scholarly journals Model-driven design and evolution of non-trivial synthetic syntrophic pairs

2018 ◽  
Author(s):  
Colton J. Lloyd ◽  
Zachary A. King ◽  
Troy E. Sandberg ◽  
Ying Hefner ◽  
Connor A. Olson ◽  
...  
Keyword(s):  
Time Course ◽  
Computational Method ◽  
Community Formation ◽  
Healthcare Applications ◽  
Adaptive Laboratory Evolution ◽  
Genetic Changes ◽  
E Coli ◽  
Model Driven ◽  
Metabolic Functions ◽  
Community Fitness

AbstractSynthetic microbial communities are attractive for applied biotechnology and healthcare applications through their ability to efficiently partition complex metabolic functions. By pairing auxotrophic mutants in co-culture, nascentE. colicommunities can be established where strain pairs are metabolically coupled. Intuitive synthetic communities have been demonstrated, but the full space of cross-feeding metabolites has yet to be explored. A novel algorithm, OptAux, was constructed to design 66 multi-knockoutE. coliauxotrophic strains that require significant metabolite cross-feeding when paired in co-culture. Three OptAux predicted auxotrophic strains were co-cultured with an L-histidine auxotroph and validated via adaptive laboratory evolution (ALE). Time-course sequencing revealed the genetic changes employed by each strain to achieve higher community fitness and provided insights on mechanisms for sharing and adapting to the syntrophic niche. A community model of metabolism and gene expression was utilized to predict the relative community composition and fundamental characteristics of the evolved communities. This work presents a novel computational method to elucidate metabolic changes that empower community formation and thus guide the optimization of co-cultures for a desired application.

scholarly journals Model-driven discovery of underground metabolic functions inEscherichia coli

2015 ◽  
Vol 112 (3) ◽  
pp. 929-934 ◽  
Author(s):  
Gabriela I. Guzmán ◽  
José Utrilla ◽  
Sergey Nurk ◽  
Elizabeth Brunk ◽  
Jonathan M. Monk ◽  
...  
Keyword(s):  
Strain Analysis ◽  
Cross Reactivity ◽  
Enzyme Promiscuity ◽  
Adaptive Laboratory Evolution ◽  
Model Driven ◽  
Bioinformatic Tools ◽  
Metabolic Functions ◽  
Biological Discovery ◽  
Constraint Based Modeling ◽  
Genome Scale

Enzyme promiscuity toward substrates has been discussed in evolutionary terms as providing the flexibility to adapt to novel environments. In the present work, we describe an approach toward exploring such enzyme promiscuity in the space of a metabolic network. This approach leverages genome-scale models, which have been widely used for predicting growth phenotypes in various environments or following a genetic perturbation; however, these predictions occasionally fail. Failed predictions of gene essentiality offer an opportunity for targeting biological discovery, suggesting the presence of unknown underground pathways stemming from enzymatic cross-reactivity. We demonstrate a workflow that couples constraint-based modeling and bioinformatic tools with KO strain analysis and adaptive laboratory evolution for the purpose of predicting promiscuity at the genome scale. Three cases of genes that are incorrectly predicted as essential inEscherichia coli—aspC,argD, andgltA—are examined, and isozyme functions are uncovered for each to a different extent. Seven isozyme functions based on genetic and transcriptional evidence are suggested between the genesaspCandtyrB,argDandastC,gabTandpuuE, andgltAandprpC. This study demonstrates how a targeted model-driven approach to discovery can systematically fill knowledge gaps, characterize underground metabolism, and elucidate regulatory mechanisms of adaptation in response to gene KO perturbations.

scholarly journals Computational Design and Analysis of Modular Cells for Large Libraries of Exchangeable Product Synthesis Modules

2021 ◽  
Author(s):  
Sergio Garcia ◽  
Cong T Trinh
Keyword(s):  
Renewable Resources ◽  
Plant Biomass ◽  
New Product ◽  
Computational Design ◽  
Computational Method ◽  
E Coli ◽  
Genetic Manipulations ◽  
Endogenous Production ◽  
Target Molecules ◽  
Rapid Generation

Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method,named ModCell-HPC, capable of designing modular cells for large libraries with hundredths of products with a highly-parallel and multi-objective evolutionary algorithm. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner under different carbons sources. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells. Furthermore, we used ModCell-HPC to identify design features that allow an existing modular cell to be re-purposed towards production of new molecules. Overall, ModCell-HPC is a useful tool towards more efficient and generalizable design of modular cells to help reduce research and development cost in biocatalysis.

Participation of central alpha-receptors on hemodynamic response to E. coli endotoxin

1984 ◽  
Vol 247 (4) ◽  
pp. R655-R662
Author(s):  
S. Koyama
Keyword(s):  
Blood Pressure ◽  
Central Nervous System ◽  
Heart Rate ◽  
Time Course ◽  
Hypotensive Effect ◽  
Control Group ◽  
E Coli ◽  
Alpha Receptors ◽  
Anesthetized Dogs ◽  
The Central Nervous System

The time course of changes in mean blood pressure (MBP), heart rate (HR), and renal blood flow (RBF) in a control group of anesthetized dogs given only endotoxin (1 mg/kg iv) was compared with groups pretreated with alpha-antagonists either intravenously or intracisternally (ic). The decreases in MBP and RBF in the control group were abolished by intracisternal prazosin (0.1 mg/kg ic). MBP response to endotoxin after intravenous prazosin did not differ from that of the control group; however, the endotoxin-induced decrease in RBF after intravenous prazosin was significantly greater than that in the control group. HR responses to endotoxin were not altered by either intracisternal or intravenous prazosin. MBP and RBF responses to endotoxin after intravenous or intracisternal yohimbine (0.5 mg/kg iv or ic) did not differ from the control responses. However, significant differences occurred in the time course of changes in HR only when yohimbine was administered intracisternally. These observations suggest that the hypotensive effect and reduction of RBF due to endotoxin may be mediated by alpha 1-adrenoceptors at least in the central nervous system and that of HR response may be mediated alpha 2-adrenoceptors.

scholarly journals Thymol tolerance in Escherichia coli induces morphological, metabolic and genetic changes

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Fatemah Al-Kandari ◽  
Rabeah Al-Temaimi ◽  
Arnoud H. M. van Vliet ◽  
Martin J. Woodward
Keyword(s):  
Antimicrobial Activity ◽  
Efflux Pump ◽  
Wide Spectrum ◽  
Genetic Changes ◽  
E Coli ◽  
Nmr Data ◽  
Stop Mutation ◽  
In The Wild ◽  
Cellular Integrity ◽  
Acrab Efflux Pump

Abstract Background Thymol is a phenolic compound used for its wide spectrum antimicrobial activity. There is a limited understanding of the antimicrobial mechanisms underlying thymol activity. To investigate this, E. coli strain JM109 was exposed to thymol at sub-lethal concentrations and after 16 rounds of exposure, isolates with a 2-fold increased minimal inhibitory concentration (MIC) were recovered (JM109-Thyr). The phenotype was stable after multiple sub-cultures without thymol. Results Cell morphology studies by scanning electron microscopy (SEM) suggest that thymol renders bacterial cell membranes permeable and disrupts cellular integrity. 1H Nuclear magnetic resonance (NMR) data showed an increase in lactate and the lactic acid family amino acids in the wild type and JM109-Thyr in the presence of thymol, indicating a shift from aerobic respiration to fermentation. Sequencing of JM109-Thyr defined multiple mutations including a stop mutation in the acrR gene resulting in a truncation of the repressor of the AcrAB efflux pump. AcrAB is a multiprotein complex traversing the cytoplasmic and outer membrane, and is involved in antibiotic clearance. Conclusions Our data suggests that thymol tolerance in E. coli induces morphological, metabolic and genetic changes to adapt to thymol antimicrobial activity.

scholarly journals Chitosan & Conductive PANI/Chitosan Composite Nanofibers - Evaluation of Antibacterial Properties

2019 ◽  
Vol 4 (1) ◽  
pp. 6-20 ◽  
Author(s):  
Panagiota Moutsatsou ◽  
Karen Coopman ◽  
Stella Georgiadou
Keyword(s):  
Chronic Wounds ◽  
Antibacterial Properties ◽  
Wound Dressings ◽  
Bacterial Strains ◽  
Healthcare Applications ◽  
E Coli ◽  
Jet Stability ◽  
Electrospun Membranes ◽  
New Treatments ◽  
Chitosan Composite

Background: Within the healthcare industry, including the care of chronic wounds, the challenge of antimicrobial resistance continues to grow. As such, there is a need to develop new treatments that can reduce the bioburden in wounds. Objective: The present study is focused on the development of polyaniline (PANI) / chitosan (CH) nanofibrous electrospun membranes and evaluates their antibacterial properties. Methods: To this end, experimental design was used to determine the electrospinning windows of both pure chitosan and PANI/CH blends of different ratios (1:3, 3:5, 1:1). The effect of key environmental and process parameters (relative humidity and applied voltage) was determined, as well as the effect of the PANI/CH ratio in the blend and the molecular interactions between PANI and chitosan that led to jet stability. Results: The nanofibrous mats were evaluated regarding their morphology and antibacterial effect against model gram positive and gram negative bacterial strains, namely B. subtilis and E. coli. High PANI content mats show increased bactericidal activity against both bacterial strains. Conclusion: The blend fibre membranes combine the materials’ respective properties, namely electrical conductivity, biocompatibility and antibacterial activity. This study suggests that electrospun PANI/CH membranes are promising candidates for healthcare applications, such as wound dressings.

scholarly journals Estimation of Time-Course Core Temperature and Water Loss in Realistic Adult and Child Models with Urban Micrometeorology Prediction

2019 ◽  
Vol 16 (24) ◽  
pp. 5097 ◽  
Author(s):  
Toshiki Kamiya ◽  
Ryo Onishi ◽  
Sachiko Kodera ◽  
Akimasa Hirata
Keyword(s):  
Core Temperature ◽  
Water Loss ◽  
Urban Areas ◽  
Time Course ◽  
The Body ◽  
Computational Method ◽  
Heat Index ◽  
Computational Techniques ◽  
Ambient Conditions ◽  
Urban Micrometeorology

Ambient conditions may change rapidly and notably over time in urban areas. Conventional indices, such as the heat index and wet bulb globe temperature, are useful only in stationary ambient conditions. To estimate the risks of heat-related illness, human thermophysiological responses should be followed for ambient conditions in the time domain. We develop a computational method for estimating the time course of core temperature and water loss by combining micrometeorology and human thermal response. We firstly utilize an urban micrometeorology prediction to reproduce the environment surrounding walkers. The temperature elevations and sweating in a standard adult and child are then estimated for meteorological conditions. With the integrated computational method, we estimate the body temperature and thermophysiological responses for an adult and child walking along a street with two routes (sunny and shaded) in Tokyo on 7 August 2015. The difference in the core temperature elevation in the adult between the two routes was 0.11 °C, suggesting the necessity for a micrometeorology simulation. The differences in the computed body core temperatures and water loss of the adult and child were notable, and were mainly characterized by the surface area-to-mass ratio. The computational techniques will be useful for the selection of actions to manage the risk of heat-related illness and for thermal comfort.

scholarly journals Genesis of the ultradian rhythm of GH secretion: a new model unifying experimental observations in rats

1998 ◽  
Vol 275 (6) ◽  
pp. E1046-E1054 ◽  
Author(s):  
Clemens Wagner ◽  
S. Roy Caplan ◽  
Gloria S. Tannenbaum
Keyword(s):  
Time Course ◽  
Male Rat ◽  
Peripheral Tissues ◽  
Feedback Mechanisms ◽  
Gh Secretion ◽  
Metabolic Functions ◽  
Neuroendocrine Axis ◽  
Two Peaks ◽  
The Brain ◽  
Gh Receptors

Growth hormone (GH) induces growth in animals and humans and also has important metabolic functions. The GH neuroendocrine axis consists of a signaling cascade from the hypothalamus to the pituitary, the liver, and peripheral tissues, including two major feedback mechanisms. GH is secreted from the pituitary into the circulating blood according to the effect on the somatotrophs of two hypothalamic peptides, GH-releasing hormone (GHRH) and its antagonist, somatostatin (SRIF). The typical GH profile in the male rat shows secretory episodes every 3.3 h, which are subdivided into two peaks. Focusing on the mechanisms for generation of this ultradian GH rhythm, we simulated the time course of GH secretion under a variety of conditions. The model that we propose is based on feedback of GH on its own release mediated both by GH receptors on SRIF neurons in the brain and by a delayed SRIF release into both the brain and portal blood. SRIF, with a resultant periodicity of 3.3 h, affects both the somatotroph cells in the pituitary and the GHRH neurons in the hypothalamus. The secretion of GHRH is postulated to occur in an ∼1-h rhythm modulated by the level of SRIF in the hypothalamus. The model predicts a possible mechanism for the feminization of the male GH rhythm by sex steroids and vice versa, and suggests experiments that might reveal the proposed intrinsic 1-h GHRH rhythm.

scholarly journals The circadian dynamics of small nucleolar RNA in the mouse liver

2017 ◽  
Vol 14 (130) ◽  
pp. 20170034 ◽  
Author(s):  
Stuart Aitken ◽  
Colin A. Semple
Keyword(s):  
Transcriptional Activation ◽  
Ribosome Biogenesis ◽  
Time Course ◽  
Environmental Changes ◽  
Regulation Of Gene Expression ◽  
Computational Method ◽  
Circadian Regulation ◽  
Small Nucleolar Rna ◽  
Rrna Maturation ◽  
Nucleolar Rna

The circadian regulation of gene expression allows plants and animals to anticipate predictable environmental changes. While the influence of the circadian clock has recently been shown to extend to ribosome biogenesis, the dynamics and regulation of the many small nucleolar RNA that are required in pre-ribosomal RNA folding and modification are unknown. Using a novel computational method, we show that 18S and 28S pre-rRNA are subject to circadian regulation in a nuclear RNA sequencing time course. A population of snoRNA with circadian expression is identified that is functionally associated with rRNA modification. More generally, we find the abundance of snoRNA known to modify 18S and 28S to be inversely correlated with the abundance of their target. Cyclic patterns in the expression of a number of snoRNA indicate a coordination with rRNA maturation, potentially through an upregulation in their biogenesis, or their release from mature rRNA at the end of the previous cycle of rRNA maturation, in antiphase with the diurnal peak in pre-rRNA. Few cyclic snoRNA have cyclic host genes, indicating the action of regulatory mechanisms in addition to transcriptional activation of the host gene. For highly expressed independently transcribed snoRNA, we find a characteristic RNA polymerase II and H3K4me3 signature that correlates with mean snoRNA expression over the day.

scholarly journals A Recombinant Multiepitope Protein for Hepatitis B Diagnosis

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Marilen Queiroz de Souza ◽  
Alexsandro Sobreira Galdino ◽  
José Carlos dos Santos ◽  
Marcus Vinicius Soares ◽  
Yanna C. de Nóbrega ◽  
...  
Keyword(s):  
Hepatitis B ◽  
Time Course ◽  
Clinical Stage ◽  
Acute Infection ◽  
Single Step ◽  
Liver Inflammation ◽  
E Coli ◽  
Terminal Time ◽  
Gene Coding ◽  
B Virus

Hepatitis B is a liver inflammation caused by hepatitis B virus (HBV) and can be diagnosed in clinical stage by hepatitis B core antibody from IgM class (anti-HBcIgM). Hepatitis B core antibody from IgG class (Anti-HBcIgG) appears quickly after IgM, reaching high titers in chronic hepatitis, and remains even after cure. Since hepatitis B core antibody (anti-HBc) is the first antibody identified and sometimes the only marker detected during the course of infection, it can be used both to indicate HBV acute infection (anti-HBc-IgM) and to identify individuals who have come into contact with the virus (anti-HBc-IgG). In this work we propose a recombinant hepatitis B core multiepitope antigen (rMEHB) to be used for diagnosis of hepatitis B. For this purpose, a synthetic gene coding for rMEHB was designed and cloned into vector pET21a with a 6xHis tag at the C-terminal. Time course induction inE. colishowed an induced protein with an apparent molecular mass of ~21 kDa. Protein purification was performed by a single step with affinity chromatography Ni-NTA. Circular dichroism spectroscopy indicated rMEHB as a thermal stable protein at pH 7.0 and 8.0. In these conditions rMEHB was successfully used to perform an enzyme linked immuno sorbent assay (ELISA) with positive and negative sera.

scholarly journals Evolutionary Changes of the flhDC Flagellar Master Operon in Shigella Strains

2005 ◽  
Vol 187 (12) ◽  
pp. 4295-4302 ◽  
Author(s):  
Akira Tominaga ◽  
Ruiting Lan ◽  
Peter R. Reeves
Keyword(s):  
Dna Sequences ◽  
Gene Clusters ◽  
Housekeeping Gene ◽  
Genetic Damage ◽  
Flagellar Motility ◽  
Genetic Changes ◽  
Mutational Change ◽  
E Coli ◽  
Evolutionary Changes ◽  
Cluster 2

ABSTRACT Shigella strains are nonmotile. The master operon of flagellar synthesis, flhDC, was analyzed for genetic damage in 46 Shigella strains representing all known serotypes. In 11 strains (B1, B3, B6, B8, B10, B18, D5, F1B, D10, F3A, and F3C) the flhDC operon was completely deleted. PCR and sequence analysis of the flhDC region of the remaining 35 strains revealed many insertions or deletions associated with insertion sequences, and the majority of the strains were found to be defective in their flhDC genes. As these genes also play a role in regulation of nonflagellar genes, the loss may have other consequences or be driven by selection pressures other than those against flagellar motility. It has been suggested that Shigella strains fall mostly into three clusters within Escherichia coli, with five outlier strains, four of which are also within E. coli (G. M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567-10572, 2000). The distribution of genetic changes in the flhDC region correlated very well with the three clusters and outlier strains found using housekeeping gene DNA sequences, enabling us to follow the sequence of mutational change in the flhDC locus. Two cluster 2 strains were found to have unique flhDC sequences, which are most probably due to recombination during the exchange of the adjacent O-antigen gene clusters.

Sign in / Sign up

Export Citation Format

Share Document