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Back to Current MBI Seminars
Past MBI Seminars: 2003-2004
Friday, June 18, 11:00-12:00PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Vitaly Ganusov, Emory University
Title: Mathematical Models of Maintenance of Immunological Memory
Immunological memory --- the ability to "remember" previously
encountered pathogens and respond faster upon re-exposure is a central
feature of the immune response of vertebrates. We use models to
consider the role of different factors such as exposure to pathogens,
cross-reactive and bystander stimulation and homeostasis on the
longevity of memory in the CD8 T cell population. We show that the
longevity of memory, defined as the decline in the population of
memory cell lineages is governed by the following rules:
1. The average loss of cells in memory lineages is proportional
to the number of cells of new (memory) specities generated following
stimulation by new pathogens and inversely proportional to the size
of the memory compartment.
2. Cross reactive stimulation (i) reduces the average rate
of loss of memory by reducing the magnitude of expansion of new
naive lineages; (ii) the variation in the rate of decline in the
populations of cells to different lineages is greatest at intermediate
levels of cross-reactivity.
3. The loss of memory is independent of bystander stimulation
and the precise mechanism for the maintenance of homeostasis.
Samuel S.-H. Wang Seminar
Wednesday, June 16, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Title: Functional Dissection of the CA3-CA1 Learning Rule
Speaker: Samuel S.-H. Wang, Princeton University
Wang Lab Homepage: http://synapse.princeton.edu
I will talk about learning rules in general. The abstract below
focuses on one aspect of the work, but I will talk about more than
this. For instance, I will cover STDP at these synapses, which is
far more complex than suggested by other investigators, but is still
tractable.
In populations of synapses, long-term potentiation and long-term
depression reflect the sum of many individual plasticity events.
We have found that at individual hippocampal CA3-CA1 synapses, upward
or downward transitions in strength are all-or-none and sudden,
thus allowing each synapse two levels of strength. Under native
conditions, three-fourths of synapses begin in a low-strength state.
Downward transitions are reversible, but after upward transitions
synapses can be locked quickly into a high-strength state. Upward
and downward transitions could be isolated by blocking or saturating
potentiation or depression. This resolves plasticity into component
processes that, when recombined, yield the native learning rule.
Under realistic spiking conditions, these processes have activity-
and timing-dependence predicting that when a rat runs through a
place field the only possible form of plasticity is LTP. A three-state
model (low, high and locked-in) accounts for our observations and
for a variety of previous physiological, pharmacological and genetic
manipulations.
Thursday, June 10, 11:00-12:00PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Daniel Coombs, University of British Columbia, Vancouver,
Canada
Title: Viral optimisation within and between hosts
Natural selection acts on viruses at a variety of levels: within
cells, within hosts, and between hosts. We examine how viruses can
optimise their behavior within a host under pressure from the immune
system, and how this optimal within-host behavior may not be ideal
from the point of view of transmission between hosts. This is a
preliminary presentation of ongoing work with Michael Gilchrist
(University of Tennessee) and Alan Perelson (LANL).
Tuesday, June 8, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Daniel Coombs, University of British Columbia, Vancouver,
Canada
Title: Equilibrium behavior of cell-cell synapses
In many situations, cell-cell adhesion is mediated by multiple
ligand-receptor pairs. For example, the interaction between T cells
and antigen-presenting cells of the immune system is mediated not
only by T cell receptors and their ligands (peptide-major histocompatibility
complex) but also by binding of intracellular adhesion molecules.
Interestingly, these binding pairs have different resting lengths.
Fluorescent labelling reveals segregation of the longer adhesion
molecules from the shorter T cell receptors in this case. We explore
the thermal equilibrium of a general cell-cell interaction mediated
by two ligand-receptor pairs to examine competition between the
elasticity of the cell wall, non-specific intercellular repulsion
and bond formation, leading to segregation at equilibrium. We make
detailed predictions concerning the relationship between physical
properties of the membrane and ligand-receptor pairs and equilibrium
pattern formation and suggest experiments to refine our understanding
of the system. We demonstrate our model by application to the T
cell-antigen-presenting-cell system and natural killer cell-target
cell adhesion. Our results underline the importance of active, energy-consuming
processes in this system.
Thursday, June 3, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Title: Elemental Dynamics across the Scales of Biological Organization
Speaker: Dr. Irakli Loladze, University of Nebraska, Lincoln
New insights in such diverse topics as RNA to protein ratio in
cells, predator-prey interactions, and effects of globally rising
CO2 on humans come from mathematical models that rely on biological
stoichiometry. Biological stoichiometry is founded on rigorous scale-invariant
principles such as mass balance law and the fact that for all life
forms, from viruses to humans, carbon (C), nitrogen (N) and phosphorus
(P) are essential. The rigor and the universality of these principles
provide a framework that is particularly appealing to mathematicians
that want to venture into mathematical biology. In this talk, I
will present three examples of stoichiometrically based ODE models
together with their mathematical analysis and biological implications.
Thursday, May 27, 11:30-12:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Title: A New Approach to Modeling Multiple Influenza Strain Dynamics
Speaker: Miriam Nuno, Cornell University
Authors: Miriam Nuno, Maia Martcheva, Paulo Parra, and Carlos Castillo-Chavez
Models that incorporate host dynamics to study the evolving nature
of pathogens such as influenza face major computational challenges.
We develop a mathematical model that allows for the study of several
strain structures and show how these may influence disease dynamics.
In particular, partial cross-immunity to next-to-kin strains leaves
hosts less likely to be infected by antigenically similar strains
while providing no immunity against all other strains. The status
of the host is determined by immune-competence levels corresponding
to all the strains that each host has immunity to. Immunity of the
host population is captured by an index-set notation where the index
specifies the immune-competence level against each particular strain.
In contrast to previous modeling approaches, the population here
is structured into non-intersecting subclasses. That is, since multiple
infection with influenza strains is uncommon, we do not imbed superinfection
with the same or different strains as part of our model. We provide
threshold quantities that allows us to determine conditions for
the invasion of a single strain or multiple co-existence of strains.
Furthermore we provide stability conditions for the disease-free
and endemic state equilibrium.
Tuesday, May 25, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Title:Dynamics of Two-Strain Influenza with Isolation and Partial
Cross-Immunity
Speaker: Miriam Nuno, Cornell University
Authors: Miriam Nuno, Zhilan Feng, Maia Martcheva, and Carlos Castillo-Chavez
The time evolution of influenza A virus is linked to a non-fixed landscape
driven by tight co-evolutionary interactions between hosts and competing
influenza strains. Herd-immunity, cross-immunity and age-structure
are among the factors that have been shown to support strain coexistence
and/or disease oscillations. In this study, we put two influenza strains
under various levels of (interference) competition. We establish that
cross-immunity and host isolation lead to periodic epidemic outbreaks
(sustained oscillations) in this multi-strain system. We compute the
basic reproductive number for each strain independently, as well as
for the full system and show that when the basic reproductive number
of both strains is less than 1, the disease dies out. Sub-threshold
coexistence driven by cross-immunity is possible even when the basic
reproductive number of one strain is below one. Conditions that guarantee
a winning type or coexistence are established in general. Oscillatory
coexistence is established via Hopf-bifurcation theory and numerical
simulations using realistic parameter values.
Monday, May 3, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Title:Structured models of microbial growth: single and mixed substrate
cultures
Speaker: Sergei Pilyugin, Mathematical Biosciences Institute, The
Ohio State University
Presentation materials: PDF
The dynamics of continuous cultures (or bioreactors) has been a
problem of considerable interest to many mathematicians. The standard
modeling approach was developed following the pioneering work of
J. Monod. Models of this class include only extracellular variables
such as cell and substrate concentrations. These simple unstructured
models typically fail to accurately describe the transient behavior
of bioreactors. Understanding such transients is crucial for such
applications as waste water treatment and food processing where
bioreactors are widely used.
In this talk, I will report on our recent progress in formulating
and analyzing structured models of microbial growth which explicitly
consider intracellular variables that determine the physiological
state of the cell.
Specifcally, I will discuss such topics as
1. General description and formualtion of structured models;
2. The role of transport enzymes;
3. Dynamics of single and mixed cultures;
4. Connections between theory and experiments.
References:
[1] Shoemaker, J., Reeves, G.T., Gupta, S., Pilyugin, S.S., Egli,
T., & Narang, A. (2003). The dynamics of single-substrate continuous
cultures: The role of transport enzymes. J. Theor. Biol., 222,
307-322.
[2] Reeves, G.T., Narang, A., & Pilyugin, S.S. (2003). Growth of
mixed cultures on mixtures of substitutable substrates: The operating
diagram for a structured model. Journal of Theoretical Biology,
226 (2), 143-157.
[3] Pilyugin, S.S., Reeves, G.T., & Narang, A. Stability of
mixed microbial cultures: connecting theory and experiments. Part
1. Unstructured model. Manuscript submitted for publication.
[4] Pilyugin, S.S., Reeves, G.T., & Narang, A. Stability of
mixed microbial cultures: connecting theory and experiments. Part
2. Structured model. Manuscript submitted for publication.
MBI Postdoctorate Seminar
Thursday, April 29, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Sanjay Danthi, Mathematical
Biosciences Institute, The Ohio State University
Title: The Excitability of Adrenal Cortical Cells
Adrenal Zona Fasciculata (AZF) cells release the hormone Cortisol
in conditions of physical or psychological stress. Cortisol release
is governed by the action of ion channels expressed in the AZF cells.
Using the method of patch clamp, the ion channels expressed in bovine
AZF cells were analyzed. Modeling of these ion channels will involve
fitting mathematical equations that describe the empirical data.
Creating a mathematical model that mimics the behavior of these
ion channels will provide a unique understanding of the process
of cortisol release and will help in predicting the possibility
of membrane excitability of the AZF cells.
Friday, April 23, 2:00-3:00pm (talk),
3:00-5:00pm (discussion)
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Alexander D Varshavsky, Eli Lilly
Presentation: PPT
Monday, April 19, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Sergei Pilyugin, Mathematical Biosciences Institute, The
Ohio State University
Title: Dynamics of chemostats with variable yield
The classical Monod model of microbial growth in a chemostat assumes
that the yield coecient, dened as the ratio of biomass production
to nutrient consumption, is constant. In this talk, I will discuss
the generalization of the Monod model to the case where the yield
coeffcient is an increasing function of the nutrient concentration.
In contrast to the Monod model, the variable yield model exhibits
sustained oscillations. Moreover, the variable yield model may undergo
a subcritical Hopf bifurcation and feature multiple limit cycles.
I will present the mathematical methods that were derived to analyze
this model. I will also discuss the implications of variable yield
for the coexistence of two competing populations.
Specifcally, the talk will include:
1. Formulation and stability analysis of the variable yield model;
2. A subcritical bifurcation lemma, divergence criterion;
3. Several examples involving the divergence criterion;
4. Examples of complicated dynamics for two competitors, period-doubling
cascades, Neimark-Sacker bifurcation.
References:
[1] Pilyugin, S.S., & Waltman, P. (2003). Multiple limit cycles
in the chemostat with variable yield. Math. Biosci., 182
, 151-166.
[2] Pilyugin, S.S., & Waltman, P. (2003). Divergence criterion
for generic planar systems. SIAM Journal on Applied Mathematics,
64 (1), 81-93.
[3] Arino, J., Pilyugin, S.S., & Wolkowicz, G. S. K. Considerations
on yield, nutirent uptake, cellular growth, and competition in chemostat
models. Manuscript submitted for publication.
MBI Postdoctorate Seminar
Thursday, April 15, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Yixin Guo, Mathematical
Biosciences Institute, The Ohio State University
Title: Existence and stability of standing pulses in neural networks
We consider the existence and the stability of standing pulse solutions
of an integro-differential equation used to describe the activity
of neuronal networks. The network consists of a single-layer of
neurons with non-saturating piecewise linear gain function, synaptically
coupled by lateral inhibition. The existence condition for pulses
can be reduced to the solution of an algebraic system and using
this condition we map out the shape of the pulses for different
weight kernels and gains. We also find conditions for the existence
of pulse with a 'dimple' on top and for a double-pulse. For a fixed
gain and connectivity, we find two single-pulse solutions-a ``large''
one and a ``small'' one. We derive conditions to show that the large
one is stable and the small one is unstable. Using the same conditions,
we also show that the dimple-pulse is stable. More importantly,
the large single-pulse and the dimple pulse are bistable with the
all-off state. This bistable localized activity may have strong
implications for the mechanism underlying of working memory.
Monday, April 12, 2:00-3:00PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Sergei Pilyugin, Mathematical Biosciences Institute, The
Ohio State University
Title: Estimating parameters of cell turnover: Smith-Martin type
models and method of rescaling
Presentation Materials: PDF
The dynamic nature of immune responses requires the development
of appropriate experimental and theoretical tools to quantitatively
estimate the division and death rates which determine the turnover
of immune cells. A number of papers have used experimental data
from BrdU and D-glucose labels together with a simple random birth-death
model to quantify the turnover of immune cells focusing on HIV/SIV
infections.
In this talk, I will discuss how the uncertainties in the assumptions
of the random birth-death model may lead to substantial errors in
the parameters estimated. I will show how more accurate estimates
can be obtained from the more recent CFSE data which allow to track
the number of divisions each cell has undergone.
Specifcally, the talk will include:
1. Biological background;,
2. Description of a mathematical model;
3. Several examples;
4. Analysis of the Smith-Martin model;
5. Method of rescaling;
6. Application to experimental datasets;
7. Discussion.
References:
[1] Pilyugin, S.S., Ganusov, V. V., Murali-Krishna, K., Ahmed,
R., & Antia, R. (2003). The rescaling method for quantifying the
turnover of cell populations. J. Theor. Biol., 225, 275-283.
[2] Ganusov, V.V., Pilyugin, S.S., de Boer, R., Murali-Krishna,
K., Ahmed, R., & Antia, R. Quantifying the cell turnover using
CFSE data. Manuscript submitted for publication.
Tuesday, March 23, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Scott Camazine
Title: Self-Organization in Biological Systems
The living world is filled with striped and mottled patterns of
contrasting colors; with sculptural equivalents of those patterns
realized as surface crests and troughs; with patterns of organization
and behavior even among individual organisms. People have long been
tempted to find some obscure "intelligence" behind all these biological
patterns. In the early twentieth century the Belgian Symbolist playwright
Maurice Maeterlinck, pondering the efficient organization of bee
and termite colonies, asked:
"What is it that governs here? What is it that issues orders,
foresees the future, elaborates plans and preserves equilibrium,
administers, and condemns to death?"
The natural world, it turns out, is replete with patterns and processes
that exhibit organization without an organizer, coordination without
a coordinator.
For some people who come to appreciate this point, it then becomes
tempting to attribute such complex patterns and processes to innate
behaviors, instincts, or genetic information encoded deep within
the chromosomes of the organism. But such "simple explanations"
are not likely and, in the best of cases, they merely sweep the
question under the carpet. What then is the origin of all this stunning
complexity?
Excerpted from:
http://www.naturalhistorymag.com/0603/0603_feature.html
MBI Postdoctorate Seminar
Thursday, February 26th, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Sookkyung Lim, Mathematical
Biosciences Institute
Title: Whirling instability of an elastic filament by the immersed
boundary method
When an elastic filament spins in a viscous incompressible fluid
at varying angular frequency it may undergo a whirling instability
and a bifurcation occurs, as studied asymptotically by Wolgemuth,
Powers, Goldstein. We use the Immersed Boundary (IB) method to study
the interaction between the elastic filament and the surrounding
viscous incompressible fluid as governed by the Navier-Stokes equations,
and to determine the nature of the bifurcation, which turns out
to be subcritical. This allows the study of the whirling motion
when the shape of the filament is very different from the unperturbed
straight state. The numerical method shows two dynamical motions
of the rotating elastic filament depending on the angular frequency
and also on the initial bend. These are in which the filament rotates
in place around a straight axis, and in which the axis of the filament
becomes drastically bent and precesses about the symmetry axis of
the system.
Monday, February 23, 2:30-3:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Professor Giuseppe
Lancia, University of Udine, Italy
Title: Combinatorial Optimization Problems in the Study of Human
Polymorphisms
A polymorphism is a trait which shows variability in a population
(e.g., the blood type): without polymorphisms, we would all look
the same! The possible values of the trait are called alleles.
At genomic level, a polymorphism is a DNA region (string of A, T,
C and Gs) whose content varies in a population. The smallest such
polymorphism consists of a single base, and is called Single Nucleotide
Polimorphism (SNP, pronounced "snip").
Trying to determine the allele values for a set of SNPs, for either
an individual or an entire population, gives rise to several nice
and challenging combinatorial problems. These problems, called "haplotyping"
problems, have been extensively studied in the last few years. In
this talk, we will illustrate the most important haplotyping problems
and mention the results that have been obtained for their solution.
In particular, some of such problems have been proved NP-hard and
solved by (worst case) exponential-time algorithms, while others
are solvable in polynomial time.
MBI Postdoctorate Seminar
Thursday, February 19th, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Iris Meier, Department
of Plant Biology, Ohio State University
Title: Spatial Organization of Ran Signaling in plants
Ran is a small GTPase with functions in nuclear transport, spindle
formation, and nuclear envelope re-assembly. It exists in two forms,
Ran-GTP and Ran-GDP, which are interconverted by the activity of two
proteins. RanGAP turns RanGTP into RanGDP while RCC1 turns RanGDP
into RanGTP. The spatial separation of RanGAP and RCC1 in the cell
leads to the establishment of a gradient between Ran-GTP and Ran-GDP,
which is important for the function of Ran. During interphase, RanGAP
is cytoplasmic while RCC1 is located in the nucleus. This establishes
a gradient of RanGTP to RanGDP across the nuclear envelope, which
is involved in the directionality of transport between nucleus and
cytoplasm. During animal mitosis, RCC1 remains bound to the chromosomes
while RanGAP migrates to the spindle apparatus. The resulting mitotic
gradient of Ran has been shown by imaging methods in live cells. We
have found that like animal RanGAP, plant RanGAP is associated with
the nuclear envelope during interphase. However, during mitosis, it
appears at the newly forming cell plate, a structure unique to plants.
A specific N-terminal domain of plant RanGAP is necessary and sufficient
for targeting the protein to the plant nuclear envelope in interphase
and to the cell plate in mitosis. We conclude that the spatial re-organization
of the Ran gradient during mitosis differs in plants and animals.
We are interested in measuring and possibly modeling the gradient
in plant cells.
MBI Postdoctorate Seminar
Thursday, February 12th, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Edward Givelberg,
Computer Science Division, University of California at Berkeley
Title: Fluid-Structure Interaction in Complex Biological Systems
Complex biological systems containing tissue immersed in a viscous
incompressible fluid are ubiquitous. Understanding the dynamics
of such systems is crucial in a vast array of scientific and engineering
problems, such as the function of the heart, the mechanism of hearing,
the dynamics of biological membranes, cell morphology and insect
flight, to name a few. In such systems the tissue may be elastic
or active, and it may posess complicated internal structure. Its
interaction with the fluid is often coupled with other physical
processes, such as biochemical reactions, electrical currents and
heat diffusion. In this talk I will survey my work on large-scale
computer modeling of such systems using the immersed boundary method.
I will discuss the application of this work to modeling the fluid
dynamics of the heart and (in more detail) the construction of a
computational model of the cochlea (the inner ear).
Tuesday, December 2, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Christiane Linster,
Department of Neurobiology and Behavior, Cornell University
Title: Olfactory coding and spike-timing-dependent plasticity
Spatial patterns of glomerular activity in the vertebrate olfactory
bulb and arthropod antennal lobe are believed to reflect an important
component of the first-order olfactory representation and contribute
to odorant identification. Higher-concentration odorant stimuli
evoke broader glomerular activation patterns, resulting in greater
spatial overlap among different odor representations. However, behavioral
studies demonstrate results contrary to what these data might suggest:
honeybees are more, not less, able to discriminate among odorants
when they are applied at higher concentrations. Using a computational
model of the honeybee antennal lobe, we here show that changes in
synchronization patterns among antennal lobe projection neurons,
as observed electrophysiologically in response to odor stimuli of
different concentrations, could parsimoniously underlie these behavioral
observations. We suggest that "stimulus salience," as defined behaviorally,
is directly correlated with the degree of synchronization among
second-order olfactory neurons.
Tuesday, November 25, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Tim Lewis, Courant
Institute and Center for Neural Science, New York University
Title: Dendritic Effects in Networks of Electrically Coupled Spiking
Neurons
Recently, direct electrical coupling between inhibitory neurons
has been found to be widespread in the brain. The effects of electrical
coupling between neurons has been the focus of much experimental
and theoretical work, however the functional role that electrical
coupling plays in neuronal networks remains unclear. It has been
suggested that electrical coupling can help coordinate synchronous
oscillatory behavior in inhibitory networks, which has been hypothesized
to be important for sensory and cognitive processes. However, it
has been shown that electrical coupling can desynchronize activity
as well. Previous theoretical studies have examined the effects
of electrical coupling on synchronization patterns between single-compartment
model neurons. The applicability of these studies to dynamics in
real inhibitory neuronal networks depends on whether or not a single-compartment
description is a sufficient model. Single-compartment models neglect
the spatial structure of neurons, and when neurons are not sufficiently
electrotonically compact, the spatial structure cannot be ignored.
In this talk, I will discuss how the spatial structure of neurons
(dendritic processing) can affect network dynamics and I will show
how the location of electrical coupling influences phase-locking
in networks of neurons.
MBI Postdoctorate Seminar
Thursday, November 6th, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Mike Zhu, Neuroscience
Department and Neurobiotechnology Center, The Ohio State University
http://www.med.ohio-state.edu/neuroscience/grad/zhu.htm
Ca2+ ions play a very important role in cellular function, ranging
from contraction, differentiation, secretion to transcriptional
regulation and programmed cell death. My lab focuses on studying
the structure and functional regulation of Ca2+ permeable channels,
which are essential for increasing intracellular Ca2+ concentrations.
Molecular cloning and genome sequencing have revealed the existence
of a novel family of Ca2+ permeable cation channels formed by homologues
of transient receptor potential (TRP) protein initially identified
from eyes of fruit flies. The TRP superfamily currently consists
of several subfamilies including TRPC, TRPV and TRPM, each of which
contains multiple family members. These channels are involved in
many important physiological functions ranging from taste transduction,
vision, muscle contraction, synaptic transmission fertilization
to temperature, pressure, and pain sensations. The TRP channels
have been the main focus of my research. Here, I will present two
topics concerning with the functions of TRPV channels. First, I
will describe a naturally occurring dominant-negative isoform of
TRPV1, also know as vanilloid receptor type 1. Then I will discuss
a number of potential activation signals for TRPV3. Both channels
are considered to be thermal sensitive channels involved in inflammatory
and nociceptive pain pathways of the somatosensory system. Integration
of signals coming from various thermal sensitive channels could
be an area for mathematical modeling. In the last third of my talk,
I will present our study on the regulation of Cav2.1 voltage-gated
channel by L7/Pcp2, a cerebellar specific protein known to regulate
Gi/o family of the heterotrimeric G proteins. Our data suggest that
L7/Pcp2 regulates the activity of the Ca2+ channel in a dose dependent
manner. This type of regulation is likely to occur in the cerebellar
Purkinje cells in consequence to the activity-dependent local synthesis
L7 proteins and thus implicated in learning and memory. Mathematical
modeling is commonly used to predict cerebellar output associated
with changes in the activity of different ion channels in Purkinje
cells.
Neuroscience Journal Club
Wednesday, November 5, 12:30-1:30PM
MBI Conference Room- Mathematics Building, Room 222
1. Nicolelis,M.A.L. (2003). Brain-machine interfaces to restore
motor function and probe neural circuits. Nature Reviews Neuroscience,
4, 417-422.
2. Chapin, J.K., Moxon, K.A., Markowitz, R.S., & Nicolelis,
M.A.L. (1999). Real-time control of a robot arm using simultaneously
recorded neurons in the motor cortex. Nature Neuroscience, 2,
664-670.
Tuesday, November 4, 2:30-3:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Bruce I. Terman,
Departments of Medicine and Pathology, Albert Einstein College of
Medicine
Angiogenesis, the formation of new blood vessels, is required for
several normal physiological process including development and wound
healing. Angiogenesis also contributes to the progression of several
diseases because it is a mechanism for providing diseased tissue
with the nutrients required for cellular viability. For example,
angiogenesis is required for tumors to grow beyond 1 mm in size.
Pharmaceuticals that target angiogenesis block tumor growth in animal
models and certain of these drugs are currently under clinical evaluation.
Angiogenesis is a complex physiological process that is mediated
by the endothelial cells that form existing blood vessels. Component
of this process include the degradation of the extracellular matrix,
endothelial cell migration, cell proliferation, and vessel formation.
These cellular activities are activated by extracellular stimuli,
and both growth factors and the extracellular matrix regulate cell
function. These activators do not enter the endothelial cells, but
instead activate cell surface receptors triggering intracellular
cell signal transduction pathways.
Vascular Endothelial Growth Factor (VEGF) has received considerable
attention as a potent angiogenic growth factor. This is due in part
to the observations that inhibition of VEGF function blocks both
angiogenesis and tumor growth in animal models. VEGF binding to
its high affinity receptor activates multiple signal transduction
pathways and endothelial cell activities. Clarification of these
signaling pathways may allow for the identification of new pharmaceutical
targets and the development of more efficacious inhibitors.
MBI Postdoctorate Seminar
Thursday, October 30th, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Jyan-Chyun Jang,
Dept of Horticulture and Crop Sciences, The Ohio State University
Title: Global transcription profiling reveals
carbon and nitrogen interaction, sugar status and stress response,
and the differential regulation of glucose induction versus glucose
repression in model plant Arabidopsis thaliana
http://www.ag.ohio-state.edu/~jcjang/
Complex and interconnected signaling networks allow cells to integrate
information that regulates growth, differentiation, cell division
or programmed cell death. Plants can sense levels of nutrients such
as carbon and nitrogen and accordingly adjust gene expression, which
in turn affects metabolic and cellular activities. Numerous physiological
studies have demonstrated that the availability and ratio of carbon
and nitrogen are key determinants for plant growth and development.
While this nutrient response is critical, our understanding of the
molecular mechanisms underlying sugar or nitrogen signal transduction
in plants is obscure. To begin unraveling complex sugar signaling
networks in plants, DNA microarray analysis was used to determine
the effects of glucose and nitrate on gene expression on a global
scale in model plant Arabidopsis. Under the conditions used, glucose
is a much more potent signal in regulating transcription than inorganic
nitrogen, and that other than genes associated with nitrate assimilation,
glucose had a greater effect in regulating nitrogen metabolic genes
than nitrogen itself. Glucose also regulated a broader range of genes,
including genes associated with carbohydrate metabolism, transcriptional
regulation, and metabolite transport. Cluster analysis revealed significant
interaction between glucose and nitrogen in regulating gene expression,
because a combination of glucose and nitrogen could modulate the expression
of many genes responsive either to glucose or nitrogen individually.
A large number of genes associated with stress response were induced
by glucose-we postulate that glucose signaling regulates these genes
either via crosstalk with stress hormone ABA or ethylene signaling
or via independent signal transduction mechanisms. Using cycloheximide,
an inhibitor of protein synthesis, we have found that glucose repression
appears to be a primary response while glucose induction is largely
a secondary response requiring de novo protein synthesis. We conclude
that glucose and inorganic nitrogen have dual roles in plants, acting
as both metabolites and effective signaling molecules. Our long-term
goal is to reveal the transcriptional cascades underlying sugar regulated
gene expression in plants.
Tuesday, October 28, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Mitch Masters, Department
of Zoology, The Ohio State University
Title: Bat Sonar: Seeing with Sound
Echolocation -- "seeing" using sound -- is a remarkable ability
bats (and toothed whales) have and we don't. We know some of what
bats can do with echolocation but are still in a fairly unenlightened
state when in comes to explaining how they do it. This talk will
focus on some of what we have learned from bats in psychophysical
experiments that raise questions about their signal-processing strategy.
MBI Postdoctorate Seminar
Thursday, October 23th, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Sung Ok Yoon, Neuroscience
Department and Neurobiotechnology Center, The Ohio State University
http://www.med.ohio-state.edu/neuroscience/grad/yoon.htm
Tuesday, October 21, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: George Billman,
Physiology and Cell Biology, The Ohio State University
Title: Mechanisms Responsbile for Sudden Cardiac Death: Alterations
in the Automonic Neural Regulation of the Heart can Provoke Ventricular
Fibrillation
Sudden cardiac death resulting from disturbance in the normal rhythmic
beating of the heart (i.e., ventricular fibrillation) remains the
leading cause of death in industrially developed countries, accounting
for between 300,000 and 500,000 deaths each year in the United States.
Yet, despite the enormity of this problem, the mechanisms responsible
for these lethal changes in the cardiac rhythm remain largely to
be determined. Alterations in the autonomic neural regulation of
heart may play a critical role in sudden cardiac death, particularly
during myocardial ischemia. It is now generally accepted that the
activation of cardiac sympathetic nerves reduce cardiac electrical
stability, while the activation of parasympathetic nerves may counteract
sympathetic activation and protect against ventricular fibrillation.
However, the mechanisms by which alterations in cardiac autonomic
activity provoke these lethal cardiac rhythm disturbances remain
to be determined. Ultimately, transmitter substances released from
the autonomic nerve terminals must bind to post-synaptic receptors
triggering a cascade of intracellular events that, in turn, provoke
changes in the flux of ions across the cell membrane. These changes
in ion flux may reduce cardiac electrical stability and increase
the probability for catastrophic rhythm disturbances. For over 20
years, I have used a canine model of sudden cardiac death to investigate
the role alterations in the autonomic control of the heart and the
resulting changes in intracellular and extracellular cations play
in the induction of ventricular fibrillation during myocardial ischemia.
MBI Postdoctorate Seminar
Thursday, October 16th, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: David Somers, Plant
Biology Department, The Ohio State University
Title:The Role of ZEITLUPE in the Control
of Circadian Period in Plants
http://www.biosci.ohio-state.edu/~plantbio/Faculty/somers.html
At the molecular core of the circadian clock lies a transcription/translation
autoregulatory feedback loop. Cyclic expression of at least some of
the components of the circadian central oscillator is essential to
maintain circadian rhythmicity. High amplitude cycling of mRNA and
protein abundance, protein phosphorylation and nuclear/cytoplasmic
shuttling have all been implicated in the maintenance of circadian
period. We have used a newly characterized Arabidopsis suspension
cell culture to establish that the rhythmic changes in the levels
of the novel clock-associated F-box protein, ZEITLUPE, are post-transcriptionally
controlled through different circadian phase-specific degradation
rates. This proteolysis is proteasome dependent, implicating ZTL itself
as substrate for ubiquitination. This demonstration of circadian phase-regulated
degradation of an F-box protein, which itself controls circadian period,
suggests a novel regulatory feedback mechanism among known circadian
systems. Evidence for an additional level of light- and dark-dependent
control of ZTL function will also be presented.
Tuesday, October 14, 3:00-4:00PM
MBI Lecture Hall - Mathematics Building, Room 240
Speakers: Thomas Powers,
Division of Engineering, Brown University
Title: Dynamics of bacterial flagella: bundling and polymorphism
E. coli and Salmonella swim using several flagella, each of which
consist of a rotary motor, a universal joint known as the hook,
and a helical filament which acts a propeller. For propulsion, the
filaments wrap into a bundle when the motors turn counter-clockwise.
We built a scale model to study the interplay of hydrodynamics and
elasticity in this process. Our model shows how the filaments wrap
around each other, and allows us to determine which characteristic
timescales govern bundling. The filament is normally left-handed
in the absence of external stress, but undergoes mechanical phase
transitions to other helical states ("polymorphs") in response to
external torque. The filament is made of identical flagellin protein
subunits which are organized into eleven protofilaments which wind
around the filament. We develop an effective theory in which the
flagellin subunits and their connections along the protofilaments
are modeled with a non-convex potential. A helical spring represents
the other connections of the subunits, and introduces a twist-stretch
coupling and an element of frustration in our model. We solve for
the ground states and the phase diagram for filament shapes.
MBI Postdoctorate Seminar
Thursday, October 9th, 11:30AM
MBI Lecture Hall - Mathematics Building, Room 240
Speaker: Mike Ostrowski,
Molecular Genetics Department, The Ohio State University
Title: Functional genomic approaches for defining transcriptional
networks important for cell growth and differentiation
http://www.osumolgen.org/faculty/ostrowski.htm
My lab has a long-standing interest in understanding how signaling
pathways elicit selective changes in gene transcription in mammalian
cells. We use a combination of genetic mouse models, molecular genetics,
biochemistry and cell biology to attack these problems. Most recently,
we have become interested in understanding interactions between
signaling pathways locating in the different cell types involved
in complex biological processes of cancer cell progression and normal
cellular differentiation. For example, in vertebrate animals, bone
is formed through the interactions between two cell types, cells
that make bone (the osteoblasts) and cells that remodel bone (the
osteoclast). There is exquisite communication between these cell
types throughout life, and upsetting this balance results in disease
states, for example, osteoporosis in humans. Understanding and targeting
such intercellular networks of communication holds great promise
for new advances in the diagnosis and treatment of many human diseases.
Recent advances in genomics and functional genomics makes it possible
to begin studying such complex networks of interaction that control
the overall behavior of different cell types. It is clear that computational
and statistical tools will be necessary to model these complex interactions.
Neuroscience Journal Club
Wednesday, October 7th, 12:30-1:30PM
MBI Conference Room- Mathematics Building, Room 222
Brainard, M.S. & Doupe, A.J. (2000). Auditory feedback in learning
and maintenance of vocal behavior. Nature Reviews Neuroscience,
1, 31-40.
Brainard, M.S. & Doupe, A.J. (2000). Interruption of a basal ganglia-forebrain
circuit prevents plasticity of learned vocalizations. Nature,
404, 762-766.
Tuesday, October 7, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building Room 240
Speaker: James Sneyd, University
of Auckland
Title: Modulation of calcium oscillations by membrane currents
I'll begin with a brief discussion of the physiology of intracellular
calcium signalling, and then present a model of calcium oscillations
in secretory epithelial cells. I'll show how we used the model to
address one particular controversy in the field, that of how calcium
oscillations are affected by membrane calcium transport. I'll briefly
describe how we used the model to make a number of predictions, and
the experiments we did to test the predictions.
Neuroscience Journal Club
Wednesday, September 24, 12:00-1:00PM
MBI Conference Room- Mathematics Building, Room 222
The papers for discussion:
64: Schultz W, Dayan P, Montague PR.
A neural substrate of prediction and reward.
Science. 1997 Mar 14;275(5306):1593-9. Review.
7: Fiorillo CD, Tobler PN, Schultz W.
Discrete coding of reward probability and uncertainty by dopamine
neurons.
Science. 2003 Mar 21;299(5614):1898-902.
Tuesday, September 23, 3:30-4:30PM
MBI Lecture Hall - Mathematics Building, Room 240
Speakers: Howard Levine,
Department of Mathematics, Iowa State University
Title: Mathematical modeling of capillary formation and development
in tumor angiogenesis
We present a mathematical model for the tumor vascularization theory
of tumor growth proposed by Judah Folkman in the early 70's and
subsequently established experimentally by him and his coworkers.
In the simplest version of this model, an avascular tumor secretes
a tumor growth factor, (TGF) which is transported across an extracellular
matrix (ECM) to a neighboring vasculature where it stimulates endothelial
cells to produce a protease that acts as a catalyst to degrade the
bronectin of the capillary wall and the ECM. The endothelial cells
then move up the TGF gradient back to the tumor, proliferating and
forming a new capillary network.
In this, we include two mechanisms for the action of angiostatin.
In the first mechanism, substantiated experimentally, the angiostatin
acts as a protease inhibitor. A second mechanism for the production
of protease inhibitor from angiostatin by endothelial cells is proposed
to be of Michaelis- Menten type. Mathematically, this mechanism
includes the former as a sub case.
Our model is different from other attempts to model the process
of tumor angiogenesis in that it focuses (1) on the biochemistry
of the process at the level of the cell; (2) the movement of the
cells is based on the theory of reinforced random walks; (3) standard
transport equations for the diffusion of molecular species in porous
media.
One consequence of our numerical simulations is that we obtain
very good computational agreement with the time of the onset of
vascularization and the rate of capillary tip growth observed in
rabbit cornea experiments. Furthermore, our numerical experiments
agree with the observation that the tip of a growing capillary accelerates
as it approaches the tumor.
Postdoctoral
Research Forum
(short talk series held September 18, 22, and 25, 2003)
Neuroscience Journal Club
Wednesday, September 17, 12:00-1:00PM
MBI Conference Room- Mathematics Building, Room 222
The papers for discussion:
1. The beginning (FIRST 5.5 PAGES - up to 'summation') of Pearce,
JM. (2002). Evaluation and development of a connectionist theory
of configural learning. Animal learning and behavior, 30(2),
73-95.
2. Review: Menzel, R. (2001). Searching for the memory trace in
a mini-brain, the honeybee. Learning and memory, 8, 53-62.
Extra-reading:
1. Menzel, R. & Giurfa, M. (2001). Cogntitive architecture
of a mini-brain: the honeybee. Trends in Cognitive Sciences,
5(2), 62-71.
2. Fanselow, MS. (1998). Pavlovian conditioning, negative feedback,
and blocking: mechanisms that regulate association formation. Neuron,
20, 625-627.
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