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RESEARCH LITERATURE IN MOLECULAR AND CELL BIOLOGY
MCB 3841W Section 002
Fall 2010
Mary K. Bruno, Ph.D.
Office:
BPB 304 (Biology-Physics Building)
Phone:
486-0360
E-mail:
[email protected]
Office hours: By appointment
Lecture:
MWF 9:00-9:50 AM
TLS 263
TEXT:
Readings for the course will include papers from the primary literature posted as PDF files on
HuskyCT.
Living Downstream, 2nd edition
(written by Sandra Steingraber, Da Capo Press [Perseus Books Group], ISBN 978-0-30681869-1)
Writing Papers in the Biological Sciences—Fourth Edition
(Victoria E. McMillan Bedford/St. Martin’s Publishers, ISBN-13: 978-0-312-44083-1)
PRIMARY COURSE OBJECTIVE:
“Learning to write in a discipline means learning to think, argue, research and communicate with the
community of scholars in a given field.” (excerpted from The Writing Center FAQ)
ADDITIONAL COURSE OBJECTIVES:
• To examine in detail current hypotheses addressing cell transformation and mechanisms of tumor
development. To acquire an appreciation for the intricacy and balance that governs all of life’s processes.
• To critically evaluate environmental factors as they impact on cancer risk.
• To develop skill in analyzing and presenting research literature.
• To foster good communication skills. All disciplines need excellent communicators. Scientists not only
need to communicate the complexities of their field to fellow colleagues, but also to non-scientists, such as
policy makers in government, industry, or in the biomedical field, to patients.
MCB 3841W
Fall 2010
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ASSIGNMENTS:
A minimum of 15 revised and edited pages of writing is a standard requirement for W courses. For MCB
3841W-002, this will consist of:
• ONE 3-page paper in the style of a scientific commentary or editorial
• ONE 5-page mini-review paper on a selective aspect of cancer biology (see list of topics)
• ONE 5-page analysis of either environmental or epigenetic factors on cancer development
• ONE 3-page essay based on Living Downstream
• Two consecutive rounds of revisions for the writing assignment listed above
Format:
•
•
•
•
The type of paper (commentary, review, essay) must be indicated on the first page before the
title
The assignments should use a 10-12 point font and the text should be double spaced with 1
inch side and top/bottom margins
Number pages.
Header: Include your Name, Date that the paper is submitted followed by “Draft”,
“Revision 1”, or “Final Version”.
Other considerations:
• As students in MCB, you are encouraged to read the primary scientific literature. It takes practice to
become proficient or comfortable. Review articles have been provided to get you started. Bring
questions to class if you are having difficulty with the reading.
• Avoid the use of web sites in your citation list. Not all of them are reliable and you would be basing
your paper on filtered, pre-digested information. (see URL info below to get started)
• Do not rely heavily on one source for the basis of your paper. This introduces bias. Learn to
understand arguments. Experimental data from different laboratories do not always agree.
• Use the most current references (2008-2010) then work backwards if needed. This field moves at a
very rapid pace. Older papers may give a perspective on the problem, but the conclusions or
interpretations may have advanced considerably since that time—or may no longer be valid in the
context of recent findings.
Useful sites:
•
•
•
•
**** http://www.ncbi.nlm.nih.gov/
http://www.plos.org
http://www.cancer.gov/
http://www.cancer.org/
PubMed
Public Library of Science
National Cancer Institute
American Cancer Society
EVALUATION:
• Your grade in the course will be composed of several components with the writing assignments
comprising 70% of your grade. Class participation (see below) and the Final exam each will each
represent 15% of your grade.
•
MCB 3841W
Specific criteria will be provided with the assignment, however, general criteria for the evaluation of
your assignments include:
o Concise, focused thesis statement
o Clarity, organized development of ideas or arguments
o Transitions
o Concise summary/conclusion—the bottom-line.
o Grammatical errors, proofreading, incorporation of comments made on your drafts
o Use of resources and appropriate documentation.
Fall 2010
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NOTE: A final submission for each assignment that contains multiple errors will not receive a
passing grade.
Statement from the Writing Center follows:
According to university-wide policies for W courses, you cannot pass this course unless you receive a passing grade for its
writing components.
•
Individual conferences may be scheduled outside of class time to further review and elaborate on
improvement in writing practices. The conferences may be instructor or student-initiated.
•
Preparation and class participation are important components of the course; 15% of your grade will
be based on this component.
o
o
Readings for each topic should be done in advance to allow for class discussion.
Each person will have an opportunity to present a segment of a published research paper
for a journal club format discussion.
Final exam: Rescheduling of the final exam requires the approval of the Office of Student
Services and Advocacy.
Statement from Office of Student Services and Advocacy follows:
Final exam week for Fall 2010 takes place from Monday, December 13th through Saturday, December 18th. Students
are required to be available for their exam during the stated time. If you have a conflict with this time you must visit
the Office of Student Services and Advocacy to discuss the possibility of rescheduling this exam.
Please note that vacations, previously purchased tickets or reservations, graduations, social events, misreading the
exam schedule and over-sleeping are not viable excuses for missing a final exam. If you think that your situation
warrants permission to reschedule, please contact the Office of Student Services and Advocacy with any questions.
Thank you in advance for your cooperation.
Colleges Against Cancer (CAC)
For those of you with an interest in volunteering and writing reflectively about your experience, participation in
UConn’s Chapter of Colleges Against Cancer may be an opportunity for you. More information can be found at
the American Cancer Society’s web site as well as the Student Activities Involvement Office.
DISABILITIES:
Any student with disabilities that he/she would like the faculty to be aware of should communicate that
information in confidence to the faculty and any issues arising will be addressed in accordance with the policy
of the University. For more information, please go to http://www.csd.uconn.edu/
MCB 3841W
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ACADEMIC MISCONDUCT STATEMENT:
“Academic misconduct in any form is in violation of the University of Connecticut Student Conduct Code and
will not be tolerated. This includes, but is not limited to: copying or sharing answers on tests or assignments,
plagiarism, and having someone else do your academic work. Depending on the act, a student could receive
an F grade on the test/assignment, F grade for the course, or could be suspended or expelled.”
Policy On Plagiarism
Plagiarizing is defined as “To steal and pass off (the ideas or words of another) as one's own : use
(another's production) without crediting the source”(www.Merrian-Webster.com, 2005)
Plagiarism violates the Academic Misconduct section of “The Student Code” of the University of
Connecticut (http://web.uconn.edu/mcb201/misconduct.html) and will not be tolerated in MCB courses.
The instructors of MCB 241W will adhere to the guidelines laid out in “The Student Code”; therefore,
students should read and understand these policies and the consequence of violations.
The definition of plagiarism extends to all aspects of evaluated work in this course. Copying another
student's work is plagiarism. Failure to give full and proper citation to other people's work is
plagiarism. Full and proper citation includes putting quotation marks around any quoted passage, including a
correct citation to the publication from where the ideas originated and a complete reference to that publication
in the "literature cited" section. This applies to all forms of communication including websites or personal
communication from someone, such as would occur in verbal discussions of scientific data. Direct quotations
are appropriate when the original statements would lose clarity or intent. However, your assignment should not
include multiple direct quotations. Paraphrasing of other authors' work is acceptable given that the ideas
contained in the paraphrased passage are properly attributed to the author and the ideas are reworded into the student's own original language.
There are many resources available to students:
PLEASE COMPLETE THE PLAGIARISM MODULE IN HUSKYCT.
Should you need additional information the following web sites may be of help:
http://www.lib.uconn.edu/using/tutorials/LILT/plagiarism.htm
http://owl.english.purdue.edu/handouts/print/research/r_plagiar.html
See also pp 29-30 and 124-126 in Victoria McMillan’s book
The penalties for copying another students work are:
1. The first violation will result in a "0" for the entire assignment.
2. The second violation may result in an ‘F’ for the course.
The penalties for failure to cite properly are:
1. The first violation will result in a written warning.
2. The second violation will result in a "0" for that assignment.
3. The third violation will result in a "0" for the assignment and failure in the course.
MCB 3841W
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Part 1:
Why, when, how??? Development of cancer: old vs. current hypotheses
“The chaos of cancer is not a modern affliction but a risk run by all multicellular organisms from ancient to modern.”
Robert A. Weinberg, One Renegade Cell: How Cancer Begins
DATE
LECTURE TOPIC
READING
ASSIGNMENT
# Numbers refer to
reference list
Aug 30
Sept 1
Sept 3
Sept 6
Sept 8
Sept 10
Sept 13
Sept 15
Sept 17
Sept 20
Sept 22
Sept 24
Sept 27
Sept 29
Oct 1
Oct 4
Oct 6
Oct 8
Oct 11
Oct 13
Oct 15
Oct 18
Oct 20
Oct 23
Oct 25
Oct 27
Oct 29
MCB 3841W
Introduction / Historical Overview
Free write / Discussion
Properties of cancer cells / Hallmarks of
Cancer
LABOR DAY
Controversies in cancer research
Writing Workshop
Examples of scientific writing
Characteristics of scientific writing
Review of grading rubric
Hypotheses for cancer development
Cancer stem cell hypothesis
Cell signaling & the tumor
microenvironment
The tumor microenvironment
Role of the EMT (epithelial-mesenchymal
transition)
The cell cycle and its regulation
Oncogenes and tumor suppressor genes
p53 and multi-tasking
Journal club discussion
Epigenetic mechanisms
Milestones 1,2,4
#1
Milestones 9-12,14,17
#2-8
Review / skim
Chapts 1,6, 7 in McMillan
#9
#10.11
#12
Draft of Commentary Due
Draft returned
Chapt 7 in McMillan
#13
Revision 1 Due
#14
Revision returned
#15
Chapt 5 in McMillan
Commentary Final Version
Due; Select topic for minireview & begin research
Telomeres
DNA damage:
Apoptosis vs. Senescence?
Angiogenesis and hypoxia
Hypoxia and bioenergetics
Metabolic requirements of cancer cells
Metabolic requirements of cancer cells
Journal club discussion
Cancer and Inflammation
MicroRNAs
#16
#17
Chapts 6 & 7 in McMillan
#18, 19
#20
#21-23
#24
Metastasis & the role of chemokines
Writing workshop / Peer Review of Minireview Revision 1
#27, 28
Begin Living
Downstream Forward &
Chapts 1-4 (pp. 1-87) for
Discussion on 11/10
Mini-review Draft Due
Draft returned
#25
#26
Mini-review Revision 1
Due
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Part 2:
Cancer—a preventable disease?
Genetic, Environmental and Nutritional Factors
“From the right to know and the duty to inquire flows the obligation to act.” Sandra Steingraber
DATE
LECTURE TOPIC
READING
ASSIGNMENT
Nov 1
The cytochrome P450 system and
genetic polymorphisms
The cytochrome P450 system and
genetic polymorphisms
TBA
Mini-review Revision 1
returned
Mini-review Final Version
Due
Select Topic for Paper 3 &
begin research
Nov 3
Nov 5
Nov 8
Nov 10
Nov 12
Nov 15
Nov 17
Chemical carcinogenesis / Cancer
clusters
Environmental causes of cancer
controversy
Long Island Breast Cancer Study
Discussion—Living Downstream (LD)
Part 1
Epigenetics revisited
Nutritional factors
Discussion—Living Downstream Part 2
Nov 19
Writing Workshop / Peer Review of Paper
3 Draft
Nov 2226
Nov 29
THANKSGIVING BREAK
Living Downstream
Chapts 5-6 (pp.89-141)
for Discussion on 11/17
Paper 3 Draft Due
Essay Questions for LD
Paper 3 Draft returned
Living Downstream
Chapts 7-12, Afterword
(pp.143-290)
For Discussion on 11/29
Discussion—Living Downstream
Parts 3 & 4
Paper 3 Revision 1 Due
Part 3:
Challenges of Therapeutic Measures
“We propose that without a truly robust mechanism for selecting the right treatment for the right patient at the right time---the central
concepts of personalized medicine---we will continue to see only incremental improvements and have little hope for substantial
survival gains.” A.Potti, R.L.Schilsky, and J.R.Nevins (Science Translational Medicine, 2 (28), 1-3, 2010)
DATE
LECTURE TOPIC
READING
Dec 1
Dec 3
Overview of therapeutic approaches
Multi-drug resistance
TBA
Dec 6
Dec 8
Dec 10
Dec 15
tentative
Immunotherapies
Personalized tumor biomarkers
Course summary
FINAL EXAM
8:00-10:00 AM
MCB 3841W
ASSIGNMENT
Essay for LD due
Paper 3 Revision 1
returned
Essay for LD returned
Paper 3 Final Version Due
Revision of Essay Due
Fall 2010
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Reading List Part 1
1. Hanahan, D. and Weinberg, R.A. (2000) The hallmarks of cancer. Cell 100, 57-70.
2. Matloff, E.T. and Brierly, K.L. (2010) The double helix derailed: the story of the BRCA patent. Lancet
376, 314-315.
3. Kesselheim, A.S. and Mello, M. (2010) Gene Patenting—Is the pendulum swinging back? New
England Journal of Medicine 362, 1855-1858.
4. Watson, J.D. NY Times Op-Ed:
http://www.nytimes.com/2009/08/06/opinion/06watson.html?_r=1&sq=Cancer&st=cse&scp=6&pagewanted=print
5. Potti, A., Schilsky, R.L., and Nevins, J.R. (2010) Refocusing the War on Cancer: The critical role of
personalized treatment. Science Translational Medicine 2 (28), 1-3.
6. Ledford, H. (2010) The cancer genome challenge. Nature 464, 972-974.
7. Weinberg, R.A. (2010) Point: Hypotheses first. Nature 464, 678.
8. Golub, T.R. (2010) Counterpoint: Data first. Nature 464, 679.
9. Negrini, S., Gorgoulis, V.G., and Halazonetis, T.D. (2010) Genomic instability—an evolving hallmark of
cancer. Nature 11, 220-228.
10. O’Brien, C.A., Kreso, A., and Jamieson, C.H.M. (2010) Cancer stem cells and self-renewal. Clinical
Cancer Research 16 (12), 3223-3120.
11. Korkaya, H. and Wicha, M.S. (2010) Cancer stem cells: nature versus nurture. Nature Cell Biology
12 (5), 419-421.
12. Li, L. and Neaves, W.B. (2006) Normal stem cells and cancer stem cells: The niche matters. Cancer
Research 66 (9), 4553-4556.
13. Kalluri, R. and Weinberg, R.A. (2009) The basics of epithelial-mesenchymal transition. Journal of
Clinical Investigation 119 (6) 1420-1428.
14. Vousden, K.H. and Prives, C. (2009) Blinded by the Light: The growing complexity of p53. Cell 137,
413-431.
15. Esteller, M. (2008) Epigentics in cancer. N. Engl. J. Med. Vol. 358, 1148-1159.
16. Artandi, S.E. and DePinho, R.A. (2010) Telomeres and telomerase in cancer. Carcinogenesis 31
(1), 9-18.
17. Cotter, T.G. (2009) Apoptosis and cancer: the genesis of a research field. Nature Reviews Cancer
9, 501-507.
18. Zetter, B.R. (2008) The scientific contributions of M. Judah Folkman to cancer research. Nature
Reviews Cancer 8, 647-654.
19. Jain, R.K. (2005) Normalization of tumor vasculature: An emerging concept in antiangiogenic
therapy. Science Vol 307, 58-62.
MCB 3841W
Fall 2010
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20. Denko, N.C. (2008) Hypoxia, HIF-1 and glucose metabolism in the solid tumor. Nature Reviews
Cancer 8, 705-713.
21. Vander Heiden, M.G., Cantley, L.C. and Thompson, C.B. (2009) Understanding the Warburg effect:
The metabolic requirements of cell proliferation. Science Vol 324, 1029-1033.
22. Pollard, P.J. and Ratcliffe, P.J. (2009) Puzzling patterns of predisposition. Science 324, 192-194.
23. Thompson, C.B. (2009) Metabolic enzymes as oncogenes or tumor suppressors. New England
Journal of Medicine 360, 813-815.
24. Olovnikov, I.A., Kravchenko, J.E. and Chumakov, P.M. (2009) Homeostatic functions of p53 tumor
suppressor: Regulation of energy metabolism, and antioxidant defense. Seminars in Cancer Biology
19, 32-41
25. Grivennikov, S.I., Greten, F.R., and Karin, M. (2010) Immunity, inflammation, and cancer. Cell 140,
883-899.
26. Koturbash, I. et al. (2010) Small molecules with big effects: The role of the microRNAome in cancer
and carcinogenesis. Mutation Research doi:10.1016/j.mrgentox.2010.05.006
27. Weinberg, R.A. (2008) Mechanisms of malignant progression. Carcinogenesis 29 (6), 1092-1095.
28. Teicher, B.A. and Fricker, S.P. (2010) CXCL12 (SDF-1)/CXCR4 pathway in cancer. Clinical Cancer
Research, 16 (11), 2927-2931.
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