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Jean-Jacques Kengwoung-Keumo
We propose a model of two-species competition in the chemostat for a single growth-limiting, nonreproducing resource that extends that of Roy [38]. The response functions are specified to be Michaelis-Menten, and there is no predation in Roy's work. Our model generalizes Roy's model to general uptake functions. The competition is exploitative so that species compete by decreasing the common pool of resources. The model also allows allelopathic effects of one toxin-producing species, both on itself (autotoxicity) and on its nontoxic competitor (phytotoxicity)...
August 1, 2016: Mathematical Biosciences and Engineering: MBE
Nahla Abdellatif, Radhouane Fekih-Salem, Tewfik Sari
We study a model of the chemostat with several species in competition for a single resource. We take into account the intra-specific interactions between individuals of the same population of micro-organisms and we assume that the growth rates are increasing and the dilution rates are distinct. Using the concept of steady-state characteristics, we present a geometric characterization of the existence and stability of all equilibria. Moreover, we provide necessary and sufficient conditions on the control parameters of the system to have a positive equilibrium...
August 1, 2016: Mathematical Biosciences and Engineering: MBE
Ngoc-Phuong-Thao Nguyen, Sonja Linder, Stefanie K Flitsch, Bettina Schiel-Bengelsdorf, Peter Dürre, Philippe Soucaille
: An operon comprising two genes, CA_P0037 and CA_P0036, that encode proteins of unknown function that were previously shown to be highly expressed in acidogenic cells and repressed in solventogenic and alcohologenic cells is located on the pSOL1 megaplasmid of Clostridium acetobutylicum upstream of adhE2 A CA_P0037::int (189/190s) mutant in which an intron was inserted at position 189/190 in the sense strand of CA_P0037 was successfully generated by the Targetron technique. The resultant mutant showed significantly different metabolic flux patterns in acidogenic (producing mainly lactate, butyrate, and butanol) and alcohologenic (producing mainly butyrate, acetate, and lactate) chemostat cultures but not in solventogenic or batch cultures...
October 4, 2016: MBio
Hongzhong Lu, Weiqiang Cao, Liming Ouyang, Jianye Xia, Mingzhi Huang, Ju Chu, Yingping Zhuang, Siliang Zhang, Henk Noorman
Aspergillus niger is one of the most important cell factories for industrial enzymes and organic acids production. A comprehensive genome-scale metabolic network model (GSMM) with high quality is crucial for efficient strain improvement and process optimization. The lack of accurate reaction equations and gene-protein-reaction associations (GPRs) in the current best model of A. niger named GSMM iMA871, however, limits its application scope. To overcome these limitations, we updated the A. niger GSMM by combining the latest genome annotation and literature mining technology...
October 3, 2016: Biotechnology and Bioengineering
Haeyoung Jeong, Sang J Lee, Pil Kim
Natural evolution involves genetic diversity such as environmental change and a selection between small populations. Adaptive laboratory evolution (ALE) refers to the experimental situation in which evolution is observed using living organisms under controlled conditions and stressors; organisms are thereby artificially forced to make evolutionary changes. Microorganisms are subject to a variety of stressors in the environment and are capable of regulating certain stress-inducible proteins to increase their chances of survival...
2016: Journal of Visualized Experiments: JoVE
H F Cueto-Rojas, R Maleki Seifar, A Ten Pierick, W van Helmond, M Pieterse M, J J Heijnen, S A Wahl
: Ammonium is the most common N-source for yeast fermentations. Although, its transport and assimilation mechanisms are well documented, there have been only few attempts to measure the in vivo intracellular concentration of ammonium and assess its impact on gene expression. Using an isotope dilution mass spectrometry (IDMS)-based method we were able to measure the intracellular ammonium concentration in N-limited aerobic chemostat cultivations using three different N-sources (ammonium, urea and glutamate) at the same growth rate (0...
September 16, 2016: Applied and Environmental Microbiology
Ruilian Yao, Dewang Xiong, Hongbo Hu, Masataka Wakayama, Wenjuan Yu, Xuehong Zhang, Kazuyuki Shimizu
BACKGROUND: Glycerol, a byproduct of biodiesel, has become a readily available and inexpensive carbon source for the production of high-value products. However, the main drawback of glycerol utilization is the low consumption rate and shortage of NADPH formation, which may limit the production of NADPH-requiring products. To overcome these problems, we constructed a carbon catabolite repression-negative ΔptsGglpK* mutant by both blocking a key glucose PTS transporter and enhancing the glycerol conversion...
2016: Biotechnology for Biofuels
William Tottey, David Feria-Gervasio, Nadia Gaci, Brigitte Laillet, Estelle Pujos, Jean-François Martin, Jean-Louis Sebedio, Benoit Sion, Jean-François Jarrige, Monique Alric, Jean-François Brugère
Background/Aims: Human gut microbiota harbors numerous metabolic properties essential for the host's health. Increased intestinal transit time affects a part of the population and is notably observed with human ageing, which also corresponds to modifications of the gut microbiota. Thus we tested the metabolic and compositional changes of a human gut microbiota induced by an increased transit time simulated in vitro. Methods: The in vitro system ECSIM (Environmental Control System for Intestinal Microbiota) was used to simulate the environmental conditions of three different anatomical parts of the human colon in a continuous process...
August 16, 2016: Journal of Neurogastroenterology and Motility
Torsten Lindström, Yuanji Cheng
The Rosenzweig-MacArthur (1963) criterion is a graphical criterion that has been widely used for elucidating the local stability properties of the Gause (1934) type predator-prey systems. It has not been stated whether a similar criterion holds for models with explicit resource dynamics (Kooi et al. (1998)), like the chemostat model. In this paper we use the implicit function theorem and implicit derivatives for proving that a similar graphical criterion holds under chemostat conditions, too.
2016: TheScientificWorldJournal
Janne Wallenius, Hannu Maaheimo, Tero Eerikäinen
The metabolism of butanol producing bacteria Clostridium acetobutylicum was studied in chemostat with glucose limited conditions, butanol stimulus, and as a reference cultivation. COnstraint-Based Reconstruction and Analysis (COBRA) was applied using additional constraints from (13)C Metabolic Flux Analysis ((13)C-MFA) and experimental measurement results. A model consisting of 451 metabolites and 604 reactions was utilized in flux balance analysis (FBA). The stringency of the flux spaces considering different optimization objectives, i...
November 2016: Bioresource Technology
Chaoqun Xu, Sanling Yuan
In this paper, a stochastic chemostat model in which n-species compete for a single growth-limiting substrate is considered. We first prove that the stochastic model has an unique global positive solution by using the comparison theorem for stochastic differential equations. Then we show that when the noise intensities are small, the competition outcome in the chemostat is completely determined by the species' stochastic break-even concentrations: the species with the lowest stochastic break-even concentration survives and all other species will go to extinction in the chemostat...
October 2016: Mathematical Biosciences
Yi-Ywan M Chen, Yueh-Ying Chen, Jui-Lung Hung, Pei-Min Chen, Jean-San Chia
GlnR-mediated repression of the GlnR regulon at acidic pH is required for optimal acid tolerance in Streptococcus mutans, the etiologic agent for dental caries. Unlike most streptococci, the GlnR regulon is also regulated by newly identified PmrA (SMUGS5_RS05810) at the transcriptional level in S. mutans GS5. Results from gel mobility shift assays confirmed that both GlnR and PmrA recognized the putative GlnR box in the promoter regions of the GlnR regulon genes. By using a chemostat culture system, we found that PmrA activated the expression of the GlnR regulon at pH 7, and that this activation was enhanced by excess glucose...
2016: PloS One
Eashwar Rajaraman, Ankit Agarwal, Jacob Crigler, Rebecca Seipelt-Thiemann, Elliot Altman, Mark A Eiteman
Eighteen strains of Escherichia coli were compared for maximum specific growth rate (μ MAX) on 85 mM acetate as the sole carbon source. The C strain ATCC8739 had the greatest growth rate (0.41 h(-1)) while SCS-1 had the slowest growth rate (0.15 h(-1)). Transcriptional analysis of three of the strains (ATCC8739, BL21, SMS-3-5) was conducted to elucidate why ATCC8739 had the greatest maximum growth rate. Seventy-one genes were upregulated 2-fold or greater in ATCC8739, while 128 genes were downregulated 2-fold or greater in ATCC8739 compared to BL21 and SMS-3-5...
September 2016: Applied Microbiology and Biotechnology
Pamela Vrabl, Desiree J Artmann, Christoph W Schinagl, Wolfgang Burgstaller
BACKGROUND: Many issues concerning sample processing for intracellular metabolite studies in filamentous fungi still need to be solved, e.g. how to reduce the contact time of the biomass to the quenching solution in order to minimize metabolite leakage. Since the required time to separate the biomass from the quenching solution determines the contact time, speeding up this step is thus of utmost interest. Recently, separation approaches based on cold-filtration were introduced as promising alternative to cold-centrifugation, which exhibit considerably reduced contact times...
2016: SpringerPlus
Rémi Dupas, Seifeddine Jomaa, Andreas Musolff, Dietrich Borchardt, Michael Rode
Despite extensive efforts to reduce nitrate transfer in agricultural areas, limited response is often observed in the nitrate concentration in rivers. To investigate the reasons for this limited response, nitrate dynamics in a 100km(2) agricultural catchment in eastern Germany was analysed from sub-hourly to decadal time-scales. Sub-hourly analysis of storm event dynamics during a typical hydrological year (2005-2006) was performed to identify periods of the year with high leaching risk and to link the latter to agricultural management practices in the catchment...
November 15, 2016: Science of the Total Environment
W O Draghi, M F Del Papa, C Hellweg, S A Watt, T F Watt, A Barsch, M J Lozano, A Lagares, M E Salas, J L López, F J Albicoro, J F Nilsson, G A Torres Tejerizo, M F Luna, M Pistorio, J L Boiardi, A Pühler, S Weidner, K Niehaus, A Lagares
Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat...
2016: Scientific Reports
Meike T Wortel, Evert Bosdriesz, Bas Teusink, Frank J Bruggeman
Protein expression is shaped by evolutionary processes that tune microbial fitness. The limited biosynthetic capacity of a cell constrains protein expression and forces the cell to carefully manage its protein economy. In a chemostat, the physiology of the cell feeds back on the growth conditions, hindering intuitive understanding of how changes in protein concentration affect fitness. Here, we aim to provide a theoretical framework that addresses the selective pressures and optimal evolutionary-strategies in the chemostat...
2016: Scientific Reports
Sarah J Hurley, Felix J Elling, Martin Könneke, Carolyn Buchwald, Scott D Wankel, Alyson E Santoro, Julius Sebastian Lipp, Kai-Uwe Hinrichs, Ann Pearson
Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate...
July 12, 2016: Proceedings of the National Academy of Sciences of the United States of America
Sarah E Barchinger, Sahand Pirbadian, Christine Sambles, Carol S Baker, Kar Man Leung, Nigel J Burroughs, Mohamed Y El-Naggar, John H Golbeck
UNLABELLED: In limiting oxygen as an electron acceptor, the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 rapidly forms nanowires, extensions of its outer membrane containing the cytochromes MtrC and OmcA needed for extracellular electron transfer. RNA sequencing (RNA-Seq) analysis was employed to determine differential gene expression over time from triplicate chemostat cultures that were limited for oxygen. We identified 465 genes with decreased expression and 677 genes with increased expression...
September 1, 2016: Applied and Environmental Microbiology
Tim Vos, Xavier D V Hakkaart, Erik A F de Hulster, Antonius J A van Maris, Jack T Pronk, Pascale Daran-Lapujade
BACKGROUND: Saccharomyces cerevisiae is an established microbial platform for production of native and non-native compounds. When product pathways compete with growth for precursors and energy, uncoupling of growth and product formation could increase product yields and decrease formation of biomass as a by-product. Studying non-growing, metabolically active yeast cultures is a first step towards developing S. cerevisiae as a robust, non-growing cell factory. Microbial physiology at near-zero growth rates can be studied in retentostats, which are continuous-cultivation systems with full biomass retention...
2016: Microbial Cell Factories
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