<span class=strong>Reception and Poster Session</span>
Monday, April 21, 2008 - 5:00pm - 6:30pm
- Evolution of song culture in the zebra finch
Haibin Wang (Cold Spring Harbor Laboratory)
A number of Oscine songbirds are vocal learners. In these species, song shares a remarkable characteristic with human language: both are acquired through imitative learning. When reared in social and acoustic isolation, the Zebra Finch (the species of songbird under study here) can still sing, revealing the genetically encoded aspect of song. However, the isolate songs usually have longer syllables, and appear to be more variable than the wild type (WT) songs found in the wild or in laboratory colonies.
In order to understand how the isolate song might evolve over multiple generations, we successively trained naïve juveniles starting with an isolate founding father. The first generation learners are in turn used as tutors to train the next generation, and so on. Thus, tutoring lineages are established through a recursive training processes. We found that small, yet systematic variations accumulate over generations of training. Remarkably, the descendants’ song structures are gradually transformed towards WT songs.
- The advantage of two step transport problem
Ezio Marchi (Instituto de Matemática Aplicada)
Here, we present a transport model which indroduce a variant in
the transport theory. Here the mass or merchandize in order to
go from a port to a destination must pass through a deposit,
without accumulation. It is possible to consider deposit
constraint. We obtain the corresponding linear program
associated to it, as well as the dual. The application of this
model to biological sciences, specially in human body, lungs, blood and biological systems seems promising.
We obtain the dual, which appear in a natural way from the
incidence matrix, which has many interesting properties.
The rank is the number of the ports, deposits plus the
destination minus on.
We study and characterize all the extremals extending the ideas
of Jurkar-Ryser, and von Neumann in the case of the classical
transpot model. A relation with the material in the papers by
E. Marchi:Z.Wahrscheinlichtheorie verww. geb,12,220-230
(1969) and 23,7-17, (1972), is underway.
We were succesful to extend this theory to mixed model
considering that in a deposit, there exists the possibility to
stay or passing. This rich study permits more potentiality to
the tools. An extension to several steps has been performed and
its potentiality for applications is vast.
- Trajectory measures describing the locomotor behavior of Drosophila melanogaster in a circular arena
Dan Valente (Cold Spring Harbor Laboratory)
Measuring locomotor behavior of Drosophila in enclosed arenas is a powerful way to obtain a quantitative behavioral phenotype. The measures previously used for this purpose are relatively coarse, thus ignoring fine scale movements of the fly. More importantly, they do not explicitly take into account how the arena shapes the dynamics of the locomotion. We acquired data using a video-tracking system to measure the trajectory of a fly over extended periods as it explores a circular arena. Based on this data, we present some metrics that take into consideration the dynamics of the trajectory, as well as the interactions of the trajectory with the geometry of the arena. The basic idea is to treat the locomotor trajectory of the fly as a stochastic process, and then estimate a set of marginal distributions of the probability measure describing this process. The measures include joint or individual distributions of position, speed, path curvature, inter-event times and re-orientation angles after stopping. These probability measures can be worked into other behavioral setups, are relatively easy to calculate using robust statistical estimation procedures, and can account for environmental effects on the behavior. They also serve as foundation for a quantitative stochastic process model of the walking behavior.
- Biological project: The construction of the cycle in Lotka-Volterra of n-species
Ezio Marchi (Instituto de Matemática Aplicada)
Lotka-Volterra equations are very famous by two biological
spices. Generally the most common presentations are in ecology
science. We study this models without considering the
antisymmetric condition among the parameters.(see Marchi and
Velasco Revista Mexicana de Fisica,36,No4(1990)665-679).We
obtain a movement constant for the systems which satisfies the
Hamilton equation. For more than two interacting species the
result the Volterra result are biologically improper. This is
due to the antisymetric conditions. Following Volterra original
methods combined with the variation of Montroll et. all, who
applied such equation to maser and laser, we obtain some
powerful personal procedure that we applied to the three and
four species obtaining and general condition and build the
cycle. Moreover this can be extended for an arbitrary number of
biological species obtaining constructively the cycle. The
background idea is to delete one variable at that time using
partial differentials equations of second power of the first
order. Furthermore we consider the conservation of the density
of point in the fase space (LIoville theorem) an we postulate
that the same distributions following the Gibbs Canonical Law.
By the way Prigogyne at all applied Lotka-Volterra system in
non-equilibrium thermodynamics. Moreover, there are several
applications of Lotka-Volterra to the theory of membrane. We
can show you some of them. Finally, we point out that
there are about four hundred papers in the subject in the last
ten years, and non of them apply our methods. The potentiality
for real application is very important even if the system of
Lotka-Volterra is asymptotically unstable.
- A design principle in biochemical reaction networks
based on realization theory
Bassam Bamieh (University of California)
We attempt to address the question of why there are so many intermediate species in biochemical
reaction networks using an idea from realization theory. We describe how prescribed biological
function can be designed with very low dimensional models, which are however not implementable
with the physically allowable biochemical reaction mechanisms. It then becomes apparent that
the introduction of a large number of intermediate species can be interpreted as a realization technique
to enable the implementation of prescribed function with the available dynamical building blocks.
By reversing this realization scheme, we propose a model reduction paradigm for biochemical reaction networks.
- Architecture and inherent robustness of a bacterial cell cycle control system
David Dill (Stanford University)
Joint work with Xiling Shen, Justine Collier, Lucy Shapiro, Mark Horowitz, and Harley H. McAdams.
We developed a mechanistic model of the cell cycle control of Caulobacter Crescentus. Symbolic model checking reveals that the cell cycle is extremely robust to parameter variations, and that the cell cycle starts and stops reliably to accommodate arbitrary starvation periods.
- A transcriptional regulatory switch underlying B-cell terminal
differentiation and its disruption by dioxin
Sudin Bhattacharya (The Hamner Institutes for Health Sciences)
Joint work with Qiang Zhang(1), Melvin E. Andersen(1)
and Rory B.
The terminal differentiation of B cells in lymphoid organs into
antibody-secreting plasma cells upon antigen stimulation is a
step in the humoral immune response. The architecture of the
transcriptional regulatory network consists of coupled
mutually-repressive feedback loops involving the three
factors Bcl6, Blimp1 and Pax5. This structure forms the basis
irreversible bistable switch directing the B-cell to plasma
differentiation process - i.e., the switch remains on even
activating stimulus (antigen) is removed. The environmental
2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is known to suppress
humoral immune response by interfering with this
program. We have developed a computational model of the
pathways that regulate B-cell differentiation, and the
mechanism by which TCDD impairs this process through the action
aryl hydrocarbon receptor (AhR). Using a kinetic model and
analysis, we propose that TCDD regulates the proportion of
differentiate into plasma cells by raising the threshold dose
lipopolysaccharide (LPS) required to trigger the
We also show that stochastic modeling of gene expression, which
cell-to-cell differences in content of signaling proteins,
distributional characteristics to the timing and probability of
differentiation among a population of B-cells. This
variability is likely to be a key determinant of dose-response
sensitivity of individual cells to differentiation.
(1) Division of Computational Biology, The Hamner Institutes
Sciences, Research Triangle Park, NC 27709, USA
National Center for Computational Toxicology, U.S.
Protection Agency, Research Triangle Park, NC 27711, USA
- Computational hemodynamics analysis in large blood
vessels: Effects of hematocrit variation on flow stability
Oluwole Makinde (University of Limpopo)
Understanding the effects of blood viscosity
a very crucial role in hemodynamics, thrombosis and
could provide useful information for diagnostics and therapy of
vascular disease. Blood viscosity, which arises from frictional
interactions between all major blood constituents, i.e. plasma,
proteins and red blood cells, constitutes blood inherent
flow in the blood vessel. Because red blood cells (RBCs) are
constituent of the cellular phase of blood, white blood cells
platelets normally do not have a great influence on whole blood
viscosity. When blood flows through a vessel, it tends to
two different phases. In direct contact with the wall a low
phase exists, which is deficient in cells and rich in plasma
and acts as
a lubricant for the blood transport. In the central core region
vessel a high viscosity phase exists, which depends on the
In this paper, the nature and stability of blood flow in a
is investigated numerically using a spectral collocation
expansions in Chebyshev polynomials. The study reveals that a
hematocrit concentration in the central core region of a large
has a stabilizing effect on the flow.
Keywords: Arterial blood flow; Hematocrit; Variable viscosity;
stability; Chebyshev spectral collocation technique
1.) Pedley T. J.: The Fluid Mechanics of Large Blood Vessels.
University Press, London, 1980.
2.) Makinde O. D.: Magneto-Hydromagnetic Stability of plane-
flow using Multi-Deck asymptotic technique. Mathematical &
Modelling Vol. 37, No. 3-4, 251-259, 2003.
3.) Makinde O. D. and Mhone P. Y.: Temporal stability of small
disturbances in MHD Jeffery-Hamel flows. Computers and
Applications, Vol. 53, 128–136, 2007.
4.) Makinde O. D.: Entropy-generation analysis for
channel flow with non-uniform wall temperature. Applied Energy,
- Recurrent and robust patterns underlying human relative preference, and associations with brain circuitry plus genetics
Hans Breiter MD (Massachusetts General Hospital)
Joint work with BW Kim.
The Phenotype Genotype Project on Addiction and Depression (PGP), with support from the Departments of Neurology, Psychiatry, and Radiology, and Center for Human Genetic Research; Massachusetts General Hospital and Harvard Medical School; Boston, MA, USA
Positive and negative preferences can be assessed by keypress procedures that quantify (i) decision-making regarding approach, avoidance, indifference, and ambivalence responses, and (ii) judgments that determine the magnitude of approach and avoidance. Most prior studies of relative preference have not used keypress procedures, but have used ratings of personal utility, as a composite index of approach and avoidance. Such composite ratings can be calibrated against an absolute framework such as the macroeconomic pricing of commodities, as is done with Prospect Theory. It leaves open questions of whether or not splitting composite ratings of utility into approach and avoidance measures reveals any patterns in behavior, as observed for Prospect Theory. Such patterns might include a trade-off relationship between approach and avoidance, or a value function that might not need an absolute macroeconomic framework. We assessed these questions across multiple sets of healthy control sub
jects with a keypress procedure, and found a set of patterns for approach and avoidance are (i) recurrent across many stimulus types, and (ii) robust to the injection of noise. These patterns include: (a) a preference trade-off plot that counterbalances approach and avoidance responses and represents biases in preference and consistency/uncertainty of preference, (b) a value function linking preference intensity to uncertainty about preference, and (c) a preference saturation plot that represents how avoidance actions are over-determined relative to approach actions. One can consider this set of patterns to be a form of relative preference theory (RPT), since they meet the same requirements for recurrency and robustness to noise as the Weber-Fechner-Stevens Law. As with the value function for Prospect Theory, the value function in RPT has a steeper slope for negative relative to positive preferences (i.e., loss aversion), and can be described as a power law, or a logarithmic functi
on. All of these patterns show symmetry between group and individual data in that they have similar mathematical formulations as manifolds or boundary asymptotes for group data, or as fitted functions for individual data across multiple variables. These patterns verify known biases between females and males regarding viewing beautiful and average faces. When used to evaluate cocaine dependent subjects versus healthy controls, these patterns quantify the phenotype of the restricted behavioral repertoire observed in addiction. When used as regressors in the analysis of fMRI data, RPT measures are associated with significant BOLD signal change across a set of reward/aversion brain regions. Both keypress behavior and fMRI BOLD signal can be further associated with polymorphisms is genes such as CREB1 and BDNF. Given RPT scaling between groups of subjects and individuals, further work is warranted to assess if scaling can be achieved to brain circuitry and genetics.
- Quantitative systems analysis of multicellular morphodynamics
Anand Asthagiri (California Institute of Technology)
The goal of my research program is to better understand how biological circuits program multicellular phenotypes. While a major focus of the group involves phenotypes associated with human epithelial systems, we have also drawn upon more tractable model systems, such as C. elegans and yeast, to glean deeper fundamental insights. Each of these three biological systems provides unique advantages that my lab has sought to exploit using a combination of computational and quantitative experimental approaches.