Biology on the Edge Past seminars
2008 Dr. Stuart Kauffman, Professor of Biological Science, Physics and Astronomy, University of Calgary, Canada
"Reinventing the Sacred: A reductionsist's conviction in a complex world"
April 11, 2008, 4:00-5:00 PM
Building 517, Room 147
Abstract: I would like to begin a discussion about the first glimmerings of a new scientific world view - beyond reductionism to emergence and radical creativity in the biosphere and human world. This emerging view finds a natural scientific place for value and ethics, and places us as co-creators of the enormous web of emerging complexity that is the evolving biosphere and human economics and culture. In this scientific world view, we can ask: Is it more astonishing that a God created all that exists in six days, or that the natural processes of the creative universe have yielded galaxies, chemistry, life, agency, meaning, value, consciousness, culture without a Creator. In my mind and heart, the overwhelming answer is that the truth as best we know it, that all arose with no Creator agent, all on its wondrous own, is so awesome and stunning that it is God enough for me and I hope much of humankind Andre Cavalcanti
"Evolution of Alternative Genetic Codes in Ciliates"
April 23, 2008
1:00-2:00 PM
Building 535, Room 152/154
Dr. Eric Winfree, Associate Professor of Computer Science, Caltech
"Programming a DNA World"
April 9, 2008, 1:00-2:00 PM
Building 535, Room 152/154
Abstract: Biological organisms are a beautiful example of programming. The program and data are stored in biological molecules such as DNA, RNA, and proteins; the algorithms are carried out by molecular and biochemical processes; and the end result is the creation and function of an organism. If we understood how to program biomolecular systems, what could we create? DNA nanotechnology provides fertile ground for exploring this notion. It has given us DNA molecules that self-assemble precisely, that fold into complex nanoscale objects, that act as mechanical actuators and molecular motors, and that make decisions based on digital and analog logic. These DNA devices appear to be the building blocks for creating ever more sophisticated programmable molecular systems, with potential applications in synthetic chemistry, nanotechnology, and biotechnology. But how can we take the DNA devices and put them together into integrated systems that carry out desired functions? This requires abstractions for specifying system behavior and compilers for automatically designing the required DNA sequences. I will describe our initial efforts developing abstractions and compilers for programming DNA self-assembly and DNA logic circuits.
Dr. Clarissa (Cris) Cheney, Associate Professor of Biology, Pomona College
"Targeting rab GTPases in Vesicle Transport"
March 12, 2008, 1:00-2:00 PM
Building 535, Room 152/154
Abstract: Rab GTPases play multiple roles in vesicle transport. Rab GDP dissociation inhibitor (GDI) regulates rab placement by retrieving rabs from target membranes and delivering rabs through the cytoplasm to donor membranes. The mechanisms by which GDI retrieves rabs and then delivers them are not fully understood. To identify proteins that interact with GDI, we have carried out screens for GDI interactors, using Drosophila as the model system, since the fly genome has a single GDI, but multiple rabs. In a yeast two-hybrid (Y2H) screen, a protein with a ubiquitin-like UBX domain was identified as a GDI interactor. This protein was named Gint3, for GDI interacting protein 3. Gint3 has a PUG N-glycanase-associated domain and a UBX ubiquitin-like domain, but no obvious transmembrane domain. Gint3 did interact with T248A mutant GDI in the yeast two hybrid system. T248A GDI has a mutation in a rab-binding residue of GDI and shows reduced rab retrieval from membranes, suggesting that rab is not an essential partner for the GDI-Gint3 interaction. Gint3 did not interact with Hsp83, the Drosophila Hsp90 homolog. Hsp90 has been shown to interact with GDI (Chen and Balch, 2006). GST-GDI and GST-Gint3 expressed in bacteria were purified and were found to interact using a quartz crystal microbalance with dissipation monitoring (QCM-D). Dr. Todd Oakley, Assistant Professor of Ecology and Evolutionary Biology, University of California, Santa Barbara
"How did evolution build complex traits? The origins of animal synapses and phototransduction"
March 19, 2008, 1:00-2:00 PM
Building 535, Room 152/154
Abstract: Biologists are amazed by the intricacy and complexity of biological interactions between molecules, cells, organisms, and ecosystems. Yet underlying all biodiversity is a universal common ancestry. How does evolution proceed from common starting points to generate the riotous biodiversity we see today? This "novelty problem" - understanding how novelty and common ancestry relate - has become of critical importance, especially since the realization that genes and developmental processes are often conserved across vast phylogenetic distances. In particular, two processes have emerged as the primary generators of diversity in organismal form: duplication plus divergence and co-option. I will illustrate how phylogenetic methodology and "tree thinking" can be used to distinguish duplication plus divergence from co-option. In addition, I will review two case studies in animal evolution -- both illustrating co-option of existing components was involved in the origins of animal synapses and phototransduction; two traits that have had enormous impact on the evolution of all animals. Dr. Eliot Bush, Assistant Professor of Molecular Evolution and Computational Biology, Harvey Mudd College
"A computational screen for regulatory elements important in human evolution."
March 5, 2008, 1:00-2:00 PM
Building 535, Room 152/154
Abstract: A major goal in the study of human evolution is to identify key genetic changes which occurred over the course of primate evolution. According to one school of thought, many such changes are likely to be found in noncoding sequence. An approach to identifying these involves comparing multiple genomes to identify conserved regions with an accelerated substitution rate in a particular lineage. Such acceleration could be the result of positive selection. I will present a likelihood ratio test method to identify such regions. I've applied it to the human terminal lineage as well as several other branches in the primate tree. I will also present resequencing data from one particular element accelerated on the human lineage. These data indicate that the element lies in a region of low polymorphism in humans, consistent with the possibility of a recent selective sweep. They also show that the AT to GC bias for polymorphism in this region differs dramatically from that for substitutions. "Evolution of Insect Water Balance in Natural and Artificial Deserts"
Dr. Allen Gibbs
Professor of Ecology and Evolutionary Biology, University of Nevada, Las Vegas
February 13, 2008, 1:00-2:00 PM
Building 535, Room 152/154 Abstract
Insects are especially susceptible to dehydration because of their small body size. Despite this limitation, they are also the most abundant and diverse animals in desert habitats. I will discuss Drosophila as a model for physiological and genetic analyses of adaptation to desert conditions, in three contexts. Firstly, Drosophila species have invaded North American deserts on several occasions, where they breed and develop in cacti. The phylogenetic relationships of these species are well studied, providing the opportunity to apply rigorous comparative methods to the evolution of water balance in nature. Secondly, we have subjected replicated populations of Drosophila melanogaster to selection for desiccation resistance in the laboratory. This provides a laboratory model for natural populations, with the added advantage that the experimental toolkit available for this species can be used to identify and test hypotheses about the molecular mechanisms of adaptation. Finally, the genome of a desert species, Drosophila mojavensis, has been sequenced. This is the "bionic" fly, able to withstand extreme temperatures, lack of food and water, and highly toxic dietary compounds made by its host plants. Microarrays to study the effects of environmental stress on gene expression in Drosophila mojavensis are available, and I will discuss our current and future plans to take functional genomics out of the lab and into the real world. "Immunoglobulin Gene Diversification: Evolution in Real Time"
February 8, 2008, 4:00-5:00 PM
Building 517, Room 147
Dr. Nancy Maizels
Professor of Immunology and Biochemistry; Director, Molecular Medicine Program, University of Washington Seattle Abstract
B cells diversify their immunoglobulin genes to respond rapidly and dynamically to ever-changing pathogens. Diversification uses conserved mechanisms that maintain and modify DNA structure in all cells. Understanding these mechanisms is revealing about events that lead to cancer; and harnessing them may provide new approaches to targeted gene therapy. 2007 "A Fundamental Difficulty in Evolutionary Reconstruction: Deducing Both Alignment and Phylogeny from Molecular Sequences"
Marc Suchard, MD, PhD
Assistant Professor, Department of Biomathematics and Human Genetics, David Geffen School of Medicine, UCLA
December 12, 2007
1:00-2:00pm "Objects that Make Objects: The Population Dynamics of Structural Complexity"
James P. Crutchfield
Complex Systems Center and Physics Department, University of California, Davis
November 30, 2007
4:00-5:00pm "Ataxia- Telangiectasia: how an orphan disease led to the cloning of a major DNA repair gene"
Dr. Richard Gatti
Professor of Pediatrics and Laboratory Medicine, UCLA School of Medicine
November 2, 2007
4:00-5:00 PM
Building 517, Room 147 Abstract
Because the disorder called 'ataxia-telangiectasia' involved at least five seemingly unrelated systems and was a single gene defect, we invested 14 years in the positional cloning of the ATM gene. This opened a logjam of research that has begun to elucidate how these five systems are interrelated: cell cycle checkpoints, DNA repair, cancer, immunodeficiency, and neurological development. Many translational opportunities have also become apparent, including mutation-targeted therapy, whereby certain drugs can correct specific types of mutations to induce the missing ATM protein. ATM carriers are prone to breast cancer; over 30 million carriers exist in the U.S. alone. Carrier testing is yet another application of this new understanding. "Profile context-sensitive HMMs: An effective framework for RNA homology search"
Byung-Jun Yoon
California Institute of Technology
October 17, 2007 "Functional and genomic analyses of Drosophilia sex hierarchy regulated genes"
Dr. Michelle Arbeitman
Associate Professor of Molecular Biology and Computational Biology, University of Southern California
September 28, 2007 "The Theory of Lethal Mutagenesis"
Claus Wilke
University of Texas at Austin
May 18, 2007 "MicroRNAs: From Scale Invariance to Stem Cells"
Jonathan Miller
Professor, Baylor College of Medicine
May 11, 2007 "Topological Modeling of Nonlinear Systems through Active Interrogation"
Josh Bongard
University of Vermont
May 4, 2007 "Engineering Biological Simplicity"
Drew Endy
Cabot Assistant Professor, MIT
April 20, 2007 "Carbon Nanotubes and Biotechnology Applications: Current Research and Future Technology"
Eric Tan
Keck Graduate Institute
April 6, 2007 "Measures of inflammation in chronic inflammatory diseases of the airways (e.g. asthma): Time for a paradigm shift?"
Jeff Irvine
Medical Assistant, Cerberus Ltd.
February 20, 2007 2006 "Ultra-Sensitive Reagentless Biological and Organic Contamination Sensors Using Deep UV Laser Induced Native Fluorescence and Resonance Raman Spectroscopy"
William Hug
Photon Systems, Inc.
November 17, 2006 "Label-free detection of biomolecules by a field-effect transitor with bio-functionalized gate surfaces"
Yinhua Han
Keck Graduate Institute
November 10, 2006 "Synthetic Biology. Understanding the Connection between Chemistry and Biology by Generating Artificial Life Forms"
Steven A. Benner
The Westheimer Institue for Science and Technology
October 27, 2006 "Developmental Information Processing"
C. Titus Brown
California Institute of Technology
October 20, 2006 "Selection Pressures on Microbial Proteins"
Joshua B. Plotkin
Harvard Society of Fellows
October 13, 2006 "Extending Blood Safety with Pathogen Reduction Technology For All Three Blood Components"
Raymond Goodrich
Chief Science Officer, Navigant Biotechnologies
October 6, 2006 "Structure -function studies of claudins, tight junction proteins that form epithelial ion pores"
Alan Yu
Professor, University of Southern California Keck School of Medicine
September 26, 2006 "Molecular Information Theory: From Clinical Applications to Binding Site Evolution"
Tom Schneider
Research Biologist, National Cancer Institute
September 22, 2006 "The Cytoskeleton as a Target in the Treatment of Hypertension and Cancer"
Primal de Lanerolle
Professor of Physiology, University of Illinois at Chicago
August 3, 2006 "Photochemical Triggers and Probes of Protein Folding"
Jennifer Lee
Doctor
June 30, 2006 "The homing of adult cardiac stem cells"
Yao-Liang Tang
Doctor
May 26, 2006
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