Instructor’s Guide
The Relationship Between Genes and
Proteins: Transcription and
Translation
Accompanying Laboratory: Effects of Antibiotics on Bacterial Growth
and Protein Synthesis
IG001
Printed in USA. Revised 2/08
The Relationship Between Genes
and Proteins: Transcription and
Translation
Instructor’s Guide
I.
About This Resource ............................................................................................2
A.
B.
C.
II.
Writing Assignments and Grading Rubrics .......................................................3
A.
B.
C.
D.
E.
F.
III.
I.
Introduction......................................................................................................2
Learning Objectives.........................................................................................3
Using the Accompanying Laboratory...............................................................3
Reporting Experimental Results......................................................................4
Science Journalism Based on Published Research ........................................8
Writing a Letter of Transmittal ..........................................................................9
Grading Rubric for Reporting Experimental Results .....................................10
Grading Rubric for Science Journalism Based on Published Research........11
Grading Rubric for Writing a Letter of Transmittal..........................................11
Suppliers and Ordering Information .................................................................12
About This Resource
I.A. Introduction
The relationship between genes and proteins: Transcription and translation is an
instructional unit designed to supplement courses that introduce students to the
basic molecular biology of transcription and translation. The accompanying laboratory, Effects of antibiotics on bacterial growth and protein synthesis, reinforces
concepts presented in class and may be used as a jumping point to studentdesigned, inquiry-based investigation. The modular nature of this instructional
unit allows instructors to adapt individual components for their existing courses.
Writing assignments are included in this instructor’s guide for courses that must
meet “writing across the curriculum” or “write to learn” requirements.
Pages of this instructor’s guide, such as “Reporting Experimental Results” or the
descriptions of writing assignments, can be printed and distributed directly to
students. Grading rubrics are provided as guidelines for instructors.
This teaching resource is
made available to educators free of charge by
Promega Corporation.
Copyright 2008 Promega
Corporation. All rights
reserved.
Reproduction for noncommericial educational
purposes only.
Editor:
Michele Arduengo, PhD
Laboratory:
Terri Sundquist, MS
Michele Arduengo, PhD
Animations:
Sara Klink, MS
Web:
Tim Rickey, PhD
Chris Murvine
www.promega.com
! Note: This instructor’s manual is available
online only.
Instructors in the United States who are using Promega products for teaching laboratories may be eligible to participate in the Promega Training Support Program.
Visit the web site at: www.promega.com/us/trainingsupport/default.htm for discounts on products used in teaching activities.
If you have feedback, including suggestions for other topics you would like to see
covered, please contact Michele Arduengo ([email protected]).
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
Printed in USA.
8/07
IG001
Page 2
I.B. Learning Objectives
Depending upon which parts of this instructional unit are used, students will:
1.
become familiar with the basic events of transcription and translation (lecture, animations, laboratory, writing assignments)
2.
be able to identify major differences of transcription and translation in
prokaryotic and eukaryotic organisms (lecture, writing assignments)
3.
appreciate the historical development of scientists’ understanding of transcription, translation and the genetic code (lecture, writing assignments)
4.
gain familiarity with seminal primary literature in the field of transcription and
translation (lecture, writing assignments)
5.
understand that chemical reactions can be catalyzed by molecules other
than proteins (i.e., ribozymes) (lecture)
6.
be able to report experimental data in a standard scientific format (laboratory, writing assignments)
7.
improve science writing skills (writing assignments)
8.
demonstrate subject mastery (writing assignments)
9.
explore theoretical knowledge using the linked laboratory exercise (laboratory, writing assignments)
10. relate results from in vitro and in vivo experiments (laboratory)
11. formulate original questions based on experimental data (laboratory, writing
assignments)
I.C. Using the Accompanying Laboratory
The laboratory protocol that accompanies this instructional unit has two parts:
an in vitro experiment to explore the effect of various antibiotics on translation
and an “in vivo” experiment that will allow students to make connections
between what happens on the molecular level (in the test tube) and what happens to the whole organism (bacteria grown on plates). Students will add various
antibiotics to E. coli S30 extract to determine their effect on transcription and
translation using the production of active luciferase as a reporter for the system.
Production of luciferase can be monitored by luminescence or a colorimetric
assay, depending on available laboratory equipment and supplies. Both the luminescent and the alternative colorimetric protocols are provided in the laboratory
instructor’s manual.
This unit provides an instructor’s manual for the laboratory as well as a separate
student’s manual. Both manuals are available as PDF files and can be downloaded and printed for educational use. We have included postlab “thought”
questions to foster student inquiry or to serve as prompts for student-designed,
inquiry-based laboratory exercises.
II.
Writing Assignments and Grading Rubrics
Three writing assignments are included in this instructor’s guide. These assignments are written for students and can be distributed directly to students without
modification. We have also included grading rubrics for the convenience of the
instructors.
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
IG001
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Printed in USA.
Revised 2/08
II.A. Reporting Experimental Results
Your laboratory report should include the following components:
Title. Your title should be specific so that a reader can know at a glance what the
report is about. Specificity does not necessarily equate with length.
Abstract. Abstracts are short (50 to 100 words) summaries of the work. They
often include one sentence to provide context. They state what was tested and
why, the system used, and they briefly describe the results. They are written as one
paragraph, except in some medical literature where structured abstracts are
used.
Introduction. A short section that clearly states your question or hypothesis.
This section will answer the question “who cares?” by providing context and
background that show why your study is important.
Materials and Methods. This section should be written so that someone can
duplicate your experiment. It should be brief but informative. Any special steps
taken should be explained, but standard details (e.g., how to use a pipettor)
should be omitted. Quite often this section is written using the passive voice,
because who did the work is not as important as what was done.
Results. This part of your report presents the experimental data obtained; it
does NOT interpret that data. Quite often this section will use tables and graphs.
Make sure that any tables you construct for your data are easily understandable.
Label columns and rows. Generally put the known information (context) to the
left and the new information to the right.
For example, the sample table below summarizes data from experiments to
purify DNA from a variety of organisms. The organisms used are “known” and
presented first (on the left); what is new is how much DNA was obtained, and it
is presented to the right.
Table 1. Quantity of DNA Purified from Various Sample Types Using the
Automated Purification Method.
Organism (Tissue)
Starting Material
DNA Yield (µg)
D. melanogaster (whole fly)
Artemia fransciscana (whole
shrimp)
5 flies
1.52
1 shrimp, 3–4 mm
1.72
C. elegans (whole worm)
50,000 worms
0.08
Graphs are used to illustrate trends in the data that are not immediately obvious
when you put your data in a table format. Do not include graphs in your laboratory report merely for the sake of including a graph. Make sure that the graph,
tells an important story or shows a trend that you cannot call to your readers’
attention by any other medium.
When plotting data to create graphs, make sure that you are representing your
data correctly. For instance, do not plot categorical data as a continuous line.
Consider the example below where categories (drug treatment) are plotted as
points connected by lines:
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
Printed in USA.
Revised 2/08
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Page 4
A.
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B.
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40
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20
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0
25 mg Demerol,
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Hydroxyzine
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25 mg Morphine
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10 mg Morphine,
0.8 mg Atropine
Drug Treatment Given
You could argue, of course, that the data presented above do not show any particular trend and might best be presented in a table.
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
IG001
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8/07
II.A. Reporting Experimental Results (continued)
When writing the text portion of your results section, draw your reader’s attention
to the key patterns or trends in the data, but do not recreate your graphs in
words. When you write your results section, make sure that you know what you
want your reader to notice in your data.
Avoid the temptation to sum things up by saying the experiment “worked” or
“didn’t work”. The data may not be what you expected, but if the experiment was
performed correctly with all of the appropriate controls, you have results that
should be presented.
Discussion. Here is where you will interpret your results against the backdrop
of the original hypothesis or question you set out to investigate. Your discussion
can be built around the following questions:
1.
What were the predictions of your original hypothesis (or expectations in a
descriptive study)?
2.
How did the results you obtained compare to your original predictions or
expectations?
3.
How might you explain any unexpected results? Be sure to include information about how your positive and negative controls performed.
4.
Can you suggest ways to test your explanations?
5.
Do your results raise any questions for future study?
Literature Cited. This section lists all of the papers or communication that you
are using to support your statements in the introduction and discussion sections.
There are some standards for using references in scientific writing:
1.
Do not use footnotes within the text. You can cite sources using a numerical
method, where each source is assigned a number based on the first place
in the paper where the source is used. Or, you can use the “author, date”
format within the text and alphabetize your list of references at the end of
the paper. Your instructor will tell you which style to use.
2.
You can cite information from a lecture, presentation or conversation as
“personal communication”. You should have permission of the person you
are citing before you do so.
3.
Make sure that you have read the ENTIRE paper if you cite it. Do not read
the abstract from a PubMed search and then cite the paper without reading
the actual paper.
4.
If you are citing an online source, do your homework. Who is the author or
sponsor of the web site? Do they have the credentials necessary to be an
authoritative voice on the subject? When was the information last updated?
5.
Although Wikipedia is an excellent starting point for most research, it should
not be a primary source for your work.
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
Printed in USA.
Revised 2/08
IG001
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II.A. Reporting Experimental Results (continued)
Style. Good science writing, like any good writing, must communicate an idea to
the reader clearly, which means that the writer needs to use good grammar, use
language correctly and proofread the work. Good science writing is judged by
the readers’ responses to the writing. Can the reader easily find needed information? Can the reader recall the message of the text? Can the reader make a
decision or take an appropriate action after reading the text?
There are many excellent resources for writers. One of the best is the writing
center at your college or university. Most writers also have one or two key style
guides on hand for reference as they write.
Below are some style guides that are useful for writers in the life science and
medical fields. Your instructor may assign a specific style for you to follow. If not,
use one of the style guides below to guide you with your writing.
Science Writing
Council of Science Editors, Style Manual Committee. 2006. Scientific style and
format: The CSE manual for authors , editors , and publishers. 7th ed. Reston (VA):
The Council.
Dodd, J.S., ed. 1997. The ACS style guide. 2nd ed. Washington (DC): American
Chemical Society.
Iverson, C. et al. 2007. AMA manual of style: A guide for authors and editors.
10th ed. New York (NY): Oxford University Press.
General Writing Style
Sabin, W.A. 2004. The Gregg Reference Manual. 10th ed. New York (NY):
McGraw-Hill Irwin.
Sabin, W.A. 2008. The Gregg Reference Manual, online. 10th ed. New York (NY):
McGraw-Hill Irwin. http://highered.mcgraw-hill.com/sites/0073545430/information_center_view0/ (accessed 7/27/2007)
Strunk, W. and White, E.B. 1979. The Elements of Style. 4th ed. Boston (MA):
Allyn and Bacon.
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
IG001
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Printed in USA.
Revised 2/08
II.B. Science Journalism Based on Published Research
Explaining science to the nonscientist is one of the most difficult tasks that a
scientist may undertake and perhaps one of the most important. Decisions about
which projects to fund are often made by board members or administrators who
do not have a scientific background; legislation covering the conduct of research
is drafted by lawmakers who most often are not scientists. Science and technology affect everyone in society from the patient in the hospital to the road construction crew marking gas pipes and electrical cables.
To explain science to the nonscientist, a person must have a thorough grasp of
the scientific concepts involved and be able to simplify them without omitting so
much detail or nuance that the story becomes inaccurate.
Assignment
Table 1 lists some “historical” peer-reviewed papers related to the general topics
of transcription and translation. Choose one of these papers and write a 400word newspaper article describing the findings and their relevance for the nonscientist.
Most often journalistic pieces are written in an “inverted pyramid” style with the
main message coming at the beginning. The remainder of the article expands on
the summary at the beginning. Since you are writing for a nonscientist, you will
explain to the reader what was done and why, and importantly, why the results
are interesting and relevant to your reader.
Table 1. Historical Papers in the Field of Transcription and Translation Research.
Ingram, V.M. 1957. Gene mutations in human hemoglobin: The chemical difference between
normal and sickle cell hemoglobin. Nature. 180, 326–328.
Crick, F.H.C. et al. 1961. General nature of the genetic code for proteins. Nature. 192,
1227–1232.
Murayama, M. 1967. Structure of sickle cell hemoglobin and molecular mechanism of sickling
phenomenon. Clinical Chemistry. 14, 578–588.
Beadle, G.W. and Tatum, E.L. 1941. Genetic control of biochemical reactions in Neurospora.
Proc. Natl. Acad. Sci. USA 27, 499–506.
Maling, B.D. and Yanofsky, C. 1961. The properties of altered proteins from mutants bearing
one or two lesions in the same gene. Proc. Natl. Acad. Sci. USA 47, 551–566.
Sarabhai, A.S. et al. 1964. Colinearity of the gene with the polypeptide chain. Nature 201,
13–17.
Dintzis, H.M. 1961. Assembly of the peptide chains of hemoglobin. Proc. Natl. Acad. Sci. USA.
47, 247–261.
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
Printed in USA.
Revised 2/08
IG001
Page 8
II.C. Writing a Letter of Transmittal
Letters of transmittal are used in professional settings to introduce experimental
reports. These letters are important documents for record keeping. A well written
letter of transmittal will provide an “executive summary” of the work undertaken
and the major results achieved. Well written letters may even be used as the primary source of information for a corporate board of nonscientists who must
make funding or investment decisions about the research. A letter of transmittal
should not exceed one page in length. In addition to containing information
about the research conducted, it may also contain information regarding contractual arrangements agreed upon for funding or timelines, or the letter may
even solicit additional research funding. Letters of transmittal are formal business letters; as such, the letter should be printed on formal letterhead, include
dates, names and positions of correspondents, etc.
Assignment
Your research group has been contracted by a major pharmaceutical company
to determine the mechanism of action of a number of antibiotic compounds that
they have synthesized in their basic research laboratories. Write a letter of transmittal from your research group to B. Lactam, MD, Director of Lead-Compound
Testing at AntiBac, Inc. The letter should describe the experiments you performed to determine the mechanism of action of the antibiotics you tested in the
laboratory.
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IG001
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Printed in USA.
Revised 2/08
II.D. Grading Rubric for Reporting Experimental Results
•Introduction has adequate background information and clearly states the
Introduction (10)
-"Who Cares" statement: why the study was done (relevance)
-Brief summary of relevant background facts
-Background clearly leads to the problem or question being addressed
-Clearly stated hypothesis with predictions
question being investigated or the hypothesis being tested. 10 points
•Hypothesis or question being investigated is clearly articulated and relevance described, but background information is incomplete. 7–9 points
•Introduction provides adequate background but hypothesis/question not
clearly articulated. 0–7 points
•Introduction is absent or plagiarized. 0 points
Materials and Methods (20)
•Equipment and Supplies list complete; procedure could be replicated
someone else as described; report of actual experimental methods accurate. 20 points.
-Equipment and supplies required
•Equipment and supplies list incomplete; procedure could be replicated
-What the scientists (students) ACTUALLY did
-Detailed enough that someone else with the same knowledge and experi- as described; description of actual experimental methods accurate. 18–19
points.
ence could repeat the experiment exactly
•Equipment and supplies list absent; procedure could be replicated as
described; description of actual experimental methods accurate. 16–18
points
•Equipment and supplies list complete; but procedure is missing key
information for replication or report of methods not accurate. 10–16 points
•Procedure is minimally described or absent; equipment and supplies list
is provided. 1–10 points
•Materials and Methods section is absent or copied verbatim from
existing protocol. 0 points
Results (10)
-Presents major findings of the study
-Presents data and summarizes observations using graphs and tables
-Any trends noticed are clearly indicated
-Data should not be interpreted in this section
•Data presented clearly and with appropriate graph, table or illustration;
trends identified. 10 points
•Data presented in an unclear fashion; format for data may not be the
best. 1–9 points
•Results section missing or plagiarized. 0 points
Discussion (10)
•Results are clearly tied back to original hypothesis. New
questions/hypotheses presented and future work is presented. 10 points.
•Missing either linkage to original hypothesis/question or new ques-How do the results relate to the hypothesis or goals of the study?
-What new questions does the study raise? or What new hypotheses might tions/future work not presented. 5–9 points.
•Results not tied back to original hypothesis or question investigated.
now be formulated? What are the future directions for the work?
•Future questions /directions not discussed. 1–5 points.
•Discussion section missing or plagiarized. 0 points
Literature Cited (5)
-Full citations for any references cited in the report using the Scientific
Style and Format or other assigned style manual.
Abstract (5)
-Summarizes the problem addressed; the approach and major findings
and conclusions. This will be at the beginning of the report but is often
written last. No more than 120 words.
Writing Quality (20)
-Grammar, spelling and punctuation are correct.
-Writing is clear and reader-centered.
Scientific Accuracy (20)
-Scientific concepts are presented clearly and explained accurately.
•Required style format followed; references are accurate and correctly
cited in text. 5 points.
•Either format not followed or references were not accurately cited. 1–4
points.
•Literature cited section is absent. 0 points
•All parts present. Length limitation met. 5 points.
•Missing one or more elements or too long. 1–5 points.
•Abstract is missing. 0 points.
•Clear, reader-centered writing; all jargon is defined; language is precise;
grammar, spelling and punctuation are stellar. 20 points.
•Clear, reader-centered writing; jargon is defined; precise language; some
minor grammar, spelling or punctuation errors. 16–20 points.
•Writing is sometimes muddled; imprecise language; minor grammar,
spelling or punctuation errors. 12–16 points
•Major grammatical errors; muddled writing; imprecise language. 0–10
points
•Jargon clearly defined and defined correctly; background correctly
describes previous work; no scientific gaffes or inaccuracies. 20 points
•Some problems with interpreting primary literature cited in report;
science mostly correct and accurate. 13–19 points
•Inaccuracies in interpreting previous work; scientific concepts
inaccurate; materials and methods inaccurate. 0–13 points.
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
Printed in USA.
Revised 2/08
IG001
Page 10
II.E. Grading Rubric for Science Journalism Based on Published Research
Content (30)
•Clearly states the take-home message, explains the science to the nonscientist, clearly indicates the relevance of the research to the reader. (30
points)
The news story opens with a lead that clearly states the take-home message of the research. The news story clearly explains the study conducted •Missing a lead, fails to explain the science, fails to show relevance or
generate interest. (0–29 points)
and the science behind it in a concise manner. The piece shoud give a
nonscientist a rudimentary understanding of the research and, importantly,
its relevance to his or her life.
Writing Quality (35)
-Grammar, spelling and punctuation are correct.
-Writing is clear and reader-centered.
Scientific Accuracy (35)
-Scientific concepts are presented clearly and explained accurately.
•Clear, reader-centered writing; all jargon is defined; language is precise;
grammar, spelling and punctuation are stellar. (35 points)
•Clear, reader-centered writing; jargon is defined; precise language; some
minor grammar, spelling or punctuation errors. (25–34 points)
•Writing is sometimes muddled; imprecise language; minor grammar,
spelling or punctuation errors. (1–24 points)
•Major grammatical errors; muddled writing; imprecise language. (0–10
points)
•Jargon clearly defined and defined correctly; science explained
accurately; no scientific gaffes or inaccuracies. (35 points)
•Science mostly correct and accurate. (25–34 points)
•Scientific inaccuracies. (0–24 points)
II.F. Grading Rubric for Writing a Letter of Transmittal
Letter Contents (30)
•Contains an accurate, precise summary of the study and major findings,
and a statement of relevance of the work, professional tone. (30 points)
-The letter clearly explains the study conducted and the science behind it •Missing either summary of the study, the major findings or statement of
in a concise manner. The letter should give a nonscientist executive a rudi- relevance for the work. (0–29 points)
mentary understanding of the research and its relevance.
Writing Quality (35)
-Grammar, spelling and punctuation are correct.
-Writing is clear and reader-centered.
Scientific Accuracy (35)
-Scientific concepts are presented clearly and explained accurately.
•Clear, reader-centered writing; all jargon is defined; language is precise;
grammar, spelling and punctuation are stellar. (35 points)
•Clear, reader-centered writing; jargon is defined; precise language; some
minor grammar, spelling or punctuation errors. (25–34 points)
•Writing is sometimes muddled; imprecise language; minor grammar,
spelling or punctuation errors. (1–24 points)
•Major grammatical errors; muddled writing; imprecise language. (0–10
points)
•Jargon clearly defined and defined correctly; science explained
accurately; no scientific gaffes or inaccuracies. (35 points)
•Science mostly correct and accurate. (25–34 points)
•Scientific inaccuracies. (0–24 points)
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
IG001
Page 11
Printed in USA.
Revised 2/08
III. Suppliers and Ordering Information
Product
E. coli S30 Extract System for Circular DNA
Cat.#
L1020
Provides enough control plasmid for 20 student reactions. (Each student group will perform 10 reactions.) Be sure to
request an additional vial of pBESTluc™ DNA to ensure that you have enough DNA template.
Steady-Glo® Luciferase Assay System
E2510
Provides enough reagent for 100 luciferase assays. (Each student group will perform 10 luciferase assays.)
Transcend™ Non-Radioactive Translation Detection System
L5070
For Laboratory Use. For laboratories that do not have access to a luminometer or multimode instrument that can measure luminescence. Also, instructor’s who wish to introduce students to SDS-PAGE can use this system.
Nuclease-Free Water
P1193
For Laboratory Use.
Promega Training Support Program:
Discounts for Educators in the United States
To order Promega products for your teaching laboratory (U.S. only) at a significant educational discount, visit www.promega.com/us/trainingsupport/default.htm
Materials required from vendors other than Promega
Product
Mueller Hinton Agar
Mueller Hinton Broth (dehydrated medium)
Ampicillin antibiotic disks (10 µg)
Chloramphenicol antibiotic disks (30 µg)
Streptomycin antibiotic disks (10 µg)
Tetracycline antibiotic disks (30 µg)
Erythromycin antibiotic disks (15 µg)
Neomycin antibiotic disks (30 µg)
Blank paper disks
Ampicillin sodium salt
Chloramphenicol
Streptomycin sulfate salt
Tetracycline hydrochloride
Erythromycin
Neomycin solution
Cycloheximide ready-made solution
Petri dishes (10 cm)
Vendor
Cat.#
BBL Microbiology
211438
BBL Microbiology
211443
BBL Microbiology
230705
BBL Microbiology
230733
BBL Microbiology
230942
BBL Microbiology
231344
BBL Microbiology
230793
BBL Microbiology
230882
BBL Microbiology
231039
Sigma-Aldrich
A2084
Sigma-Aldrich
C7795
Sigma-Aldrich
S8090
Sigma-Aldrich
T7660
Sigma-Aldrich
E5389
Sigma-Aldrich
N1142
Sigma-Aldrich
C4859
Fisher Scientific 08-757-9B
Products may be covered by pending or issued patents or may have certain limitations. Please visit our Web
site for more information.
Promega Corporation · 2800 Woods Hollow Road · Madison, WI 53711-5399 USA · Toll Free in USA 800-356-9526 · Telephone 608-274-4330 · Fax 608-277-2516 · www.promega.com
Printed in USA.
Revised 2/08
IG001
Page 12