Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1321310 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This work describes the development of the first microarray detection system that simultaneously identifies common pathogens associated with STDs from clinical samples, and paves the way for establishing a time-saving, accurate and high-throughput diagnostic tool. The target genes are 16S rRNA gene for N. gonorrhoeae, M. genitalium, M. hominism, and Ureaplasma, the major outer membrane protein gene (ompA) for C. trachomatis, the glycoprotein B gene (gB) for HSV; and the L1 gene for HPV. 34 probes that reproducibly detected multiple Legionella species with high specificity were included in the array.
2015-12-31 | E-GEOD-69508 | biostudies-arrayexpress
Project description:To understand the changes in gene expression by oral immunotherapy to a multi-antigenic construct consisting AHC (ApoB, HSP60 and chlamydia pneumonia outer membrane protein) at different stages of atherosclerotic development, double knock out Apobtm2Sgy/Ldltm1Her mice were fed with high-fat after 5 oral doses with respective highfat diet alone controls at 0,6,18 and 30 weeks.
2022-08-31 | GSE110670 | GEO
Project description:OmpA, a predominant outer membrane protein (OMP) in Gram-negative bacteria, plays a crucial role in maintaining the integrity and functionality of the bacterial outer membrane (OM). Despite its significance in virulence, adhesion, and OM stability, the specific role of OmpA has remained unclear since its discovery 50 years ago. In this study, we demonstrate that OmpA organizes the OMP lattice and mechanically connects it to the cell wall. Using atomic force microscopy, simulations, and microfluidics, we show that while the β-barrel domain of OmpA is essential for maintaining the permeability barrier, both the β-barrel and cell wall-binding domains are necessary to enhance the cell envelope's strength. We propose that OmpA integrates the compressive properties of the OMP lattice with the tensile strength of the cell wall, forming a mechanically robust composite that enhances overall envelope integrity. This coupling likely underpins the ability of the entire envelope to function as a cohesive and resilient structure, critical for the survival and pathogenicity of Gram-negative bacteria.
2024-11-20 | PXD054033 | Pride
Project description:Escherichia coli is a major cause of blood stream and urinary tract infections. Owing to the spread of antimicrobial resistance, it is often treated with an inadequate antibiotic. With the aim to accelerate the diagnostics of this key pathogen, we used the flycode technology to generate nanobodies against the conserved and highly abundant outer membrane protein OmpA. Two nanobodies each recognizing a different isoform of OmpA were shown by flow cytometry to recognize > 91% of 85,680 E. coli OmpA sequences deposited in a large bacterial genome database. Crystal structures of these nanobodies in complex with the respective OmpA isoform revealed interactions with all four surface accessible loops of OmpA. Steric hindrance caused by dense O-antigen layers initially impeded reliable capture of clinical E. coli strains. By generating nanobody constructs with long linkers and by thinning the O-antigen layer through alterations to growth medium and buffers, we achieved to capture <50 CFU/mL. Our work provides a framework to generate nanobodies for the specific and sensitive detection and capture of clinically relevant pathogenic bacteria.
2025-06-11 | PXD054264 | Pride
Project description:Dengue virus 1 isolate envelope protein(E), partial cds
| PRJNA643890 | ENA
Project description:Transcriptome profiles were analyzed using the samples taken at the exponential and stationary phases during the cultivation of REL606 and MG1655 in LB medium. At the exponential growth phase, most highly expressed genes of B were those for replication, translation, or nucleotide transport and metabolism, while many of the K-12 genes were involved in cell motility, transcription, carbohydrate transport, or energy production. At the stationary phase, many of the genes highly expressed in B were for transport and metabolism of various amino acids and carbohydrates, whereas those in K-12 had functions related to cell motility, ribosomal subunit protein production, or energy generation. Many genes in REL606 and MG1655 showed highly distinct expression levels irrespective of growth conditions. Highly expressed genes in REL606 included those encoding enzymes for biosynthesis of L-arginine (argAGDECBHI) and branched-chain amino acid (ilvGMEDA), and those encoding a subunit of the L-arginine transporter (artJ), cytochrome b562 (cybC), subunits of the histidine ABC transporter (hisPJ), cytotoxins (hokED), outer membrane porin (ompF), L-arginine decarboxylase (speA), and cell division inhibitor (sulA). Highly expressed genes in MG1655 included those for chemotaxis (cheZYRWA, tap, trg, tsr), Lon protease (lon), C4-dicarboxylate-sensing histidine kinase (dcuS), chaperones (clpB, dnaK, groES, htpG, ibpA), the major subunit of type 1 fimbriae (fimA), a regulator of flagellar biosynthesis (flhC), glycerol-3-phosphate-dehydrogenase (glpABCD), glycerophosphoryl diester phosphodiesterase (glpQ), glycerol-3-phosphate transporter (glpT), hydrogenase 2 (hybCBO), outer membrane porins (nmpC, ompA, ompC), and galactitol transport and metabolism (gatYZC).
2009-09-28 | GSE13011 | GEO
Project description:Transcriptome profiles were analyzed using the samples taken at the exponential and stationary phases during the cultivation of REL606 and MG1655 in LB medium. At the exponential growth phase, most highly expressed genes of B were those for replication, translation, or nucleotide transport and metabolism, while many of the K-12 genes were involved in cell motility, transcription, carbohydrate transport, or energy production. At the stationary phase, many of the genes highly expressed in B were for transport and metabolism of various amino acids and carbohydrates, whereas those in K-12 had functions related to cell motility, ribosomal subunit protein production, or energy generation. Many genes in REL606 and MG1655 showed highly distinct expression levels irrespective of growth conditions. Highly expressed genes in REL606 included those encoding enzymes for biosynthesis of L-arginine (argAGDECBHI) and branched-chain amino acid (ilvGMEDA), and those encoding a subunit of the L-arginine transporter (artJ), cytochrome b562 (cybC), subunits of the histidine ABC transporter (hisPJ), cytotoxins (hokED), outer membrane porin (ompF), L-arginine decarboxylase (speA), and cell division inhibitor (sulA). Highly expressed genes in MG1655 included those for chemotaxis (cheZYRWA, tap, trg, tsr), Lon protease (lon), C4-dicarboxylate-sensing histidine kinase (dcuS), chaperones (clpB, dnaK, groES, htpG, ibpA), the major subunit of type 1 fimbriae (fimA), a regulator of flagellar biosynthesis (flhC), glycerol-3-phosphate-dehydrogenase (glpABCD), glycerophosphoryl diester phosphodiesterase (glpQ), glycerol-3-phosphate transporter (glpT), hydrogenase 2 (hybCBO), outer membrane porins (nmpC, ompA, ompC), and galactitol transport and metabolism (gatYZC). All microarray experiments were performed in duplicate with dye-swapping. The probes were spotted in duplicate onto the microarray. Thus, the log2 of the intensity ratio with the two dyes for each spot was calculated from up to four values from the duplicated spot on the microarray and the dye-swap experiment.
2010-05-22 | E-GEOD-13011 | biostudies-arrayexpress