EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search

Background Elementary flux mode (EFM) analysis is a well-established, yet computationally challenging approach to characterize metabolic networks. Standard algorithms require huge amounts of memory and lack scalability which limits their application to single servers and consequently limits a comprehensive analysis to medium-scale networks. Recently, Avis et al. developed —a parallel version of the lexicographic reverse search (lrs) algorithm, which, in principle, enables an EFM analysis on high-performance computing environments (Avis and Jordan. mplrs: a scalable parallel vertex/facet enumeration code. arXiv:1511.06487, 2017). Here we test its applicability for EFM enumeration. Results We developed , a Python package that gives users access to the enumeration capabilities of . uses COBRApy to process metabolic models from sbml files, performs loss-free compressions of the stoichiometric matrix, and generates suitable inputs for as well as , providing support not only for our proposed new method for EFM enumeration but also for already established tools. By leveraging COBRApy, also allows the application of additional reaction boundaries and seamlessly integrates into existing workflows. Conclusion We show that due to ’s properties, the algorithm is perfectly suited for high-performance computing (HPC) and thus offers new possibilities for the unbiased analysis of substantially larger metabolic models via EFM analyses. is an open-source program that comes together with a designated workflow and can be easily installed via pip.

Effect of Initial Water Flux on the Performance of Anaerobic Membrane Bioreactor: Constant Flux Mode versus Varying Flux Mode

Anaerobic membrane bioreactors (AnMBRs) have aroused growing interest in wastewater treatment and energy recovery. However, serious membrane fouling remains a critical hindrance to AnMBRs. Here, a novel membrane fouling mitigation via optimizing initial water flux is proposed, and its feasibility was evaluated by comparing the membrane performance in AnMBRs between constant flux and varying flux modes. Results indicated that, compared with the constant flux mode, varying flux mode significantly prolonged the membrane operating time by mitigating membrane fouling. Through the analyses of fouled membranes under two operating modes, the mechanism of membrane fouling mitigation was revealed as follows: A low water flux was applied in stage 1 which slowed down the interaction between foulants and membrane surface, especially reduced the deposition of proteins on the membrane surface and formed a thin and loose fouling layer. Correspondingly, the interaction between foulants was weakened in the following stage 2 with a high water flux and, subsequently, the foulants absorbed on the membrane surface was further reduced. In addition, flux operating mode had no impact on the contaminant removal in an AnMBR. This study provides a new way of improving membrane performance in AnMBRs via a varying flux operating mode.

Metabolic Efficiency of Sugar Co-Metabolism and Phenol Degradation in Alicyclobacillus acidocaldarius for Improved Lignocellulose Processing

Substrate availability plays a key role in dictating metabolic strategies. Most microorganisms consume carbon/energy sources in a sequential, preferential order. The presented study investigates metabolic strategies of Alicyclobacillus acidocaldarius, a thermoacidophilic bacterium that has been shown to co-utilize glucose and xylose, as well as degrade phenolic compounds. An existing metabolic model was expanded to include phenol degradation and was analyzed with both metabolic pathway and constraint-based analysis methods. Elementary flux mode analysis was used in conjunction with resource allocation theory to investigate ecologically optimal metabolic pathways for different carbon substrate combinations. Additionally, a dynamic version of flux balance analysis was used to generate time-resolved simulations of growth on phenol and xylose. Results showed that availability of xylose along with glucose did not predict enhanced growth efficiency beyond that of glucose alone, but did predict some differences in pathway utilization and byproduct profiles. In contrast, addition of phenol as a co-substrate with xylose predicted lower growth efficiency. Dynamic simulations predicted co-consumption of xylose and phenol in a similar pattern as previously reported experiments. Altogether, this work serves as a case study for combining both elementary flux mode and flux balance analyses to probe unique metabolic features, and also demonstrates the versatility of A. acidocaldarius for lignocellulosic biomass processing applications.

Towards scaling elementary flux mode computation

While elementary flux mode (EFM) analysis is now recognized as a cornerstone computational technique for cellular pathway analysis and engineering, EFM application to genome-scale models remains computationally prohibitive. This article provides a review of aspects of EFM computation that elucidates bottlenecks in scaling EFM computation. First, algorithms for computing EFMs are reviewed. Next, the impact of redundant constraints, sensitivity to constraint ordering and network compression are evaluated. Then, the advantages and limitations of recent parallelization and GPU-based efforts are highlighted. The article then reviews alternative pathway analysis approaches that aim to reduce the EFM solution space. Despite advances in EFM computation, our review concludes that continued scaling of EFM computation is necessary to apply EFM to genome-scale models. Further, our review concludes that pathway analysis methods that target specific pathway properties can provide powerful alternatives to EFM analysis.

Genetic and pharmacological inactivation of apical Na+-K+-2Cl− cotransporter 1 in choroid plexus epithelial cells reveals the physiological function of the cotransporter

Choroid plexus epithelial cells (CPECs) secrete cerebrospinal fluid (CSF). They express Na+-K+-ATPase and Na+-K+-2Cl− cotransporter 1 (NKCC1) on their apical membrane, deviating from typical basolateral membrane location in secretory epithelia. Given this peculiarity, the direction of basal net ion fluxes mediated by NKCC1 in CPECs is controversial, and cotransporter function is unclear. Determining the direction of basal NKCC1-mediated fluxes is critical to understanding the function of apical NKCC1. If NKCC1 works in the net efflux mode, it may be directly involved in CSF secretion. Conversely, if NKCC1 works in the net influx mode, it would have an absorptive function, contributing to intracellular Cl− concentration ([Cl−]i) and cell water volume (CWV) maintenance needed for CSF secretion. We resolve this long-standing debate by electron microscopy (EM), live-cell-imaging microscopy (LCIM), and intracellular Na+ and Cl− measurements in single CPECs of NKCC1+/+ and NKCC1−/− mouse. NKCC1-mediated ion and associated water fluxes are tightly linked, thus their direction is inferred by measuring CWV changes. Genetic or pharmacological NKCC1 inactivation produces CPEC shrinkage. EM of NKCC1−/− CPECs in situ shows they are shrunken, forming large dilations of their basolateral extracellular spaces, yet remaining attached by tight junctions. Normarski LCIM shows in vitro CPECs from NKCC1−/− are ~17% smaller than NKCC1+/+. CWV measurements in calcein-loaded CPECs show that bumetanide (10 μM) produces ~16% decrease in CWV in NKCC1+/+ but not in NKCC1−/− CPECs. Our findings suggest that under basal conditions apical NKCC1 is continuously active and works in the net inward flux mode maintaining [Cl−]i and CWV needed for CSF secretion.