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  • mRNA
  • MICROB Enrich employs hybridization capture technology (patent pending) to remove human, mouse, and rat RNA (both mRNA and rRNA) from complex host-bacterial RNA populations, leaving behind enriched microbial total RNA. (bio-medicine.org)
  • If desired, upon completion of the MICROB Enrich procedure bacterial mRNA can be purified from the total RNA through the seamless integration of Ambion's MICROB Express technology. (bio-medicine.org)
  • The absence of poly(A) tails on bacterial mRNA prevents the use of oligo(dT) primed reverse transcription, which is at the heart of most amplification methods. (thermofisher.com)
  • As little as 10 ng of enriched bacterial mRNA or 100 ng of total RNA can be amplified to yield sufficient antisense amplified RNA (aRNA) for microarray analysis. (thermofisher.com)
  • Co‐immunoprecipitation of cellular RNA followed by deep sequencing (RIP‐seq) has yielded semi‐quantitative snapshots of sRNA and mRNA association patterns with Hfq in different growth phases of Salmonella (Chao et al , 2012 ). (embopress.org)
  • GRIL‐seq works similarly but additionally seeks to seal the typically short sRNA-mRNA duplexes in vivo by expressing an RNA ligase prior to RNA capture (Han et al , 2016 ). (embopress.org)
  • DNA TATA box Pribnow box SOS box CAAT box CCAAT box Operator (biology) Upstream activation sequence RNA List of cis-regulatory RNA elements Polyadenylation signals, mRNA AU-rich element, mRNA Other Regulation of gene expression cis-regulatory module Gene regulatory network Operon Promoter Trans-acting factor Rfam Transterm Butler JE, Kadonaga JT (October 2002). (wikipedia.org)
  • The ibs gene is on the opposite strand to sib and is completely complimentary, so the antisense-binding of Sib RNA with the ibs mRNA brings about dsRNA-mediated degradation. (wikipedia.org)
  • sRNA
  • Global transcript profiling by RNA‐seq has been amply used to map bacterial regulons, but sRNA‐mediated control seldom causes strong alterations in transcript abundance and observed changes may not always be a direct consequence of sRNA activity. (embopress.org)
  • Subsequently, the resulting hybrid RNAs of either protocol are sequenced, allowing in silico analysis of sRNA-target interactions. (embopress.org)
  • Bottom middle: Sequencing of RNA hybrids reveals global sRNA interactomes. (embopress.org)
  • In the 1960s, the abbreviation sRNA was used to refer to "soluble RNA," which is now known as transfer RNA or tRNA (for an example of the abbreviation used in this sense, see). (wikipedia.org)
  • The first bacterial sRNA was discovered and characterized in 1984. (wikipedia.org)
  • Northern blotting can reveal possible sRNA transcript size and expression levels by running a mixed RNA sample on an agarose gel and probing for a desired sRNA. (wikipedia.org)
  • cDNA
  • Cellular RNA is extracted and converted to cDNA, which is used to prepare sequencing libraries. (illumina.com)
  • High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. (biomedcentral.com)
  • 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)
  • 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)
  • long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. (rna-seqblog.com)
  • Total RNA
  • 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)
  • microbial
  • Bacterial, viral, and other microbial RNA-Seq experiments enable annotation and quantification of comprehensive microbial transcripts. (illumina.com)
  • A wide dynamic range enables confident identification of both high and low expressors in a single bacterial, viral, or other microbial RNA-Seq experiment. (illumina.com)
  • transcripts
  • A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance. (biomedcentral.com)
  • The relative abundances of individual transcripts in a bacterial transcriptome can differ by several orders of magnitude. (biomedcentral.com)
  • Detection and quantification of low abundance transcripts by RNA-Seq can be enhanced in two main ways. (biomedcentral.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)
  • 2016
  • Holmqvist et al , 2016 ), showing more precisely where Hfq recognizes its RNA targets. (embopress.org)
  • small
  • 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)
  • The small RNA nitrogen stress-induced RNA 1 (NsiR1) is produced by Cyanobacteria under conditions of nitrogen deprivation. (wikipedia.org)
  • Strong σ70 promoters were predicted upstream of all novel small RNAs, indicating the potential for transcriptional activity. (biomedcentral.com)
  • These defense systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids. (sciencemag.org)
  • 1984 Rajneeshee bioterror attack AsrC small RNA Bacterial small RNA HilD 3'UTR PinT small RNA Typhoid Mary Giannella RA (1996). (wikipedia.org)
  • It was originally identified along with 26 other non-coding RNAs using a tiled Caulobacter microarray protocol specifically aimed at detecting small RNAs. (wikipedia.org)
  • rifampicin
  • Mutations in rpoB that confer resistance to rifamycins do so by altering residues of the rifamycin binding site on RNA polymerase, thereby reducing rifamycin binding affinity for rifamycins Initial studies were done by Jin and Gross to generate rpoB mutations in E. coli that conferred resistance to rifampicin. (wikipedia.org)
  • Rifampicin, also known as rifampin, is an antibiotic used to treat several types of bacterial infections, including tuberculosis, leprosy, and Legionnaire's disease. (wikipedia.org)
  • experiments
  • 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)
  • Sequencing
  • 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)
  • agarose
  • RNA was precipitated and an equal fraction of each sample was analyzed by denaturing agarose gel electrophoresis. (bio-medicine.org)
  • A 1 µg aliquot of DNA from each respective bacterial sample was resolved on a 1% agarose gel in 0.5X TBE at 150 volts for 16 hours using a BioRad CHEF DRII system. (sigmaaldrich.com)
  • coli
  • In E. coli, the direction for orisome assembly are built into a short stretch of nucleotide sequence called as origin of replication (oriC) which contains multiple binding sites for the initiator protein DnaA (a highly homologous protein amongst bacterial kingdom). (wikipedia.org)
  • It was shown in a study using the enterohemorrhagic E. coli that unusually short (between 50 and 60 nucleotide long) small RNAs are expressed by bacteriophages and bacteriophage-derived pathogenicity islands. (wikipedia.org)
  • genes
  • Another cellular enzyme, RNAse L-also induced by interferon action-destroys RNA within the cells to further reduce protein synthesis of both viral and host genes. (wikipedia.org)
  • In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some, if not most, of them are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution. (wikipedia.org)
  • PcrZ (photosynthesis control RNA Z) identified in R. sphaeroides, is a trans-acting sRNA which counteracts the redox-dependent induction of photosynthesis genes, mediated by protein regulators. (wikipedia.org)
  • While identifying these small RNAs, her lab discovered that some of these small RNAs encode small proteins that had previously been overlooked because they are not detected in many traditional biochemical assays and the corresponding genes are poorly annotated. (wikipedia.org)
  • motif
  • A cluster of four homologous sRNAs called CcsR for conserved CCUCCUCCC motif stress-induced RNA has been shown to play a role in photo-oxidative stress resistance as well. (wikipedia.org)
  • viruses
  • In November 8-11, the Research Training Center on animal disease diagnostics of the IVM hosts workshop on the theoretical training on molecular virology of RNA viruses for representatives of the Ministry of Health of Ukraine: regional laboratory centers, the Ukrainian Center for Disease Control and Monitoring, the Lviv Research Institute of Epidemiology and Hygiene. (kiev.ua)
  • Noroviruses (NoV) are a genetically diverse group of single-stranded positive-sense RNA, non-enveloped viruses belonging to the Caliciviridae family. (wikipedia.org)
  • infection
  • Comparison of Asian porcine high fever disease isolates of porcine reproductive and respiratory syndrome virus to United States isolates for their ability to cause disease and secondary bacterial infection in swine. (usda.gov)
  • Those that remain can be eluted, used to produce more phage (by bacterial infection with helper phage) and so produce a phage mixture that is enriched with relevant (i.e. binding) phage. (wikipedia.org)
  • cells
  • For instance, Dr. Stephen Meyer of Discovery Institute says that "bacterial cells are propelled by rotary engines called flagellar motors that rotate at 100,000 rpm," which is powerful evidence for design by an intelligent cause. (blogspot.fi)
  • The activity of this thermoregulator was confirmed in vitro but was not found in vivo, suggesting more complicated operon regulation exists in bacterial cells. (wikipedia.org)
  • found
  • Although no PhotoRC-II RNA has been detected in cyanobacteria, one is found in the genome of a purified phage that infects cyanobacteria. (wikipedia.org)
  • The IbpB thermometer is an RNA thermometer element found in the ibpAB operon. (wikipedia.org)
  • specific
  • The RNase H1 is a non-specific endonuclease and catalyzes the cleavage of RNA via a hydrolytic mechanism. (wikipedia.org)
  • shows
  • The above picture shows the vector field of bacterial velocities at the bottom of a drop hanging from the bottom of a petri dish, at high magnification, with prominent regions of circulation evident. (blogspot.com)