Microbial communities are essential for global ecosystems and human health. Computational modeling of microbial consortia is thus a major goal in systems biology and microbial ecology. BacArena is a project to simulate bacterial behavior in communities. A lot of progress is done in the last years to create genome wide metabolic reconstructions of certain organisms, which open a wide field of ma...

After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli grows as predicted using flux balance analysis (FBA) on genome-scale metabolic models (GEMs). However, it is not known whether the predicted pathway usage in FBA solutions is consistent with gene and protein expression in the wild-type and evolved strains. Here, we report that >98% of active reactions fr...

This paper presents the MINDED-FBA, a remote-sensing-based tool for determination of both flooded and burned areas. The tool, freely distributed as QGIS plugin, consists an adaptation development previously published Multi Index Image Differencing methods (MINDED MINDED-BA). MINDED-FBA allows integration combination wider diversity satellite sensor datasets, now including synthetic aperture rad...

Foreign body aspiration (FBA) often causes a delay in management due to asymptomatic clinical manifestations, seeking medical care, less competent personnel, and inadequate healthcare facilities.

The hormone 17beta-estradiol (E2) can cause endocrine disruption in sensitive species at part per trillion concentrations. The persistence and transport pathways of manure-borne E2 in agricultural soils were determined by comparing its occurrence with the transfer of water and the transport of non-sorbing fluorobenzoic acid (FBA) tracers. This comparison was done using capillary wick lysimeters...

This paper presents a new method, steady-state regulatory flux balance analysis (SR-FBA), for predicting gene expression and metabolic fluxes in a large-scale integrated metabolic-regulatory model. Using SR-FBA to study the metabolism of Escherichia coli, we quantify the extent to which the different levels of metabolic and transcriptional regulatory constraints determine metabolic behavior: me...

Motivated by flexible resource allocation in emerging network technologies, we study the following variant of the classic storage allocation problem. We are given a set of flexible axis-parallel rectangles (corresponding to activities), and a linear resource. Each rectangle has a maximum possible height, as well as the profit accrued per allocated unit of the resource. The goal is to feasibly a...

Flux Balance Analysis (FBA) has been successfully applied to facilitate the understanding of cellular metabolism in model organisms. Standard formulations of FBA can be applied to large systems, but the accuracy of predictions may vary significantly depending on environmental conditions, genetic perturbations, or complex unknown regulatory constraints. Here we present an FBA-based approach to i...

Tea oil tree (Camellia oleifera, Co) provides a fine edible oil source in China. Tea oil from the seeds is very beneficial to human health. Fructose-1,6-bisphosphate aldolase (FBA) hydrolyzes fructose-1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, two critical metabolites for oil biosynthesis. The objectives of this study were to identify FBA genes and investig...

Repetition of the same stimulus leads to a reduction in neural activity known as repetition suppression (RS). In functional magnetic resonance imaging (fMRI), RS is found for multiple object categories. One proposal is that RS reflects locally based "within-region" changes, such as neural fatigue. Thus, if a given region shows RS across changes in stimulus size or view, then it is inferred to h...