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The goal of Caltech's Cell Center (Center for Integrative Study of Cell Regulation) is to develop new computational methods for understanding how the many genes and proteins that make up individual cells work together to carry out specilized functions of different cell tyeps, including neurons, plant cells, and bacteria.
The project focus within the Cell Center is dynamic and this early list is not exhaustive. Some initial research science drivers of the center include:
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Spatially explicit simulations of cellular and viral ultrastructure
Spatial organization of cellular ultrastructure determines major physical properties of cells, is a prerequisite for some functions of cell metabolism and division and also influences characteristics of viruses such as HIV-1. Using a powerful miscroscopy technique known as electron cryotomography, the lab of Grant Jensen collects images of both bacterial subcellular structures and viruses. The images are then used to generate reconstructions in three dimensions. These 3D reconstructions inform spatially explicit biosimulations designed to test hypotheses regarding the interplay of spatially extended protein assemblies and functional behavior.
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Modeling of synaptic plasticity
Synaptic plasticity refers to the process whereby neuronal connections in the brain are modified in response to stimuli; it is the fundamental physiological basis of learning and memory. Changes in synaptic strength are the result of a complex biochemical signaling network that is sensitive to the discrete distributions in both space and time of the component molecules. The lab of Mary M. Kennedy combines experiments that characterize the reaction kinetics of key players in this biochemical network with Monte Carlo simulations of molecular dynamics and interactions within a model cell to understand synaptic plasticity.
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Modeling of plant development
One of the great unanswered questions of biology is the mechanism of organismal growth and development. The Meyerowitz group, working with Eric Mjolsness at the University of California at Irvine, is studying the growth of plan shoots at the cellular level, obtaining new dynamic descriptions of patterns of cell division and gene expression by using real-time laser scanning confocal microscopy of plant meristems that have been marked with fluorescent reporters. Specific problems of interest include control of stem cell subpopulations in the developing shoot and parameterization of models of root meristem behavior.
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Evolution of developmental mechanisms in vertebrates
The neural crest is a cell population that is migratory and multipotent during development of the organism. Neural crest cells ultimately give rise to many defining characteristics of vertebrates, including a well-defined head and peripheral neural ganglia. Thus, understanding the genetic changes driving the evolution of definitive neural crest cells from their early evolutionary precursors is critical to understanding vertebrate origins. Professor Marianne Bronner-Fraser examines orthologous gene regulatory proteins in various species in order to define mechanisms leading to evolution of the neural crest.
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