GSE134667 Condensation of nucleoid during environmental adaptation is regulated by dynamic HU interactions

Contributors : Subhash C Verma ; Sankar Adhya ; Soumya G Remesh ; Michal HammelSeries Type : Expression profiling by high throughput sequencingOrganism : Escherichia coliNucleoid remodeling facilitated by DNA supercoiling results in changes in nucleoid configuration and involves nucleoid-associated proteins (NAPs) and structural maintenance of chromosomes (SMC) proteins among others. Changes in nucleoid configurations regulated by NAPs are synchronized with cellular adaptation and influence the simultaneous expression of several genes. HU, a ubiquitous bacterial histone-like protein, is among the most conserved and abundant NAPs in eubacteria. In Escherichia coli, HU forms dimers by HU α self-association (HUαα) or by HUα-HUβ interactions (HUαβ). HUα is mostly expressed during lag and early exponential growth phase and HUβ is expressed only during the later exponential and stationary phase, pointing to distinct HUαα/DNA and HUαβ/DNA packaging of the nucleoid in regulat ing expression patterns during growth and stasis. Mutations or the deletion of HU transform the E. coli nucleoid to a different form and alter overall transcription program; thus, HU interactions with DNA directly affect global gene regulation. Recently, analysis of high-resolution contact maps of t he E. coli nucleoid revealed an important role of HU to promote long-range DNA-DNA contacts within the nucleoid. Yet, the molecular connectio...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Escherichia coli Source Type: research

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In conclusion, the information on bioavailable mercury estimated by bioreporter E. coli ARL1 is valuable, but the results must be interpreted with caution. The route to functional bioavailability bioassay remains long.
Source: Sensors - Category: Biotechnology Authors: Tags: Article Source Type: research
Publication date: Available online 31 May 2020Source: Biochemical Engineering JournalAuthor(s): Chengfeng Xue, Kai-Min Hsu, Wan-Wen Ting, Shih-Fang Huang, Hung-Yi Lin, Sheng-Feng Li, Jo-Shu Chang, I-Son Ng
Source: Biochemical Engineering Journal - Category: Biochemistry Source Type: research
Contributors : Sin éad O’Loughlin ; Mark C Capece ; Mariia Klimova ; Norma M Wills ; Arthur Coakley ; Ekaterina Samatova ; Patrick O’Connor ; Gary Loughran ; Jonathan S Weissman ; Pavel V Baranov ; Marina V Rodnina ; Joseph D Puglisi ; John F AtkinsSeries Type : OtherOrganism : Escherichia coli ; Escherichia virus T4Ribosome profiling analysis of phage T4 infected E. coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. Ribosomes at this position also yielded some 53 nucleotide fragments, 16 longer. These were due to protection of the nuc...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Other Escherichia coli Escherichia virus T4 Source Type: research
Contributors : Guillaume Urtecho ; Kimberly D Insigne ; Arielle D Tripp ; Marcia S Brinck ; Nathan Lubock ; Chan Tracey ; Hwangbeom Kim ; Kosuri SriramSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Escherichia coli DH5[alpha] ; Escherichia coli str. K-12 substr. MG1655Using a novel multiplexed reporter assay, we characterize promoter activity of hundreds of thousands of DNA sequences spanning the entire E. coli genome. We use this powerful assay to identify promoters throughout the E. coli genome and systematically dissect their regulatory motifs which encode promoter activity using a series of experiments.
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Other Expression profiling by high throughput sequencing Escherichia coli DH5[alpha] Escherichia coli str. K-12 substr. MG1655 Source Type: research
Journal of Agricultural and Food ChemistryDOI: 10.1021/acs.jafc.0c01846
Source: Journal of Agricultural and Food Chemistry - Category: Food Science Authors: Source Type: research
The objective of this study was to evaluate the phylogeny and the gene content of Brazilian aEPEC genomes compared to a global aEPEC collection. MethodologySingle nucleotide polymorphism (SNP)-based phylogenomic analysis was used to compare 106 sequenced Brazilian aEPEC with 221 aEPEC obtained from other geographic origins. Additionally, Large-Scale BLAST Score Ratio was used to determine the shared versus unique gene content of the aEPEC studied. Principal FindingsPhylogenomic analysis demonstrated the 106 Brazilian aEPEC were present in phylogroups B1 (47.2%, 50/106), B2 (23.6%, 25/106), A (22.6%, 24/106), and E (6.6%, 7...
Source: PLoS Neglected Tropical Diseases - Category: Tropical Medicine Authors: Source Type: research
m Tae-Joon Jeon A colorimetric polydiacetylene (PDA) paper strip sensor that can specifically recognize Bacillus thuringiensis (BT) HD-73 spores is described in this work. The target-specific aptamer was combined with PDA, and the aptamer-conjugated PDA vesicles were then coated on polyvinylidene fluoride (PVDF) paper strips by a simple solvent evaporation method. The PDA-aptamer paper strips can be used to detect the target without any pre-treatment. Using the paper strip, the presence of BT spores is directly observable by the naked eye based on the unique blue-to-red color transition of the PDA. Quantitative studi...
Source: Sensors - Category: Biotechnology Authors: Tags: Article Source Type: research
Gram-negative bacteria possess an asymmetric outer membrane (OM) composed primarily of lipopolysaccharides (LPSs) on the outer leaflet and phospholipids (PLs) on the inner leaflet. The loss of this asymmetry due to mutations in the LPS biosynthesis or transport pathways causes the externalization of PLs to the outer leaflet of the OM and leads to OM permeability defects. Here, we used metabolic labeling to detect a compromised OM in intact bacteria. Phosphatidylcholine synthase expression in Escherichia coli allowed for the incorporation of exogenous propargylcholine into phosphatidyl(propargyl)choline and exogenous 1-azid...
Source: The Journal of Lipid Research - Category: Lipidology Authors: Tags: Research Articles Source Type: research
A 61-year-old man from Georgia, with common variable immunodeficiency (CVID), presented with generalized weakness, multiple diarrheal episodes day and night, and 120-lb weight loss over 4 years in the context of chronic giardiasis refractory to multiple treatments with metronidazole. He was deficient in vitamins A, D, and K, as well as iron and zinc. Magnetic resonance imaging of his abdomen showed small-bowel thickening, dilated portal vein, and splenomegaly characteristic of CVID (Figure  1). Upper endoscopy revealed diffusely thickened duodenal folds (Supplemental Figure, available online at http://www.mayoclinicproceedings.org).
Source: Mayo Clinic Proceedings - Category: Internal Medicine Authors: Tags: Medical image Source Type: research
mente Capasso The interconversion of CO2 and HCO3− is catalyzed by a superfamily of metalloenzymes, known as carbonic anhydrases (CAs, EC 4.2.1.1), which maintain the equilibrium between dissolved inorganic CO2 and HCO3−. In the genome of Escherichia coli, a Gram-negative bacterium typically colonizing the lower intestine of warm-blooded organisms, the cyn operon gene includes the CynT gene, encoding for a β-CA, and CynS gene, encoding for the cyanase. CynT (β-CA) prevents the depletion of the cellular bicarbonate, which is further used in the reaction catalyzed by cyanase. A secon...
Source: Molecules - Category: Chemistry Authors: Tags: Article Source Type: research
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