MCB 5255 Course organization 2014 spring
Jan 22
Introduction to the course, expectations, resources for the course
assigned reading for general discussion on 1/29 (come prepared on to
discuss the first pair of assigned papers)
Jan 29
Grantsmanship: Who, What , When, How and Why
extra reading: "Sidestep These Application Missteps: Unfocused
Hypothesis or Specific Aims" Selection/Assignment of Student
presentation topics Group discussion of assigned papers (papers 1-2)
Feb 5
Group discussion of assigned papers (papers 3-4) Discussion of what
a specific aim is designed to express in a grant proposal
Feb 12
Group discussion of assigned papers (papers 5-6) (Sadie leading
discussion)
Feb 19
Joerg Graf presentation: the gut microbiome
Lawrence Silbart presentation: mucosal immunity
Feb 26
Charles Giardina presentation: gut differentiation and remodeling
Group discussion of assigned papers (papers 7,8)
Discussion of what a specific aim is designed to express in a grant
proposal
Mar 5
Group discussion of assigned papers (papers 9,10,11) Specific aims
discussion (come with your hypothesis and grant specific aim thought
out and written down; email of this aim due to Dr Lynes by 5pm of
March 4th
Mar 12
Student presentation #1 : Jaimee Doucette – T helper cells and IBD
Sun.
Sat.
Mar. 16
Mar. 22
Spring recess begins
Spring recess ends
Mar 26
NO CLASS; work on your grant proposal and presentation
April 2
Student presentation #2 : Kristen Dostie : Alteration of chemotaxis in
the gut of IBD patients
April 9
Student presentation #3 : Alexander Lind : Acute phase cytokines
and Inflammatory Bowel Disease
April 16
Student presentation #4: Christina Philips : Opportunistic bacterial
infections during the course of IBD
Student presentation # 5: Jennifer McCluskey : Interaction of gut
micro biota and epithelial cells in IBD
April 23
Student presentation #6: Jianping Li : Role of autophagy in the
pathogenicity of Crohn’s disease
Student presentation # 7: Ziyan (Eureka) Zhao : Endoplasmic
reticulum stress and IBD
April 30
Student presentation #8: Jessie Scott : Asthma and anti-TNF
therapeutics
Student presentation #9: Zuleyha Ozen : Chronic obstructive
pulmonary disease
May 2
May 5-10
last day of spring semester classes
Examination period
Schedule guest lectures
Charlie
Silbart
Joerg
Some student topics:
1. Acute phase cytokines and Inflammatory Bowel Disease
2. Role of anti-oxidants in the progression of IBD
3. Opportunistic bacterial infections during the course of IBD
4. T helper cells and IBD
5. Alteration of chemotaxis in the gut of IBD patients
6. Role of autophagy in the pathogenicity of Crohn’s disease
7. Interaction of gut micro biota and epithelial cells in IBD
8. Endoplasmic reticulum stress and IBD
9. Asthma and anti-TNF therapeutics
10. Chronic obstructive pulmonary disease
Assigned papers:
1.
2.
Chiarugi, P. and P. Cirri, Redox regulation of protein tyrosine phosphatases
during receptor tyrosine kinase signal transduction. Trends Biochem Sci, 2003.
28(9): p. 509-14.
Daynes, R.A., E.Y. Enioutina, and D.C. Jones, Role of redox imbalance in the
molecular mechanisms responsible for immunosenescence. Antioxid Redox
Signal, 2003. 5(5): p. 537-48.
3.
4.
5.
6.
7.
8.
9.
10.
11.
Smith, P.M., et al., The microbial metabolites, short-chain fatty acids, regulate
colonic Treg cell homeostasis. Science. 341(6145): p. 569-73.
Javed, S., et al., Helicobacter bilis gamma-glutamyltranspeptidase enhances
inflammatory stress response via oxidative stress in colon epithelial cells. PLoS
One. 8(8): p. e73160.
Planell, N., et al., Transcriptional analysis of the intestinal mucosa of patients
with ulcerative colitis in remission reveals lasting epithelial cell alterations. Gut.
62(7): p. 967-76.
Roman, J., et al., Evaluation of responsive gene expression as a sensitive and
specific biomarker in patients with ulcerative colitis. Inflamm Bowel Dis.
19(2): p. 221-9.
Guidi, L., et al., FOXP3(+) T regulatory cell modifications in inflammatory
bowel disease patients treated with anti-TNFalpha agents. Biomed Res Int.
2013: p. 286368.
Nancey, S., et al., Blockade of LTB(4) /BLT(1) pathway improves CD8(+) T-cellmediated colitis. Inflamm Bowel Dis. 17(1): p. 279-88.
Boschetti, G., et al., Therapy with anti-TNFalpha antibody enhances number
and function of Foxp3(+) regulatory T cells in inflammatory bowel diseases.
Inflamm Bowel Dis. 17(1): p. 160-70.
Morgan, A.R., A.G. Fraser, and L.R. Ferguson, Metallothionein genes: no
association with Crohn's disease in a New Zealand population. J Negat Results
Biomed. 11: p. 8.
Brant, S.R. and Y.Y. Shugart, Inflammatory bowel disease gene hunting by
linkage analysis: rationale, methodology, and present status of the field.
Inflamm Bowel Dis, 2004. 10(3): p. 300-11.
POTENTIAL PAPERS FOR MCB 5255
IBD review
1. http://gut.bmj.com/content/62/11/1653.full.pdf+html
2. http://europepmc.org/articles/PMC3347037
TNF therapies
1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726555/pdf/nihms45885
5.pdf
2. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766994/
3. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774925/
4. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3674701/
Microbes and inflammation
1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807819/
2. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256734/
3. http://www.ncbi.nlm.nih.gov/pubmed/24009737
Genetics
1. http://gut.bmj.com/content/62/7/967.full.pdf+html
2. http://www.sciencedirect.com/science/article/pii/S0009898113000697
3. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616873/
4. http://www.ncbi.nlm.nih.gov/pubmed/21900546
Biochemistry of inflammation (ROS)
1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868631/
2. http://journals.cambridge.org/download.php?file=%2FBJN%2FS000711451
3002663a.pdf&code=618de12bcbde9f98d990e75cf703ee45
3. http://ebm.sagepub.com/content/237/5/474.full.pdf+html
4. http://www.biochemsoctrans.org/bst/039/1102/0391102.pdf
MT genes and IBD
1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280932/pdf/1477-575111-8.pdf