MBI Videos

Videos by 2010

  • Road signs for kinesin transport
    Kristen Verhey
    We probe the transport properties in protein solutions stable with respect to any, solid or liquid, phase separation as a step in the understanding of transport in the cytosol of live cells. We determine the mean squared displacement of probe particles in the time range 1 millisecond - 10 seconds in solutions of a model protein. The tested solutions exhibit significant ela...
  • Mechanics of Actomyosin Interaction and the Role of Substrate Stiffness on Actin Network Dynamics
    Sean Sun
    Myosin is a major molecular force generator in the cell. The essential features of myosin interaction with actin filaments are understood. In the cell, the interactions of myosin with F-actin, substrate adhesions and other actin-associated proteins are less clear. We will borrow ideas from mathematical models of skeletal muscle to develop simple models for integrin focal a...
  • The conserved L5 loop establishes the pre-powerstroke conformation of the kinesin-5 motor, Eg5
    Sarah Rice
    Kinesin superfamily motor proteins contain a structurally conserved loop near the ATP binding site, termed L5. The function of L5 is unknown, although several drug inhibitors of the mitotic kinesin Eg5 bind to L5. We used electron paramagnetic resonance spectroscopy (EPR) to investigate the function of L5 in Eg5. We site-specifically attached EPR probes to ADP, to L5, and ...
  • The Function of Dynein in Budding Yeast: Mechanism, Regulation and Checkpoint Activity
    John Cooper
    I will discuss work from our lab and other labs on how dynein functions to position the mitotic spindle and the nucleus in budding yeast. Interactions of cytoplasmic microtubules with the cortex control spindle position, and dynein represents one of the major pathways by which spindle position is controlled. Dynein functions by an "offloading" mechanism in which ...
  • Does Neuroscience Need Mathematics? And vice-versa?
    David Terman
    To a mathematical biologist, the answer to both of these questions is (no surprise) 'of course'. The brain is after all an extremely complicated network with hundreds of billions of neurons interacting in highly nonlinear ways, generating complex firing patterns that depend nontrivially on parameters. How can one possibly understand mechanisms underlying those pa...
  • DNA chasing DNA: physics of homology recognition and the secret of perfect match
    Alexei Kornyshev
    DNA chasing DNA: physics of homology recognition and the secret of perfect match...
  • Motoring along a nucleic acid strand: template-dictated polymerization of macromolecules of life
    Debashish Chowdhury
    Polymerases and ribosome are molecular machines which perform three important biological functions. Like cytoskeletal motors, each of these moves along a track using chemical energy for performing mechanical work. Moreover, it decodes genetic information chemically-encoded in the sequence of the subunits of the track. Furthermore, it polymerizes a macromolecule (DNA, RNA o...
  • The Freter Model of Biofilm Formation
    Hal Smith
    Driven by recent advances in noninvasive microscopy, staining techniques, and genetic probes, there has been enormous increase in our understanding of biofilms. Along with this increase in understanding, has been increasing interest in mathematical models of biofilms to get at important mechanisms. Most recent modeling in the field has been directed towards understanding t...
  • A novel signaling network essential for regulating Pseudomonas aeruginosa biofilm development
    Karin Sauer
    The important human pathogen Pseudomonas aeruginosa has been linked to numerous biofilm-related chronic infections Biofilms are complex communities of microorganisms encased in a matrix and attached to surfaces. It is well recognized that biofilm cells differ from their free swimming counterparts with respect to gene expression, protein production, and resistance to antibi...
  • Modeling and predicting DNA-binding specificity
    Gary Stormo
    Many different kinds of data are available for modeling the specificity of a DNA-binding protein, and the quality of the model depends on both the type of data used and the algorithms for estimating binding energies. We discuss our approaches for modeling from several different types of data, and assess the accuracy of each based on experimental measurements. Given specifi...
  • DNA Architecture and Transcriptional Regulation: The Physics of Genome Management
    Hernan Garcia
    DNA architecture plays a key role in determining spatial and temporal patterns of gene expression. This architecture encompasses both the nucleotide sequence (i.e., the information content) and the physical state of the DNA such as its spatial organization and mechanical properties. We study several regulatory motifs in E. coli using a three pronged approach: theoretical m...
  • DNA Looping Probabilities and Semi-Classical Path Integrals
    John Maddocks
    (Joint work with L. Cotta-Ramusino and R. Manning)

    DNA interactions with proteins frequently involves looping in which the location and orientation of the two ends of a DNA segment are prescribed. I will show how path integral methods can be used to obtain a sequence-dependent formula for the probability of loop formation, including the case of minicircle cy...
  • Models for Amino Acid Substitution and Gene Duplication With Roots in Molecular and Evolutionary Processes
    David Liberles
    In Darwinian evolution, mutations occur approximately at random in a gene, turned into amino acid mutations by the genetic code. Some mutations are fixed to become substitutions and some are eliminated from the population. Partitioning pairs of closely related species with complete genome sequences by population size, we look at the PAM matrices generated for these partiti...
  • Bayesian Gene-tree Reconstruction and Learning in Phylogenomics
    Matthew Rasmussen
    Advances in genome sequencing have enabled the study of evolution across both genomes and large clades of species, and has been especially useful for studying gene families as they expand and contract over evolutionary time by gene duplication and loss events. Here, we present a new approach for the reconstruction of gene-tree phylogenies that models simultaneously gene an...
  • Estimation of ancestral population divergence times and effective population sizes from complete human genome sequences
    Adam Siepel
    Complete genome sequences are now available for individuals representing several distinct human populations. The primary motivation for collecting these sequences has been to characterize human diversity, facilitate disease association studies, and pave the way for an era of "personalized medicine". However, these data also contain valuable information about huma...
  • Model fitting for mixture models
    Anna Kedzierska
    Phylogenetic data arising on different tree topologies might be mixed on a given alignment. Models taking into it account usually contain a large number of parameters and the usual tests for model fitting cannot deal with them. Here we discuss an approach for model fitting of algebraic models on m-tree mixtures. This is joint work in progress with Marta Casanellas and Jesu...
  • Inference of population structure using dense genotype data
    Daniel Falush
    Inference of population structure using dense genotype data...
  • Transposable elements: germline invaders with a lasting impact on genome evolution
    Cedric Feschotte
    I will provide an overview of our studies of the evolutionary dynamics of transposable elements and their impact on eukaryotic evolution. The emphasis will be on class 2 or DNA transposons in mammalian genomes. Genomic analyses reveal that a vast diversity of DNA transposons exists in mammalian genomes and that large cohorts of elements have been integrated in a lineage-sp...
  • Many-Core Algorithms for Statistical Phylogenetics
    Marc Suchard
    Massive numerical integration plagues the statistical inference of partially observed stochastic processes. An important biological example entertains partially observed continuous-time Markov chains (CTMCs) to model molecular sequence evolution. Joint inference of phylogenetic trees and codon-based substitution models of sequence evolution remains computationally impracti...
  • Parameter estimation in models for sequence alignment
    Ana Arribas-Gil
    Models for pairwise alignment based on the TKF (Thorne, Kishino and Felsenstein 1991) indel process fit into the pair-Hidden Markov Model (pair-HMM). Observations in a pair-HMM are formed by the couple of sequences to be aligned and the hidden alignment is a Markov chain. Many efficient algorithms have been developed to estimate alignments and evolution parameters in this ...
  • Using empirical codon models to understand the patterns and pressures of natural variation reflected in genomic re-sequencing data
    Carolin Kosiol
    In the past, two kinds of Markov models have been considered to describe protein sequence evolution. Codon-level models have been mechanistic, with a small number of parameters designed to take into account features such as transition-transversion bias, codon frequency bias and synonymous-nonsynonymous amino acid substitution bias. Amino acid models have been empirical, at...
  • A coalescent process Markov in time and space
    Thomas Mailund
    A coalescent process Markov in time and space...
  • First-principles calculation of DNA looping in tethered particle experiments
    Phil Nelson
    We show how to calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor, using a mathematical model of DNA elasticity. Our approach has new features enabling us to compute quantities directly observable in Tethered Particle Motion (TPM) experiments; e.g. it accounts for all the entropic forces present in such experiments. Our mo...
  • Persister Cells and the Paradox of Relapsing Chronic Infection
    Kim Lewis
    Pathogen populations produce persisters, specialized survivor cells that are dormant and highly tolerant to all known antibiotics. Molecular mechanisms of persister formation will be discussed, as well as their role in disease, such as biofilm infections of catheters, cystic fibrosis, and oropharyngeal candidiasis. Approaches to eradicating persisters will be discussed as ...
  • Communication and cooperation in bacterial populations: Mechanistic and evolutionary perspectives
    Martin Schuster
    There has been an explosion in research directed at understanding the mechanisms of how bacteria communicate and cooperate to perform a variety of multicellular behaviors, including biofilm formation. Not until very recently have microbiologists also begun to investigate these behaviors from the perspective of social evolution. Our goal is to integrate mechanistic and evol...
  • Role of microbial biofilms in device-related and other chronic diseases
    Bill Costerton
    Direct observations have revealed that the bacteria that cause device-related and other chronic diseases grow in matrix-enclosed biofilms, adherent to the surfaces of biomaterials and tissues. In this biofilm mode-of-growth, the organisms are virtually impervious to antibiotics, and to the antibodies and phagocytes that constitute the defense systems of virtually all mamma...
  • A simple biophysical model of nucleosome positioning and energetics
    Alexandre Morozov
    Genomic DNA is packaged into chromatin in eukaryotic cells. The fundamental building block of chromatin is the nucleosome, a 147 bp-long DNA segment wrapped around the surface of a histone octamer. Nucleosomes function to compact genomic DNA and to regulate access to it both by physical occlusion and by providing the substrate for numerous covalent epigenetic tags. We have...
  • Parallel mutations and partial sweeps
    Graham Coop
    Parallel mutations and partial sweeps...
  • Allocation dilemmas in plants
    Jan Kozlowski
    There are annual and perennial plants; perennials may reproduce once in life (semelparity, monocarpic perennials) or repeatedly (iteroparity). Perennial herbs lose virtually all vegetative parts but storage organs before winter, whereas shrubs and trees retain large part or even most of vegetative mass. Theory of optimal resource allocation helps to predict important featu...
  • No Title Available
    Hamlyn (Lyn) Jones
    No description available...
  • A brief review of progress and some remaining challenges in modelling plant development
    Vince Gutschick
    As part of a selective review of progress in modelling of plant development, I wish to offer a larger context, extending to the evolutionary scale, and mostly to pose a set of questions or challenges to modellers.

    First, I would like to affirm some premises that I believe are widely shared by modellers. Why do we make models?: 1) to predict plant (or stand o...
  • Model-assisted integration of physiological and environmental constraints affecting the dynamic and spatial patterns of root water uptake from soils
    Xavier Draye
    Due in part to recent progress in root genetics and genomics, increasing attention is being devoted to root system architecture (RSA) for the improvement of drought tolerance. The focus is generally set on deep roots, expected to improve access to soil water resources during water deficit episodes. Surprisingly, our quantitative understanding of the role of RSA in the upta...
  • Using models of plant hydraulic function to predict gas exchange, growth, and survival in response to environment and ontogeny
    John Sperry
    Models of plant hydraulic resistance are useful because they provide mechanistically anchored predictions of plant gas exchange and survival in response to environmental stress and ontogeny. Flow resistance in soil and plant xylem can be modeled relatively easily because the processes are largely physical and linked to environment and plant size in ways that can be readily...
  • Using functional-structural plant modeling to study, understand and simulate fruit tree physiology, architecture, growth and production responses to changes in genetics, environment and management
    Ted DeJong
    Perennial deciduous fruit trees are very complex organisms that are governed and influenced by a multitude of factors. Empirical research approaches are generally limited to dealing with a couple factors at a time and integration of the effects of multiple factors affecting tree growth and productivity are generally limited to verbal descriptions and displaying data with t...
  • On functional-structural plant modelling
    Jan Vos
    Models are simplified representations of a system, i.e. a limited part of reality. Structure and properties of specific models are chosen depending on the purpose they serve. These purposes include: summarizing data, assisting in the analysis of experimental data, testing of hypotheses, extrapolation of system behaviour beyond the conditions that were covered experimentall...
  • At which scale modeling plant-climate-pathogen interactions to find new levers in pest management? - Phylloclimate a key variable to study interactions?
    Michael Chelle
    Fungal diseases are a major concern for crop production. Up to now crop protection has mainly relied on fungicide sprays and host genetic resistance. However, their intensive use boosts the adaptation of fungal populations, causing the decrease of pathogen sensivity to fungicides and the breakdown of host resistance. Therefore, novel crop management techniques have to be d...
  • Combining multiple modeling approaches to design plant ideotypes for specific climates
    Thierry Simonneau
    Modeling plant growth and development underwent considerable development with strong incentives from various consortia. It emerged as an efficient tool in ecology and genetics to face new challenges raised by competition for resources and to benefit from breakthroughs in biotechnology. In this presentation, we propose a classification of approaches used in modeling plants ...
  • Modelling tree development : overview of open questions specific to fruit species
    Evelyne Costes
    Fruit trees present developmental characteristics which are similar to other perennials, such as the existence of ontogenetic gradients and dependencies between consecutive growth. However, because of their agronomical use, fruit tree species also raise specific issues. For instance, the practice of grafting on dwarfing rootstock considerably reduces the juvenile period du...
  • Circadian Control at the Post-Transcriptional Level: the Gonyaulax story
    Woody Hastings
    Several different circadian rhythms, as well as an annual rhythm, have been studied in the marine dinoflagellate Gonyaulax polyedra (now Lingulodinium polyedrum), many features of which may be grist for modeling mills, whatever they may be. The rhythm of bioluminescence provides an easy "hand" for the automation of its measurement in vivo, and the luciferase and ...
  • How Fungi Keep Time: Circadian Oscillators And Rhythmic Outputs
    Deborah Bell-Pedersen
    About 20% of Neurospora genes are under control of the circadian clock system at the level of transcript accumulation, and the bulk of the clock-controlled mRNAs have peak accumulation in the late night to early morning. These data suggested the existence of global mechanisms for rhythmic control of gene expression. Consistent with this idea, we found that the Neurospora O...
  • Optimal Control of Dynamical Biological System: Simplified Model of Balanced Growth and Development
    Ilya Ioslovich
    A dynamical biological system containing a vegetable crop and control tools for protected and intensive cultivation is considered. To optimize an economical criterion along the growing season, model based control must be designed. A special simplified biological model was developed for the purpose of determining the control inputs. This model uses the main biological prope...
  • It's not just genes: how interactions drive cancer progression
    Alexander Anderson
    No description available....
  • Evolution of body size in food webs
    Rosalyn Rael
    Body size has been shown to be a significant factor in shaping the structure of food webs, which are network models of the flow of energy in an ecosystem. Recent studies have shown that body size constraints can influence food web dynamics through prey preference and foraging behavior, and can thereby influence the stability of these ecosystem models. Because of its signif...
  • Asymmetric stable droplets in a fish patterning model.
    Thomas Woolley
    Soliton like structures called "stable droplets" are found to exist within a paradigm reaction diffusion model which can be used to describe the patterning in a number of fish species. It is straightforward to analyse this phenomenon in the case when two non-zero stable steady states are symmetric, however the asymmetric case is more challenging. We use a recentl...
  • Kinesin-Microtubule Interactions: Transport and Spindle Formation
    Peter Bates
    This talk consists of two parts: Pattern formation in families of microtubules under the action of kinesin and the detailed motion of kinesin along a microtubule.

    Microtubules are long cylindrical structures (lengths being tens of microns and diameter approximately 25 nm) comprised of tubulin dimers, which self-assemble, 13 protofilaments being required side...
  • Algebraic models in systems biology
    Reinhard Laubenbacher
    Progress in systems biology relies on the use of mathematical and statistical models for system level studies of biological processes. Several different modeling frameworks have been used successfully, including traditional differential equations based models, a variety of stochastic models, agent-based models, and Boolean networks, to name some common ones. This talk will...
  • Yes, Even You Can Bend It Like Beckham
    Edray Goins
    In the 2002 film by Gurinder Chadha, character Jesminder 'Jess' Bhamra states "No one can cross a ball or bend it like Beckham" in a reference to the international soccer star's ability to cause the ball to swerve. French researchers Guillaume Dupeux, Anne Le Goff, David Quere and Christophe Clanet published a paper earlier this year in the New Jou...
  • A new SIS malaria model with vector demography showing natural occurring oscillations
    Miranda Teboh-Ewungkem
    A new way to model the dynamics of malaria transmission that takes into consideration the demography of the transmitting vector will be presented. Model results indicate the existence of nontrivial disease free and endemic steady state solutions which can be driven to instability via a Hopf bifurcation as a parameter is varied in parameter space. The model therefore captur...
  • Differential Regulation of FSH(beta) Transcription by Changes in GnRH Pulse Frequency
    Ursula Kaiser
    The gonadotropins, luteinizing hormone (LH) and follicle-stimulating hormone (FSH) play an integral role in the reproductive axis, translating neural and hormonal input into precisely regulated output to achieve normal sexual development and regulation of gonadal function. In recent years, considerable progress has been made in the elucidation of the molecular mechanisms u...
  • Nonlinear partial differential equation and stochastic singular control
    Ryan Hynd
    Nonlinear partial differential equations arise in stochastic optimal control via dynamic programming equations. In many cases, solutions of these equations aid in the design of optimal controls. We discuss a class of equations where the associated control processes are "singular" with respect to the time variable. These equations arise in models for spacecraft co...
  • How can changes in protein isomer concentration trigger protein aggregation diseases?
    Conner Sandefur
    Conformational diseases result from the failure of a specific protein to fold into its correct functional state. The misfolded proteins can lead to the toxic aggregation of proteins. In some cases, misfolded proteins interact with bystanders proteins (unfolded and native folded proteins), eliciting a misfolded phenotype. These bystander polypeptides would follow their norm...
  • Young Women and Mathematical Biology: A Personal Perspective
    Carlos Castillo-Chavez
    Lee Segel one of the greatest applied mathematicians of our time passed away on January 31, 2005. His obituary (SIAM News, 03-10-2005) read "With his death, the applied mathematics community lost one of its finest practitioners, and the theoretical biology community lost a true pioneer who was still a leader at the cutting edge of so many subjects. And most importantl...
  • Modeling of Exocytosis in Endocrine and Neuroendocrine Cells
    Arthur Sherman
    Secretion, whether from nerve terminals or hormone-secreting cells, is determined by the product of the number of release-ready vesicles and the probability of release per vesicle. The probability of release is in turn dependent on both the concentration of calcium seen by the vesicles and the affinity of the release mechanism for calcium. All of these factors vary in time...
  • An introduction to the analysis of biomathematical models
    Richard Bertram
    An introduction to the analysis of biomathematical models...
  • Introduction to neuroendocrinology
    Arturo Iglesias
    Introduction to neuroendocrinology...
  • Modeling Neural Circuitry for Early Olfactory Processing
    William Sherwood
    The neuronal networks of the olfactory system transduce and transform complex mixtures of odorant molecules into patterns of the neural activity representing smells. We explore two important aspects of how this process works, at the cellular and the neural circuit level, in modeling studies that produce experimental testable predictions.

    1) It has long been ...
  • Circadian gating of cell divisions revealed in single cyanobacterial cells
    Qiong Yang
    Cyclic processes in biology span a wide dynamic range, from the sub-second periods of neural spike trains to annual rhythms in animal and plant reproduction. Even an individual cell exposed to a constant environment may exhibit many parallel periodic activities with different frequencies. It is therefore important to elucidate how multiple clocks coordinate their oscillati...
  • Mathematical modeling of cell cycle and circadian rhythms as a coupled oscillator
    Chris Hong
    In most eukaryotic organisms, networks of cell cycle and circadian rhythms coexist and work coordinately to create optimal conditions for cells to grow and adapt to the surrounding environment. Cell cycle regulatory mechanisms include multiple checkpoints for controlled growth and cell divisions. The period of this oscillation, however, varies with external conditions such...
  • Dynamic Motifs in Cell Biological Systems
    Helen Byrne
    No description available....
  • Using Somatic Genomic Variation To Reconstruct Somatic Cell Evolution
    Darryl Shibata
    No description available....
  • Homeostatic and Oscillatory Mechanisms in Plant and Fungal Nitrate Assimilation
    Peter Ruoff
    Homeostatic control mechanisms are essential to keep cells and organisms fit in a changing and challenging environment. An important task is to identify the factors which contribute to the functionality and robustness of homeostatic mechanisms in the presence of environmental perturbations. Kinetic conditions which lead to robust homeostasis and perfect adaptation together...
  • Symbiosis of tumor growth dynamics and radiotherapy modeling
    Heiko Enderling
    No description available....
  • Can mathematical analysis help uncover the design principles behind circadian rhythms?
    David Rand
    I will survey what some recent mathematical results suggest about the design principles behind circadian clocks. In particular, I will discuss flexibility, robustness, buffering mechanisms against environmental heterogeneity, temperature compensation in physiological entrained conditions and tracking of multiple phases. If time permits I will also discuss new methods for f...
  • The Mathematics of Radiobiology
    Philip Hahnfeldt
    No description available....
  • Amplitude/Temperature-Compensation: Data and Models
    Stuart Brody
    Amplitude is a measurable parameter of an oscillator, yet it is often not considered as a variable, Amplitude can be measured in several ways: 1) as an output of an oscillator; 2) directly as the amplitude of a "key" clock protein; or 3) indirectly via a Phase-response curve. Data will be presented for a particular mutant (frq7) of Neurospora which shows how the ...
  • Scaling in Vascular Networks: Curvature, Finite-Size Effects, and Applications to Tumor Angiogenesis and Growth
    Van Savage
    Metabolic rate, heart rate, and lifespan depend on body size according to scaling relationships that extend over ~21 orders of magnitude and that represent diverse taxa and environments. These relationships for body mass have long been approximated by power laws, but there has been intense debate about the values of exponents (e.g., 1/4 versus 1/3). I will show for mammals...
  • Understanding Conflicting Zeitgeber Experiments
    Gisele Oda
    Several experimental studies have altered the natural phase relationship between photic and non-photic zeitgebers, in order to assess their hierarchy in the entrainment of circadian rhythms. In order to interpret the complex results that emerge from these conflicting zeitgeber protocols, we present computer simulations of two coupled oscillator systems forced by two indepe...
  • Modeling the mammalian circadian clock: from single cells to cell populations
    Didier Gonze, Didier Gonze

    Circadian rhythms represent one of the more conspicuous examples of biological rhythms. Manifested at the physiological, behavioral, and cellular levels, these 24-hour rhythms originate at the molecular level, through a complex gene regulatory network. In mammals, the circ...

  • Modeling the mammalian circadian clock: from single cells to cell populations
    Didier Gonze, Didier Gonze

    Circadian rhythms represent one of the more conspicuous examples of biological rhythms. Manifested at the physiological, behavioral, and cellular levels, these 24-hour rhythms originate at the molecular level, through a complex gene regulatory network. In mammals, the circ...

  • Wavelet Analysis of Circadian Oscillations
    Tanya Leise
    No description available....
  • A Primer to Radiobiology in Radiotherapy
    Tyson McDonald
    No description available....