
#/grp[5] |
|
1.1.1 |
Mon |
3-1.74 |
start[6] |
intro to light microscopy[7] |
-- |
-- |
1[8] |
|
1. intro to micro, 2. molecules
of life, and 3. microscopy |
|||||||
|
3. microscopy and 4. prokaryotic
growth |
|||||||
|
2.1.2 |
Thurs |
3-4.93 |
simple stains[11] |
-- |
-- |
1 |
|
|
2.1.2 |
Thurs |
1-2.34 |
start |
aseptic transfers[12] |
25, 37 |
next |
1 |
|
2.1.2 |
Thurs |
3-1.74 |
complete |
intro to light microscopy |
-- |
-- |
1 |
|
2.1.2 |
Thurs |
--- |
complete |
phase contrast, Pseudomonas[13] |
-- |
-- |
1 |
|
weekend 1 / week 2 below |
|||||||
|
3.2.1 |
Mon |
1-2.13 |
finish[14] |
aseptic transfers |
-- |
-- |
1 |
|
3.2.1 |
Mon |
3-6.98 |
complete |
Gram stain[15] |
-- |
-- |
1 |
|
3.2.1 |
Mon |
3-7.102 |
complete |
acid-fast stains[16] |
-- |
-- |
1 |
|
3.2.1 |
Mon |
--- |
complete |
phase contrast, hay infusion[17] |
-- |
-- |
1 |
|
4. prokaryotic growth and 5. control
of microbial growth |
|||||||
|
5. control of microbial growth and
6. metabolism |
|||||||
|
4.2.2 |
Thurs |
2-13.67 |
start |
effectiveness hand washing[18] |
25 |
48 |
2 |
|
4.2.2 |
Thurs |
4-1.120 |
start |
streak plate[19] |
37 |
24-48 |
1 |
|
4.2.2 |
Thurs |
6-1.242 |
start |
standard plate count[20] |
37 |
24-48 |
2 |
|
4.2.2 |
Thurs |
2-12.64 |
start |
disinfectants[21] |
37 |
48 |
2 |
|
4.2.2 |
Thurs |
6-3.250 |
complete |
direct count[22] |
-- |
-- |
2 |
|
weekend 2 / week 3 below |
|||||||
|
5.3.1 |
Mon |
MLK Jr. |
none |
-- |
-- |
-- |
-- |
|
6. metabolism and 7. DNA to
protein |
|||||||
|
7. DNA to protein and 8. bacterial
genetics |
|||||||
|
6.3.2 |
Thurs |
8-1.288 |
complete |
extraction of DNA[23] |
-- |
-- |
2 |
|
6.3.2 |
Thurs |
4-2.123 |
start |
37 |
24-48 |
4 |
|
|
6.3.2 |
Thurs |
4-3.125 |
start |
phenylethyl agar |
37 |
24-48 |
4 |
|
6.3.2 |
Thurs |
2-13.67 |
finish |
effectiveness hand washing[26] |
-- |
-- |
2 |
|
6.3.2 |
Thurs |
6-1.242 |
finish |
standard plate count |
-- |
-- |
2 |
|
6.3.2 |
Thurs |
2-12.64 |
finish |
disinfectants[27] |
-- |
-- |
2 |
|
6.3.2 |
Thurs |
4-1.120 |
finish |
streak plate |
-- |
-- |
1 |
|
weekend 3 / week 4 below |
|||||||
|
7.4.1 |
Mon |
2-4.45 |
start |
evaluation of media[28] |
37 |
24-48 |
4 |
|
7.4.1 |
Mon |
4-5.129 |
start |
endo agar |
37 |
24-48 |
4 |
|
7.4.1 |
Mon |
4-6.131 |
start |
eosin methylene blue agar[29] |
37 |
24-48 |
4 |
|
7.4.1 |
Mon |
4-8.135 |
start |
MacConkey agar[30] |
37 |
24-48 |
4 |
|
7.4.1 |
Mon |
2-5.47 |
start |
aerotolerance[31] |
37 |
24-48 |
4 |
|
7.4.1 |
Mon |
2-7.52 |
start |
effect of temp. on growth[32] |
25,37 |
24-48 |
4 |
|
7.4.1 |
Mon |
4-2.123 |
finish[33] |
mannitol salt agar |
-- |
-- |
2 |
|
7.4.1 |
Mon |
4-3.125 |
finish |
phenylethyl agar[34] |
-- |
-- |
2 |
|
review/catch
up |
|||||||
|
midterm
exam #1 |
|||||||
|
8.4.2 |
Thurs |
2-4.45 |
finish |
evaluation of media |
-- |
-- |
2 |
|
8.4.2 |
Thurs |
4-5.129 |
finish |
endo agar |
-- |
-- |
2 |
|
8.4.2 |
Thurs |
4-6.131 |
finish |
eosin methylene blue agar[35] |
-- |
-- |
2 |
|
8.4.2 |
Thurs |
4-8.135 |
finish |
MacConkey agar |
-- |
-- |
2 |
|
8.4.2 |
Thurs |
2-5.47 |
finish |
aerotolerance[36] |
-- |
-- |
2 |
|
8.4.2 |
Thurs |
2-7.52 |
finish |
effect of temp. on growth[37] |
-- |
-- |
2 |
|
weekend 4 / week 5 below |
|||||||
|
9.5.1 |
Mon |
3-5.96 |
complete |
negative stain[38] |
-- |
-- |
1 |
|
9.5.1 |
Mon |
3-9-109 |
complete |
endospore stain[39] |
-- |
-- |
1 |
|
9.5.1 |
Mon |
3-8.107 |
complete |
-- |
-- |
1 |
|
|
10. prokaryote ID and 11. prokaryote
diversity |
|||||||
|
11. prokaryote diversity and 12. eukaryote
microbes |
|||||||
|
10.5.2 |
Thurs |
lab exam # 1 |
none |
exam on first 9 labs[42] |
-- |
-- |
1 |
|
weekend 5 / week 6 below |
|||||||
|
11.6.1 |
Mon |
6-4.251 |
start |
plaque assay[43] |
37 |
24-48 |
2 |
|
11.6.1 |
Mon |
5-13-177 |
start |
starch hydrolysis[44] |
37 |
48 |
4 |
|
11.6.1 |
Mon |
5-7.159 |
start |
nitrate reduction test[45]** |
37 |
24-48 |
4 |
|
11.6.1 |
Mon |
5-1.140 |
start |
oxidation fermentation test[46]** |
37 |
48 |
4 |
|
11.6.1 |
Mon |
5-20.194 |
start |
SIM medium** |
27 |
24-48 |
4 |
|
11.6.1 |
Mon |
5-4.149 |
start |
MRVP** |
37 |
120 |
4 |
|
11.6.1 |
Mon |
5-8.164 |
start |
citrate test** |
37 |
168 |
4 |
|
11.6.1 |
Mon |
5-17.187 |
start |
gelatinase test** |
25 |
168 |
4 |
|
12. eukaryote microbes and 13. viruses
of bacteria |
|||||||
|
13. viruses of bacteria and 14. infectious
agents |
|||||||
|
12.6.2 |
Thurs |
6-4.251 |
finish |
plaque assay[47] |
-- |
-- |
2 |
|
12.6.2 |
Thurs |
5-13-177 |
finish |
starch hydrolysis[48] |
-- |
-- |
2 |
|
12.6.2 |
Thurs |
5-7.159 |
finish |
nitrate reduction test[49]** |
-- |
-- |
2 |
|
12.6.2 |
Thurs |
5-1.140 |
continue |
oxidation fermentation test** |
37 |
48 |
2 |
|
12.6.2 |
Thurs |
5-20.194 |
finish |
SIM medium** |
-- |
-- |
2 |
|
weekend 6 / week 7 below |
|||||||
|
13.7.1 |
Mon |
5-1.140 |
finish |
oxidation fermentation test[50]** |
-- |
-- |
2 |
|
13.7.1 |
Mon |
5-4.149 |
finish |
MRVP[51]** |
-- |
-- |
2 |
|
13.7.1 |
Mon |
5-8.164 |
finish |
citrate test** |
-- |
-- |
2 |
|
13.7.1 |
Mon |
5-17.187 |
finish |
gelatinase test[52]** |
-- |
-- |
2 |
|
13.7.1 |
Mon |
10-1.320 |
start |
the fungi[53] |
-- |
-- |
1 or 2 |
|
13.7.1 |
Mon |
10-2.326 |
start |
protozoans[54] |
-- |
-- |
1 or 2 |
|
13.7.1 |
Mon |
10-3.334 |
start |
helmith parasites[55] |
-- |
-- |
1 or 2 |
|
review/catch
up |
|||||||
|
midterm
exam #2 |
|||||||
|
14.7.2 |
Thurs |
5-5.154 |
start |
catalase test[56]** |
37 |
24 |
4 |
|
14.7.2 |
Thurs |
5-15.182 |
start |
urease test (broth only)[57]** |
37 |
24 |
4 |
|
14.7.2 |
Thurs |
5-16.185 |
start |
casease test** |
37 |
24 |
4 |
|
14.7.2 |
Thurs |
5-21.199 |
start |
triple sugar iron agar** |
37 |
18-24 |
4 |
|
14.7.2 |
Thurs |
5-2.143 |
start |
phenol red broth[58]** |
37 |
18 |
4 |
|
14.7.2 |
Thurs |
5-28.218 |
start |
motility test[59]** |
37 |
24-48 |
4 |
|
14.7.2 |
Thurs |
5-23.204 |
start |
litmus milk test** |
37 |
168 |
4 |
|
14.7.2 |
Thurs |
10-1.320 |
continue |
the fungi |
-- |
-- |
1 or 2 |
|
14.7.2 |
Thurs |
10-2.326 |
continue |
Protozoans |
-- |
-- |
1 or 2 |
|
14.7.2 |
Thurs |
10-3.334 |
continue |
helmith parasites |
-- |
-- |
1 or 2 |
|
weekend 7 / week 8 below |
|||||||
|
15.8.1 |
Mon |
5-27.215 |
start |
coagulase test[60] |
37 |
24 |
2 |
|
15.8.1 |
Mon |
2-14.69 |
start |
antimicrobial susceptibility[61] |
37 |
16-18 |
2 |
|
15.8.1 |
Thurs |
5-6.157 |
complete |
oxidase test[62]** |
-- |
-- |
2 |
|
15.8.1 |
Mon |
5-5.154 |
finish |
catalase test[63]** |
-- |
-- |
2 |
|
15.8.1 |
Mon |
5-15.182 |
finish |
urease test (broth only)[64]** |
-- |
-- |
2 |
|
15.8.1 |
Mon |
5-16.185 |
finish |
casease test[65]** |
-- |
-- |
2 |
|
15.8.1 |
Mon |
5-21.199 |
finish |
triple sugar iron agar[66]** |
-- |
-- |
2 |
|
15.8.1 |
Mon |
5-2.143 |
finish |
phenol red broth[67]** |
-- |
-- |
2 |
|
15.8.1 |
Mon |
5-28.218 |
finish |
motility test[68]** |
-- |
-- |
2 |
|
15.8.1 |
Thurs |
10-1.320 |
continue |
the fungi |
-- |
-- |
1 or 2 |
|
15.8.1 |
Thurs |
10-2.326 |
continue |
protozoans |
-- |
-- |
1 or 2 |
|
15.8.1 |
Thurs |
10-3.334 |
continue |
helmith parasites |
-- |
-- |
1 or 2 |
|
15. innate immunity and 16. adaptive
immunity |
|||||||
|
16. adaptive immunity and 17. immunology
applications |
|||||||
|
16.8.2 |
Thurs |
5-26.212 |
start |
blood agar |
25 |
24 |
4 |
|
16.8.2 |
Thurs |
2-01-36 |
start |
ubiquity of microorganisms |
25,37 |
24-48 |
2 |
|
16.8.2 |
Thurs |
-- |
start |
bacterial unknown[69] |
many |
many |
1 |
|
|
|
5-4.149 |
start |
MRVP |
37 |
120 |
1 |
|
|
|
5-8.164 |
start |
citrate test |
37 |
168 |
1 |
|
|
|
5-17.187 |
start |
gelatinase test |
25 |
168 |
1 |
|
|
|
5-23.204 |
start |
litmus milk test** |
37 |
168 |
1 |
|
16.8.2 |
Thurs |
5-27.215 |
finish |
coagulase test |
-- |
-- |
2 |
|
16.8.2 |
Thurs |
10-1.320 |
continue |
the fungi |
-- |
-- |
1 or 2 |
|
16.8.2 |
Thurs |
10-2.326 |
continue |
protozoans |
-- |
-- |
1 or 2 |
|
16.8.2 |
Thurs |
10-3.334 |
continue |
helmith parasites |
-- |
-- |
1 or 2 |
|
weekend 8 / week 9 below |
|||||||
|
20.10.2 |
Thurs |
5-14.180 |
complete |
ONPG test[70] |
-- |
-- |
2 |
|
17.9.1 |
Mon |
5-26.212 |
finish |
blood agar |
-- |
-- |
2 |
|
17.9.1 |
Mon |
2-01-36 |
finish |
ubiquity of microorganisms |
-- |
-- |
2 |
|
17.9.1 |
Mon |
5-23.204 |
finish |
litmus milk test[71]** |
-- |
-- |
2 |
|
17.9.1 |
Mon |
-- |
continue |
bacterial unknown[72] |
many |
many |
1 |
|
|
|
5-1.140 |
start |
oxidation fermentation test |
37 |
48 |
1 |
|
|
|
5-2.143 |
start |
phenol red broth |
37 |
18 |
1 |
|
|
|
5-5.154 |
start |
catalase test |
37 |
24 |
1 |
|
|
|
5-7.159 |
start |
nitrate reduction test |
37 |
24-48 |
1 |
|
|
|
5-15.182 |
start |
urease test (broth only) |
37 |
24 |
1 |
|
|
|
5-16.185 |
start |
casease test |
37 |
24 |
1 |
|
|
|
5-20.194 |
start |
SIM medium |
|||