TY - JOUR. T1 - Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. AU - Yoon, Sung H.. AU - Han, Mee Jung. AU - Jeong, Haeyoung. AU - Lee, Choong H.. AU - Xia, Xiao Xia. AU - Lee, Dae Hee. AU - Shim, Ji H.. AU - Lee, Sang Y.. AU - Oh, Tae K.. AU - Kim, Jihyun F.. PY - 2012/5/25. Y1 - 2012/5/25. N2 - Background: Elucidation of a genotype-phenotype relationship is critical to understand an organism at the whole-system level. Here, we demonstrate that comparative analyses of multi-omics data combined with a computational modeling approach provide a framework for elucidating the phenotypic characteristics of organisms whose genomes are sequenced.Results: We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome, proteome, and phenome - to determine the differences between Escherichia coli B and K-12 strains. A genome-scale metabolic network of E. coli B was reconstructed and used to identify genetic ...
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The structure of the O-antigen polysaccharide (PS) from the enteroaggregative Escherichia coli strain 180/C3 has been determined. Sugar and methylation analysis together with 1H and 13C NMR spectroscopy were the main methods used. The PS is composed of tetrasaccharide repeating units with the following structure:→2)-β-d-Quip3NAc-(1→3)-β-d-Ribf-(1→4)-β-d-Galp-(1→3)-α-d-GalpNAc-(1→Analysis of NMR data indicates that the presented sequence of sugar residues also represents the biological repeating unit of the O-chain. The structure is closely related to that of O-antigen polysaccharide from E. coli O5 and partially to that of E. coli O65. The difference between the O-antigen from the 180/C3 strain and that of E. coli O5 is the linkage to the d-Quip3NAc residue, which in the latter strain is 4-O-substituted. The E. coli O65 O-antigen contains as part of its linear pentasaccharide repeating unit a similar structural element, namely ...
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in Journal of the American Chemical Society (2008), 130(17), 5618-9. Solid-state NMR spectroscopy is applied to intact peptidoglycan sacculi of the Gram-negative bacterium Escherichia coli. High-quality solid-state NMR spectra allow atom-resolved investigation of the ... [more ▼]. Solid-state NMR spectroscopy is applied to intact peptidoglycan sacculi of the Gram-negative bacterium Escherichia coli. High-quality solid-state NMR spectra allow atom-resolved investigation of the peptidoglycan structure and dynamics as well as the study of protein-peptidoglycan interactions. [less ▲]. Detailed reference viewed: 70 (1 ULiège) ...
e coli protein e coli host cell protein elisa | order e coli protein e coli host cell protein elisa | How to use: e coli protein e coli host cell protein elisa |
The novel sigma factor (sigma S) encoded by rpoS (katF) is required for induction of many growth phase-regulated genes and expression of a variety of stationary-phase phenotypes in Escherichia coli. Here we demonstrate that wild-type cells exhibit spherical morphology in stationary phase, whereas rpoS mutant cells remain rod shaped and are generally larger. Size reduction of E. coli cells along the growth curve is a continuous and at least biphasic process, the second phase of which is absent in rpoS-deficient cells and correlates with induction of the morphogene bolA in wild-type cells. Stationary-phase induction of bolA is dependent on sigma S. The "gearbox" a characteristic sequence motif present in the sigma S-dependent growth phase- and growth rate-regulated bolAp1 promoter, is not recognized by sigma S, since stationary-phase induction of the mcbA promoter, which also contains a gearbox, does not require sigma S, and other sigma S-controlled promoters do not contain gearboxes. However, ...
Surgical stress shifts the intestinal Escherichia coli population to that of a more adherent phenotype: role in barrier regulation.: The combination of surgical
E. coli bacteria. Coloured scanning electron micrograph of the rod-shaped, Gram-negative bacteria, Escherichia coli, known as E. coli. These bacteria are normal inhabitants of the human intestine (they also occur in the intestine of animals) and are usually harmless. Under certain conditions, however, E. coli might increase in number and cause infection. Serotypes of E. coli are responsible for gastro-enteritis in children, particularly in tropical countries. In adults it causes travellers diarrhoea and 80% of all urinary tract infections. It is also the organism most used in genetic engineering studies. Magnification: x2400 at 6x7cm size. - Stock Image B230/0143
e coli protein biotin labeled anti e coli host cell protein antibody | order e coli protein biotin labeled anti e coli host cell protein antibody | How to use:
The susceptibility of the E. coli B strain to a variety of stressful conditions and antibiotics revealed by PM tests (Figure S3 in Additional file 1) can be explained by several observations (Figure 5). First, differences in the composition of the LPS core and expression of outer membrane proteins may influence the permeability and integrity of the cell envelope. B strains produce more OmpF porin than K-12 strains because the B genome lacks micF, which post-transcriptionally prevents production of OmpF [24]. This is further supported by the transcriptome data showing high levels of ompF expression in the B strain and high expression of ompC and ompA in the K-12 strain (Figure 4). These observations were also consistent with results of proteome analysis of the outer membrane fractions (Figure S2B in Additional file 1). Noxious agents such as antibiotics and bile acids diffuse more easily through OmpF than OmpC because the former produces a channel with a larger pore size [25]. Second, synthesis ...
A strain of human invasive Escherichia coli 0143 (HlnvEC) which was found to lack pili and flagella was orally administered to rabbits weighing 0.7 to 1.1 kg in doses ranging from 1.5 x 108 to 2.5 x 10 10 bacteria. HInvEC colonized the ileum, cecum, and colon in large numbers for one to three days and produced diarrhea depending on the dose in 124 (65%) of 189 rabbits. A dose of 2.5 x 10 10 bacteria elicited diarrheal disease in 91 (87%) of 105 rabbits, The acute pathohistology as determined by light microscopy, transmission and scanning electron microscopy, and immune-fluorescent microscopy was manifested in the distal ileum, cecum, and colon. The pathohistology involved the epithelial mucosa which developed mucosal ulcers characterized by a polymorphonuclear leucocyte response, especially at sites where HlnvEC invaded the lamina propria. Thus, we have developed and characterized in young rabbits a model of HlnvEC diarrhea that is similar clinically and pathohistologically to the same disease ...
Studies using isogenic transductant strains mlpA+ and mlpA as well as reversion analysis suggested that the physiological consequences of a structural gene mutation in murein lipoprotein include (i) increased sensitivity toward chelating agents ethylenediaminetetraacetic acid and ethyleneglycol-bis (beta-aminoethyl ether)-N,N-tetraacetic acid, (ii) leakage of periplasmic enzyme ribonuclease, (iii) weakened association between the outer membrane and the rigid layer accentuated by Mg2+ starvation, resulting in the formation of outer membrane blebs, and (iv) decreased growth rate in media of low ionic strength or low osmolarity. It is suggested that the bound form of lipoprotein plays an important role in the maintenance of the structural integrity of the outer membrane of the Escherichia coli cell envelope. Other outer membrane components may also contribute to the anchorage of outer membrane to the rigid layer, probably through ionic interactions with divalent cations. Using the phenotype of ...
Can get into food, like beef andescherichia . Common type of several types or strains of bacteria and fecaloral found. . Bacteria thatnov , get into. russian blue cat for sale in michigan, Escherichia coli characteristics types of the enteroaggregative shiga toxin verotoxin producing escherichia. Gram negative, rod shaped bacteria and related bacteria thatnov . Can get into food, like beef andescherichia e an aerobic gram. Like beef andescherichia e food like ...
The ribosome is a complex macromolecule consisting of RNA and protein subunits that is responsible for translating the genetic code and protein synthesis. Within its large subunit, the exit tunnel exists as a conduit for nascent peptides to traverse before reaching the cytoplasm or membrane translocon. The tips of the extended loops (also called tentacles) of two proteins, L4 and L22, contribute to the surface of the narrowest portion of Escherichia colis exit tunnel. Mutations in the tentacles of the L4 and L22 proteins promote resistance to a class of antibiotics referred to as macrolides. Although the mutant strains have the advantage of growing in the presence of the antibiotic, erythromycin, they have the disadvantage of growing slower than the wildtype. The decreased rate of growth may be a reflection of structural changes within the 23S rRNA component of the large subunit induced by structural changes in L4 and L22, which in turn result in defects in ribosomal assembly and/or peptide ...
Chromosomal DNA from several Escherichia coli reference (ECOR) strains was transduced by bacteriophage P1 into E. coli strain K12 W3110 trpA33. Recombination patterns of the transductants were determined by restriction fragment length polymorphism over a 40-kb region centering on a single marker (trpA+) in the tryptophan operon. These experiments demonstrate that transduction between different strains of E. coli can result in recombinational replacements that are small in comparison to the entrant molecule (replacements average 8-14 kb, whereas P1 packages approximately 100 kb) often in a series of discrete segments. The transduction patterns generated resemble the natural mosaic sequence patterns of the ECOR strains described in previous work. Extensive polymorphisms in the restriction-modification systems of the ECOR strains are a possible explanation for the sequence patterns in nature. To test this possibility two transductants were back-transduced into strain K12 W3110 trpA33. The resulting ...
Summary Nine hundred and twenty-five Escherichia coli isolates from cases of diarrhoea in the United Kingdom and belonging to enteropathogenic E. coli (EPEC) O serogroups were examined for virulence properties. The tests included adhesion to HEp-2 cells, the fluorescence actin staining (FAS) test (which correlates with the ability to cause attaching and effacing lesions) and DNA hybridisations with probes to detect sequences for eaeA (E. coli attaching and effacing factor), EAF (EPEC adherence factor), verocytotoxins VT1 and VT2, enteroaggregative E. coli and diffusely adherent E. coli. The O serogroups examined were 18, 26, 44, 55, 86, 111, 114, 119, 125, 126, 127, 128 and 142. Six hundred and sixty strains (71.4%) hybridised with at least one of the DNA probes. Over 80% of strains in O serogroups 26, 55, 119, 125, 127 and 142 and 41% of strains of serogroups 86, 111, 114, 126 and 128 hybridised with the eae probe and most showed localised attachment and were FAS-positive. However, |10% of these eae
E. coli bacterium, artwork. The Escherichia coli bacterium is a Gram-negative bacillus (rod-shaped bacterium). It commonly has a single long flagellum (thin thread-like structure) that is used for movement. However, this strain has numerous flagella, giving it greater mobility. E. coli is a normal inhabitant of the human intestine however, under certain conditions, its numbers may increase, causing infection. - Stock Image C011/1351
Optimisation of Bacillus subtilis for the secretion of heterologous proteins Therapeutic proteins (including those required for experimental purposes and clinical trials) are major products of biomanufacturing processes and considerable time and expense are expended to maximise the yield and quality of proteins produced in heterologous hosts. The production host of choice is the Gram-negative bacterium Escherichia coli for which many strains and expression systems have been developed. However ...
Optimisation of Bacillus subtilis for the secretion of heterologous proteins Therapeutic proteins (including those required for experimental purposes and clinical trials) are major products of biomanufacturing processes and considerable time and expense are expended to maximise the yield and quality of proteins produced in heterologous hosts. The production host of choice is the Gram-negative bacterium Escherichia coli for which many strains and expression systems have been developed. However ...
BioAssay record AID 585432 submitted by ChEMBL: Antimicrobial activity against oqxAB positive Escherichia coli DH5[alpha] harboring pMD18-T::oqxAB by CLSI agar dilution method.
DNA damaging alkylating agents are present abundantly in the environment and also produced endogenously.The majority of the DNA adducts caused by such alkylating agents would be in double-stranded DNA. However, single-strand- specific lesions canarise when DNA double helix is temporarily unwound during replication or recombination. The N1 position of purines and the N3 of pyrimidines, which are normally protected from alkylation by base pairing in duplex DNA, can be alkylated in single-stranded DNA. The Escherichia coliAlkB protein is an oxidative demethylase that repairs such alkylatedbases present in single stranded DNA. Although AlkB function was known in great detail, its regulation was poorly characterized. I hypothesized that some proteins might directly interact with AlkB to regulate its function.. ...
Results of this study provided an example of how ESBL determinants in general and CTX-M in particular are rapidly spreading among commensal E. coli strains in healthy subjects from low-resource settings. In the surveyed area, including urban settings in Bolivia and Peru, the prevalence of healthy children carrying ESBL-positive E. coli strains in their commensal microbiota underwent a dramatic (17-fold) increase over a 3-year time period that was mostly contributed by CTX-M-type determinants. This phenomenon is a matter of concern, since commensals can act as a reservoir of resistance genes (Reservoirs of Antibiotic Resistance Network [http://www.roarproject.org]; Alliance for Prudent Use of Antibiotics), while intestinal colonization by ESBL-producing isolates can be a source for influx of ESBL determinants into the hospital setting and represents a risk factor for subsequent infections caused by ESBL-producing strains in hospitalized patients (3). The reasons for this alarming evolution remain ...
Understanding the mechanisms behind translation and its rate-limiting steps is crucial for both the development of drug targets and improvement of heterologous protein production with many biotechnological applications, such as in pharmaceutical and biofuel industries. Despite many advances in the knowledge of the ribosome structure and function, there is still much discussion around the determinants of translation elongation with experiments and computational studies pointing in different directions. Here, we use a stochastic framework to simulate the process of translation in the context of an Escherichia coli cell by gathering the available biochemical data into a ribosome kinetics description. Our results from the study of translation in E. coli at different growth rates contradict the increase of mean elongation rate with growth rate established in the literature. We show that both the level of tRNA competition and the type of cognate binding interaction contribute to the modulation of ...
Most of us associate the bacteria E. coli with nasty stomach ailments. But a new study published in Nature magazine suggests E. coli can not just turn stomachs, but could potentially turn the wheels of your car, since a genetically engineered strain of the bacteria has produced clean, road-ready biodiesel.. The bacteria can work on any type of biomass, including wood chip, switchgrass, and the plant parts that are left behind after a harvest-all contain cellulose, a structural material that comprises much of a plants mass. Study coauthor Jay Keasling and his colleagues report engineering E. coli bacteria to synthesize and excrete the enzyme hemicellulase, which breaks down cellulose into sugars. The bacteria can then convert those sugars into a variety of chemicals-diesel fuel among them. The final products are excreted by the bacteria and then float to the top of the fermentation vat before being siphoned off [Technology Review]. E. coli bacteria naturally turn sugars into fatty acids to build ...
Methionine is an essential amino acid for animals and is typically considered one of the first limiting amino acids in animal feed formulations. Methionine deficiency or excess in animal diets can lead to sub-optimal animal performance and increased environmental pollution, which necessitates its accurate quantification and proper dosage in animal rations. Animal bioassays are the current industry standard to quantify methionine bioavailability. However, animal-based assays are not only time consuming, but expensive and are becoming more scrutinized by governmental regulations. In addition, a variety of artifacts can hinder the variability and time efficacy of these assays. Microbiological assays, which are based on a microbial response to external supplementation of a particular nutrient such as methionine, appear to be attractive potential alternatives to the already established standards. They are rapid and inexpensive in vitro assays which are characterized with relatively accurate and consistent
Purchase Recombinant Escherichia coli UPF0073 inner membrane protein yqfA(yqfA). It is produced in in vitro E.coli expression system. High purity. Good price.
Hi there, I need an antibody which would recognize the E coli cell surface (I am thinking, for instance, about an anti-flagellae, or and anti-LPS or an anti-porin), that could be use in Elisa experiment where I coat the multiplate with entire and intact E coli cells. Anybody has an answer and/or the antibody? Many thanks in advance! Jean-Yves Paquet jean-yves.paquet at fundp.ac.be ...
In animal diets optimal amino acid quantities and balance among amino acids is of great nutritional importance. Essential amino acid deficiencies have negative impacts on animal physiology, most often expressed in sub-optimal body weight gains. Over supplementation of diets with amino acids is costly and can increase the nitrogen emissions from animals. Although in vivo animal assays for quantification of amino acid bioavailability are well established, Escherichia coli-based bioassays are viable potential alternatives in terms of accuracy, cost, and time input. E. coli inhabits the gastrointestinal tract and although more abundant in colon, a relatively high titer of E. coli can also be isolated from the small intestine, where primary absorption of amino acids and peptides occur. After feed proteins are digested, liberated amino acids and small peptides are assimilated by both the small intestine and E. coli. The similar pattern of uptake is a necessary prerequisite to establish E. coli cells as
Economic Importance of E Coli Bacteria 1) E coli bacteria break down glucose and lactose to from acid and gas by fermentation 2) In human intestine E coli
P.514 left column top paragraph: The bacterial (and archaeal) small (30S) subunit contains the 16S rRNA and 21 r-proteins (Escherichia coli), whereas the eukaryotic small subunit contains the 18S rRNA and 32 r-proteins (Saccharomyces cerevisiae although the numbers vary between species). The bacterial large (50S) subunit contains the 5S and 23S rRNAs and 34 r-proteins (E. coli), with the eukaryotic large subunit containing the 5S, 5.8S and 25S/28S rRNAs and 46 r-proteins (S. cerevisiae again, the exact numbers vary between species ...
SlyA is a member of the MarR family of bacterial transcriptional regulators. Previously, SlyA has been shown to directly regulate only two operons in Escherichia coli K-12 MG1655, fimB and hlyE (clyA). In both cases, SlyA activates gene expression by antagonizing repression by the nucleoid-associated protein H-NS. Here, the transcript profiles of aerobic glucose-limited steady-state chemostat cultures of E. coli K-12 MG1655, slyA mutant and slyA over-expression strains are reported. The transcript profile of the slyA mutant was not significantly different from that of the parent; however, that of the slyA expression strain was significantly different from that of the vector control. Transcripts representing 27 operons were increased in abundance, whereas 3 were decreased. Of the 30 differentially regulated operons, 24 have previously been associated with sites of H-NS binding, suggesting that antagonism of H-NS repression is a common feature of SlyA-mediated transcription regulation. Direct binding of
The Escherichia coli DnaA protein is a sequence-specific DNA binding protein that promotes the initiation of replication of the bacterial chromosome, and of several plasmids including pSC101. Twenty-eight novel missense mutations of the E. coli dnaA gene were isolated by selecting for their inabilit …
SINGAPORE, Jun. 4 (Korea Bizwire) - Every day, we are exposed to millions of harmful bacteria that can cause infectious diseases, such as the E. coli bacteria. Now, researchers at the Institute of Bioengineering and Nanotechnology (IBN) of A*STAR have developed a new material that can kill the E. coli bacteria within 30 seconds. This finding has been published in the peer-reviewed journal, Small.. "The global threat of drug-resistant bacteria has given rise to the urgent need for new materials that can kill and prevent the growth of harmful bacteria. Our new antimicrobial material could be used in consumer and personal care products to support good personal hygiene practices and prevent the spread of infectious diseases," said IBN Executive Director, Professor Jackie Y. Ying.. Triclosan, a common ingredient found in many products such as toothpastes, soaps and detergents to reduce or prevent bacterial infections, has been linked to making bacteria resistant to antibiotics and adverse health ...
Using a genetic selection for mutations which allow large maltodextrins to cross the outer membrane of Escherichia coli in the absence of the LamB maltoporin, we have obtained and characterized two mutations that define a new locus of E. coli. We have designated this locus imp for increased membrane permeability. Mapping studies show that the imp gene resides at approximately 1.2 min on the E. coli chromosome. The mutations alter the permeability of the outer membrane resulting in increased sensitivity to detergents, antibiotics and dyes. The mutations are nonreverting and codominant. Genetic analysis of the mutations suggest that the imp gene is an essential gene. We describe a general cloning strategy that can be used to clone both dominant and recessive alleles. Using this technique, we have cloned the wild-type and mutant imp alleles onto a low copy number plasmid. ...
Results: Our goal was to develop a high-throughput recombineering system, primarily for the coupling of genes to epitope tags, which could also be used for deletion of genes in both pathogenic and K-12 E. coli strains. To that end we have designed a series of donor plasmids for use with the lambda-Red recombination system, which when cleaved in vivo by the I-SceI meganuclease generate a discrete linear DNA fragment, allowing for C-terminal tagging of chromosomal genes with a 6xHis, 3xFLAG, 4xProteinA or GFP tag or for the deletion of chromosomal regions. We have enhanced existing protocols and technologies by inclusion of a cassette conferring kanamycin resistance and, crucially, by including the sacB gene on the donor plasmid, so that all but true recombinants are counter-selected on kanamycin and sucrose containing media, thus eliminating the need for extensive screening. This method has the added advantage of limiting the exposure of cells to the potential damaging effects of the lambda-Red ...
B Per for total bacterial protein extraction - posted in Protein and Proteomics: Hi all, I am in need of clarification of something that is concerning me. I am wanting to extract a transmembrane protein localised in the cytoplasmic membrane of E. coli for western blotting and hence I bought B Per from Pierce Scientific. It states that it is an easy to use, one reagent method for gentle lysis of bacterial cells to extract both soluble and insoluble proteins and soluble pr...
Chinese scientists who have fully sequenced the genome of the new E. Coli spreading through Europe said Saturday they found genes in the bacteria that gave it resistance to eight classes of antibiotics. Researchers with the Beijing Genomics Institute, the worlds largest DNA sequencing center, have found genes in the newly identified 0104 strain of E. Coli bacteria that made it resistant to major classes of antibiotics including sulfonamide, cephalothin, penicillin and streptomycin.. This helped explain why doctors in Europe had difficulties in fighting the bug that has killed 18 people and sickened nearly 2,000, BGIs major research arm in Shenzhen said on its website Saturday.. This would help doctors choose right medicines for the treatment, it said.. The researchers are developing a diagnostic kit which will be used to detect the bacteria and prevent the epidemic from spreading further.. The Chinese researchers obtained DNA samples of the bacteria from collaborating scientists in Germany and ...
RecA is important in recombination, DNA repair and repair of replication forks. It functions through the production of a protein-DNA filament. To study the localization of RecA in live Escherichia coli cells, the RecA protein was fused to the green fluorescence protein (GFP). Strains with this gene …
E. coli growth and anaerobic expression of heterologous active [FeFe] hydrogenases.All data are for cultures of E. coli strain BL21(DE3) ΔiscR, and both iron a
Utilizing the bicistronic reporter transposon mini-Tn5 lacZ-tet/1, we have identified lacZ fusions to four Escherichia coli genes/operons that are strongly activated by the accumulation of self-produced extracellular signals. These fusions were designated cma9, cma48, cma113, and cma114 for conditioned medium activated. Each of the cma fusions was expressed in a growth phase-dependent manner, and the presence of conditioned medium from a stationary phase E. coli culture resulted in the premature activation of these fusions in cells at early to mid-logarithmic phase. The cma48 and cma114 fusions were dependent on RpoS for growth phase expression and response to extracellular factors. The extracellular factors that activated the cma9, cma48, and cma114 fusions were produced in both rich complex and defined minimal media. The cma fusions were shown to be within the cysK (cma9), astD (cma48), tnaB (cma113), and gabT (cma114) genes. These genes function in the uptake, synthesis, or degradation of ...
The effect of quindoxin on the synthesis of deoxyribonucleic acid (DNA), ribonucleic acid, and protein in Escherichia coli KL 399 was examined under aerobic and anaerobic conditions. In the absence of oxygen the synthesis of DNA was completely inhibited by 10 ppm of quindoxin, whereas the syntheses of ribonucleic acid and protein were not affected. Quinoxalin-di-N-oxides (QdNO) induce degradation of DNA in both proliferating and non-proliferating cells. polA, recA, recB, recC, exrA, and uvrA mutants were more susceptible than the corresponding repair-proficient strains. All strains were more resistant in the presence of oxygen. Quindoxin was reduced to quinoxalin-N-oxide by intact E. coli cells or by a cell-free E. coli extract. Electron spin resonance measurements demonstrated the generation of free radicals during the reduction of quindoxin. Oxygen or deficiency of energy sources impaired the antibiotic activity and the reduction of QdNO. The QdNO reductase activity was demonstrated to be ...
Improving Soluble Expression of β-Galactosidase in Escherichia coli by Fusion with Thioredoxin - $\beta$-Galactosidase;Thioredoxin;Inclusion Body;IPTG;
BioAssay record AID 1094529 submitted by ChEMBL: Antimicrobial activity against Escherichia coli at 100 ppm after 24 hr by disk diffusion method.
The genomes of species of Escherichia coli (E. coli) show an extraordinary amount of diversity, which include commensal strains and strains belonging to different pathovars. Many strains of E. coli, which can cause mild or severe pathologies in humans, have a commensal ancestor. Understanding the evolutionary changes that can lead to a transition from commensal to pathogen is an important task, which requires integration of different methodologies. One method is experimental evolution of bacteria, in controlled environments, that mimic some of the selective pressures, likely to be important during the transition to pathogenesis. The success of such a transition will depend, at least partially, on ability of E. coli to adapt to the presence of cells of the immune system. Here, we describe a protocol for performing experimental evolution of a commensal strain of E. coli, a derivative of the well studied K12, under the constant selective pressure imposed by cells of the innate immune system, specifically
p.1602 right column bottom paragraph: Considering the fast transcription (∼45 bases/s) and translation (∼15 residues/s) rates, [investigators] tentatively assign 1/κ to the fluorophore maturation process (SOM Text). Although [they] can only spatially resolve a few molecules within an E. coli cell because of the diffraction limit, the long spread of the stochastic arrival times of Venus allows many more protein molecules per expression burst to be counted in several consecutive images ...
Alkylating agents constitute a large class of DNA‐damaging agents that generate both mutagenic and cytotoxic DNA lesions. Much of our understanding of alkylation damage repair is from studies on Escherichia coli, in particular on the adaptive (Ada) response, which involves the upregulation of four genes: ada, aidB, alkA and alkB (Sedgwick et al, 2007). The Ada protein is a multifunctional DNA methyltransferase that also acts as a transcriptional activator of the response. The exact function of AidB, a flavin‐binding protein, remains to be explained and AlkA is a DNA glycosylase with a broad specificity. AlkB catalyses the demethylation of 1‐methyladenine and 3‐methylcytosine in DNA and RNA, coupled to the decarboxylation of 2‐oxoglutarate (2OG) to succinate and CO2 (Falnes et al, 2002; Trewick et al, 2002). Homologues of AlkB have been identified in species ranging from bacteria to humans; eight human homologues (ABH) have been described, but only two, ABH2 and ABH3, are known to ...
Escherichia coli (E. coli) O157, sometimes called VTEC, is a bacterial infection that can cause severe stomach pain , bloody diarrhoea and kidney failure.
E. coli host cells, the phage λ genome circularizes by joining of the cohesive .... construction of recombinant DNA "designer weapons. ... The restriction endonuclease is loosely bound and its catalytic center is kept ... the presence of the essential cofactor Mg2+, the enzyme cleaves the DNA on both strands at the same time. ...
Growth characteristics of coliphage viruses indicate that they are adapted to live with their Eschericia coli hosts in the intestinal tract. However, coliphage experimentally introduced by ingestion persist only transiently if at all in the gut of humans and other animals. This study attempted to identify the barriers to long term establishment of exogenous coliphage in the gastrointestinal (GI) tracts of laboratory mice. Intestinal contents were screened for the presence of coliphage and host bacteria, and strains of E. coli bacteria from different segments of the GI tract were tested for susceptibility to six common laboratory coliphages. Contrary to expectations, coliphage were not evident in the GI tracts of laboratory mice, although they were occasionally detected in feces. Commensal flora showed extreme variability within groups of mice despite identical handling and diet. Less than 20% of 48 mice tested carried E. coli in their gut, and of 22 commensal E. coli strains isolated and tested, 59%
E. coli long-term evolution experiment. This is an ongoing study in experimental evolution led by Richard Lenski that has been tracking genetic changes in 12 initially identical populations of asexual Escherichia coli bacteria since 24 February 1988. The populations reached the milestone of 60,000 in April 2014, the equivalent of 1-million years of human evolution (based on 16-years between generations). Lenski and his colleagues have reported a wide array of genetic changes. Some changes have occurred in all 12 populations and others have only appeared in one or a few populations. At the present time though, the E-coli bacteria are still E-coli bacteria. Not one of them has grown fins to swim around the petri dish or limbs to help it climb out ...
LB Broth is a low-salt formulation in comparison to its counterpart LB Broth, Bertani Miller. Lennox is also nutrient rich containing peptides, amino acids, water soluble vitamins and carbohydrates.LB Broth, Lennox is useful for molecular genetic studies, as well as maintenance and propagation of bacteriological stocks.. ...
BL21 (DE3) is an E.coli Expression strain, which is a protein expression host with T7 RNA polymerase as the expression system. The expression of T7 phage RNA polymerase gene is controlled by lacuv5 promoter in DE3 region of λ phage, which is integrated on the chromosome of BL21. The strain is suitable for the expression of nontoxic proteins.
At Technovelgy: the Guardian reports on solving the Hamiltonian path problem with E. coli. Programming such a computer is no easy task, however. The researchers coded a simplified version of the problem, using just three cities, by modifying the DNA of Escherichia coli bacteria. The cities were represented by a combination of genes causing the bacteria to glow red or green, and the possible routes between the cities were explored by the random shuffling of DNA. Bacteria producing the correct answer glowed both colours, turning them yellow. The experiment worked, and the scientists checked the yellow bacterias answer by examining their DNA sequence. By using additional genetic differences such as resistance to particular antibiotics, the team believe their method could be expanded to solve problems involving more cities. This is not the only problem bacteria can solve. The research builds on previous work by the same team, who last year created a bacterial computer to solve the Burnt Pancake Problem.
To resurrect these enzymes, which are found in nearly all known modern organisms and are essential for life in mammals, the researchers first constructed a family tree of the more than 200 thioredoxin sequences available from the three domains of life. Then they reconstructed the sequences of the ancestral thioredoxin enzymes using statistical methods based on maximum likelihood. Finally, they synthesized the genes that encoded these sequences, expressed the ancient proteins in the cells of modern Escherichia coli bacteria and then purified the proteins ...
High molecular weight synthetic poly(peptides) of precisely controlled amino acid composition and sequence can be produced by the genetic engineering of Escherichia coli bacteria. By this route, novel
Recombinant DnaK Substrate Binding Domain produced in E.Coli is a single, non-glycosylated polypeptide chain containing 384 amino acids and having a molecular mass of 48.1 kDa.
Specific assembly proteins are required for the folding and integration of autotransporters into the outer membrane. Employing x-ray crystallography, the authors of the study decoded the atomic structure of the autotransporter assembly protein TamA of the intestinal bacterium Escherichia Coli.. "The protein TamA", explains Fabian Gruss, first author and recipient of a Werner-Siemens PhD fellowship, "also forms a barrel with a pore. The pore is closed to the outside by a lid but a particular kink in the barrel wall provides a gate for autotransporter substrates." When an unfolded autotransporter is delivered, TamA hooks onto one end of the substrate polypeptide chain and integrates it step by step via the gate into its own barrel structure. The TamA barrel is thus expanded; the pore widens and opens such that passenger substrates traverse to the exterior. The assembly process ends when TamA releases the autotransporter into the surrounding membrane. "The autotransporter insertion mechanism was ...
This thesis presents two new concepts for separation of micro particles using dielectrophoresis, demonstrated by calculated examples, as well as a new method for obtaining dielectric data on living cells. The thesis is based on four papers.. Paper I describes how the trapping efficiency of micro particles may be significantly increased when superpositioned electric fields are employed in a high conductivity medium. Avoiding low conductivity media is important when working with living cells. Calculations were performed to predict trajectories of Escherichia coli bacteria in the system with superpositioned electric fields, and a model was developed which employed two arrays of interdigitated electrodes in a micro channel.. Paper II proposes a new concept for separation of micro particles, based on repetitive dielectrophoretic trapping and release in a flow system. Calculations show that the resolution increases as a direct function of the number of trap and release steps, and that a difference in ...
Recombinant Dnak produced in E.Coli is a single, non-glycosylated polypeptide chain containing 638 amino acids and having a molecular mass of 69 kDa.
Involved in the biogenesis of TorA. Acts on TorA before the insertion of the molybdenum cofactor and, as a result, probably favors a conformation of the apoenzyme that is competent for acquiring the cofactor.
KOHLENHYDRATKATABOLISMUS (METABOLISMUS); WACHSTUM UND ENTWICKLUNG VON MIKROORGANISMEN (MIKROBIOLOGIE); MIKROBIELLER ABBAU UND KATABOLISMUS (METABOLISMUS); ESCHERICHIA (MIKROBIOLOGIE); CARBOHYDRATE CATABOLISM (METABOLISM); GROWTH AND DEVELOPMENT OF MICROORGANISMS (MICROBIOLOGY); MICROBIAL DEGRADATION AND CATABOLISM (METABOLISM); ESCHERICHIA (MICROBIOLOGY ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
Escherichia coli is a Gram-negative rod-shaped bacterium [Plural: Bacteria] that is commonly found in the lower intestine of human n animal. This bacterium is the most human friendly and environment friendy bug. Most E. coli strains are harmless, but some [grand-childrens of E coli], such as serotype EHEC O157:H7, O104:H4 strains , can cause serious food poisoning in humans. The harmless strains are part of the normal flora [bacteria which are found in or on our bodies without causing disease] of the gut, and can benefit their hosts by producing vitamin K and by preventing the establishment of pathogenic bacteria within the intestine and hell lot other beneficial ...
Actually Id like to compare a metal reduction process between different engineered E. coli strains which membrane permeability is impaired. These mutants are derived from MC4100, so I need to use this one as a control. Some of these strains carry a pET vector in which a gene encoding a metal reductase was cloned. My preliminary experiments suggest that the IPTG induction may have not worked as expected. Before I check the protein production by western blot, I was just wondering if somebody had expertise in using the T7 expression system with MC4100 and derived strains. Thanks !. ...
There are many human feeding studies of various E. coli types and strains, which can be pooled in various ways to yield different dose response models. Many of these have small sample sizes and cannot be used on their own to reliably fit a dose response model. Most datasets for E. coli infections describe high levels of infection resulting from high doses. Lower doses remain to be investigated, and dose response models for infection are therefore uncertain. Another important factor is whether the dose was given with bicarbonate, which would neutralize some stomach acid and possibly increase infectivity.. Haas, Rose, and Gerba (1999) fitted beta-Poisson models to several pooled datasets describing the disease response from ETEC, EPEC and EIEC. [6]Among these datasets were the EPEC strains O111[7] and O55, as well as EIEC strains 4608 and 1624[8] with diarrhea as the end point. However, it mixed data from experiments in which bacteria were given with and without bicarbonate.. The best available ...
Science breaks the news again. What if, instead of storing information in computers, we were able to do so in living organisms? This has been proven to be
... A mathematical model of aerobic bacterial metabolic processes is developed and used to derive the Monod equation, a second-order differential BOD equation, an equation relating specific bacterial growth rate to specific bacterial respiration rate, and a rationale for continuous respirometric growth rate control of the activated sludge process. The model consists of rate equations for both viable and nonviable cells. It is shown that the continuous respirometric data could be used to calculate the amount of new protoplasm synthesized over a day's time.
Cloning recombinants. A restriction enzyme is used to insert a hummingbird gene into a plasmid, which acts as a cloning vector and placed back into E. coli cells. The plasmid genes ampR (ampicillin resistance) and lacZ are used as genetic markers to screen for E. coli cells containing the recombinant gene of interest. Once identified, the recombinant E. coli cells are cloned to make many copies of the gene of interest. Tutorial: ...
LB broth is used for maintaining and cultivating recombinant strains of Escherichia coli. The ingredients of LB broth are tryptone, yeast extract and Sodium Chloride. We show you how to prepare the LB medium. - LB Medium Preparation - AbVideo™ - Support - Abnova
Ours is the only existing genome-scale model of E. coli," says Palsson. In addition, while many approaches to genetics experiments "knock out" individual genes and track the results, the new model takes a whole-system approach. Changing one aspect of a genetic code could be irrelevant if an organism adapts and evolves, says Palsson. The constraints-based models allow the E. coli to evolve more naturally along several possible paths ...
EUPROTEIN provides expression and production services in the E.coli expression system. Learn more about it, by submitting an initial inquiry to us.
Two hundred and thirty-two strains of Escherichia coli belonging to infantile enteropathogenic serotypes isolated in the United Kingdom during 1980 and 1981 were tested for resistance to 10 antimicrobial drugs. Resistance to one or more drugs was found in 134 (57.8%) of the strains, with resistance to sulphonamides, streptomycin, tetracycline, and ampicillin occurring most commonly. Resistance was transferable in 65 out of 104 resistant strains. These findings are a cause for concern because they indicate that the choice of treatment for severe illness is limited and suggest that a large pool of drug-resistant organisms exists in the community. ...
Can a bacterial cell model vet large datasets from disparate sources? Macklin et al. explored whether a comprehensive mathematical model can be used to verify or find conflicts in massive amounts of data that have been reported for the bacterium Escherichia coli , produced in thousands of papers from hundreds of labs. Although most data were consistent, there were data that could not accommodate known biological results, such as insufficient output of RNA polymerases and ribosomes to produce measured cell-doubling times. Other analyses showed that for some essential proteins, no RNA may be transcribed or translated in a cells lifetime, but viability can be maintained without certain enzymes through a pool of stable metabolites produced earlier. Science , this issue p. [eaav3751][1] ### INTRODUCTION The generation of biological data is presenting us with one of the most demanding analysis challenges the world has ever faced, not only in terms of storage and accessibility, but more critically in ...
Hi Everyone. (I do have questions, but want to give you my background info first.) I am planning on doing an experiment to make one species of bacteria into another. I plan to: Take E. coli bacteria and extract all of their DNA; their entire genome. Then, I will take another species of bacteria (strep) and remove ALL DNA from them. I shall next take the E. coli DNA and force it into the strep. I want to see if the strep cells will indeed turn into the E. coli bacteria. None of this is finalized. The bacteria species and types may vary if it is easier to do this experiment. The DNA may be cut with enzymes, or whatever, as long as it goes into the 2nd bacteria type. Efficiency rates are not a problem, as long as there is a small or some percent of chance of success. ===== MY QUESTIONS: What are the lab methods of extracting a full "loop" of DNA from bacteria? Is there a way at all to extract all of the DNA in a cell (many cells will be used when I do this.) If the bacterial DNA is broken into many ...
Much research has been done on the ebg operon of the bacterium Escherichia coli over the last 30 years. specific mutations within this operon enable the bacterium to metabolize lactose.. PDF Download ...
Much research has been done on the ebg operon of the bacterium Escherichia coli over the last 30 years. specific mutations within this operon enable the bacterium to metabolize lactose.. PDF Download ...
New template-based self-propelled gold/nickel/polyaniline/platinum (Au/Ni/PANI/Pt) microtubular engines, functionalized with the Concanavalin A (ConA) lectin bioreceptor, are shown to be extremely useful for the rapid, real-time isolation of Escherichia coli (E. coli) bacteria from fuel-enhanced environmental, food, and clinical samples. These multifunctional microtube engines combine the selective capture of E. coli with the uptake of polymeric drug-carrier particles to provide an attractive motion-based theranostics strategy. Triggered release of the captured bacteria is demonstrated by movement through a low-pH glycine-based dissociation solution. The smaller size of the new polymer-metal microengines offers convenient, direct, and label-free optical visualization of the captured bacteria and discrimination against nontarget cells. ...
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DH5-alpha Chemically Competent E. coli cells are suitable for high efficiency transformation in a wide variety of routine applications such as plasmid isolation, cloning, and subcloning.
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LA Testing provides environmental and food testing services to help prevent deadly E. coli outbreaks., , , , Garden Grove, CA, , , , According to a recent article in the Microbial Drug Resistance journal, the...
Escherichia coli, commonly referred to as E. coli, has many different strains. The most commonly known serotypes of these bacteria can cause serious food poisoning or even fatality in humans. However, most strains are completely harmless. These strains are usually found in the gut of the host and help by producing K2 and helping with digestion. The presence of these bacteria is very beneficial for it helps to prevent pathogenic bacteria from being present in the intestine.[1] The Lac switch that we have created in the genetic coding of E. coli bacteria produces a glowing blue color that initially runs off of glucose and eventually runs off of lactose. With this technology, we can create a glow stick that can be used in emergency kits that will provide light in dire situations. By using a non-harmful strain of E. coli, we can create an environmental conscious and biodegradable glow stick that will not cause harm to the surroundings. This model would act as a proof-of-concept in the development of ...
Escherichia coli, commonly referred to as E. coli, has many different strains. The most commonly known serotypes of these bacteria can cause serious food poisoning or even fatality in humans. However, most strains are completely harmless. These strains are usually found in the gut of the host and help by producing K2 and helping with digestion. The presence of these bacteria is very beneficial for it helps to prevent pathogenic bacteria from being present in the intestine.[1] The Lac switch that we have created in the genetic coding of E. coli bacteria produces a glowing blue color that initially runs off of glucose and eventually runs off of lactose. With this technology, we can create a glow stick that can be used in emergency kits that will provide light in dire situations. By using a non-harmful strain of E. coli, we can create an environmental conscious and biodegradable glow stick that will not cause harm to the surroundings. This model would act as a proof-of-concept in the development of ...
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a protein, called MscL, found in the membrane of the single-cell bacterium Escherichia coli. The protein is essentially an emergency-response valve that changes shape to let salts and other solutes in and out of the cell through a process called gating in order to keep tension on the membrane steady. This gating process allows some of the cells innards to spill out or liquid from the surrounding environment to rush in ...
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Its difficult to make predictions, especially about the future, and even more so when they involve the reactions of living cells - huge numbers of genes, proteins and enzymes, embedded in complex pathways and feedback loops. Yet researchers at the University of California, Davis, Genome Center and Department of Computer Science are attempting just that, building a computer
A newly discovered receptor in a strain of Escherichia coli can be blocked to avert infection, a finding that might aid in developing better therapies to treat bacterial infections resulting in food poisoning, diarrhoea or plague.
Hi, Patrice: In a past I found useful the following technique: 1. Spin down 1.5 ml of stationary-phase E. coli culture in Eppendorf tube 2. Resuspend pellet in 0.5 ml ice-cold 20 mM Tris pH 7.4-7.6, 50 mM NaCL, 5-10 mM 2-mercaptoethanol 3. sonicate on ice (time and intensity depends on culture and model of sonicator, generally 6 x 10 sec with 10 sec. intervals, 50% pulse duration and 50-90 power is OK in most cases) 4. spin down in microcentrifuge for 2 min @ max speed at 4 C (room t works as well) 5. incubate 10 ul of lambda DNA (0.1 ug/ul in appropriate restriction buffer) with 3 ul of resulting lysate for 10-30 min @ 37 C 6. run the gel This procedure worked in my hands with about dosen of naturally occuring producers of restriction enzymes as well as with genes cloned in E. coli. In a latter case contaminating nucleases never presented a problem. However, if this happens, some old remedy suggests to add t-RNA to titer out nonspecific nucleases. Some adjustments might be necessary with above ...
Misc.Comments : Open reading frame vector. E.coli MC1000 = F- araD139 delta[ara,leu]7697 delta[lac]chi74 galK- galU- rpsL. Medium is 1227 LB plus ampicillin ...
Fitting Inside a Cell - E-coli is able to house a long strand of DNA because of DNAs relationship with proteins called histones. Learn about E-coli and find out how DNA wraps around histones.
i. α-helix: In an α-helix, the protein chain is coiled like a loosely-coiled spring (just like the telephone cable). Why it is called "alpha"? Alpha measn that if you look down the length of the spring, the coiling happens in a clockwise direction as it goes away from you. An α-helix is stabilized by hydrogen bonds between the (backbone) amino and carbonyl groups. The H-atom of amide group forms the bond with the OH atoms of carbonyl group. There is regularity in the arrangement of hydrogen atoms. All the N-H groups point upwards as against the C=O groups that point downwards (as in the figure). In an α-helix, the R-groups (side chains) of amino acids protrude out from the helically coiled polypeptide backbone. Also, each complete turn of the spiral has approximately 3.6 amino acids residues in it and the distance between two turns is 0.54nm ...
SWISS-MODEL Repository entry for C4ZY62 (MDTI_ECOBW), Spermidine export protein MdtI. Escherichia coli (strain K12 / MC4100 / BW2952)
SWISS-MODEL Repository entry for C4ZU95 (ARNB_ECOBW), UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase. Escherichia coli (strain K12 / MC4100 / BW2952)
Protein expression in the bacterium E. coli has been the most popular means of producing recombinant proteins for over two decades.
Recombinant Human Cytokeratin-8 / KRT8, expressed in E. coli protein - 230-00241. Liquid . Expression system is Escherichia coli (E.coli).
E coli dosH protein: DOS=direct oxygen sensor; a Heme-binding PAS-domain protein from E. coli; dosH is the sensor domain; amino acid sequence in first source