BEGIN:VCALENDAR CALSCALE:GREGORIAN METHOD:PUBLISH PRODID:-//The Biocomplexity Institute\, Indiana University//NONSGML Biocomplexity Calendar Exporter\, PHP//EN VERSION:2.0 BEGIN:VTIMEZONE TZID:US-Eastern BEGIN:STANDARD TZOFFSETFROM:-0400 TZOFFSETTO:-0500 TZNAME:EST DTSTART:19701025T020000 RRULE:FREQ=YEARLY;BYMONTH=10;BYDAY=-1SU END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:-0500 TZOFFSETTO:-0400 TZNAME:EDT DTSTART:19700405T020000 RRULE:FREQ=YEARLY;BYMONTH=4;BYDAY=1SU END:DAYLIGHT END:VTIMEZONE BEGIN:VEVENT UID:20091123T154047Z-000312@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070109T160000 DTEND;TZID=US-Eastern:20070109T170000 SUMMARY:Biocomplexity Seminar: Tinri Aegerter-Wilmsen DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Model for the regulation of size in the wing imaginal disc of Drosophila'\nTinri Aegerter-Wilmsen\nInstitute of Molecular Systems BiologySwiss Federal Institute of Technology Zurich\n\nAbstract\nFor development it is necessary that organs stop growing after they reach a certain size. However\, it is still largely unknown how this termination of growth is regulated. The wing imaginal disc of Drosophila serves as a commonly used model system to study the regulation of growth. Paradoxically\, it has been observed that growth occurs uniformly throughout the disc\, even though Decapentaplegic (Dpp)\, a key inducer of growth\, forms a gradient. We have formulated a model for the control of growth in which mechanical forces play a key role. With the use of numerical simulations we show that the model can indeed account for the termination of growth and that it does yield uniform growth. Furthermore\, we argue that the model can explain the available experimental results where the wing disc has been manipulated genetically. LOCATION:Swain Hall West 238 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=312 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT BEGIN:VEVENT UID:20091123T154047Z-000313@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070213T140000 DTEND;TZID=US-Eastern:20070213T150000 SUMMARY:Biocomplexity Seminar: Hanna Salman DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Emergence of collective behavior and diversity in gene expression: A study in bacterial culture'\nHanna Salman\nCenter for Studies in Physics and BiologyThe Rockefeller University\n\nAbstract\nThe focus of my research is the early stages of collective behavior in cultures of bacteria. It aims to understand the behavior and underlying molecular mechanisms of the transition from a state where bacteria act independently\, to a state in which they start interacting and move to form complex structures. This is done by exploring the effects of cell density on gene expression and the formation of multi-cellular structures. \n \nIn this regard\, we have studied how the concentration of bacteria affects their response to temperature changes. The bacteria are grown in a batch mode culture\, which affects their physiological state due to nutrient depletion. \n \nFor bacteria at a constant physiological state\, we observe a critical transition in behavior in a one-dimensional temperature gradient as their initial concentration in the sample increases. Above a concentration of 108cells/cm3\, an early accumulation near their favored temperature\, caused by thermotaxis\, develops into a sharp pulse moving at a fast velocity (~3.5 µm/sec). This mode is the result of a positive feedback mechanism provided by inter-bacterial communication. A theoretical model describing this interaction shows good agreement with the experimental results. \n \nFor different physiological states\, we observe a critical transition in the bacterial response to localized heating by infrared laser. When the bacteria are grown to concentrations below 2x108cells/cm3 they swim towards the heated region\; when they are grown beyond this concentration they escape from the heated region. This effect is reversible. Also\, mixing populations from different physiological states does not affect the response of either population. A genetic switch controlled by the nutrients’ availability seems to be responsible for this behavior. \n \nThis work will be expanded to consider other environmental changes\, such as food sources. Also\, special attention will be paid to the regulation of gene expression and its variation among the colony members. Such variation can play an important role in phenotypic variation as well as the survival of the population through adaptation to transient stress.\n\nOther Information\nHanna Salman is a Biocomplexity CTE Faculty Search Candidate. Note: this seminar's time has been moved from its original time to 2:00 PM. LOCATION:Swain Hall West 238 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=313 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT BEGIN:VEVENT UID:20091123T154047Z-000314@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070220T160000 DTEND;TZID=US-Eastern:20070220T170000 SUMMARY:Biocomplexity Seminar: Oscar N. Mesquita DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Living cell motility studied with defocusing microscopy'\nOscar N. Mesquita\nDepartamento de Física —\; ICEXUniversidade Federal de Minas Gerais\, Brazil\n\nAbstract\nTransparent objects (phase objects) can be seen in a conventional bright-field optical microscope\, if the microscope is slightly defocused. Recently\, we have carried out the optical calculations for a defocused microscope\, and have shown that the image contrast observed is proportional to the defocus distance and to the two-dimensional Laplacian of the phase difference introduced by the phase object. If the refractive index is homogeneous the contrast is proportional to the local curvature of the phase object. We named this technique "\;defocusing microscopy"\;. \n \nBy using defocusing microscopy we are able to measure cell surface dynamic fluctuations both in macrophages and in red blood cells. In macrophages we observe two main types of curvature fluctuations: one with large amplitude\, which propagates along the cell surface (ruffles) and the other random with small amplitudes (of the order of 3 nm) which permeate the whole cell. We also studied how these fluctuations correlate with the phagocytosis process. We discuss these observations under the light of recent physical models of motility. \n \nAs another example of applicability of defocusing microscopy we obtain shape\, index of refraction and bending modulus of red blood cells. LOCATION:Swain Hall West 238 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=314 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT BEGIN:VEVENT UID:20091123T154047Z-000316@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070227T160000 DTEND;TZID=US-Eastern:20070227T170000 SUMMARY:Biocomplexity Seminar: Marta Sales-Pardo DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Topology and Dynamics of Complex Biological Systems'\nMarta Sales-Pardo\nDepts. of Chemical & Biological Engineering\,Northwestern Institute on Complex SystemsNorthwestern University\n\nAbstract\nThe myriad of high-throughput methods available for probing biological samples has drastically boosted our ability to gather comprehensive molecular-level information on an increasing number of organisms. Unfortunately\, our understanding of biological systems has not grown proportionally. I will talk about two different problems in which the analysis of large pools of data can help us extract knowledge from the "sea" of available information: evolutionary processes and the organization of complex networks. First\, I show that the systematic analysis of protein families enables us to assess evolutionary relationships between species and to discriminate between theories about the tree of life. Second\, I will present a set of methods that is able to accurately extract the hierarchical organization of complex networks and how such methods are able to summarize the information stored in biochemical networks.\n\nOther Information\nMarta Sales-Pardo Biocomplexity CTE Faculty Search Candidate. LOCATION:Swain Hall West 238 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=316 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT BEGIN:VEVENT UID:20091123T154047Z-000317@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070301T160000 DTEND;TZID=US-Eastern:20070301T170000 SUMMARY:Biocomplexity Seminar: Francis Lin DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Targeting Immune Cell Trafficking Using an Integrative Approach'\nFrancis Lin\nLaboratory of Immunology and Vascular BiologyStanford University School of Medicine\n\nAbstract\nThe trafficking of immune cells is important in defining the cell’s physiological functions\, and is connected with a variety of diseases. Cells\, chemotactic factors and adhesion molecules form a complex biological system and their spatiotemporal interactions result in the diverse\, specific and dynamic trafficking patterns of immune cells. My research targets the complexity of the immune cell trafficking system using an integrative approach. This approach involves the development of novel microfluidic systems for in-vitro cell migration studies\, biological and immunological methods for cellular manipulations and measurements\, and quantitative modeling. We have developed several microfluidics-based strategies for generating highly-controlled concentration gradients of extracellular soluble factors. Using the microfluidic devices\, we have studied the migration and chemotaxis of blood cells in different gradient configurations. In addition\, we have identified an important cellular mechanism for chemotactic navigation of immune cells in complex gradient environments by modeling and experimental studies. Finally\, using a combination of molecular biology approach and a microfluidic electrokinetic system\, we have investigated the influence of externally applied DC electric field on immune cell migration\, and the results of this study suggested a new dimension to the regulations of immune cell trafficking. My future research will continue to investigate the regulating mechanisms of immune cell trafficking with an emphasis on the combinatorial regulation of different environmental factors\, in connection with further development and integration of the experimental and theoretical approaches. The outcomes of these studies will advance the understanding of immune cell trafficking at the system level\, and may lead to novel therapeutic approaches for cell migration related diseases such as autoimmune diseases and cancers. Furthermore\, it will result in advanced experimental platforms\, which will facilitate a broad range of systems biology oriented research.\n\nOther Information\nFrancis Lin is a Biocomplexity CTE Faculty Search Candidate. LOCATION:Swain Hall West 238 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=317 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT BEGIN:VEVENT UID:20091123T154047Z-000315@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070306T160000 DTEND;TZID=US-Eastern:20070306T170000 SUMMARY:Biocomplexity Seminar: Virgil Griffith DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Quantifying Evolvability in Computer Programming Languages'\nVirgil Griffith\nIndiana University School of Informatics\n\nAbstract\nQuantifying Evolvability in Computer Programming Languages\n\nOther Information\nQuantifying Evolvability in Computer Programming Languages LOCATION:Swain Hall West 238 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=315 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT BEGIN:VEVENT UID:20091123T154047Z-000320@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070320T160000 DTEND;TZID=US-Eastern:20070320T170000 SUMMARY:Biocomplexity Seminar: Brian DiDonna DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Filamin cross-linkers in the cytoskeleton: fragility under strain'\nBrian DiDonna\n\nAbstract\nThe cytoskeleton is a network of stiff polymers which fills our cells and plays an important role in many cell processes. It is a dynamic structure\, in a continual process of reorganization and regeneration. Cells optimize the local elasticity and chemical functionality of the cytoskeleton on the fly for different tasks by adjusting its topologyand chemical composition. In my talk I will examine the function of a highly structured chemical cross-linker (filamin) which contains unfolding protein domains. I will show\, through simulations and mean field theory\, that the inclusion of these cross-linkers drastically alters the mechanical properties of the cytoskeleton\, in a manner which explains recent experimentally observed power law behavior of its visco-elactic moduli. We have discovered a new form of fragile mechanical state in random elastic networks built with such unfolding cross-linkers. The action of protein domain unfolding\, combined with the geometric disorder of the network\, causes the cross-linkers to self-organize into a fragile state characterized by an enhanced sensitivity to mechanical perturbation. I will discuss the origins of this fragile state and its possible function in cells. \n \nGraduate students and post-docs may meet with Brian DiDonna in Swain Hall West 238 from 5:00-6:00 PM after the seminar. If you would like to meet with Dr. DiDonna\, please e-mail bioc@indiana.edu to arrange the meeting.\n\nOther Information\nBrian DiDonna is a Biocomplexity CTE Faculty Search Candidate. If you would like to meet with Dr. DiDonna\, please see the end of the abstract for more details. LOCATION:Swain Hall West 238 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=320 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT BEGIN:VEVENT UID:20091123T154047Z-000319@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070322T140000 DTEND;TZID=US-Eastern:20070322T150000 SUMMARY:Biocomplexity Seminar: Sunghwan Jung DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Swimming\, towing\, tumbling in viscous fluids'\nSunghwan Jung\n\nAbstract\nI will present three topics related to bio-locomotions (fluid-structure interactions) at low Reynolds number. First\, motivated by numerical simulations of sedimenting rod suspensions\, I will discuss experimental observations of the sedimentation of two identical but anisotropic particles. For a wide variety of body shapes\, we find surprisingly stable "\;tumbling orbits"\; where the two bodies rotate in phase\, alternately speeding up and slowing down as they fall. In the next study\, motivated by the shape and locomotion of superhelically shaped spirochete bacteria (Leptospira)\, we consider instead single bodies of high geometric complexity. We consider the rotational dynamics of towed bodies whose shape is a superposition of two oppositely handed helices\, finding that the direction and rate of body rotation is a result of competition between the two helices. Lastly\, we investigate how swimming C. elegans nematodes respond to the systematic changes in their fluid environment. We find that stroke form and Strouhal number remain invariant over many orders of magnitude change in viscosity\, and that the stroke form lies near that of peak mechanical efficiency. We also find a power-law relation between swimming power-output and viscosity. I will also discuss the swimming of two interacting C. elegans and in confined geometries and more. \n \nGraduate students and post-docs may meet with Sunghwan Jung in Swain Hall West 238 from 3:00-4:00 PM after the seminar. If you would like to meet with Dr. Jung\, please e-mail bioc@indiana.edu to arrange the meeting.\n\nOther Information\nSunghwan Jung is a Biocomplexity CTE Faculty Search Candidate. If you would like to meet with Dr. Jung\, please see the end of the abstract for more details. Note also that this seminar is on Thursday and begins at 2:00 PM. LOCATION:Swain Hall West 238 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=319 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT BEGIN:VEVENT UID:20091123T154047Z-000321@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070403T160000 DTEND;TZID=US-Eastern:20070403T170000 SUMMARY:Biocomplexity Seminar: András Czirók DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Pattern formation during embryonic development'\nAndrás Czirók\n\nAbstract\nLiving organisms\, from bacteria to vertebrates\, are well known to generate sophisticated multicellular patterns. The formation and regulation of these structures\, together with the emergence of associated functions\, became the focus of numerous recent interdisciplinary research. Advances in automatized microscopy allow the time-resolved tracking of embryonic development at cellular resolution over an extended area covering most of the embryo. The resulting images yield us information on the motion of multiple tissue components -- both cells and extracellular matrix (ECM) proteins. In bird embryos\, our studies on ECM displacements resulted in a method to distinguish tissue deformation and cell-autonomous motion. The smooth\, large-scale tissue movements of gastrulation/neurulation stage embryos were shown to exhibit a sustained\, vortex-like velcity pattern. Cellular rearrangements are superimposed upon the macroscopic tissue movement -- as seen during the assembly of ECM filaments\, or during the formation of the primordial vascular bed. ECM filament assembly is a hierarchical process\, where coordinated cell motility joins increasingly larger ECM structures into linear structures. Patterning of the primary vascular plexus is a collective action of primordial endothelial cells. The emerging "\;polygonal"\; vascular structure is shown to be formed by cell-cell and cell-ECM interactions: adhesion and protrusive activity (sprouting). Utilizing avb3 integrins\, multicellular sprouts invade rapidly into avascular areas. Sprout elongation\, in turn\, depends on a continuous supply of endothelial cells. These cells migrate along the sprout\, towards its tip\, in a VE cadherin-dependent process. The observed abundance of multicellular sprout formation in various in vitro and in vivo systems can be explained by a generic mechnism based on preferential attraction to elongated structures. Our interacting particle model exhibits robust sprouting dynamics and results in patterns with morphometry similar to native primordial vascular plexuses — without ancillary assumptions involving chemotaxis or chemomechanical signaling.\n\nOther Information\nAndrás Czirók is a Biocomplexity CTE Faculty Search Candidate. LOCATION:Swain Hall West 238 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=321 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT BEGIN:VEVENT UID:20091123T154047Z-000318@biocomplexity.indiana.edu DTSTAMP:20091123T154047Z DTSTART;TZID=US-Eastern:20070423T160000 DTEND;TZID=US-Eastern:20070423T170000 SUMMARY:Biocomplexity Seminar: Luis Bettencourt DESCRIPTION:Biocomplexity Seminar/Spring 2007\n'Detecting the onset of human transmission in avian influenza outbreaks'\nLuis Bettencourt\nTheoretical DivisionLos Alamos National Laboratory\n\nAbstract\nAs the world population grows and becomes more mobile the threat of new and emerging infectious diseases gains increasing importance. Calls for better international surveillance must be met with new methods for the assessment and prediction of emergent disease evolution\, before they becomes epidemic. Presently\, the H5N1 highly pathogenic avian influenza virus is singular among other emerging diseases\, infecting millions of birds worldwide and having caused more than 270 confirmed human infections\, with over 60% observed case mortality. There is worldwide alert for the possibility that H5N1 will become as transmissible in humans as seasonal influenza strains\, possibly causing a worldwide pandemic of unprecedented proportions. Here we develop a new general class of methods for estimating quantitatively the evolution of the epidemic potential of emerging diseases. Estimates are performed as new cases are reported\, without need for knowledge of outbreak size\, as is characteristic of most present approaches. We use current worldwide surveillance data to place bounds on the basic reproductive number of H5N1 influenza in humans\, and to establish a basis for monitoring the future evolution of human-to-human transmissibility by detecting quantitative shifts in its epidemiology. LOCATION:Swain Hall West 113 URL:http://biocomplexity.indiana.edu/events/seminars.php?v=abstract&sid=318 CLASS:PUBLIC TRANSP:TRANSPARENT END:VEVENT END:VCALENDAR