scholarly journals Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli

2020 ◽  
Author(s):  
Michaëlle N. Mayalu ◽  
Richard M. Murray
Keyword(s):  
Quorum Sensing ◽  
Cooperative Control ◽  
Population Control ◽  
Mathematical Framework ◽  
Molecular Control ◽  
E Coli ◽  
Environmental Perturbations ◽  
Theoretical Design ◽  
Synthetic Circuit ◽  
The Relationship

SummaryWe have developed a mathematical framework to analyze the cooperative control of cell population homeostasis via paradoxical signaling in synthetic contexts. Paradoxical signaling functions through quorum sensing (where cells produce and release a chemical signal as a function of cell density). Precisely, the same quorum sensing signal provides both positive (proliferation) and negative (death) feedback in different signal concentration regimes. As a consequence, the relationship between intercellular quorum sensing signal concentration and net growth rate (cell proliferation minus death rates) can be non-monotonic. This relationship is a condition for robustness to certain cell mutational overgrowths and allows for increased stability in the presence of environmental perturbations. Here, we explore stability and robustness of a conceptualized synthetic circuit. Furthermore, we asses possible design principles that could exist among a subset of paradoxical circuit implementations. This analysis sparks the development a bio-molecular control theory to identify ideal underlying characteristics for paradoxical signaling control systems.

The relationship between health effects in triathletes and microbiological quality of freshwater

1995 ◽  
Vol 31 (5-6) ◽  
pp. 19-26 ◽  
Author(s):  
G. J. Medema ◽  
I. A. van Asperen ◽  
J. M. Klokman-Houweling ◽  
A. Nooitgedagt ◽  
M. J. W. van de Laar ◽  
...  
Keyword(s):  
Water Quality ◽  
Geometric Mean ◽  
Microbiological Quality ◽  
Quality Parameters ◽  
Health Complaints ◽  
E Coli ◽  
Thermotolerant Coliforms ◽  
Microbiological Water Quality ◽  
The Relationship ◽  
Faecal Streptococci

This pilot study was carried out to determine the relationship between microbiological water quality parameters and the occurrence of health complaints among triathletes. Data were collected at an Olympic distance triathlon (n=314) and a run-bike-run (n=81; controls for exposure to fresh water). At the time of the triathlon, the concentrations of Escherichia coli , thermotolerant coliforms, faecal streptococci, entero- and reoviruses, F-specific RNA phages, Salmonella, Campylobacter, Aeromonas, Plesiomonas shigelloides, Pseudomonas aeruginosa and Staphylococcus aureus were examined over the swimming course. Information on the occurrence of health complaints during the competition and in the week thereafter was collected through a written questionnaire. The results show that triathletes and run-bike-runners are comparable with respect to factors other than water exposure (age, sex, training history, physical stress, lower intestinal health complaints during the competition) that may influence the occurrence of health complaints in the week after the competition. Triathletes and run-bike-runners reported gastro-intestinal (7.7% vs 2.5%), respiratory (5.5% vs 3.7%), skin/mucosal (2.6% vs 1.2%), general (3.5% vs 1.2%) and total symptoms (14.8% vs 7.4%) in the week after the event. The health risks for triathletes for all symptom groups are not significantly higher than for run-bike-runners. The geometric mean concentration of faecal indicator bacteria is relatively low: E. coli 170/100 ml; faecal streptococci 13/100 ml, enteroviruses were present at concentrations of 0.1/l. The group of triathletes was homogeneusly and relatively intensely exposed to water; they all swam in the same body of water at the same time and 75% reported to have swallowed freshwater. It was concluded that this study design is suitable to study the relationship between health complaints and microbiological water quality. In the summers of 1993 and 1994, a study will be carried out concerning several run-bike-runs and triathlons in freshwaters of different quality.

The effect of type of water supply on water quality in a developing community in South Africa

1997 ◽  
Vol 35 (11-12) ◽  
pp. 35-40 ◽  
Author(s):  
B. Genthe ◽  
N. Strauss ◽  
J. Seager ◽  
C. Vundule ◽  
F. Maforah ◽  
...  
Keyword(s):  
Water Quality ◽  
Water Supply ◽  
Cross Sectional Study ◽  
Cross Sectional ◽  
E Coli ◽  
Guideline Values ◽  
Developing Communities ◽  
Quality Guideline ◽  
And Control ◽  
The Relationship

Efforts to provide water to developing communities in South Africa have resulted in various types of water supplies being used. This study examined the relationship between the type of water supply and the quality of water used. Source (communal taps, private outdoor and indoor taps) and point-of-use water samples were examined for heterotrophic plate counts (HPC), total and faecal coliforms, E. coli, and coliphages. Ten percent of samples were also analysed for enteric viruses, Giardia and Cryptosporidium. Approximately 320 households were included in a case-control study. In addition, a cross-sectional study was conducted. Both studies examined the relationship between different types of water facilities and diarrhoea among pre-school children. The source water was of good microbial quality, but water quality was found to have deteriorated significantly after handling and storage in both case and control households, exceeding drinking water quality guideline values by 1-6 orders of magnitude. Coliphage counts were low for all water samples tested. Enteric viruses and Cryptosporidium oocysts were not detected. Giardia cysts were detected on one occasion in case and control in-house samples. Comparisons of whether in-house water, after handling and storage, complied with water quality guideline values demonstrated households using communal taps to have significantly poorer quality than households using private outdoor or indoor taps for HPC and E. coli (χ2 = 14.9, P = 0.001; χ2 = 6.6, P = 0.04 respectively). A similar trend (although not statistically significant) was observed for the other microbial indicators. The cross-sectional study demonstrated an apparent decrease in health risk associated with private outdoor taps in comparison to communal taps. This study suggests that a private outdoor tap is the minimum level of water supply in order to ensure the supply of safe water to developing communities.

Design of Synthetic Quorum Sensing Achieving Induction Timing-Independent Signal Stabilization for Dynamic Metabolic Engineering of E. coli

2021 ◽  
Author(s):  
Yuki Soma ◽  
Masatomo Takahashi ◽  
Yuri Fujiwara ◽  
Tamaki Shinohara ◽  
Yoshihiro Izumi ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Quorum Sensing ◽  
E Coli

scholarly journals Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
María-Eugenia DeCastro ◽  
Michael P. Doane ◽  
Elizabeth Ann Dinsdale ◽  
Esther Rodríguez-Belmonte ◽  
María-Isabel González-Siso
Keyword(s):  
Microbial Community ◽  
Hot Spring ◽  
Functional Characterization ◽  
Tca Cycle ◽  
Maximal Activity ◽  
Sulfur Cycle ◽  
E Coli ◽  
Complex Microbial Community ◽  
Relationship Of ◽  
The Relationship

AbstractIn the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquificae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter, was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin–Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta-galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli. The pTsbg enzyme had activity towards o-Nitrophenyl-β-d-galactopyranoside (ONPG) and p-Nitrophenyl-β-d-fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This finding highlights the challenge of finding novel active enzymes based only on their sequence.

scholarly journals Cryo-EM structure of mycobacterial cytochrome bd reveals two oxygen access channels

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Weiwei Wang ◽  
Yan Gao ◽  
Yanting Tang ◽  
Xiaoting Zhou ◽  
Yuezheng Lai ◽  
...  
Keyword(s):  
Rational Design ◽  
Pathogenic Bacteria ◽  
Structural Topology ◽  
Antimicrobial Drugs ◽  
E Coli ◽  
Cytochrome Bd ◽  
Cryo Electron Microscopy ◽  
Functional Mechanisms ◽  
The Relationship ◽  
Potential Oxygen

AbstractCytochromes bd are ubiquitous amongst prokaryotes including many human-pathogenic bacteria. Such complexes are targets for the development of antimicrobial drugs. However, an understanding of the relationship between the structure and functional mechanisms of these oxidases is incomplete. Here, we have determined the 2.8 Å structure of Mycobacterium smegmatis cytochrome bd by single-particle cryo-electron microscopy. This bd oxidase consists of two subunits CydA and CydB, that adopt a pseudo two-fold symmetrical arrangement. The structural topology of its Q-loop domain, whose function is to bind the substrate, quinol, is significantly different compared to the C-terminal region reported for cytochromes bd from Geobacillus thermodenitrificans (G. th) and Escherichia coli (E. coli). In addition, we have identified two potential oxygen access channels in the structure and shown that similar tunnels also exist in G. th and E. coli cytochromes bd. This study provides insights to develop a framework for the rational design of antituberculosis compounds that block the oxygen access channels of this oxidase.

scholarly journals Quorum Sensing Is a Global Regulatory Mechanism in Enterohemorrhagic Escherichia coli O157:H7

2001 ◽  
Vol 183 (17) ◽  
pp. 5187-5197 ◽  
Author(s):  
Vanessa Sperandio ◽  
Alfredo G. Torres ◽  
Jorge A. Girón ◽  
James B. Kaper
Keyword(s):  
Escherichia Coli ◽  
Quorum Sensing ◽  
Type Strain ◽  
Wild Type Strain ◽  
Regulatory Mechanism ◽  
Sos Response ◽  
Enterohemorrhagic Escherichia Coli ◽  
Trna Genes ◽  
Wild Type ◽  
E Coli

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is responsible for outbreaks of bloody diarrhea and hemolytic-uremic syndrome in many countries. EHEC virulence mechanisms include the production of Shiga toxins (Stx) and formation of attaching and effacing (AE) lesions on intestinal epithelial cells. We recently reported that genes involved in the formation of the AE lesion were regulated by quorum sensing through autoinducer-2, which is synthesized by the product of the luxS gene. In this study we hybridized an E. coli gene array with cDNA synthesized from RNA that was extracted from EHEC strain 86-24 and its isogenicluxS mutant. We observed that 404 genes were regulated by luxS at least fivefold, which comprises approximately 10% of the array genes; 235 of these genes were up-regulated and 169 were down-regulated in the wild-type strain compared to in theluxS mutant. Down-regulated genes included several involved in cell division, as well as ribosomal and tRNA genes. Consistent with this pattern of gene expression, theluxS mutant grows faster than the wild-type strain (generation times of 37.5 and 60 min, respectively, in Dulbecco modified Eagle medium). Up-regulated genes included several involved in the expression and assembly of flagella, motility, and chemotaxis. Using operon::lacZ fusions to class I, II, and III flagellar genes, we were able to confirm this transcriptional regulation. We also observed fewer flagella by Western blotting and electron microscopy and decreased motility halos in semisolid agar in the luxS mutant. The average swimming speeds for the wild-type strain and the luxS mutant are 12.5 and 6.6 μm/s, respectively. We also observed an increase in the production of Stx due to quorum sensing. Genes encoding Stx, which are transcribed along with λ-like phage genes, are induced by an SOS response, and genes involved in the SOS response were also regulated by quorum sensing. These results indicate that quorum sensing is a global regulatory mechanism for basic physiological functions of E. coli as well as for virulence factors.

P. vortex-mediated strategies for polysaccharides decomposition

TECHNOLOGY ◽  
2015 ◽  
Vol 03 (02n03) ◽  
pp. 80-83
Author(s):  
Mark Polikovsky ◽  
Eshel Ben-Jacob ◽  
Alin Finkelshtein
Keyword(s):  
Degradation Products ◽  
Cellulose Degradation ◽  
Cellulose Hydrolysis ◽  
Industrial Applications ◽  
Biofuel Production ◽  
E Coli ◽  
Novel Approach ◽  
Textile Manufacture ◽  
Hydrolysis Of Cellulose ◽  
The Relationship

Cellulose hydrolysis has many industrial applications such as biofuel production, food, paper and textile manufacture. Here, we present a novel approach to cellulose hydrolysis using a consortium of motile bacteria, Paenibacillus vortex, that can swarm on solid medium carrying a non-motile recombinant E. coli cargo strain expressing the β-glucosidase and cellulase genes that facilitate the hydrolysis of cellulose. These two species cooperate; the relationship is mutually beneficial: the E. coli is dispersed over long distances, while the P. vortex bacteria gain from the supply of cellulose degradation products. This enables the use of such consortia in this area of biotechnology.

scholarly journals Evaluation of bacterial proliferation with a microfluidic-based device: Antibiochip

2019 ◽  
Author(s):  
Valentina Gallo ◽  
Alessia Ruiba ◽  
Massimo Zanin ◽  
Paolo Begnamino ◽  
Sabina Ledda ◽  
...  
Keyword(s):  
Laboratory Medicine ◽  
Culture Conditions ◽  
Inhibition Of Proliferation ◽  
Standard Methods ◽  
E Coli ◽  
Bacterial Proliferation ◽  
Microbial Cultures ◽  
Novel Approach ◽  
Microbial Strains ◽  
The Relationship

AbstractThe measurement of the proliferation (and the relevant inhibition of proliferation) of microbes is used in different settings, from industry to laboratory medicine. Thus, in this study, the capacity of the Antibiochip (ELTEK spa), a microfluidic-based device, to measure the amount of E. coli in certain culture conditions, was evaluated. An Antibiochip is composed of V-shaped microchannels, and the amount of microparticles (such as microbes) is measured by the surface of the pellet after centrifugation. In the present study, different geometries, volumes and times were analyzed. When the best conditions were identified, serial dilutions of microbial cultures were tested to validate the linearity of the results. Then, with the use of wild E. coli strains isolated from medical samples, the relationship between bacterial susceptibility to antibiotics (gentamicin, amikacin and ceftriaxone) measured by standard methods and that measured by the Antibiochip was evaluated. In this report, the good quality performances of the methods, their linearity and the capacity to identify susceptible microbial strains after 60 minutes of incubation are shown. These results represent a novel approach for ultrarapid antibiograms in clinics.

scholarly journals Molecular Control of Sucrose Utilization in Escherichia coli W, an Efficient Sucrose-Utilizing Strain

2012 ◽  
Vol 79 (2) ◽  
pp. 478-487 ◽  
Author(s):  
Suriana Sabri ◽  
Lars K. Nielsen ◽  
Claudia E. Vickers
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Good Growth ◽  
Knockout Mutant ◽  
Sucrose Transport ◽  
Molecular Control ◽  
Content Type ◽  
E Coli ◽  
K 12 ◽  
Sucrose Utilization

ABSTRACTSucrose is an industrially important carbon source for microbial fermentation. Sucrose utilization inEscherichia coli, however, is poorly understood, and most industrial strains cannot utilize sucrose. The roles of the chromosomally encoded sucrose catabolism (csc) genes inE. coliW were examined by knockout and overexpression experiments. At low sucrose concentrations, thecscgenes are repressed and cells cannot grow. Removal of either the repressor protein (cscR) or the fructokinase (cscK) gene facilitated derepression. Furthermore, combinatorial knockout ofcscRandcscKconferred an improved growth rate on low sucrose. The invertase (cscA) and sucrose transporter (cscB) genes are essential for sucrose catabolism inE. coliW, demonstrating that no other genes can provide sucrose transport or inversion activities. However,cscKis not essential for sucrose utilization. Fructose is excreted into the medium by thecscK-knockout strain in the presence of high sucrose, whereas at low sucrose (when carbon availability is limiting), fructose is utilized by the cell. Overexpression ofcscA,cscAK, orcscABcould complement the WΔcscRKABknockout mutant or confer growth on a K-12 strain which could not naturally utilize sucrose. However, phenotypic stability and relatively good growth rates were observed in the K-12 strain only when overexpressingcscAB, and full growth rate complementation in WΔcscRKABalso requiredcscAB. Our understanding of sucrose utilization can be used to improveE. coliW and engineer sucrose utilization in strains which do not naturally utilize sucrose, allowing substitution of sucrose for other, less desirable carbon sources in industrial fermentations.

Contribution of SOS Genes to H2O2-induced Apoptosis-like Death in Escherichia Coli

2021 ◽  
Author(s):  
Heesu Kim ◽  
Dong Gun Lee
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Treatment Strategies ◽  
Sos Response ◽  
Bacterial Dna ◽  
E Coli ◽  
New Treatment ◽  
Induced Apoptosis ◽  
And Function ◽  
The Relationship

Abstract Hydrogen peroxide (H2O2) is a debriding agent that damages the microbial structure and function by generating various reactive oxygen species (ROS). H2O2-produced hydroxyl radical (OH∙) also exert oxidative stress on microorganisms. The spread of antibiotic resistance in bacteria is a serious issue worldwide, and greater efforts are needed to identify and characterize novel antibacterial mechanisms to develop new treatment strategies. Therefore, this study aimed to clarify the relationship between H2O2 and Escherichia coli and to elucidate a novel antibacterial mechanism(s) of H2O2. Following H2O2 exposure, increased levels of 8-hydroxyldeoxyguanosine and malondialdehyde indicated that H2O2 accelerates oxidation of bacterial DNA and lipids in E. coli. As oxidative damage worsened, the SOS response was triggered. Cell division arrest and resulting filamentation were identified in cells, indicating that LexA was involved in DNA replication. It was also verified that RecA, a representative SOS gene, helps self-cleavage of LexA and acts as a bacterial caspase-like protein. Our findings also showed that dinF is essential to preserve E. coli from H2O2-induced ROS, and furthermore, demonstrated that H2O2-induced SOS response and SOS genes participate differently in guarding E. coli from oxidative stress. As an extreme SOS response is considered apoptosis-like death (ALD) in bacteria, additional experiments were performed to examine the characteristics of ALD. DNA fragmentation and membrane depolarization appeared in H2O2-treated cells, suggesting that H2O2 causes ALD in E. coli. In conclusion, our investigations revealed that ALD is a novel antibacterial mode of action(s) of H2O2 with important contributions from SOS genes.

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