A New Approach to Modeling Morphogenesis Using Control Theory

It has been proposed that biological structures termed fractones may govern morphogenic events of cells; that is, fractones may dictate when a cell undergoes mitosis by capturing and concentrating certain chemical growth factors created by cells in their immediate vicinity. Based on this hypothesis, we present a model of cellular growth that incorporates these fractones, freely-diffusing growth factor, their interaction with each other, and their effect on cellular mitosis. The question of how complex biological cell structures arise from single cells during development can now be posed in terms of a mathematical control problem in which the activation and deactivation of fractones determines how a cellular mass forms. Stated in this fashion, several new questions in the field of control theory emerge. We present this new class of problems, as well as an initial analysis of some of these questions. Also, we indicate an extension of the proposed control method to layout optimization.

The development of HISPEC for Keck and MODHIS for TMT: science cases and predicted sensitivities

HISPEC is a new, high-resolution near-infrared spectrograph being designed for the W.M. Keck II telescope. By offering single-shot, R=100,000 between 0.98 - 2.5 um, HISPEC will enable spectroscopy of transiting and non-transiting exoplanets in close orbits, direct high-contrast detection and spectroscopy of spatially separated substellar companions, and exoplanet dynamical mass and orbit measurements using precision radial velocity monitoring calibrated with a suite of state-of-the-art absolute and relative wavelength references. MODHIS is the counterpart to HISPEC for the Thirty Meter Telescope and is being developed in parallel with similar scientific goals. In this proceeding, we provide a brief overview of the current design of both instruments, and the requirements for the two spectrographs as guided by the scientific goals for each. We then outline the current science case for HISPEC and MODHIS, with focuses on the science enabled for exoplanet discovery and characterization. We also provide updated sensitivity curves for both instruments, in terms of both signal-to-noise ratio and predicted radial velocity precision.Comment: 25 pages, 9 figures. To appear in the Proceedings of SPIE: Techniques and Instrumentation for Detection of Exoplanets XI, vol. 12680 (2023

A Hybrid Control Model of Fractone-Dependent Morphogenesis

Ph.D. University of Hawaii at Manoa 2015.Includes bibliographical references.It has been hypothesized that the generation of new neural cells (neurogenesis) resulting from cell proliferation and differentiation in the developing and adult brain is guided by the extracellular matrix. The extracellular matrix of the neurogenic niches comprises specialized structures termed fractones, which are scattered in between stem/progenitor cells. Fractones have been found to bind and activate growth factors at the surface of stem/progenitor cells to influence their proliferation. We present a mathematical control model that considers the role of fractones as captors and activators of growth factors, controlling the rate of proliferation and directing the location of the newly generated neuroepithelial cells in the forming brain. The model is a hybrid control system that incorporates both continuous and discrete mechanics. The continuous portion of the model features the diffusion of multiple growth factor concentrations through the mass of cells, with fractones acting as sinks that absorb and hold growth factor. When a sufficient amount has been captured, growth is assumed to occur instantaneously in the discrete portion of the model, causing an immediate rearrangement of cells, and potentially altering the dynamics of the diffusion. The fractones in the model are represented by controls that allow for their dynamic placement in and removal from the evolving cell mass. These controls allows us to govern its developing shape. A version of the model has been implemented for computer simulation and initialized with real biological data. We hope to show the potential usefulness of such a model to verify the plausibility of the fractone hypothesis

Allelic analysis of sheath blight resistance with association mapping in rice

Citation: Jia, Limeng, Wengui Yan, Chengsong Zhu, Hesham A. Agrama, Aaron Jackson, Kathleen Yeater, Xiaobai Li, et al. “Allelic Analysis of Sheath Blight Resistance with Association Mapping in Rice.” PLOS ONE 7, no. 3 (March 12, 2012): e32703. https://doi.org/10.1371/journal.pone.0032703.Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r =20.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice