CINQA Seminar Series Winter 2011

Click a topic for more detailed information about the seminar.

January 12

How has evolution built complex animal visual systems?

February 1

Catastrophic eruptions and rebirth at hydrothermal vents - the role for tiny larvae

February 7

Blood Vessel Segmentation in Volumetric Ultrasound

February 10

Modeling Perceptual Biases in Sound Localization

February 17

Protein Structure Modeling via Distance Geometry & Mean Force Potentials

March 2

Eulerian Graphs and Reading DNA Sequences

March 3

Signal Transduction: Multistability, Noise, and Cell Population Dynamics

Todd Oakley , Ph.D. - Wednesday, January 12, 2011

Assistant Professor of Ecology, Evolution and Marine Biology
University of California Santa Barbara

"How has evolution built complex animal visual systems?"

The evolutionary histories of complex traits are complicated because such traits are comprised of multiple integrated and interacting components, which may have different individual histories. Phylogenetic studies of complex trait evolution often do not take this into account, instead focusing only on the history of whole, integrated traits, for example mapping eyes as simply present or absent through history. Using the biochemistry of animal vision as a model, I will present two case studies to demonstrate how investigating the individual components of complex systems can aid in elucidating both the origins and diversification of such systems. Opsin-based phototransduction underlies all visual phenotypes in animals, using complex protein cascades that translate light information into a nervous signal. First, I will discuss our recent work in the model cnidarian Hydra magnipapillata. As the only non-bilaterian lineage to possess functional opsins, our findings in cnidaria allow us to trace the history of various components to the very origin of animal phototransduction. Second, I will discuss the origin of a complex light-producing organ in a cephalopod the Hawaiian Bobtail Squid. I will show that bioluminescent organs possess the molecular, biochemical, and physiological capability for light detection. The same molecular machinery is used in squid eyes and light organ, illustrating a case of co-option of existing components in a new structure. Examining the evolutionary history of cephalopods as a whole indicates that bioluminescence and light organs evolved multiple times, providing a valuable system to address whether similar molecular changes accompany convergent morphological changes.

Time: 3:15-4:15 p.m. in Salazar Hall Room C168.

Refreshments are available before the seminar.

Follow this link to visit Dr. Oakley's homepage.                               Back to Top



Diane Adams, Ph.D. - Tuesday, February 1, 2011

Postdoctoral Fellow
National Institutes of Health / National Institute of Dental and Craniofacial Research

"Catastrophic eruptions and rebirth at hydrothermal vents - the role for tiny larvae"

On the alien, dark ocean floor, islands of strange organisms thrive off of scalding hot water full of toxic chemicals at hydrothermal vents.  These oases of life are subject to volcanic eruptions and earthquakes which can decimate entire communities.  However, the organisms return and reestablish vibrant and productive communities quickly.  It is the tiny, dispersive larval stage of the animals that enables this quick recovery.  But where do the larvae come from? How do they get there? And how can they do it so quickly?  I was lucky enough to study hydrothermal vent sites both before and after a catastrophic volcanic eruption to provide some answers to how larvae control the dynamics and structure of frequently-disturbed hydrothermal vent communities.

Time: 12:10-1:00 p.m. in Biological Sciences Room 335.                   Back to Top



Jue "Joy" Wang , Ph.D. - Monday, February 7, 2011

Visiting Assistant Professor of Mathematics
Union College,
Schenectady, NY

"Blood Vessel Segmentation in Volumetric Ultrasound"

Real-time 3D ultrasound imaging has been used to visually guide clinicians inserting central catheters into the blood vessels of neonates being cared in NICU for the delivery of medicine to the hearts. However, it is challenging to visualize the vessels in the raw images due to the heavy speckle noise and low spatial resolution.

A 3D vascular segmentation method has been developed to provide more clinically meaningful views of the catheter in real-time ultrasound. The segmentation consists of a centerline detection and cross-section delineations. A sequential Monte Carlo approach is used to trace the 3D vessel. It is seen as the maximum a posteriori (MAP) path of a group of particles driven by both an intrinsic stochastic dynamics and a statistical image data model. The cross-sectional contours are estimated using energy minimization and regularization. The efficacy of the approach will be demonstrated using simulated and in vivo animal datasets.

Time: 3:15-4:15 p.m. in Simpson Tower F213.

Refreshments are available after the seminar.

Follow this link to visit Dr. Wang's homepage.                                 Back to Top



Brian Fisher, Ph.D. - Thursday, February 10, 2011

Ecole Normale Superieure
Paris, France

"Modeling Perceptual Biases in Sound Localization "

In this talk, I will present a mathematical model for the barn owl's sound localization behavior.  The barn owl is a nocturnal hunter that uses sound localization to capture prey.  The owl is very accurate at localizing sources near the center of gaze, but makes systematic errors for sources in the periphery. This pattern of errors is not unique to owls, but rather is widely observed in other species, including humans. I will formulate the task of sound localization as an estimation problem and model the owl’s behavior as a form of statistical inference.  In particular, I will show that a Bayesian estimator that emphasizes central directions can explain the owl's behavioral bias.  This model accounts for how the owl uses the available sensory information to drive its behavior in a number of stimulus conditions.

Time: 3:15-4:15 p.m. in Simpson Tower F213.

Refreshments are available after the seminar.

Follow this link to visit Dr. Fisher's homepage.                                Back to Top



Di Wu , Ph.D. - Thursday, February 17, 2011

Assistant Professor of Mathematics
Western Kentucky University

"Protein Structure Modeling via Distance Geometry & Mean Force Potentials "

The distances for certain pairs of atoms in a protein can often be obtained based on our knowledge on various types of bond-lengths and bond-angles or from physical experiments such as nuclear magnetic resonance (NMR). The coordinates of the atoms and hence a protein structure can then be determined by using the known distances. However, it requires the solution of a mathematical problem called the distance geometry problem, which is proved to be computationally intractable in general. In addition, due to insufficient data, such as nuclear overhauser effect (NOE) data in NMR and structural information of comparative models from theoretical methods, the protein structures determined by conventional techniques usually are not as accurate as desired. Therefore, the uses of such protein structures in important applications, including homology modeling and rational drug design, have been severely limited. In this talk, I will introduce several efficient algorithms including theories for the solution of the distance geometry problem using the idea of geometric build-up. I will also introduce knowledge-based methods for protein structure refinement via constrained optimization and molecular dynamic simulation, in which we construct dedicated structural databases for studying protein inter-atomic distance distributions and derive so-called mean force potentials to refine NMR-determined protein structures and comparative models.

Time: 3:15-4:15 p.m. in Simpson Tower F213.

Refreshments are available after the seminar.                                Back to Top



Michael S. Waterman, Ph.D. - Wednesday, March 2, 2011

Professor of Biological Sciences, Mathematics, and Computer Science
University of Southern California

"Eulerian Graphs and Reading DNA Sequences "

With the discovery of the double helix in 1953, it became clear that determining DNA sequences was an important goal. The Sanger method was invented in 1975 and by 2001 refinements of that method allowed sequencing of the human genome. Today an exciting new generation of sequencing technologies are rapidly increasing the speed of DNA sequencing. This lecture will consider the mathematical and computational challenges of sequencing DNA.

Time: 3:15-4:15 p.m. in Salazar Hall Room C246.

Refreshments are available before the seminar.

Follow this link to visit Dr. Waterman's homepage.                           Back to Top



Liming (Alice) Wang , Ph.D. - Thursday, March 3, 2011

Professor of Mathematics
University of California, Irvine

Signal Transduction: Multistability, Noise, and Cell Population Dynamics

Biological networks act as biochemical computing machines in cells.
Signals are sensed from cellular and extracellular environment, and
appropriate responses are produced. Understanding the underlying
control feedback mechanism is a challenge in systems biology. In this
talk, I will start with signal transduction in single cells and then
discuss the effect of noise on signaling pathways. Finally, I will
present a multiscale model that combines the single cell dynamics,
cell division, intracellular fluctuations, and population dynamics. In
single cells, I will focus on ultrasensitivity and asymptotic
behaviors of multisite protein phosphorylations.

Time: 3:15-4:00 p.m. in Simpson Tower F213.

Refreshments are available before the seminar.

Follow this link to visit Dr. Wang's homepage.                           Back to Top


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