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Conference on Theory & Biology

SIMONS FOUNDATION

Friday, April 11, 2014 from 9:00 AM to 6:00 PM (EDT)

New York, NY

Conference on Theory & Biology

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CONFERENCE

ON

THEORY & BIOLOGY

Friday, April 11, 2014

9:00 AM – 6:00 PM

Gerald D. Fischbach Auditorium

160 5th Avenue, New York, New York, 10010

This conference will highlight a few of the many areas where theoretical ideas are having an impact on the life sciences. Lunch will be served and there will be ample time for discussion.

This conference will be of interest to established researchers, postdoctoral fellows and graduate students working in the life sciences and allied fields.


AGENDA

8:15 - 9:15 AM Check-in and breakfast

9:15 - 9:30 AM Welcome

9:30 - 10:45 AM Talks

10:45 - 11:00 AM Break

11:00 AM - 1:00 PM Talks

1:00 - 2:00 PM Lunch

2:00 - 4:00 PM Talks

4:00 - 4:15 PM Break

4:15 - 5:30 PM Talks


ABSTRACTS

9:30 - 10:45 AM

Eric WieschausPrinceton University

Mechanics of cell shape change during Drosophila gastrulation

How cells convert patterns of gene activity into the physical properties that control shape and motility is a major question in biology. In Dr. Wieschaus’s talk, he will describe recent experiments that address these questions using the Drosophila embryo as a model system. Cells in the ventral region of this embryo are assigned to the mesodermal cell fate by two transcription factors, Twist and Snail. These cell fates’ decisions are followed by immediate changes in cell shape that internalize the mesoderm. He has characterized this reorganization using computational tools that allow tracking physical properties of all 800 mesodermal cells during gastrulation. His experiments show that cell shape changes and nuclear position is driven by pulses of actin-myosin constriction in the apical surface that are somehow transmitted across the entire length of the cell by the non-compressible nature of the cytoplasm.

Surprisingly, many of the morphological changes in mesodermal cells still occur in mutants in which cellularization has been blocked. He investigates the properties of the cytoplasm that transmit force in the absence of membrane by tracking fluorescent beads in living embryos, and by locally disrupting the cytoskeleton using laser dissections.

These various experiments have led to two different approaches for modeling cell shape change and morphogenesis during gastrulation. In one approach, he uses a computational vertex model, where passive volume maintenance in cells bounded by an elastic cellular membrane can account for invagination of the furrow. The second approach eliminates the role of elastic cell membranes and relies on the Navier-Stokes equation to explain the invagination in terms of global flows in viscous cytoplasmic medium. He presents genetic data and morphological observations to distinguish between the two models.

This presentation was made in collaboration with Bing He, Konstantin Doubrovinski, Oleg Polyakov and Joshua Shaevitz.

 

Boris Shraiman, Kavli Institute for Theoretical Physics

Mechanics of morphogenesis: from theory to experiment and back 

Morphogenesis involves cell proliferation and rearrangement and has many distinctly mechanical aspects that are part and parcel of the "executable program" of development.

This talk will (a) review the experimental status of the idea of mechanical feedback regulation of growth (in an epithelial layer), (b) describe how a simple theoretical model of cell mechanics can be used to infer mechanical forces within an epithelial layer and (c) use this inference method alongside live-imaging data and phenomenological modeling to gain some insight into the mechanisms of germ-band extension and ventral furrow formation in Drosophila embryos.

 

11:00 AM - 1:00 PM

Ned S. WingreenPrinceton University

Keeping it together: Organizing the bacterial chromosome for division

Research has shown the bacterial chromosome to be highly organized in space in many bacteria, although the origins of this organization remain unclear. Chromosomal organization is further complicated by the requirement for replication and segregation. In a variety of bacteria, partitioning proteins of the ParABS system mediate chromosome and plasmid segregation. At its heart, this segregation machinery includes a large ParB–DNA complex consisting of hundreds of ParB proteins. The nature of interactions between DNA-bound ParB proteins and how these determine the structural properties of the partitioning module remains unclear. In particular, does ParB spread along the DNA to form a filamentous protein-DNA complex with a 1D character, or rather does it assemble to form a 3D complex on the DNA? And how does the presence of only one or even a few parS sites lead to robust formation and localization on the chromosome of such a large protein-DNA complex? Dr. Wingreen will present a simple model for interacting proteins on DNA, which reveals that a combination of 1D spreading bonds and a 3D bridging bond between ParB proteins constitutes a minimal model for condensation of a 3D ParB-DNA complex. These combined interactions provide an effective surface tension that prevents fragmentation of the ParB–DNA complex. Importantly, this model accounts for recent experiments on ParB-induced gene silencing and the effect of a DNA “roadblock” on ParB localization. Furthermore, the model provides a simple mechanism to explain how a single parS site is both necessary and sufficient for the formation and localization of the ParB–DNA complex.

 

Massimo VergassolaUniversity of California, San Diego

Adaptation in bacterial chemotaxis

The response of E. coli to the chemoattractant aspartate features perfect adaptation, i.e., constant stimuli are filtered out, whilst the response to the chemoattractant serine does not. Adaptation (perfect or partial) is common to many cellular and neurobiological sensory systems.

Bacterial chemotaxis has the notable advantage of being well characterized at the molecular level, making it both appropriate and timely to address the functional and selective aspects of its dynamic and adaptation properties. Dr. Vergassola shall discuss this issue, presenting past and ongoing theoretical and experimental work.

 

Michael B. ElowitzCalifornia institute of Technology; Investigator, HHMI

Circuits of unknown function

Cells use circuits of interacting genes and proteins to control their behaviors, but the design principles that govern genetic circuit architecture usually remain mysterious. Dr. Elowitz’s lab seeks to identify and understand such design principles. To do so, he and his lab combine three synergistic approaches: First, they apply time-lapse movies and quantitative image analysis to follow the dynamics of genetic circuits in individual cells. Second, they develop synthetic biology approaches in which they design and construct new genetic circuits (or rewire natural ones) to implement specific functions in cells. Finally, they use mathematical models to explore the dynamics of actual and potential genetic circuit architectures. They work with bacteria, yeast and mammalian cells, model systems that enable the precise genetic manipulation and measurement of the dynamics of cellular gene circuits. In this talk, Dr. Elowitz will discuss recent work from bacteria to mammalian cells in which careful analysis of gene circuit dynamics is beginning to shed light on the design principles of core cellular circuits.


2:00 - 4:00 PM

Dmitry RinbergNew York University Neuroscience Institute

What the mouse glomerulus tells the mouse brain

The basic questions of sensory coding are: (1) How is information about the stimulus encoded by activity of the neurons, and (2) what features of this activity can be read by the higher brain areas? We use psychophysics, electrophysiology and optogenetics to approach these questions in mouse olfaction, which is arguably the most genetically tractable and highly relevant sensory system for rodent behavior. The segregation of each of the 1000+ olfactory receptor neuron types into its respective olfactory bulb glomerulus implies that 1000+ chemical features are initially encoded separately. What is the role of these individual channels of information transmission in olfactory perception, and what specific features of olfactory stimuli do these channels transmit from the bulb to the higher brain areas? Electrophysiological recording of the activity of second order neurons, which take their input from the glomeruli, establishes that the timing of their activation carries information about odor identity and concentration. Behavioral experiments with the optogenetic stimulation of an individual glomerulus demonstrate that this timing can be read by the brain.

 

Alexei Koulakov, Cold Spring Harbor Laboratory

Deciphering the olfactory code

Olfaction is the final frontier of our senses. Unlike vision and hearing, where a relatively straightforward relationship exists between stimulus features and neural responses, the olfactory code remains unbroken. Koulakov will describe his lab’s recent attempts to understand various features of the representation of smells by networks of neurons in the mammalian olfactory bulb, including the code's sparsity, fine temporal structure and adaptation to novel stimuli.


Eero SimoncelliNew York University; Investigator, HHMI

Embedding of environmental probabilities in populations of sensory neurons

The mammalian brain is metabolically expensive and evolutionary pressures have presumably driven it to make productive use of its resources. During early stages of sensory processing, this concept can be expressed more formally as an optimality principle: the brain maximizes encoded information about relevant sensory variables given available resources. Dr. Simoncelli will describe a specific instantiation of this hypothesis that predicts a direct relationship between the distribution of sensory attributes encountered in the environment, and the selectivity and response levels of neurons within a population that encodes those attributes. This allocation of neural resources, in turn, imposes direct limitations on the organism’s ability to discriminate different values of the encoded attribute. Dr. Simoncelli will show that these physiological and perceptual predictions are borne out in a variety of visual and auditory attributes. Finally, he will show that this encoding of sensory information provides a natural substrate for subsequent computation, which can make use of the knowledge of environmental (prior) distributions that is embedded in the population structure.


4:15 - 5:30 PM

William BialekPrinceton University & Daniel FisherStanford University

Perspectives on theory and biology


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When & Where


Gerald D. Fishbach Auditorium
160 5th Avenue
New York, NY 10010

Friday, April 11, 2014 from 9:00 AM to 6:00 PM (EDT)


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SIMONS FOUNDATION

About the Simons Foundation
 
Established in 1994, the Simons Foundation is a private foundation based in New York City. With assets of $2 billion and annual grants of approximately $170 million, the foundation is dedicated to advancing the frontiers of research in basic science and mathematics.
 
Simons Foundation programs in Mathematics & Physical Sciences support mathematics, theoretical computer science and theoretical physics, and the foundation's Life Sciences programs have focused on research that promotes synergy between biology and mathematics.
 
The foundation is also committed to advancing autism research. Launched in 2005, the Simons Foundation Autism Research Initiative (SFARI) is a research campaign whose mission is to improve the diagnosis and treatment of autism spectrum disorders by funding, catalyzing and driving innovative research of the greatest quality and relevance. 

simonsfoundation.org

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