Recommended Readings: Andrew Knoll, Ph.D.

Friday Lecture Series

Systems Paleobiology

Andrew Knoll,  Ph. D., Fisher Professor of Natural History

and professor of earth and planetary sciences, Harvard University;

curator, Paleobotanical Collections, Harvard University Herbaria

April 1, 2011

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

Caspary Auditorium

Brocks, J. J., G. D. Love, R. E. Summons, A. H. Knoll, G. A. Logan, and S. A. Bowden. 2005. Biomarker evidence for green and purple sulphur bacteria in a stratified palaeoproterozoic sea. Nature 437, (7060): 866-870

Knoll, A. H., E. J. Javaux, D. Hewitt, and P. Cohen. 2006. Eukaryotic organisms in proterozoic oceans. Philosophical Transactions of the Royal Society B: Biological Sciences 361, (1470): 1023-1038

Squyres, S. W., J. P. Grotzinger, R. E. Arvidson, J. F. Bell III, W. Calvin, P. R. Christensen, B. C. Clark, et al. 2004. In situ evidence for an ancient aqueous environment at meridiani planum, mars. Science 306, (5702): 1709-1714

Tosca, N. J., A. H. Knoll, and S. M. McLennan. 2008. Water activity and the challenge for life on early mars. Science 320, (5880): 1204-1207

Yin, L., M. Zhu, A. H. Knoll, X. Yuan, J. Zhang, and J. Hu. 2007. Doushantuo embryos preserved inside diapause egg cysts. Nature 446, (7136): 661-663

UCLA Team Builds Microfluidic Platform for Measuring Protein Kinase Activity

University of California, Los Angeles, researchers have built an integrated chip-based microfluidic and imaging platform capable of measuring kinase activity in samples containing as few as 3,000 cells.

The platform, which the scientists used to measure ABL kinase activity – the target of the kinase inhibitor Gleevec – in BCR-ABL-positive leukemia patient samples, could potentially be expanded into a multiplex version for use in high-throughput kinase studies, said Thomas Graeber, assistant professor of molecular and medical pharmacology at UCLA and one of the platform’s developers.  Read more here.

The Earth Microbiome Project

The Earth Microbiome Project (EMP) is a proposed massively multidisciplinary effort to analyze microbial communities across the globe from many environments.  The first EMP Conference is scheduled for June 2011 in Shenzhen, China.  The goal is to understand microbes (Bacterial, Archaeal, Eukaryal and Viral) in terms of whom they are and what they do; it is the grand challenge of microbial ecology.  Read more at the Earth Microbiome Project website.

Recommended Readings: Lee Stirling Churchman, Ph.D.

Monday Lecture Series

Visualizing Transcription at Nucleotide Resolution Using Nascent Transcript Sequencing

Lee Stirling Churchman, Ph.D.

Post Doctoral Researcher, Department of Cellular and Molecular Pharmacology

University of California, San Francisco

April 4, 2011

4:00 – 5:00 p.m.  Caspary Auditorium

Recommended Readings:

Churchman, LS; Weissman, JS.  2011.  Nascent transcript sequencing visualizes transcription at nucleotide resolution. NATURE. 469(7330):368-

Namekawa, SH; Lee, JT.  2011.  Detection of nascent RNA, single-copy DNA and protein localization by immunoFISH in mouse germ cells and preimplantation embryosNATURE Protocols. 6(3): 10.1038/nprot.2010.195

Mortenson, KI; Churchman, LS; Spudich, JA, et al.   2010.  Optimized localization analysis for single-molecule tracking and super-resolution microscopy. NATURE Methods. 7(5):377-U59.

Ingolia, NT; Chaemmaghami, S; Newman, JRS; and Weissman, JS.  2009.  Genome-wide analysis in  vivo of translation with nucleotide resolution using ribosome profiling. SCIENCE. 324(5924):218-223.

Churchman, LS; Okten, Z; Rock, RS et al. 2005.  Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. PNAS 102(5):1419-1423.

Okten, Z; Churchman, LS; Rock, RS et al. 2004. Myosin VI walks hand-over-hand along actin NATURE Structural & Molecular Biology. 11(9):884-887.

The 40th Anniversary of “The War on Cancer”

Science this week presents a special issue to mark the 40th anniversary of the signing of the US National Cancer Act in 1971 by then-President Richard Nixon. In their introduction to the special issue, Paula Kibertsis and Eliot Marshall note that papers published in Science at the time were asking questions like, “How do abnormalities in chromosome number arise in tumor cells? Can tissue-specific markers be used to determine the epithelial versus mesenchymal origin of a solid tumor? … Do viruses play a role in human cancer?” Though there are still many questions surrounding cancer, Kibertsis and Marshall say, some have been answered. See the rest of Science‘s 40th anniversary coverage here.

Recommended Readings: Yi Zhang, Ph.D.

Friday Lecture Series

Dynamic Regulation of DNA Methylation in Stem Cell and Development

Yi Zhang,  Ph.D., investigator, Howard Hughes Medical Institute;

Kenan Distinguished Professor,

University of North Carolina at Chapel Hill

March 25, 2011

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

Caspary Auditorium

Bailey, V. J., H. Easwaran, Y. Zhang, E. Griffiths, S. A. Belinsky, J. G. Herman, S. B. Baylin, H. E. Carraway, and T. -H Wang. 2009. MS-qFRET: A quantum dot-based method for analysis of DNA methylation. Genome research 19, (8): 1455-1461

Cao, R., H. Wang, J. He, H. Erdjument-Bromage, P. Tempst, and Y. Zhang. 2008. Role of hPHF1 in H3K27 methylation and hox gene silencing. Molecular and cellular biology 28, (5): 1862-1872

Jones, B., H. Su, A. Bhat, H. Lei, J. Bajko, S. Hevi, G. A. Baltus, et al. 2008. The histone H3K79 methyltransferase Dot1L is essential for mammalian development and heterochromatin structure. PLoS Genetics 4, (9)

Klose, R. J., and Y. Zhang. 2007. Regulation of histone methylation by demethylimination and demethylation. Nature Reviews Molecular Cell Biology 8, (4): 307-318

Liang, J., M. Wan, Y. Zhang, P. Gu, H. Xin, S. Y. Jung, J. Qin, et al. 2008. Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nature cell biology 10, (6): 731-739

Wu, S. C., and Y. Zhang. 2009. Minireview: Role of protein methylation and demethylation in nuclear hormone signaling. Molecular Endocrinology 23, (9): 1323-1334

Recommended Readings: David C. Gadsby, PhD April 4, 2011

Monday Lecture Series

How CFTR, the Model ABC Protein Defective in Cystic Fibrosis, Works

 Davd C. Gadsby PhD

 Patrick A. Gerschel Family Professor

 Laboratory of Cardiac and Membrane Physiology



Recommended Readings

Wang, G. Y.  2011.  The inhibition mechanism of non-phosphorylated Ser(768) in the regulatory domain of cystic fibrosis trasnmembrane conductance regulatorJournal of Biological Chemistry.  286(3):2171-2181.

Koepikin, Z.; Sohma, Y.; Li, M.; et al.  2010.  On the mechanism of CFTR inhidition by a thiasolidinone derivativeJournal of General Physiology.  136(6):659-671.

El Hiani, Y. and  Linsdell, P.   2010.  Changes in accessibility of cytoplasmic substances to the pore associated with activation of the cystic fibrosis transmembrane conductance regulator chloride channel.  Journal of Biological Chemistry.  285(42):32126-32140. 

Szollosi, A.; Vergani. P. and Csanady, L.   2010.  Involvement of F1296 and N1303 of CFTR in induced-fit conformational change in response tp ATP binding at NBD2 Journal of General Physiology.  136(4):407-423.

Bai, Y. H.; Li, M. and Hawang, T.C.  2010.  Dual roles of the sixth transmembrane segment of the CFTR chloride channel in gating and permeation.   Journal of General Physiology.  136(3):293-309.

Gadsby, D. C.; Vergani, P.; Mense, M.; et al.  2010.  Control of CFTR’s gates by ATP binding and hydrolysis.  Pediatric Pulmonology.   Supple.  33: 114-115.    Please request from Markus Library.

Csanady, L.; Vergani, P. and Gadsby, D. C.  2010.  Strict coupling between CFTR’s catalytic cycle and gating of its CL-ion pore revealed by distributions of open channel burst durations.   PNAS.  107(3):1241-1246.

Muallem, D. and Vergani, P.  2009.  ATP hydroloysis-driven gating in cystic fibrosis trasnmembrance conductance regulator.  Philosophical Transactions of the Royal Society B-Biological Sciences.  364(1514):247-255. doi: 10.1098/rstb.2008.0191.

Aleksandrov, A. A.; Aleksandrov, L.A. and Riordan, J.R.  2007.   CFTR (ABCC7) is a hydrolysable-ligand-gated channel Pflugers Archive-European Journal of Physiology.  453(5):693-702

Scripps Research Team Discovers New Details About Medically Important Protein Family

Scientists from The Scripps Research Institute have determined a new structure from a medically important superfamily of proteins. The structure should help instruct the design of a new kind of therapeutics for conditions ranging from Parkinson’s disease to inflammation.   The study, published on March 10, 2011, in Science Express provides important insights into how this large family of proteins, called G protein-coupled receptors (GPCRs), can recognize and respond to a wide array of signals, including odors, hormones, neurotransmitters, and light.

New Measurement Into Biological Polymer Networks

The development of a new measurement technology under a research project funded by the Air Force Office of Scientific Research and the National Science Foundation is probing the structure of composite and biological materials.   Researchers at Technische Universtaet Muenchen (Technical University of Munich) used the muscle filament actin to construct a unique polymer network. In their quest to understand more about bio-polymers, they developed the rheometer and confocal microscope system (measures the mechanical properties of materials), which provide a unique and unprecedented level of precision and sensitivity for investigating polymeric systems which were previously too small to visualize during mechanical stress experiments. The rheometer and confocal microscopes clearly visualized the fluorescently labeled actin network and they filmed the polymer filaments’movement in 3-D when mechanical stress was applied.

Recommended Readings: Agata Smogorzewska M.D., PhD March 28 2011

Monday Lecture Series

Role of Ubiquitin and Nucleases in DNA Crosslink Repair

Agata Smogorzewska  M. D. , PhD

Laboratory of Genome Maintenance
March 28, 2011

4:00 p.m.-5:00 p.m. Caspary Auditorium

Recommended Readings

Tumini, E.; Plevani, P.; Muzi-Falconi, M; et al.  2011.  Physical and functional crosstalk between Fanconi anemia core components and the GINS replication complex.   DNA Repair.  10(2):149-158.

Smogorzewska, A.; Desetty, R.; Saitto, T.T.; et al.  2010.  A genetic screen identifies FAN1, a Fanconi anemia-associated nuclease necessary for DBA interstrand crosslink repairMolecular Cell.  39(1):36-47.

Kratz, K.; Schopf, B.; Kaden, S.; et al.  2010.  Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensitizes cells to interstrand crosslinking agents Cell.  142(1):77-88.

Bhagwat, N.; Olsen, A.L.; Wang, T.; et al.  2009.  XPF-ERCC1 participates in the Fanconi anemia pathway of cross-link repair.   Molecular and Cellular Biology.  29(24):6427-6437.

Thompson, L.H.; and Hinz, J. M.  2009.   Cellular and molecular consequences of defective Fanconi anemia proteins in replication-coupled DNA repair: mechanistic insightsMutation Research- Fundamental and Molecular Mechanisms of Mutagenesis.  668(1-2, Spec. Issue1):54-72.  Please request from Markus Library.

Fekairi, S.; Scaglione, S.; Chahwan, C.; et al.  2009.  Human SLX4 is a holliday junction resolvae subunit that binds multiple DNA repair/recombination endonucleases.  Cell.  138(1):78-89

Smogorzewska, A.; Matsuoka,S.; Vinciguerria, P.  2007.  Identification of the FANCI protein, a monoubiquitinated FANCD2 paralog required for DNA repair.  Cell.  129(2):289-301.

Gurtan, A.M.; and  D’Andrea, A.D.  2006.  Dedicated to the core: understanding the Fanconi anemia complexDNA Repair.  5(9-10):1119-1125.