• Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries. (nih.gov)
  • Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. (nih.gov)
  • Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. (nih.gov)
  • Moreover, they have shown that a short sequence of 13 residues within the 23S ribosomal RNA triggers this pathway and leads to the production of interleukin-1β. (elifesciences.org)
  • Other forms of ribosomal RNA are unable to trigger the production of interleukin-1β. (elifesciences.org)
  • Aminoglycosides antibiotics provoke lethal translation errors by specifically binding to the bacterial ribosomal A-site. (jbsdonline.com)
  • To estimate the contribution of demand for RNA polymerase to the cost of resistance in rifampicin-free environments, we measured the fitness of 53 rifampicin-resistant mutants of Pseudomonas aeruginosa across a range of environments where we experimentally manipulated demand for RNA polymerase by adding sublethal doses of ribosomal inhibitors. (genetics.org)
  • Initially, three ranges (Type I, Type II, and Type III) of precursor 16S ribosomal RNA levels were defined by whole cell fluorescence in situ hybridization of a pure culture of Acinetobacter calocaceticusT prepared in three culture conditions. (bepress.com)
  • Low levels of precursor 16S ribosomal RNA (Type I) corresponded to a stationary phase culture prepared overnight in Luria-Bertani medium. (bepress.com)
  • Intermediate levels of precursor 16S ribosomal RNA (Type II) corresponded to a culture transferred into fresh Luria-Bertani medium, and high levels of precursor 16S ribosomal RNA (Type III) corresponded to a culture treated with the growth inhibiting antibiotic chloramphenicol. (bepress.com)
  • This mutation significantly alters cell growth, folding of 16S ribosomal RNA, and translational fidelity. (mendeley.com)
  • Barquist L, Westermann AJ, Vogel J (2016) Molecular phenotyping of infection-associated small non-coding RNAs. (springer.com)
  • Treatment of bacterial/HIV-1 co-infection is even more challenging due to potential drug-drug interactions and the ongoing prevalence of resistant strains in HIV-1 populations [ 4 ]. (mdpi.com)
  • In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcuspyogenes and prevented bacterial dissemination. (ovid.com)
  • IsrM RNA is expressed in vitro under conditions resembling those during infection in the gastrointestinal tract. (prolekare.cz)
  • Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children. (ox.ac.uk)
  • Because clinical features do not reliably distinguish bacterial from viral infection, many children worldwide receive unnecessary antibiotic treatment, while bacterial infection is missed in others.To identify a blood RNA expression signature that distinguishes bacterial from viral infection in febrile children.Febrile children presenting to participating hospitals in the United Kingdom, Spain, the Netherlands, and the United States between 2009-2013 were prospectively recruited, comprising a discovery group and validation group. (ox.ac.uk)
  • Each group was classified after microbiological investigation as having definite bacterial infection, definite viral infection, or indeterminate infection. (ox.ac.uk)
  • RNA expression signatures distinguishing definite bacterial from viral infection were identified in the discovery group and diagnostic performance assessed in the validation group. (ox.ac.uk)
  • 62% male) included 52 with definite bacterial infection, of whom 36 (69%) required intensive care, and 92 with definite viral infection, of whom 32 (35%) required intensive care. (ox.ac.uk)
  • Analysis of RNA expression data identified a 38-transcript signature distinguishing bacterial from viral infection. (ox.ac.uk)
  • Of the children in the indeterminate groups, 46.3% (63/136) were classified as having bacterial infection, although 94.9% (129/136) received antibiotic treatment.This study provides preliminary data regarding test accuracy of a 2-transcript host RNA signature discriminating bacterial from viral infection in febrile children. (ox.ac.uk)
  • Single-cell RNA-seq studies have addressed how heterogeneity among individual host cells may determine infection outcomes. (rna-seqblog.com)
  • Furthermore, we demonstrate that viral infection of the placenta may sensitize the pregnant mother to bacterial products and promote preterm labor. (jimmunol.org)
  • As of 2017, he is the Founding Director of the Helmholtz Institute for RNA -based Infection Research in Würzburg. (helmholtz-hzi.de)
  • A cooperative study conducted by University of Jyväskylä and Natural Resources institute Finland (Luke), revealed that enriched rearing of juvenile fish significantly enhances the survival of fish from bacterial infection commonly seen in rearing conditions. (phys.org)
  • 14. The method of claim 13 in which a formulation comprised of the RNA is applied on or adjacent to a plant, and disease associated with nematode infection of the plant is thereby reduced. (google.com)
  • Despite antibiotic stewardship programs and increased awareness, clinicians continue to prescribe antibiotics without clear evidence of bacterial infection, especially in high risk populations such as immunocompromised patients, children, and the elderly. (biomedcentral.com)
  • During the past 5 years, Hfq-mediated control has been an area of increasing focus because the protein has been linked to the action of many versatile RNA-based regulators that use basepairing interactions to regulate the expression of target mRNAs. (nih.gov)
  • Altuvia S, Weinstein-Fischer D, Zhang A et al (1997) A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator. (springer.com)
  • Barquist L, Vogel J (2015) Accelerating discovery and functional analysis of small RNAs with new technologies. (springer.com)
  • These defense systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids. (sciencemag.org)
  • This approach identified covalent cap-like linkage of a specific set of small RNAs to the ubiquitous redox cofactor NAD, and a profound influence of this modification on RNA turnover. (nih.gov)
  • The small RNA nitrogen stress-induced RNA 1 (NsiR1) is produced by Cyanobacteria under conditions of nitrogen deprivation. (wikipedia.org)
  • The lack of an appropriate method for bacterial RNA amplification has hampered studies that rely on rare or limited samples, such as environmental collections, small volume cultures, and bacterial RNA isolated from host cells. (thermofisher.com)
  • We show that the difficulties in imaging the dynamics of protein expression in live bacterial cells can be overcome using fluorescent sensors based on Spinach, an RNA that activates the fluorescence of a small-molecule fluorophore. (pubmedcentralcanada.ca)
  • This method involves fusing RNA aptamers that bind metabolites to Spinach 2 , a 98-nt RNA that switches on the fluorescence of 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), an otherwise nonfluorescent small molecule. (pubmedcentralcanada.ca)
  • Strong σ70 promoters were predicted upstream of all novel small RNAs, indicating the potential for transcriptional activity. (biomedcentral.com)
  • Previous research has shown that six Hfq subunits combine to form a ring-shaped structure and has also provided some clues about the way in which Hfq can recognise a short stretch of a small RNA molecule, but the precise details of the interaction between them are not fully understood. (elifesciences.org)
  • have used a technique called X-ray crystallography to visualize the interaction between Hfq and a small RNA molecule called RydC. (elifesciences.org)
  • In order to generate comprehensive transcriptome profiles using RNA-Seq one must therefore obtain a sufficiently large number of reads to detect those biologically relevant transcripts that comprise a relatively small proportion of the cDNA library. (biomedcentral.com)
  • Is illumina small RNA-Seq strand specific? (biostars.org)
  • Because they are able to accurately make DNA copies of almost any type of RNA from very small amounts of starting material, they would do a better job of catching biomarkers for disease than anything currently available in an RNA-based liquid biopsy. (medicalautomation.org)
  • There has recently been a surge in studies, including one by Waters et al ( 2017 ) in this issue of The EMBO Journal , that have used clever variations of the RNA ‐seq technique to comprehensively map small RNA -target networks. (embopress.org)
  • total RNA from a Gram negative organism. (bio.net)
  • For microarray analysis and other sensitive applications, Ambion also recommends a DNase treatment (such as with DNA free Treatment and Removal Reagents ) to remove contaminating genomic DNA from the total RNA prior to the MICROB Enrich procedure. (bio-medicine.org)
  • In the first step of the MICROB Enrich procedure, host-bacterial total RNA is incubated with an optimized mixture of capture oligonucleotides that bind to the mammalian 18S and 28S rRNAs and polyadenylated RNAs. (bio-medicine.org)
  • Rat liver total RNA (25 g) and E. coli total RNA (2 g) were mixed together and subjected to the MICROB Enrich procedure. (bio-medicine.org)
  • Another mixed sample of total RNA was subjected to a mock MICROB Enrich procedure in which the capture oligonucleotide mix was left out of the reaction. (bio-medicine.org)
  • Even with a short 6 hour IVT incubation time, 100 ng of input total RNA results in sufficient aRNA for several replicate array experiments. (thermofisher.com)
  • Second, the proportion of reads representing rare transcripts can be increased by depleting abundant transcripts from total RNA and/or depleting cDNAs representing these abundant transcripts from cDNA libraries. (biomedcentral.com)
  • How I can to remove specific sequence from a fungu of a plant-fungu interaction of total RNA-Seq data? (usegalaxy.org)
  • Chao Y, Li L, Girodat D et al (2017) In vivo cleavage map illuminates the central role of RNase E in coding and non-coding RNA pathways. (springer.com)
  • CLASH: Following in vivo cross‐linking, RNase E is pulled down using a FLAG‐tag, the bound RNA is trimmed, and the complex is purified under denaturing conditions using a His‐tag. (embopress.org)
  • In vivo cross‐linked Hfq is pulled down using a FLAG‐tag, followed by RNA trimming and ligation of the interacting RNAs with T4 ligase. (embopress.org)
  • RNA-dependent RNA polymerases (RdRps) are key to the replication of RNA viruses. (rcsb.org)
  • They did this with great success: About one third of all typical 'common colds' and some cases of diarrhoea as well are caused by these RNA Viruses, which are the largest of their kind. (helmholtz-hzi.de)
  • Treatment with binase was shown to improve survival of laboratory animals infected with different RNA viruses. (biomedcentral.com)
  • I hope that this Commentary inspires exciting new questions that can be tested in the near future as new ways of studying RNA secondary and tertiary structure are developed (for a review of methods, see Ignatova and Narberhaus, 2017 ). (biologists.org)
  • Consolidating the protein-RNA complex is a host of distributed interactions mediated by the natively unstructured termini of Hfq. (elifesciences.org)
  • RIL-seq (RNA interaction by ligation and sequencing): a protein-RNA complex is immunoprecipitated and bound RNAs are crosslinked to the protein. (rna-seqblog.com)
  • DNA and RNA is ready for qPCR, RT-PCR and next-generation sequencing, while protein is ready for 1D SDS-PAGE and mass spectrometry following in-gel trypsin digestion. (qiagen.com)
  • Recent discoveries using next-generation sequencing (NGS) approaches have revealed unprecedented structural complexity with a pivotal role in regulating RNA function and stability. (medworm.com)
  • The steadily decreasing cost of sequencing, the growing number of and accessibility to high-throughput sequencing facilities, and the recent development of publicly available bioinformatic tools for RNA-Seq data analysis have made RNA-Seq an increasingly attractive and popular method for studying bacterial transcriptomes. (biomedcentral.com)
  • For many RNA-Seq-based projects, the budget for sequencing costs, and thus the total number of reads that can be obtained, is constrained. (biomedcentral.com)
  • Thus, researchers designing RNA-Seq experiments must often determine the correct balance between sequencing depth (the number of reads per sample) and breadth (the number of samples sequenced). (biomedcentral.com)
  • There is thus the need for computational methods to design optimal bacterial 16S primers able to take into account the knowledge provided by the new sequencing technologies. (biomedcentral.com)
  • However, our knowledge over unculturable bacterial sequences is rapidly growing thanks to Next-Generation Sequencing (NGS), a technology that is continuously evolving and improving [ 3 ]. (biomedcentral.com)
  • The purified RNA is free from any protein-bound circulating RNA, and can be used in a number of downstream applications including real-time PCR, Northern blotting, RNase protection, primer extension, expression arrays, and next-generation sequencing. (genomeweb.com)
  • The upgrades increase throughput and performance of the Sequel in applications such as de novo assembly, structural variant detection, targeted sequencing, and RNA sequencing. (genomeweb.com)
  • They enable a throughput of 10 gigabases per SMRT cell for long-insert genomic libraries and up to 20 gigabases per SMRT cell for targeted and RNA sequencing applications. (genomeweb.com)
  • The new release also improves the sensitivity of Iso-Seq, PacBio's RNA sequencing method, while software enhances help simplify the analytics for multiplexed samples, according to the company. (genomeweb.com)
  • While these processes are well understood in the messenger RNA of cells in higher organisms, Prof. Dr Andres Jäschke and his bioorganic chemistry working group now revealed these mechanisms in bacterial RNA. (xonl.de)
  • Detection and quantification of low abundance transcripts by RNA-Seq can be enhanced in two main ways. (biomedcentral.com)
  • Holmqvist et al , 2016 ), showing more precisely where Hfq recognizes its RNA targets. (embopress.org)
  • Thus, it was necessary to eliminate the human RNA, which could be done by hybridization capture using MICROBEnrich (Ambion). (asm.org)
  • Degraded human RNA cannot be removed by hybridization capture and could affect microarray analysis. (asm.org)
  • We also provide critical viewpoints on the use of NGS approaches for elucidating of RNA structuromes at the systems level. (medworm.com)
  • For some applications of RNA-Seq such as transcriptome mapping and annotation, the ability to detect rare transcripts is critical, and approaches such as the ones described above for increasing the total number of biologically relevant reads obtained per sample play a central role. (biomedcentral.com)
  • Collectively, this creates a need for global RNA biology approaches that can rapidly and comprehensively analyze the RNA composition of a bacterium of interest. (openrepository.com)
  • Using these approaches we are beginning to chart the full cosmos of RNA functions in the human microbiome. (helmholtz-hzi.de)
  • Was wondering which would be the best mapper for strand-specific RNA-seq mapping for bacterial transcriptomics? (biostars.org)
  • I am looking for mapping software to analyze directional/strand-specific RNA-seq. (biostars.org)
  • Could I map strand specific RNA-seq with non-strand specific? (biostars.org)
  • Does the order of input files matter when mapping paired-end strand specific RNA-seq reads? (biostars.org)
  • These structures refine the pathway from preinitiation through initiation to elongation for the RNA-dependent RNA polymerization reaction, explain the role of the noncatalytic divalent cation in 6 RdRp, and pinpoint the previously unresolved Mn(2+)-dependent step in replication. (rcsb.org)
  • The sequence of 13 residues is located at an active site in the RNA that catalyzes the synthesis of peptide bonds, and changing just one of these residues stops the production of interleukin-1β. (elifesciences.org)
  • Here, we review recent insights concerning RNA-based control of toxin synthesis, and discuss possible implications for persister generation. (paperity.org)
  • RNA‑based regulation in type I toxin-antitoxin systems and its implication for bacterial persistence Bork A. Berghoff 0 1 E. Gerhart H. Wagner 0 0 Department of Cell and Molecular Biology, Uppsala University , 75124 Uppsala , Sweden 1 Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität , 35392 Giessen , Germany 2 E. Gerhart H. Wagner Bacterial dormancy is a valuable survival strategy upon challenging environmental conditions. (paperity.org)