KNOWLEDGE DISCOVERY FOR IDENTIFICATION OF ENZYME WITH A PRIORY SPECIFIED PROPERTIES

Development of new products with the given properties from the known raw materials is one of the common research tasks in process engineering. Usually the first step of research is a literature survey based on the search for the specific keywords. Nowadays there exist many vast databases of articles and patents, and the traditional, keywords-based, searching tools are not always sufficient to find the desired information. The main objective of this paper is to develop methodology for identification of new materials, based on knowledge discovery. As an example, the proposed methodology is applied for identification of new enzyme of microbial origin capable of polymerizing lactose in aqueous solution, with the number of required criteria

Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142

Genome-scale metabolic models have proven useful for answering fundamental questions about metabolic capabilities of a variety of microorganisms, as well as informing their metabolic engineering. However, only a few models are available for oxygenic photosynthetic microorganisms, particularly in cyanobacteria in which photosynthetic and respiratory electron transport chains (ETC) share components. We addressed the complexity of cyanobacterial ETC by developing a genome-scale model for the diazotrophic cyanobacterium, Cyanothece sp. ATCC 51142. The resulting metabolic reconstruction, iCce806, consists of 806 genes associated with 667 metabolic reactions and includes a detailed representation of the ETC and a biomass equation based on experimental measurements. Both computational and experimental approaches were used to investigate light-driven metabolism in Cyanothece sp. ATCC 51142, with a particular focus on reductant production and partitioning within the ETC. The simulation results suggest that growth and metabolic flux distributions are substantially impacted by the relative amounts of light going into the individual photosystems. When growth is limited by the flux through photosystem I, terminal respiratory oxidases are predicted to be an important mechanism for removing excess reductant. Similarly, under photosystem II flux limitation, excess electron carriers must be removed via cyclic electron transport. Furthermore, in silico calculations were in good quantitative agreement with the measured growth rates whereas predictions of reaction usage were qualitatively consistent with protein and mRNA expression data, which we used to further improve the resolution of intracellular flux values

Simulation of Pulling the Reinforcing Bar from Concrete Block with Account of Friction and Concrete Damage

A direct finite element modeling of the pulling process of the steel reinforcing bar out from the concrete block with taking into account the cohesive behavior of steel-concrete bond and using elastic-plastic-damage constitutive equations for the concrete is considered. The comparison of obtained results of finite element simulations with experimental data is presented and discussed for the problem of pulling the reinforcing bar from the concrete block

Simulation of Pulling the Reinforcing Bar from Concrete Block with Account of Friction and Concrete Damage

A direct finite element modeling of the pulling process of the steel reinforcing bar out from the concrete block with taking into account the cohesive behavior of steel-concrete bond and using elastic-plastic-damage constitutive equations for the concrete is considered. The comparison of obtained results of finite element simulations with experimental data is presented and discussed for the problem of pulling the reinforcing bar from the concrete block

Predicted effects of varying photon uptake rates on growth and electron transport pathways.

<p>(A) 2-D phenotypic phase plane (PhPP) displaying maximum growth rates for varying photon uptake rates. The PhPP has 3 distinct regions – in regions 1 and 3, flux through a single photosystem limit growth rates, whereas in region 2 flux increases through either photosystem will increase growth rate. (B) Pathway maps of electron transfer reactions in different PhPP regions. PhPP flux variability analysis was performed to see which flux is always required (red arrows), optional (green arrows), and blocked (blue arrows) across each of the three PhPP regions.</p

Effect of nutrient limitation on biomass composition (normalized to ash-free dry weight).

<p>Effect of nutrient limitation on biomass composition (normalized to ash-free dry weight).</p

Effects of <i>in silico</i> reaction deletions on flux spans under light-limited conditions.

<p>(A) Effects of deletions are compared to the cases where no reactions were deleted (red bar), or TPD were used as constraints (green bar). The values represent the average flux span across all reactions in central metabolism. Only deletions which lower the flux span by at least >1 mmol·g⁻¹ AFDW·h⁻¹ are presented. (B) Changes in flux spans for specific reactions catalyzed by ribulose bisphosphate carboxylase (RBC) and phosphoglucose isomerase (PGI) between simulations that (i) use TPD data as a constraint (green bars), (ii) delete single reactions (blue and purple bars), (iii) delete two reactions (yellow bar) or (iv) impose no additional constraints (red bars). Reaction abbreviations match those listed in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002460#pcbi.1002460.s005" target="_blank">Table S1</a>.</p

Flux variability analysis for model simulations in light-limited and ammonium-limited chemostat conditions.

<p>Flux variability analysis for model simulations in light-limited and ammonium-limited chemostat conditions.</p

Impact of electron transport pathways on growth and metabolism of <i>Cyanothece</i> 51142.

<p>(A) Effects of removing cyclic photosynthesis (<i>via</i> NDH-1, NDH-2, FdPq, G3PD_PQ, and SUCD_PQ) and alternative reductant sinks (H₂ production, COX, QOX, and Mehler reactions). (B) Effect of removing alternative reductant sinks but including all routes for cyclic photosynthesis. Shaded regions indicate that multiple flux values can achieve maximal growth rate. (C) All photosynthetic and respiratory electron flow routes operate, except H₂ production.</p