Recommended Readings: Anne Brunet, Ph.D.

Special Seminar Series

Evolution, Ecology & Developmental Biology

Mechanisms of stem cell maintenance during aging

Anne Brunet, Ph.D.

Assistant Professor, Department of Genetics, Stanford School of Medicine 

3:45 pm – Refreshments

4:00 pm – 5:00 pm – Lecture

Wednesday, December 17, 2008

Welch Hall, 2nd Floor

Recommended Readings:

Carter, M. E., and A. Brunet. 2007. FOXO transcription factors. Current Biology. 17(4):R113-R114.

Greer, E. L., and A. Brunet. 2008. Signaling networks in aging. Journal of Cell Science. 121(4):407-412.

Calnan, D. R., and A. Brunet. 2008. The FoxO code. Oncogene. 27(16):2276-2288.

Salih, D. A., and A. Brunet. 2008. FoxO transcription factors in the maintenance of cellular homeostasis during aging. Current Opinion in Cell Biology. 20(2)126-136.

Greer, E. L., P. R. Oskoui, M. R. Banko, J. M. Maniar, M. P. Gygi, S. P. Gygi, and A. Brunet. 2007. The energy sensor AMP-activated protein kinase directly regulates the mammalian FOXO3 transcription factor. Journal of Biological Chemistry. 282(41)30107-30119.

Maiese, K., Z. C. Zhao, and C. S. Yan. 2007. “Sly as a FOXO”: New paths with forkhead signaling in the brain. Current Neurovascular Research. 4(4)295-302.
(Order copy from Markus Library)

Recommended Readings: Thomas Tuschl Ph.D.

Monday Lectures

Small RNA Sequencing Resolves Posttranscriptional

Regulatory Networks

Thomas Tuschl  Ph.D.

Howard Hughes Medical Institute

The Rockefeller University

4 p.m.  (refreshments at 3:45)

Monday, December 15, 2008

Welch Hall Level Two

Related Articles:

Zhao, Yi; Shunmin  He,; et al.    2008.  MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control    Trends in Genetics 24(7): 323-327.


Orom, Ulf Andersson; Finn Cilius Nielsen.    2008.  MicroRNA-10a binds the 5 ‘ UTR of ribosomal protein mRNAs and enhances their translation.   Molecular Cell  30 (4):460-471.


Hudder, Alice; and Raymond F. Novak. 2008.   miRNAs: Effectors of environmental influences on gene expression and disease.   Toxicological Sciences 103(2): 228-240.


Hu Shi-Jun; Yang Zeng-Ming.  2008. Mechanisms on the regulation of miRNAs expression.  Progress in Biochemistry and Biophysics  35(5): 483-487.    Request article from Markus Library


Lee, Ji Young; Soonhag Kim; et al.   2008.    Development of a dual-luciferase reporter system for in vivo visualization of microRNA biogenesis and posttranscriptional regulation.   Journal of Nuclear Medicine 49(2):285-294.  Request article from Markus Library.


Ku, Gregory; and Michael T. McManus.  2008.    Behind the scenes of a small RNA gene-silencing pathway.  Human Gene Therapy  19(1):17-26.   Request article from Markus Library.


Diederichs, Sven; and Daniel A.Haber.  2007.   Dual role for argonautes in MicroRNA processing and Posttranscriptional regulation of MicroRNA expression.  Cell  131(6): 1097-1108.


Zeng Yan; Heidi H. Sankala  et al. 2008.   Phosphorylation of Argonaute 2 at serine-387 facilitates its localization to processing bodies.  Biochemical Journal   413(part 3): 429-436.  


Ronemus, Michael; Matthew W. Vaughn;  et al.   2006.   MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by Argonaute, Dicer, and RNA-dependent RNA polymerase in Arabidopsis.   Plant Cell  18(7): 1559-1574.


 Chen, Po Yu; and Gunter Meister.    2005.   microRNA-guided posttranscriptional gene regulation.  Biological Chemistry  386(12):1205-1218.   Request article from Markus Library. 


Recommended Readings: Jeffrey M. Friedman M.D., Ph.D.

Monday Lectures

Leptin and the Homeostratic Control of

Food Intake and Body Weight

Jeffrey M. Friedman M.D., Ph.D.

Howard Hughes Medical Institute

The Rockefeller University

4 p.m.  (refreshments at 3:45)

Monday, December 8, 2008

Welch Hall Level Two

Recommended Review:

Morrison, Christopher D. and Hans-Rudolf Berthoud.  2007.  Neurobiology of nutrition and obesity. Nutrition Reviews.  65(12):517-534.

Related Articles:

Rodenheffer, Matthew S.; Birsoy, Kivanc; and Jeffrey M. Friedman.  2008.   Identification of white adipocyte progenitor cells in vivo.   Cell. 135(2):240-249.


Birsoy, Kivanc; Chen, Zhu; and Jeffrey M. Friedman.  2008.  Transcriptional regulation of adipogenesis by KLF4.  Cell Metabolism.  7(4):339-347.  


Berthoud, Hans-Rudolf.  2007.  Interactions between the “cognitive” and “metabolic” brain in the control of food intake. Physiology & Behavior.  91(5):486-498.


Ruano, G.; J.W.  Goethe, et al.  2007.  Physiogenomic comparison of weight profiles of olanzapine- and risperidone-treated patients.  Molecular Psychiatry.  12(5):474-482.


Berthoud, Hans-Rudolf.  2006. Homeostatic and non-homeostatic pathways involved in the control of food intake and energy balance.  Obesity.  14(Suppl 5):197-200.    Request article from Markus Library.



Understanding metastasis: Collective Cell Migration Controlled by Wnt and Fgf Signaling

In the November 11, 2008 issue of Developmental Cell, investigators from the University of Utah School of Medicine report the results of their studies in an article entitled Wnt/B-Catenin and Fgf Signaling Control Collective Cell Migration by Restricting Chemokine Receptor Expression.  These studies demonstrate a link between Wnt and Fgf signaling pathways in zebrafish and their impact on collective cell migration. 

The Wnt pathway regulates cell-to-cell communication in embryogenesis and cancer and Fgf influences embryongenesis, healing, and cell proliferation.  Piotrowski and Aman demonstrate for the first time that the interaction between Wnt and Fgf pathways is critical for collective cell migration.  Each pathway can restrict chemokine receptor expression and thereby elucidate how some types of cancer metastisize. 

Extracted from Developmental Cell and ScienceDaily.

Recommended Readings: Shu Man Fu, M.D., Ph.D.

Seminars in Clinical Research

Genetics and Pathogenesis of Systemic Lupus: Lessons learned from a Lupus Prone Mouse Model NZM2328

Shu Man Fu, M.D., Ph.D.

Professor of Medicine and Microbiology, Trolinger Professior of Rheumotology

University of Virginia School of Medicine

12 Noon

Wednesday, November 19, 2008

Room 110b, Nurses’ Residence Building

Recommended Articles:

Waters, S. T., M. McDuffie, H. Bagavant, U. S. Deshmukh, F. Gaskin, C. Jiang, K. S. K. Tung, and S. M. Fu. 2004. Breaking tolerance to double stranded DNA, nucleosome, and other nuclear antigens is not required for the pathogenesis of lupus glomerulonephritis. Journal of Experimental Medicine. 199(2):255-264.

Rhodes, B., and T. J. Vyse. 2008. The genetics of SLE: An update in the light of genome-wide association studies. Rheumatology. 47(11):1603-1611.
(Request copy from Markus Library)

Kono, D. H., and A. N. Theofilopoulos. 2006.Genetics of SLE in mice. Springer Seminars in Immunopathology. 28(2):83-96.
(Request copy from Markus Library)

Singh, R. R. 2005. SLE: Translating lessons from model systems to human disease. Trends in Immunology. 26(11):572-579.

Bagavant, H., and S. M. Fu. 2005. New insights from murine lupus: Disassociation of autoimmunity and end organ damage and the role of T cells. Current Opinion in Rheumatology. 17(5):523-528.
(Request copy from Markus Library)

Bagavant, H., U. S. Deshmukh, F. Gaskin, and S. M. Fu. 2004. Lupus glomerulonephritis revisited 2004: Autoimmunity and end-organ damage. Scandinavian Journal of Immunology. 60(1):52-63.

Deshmukh, U. S., H. Bagavant, and S. M. Fu. 2006. Role of anti-DNA antibodies in the pathogenesis of lupus nephritis. Autoimmunity Reviews. 5(6):414-418.
(Requestion copy from Markus Library)


Molecules “shake” into place

Electric field response of a vibrationally excited molecule in an STM junction

Michiaki Ohara, Yousoo Kim, and Maki Kawai

Phys. Rev. B 78, 201405 (Published November 11, 2008)

The ability to move single molecules around a surface with the tip of a scanning tunneling microscope (STM) has been around for many years. However, conventional techniques, which use direct interactions between the tip and the molecules or large electric fields, often damage the molecule.

In 2002, scientists found a less intrusive technique to control molecules [1]. By first exciting the internal vibrational energy of a molecule with an STM tip, they were able to convert this energy into rotational or translational motion of the molecule along a surface. Writing in Physical Review B, Michiaki Ohara, Yousoo Kim, and Maki Kawai from RIKEN, Saitama, and University of Tokyo, Kashiwa, Japan, demonstrate significantly more precise control over the motion of individual molecules with this technique.

The group places an STM tip off-center of a CH3S molecule on a Cu(111) surface. With a voltage between the tip and the copper surface of about 85 meV or higher, they excite the vibrational degree of freedom corresponding to stretching the C–S bond. The vibrating molecule is like an oscillating electric dipole that the electric field from the STM can push towards or away from the tip, depending on the polarity of the tip voltage. Ohara et al. are able to use electric fields that are an order of magnitude lower than previous methods, essentially eliminating the risk of breaking the STM tips or of molecular disassociation.

This technique is likely to have application in fields such as surface chemistry, where one could potentially manipulate chemical reactions on the single-molecule level. – Ashot Melikyan

Mysterious Microbe May Play Important Role In Ocean Ecology

ScienceDaily (Nov. 15, 2008) — An unusual microorganism discovered in the open ocean may force scientists to rethink their understanding of how carbon and nitrogen cycle through ocean ecosystems. A research team led by Jonathan Zehr, professor of ocean sciences at the University of California, Santa Cruz, characterized the new microbe by analyzing its genetic material, even though researchers have not been able to grow it in the laboratory.  The newly described organism seems to be an atypical member of the cyanobacteria, a group of photosynthetic bacteria formerly known as blue-green algae. Unlike all other known free-living cyanobacteria, this one lacks some of the genes needed to carry out photosynthesis, the process by which plants use light energy to make sugars out of carbon dioxide and water. The mysterious microbe can do something very important, though: It provides natural fertilizer to the oceans by “fixing” nitrogen from the atmosphere into a form useable by other organisms.  The new findings appear in the November 14 issue of the journal Science.

Creative Microbiology: New Enzyme Could Revolutionize Production Of Plastics

ScienceDaily (Nov. 13, 2008) — In future, polymethyl methacrylate (PMMA for short) – better known as acrylic glass – could be made from natural raw materials such as sugars, alcohols or fatty acids. Compared with the previous chemical production process, this biotechnological process is far more environmentally friendly.  A new enzyme  discovered by Dr. Thore Rohwerder und Dr. Roland H. Müller, called 2-hydroxyisobutyryl-CoA mutase, makes it possible to turn a linear C4 carbon structure into a branched one. Compounds of this type are precursors of MMA. Parent compounds may of course include intermediate products from the petrochemical industry.  This enzyme, integrated into metabolically appropriate microorganisms, can also transform sugars and other natural compounds into the products desired.   Dr Thore Rohwerder has been nominated as one of three candidates for the European Evonik research award for his discovery.

An HIV Enzyme “Bullet Train!”

HHMI researchers have found that HIV reverse transcriptase exhibits a stunning display of enzymatic dynamics as it zooms back and forth on the very DNA it is building.  Each of the DNA’s two strands serves as a rail, with reverse transcriptase – an enzyme crucial to HIV’s replication and survival – racing to the end of the rails so it can continue to extend them.  The work also provides new insights into how an important class of anti-HIV drugs, called non-nucleoside reverse transcriptase inhibitors (NNRTIs), block some functions of HIV reverse transcriptase. An editorial accompanying the article suggests that the new insights will inspire ideas for even better anti-HIV drugs.

Research to be published in the November 13, 2008, issue of Science Express or for the full story, go to

Source: HHMI News

On the Catalytic Proficiency of Enzymes….


Richard Wolfenden, Ph.D., Alumni Distinguished Professor Biochemistry and Biophysics and Chemistry at the University of North Carolina at Chapel Hill, with co-author Charles A. Lewis, Ph.D., a postdoctoral scientist in his lab, have recently published new work on the evolutionary process of creating the building blocks of RNA and DNA.  Read the full report in PNAS.