Recommended Readings: Hugo Bellen, Ph.D., D.V.M.

Friday Lecture Series

Mitochondria and Neurodegeneration

Hugo Bellen, Ph.D., D.V.M., investigator, Howard Hughes Medical Institute;

professor, departments of molecular and human

genetics and neuroscience, director, Program in Developmental Biology,

Baylor College of Medicine

March 30, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium


Recommended Readings:


Han, S. M., H. Tsuda, Y. Yang, J. Vibbert, P. Cottee, S. -J Lee, J. Winek, C. Haueter, H. J. Bellen, and M. A. Miller. 2012. “Secreted VAPB/ALS8 Major Sperm Protein Domains Modulate Mitochondrial Localization and Morphology Via Growth Cone Guidance Receptors.” Developmental Cell 22 (2): 348-362

Pesah, Y., T. Pham, H. Burgess, B. Middlebrooks, P. Verstreken, Y. Zhou, M. Harding, H. Bellen, and G. Mardon. 2004. “Drosophila Parkin Mutants have Decreased Mass and Cell Size and Increased Sensitivity to Oxygen Radical Stress.” Development 131 (9): 2183-2194

Romero, E., G. -H Cha, P. Verstreken, C. V. Ly, R. E. Hughes, H. J. Bellen, and J. Botas. 2008. “Suppression of Neurodegeneration and Increased Neurotransmission Caused by Expanded Full-Length Huntingtin Accumulating in the Cytoplasm.” Neuron 57 (1): 27-40

Venken, K. J. T., Y. He, R. A. Hoskins, and H. J. Bellen. 2006. “P[Acman]: A BAC Transgenic Platform for Targeted Insertion of Large DNA Fragments in D. Melanogaster.” Science 314 (5806): 1747-1751

Verstreken, P., C. V. Ly, K. J. T. Venken, T. -W Koh, Y. Zhou, and H. J. Bellen. 2005. “Synaptic Mitochondria are Critical for Mobilization of Reserve Pool Vesicles at Drosophila Neuromuscular Junctions.” Neuron 47 (3): 365-378

NIH News: IOM Report on the Complexities of Translating “Omics” Into Treatment

WASHINGTON — Genomics, proteomics, and other branches of molecular bioscience offer the prospect of greater precision in medical care, but some clinical tests based on “omics” research have proved invalid and highlighted the challenges of dealing with complex data.  To enhance the translation of omics-based discoveries to clinical use, a new report by the Institute of Medicine recommends a detailed process to evaluate whether the data and computational steps underlying such tests are sound and the tests are ready to be used in clinical trials.  The proposed process defines responsibilities and best practices for the investigators, research institutions, funders, regulators, and journals involved in development and dissemination of clinical omics-based technologies.

Recommended Readings: Shai Shaham PH.D. Monday, March 26, 2012

A New C. elegans Cell Death Program: Implications for

Neurodegeneration and Cancer

Shai Shaham, Ph.D.

Laboratory of Developmental Genetics

The Rockefeller University

4:00 p.m. Monday, March 26, 2012    Refreshments  3:45  Abby Lounge

Caspary Auditorium

Recommended readings:

Blum, E.S., Abraham, M.C., Yoshimura, S., Lu, Y., and S. Shaham.  2012.  Control of nonapoptotic developmental cell death in Caeanorhabditis elegans by a polyglutamic-repeat proteinScience.  335(6071):970-973.  DOI: 10.1126/science.1215156

 McCall, K.  2010.  Generic control of necrosis – another type of programmed cell death Current Opinion in Cell Biology.  22(6):882-888.  DOI: 10.1016/

 Yuan, J. and G. Kroemer.  2010.  Alternative cell death mechanisms in development and beyond.  Genes & Development.  24(23):2592-2602.  DOI: 10.1101/gad.1984410

 Vlachos, M. and  N. Tavernarakis.  2010.  Non-apoptotic cell death in Caenorhabditis elegans.  Developmental Dynamics.  239(5, S1):1337-1351.   DOI: 10.1002/dvdy.22230

 Miguel-Aliaga, I. and T. Stefan.  2009.  Programmed cell death in the nervous system – a programmed cell fate?  Current Opinion in Neurobiology.  19(2):127-133   DOI: 10.1016/j.conb.2009.04.002

Blum, E.S., M. Driscoll, and S. Shaham.  2008.  Noncanonical cell death programs in the nematode Caenorhabditis elegans.  Cell Death and Differeentiation.  15(7):1124-1131.  DOI: 10.1038/cdd.2008.56

 Abraham, M. C., L. Yun, and S. Shaham.  2007.  A morphologically conserved nonapoptotic program promotes linker cell death in Caenorhabiditis elegans.   Development Cell.  12(1):73-86.  DOI:  10.1016/j.devcel.2006.11.012


Erez Lieberman-Aiden Ph.D. Wednesday, April 4, 2012

How the Genome Folds

Erez Aiden  Ph.D.

Fellow, Harvard Society of Fellows

Prinicpal Investigator, Laboratory-at-Large

Harvard University

Visiting Faculty, Google

4:00 Wednesday, April 4, 2012  Refreshments Abby Lounge 3:45

Caspary Auditorium 

Recommended Readings

Zhang Y; McCord RP, Ho YJ; et al.  2012.  Spatial organization of the mouse genome and its role in recurrent chromosomal translocationsCell. 148(5):908-921.  DOI: 10.1016/j.cell.2012.02.002

Sung MH and  GL Hager.  2011.  More to Hi-C than meets the eye.  Nature Genetics.  43(11):1047-1048.  DOI: 10.1038/ng.984

Yaffe E and A Tanay.  2011.  Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nature Genetics.  43(11):1059-U40.  DOI: 10.1038/ng.947

Fudenberg G; Getz G; Meyerson M; et al.  2011.  High order chromatic architecture shapes the landscape of chromosomal alterations in cancer.   Nature Biotechnology. 29(12):1109-U75.  DOI: 10.1038/nbt.2049

Lieberman-Aiden E; van Berkum NL; Williams L; et al.  2009.  Comprehenesive mapping of long-range interactions reveals folding principles of the human genomeScience.  326(5950):289-293.  DOI: 10.1126/science.1181369

Guelen L; Pagie L; Brasset E; et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.   Nature.  453(7197):948-U83.  DOI: 10.1038/nature06947

Rada-Iglesias A; Ameur A; Kapronov P; et al.  2008.  Whole-genome maps opf USA and USF2 binding and histone H3 acetylation reveal new aspects of prmotoer structure and candidate genes for common human disorders.  Genome Research.  18(3):380-392.  DOI: 10.1101/gr.6880908

Xiao G; Wang X; and Ab Khodursky.  2011.  Modeling three-dimensional chromosome structures using gene expression data. Journal of the American Statistical Association.  106(493):61-72.  DOI: 10.1198/jasa.2010/ap09504   Please request copy from Markus Library.

Recommended Readings: Titia de Lange, Ph.D.

Friday Lecture Series

Cancer Biology Lecture

How Telomeres Solved the End-protection Problem

Titia de Lange, Ph.D., Leon Hess Professor and head,

Laboratory of Cell Biology and Genetics,

The Rockefeller University

March 23, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium


Recommended Readings:

Davoli, T., E. L. Denchi, and T. de Lange. 2010. “Persistent Telomere Damage Induces Bypass of Mitosis and Tetraploidy.” Cell 141 (1): 81-93

Davoli, T. and T. De Lange. 2011. The Causes and Consequences of Polyploidy in Normal Development and Cancer. Annual Review of Cell and Developmental Biology. Vol. 27: 585-610

De Lange, T. 2009. “How Telomeres Solve the End-Protection Problem.” Science 326 (5955): 948-952

Gong, Y. and T. de Lange. 2010. “A Shld1-Controlled POT1a Provides Support for Repression of ATR Signaling at Telomeres through RPA Exclusion.” Molecular Cell 40 (3): 377-387

Kabir, S., A. Sfeir, and T. De Lange. 2010. “Taking Apart Rap1: An Adaptor Protein with Telomeric and Non-Telomeric Functions.” Cell Cycle 9 (20): 4061-4067

Palm, W. and T. De Lange. 2008. How Shelterin Protects Mammalian Telomeres. Annual Review of Genetics. Vol. 42.

Sfeir, A., S. Kabir, M. Van Overbeek, G. B. Celli, and T. De Lange. 2010. “Loss of Rap1 Induces Telomere Recombination in the Absence of NHEJ Or a DNA Damage Signal.” Science 327 (5973): 1657-1661

Sfeir, A., S. T. Kosiyatrakul, D. Hockemeyer, S. L. MacRae, J. Karlseder, C. L. Schildkraut, and T. de Lange. 2009. “Mammalian Telomeres Resemble Fragile Sites and Require TRF1 for Efficient Replication.” Cell 138 (1): 90-103

Scherthan, H., A. Sfeir, and T. De Lange. 2011. “Rap1-Independent Telomere Attachment and Bouquet Formation in Mammalian Meiosis.” Chromosoma 120 (2): 151-157

Recommended Readings: Eva-Maria Schötz Ph.D. Monday, March 19, 2012

Collective Behaviors in Embryogenesis, Regeneration, and Asexual Reproduction

Eva-Maria Schötz, PH.D.

Lewis-Sigler Fellow

Lewis Sigler Institute for Integrative Genomics

Princeton University

Monday, March 19, 2012, Caspary Auditorium

4:00p.m.-5:00 p.m. (Refreshments, 3:45 p.m., Abby Lounge)

Recommended Readings

Manning ML; Foty RA; Steinberg MS; et al.  2011.  Reply to Krens et al: Cell stretching may initiate cell differentiation. PNAS.  108(3):E11.  DOI: 10.1073/pnas.1011542108

Krens SFG; Moellmert S; Heisenberg CP.  2011. Enveloping cell-layer differentiation at the surface of zebrafish germ-layer tissue explants.  PNAS. 108(3):E9-E10.  DOI: 1073/pnas.1010767108

Manning ML; Foty RA; Steinberg MS.  2010.  Coaction of intercellular adhesion and cortical tension specifies tissue surface tensionPNAS. 107(28):12517-126522.  DOI: 10.1073/pnas.1003743107

Von Dassow M; Davidson LA.  2011.  Physics and the canalization of morphogenesis: a grand challenge in organismal biology.  Physical Biology.  8(4):article 045002.  DOI: 10.1088/1478-3975/8/4/045002

Kollmannsberger P; Biden CM; Dunlop JWC: et al.  2011.  The physics of tissue patterning and extracellular matrix organization: how cells join forces. Soft Matter.  7(20);9549-9560.  DOI: 10.1039/c1s05588g

Gunsalus KC; Rhissorrakrai K.  2011.  Networks in Caenorhabditis elegansCurrent Opinion in Genetics and Development. 21(6):787-798.  DOI: 10.1016/j.gde.2011.10.003

Gonzalez-Estevez C; Salo E.  2010.   Autophagy and apoptosis in planarians.  Apoptosis.  15(3, sp. Issue S1):279-292.  DOI: 10.1007/s10495-009-0445-4

Trier SM; Davidson LA.  2011.  Quantitative microscopy and imaging tools for the mechanical analysis of morphogenesisCurrent Opinion in Genetics and Development.  21(5):664-670.  DOI: 10:1016/j.gde.2011.08.005.

Vermont J; Affolter M.  2011.  Modeling new conceptual interpretations of development.  Development.  138(19):4111-4115.  DOI: 10.1242/dev.066-084.

Recommended Readings: Jason Cyster, Ph.D.

Friday Lecture Series

Sphingolipids and Oxysterols in B Cell Immunity and Cancer

Jason Cyster, Ph.D., Professor, Department of Microbiology and Immunology,

University of California, San Francisco

March 16, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium


Recommended Readings:

Cinamon, G., M. A. Zachariah, O. M. Lam, F. W. Foss Jr., and J. G. Cyster. 2008. Follicular shuttling of marginal zone B cells facilitates antigen transport. Nature immunology 9, (1): 54-62

Cyster, J. G. 2005. Chemokines, sphingosine-1-phosphate, and cell migration in secondary lymphoid organs. Annual Review of Immunology 23 , pp. 127-159

Okada, T., and J. G. Cyster. 2006. B cell migration and interactions in the early phase of antibody responses. Current opinion in immunology 18, (3): 278-285

Pappu, R., S. R. Schwab, I. Cornelissen, J. P. Pereira, J. B. Regard, Y. Xu, E. Camerer, et al. 2007. Promotion of lymphocyte egress into blood and lymph by distinct sources of sphingosine-1-phosphate. Science 316, (5822): 295-298

Pham, T. H. M., P. Baluk, Y. Xu, I. Grigorova, A. J. Bankovich, R. Pappu, S. R. Coughlin, D. M. McDonald, S. R. Schwab, and J. G. Cyster. 2010. Lymphatic endothelial cell sphingosine kinase activity is required for lymphocyte egress and lymphatic patterning. Journal of Experimental Medicine 207, (1): 17-27

Randall, K. L., T. Lambe, A. Johnson, B. Treanor, E. Kucharska, H. Domaschenz, B. Whittle, et al. 2009. Dock8 mutations cripple B cell immunological synapses, germinal centers and long-lived antibody production. Nature immunology 10, (12): 1283-1291

Recommended Readings: Jeffrey V. Ravetch, Ph. D.

Friday Lecture Series

The Paradox of Immunity

Jeffrey V. Ravetch, M.D., Ph.D., Theresa and Eugene M. Lang Professor and head,

Leonard Wagner Laboratory of Molecular Genetics and Immunology,

The Rockefeller University

March 9, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium


Recommended Readings:

Anthony, R. M., F. Nimmerjahn, D. J. Ashline, V. N. Reinhold, J. C. Paulson, and J. V. Ravetch. 2008. Recapitulation of IVIG anti-inflammatory activity with a recombinant IgG fc. Science 320, (5874): 373-376

Durandy, A., S. V. Kaveri, T. W. Kuijpers, M. Basta, S. Miescher, J. V. Ravetch, and R. Rieben. 2009. Intravenous immunoglobulins-understanding properties and mechanisms. Clinical and experimental immunology 158, (SUPPL. 1): 2-13

Nimmerjahn, F., and J. V. Ravetch. 2010. Antibody-mediated modulation of immune responses. Immunological reviews 236, (1): 265-275

Ravetch, J. 2010. In vivo veritas: The surprising roles of fc receptors in immunity. Nature immunology 11, (3): 183-185

Sazinsky, S. L., R. G. Ott, N. W. Silver, B. Tidor, J. V. Ravetch, and K. D. Wittrup. 2008. Aglycosylated immunoglobulin G1 variants productively engage activating fc receptors. Proceedings of the National Academy of Sciences of the United States of America 105, (51): 20167-20172

Research on Use of Snake-Venom Peptide for Heart Attack Treatment

The National Heart, Lung and Blood Institute (NHLBI), a division of the National Institutes of Health (NIH), has awarded a $2.5 million grant to Mayo Clinic’s Cardiorenal Research Laboratory to conduct a highly innovative research project, “Cardiovascular Peptides and Myocardial Infarction.” The research will seek to further understand the potential of a novel, engineered guanylyl cyclase (GC) activator, cenderitide, to reduce the level of cardiac and renal injury following a myocardial infarction, or heart attack. Researchers will try to determine whether the therapy could help prevent deterioration of cardiac and renal function following a heart attack, and potentially reduce further heart failure in the future in treated patients.

Mayo researchers invented cenderitide to activate two different subtypes of GC receptors, which uniquely differentiates cenderitide from other GC stimulating peptides. Cenderitide, a designer peptide derived from the venom of the green mamba snake, may aid in the preservation of cardiac and renal function following serious cardiovascular events, such as heart attack and acute decompensated heart failure. 

See the announcement at the Mayo Clinic website.


Pediatric Clinical Studies: New Report From the NAS

WASHINGTON — Federal laws that motivate or require drug and biologic developers to conduct pediatric studies have yielded beneficial information to guide the use of medications in children, says a new report by the Institute of Medicine.  Still, studies involving children continue to be limited, especially in certain areas such as medications’ use in newborns and long-term safety and effectiveness in children.  The report identifies ways that Congress and the U.S. Food and Drug Administration could further improve the utility of clinical information obtained from pediatric studies, including expanding innovative strategies to research drugs and biologics in children, using FDA’s authority to require long-term pediatric studies of possible safety risks, and giving FDA flexibility to impose sanctions for unreasonably delayed studies.