Bios 532
Laboratory Module in Spectroscopy
http://www.bioc.rice.edu/bios532/bios532.html
Instructor: Susan Cates
Keck 312, X5777 mscates@rice.edu
• NO CLASS - November 8, 20, 22
Teaching Aims
I.
Principles of Spectroscopy (practicum)
II.
Proper Equipment Usage
III. Advanced Data Analysis
IV. Reporting Scientific Results
General Principles for Operating Specs
1.
2.
3.
Turn on instrument before CPU
Warm up lamp
a. Xenon short arc lamp? (CD and fluorometer)
Requires fan or cooling usually
b. Hot light sources burn less erratically after warm-up
Initialize software after machine has been initialized
Watch the screen most software will indicate correct initialization vs. error
4.
Trouble-shooting - try shutting everything down and
reinitializing the apparatus, carefully following
correct procedure.
Lab Reports
I.
Background/Introduction
II.
Materials and Methods
III. Results/Experimental Data
IV. Discussion/Analysis
V.
Conclusion
I. Background/Introduction
written for someone with general scientific background the point - to briefly, yet clearly identify:
“What question does this work address?”
“How does this experiment/apparatus/technique
answer the question?”
a. General background on your molecule of studypertinent details might include source organism,
localization, function.
b.
Review current knowledge of properties you will study.
For example, if you are measuring Hb O2 binding,
discuss cooperativity in Hb.
c.
Discuss why the experimental technique is appropriate for
the problem.
II. Materials and Methods
in general, the purpose of the materials
and methods section of any scientific
paper is REPRODUCIBILITY.
a.
b.
c.
d.
e.
Identify apparatus and technique
You do not have to rewrite the lab protocol for Bios 532 reports just reference the protocol. (In papers for publication,
grant proposals and progress reports, you should write out all
your protocols.)
You do have to mention any deviations from the protocol,;
e.g., spectra were collected according to the course protocol
except the increase in absorbance was monitored at 330 nm
instead of 280 because …
You do not have to mention all buffers, additives, if they are
in the lab protocol, but BE AWARE of your materials you must know your buffers, additives for proper interpretation
of data and for proper troubleshooting.
The exception to item (d) are cases where calculations are required to
determine proper concentration, or an aliquot worksheet has been
handed out with the lab - you do have to include these in the report.
III. Results/Experimental Data
a.
Raw Data
The general rule in the biosciences is NOT to include
the raw data in the write-up. There is usually an
overabundance of raw data, often in a format that is not
meaningful to the reader.
b.
Tabulated/Calculated Data
Data is usually shown in a graph, table or summary form
(mean values, etc.). You must show at least one sample
calculation and there is more chance for partial credit if
you include all your calculation columns in your data table.
(Methods - show formula, or Results - sample calculation.)
c.
Present ALL Data - if the protocol asks you to record data,
put the results in the lab report, even if there is not a specific
question about that data in the lab protocol calculations section.
Proper presentation of data requires some thought.
Examples for Data/Results Section:
Measuring affect of additive on a protein’s UV/VIS spectrum:
Instead of overlaying multiple spectroscopic wavelength scans
Taken after the addition of another aliquot of additive, you might
show a graph of the change in absorbance at one wavelength as
a function of the concentration of the additive.
In this example, it would be crucial to pick
(1) the right wavelength.
(2) the best axes ranges for your graph.
Bad graph
Poor choice of left axis range
Good graph
•Axes labels
•Units
•Proper axis range
•Legend
•Title
•Independent variable usually on bottom axis
Rice Interdisciplinary Web-Based
Teaching Laboratory Materials
http://www.ruf.rice.edu/~bioslabs/tools/tools.html
This web page contains pdf references for
proper reporting procedures for scientific
papers, laboratory reports and notebooks.
IV. Discussion/Analysis
always compare your results with the
current literature.
a.
If you have been given a paper on PMB-binding to Hb
in this course, and then you are asked to perform an
experiment measuring UV/VIS absorbance changes
in Hb as a result of addition of PMB, you definitely
should compare your results to the results in the paper.
b.
Postulate (why?) - be clear on the difference between
a postulation and a statement of fact, but discuss what you
think is happening.
V. Conclusion
Summarize the big picture. This often
involves considering the background,
adding your results/discussion and
coming up with the revised story.
Our results (do not) support the hypothesis that….
Important: proofread, spell check
Considerations while writing Bios 532 lab reports:
I.
II.
Data presentation - graph? table?
Data analysis
a.
appropriate precision (significant figures)
b.
raw data conversion (appropriate units, physically
meaningful values)
c.
appropriate analytical method(s)
d.
interpretation of relevance of results (application)
e.
integration of knowledge
f.
results and conclusions "make sense"? can you
recognize blatant errors?
III. Laboratory procedures
a.
followed protocol
b.
scientific method (controls, biased toward hypothesis in
spite of contrary evidence?)
c.
safety, awareness of environment
d.
troubleshooting, critical thinking
e.
records (log) – reproducible?
IV. Background