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Alicea B.,Orthogonal Research | Gordon R.,Wayne State University | Gordon R.,Embryogenesis Center
BioSystems | Year: 2014

Many models have been used to simplify and operationalize the subtle but complex mechanisms of biological evolution. Toy models are gross simplifications that nevertheless attempt to retain major essential features of evolution, bridging the gap between empirical reality and formal theoretical understanding. In this paper, we examine thirteen models which describe evolution that also qualify as such toy models, including the tree of life, branching processes, adaptive ratchets, fitness landscapes, and the role of nonlinear avalanches in evolutionary dynamics. Such toy models are intended to capture features such as evolutionary trends, coupled evolutionary dynamics of phenotype and genotype, adaptive change, branching, and evolutionary transience. The models discussed herein are applied to specific evolutionary contexts in various ways that simplify the complexity inherent in evolving populations. While toy models are overly simplistic, they also provide sufficient dynamics for capturing the fundamental mechanism(s) of evolution. Toy models might also be used to aid in high-throughput data analysis and the understanding of cultural evolutionary trends. This paper should serve as an introductory guide to the toy modeling of evolutionary complexity. © 2014 Elsevier Ireland Ltd. Source

Lu K.,Kyoto University | Cao T.,National University of Singapore | Gordon R.,Embryogenesis Center
BioSystems | Year: 2012

Cell fate determination and development is a biology question that has yet to be fully answered. During embryogenesis and . in vivo stem cell differentiation, cells/tissues deploy epigenetic mechanisms to accomplish differentiation and give rise to the fully developed organism. Although a biochemistry description of cellular genetics and epigenetics is important, additional mechanisms are necessary to completely solve the problem of embryogenesis, especially differentiation and the spatiotemporal coordination of cells/tissues during morphogenesis. The cell state splitter and differentiation wave working-model was initially proposed to explain the homeostatic primary neural induction in amphibian embryos. Here the model is adopted to explain experimental findings on . in vitro embryonic stem cell, pluripotency and differentiation. Moreover, since somatic cells can be reverted to a stem-cell-like pluripotent state through the laboratory procedure called epigenetic reprogramming, erection of a cell state splitter could be a key event in their successful reprogramming. Overall, the cell state splitter working-model introduces a bistable cytoskeletal mechanism that partially explains cell fate determination and biological development. It offers an interdisciplinary framework that bridges the gap between molecular epigenetics and embryogenesis. © 2012 Elsevier Ireland Ltd. Source

Gordon R.,Embryogenesis Center
Systems Biology in Reproductive Medicine | Year: 2013

The study of embryos with the tools and mindset of physics, started by Wilhelm His in the 1880s, has resumed after a hiatus of a century. The Embryo Physics Course convenes online allowing interested researchers and students, who are scattered around the world, to gather weekly in one place, the virtual world of Second Life®. It attracts people from a wide variety of disciplines and walks of life: applied mathematics, artificial life, bioengineering, biophysics, cancer biology, cellular automata, civil engineering, computer science, embryology, electrical engineering, evolution, finite element methods, history of biology, human genetics, mathematics, molecular developmental biology, molecular biology, nanotechnology, philosophy of biology, phycology, physics, self-reproducing systems, stem cells, tensegrity structures, theoretical biology, and tissue engineering. Now in its fifth year, the Embryo Physics Course provides a focus for research on the central question of how an embryo builds itself. Copyright © 2013 Informa Healthcare USA, Inc. Source

Vinayak V.,Dr Hari Singh Gour University | Gordon R.,Embryogenesis Center | Gautam S.,Dr Hari Singh Gour University | Rai A.,Diatom Research Unit
Advanced Science Letters | Year: 2014

Diadesmis confervacea produces substantial amounts of oil which could be utilized as biofuel. We discovered that oil exocytoses spontaneously from cells of D. confervacea, a new observation for diatoms. Morphological observation shows about 50% of cultured diatoms oozing oil by the 10th day of culture and about 80% oozing by the end of a month. When the 31st day plates were subcultured on fresh media they resumed active growth, division and oil production and oozing in a similar manner over the following month. GCMS (gas chromatographymass spectrometry) results showed formation of free fatty acids at retention time peak 12.91 minutes and FAME (fatty acid methyl esters) at retention time peak 18.32 minutes upon transesterification. Spontaneous oozing greatly reduces the cost of algal fuels, as separation of the oil from the cells has hitherto been an expensive, fuel requiring process, and makes it easier to design diatom biofuel solar panels. © 2014 American Scientific Publishers All rights reserved. Source

Alvare G.,University of Manitoba | Gordon R.,Embryogenesis Center | Gordon R.,Wayne State University | Gordon R.,Stellarray, Inc.
Theoretical Biology and Medical Modelling | Year: 2015

Background: X-ray dose from computed tomography (CT) scanners has become a significant public health concern. All CT scanners spray x-ray photons across a patient, including those using compressive sensing algorithms. New technologies make it possible to aim x-ray beams where they are most needed to form a diagnostic or screening image. We have designed a computer game, CT Brush, that takes advantage of this new flexibility. It uses a standard MART algorithm (Multiplicative Algebraic Reconstruction Technique), but with a user defined dynamically selected subset of the rays. The image appears as the player moves the CT brush over an initially blank scene, with dose accumulating with every "mouse down" move. The goal is to find the "tumor" with as few moves (least dose) as possible. Results: We have successfully implemented CT Brush in Java and made it available publicly, requesting crowdsourced feedback on improving the open source code. With this experience, we also outline a "shoot 'em up game" CancerZap! for photon limited CT. Conclusions: We anticipate that human computing games like these, analyzedby methods similar to those used to understand eye tracking, will lead to new object dependent CT algorithms that will require significantly less dose than object independent nonlinear and compressive sensing algorithms that depend on sprayed photons. Preliminary results suggest substantial dose reduction is achievable. © 2015 Alvare and Gordon. Source

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