Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics: differentiation in living matters.

The notion of an attractor has been widely employed in thinking about the nonlinear dynamics of organisms and biological phenomena as systems and as processes. The notion of a landscape with valleys and mountains encoding multiple attractors, however, has a rigorous foundation only for closed, thermodynamically non-driven, chemical systems, such as a protein. Recent advances in the theory of nonlinear stochastic dynamical systems and its applications to mesoscopic reaction networks, one reaction at a time, have provided a new basis for a landscape of open, driven biochemical reaction systems under sustained chemostat. The theory is equally applicable not only to intracellular dynamics of biochemical regulatory networks within an individual cell but also to tissue dynamics of heterogeneous interacting cell populations. The landscape for an individual cell, applicable to a population of isogenic non-interacting cells under the same environmental conditions, is defined on the counting space of intracellular chemical composition

Integrating multiple types of data to predict novel cell cycle-related genes

<p>Abstract</p> <p>Background</p> <p>Cellular functions depend on genetic, physical and other types of interactions. As such, derived interaction networks can be utilized to discover novel genes involved in specific biological processes. Epistatic Miniarray Profile, or E-MAP, which is an experimental platform that measures genetic interactions on a genome-wide scale, has successfully recovered known pathways and revealed novel protein complexes in <it>Saccharomyces cerevisiae</it> (budding yeast).</p> <p>Results</p> <p>By combining E-MAP data with co-expression data, we first predicted a potential cell cycle related gene set. Using Gene Ontology (GO) function annotation as a benchmark, we demonstrated that the prediction by combining microarray and E-MAP data is generally >50% more accurate in identifying co-functional gene pairs than the prediction using either data source alone. We also used transcription factor (TF)–DNA binding data (Chip-chip) and protein phosphorylation data to construct a local cell cycle regulation network based on potential cell cycle related gene set we predicted. Finally, based on the E-MAP screening with 48 cell cycle genes crossing 1536 library strains, we predicted four unknown genes (<it>YPL158C</it>, <it>YPR174C</it>, <it>YJR054W</it>, and <it>YPR045C</it>) as potential cell cycle genes, and analyzed them in detail.</p> <p>Conclusion</p> <p>By integrating E-MAP and DNA microarray data, potential cell cycle-related genes were detected in budding yeast. This integrative method significantly improves the reliability of identifying co-functional gene pairs. In addition, the reconstructed network sheds light on both the function of known and predicted genes in the cell cycle process. Finally, our strategy can be applied to other biological processes and species, given the availability of relevant data.</p

Leveraging remotely sensed non-wall-to-wall data for wall-to-wall upscaling in forest inventory

Remote sensing (RS) has enhanced forest inventory with model-based inference, that is, a family of statistical procedures rigorously estimates the parameter of a variable of interest (VOI) for a spatial population, e.g., the mean or total of forest carbon for a study area. Upscaling in earth observation, alias to this estimation, aggregates VOI from a finer spatial resolution to a coarser one with reduced uncertainty, serving decision making for natural resource management at larger scales. However, conventional model-based estimation (CMB) confronts a major challenge: it only supports RS wall-to-wall data, meaning that remotely sensed data must be available in panorama and non-wall-to-wall but quality data such as lidar or even cloud-masked satellite imagery are not supported due to incomplete coverage, impeding precise upscaling with cutting-edge instruments or for large scale applications. Consequently, this study aims to develop and demonstrate the use and usefulness of RS nonwall-to-wall data for upscaling with Hierarchical model-based estimation (HMB) which incorporates a two-stage model for bridging RS non- and wall-to-wall data; and for optimizing cost-efficiency, to evaluate the effects of non-wall-to-wall sample size on upscaling precision. Three main conclusions are relevant: (1) the HMB is a variant of the CMB estimator through trading in the uncertainty of the second-stage model to enable estimation using RS non-wall-to-wall data; (2) a quality first-stage model is key to exerting the advantage of HMB relative to the CMB estimator; (3) the variance of the HMB estimator is dominated by the first-stage model variance component, indicating that increasing the sample size in the first-stage is effective for increasing the overall precision. Overall, the HMB estimator balances tradeoffs between cost, efficiency and flexibility when devising a model-based upscaling in earth observation