PSM Biotechnology Lab I: BIOL 5503
Syllabus and outline
Room 247 Biology Building, Wednesday 4 pm -8 pm
Instructor: Seema Freer, Ph.D.,
sfreer@temple.edu
Developed by Dr. Jackie Tanaka and previously used by her as a research techniques
course for Biology Ph.D. students, this modified course has been made possible by her
generous investment of time and resources.
Learning goals of the lab
The objective of the lab is to introduce students to laboratory skills with the goal of training
them to work in the research laboratory of their interest. Students will begin by learning
basic lab skills and safety protocols and advance to an introduction of emergent techniques in
molecular biology and invertebrate model systems. Skills learnt in this laboratory will
complement the Analytical Biotechnology course BIOL 5501 and will also enable students in
the PSM program to pick potential projects/model systems for completion of their Master's
degree.
This learning objective will also be achieved through team-based learning. The lab will meet one
afternoon a week. Students use AT THE BENCH for general introduction to bio-related experiments and
general protocols. (At the Bench, A Laboratory Navigator Kathy Barker ISBN 978-087969708-2).
Information about schedule and specific week’s protocol will be posted on Blackboard.
Safety and Lab rules: Students will go to this link below and complete all online safety training
(about 8 modules on initial lab safety).
http://www.temple.edu/ehrs/training/training-instructions.asp
TEMPLE EHS Safety - Red Book Recommended but provided in the lab.
A lab notebook and lab coat will be provided for all students. It is recommended that the students
bring safety goggles or eye protection to the labs.
General Instructions and Information for students:
Office Hours: For our students who are working professionals, office hours will be by appointment
according to your availability. For students who are on campus I will also be available in my office
Room 333A, Biology Building, every Tuesday and Thursday morning by appointment. Feel free to
contact me by email sfreer@temple.edu as necessary.
Preparation for lab (pre lab and protocols):
In this lab 5503 a bound (numbered) notebook will be used for the purpose of recording
keeping. The pages should be used sequentially unless otherwise noted. Designate the first two
pages as an Index and enter the name of the Experiment and the date that it was started in that
index.
Every experiment should start with an objective, followed by materials needed and the
method or protocol that will be followed. The last portion of an experimental write up in your
lab notebook is the conclusion of your experiment. Often this conclusion will include a graph,
table or both. During the course of this 5503 you will be using Excel and Table Curve. The
printed data and analysis should be taped into the relevant pages of your notebook and
initialed with “No Writing Under Insert” or NWUI added to each sheet.
This method of reporting data that comes out of your lab notebook, will be used repetitively in
your career as a scientist. This will also become your legal record. And in some cases your only
documentation that you did the work as you claimed to have done it.
For example, one day your research may lead to a discovery of a novel function of a protein
resulting in an assay that can now be patented. For the your attorneys to prove that your
invention is “novel, useful and nonobvious: Process, Machine, Article of manufacture,
Composition of matter, Improvement of any of the above”, they will use evidence of all these
claims from your well maintained notebook showing dates, protocols, data and conclusion.
Pre lab: You will come to every lab having read the content on Blackboard, prepared a
protocol from which you can work and with understanding of the purpose of the lab and
the goals as pertaining to this course and your training as a bench scientist.
In lab: You will work from your protocol and maintain a professional and courteous
environment so that others are not hindered by your behavior.
Post lab: You will write your initial conclusions in your lab notebook. As needed you will
print a graph, table and add (by taping) the data to your lab notebook
Grading and assessment
All labs are graded out of 100 points (1750 total). 50 points come from reading the experiment
and writing a good protocol and experimental design. You will be expected to anticipate the
materials you will need to ask the relevant questions. 50 points will be given for conducting a
successful experiment and analyzing the data. Since the expected results are known in most
cases, you will be assessed for evidence of the significant data, and for critical analysis of it as
reflected in your notebook documentation of it. Also, since the expected data is known, when
an experiment fails you will be asked to repeat it to get the correct results. This may mean we
will go over the 4 hour allotted time. You will record all this in your lab notebook and maintain a
separate binder with printed protocols for all the 14 weeks of lab. The conclusions and
summary of every experiment will be typed and the printed version with be pasted onto your
lab notebook. One of the goals of this laboratory course is that you will use the protocols
generated as guidelines for future research.
The highlighted material below is subject to change based on discussions with you in lab and
suggestions from Dr. Tanaka who has helped develop this course.
Project proposal Due on Nov 20th: You will also design an experimental process that may be
combined with the writing to be submitted in Dr. Jackie Tanaka’s Course 5505. More
information will be provided in class. This may not become your project but will be part of your
assessment at the end of the semester. This will be a typed proposal with protocols (references
that this work is feasible) and will be accompanied by a short presentation the week after
Thanksgiving. The final project will be 20% of your grade (350 points).
Schedule
Week
1
Date
August 28th
2
3
September 4th
September 11th
4
September 18th
5
6
September 25th
October 2nd
7
October 9th
8
October 16th
9
October 23th
10
11
October 30th
November 6th
12
November 13th
Experiment/s
Pipetting, Bradford Protein
assay
Enzyme kinetics, Vmax, Km
Enzyme kinetics, Effect of
inhibitors
Ligand Binding (ANS –
BSA)
External Advisor’s meeting
Induction and gene
regulation using Jacob &
Monod’s 4 lac operon
mutants
Western blot, dot blot of
induction
Immunofluorescence of
genes
Restriction mapping
Molder Center
Environmental lab waste
water and detection of
Triclosan in water ( JUDY
ZHANG)
PCR and RT PCR of
evolutionary and
13
14
15
November 20th
November 27th
December 5th
developmental (evodevo)genes in Zebra fish
and Xenopus
Run Gels from evo-devo lab
No lab Thanksgiving break
Final Lab and presentations