Vertebrate Limb Chondrogenesis and Invertebrate Comparative Genomics
Mar 13, Thu 2007
2:00 pm, Nichols Hall Apollo Room
Dr. Scott Christley
Department of Computer Science and Engineering, University of Notre Dame,
The precartilage mesenchymal cells of the developing limbs, or limb buds, of embryos of vertebrate organisms such as chickens or mice, undergo a process of chondrogenic (i.e., cartilage) pattern formation whereby they first become more tightly packed at discrete sites, forming "condensations". These precartilage condensations then differentiate into nodules or bars of cartilage which form the primordia of the develop limb skeleton. We introduce a discrete, multiscale, stochastic agent-based model for the behavior of limb bud mesenchymal cells in high density ("micromass") culture. The model employs a biologically motivated reaction-diffuion process, and cell-matrix adhesion (haptotaxis), as the bases of chondrogenic pattern formation. Our model is the most successful computational model to date for pattern formation in the limb cell micromass system, and it has suggested new empirically testable hypotheses involving transient or stationary dynamical regimes for inductive patterns of morphogens. We will also discuss future directions for the model to incorporate new biological results.
Some of the worst human pathogens (malaria, West Nile, trench fever, etc.) are transmitted by small insects, or invertebrate vectors. VectorBase.org is an NIAID Bioinformatics Resource Center hosted at the University of Notre Dame for Invertebrate Vectors of Human Pathogens. VectorBase.org manages genomic data, provides web-based genome browsing, provides web-submission access to computational tools, and manages numerous other resources for the broader community of researchers studying these organisms. We will describe the back-end architectural design of VectorBase.org and the management of this community resource. VectorBase.org has also provided the opportunity for comparative genomics research of these invertebrates. We will discuss a couple projects including an algorithm and workflow for finding ultraconserved elements shared by any number of organisms regardless of genome size, and a project about the ongoing speciation of the malaria mosquito Anopheles gambiae through comparison of the newly sequenced genomes for the M and S molecular forms.