scholarly journals Comparative genomics in “Candidatus Kuenenia stuttgartiensis” reveal high genomic plasticity in the overall genome structure, CRISPR loci and surface proteins

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Chang Ding ◽  
Lorenz Adrian
Keyword(s):  
Growth Rate ◽  
Genome Structure ◽  
Draft Genome ◽  
Surface Proteins ◽  
Anammox Bacteria ◽  
Continuous Stirred Tank Reactor ◽  
Genes Encoding ◽  
Continuous Stirred Tank ◽  
The Stability ◽  
Genomic Regions

Abstract Background Anaerobic ammonium oxidizing bacteria (anammox bacteria) are contributing significantly to the nitrogen cycle and are successfully used in wastewater treatment. Due to the lack of complete genomes in the databases, little is known about the stability and variability of their genomes and how the genomes evolve in response to changing environments. Results Here we report the complete genome of the anammox bacterium “Candidatus Kuenenia stuttgartiensis” strain CSTR1 which was enriched planktonically in a semi-continuous stirred-tank reactor. A comparison of the genome of strain CSTR1 with the genome of “Ca. Kuenenia stuttgartiensis” MBR1 and the draft genome of KUST showed > 99% average nucleotide identity among all. Rearrangements of large genomic regions were observed, most of which were associated with transposase genes. Phylogenetic analysis suggests that strain MBR1 is more distantly related to the other two strains. Proteomic analysis of actively growing cells of strain CSTR1 (growth rate ~ 0.33 d− 1) failed to detect the annotated cytochrome cd1-type nitrite reductase (NirS) although in total 1189 proteins were found in the proteome. Yet, this NirS was expressed when strain CSTR1 was under stress or starvation (growth rate < 0.06 d− 1). We also observed large sequence shifts in the strongly expressed S-layer protein compared to other “Ca. Kuenenia” strains, indicating the formation of hybrids of genes encoding the surface proteins. Conclusions “Ca. Kuenenia” strains appear to be relatively stable in their basic physiological traits, but show high variability in overall genome structure and surface proteins.

scholarly journals Dynamical Analysis of a Continuous Stirred-Tank Reactor with the Formation of Biofilms for Wastewater Treatment

2015 ◽  
Vol 2015 ◽  
pp. 1-10
Author(s):  
Karen López Buriticá ◽  
Simeón Casanova Trujillo ◽  
Carlos D. Acosta ◽  
Héctor A. Granada Diaz
Keyword(s):  
Growth Rate ◽  
Wastewater Treatment ◽  
Stability Analysis ◽  
Equilibrium Points ◽  
Stirred Tank ◽  
Dynamical Analysis ◽  
Continuous Stirred Tank Reactor ◽  
Stirred Tank Reactor ◽  
Tank Reactor ◽  
Continuous Stirred Tank

This paper analyzes the dynamics of a system that models the formation of biofilms in a continuous stirred-tank reactor (CSTR) when it is utilized for wastewater treatment. The growth rate of the microorganisms is modeled using two different kinetics, Monod and Haldane kinetics, with the goal of studying the influence of each in the system. The equilibrium points are identified through a stability analysis, and the bifurcations found are characterized.

scholarly journals Lineage transcription factors co-regulate subtype-specific genes providing a roadmap for systematic identification of small cell lung cancer vulnerabilities

2020 ◽  
Author(s):  
Karine Pozo ◽  
Rahul K. Kollipara ◽  
Demetra P. Kelenis ◽  
Kathia E. Rodarte ◽  
Xiaoyang Zhang ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Transcription Factors ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Small Cell ◽  
Surface Proteins ◽  
Small Cell Lung ◽  
Specific Tumor ◽  
Genes Encoding ◽  
Genomic Regions

ABSTRACTLineage-defining transcription factors (LTFs) play key roles in tumor cell growth, making them highly attractive, but currently “undruggable”, small cell lung cancer (SCLC) vulnerabilities. Delineating LTF genomic binding sites and associated chromatin features would provide important insights into SCLC dependencies. Here we map super-enhancers (SEs) across multiple patient-derived SCLC preclinical models, and find SE patterns are sufficient to classify the models into the recently defined, LTF-based, SCLC subtypes. 3D-chromatin conformation analysis identified genes associated with SEs that define subtype-specific tumor signatures with genes functioning in diverse processes. Focusing on ASCL1-high SCLC (SCLC-A), we found ASCL1 physically interacts with NKX2-1 and PROX1. These factors bind overlapping genomic regions, and co-regulate a set of genes, including genes encoding cell surface proteins, SCN3A and KCNB2 enriched in SCLC-A. Genetic depletion of NKX2-1 or PROX1 alone, or in combinations with ASCL1, did not inhibit SCLC growth more than that achieved by depleting ASCL1 alone. We demonstrate the SE signature supports the LTF classification of SCLC, identify NKX2-1 and PROX1 as ASCL1 co-factors, and substantiate the central importance of ASCL1 as a key dependency factor in the majority of SCLC. The LTF and SE gene sets provide a molecular roadmap for future ASCL1 therapeutic targeting studies.

scholarly journals An Analysis of Microbial Population of Chemostat Model in Fuzzy Environment

2019 ◽  
Vol 36 (1-2) ◽  
pp. 1-10
Author(s):  
Harish Chandra Bhandari ◽  
Kanhaiya Jha
Keyword(s):  
Differential Equations ◽  
Microbial Population ◽  
Stirred Tank ◽  
Continuous Stirred Tank Reactor ◽  
Chemostat Model ◽  
Tank Reactor ◽  
Fuzzy Environment ◽  
Research Problems ◽  
Continuous Stirred Tank ◽  
The Stability

Chemostat is a continuous stirred tank reactor used for continuous microbial biomass production in commercial, medical and other research problems. While modeling real world phenomena through differential equations as backbone of practical problems, we need to introduce various parameters. These parameters may be vague, imprecise and uncertain. To incorporate these uncertainties, the notion of fuzzy differential equations is used in chemostat model as one of the tool. In this paper, we discuss some new results for the stability analysis of chemostat model and the results so obtained are justifiable analytically and verified graphically in fuzzy environment.

scholarly journals Global Pattern of Gene Expression of Xanthomonas axonopodis pv. glycines Within Soybean Leaves

2016 ◽  
Vol 29 (6) ◽  
pp. 508-522 ◽  
Author(s):  
Tiyakhon Chatnaparat ◽  
Sutruedee Prathuangwong ◽  
Steven E. Lindow
Keyword(s):  
Cell Surface ◽  
Draft Genome ◽  
Surface Proteins ◽  
In Planta ◽  
Cell Wall Degrading Enzymes ◽  
Global Pattern ◽  
Xanthomonas Axonopodis ◽  
Genes Encoding ◽  
Soybean Leaves

To better understand the behavior of Xanthomonas axonopodis pv. glycines, the causal agent of bacterial pustule of soybean within its host, its global transcriptome within soybean leaves was compared with that in a minimal medium in vitro, using deep sequencing of mRNA. Of 5,062 genes predicted from a draft genome of X. axonopodis pv. glycines, 534 were up-regulated in the plant, while 289 were down-regulated. Genes encoding YapH, a cell-surface adhesin, as well as several others encoding cell-surface proteins, were down-regulated in soybean. Many genes encoding the type III secretion system and effector proteins, cell wall–degrading enzymes and phosphate transporter proteins were strongly expressed at early stages of infection. Several genes encoding RND multidrug efflux pumps were induced in planta and by isoflavonoids in vitro and were required for full virulence of X. axonopodis pv. glycines, as well as resistance to soybean phytoalexins. Genes encoding consumption of malonate, a compound abundant in soybean, were induced in planta and by malonate in vitro. Disruption of the malonate decarboxylase operon blocked growth in minimal media with malonate as the sole carbon source but did not significantly alter growth in soybean, apparently because genes for sucrose and fructose uptake were also induced in planta. Many genes involved in phosphate metabolism and uptake were induced in planta. While disruption of genes encoding high-affinity phosphate transport did not alter growth in media varying in phosphate concentration, the mutants were severely attenuated for growth in soybean. This global transcriptional profiling has provided insight into both the intercellular environment of this soybean pathogen and traits used by X. axonopodis pv. glycines to promote disease.

Design of a Robust Observer with Super-Twisting Algorithm for Simultaneous Concentration Estimation and Faults Reconstruction in a CSTR

2019 ◽  
Vol 17 (8) ◽  
Author(s):  
M. Boudjellal ◽  
R. Illoul
Keyword(s):  
High Gain ◽  
Lyapunov Theory ◽  
Continuous Stirred Tank Reactor ◽  
Nonlinear Observers ◽  
Robust Observer ◽  
Fault Reconstruction ◽  
Concentration Estimation ◽  
Continuous Stirred Tank ◽  
The Stability ◽  
Twisting Algorithm

AbstractThis paper deals with the problem of simultaneous concentration and faults estimations of a continuous stirred tank reactor (CSTR) subject to unknown inputs. We propose a combination of two robust nonlinear observers for state estimation and fault reconstruction without any use of a linear approximation of the CSTR dynamic model. Based on the high-gain observer, the proposed scheme can guarantee the asymptotic estimation of the concentration inside the reactor, while, a robust term is added to the nominal plant on the basis of the super-twisting algorithm for fault reconstruction. The stability analysis is proved mathematically using the Lyapunov theory. The effectiveness and robustness of the proposed scheme are illustrated via simulations.

On the Influence of Fluctuating Flow Rate Upon the Performance and Behaviour of Isothermal Reacting Systems

1998 ◽  
Vol 63 (6) ◽  
pp. 881-898
Author(s):  
Otakar Trnka ◽  
Miloslav Hartman
Keyword(s):  
Flow Rate ◽  
Gas Flow ◽  
Fluidized Bed Reactor ◽  
Computational Techniques ◽  
Continuous Stirred Tank Reactor ◽  
Gas Flow Rate ◽  
Solid Reaction ◽  
Continuous Stirred Tank ◽  
And Performance ◽  
Reacting Systems

Three simple computational techniques are proposed and employed to demonstrate the effect of fluctuating flow rate of feed on the behaviour and performance of an isothermal, continuous stirred tank reactor (CSTR). A fluidized bed reactor (FBR), in which a non-catalytic gas-solid reaction occurs, is also considered. The influence of amplitude and frequency of gas flow rate fluctuations on reactant concentrations at the exit of the CSTR is shown in four different situations.

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