Introduction
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| This laboratory is an introduction to molecular biological techniques for those
with previous experience in organic chemistry and biology.
The first portion of the laboratory exercises develop basic techniques in
fluid measurements, sterile techniques, and laboratory equipment use and care
and safety. Basic molecular biological protocols are introduced and
wet lab skills practiced. Internet navigation and use of bioinformatic
tools are also practiced as a group in the college computer facility.
The sessions are :
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A general overview of the sequence of experiments
for the entire course is also shown at Flow
Chart. |
Reports for these laboratories should only include carefully presented results. The
instructor will often help students prepare the results in class.
The next exercises are goal oriented experiments that require several sessions
and a progression of success. Previously used basic techniques are re-enforced and new
techniques are learned. Careful notebook keeping is necessary. Formal
laboratory reports are required and will be graded. The following exercises will be
grouped together in to four reports:
Report 1:
Report 2:
Report 3:
Report 4:
An overview of the sequence of experiments is at Flow Chart.
Again, These are the labs that will be graded (print
a summary)
| Southern Analysis of Genomic and Plasmid DNA |
Includes four sessions: 1. Plasmid extraction,
2. gel electrophoresis, 3. Southern blotting, 4. DNA probe hybridization and detection |
| Lambdology |
Includes two sessions: Plating lambda plaques
for titer and extraction of lambda DNA from a plate lysate |
| Western Analysis |
Includes two sessions: 1. Extraction of
protein from maize kernels and Western blotting and 2. Antibody detection of a maize
protein |
| Polymerase Chain Reaction |
One session |
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Lab reports should contain the following sections:
Introduction – explains the importance of the exercise, the value of the
content, and its place in the general field of molecular biology, that is, the
introduction should offer perspective on the details to follow.
- Methods
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- a copy of the protocol(s)
- recipes of reagents i.e., (what is 2x SDS loading?, this is an exercise in searching
CURRENT PROTOCOLS on CD, in the library)
- step by step rationale of the protocol in parallel to the protocol
- Results
– photographs of gels, titers, blots, graphs, tables of values, etc.
Should contain no discussion or commentary
- Discussion
– discuss the interpretation of results, problems with protocols or
results, deviations from protocols, the value of results in reference to the perspective
of the Introduction in parallel to the Results.
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Particulars per session:
Your results need include (print a summary):
| Plasmid extraction |
Gel photograph, molecular weight standard
curve, and size of unknown plasmid bands, restriction map of plasmid and insert (supplied) |
| Southern transfer |
none |
| DNA probe hybridization |
Photocopy of probed blot, size of detected
band(s), size standards, standard curve |
| Lambda plating |
Titers from four plates |
| Lambda DNA extraction |
Gel photograph or photocopy, size standards,
standard curve |
| SDS PAGE electrophoresis (maize proteins) |
Photocopy of gel, size standards, standard
curve |
| Western detection |
Photocopy of blot, size standards, standard
curve of markers, size of antigen |
| Polymerase chain reaction |
Gel photograph or photocopy,
standard curve of markers, size of PCR products, data matrix of scored RAPDs, genetic
distance analysis, cladogram |
A grading form will be used for each of these four reports. Grading criteria are
defined below.
Grading criteria: 10pts for each of two sections (Introduction and Results) and 20pts@
for Methods and Discussion for 60pts total for each of 4 graded labs. All typographical
errors, missing labels, missing graph titles, spelling, word usage are circled in red and
subject to ½ pt. deductions as minor errors. Other points are awarded as outlined below
(print grading form).
| Introduction 10pts:
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- Detail: 2pts
- Perspective: 5 pts
- Plagiarism: no maybe
- Accuracy of information. 2pts
- Appropriateness: 1 pt.
- missing:____________________
Other: _____________________________ |
| Method 20 pts:
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- Copy of protocol. 1 pt
- Recipes or CponCD search: 4 pts
- Step by step rationale of protocol. 15pts
- missing:____________________
Other: _____________________________ |
| Results 10 pts: |
- Presentation –Titer, graph or table or labeled photo, standard
curve, data matrix, cladogram, calculations, etc: 5 pts
- Quality of results : 2 pts
- Completeness: 3 pts
- missing:____________________
Other: _____________________________ |
| Discussion 20 pts:
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- Detail: 2 pts
- Perspective (congruent with Intro): 2 pts
- Interpretive Accuracy: 2 pts
- Appropriateness: 2 pts
- Congruence with Results: 2 pts
- Demonstrates understanding of exercise: 5pts
- Completeness: 5pts
Missing: ____________________________
Other: _____________________________ |
| Minor errors ½ pt each: |
See content and circled errors in report text. |
| Comments: |
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Definitions:
Detail: Is the content vague, lacking detail, pleonastic? Is the exposition
substantive or just placatory fluff.
Accuracy: Is what’s written veritable? Are there statements that are befuddled,
spurious or demonstrate a lack of acumen?
Perspective: Does the student demonstrate an understanding of this specific content in
relation to the field of molecular biology? Does the student know the place or importance
of this technique or the value of what was learned.
Appropriateness: Are there statements that are superfluous, gratuitous, or pretentious
verbosity? Are unrelated subjects explored ex situ.
Plagiarism: Does it look like this content was filched verbatim from a textbook. Is
this the author’s own words? Are there appropriate citations for paraphrases?
Presentation: Is the data presented in a logical and clear fashion. Is the data neat
and explicit. Is the data free from misplaced interpretation.
Recipes or CponCD search: supply components of all solutions and/or alternative
protocols from Current Protocols.
Completeness: Are there items missing? Are there conclusions or insights on which the
student failed to comment
Good Luck!
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