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https://www.readbyqxmd.com/read/28647528/the-linkage-between-nutrient-supply-intracellular-enzyme-abundances-and-bacterial-growth-new-evidences-from-the-central-carbon-metabolism-of-corynebacterium-glutamicum
#1
Stephan Noack, Raphael Voges, Jochem Gätgens, Wolfgang Wiechert
Corynebacterium glutamicum serves as important production host for small molecular compounds that are derived from precursor molecules of the central carbon metabolism. It is therefore a well-studied model organism of industrial biotechnology. However, a deeper understanding of the regulatory principles underlying the synthesis of central metabolic enzymes under different environmental conditions as well as its impact on cell growth is still missing. We studied enzyme abundances in C. glutamicum in response to growth on: i) one limiting carbon source by sampling chemostat and fed-batch cultivations and ii) changing carbon sources provided in excess by sampling batch cultivations...
June 21, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28645580/chemostat-studies-of-bacteriophage-m13-infected-escherichia-coli-jm109-for-continuous-ssdna-production
#2
Benjamin Kick, Karl Lorenz Behler, Timm Steffen Severin, Dirk Weuster-Botz
Steady state studies in a chemostat enable the control of microbial growth rate at defined reaction conditions. The effects of bacteriophage M13 infection on maximum growth rate of Escherichia coli JM109 were studied in parallel operated chemostats on a milliliter-scale to analyze the steady state kinetics of phage production. The bacteriophage infection led to a decrease in maximum specific growth rate of 15 % from 0.74 h(-1) to 0.63 h(-1). Under steady state conditions, a constant cell specific ssDNA formation rate of 0...
June 20, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28619035/an-evolutionary-optimization-of-a-rhodopsin-based-phototrophic-metabolism-in-escherichia-coli
#3
Hyun Aaron Kim, Hyun Ju Kim, Jihoon Park, Ah Reum Choi, Kyoo Heo, Haeyoung Jeong, Kwang-Hwan Jung, Yeong-Jae Seok, Pil Kim, Sang Jun Lee
BACKGROUND: The expression of the Gloeobacter rhodopsin (GR) in a chemotrophic Escherichia coli enables the light-driven phototrophic energy generation. Adaptive laboratory evolution has been used for acquiring desired phenotype of microbial cells and for the elucidation of basic mechanism of molecular evolution. To develop an optimized strain for the artificially acquired phototrophic metabolism, an ancestral E. coli expressing GR was adaptively evolved in a chemostat reactor with constant illumination and limited glucose conditions...
June 15, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28589225/characterization-of-the-newly-isolated-%C3%AF-oxidizing-yeast-candida-sorbophila-ds02-and-its-potential-applications-in-long-chain-dicarboxylic-acid-production
#4
Heeseok Lee, Yohanes Eko Chandra Sugiharto, Seunghoon Lee, Gyuyeon Park, Changpyo Han, Hyeran Jang, Wooyoung Jeon, Heejoon Park, Jungoh Ahn, Kyungbo Kang, Hongwoen Lee
α, ω-Dicarboxylic acids (DCAs) are multipurpose chemicals widely used in polymers, perfumes, plasticizers, lubricants, and adhesives. The biotransformation of DCAs from alkanes and fatty acids by microorganisms has attracted recent interest, since synthesis via chemical oxidation causes problems in terms of the environment and safety. We isolated an ω-oxidizing yeast from a wastewater disposal facility of a petrochemical factory by chemostat enrichment culture. The haploid strain identified as Candida sorbophila DS02 grew on glucose and dodecane, exhibiting greater cell shrinkage on the latter...
June 6, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28585809/bsim-2-0-an-advanced-agent-based-cell-simulator
#5
Antoni Matyjaszkiewicz, Gianfranco Fiore, Fabio Annunziata, Claire S Grierson, Nigel J Savery, Lucia Marucci, Mario di Bernardo
Agent-based models (ABMs) provide a number of advantages relative to traditional continuum modeling approaches, permitting incorporation of great detail and realism into simulations, allowing in silico tracking of single-cell behaviors and correlation of these with emergent effects at the macroscopic level. In this study we present BSim 2.0, a radically new version of BSim, a computational ABM framework for modeling dynamics of bacteria in typical experimental environments including microfluidic chemostats...
June 23, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28585362/tailor-made-pat-platform-for-safe-syngas-fermentations-in-batch-fed-batch-and-chemostat-mode-with-rhodospirillum-rubrum
#6
Stephanie Karmann, Stéphanie Follonier, Daniel Egger, Dirk Hebel, Sven Panke, Manfred Zinn
Recently, syngas has gained significant interest as renewable and sustainable feedstock, in particular for the biotechnological production of poly([R]-3-hydroxybutyrate) (PHB). PHB is a biodegradable, biocompatible polyester produced by some bacteria growing on the principal component of syngas, CO. However, working with syngas is challenging because of the CO toxicity and the explosion danger of H2 , another main component of syngas. In addition, the bioprocess control needs specific monitoring tools and analytical methods that differ from standard fermentations...
June 6, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28572754/functional-amplification-and-preservation-of-human-gut-microbiota
#7
Nadia Gaci, Prem Prashant Chaudhary, William Tottey, Monique Alric, Jean-François Brugère
Background: The availability of fresh stool samples is a prerequisite in most gut microbiota functional studies. Objective: Strategies for amplification and long-term gut microbiota preservation from fecal samples would favor sample sharing, help comparisons and reproducibility over time and between laboratories, and improve the safety and ethical issues surrounding fecal microbiota transplantations. Design: Taking advantage of in vitro gut-simulating systems, we amplified the microbial repertoire of a fresh fecal sample and assessed the viability and resuscitation of microbes after preservation with some common intracellular and extracellular acting cryoprotective agents (CPAs), alone and in different combinations...
2017: Microbial Ecology in Health and Disease
https://www.readbyqxmd.com/read/28559741/an-effective-method-of-continuous-production-of-erythritol-from-glycerol-by-yarrowia-lipolytica-mk1
#8
Magdalena Rakicka, Aleksandra M Mirończuk, Ludwika Tomaszewska-Hetman, Anita Rywińska, Waldemar Rymowicz
This study demonstrates the potential applicability of the UV mutant Yarrowia lipolytica MK1 for the valorisation of glycerol and erythritol production in a chemostat culture. The aim of this research is to investigate the optimal C:N ratio in the feeding medium in order to enhance erythritol production. The highest erythritol concentration, at 113.1 g/L with a volumetric erythritol production rate of 1.1 g/(L·h) and a yield of 0.57 g/g, was obtained in the feeding medium with a C:N ratio of 80:1. Moreover, no residual glycerol was observed in the culture broth during cultivation...
March 2017: Food Technology and Biotechnology
https://www.readbyqxmd.com/read/28550811/influence-of-solids-residence-time-and-carbon-storage-on-nitrogen-and-phosphorus-recovery-by-microalgae-across-diel-cycles
#9
D A Gardner-Dale, I M Bradley, J S Guest
Microalgal treatment systems could advance nutrient recovery from wastewater by achieving effluent nitrogen (N) and phosphorus (P) levels below the current limit of technology, but their successful implementation requires an understanding of how design decisions influence nutrient uptake over daily (i.e., diel) cycles. This work demonstrates the ability to influence microalgal N:P recovery ratio via solids residence time (SRT) while maintaining complete nutrient removal across day/night cycles through carbon storage and mobilization...
May 18, 2017: Water Research
https://www.readbyqxmd.com/read/28545207/quality-and-reactivity-of-dissolved-organic-matter-in-a-mediterranean-river-across-hydrological-and-spatial-gradients
#10
Elisabet Ejarque, Anna Freixa, Eusebi Vazquez, Alba Guarch, Stefano Amalfitano, Stefano Fazi, Anna M Romaní, Andrea Butturini
Understanding DOM transport and reactivity in rivers is essential to having a complete picture of the global carbon cycle. In this study, we explore the effects of hydrological variability and downstream transport on dissolved organic matter (DOM) dynamics in a Mediterranean river. We sampled the main stem of the river Tordera from the source to the sea, over a range of fifteen hydrological conditions including extreme events (flood and drought). By exploring spatial and temporal gradients of DOM fluorescence properties, river hydrology was found to be a significant predictor of DOM spatial heterogeneity...
December 1, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28527885/maintenance-of-atp-homeostasis-triggers-metabolic-shifts-in-gas-fermenting-acetogens
#11
Kaspar Valgepea, Renato de Souza Pinto Lemgruber, Kieran Meaghan, Robin William Palfreyman, Tanus Abdalla, Björn Daniel Heijstra, James Bruce Behrendorff, Ryan Tappel, Michael Köpke, Séan Dennis Simpson, Lars Keld Nielsen, Esteban Marcellin
Acetogens are promising cell factories for producing fuels and chemicals from waste feedstocks via gas fermentation, but quantitative characterization of carbon, energy, and redox metabolism is required to guide their rational metabolic engineering. Here, we explore acetogen gas fermentation using physiological, metabolomics, and transcriptomics data for Clostridium autoethanogenum steady-state chemostat cultures grown on syngas at various gas-liquid mass transfer rates. We observe that C. autoethanogenum shifts from acetate to ethanol production to maintain ATP homeostasis at higher biomass concentrations but reaches a limit at a molar acetate/ethanol ratio of ∼1...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28526017/the-effect-of-hypoxia-on-the-lipidome-of-recombinant-pichia-pastoris
#12
Núria Adelantado, Pablo Tarazona, Karlheinz Grillitsch, Xavier García-Ortega, Sergi Monforte, Francisco Valero, Ivo Feussner, Günther Daum, Pau Ferrer
BACKGROUND: Cultivation of recombinant Pichia pastoris (Komagataella sp.) under hypoxic conditions has a strong positive effect on specific productivity when the glycolytic GAP promoter is used for recombinant protein expression, mainly due to upregulation of glycolytic conditions. In addition, transcriptomic analyses of hypoxic P. pastoris pointed out important regulation of lipid metabolism and unfolded protein response (UPR). Notably, UPR that plays a role in the regulation of lipid metabolism, amino acid metabolism and protein secretion, was found to be upregulated under hypoxia...
May 19, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28499906/a-numerical-approach-to-determine-mutant-invasion-fitness-and-evolutionary-singular-strategies
#13
Coralie Fritsch, Fabien Campillo, Otso Ovaskainen
We propose a numerical approach to study the invasion fitness of a mutant and to determine evolutionary singular strategies in evolutionary structured models in which the competitive exclusion principle holds. Our approach is based on a dual representation, which consists of the modeling of the small size mutant population by a stochastic model and the computation of its corresponding deterministic model. The use of the deterministic model greatly facilitates the numerical determination of the feasibility of invasion as well as the convergence-stability of the evolutionary singular strategy...
June 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28497287/role-of-nitrite-in-the-competition-between-denitrification-and-dnra-in-a-chemostat-enrichment-culture
#14
Eveline M van den Berg, Julius L Rombouts, J Gijs Kuenen, Robbert Kleerebezem, Mark C M van Loosdrecht
Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two microbial processes that compete for oxidized nitrogen compounds in the environment. The objective of this work was to determine the role of nitrite versus nitrate as terminal electron acceptor on the competition between DNRA and denitrification. Initially, a mixed culture chemostat was operated under nitrate limitation and performed DNRA. Stepwise, the influent nitrate was replaced with nitrite until nitrite was the sole electron acceptor and N-source present...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28497245/single-species-growth-consuming-inorganic-carbon-with-internal-storage-in-a-poorly-mixed-habitat
#15
Sze-Bi Hsu, King-Yeung Lam, Feng-Bin Wang
This paper presents a PDE system modeling the growth of a single species population consuming inorganic carbon that is stored internally in a poorly mixed habitat. Inorganic carbon takes the forms of "CO2" (dissolved CO2 and carbonic acid) and "CARB" (bicarbonate and carbonate ions), which are substitutable in their effects on algal growth. We first establish a threshold type result on the extinction/persistence of the species in terms of the sign of a principal eigenvalue associated with a nonlinear eigenvalue problem...
May 11, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28495957/resolving-the-complex-genetic-basis-of-phenotypic-variation-and-variability-of-cellular-growth
#16
Naomi Ziv, Bentley M Shuster, Mark L Siegal, David Gresham
In all organisms, many traits vary continuously between individuals. Explaining the genetic basis of quantitative trait variation requires comprehensively accounting for genetic and non-genetic factors as well as their interactions. The growth of microbial cells can be characterized by a lag duration, an exponential growth phase and a stationary phase. Parameters that characterize these growth phases can vary among genotypes (phenotypic variation), environmental conditions (phenotypic plasticity) and among isogenic cells in a given environment (phenotypic variability)...
May 11, 2017: Genetics
https://www.readbyqxmd.com/read/28494362/transformation-of-carbon-tetrachloride-and-chloroform-by-trichloroethene-respiring-anaerobic-mixed-cultures-and-supernatant
#17
Kyle E Vickstrom, Mohammad F Azizian, Lewis Semprini
Carbon tetrachloride (CT) and chloroform (CF) were transformed in batch reactor experiments conducted with anaerobic dechlorinating cultures and supernatant (ADC + S) harvested from continuous flow reactors. The Evanite (EV) and Victoria/Stanford (VS) cultures, capable of respiring trichloroethene (TCE), 1,2-cis-dichloroethene (cDCE), and vinyl chloride (VC) to ethene (ETH), were grown in continuous flow reactors receiving an influent feed of saturated TCE (10 mM; 60 mEq) and formate (45 mM; 90 mEq) but no CT or CF...
April 29, 2017: Chemosphere
https://www.readbyqxmd.com/read/28490602/processes-on-the-emergent-landscapes-of-biochemical-reaction-networks-and-heterogeneous-cell-population-dynamics-differentiation-in-living-matters
#18
REVIEW
Sui Huang, Fangting Li, Joseph X Zhou, Hong Qian
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...
May 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28474106/asymptotic-behavior-of-a-chemostat-model-with-constant-recycle-sludge-concentration
#19
Mohamed Amine Hamra, Karim Yadi
In this work, we study a several species aerobic chemostat model with constant recycle sludge concentration in continuous culture. We reduce the number of parameters by considering a dimensionless model. First, the existence of a global positive uniform attractor for the model with different removal rates is proved using the theory of dissipative dynamical systems. Hence, we investigate the asymptotic behavior of the model under small perturbations using methods of singular perturbation theory and we prove that, in the case of two species in competition, the unique equilibrium which is positive is globally asymptotically stable...
May 4, 2017: Acta Biotheoretica
https://www.readbyqxmd.com/read/28456462/analysis-of-stability-to-cheaters-in-models-of-antibiotic-degrading-microbial-communities
#20
András Szilágyi, Gergely Boza, István Scheuring
Antibiotic resistance carried out by antibiotic degradation has been suggested recently as a new mechanism to maintain coexistence of microbial species competing on a single limiting resource, even in well-mixed homogeneous environments. Species diversity and community stability, however, critically depend on resistance against social cheaters, mutants that do not invest in production, but still enjoy the benefits provided by others. Here we investigate how different mutant cheaters affect the stability of antibiotic producing and degrading microbial communities...
April 27, 2017: Journal of Theoretical Biology
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