A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
RNA, Small Interfering
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
DNA-Directed RNA Polymerases
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
RNA Polymerase II
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.
RNA Processing, Post-Transcriptional
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
RNA, Small Nuclear
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
Nucleic Acid Conformation
Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.
Sequence Analysis, RNA
RNA Ligase (ATP)
DEAD-box RNA Helicases
RNA Polymerase III
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 22.214.171.124.
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
RNA Polymerase I
RNA, Ribosomal, 28S
RNA, Ribosomal, 18S
RNA, Ribosomal, 23S
RNA, Spliced Leader
Small, linear single-stranded RNA molecules functionally acting as molecular parasites of certain RNA plant viruses. Satellite RNAs exhibit four characteristic traits: (1) they require helper viruses to replicate; (2) they are unnecessary for the replication of helper viruses; (3) they are encapsidated in the coat protein of the helper virus; (4) they have no extensive sequence homology to the helper virus. Thus they differ from SATELLITE VIRUSES which encode their own coat protein, and from the genomic RNA; (=RNA, VIRAL); of satellite viruses. (From Maramorosch, Viroids and Satellites, 1991, p143)
RNA, Ribosomal, 16S
Amino Acid Sequence
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
RNA, Heterogeneous Nuclear
RNA, Small Cytoplasmic
RNA 3' End Processing
RNA, Small Untranslated
RNA, Ribosomal, 5.8S
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
RNA, Long Noncoding
A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.
RNA, Small Nucleolar
Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.
Promoter Regions, Genetic
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Reverse Transcriptase Polymerase Chain Reaction
Single-Strand Specific DNA and RNA Endonucleases
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
Gene Expression Regulation
RNA, Transfer, Phe
RNA, Transfer, Lys
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
5' Untranslated Regions
RNA, Transfer, Tyr
Sequence Homology, Nucleic Acid
3' Untranslated Regions
Cyclic peptides extracted from carpophores of various mushroom species. They are potent inhibitors of RNA polymerases in most eukaryotic species, blocking the production of mRNA and protein synthesis. These peptides are important in the study of transcription. Alpha-amanitin is the main toxin from the species Amanitia phalloides, poisonous if ingested by humans or animals.
Nucleic Acid Denaturation
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
Sequence Homology, Amino Acid
Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Gene Expression Regulation, Viral
Viral Nonstructural Proteins
RNA, Transfer, Amino Acyl
RNA Splice Sites
RNA, Transfer, Ala
A species of ENTEROVIRUS which is the causal agent of POLIOMYELITIS in humans. Three serotypes (strains) exist. Transmission is by the fecal-oral route, pharyngeal secretions, or mechanical vector (flies). Vaccines with both inactivated and live attenuated virus have proven effective in immunizing against the infection.
Centrifugation, Density Gradient
RNA-Directed DNA Polymerase
A compound composed of a two CYCLIC PEPTIDES attached to a phenoxazine that is derived from STREPTOMYCES parvullus. It binds to DNA and inhibits RNA synthesis (transcription), with chain elongation more sensitive than initiation, termination, or release. As a result of impaired mRNA production, protein synthesis also declines after dactinomycin therapy. (From AMA Drug Evaluations Annual, 1993, p2015)
Open Reading Frames
Gene Expression Profiling
Electrophoresis, Polyacrylamide Gel
RNA, Transfer, Asp
RNA, Transfer, Met
Regulatory Sequences, Ribonucleic Acid
A multiribosomal structure representing a linear array of RIBOSOMES held together by messenger RNA; (RNA, MESSENGER); They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
RNA, Transfer, Gly
RNA, Transfer, His
Saccharomyces cerevisiae Proteins
RNA, Transfer, Val
Nucleic Acid Precursors
Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.
RNA, Transfer, Arg
Sequence Analysis, DNA
A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Ribonucleoproteins, Small Nuclear
Hepatitis Delta Virus
RNA, Transfer, Trp
Oligonucleotide Array Sequence Analysis
Recombinant Fusion Proteins
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Trypanosoma brucei brucei
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Gene Expression Regulation, Bacterial
The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.
RNA, Transfer, Leu
Chlamydia pneumoniae infection in human monocytes. (1/10063)Chlamydia pneumoniae infection has been associated with cardiovascular diseases in seroepidemiological studies and by demonstration of the pathogen in atherosclerotic lesions. It has the capacity to infect several cell types, including monocyte-derived macrophages, which play an essential role in the development of atherosclerosis. However, the persistence of C. pneumoniae in mononuclear cells is poorly understood. To study the morphology and biological characteristics of the infection, human peripheral blood monocytes were infected with C. pneumoniae. Freshly isolated monocytes resisted the development of infectious progeny, and confocal and transmission electron microscopy showed that the morphology of the inclusions and chlamydial particles was abnormal. Addition of tryptophan or antibodies against gamma interferon did not diminish the inhibition of C. pneumoniae, suggesting that other factors are involved in the chlamydiostatic activity of the monocytes. Chlamydial mRNA was expressed at least 3 days after infection, however, and a capability for infected monocytes to induce a positive lymphocyte proliferative response was detected for up to 7 days, indicating that C. pneumoniae remains metabolically active in the monocytes in vitro. These results are in accordance with the hypothesis that C. pneumoniae may participate in the maintenance of local immunological response and inflammation via infected monocytes and thus enhance atherosclerosis. (+info)
Synthesis of bacteriophage phi6 double-stranded ribonucleic acid. (2/10063)Uracil was incorporated into all three bacteriophage phi6 dsRNA segments throughout the infection cycle; the rates of incorporation into each of the three segments were approx. constant for the first 15 to 20 min and then increased rapidly until 50 min after infection. The medium and small dsRNA segments were produced in greater amounts than the large dsRNA segment at all times in the infection cycle. Inhibition of host RNA and protein synthesis with rifampin and chloramphenicol revealed that virus dsRNA synthesis immediately after infection was independent of either host function. (+info)
Characterization of an insertion sequence element associated with genetically diverse plant pathogenic Streptomyces spp. (3/10063)Streptomycetes are common soil inhabitants, yet few described species are plant pathogens. While the pathogenicity mechanisms remain unclear, previous work identified a gene, nec1, which encodes a putative pathogenicity or virulence factor. nec1 and a neighboring transposase pseudogene, ORFtnp, are conserved among unrelated plant pathogens and absent from nonpathogens. The atypical GC content of nec1 suggests that it was acquired through horizontal transfer events. Our investigation of the genetic organization of regions adjacent to the 3' end of nec1 in Streptomyces scabies 84.34 identified a new insertion sequence (IS) element, IS1629, with homology to other IS elements from prokaryotic animal pathogens. IS1629 is 1,462 bp with 26-bp terminal inverted repeats and encodes a putative 431-amino-acid (aa) transposase. Transposition of IS1629 generates a 10-bp target site duplication. A 77-nucleotide (nt) sequence encompassing the start codon and upstream region of the transposase was identified which could function in the posttranscritpional regulation of transposase synthesis. A functional copy of IS1629 from S. turgidiscabies 94.09 (Hi-C-13) was selected in the transposon trap pCZA126, through its insertion into the lambda cI857 repressor. IS1629 is present in multiple copies in some S. scabies strains and is present in all S. acidiscabies and S. turgidiscabies strains examined. A second copy of IS1629 was identified between ORFtnp and nec1 in S. acidiscabies strains. The diversity of IS1629 hybridization profiles was greatest within S. scabies. IS1629 was absent from the 27 nonpathogenic Streptomyces strains tested. The genetic organization and nucleotide sequence of the nec1-IS1629 region was conserved and identical among representatives of S. acidiscabies and S. turgidiscabies. These findings support our current model for the unidirectional transfer of the ORFtnp-nec1-IS1629 locus from IS1629-containing S. scabies (type II) to S. acidiscabies and S. turgidiscabies. (+info)
Inhibition of translation and cell growth by minigene expression. (4/10063)A random five-codon gene library was used to isolate minigenes whose expression causes cell growth arrest. Eight different deleterious minigenes were isolated, five of which had in-frame stop codons; the predicted expressed peptides ranged in size from two to five amino acids. Mutational analysis demonstrated that translation of the inhibitory minigenes is essential for growth arrest. Pulse-labeling experiments showed that expression of at least some of the selected minigenes results in inhibition of cellular protein synthesis. Expression of the deleterious minigenes in cells deficient in peptidyl-tRNA hydrolase causes accumulation of families of peptidyl-tRNAs corresponding to the last minigene codon; the inhibitory action of minigene expression could be suppressed by overexpression of the tRNA corresponding to the last sense codon in the minigene. Experimental data are compatible with the model that the deleterious effect of minigene expression is mediated by depletion of corresponding pools of free tRNAs. (+info)
Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. (5/10063)We examined the effectiveness of antisense RNA (as RNA) strategies for metabolic engineering of Clostridium acetobutylicum. Strain ATCC 824(pRD4) was developed to produce a 102-nucleotide asRNA with 87% complementarity to the butyrate kinase (BK) gene. Strain ATCC 824(pRD4) exhibited 85 to 90% lower BK and acetate kinase specific activities than the control strain. Strain ATCC 824(pRD4) also exhibited 45 to 50% lower phosphotransbutyrylase (PTB) and phosphotransacetylase specific activities than the control strain. This strain exhibited earlier induction of solventogenesis, which resulted in 50 and 35% higher final concentrations of acetone and butanol, respectively, than the concentrations in the control. Strain ATCC 824(pRD1) was developed to putatively produce a 698-nucleotide asRNA with 96% complementarity to the PTB gene. Strain ATCC 824(pRD1) exhibited 70 and 80% lower PTB and BK activities, respectively, than the control exhibited. It also exhibited 300% higher levels of a lactate dehydrogenase activity than the control exhibited. The growth yields of ATCC 824(pRD1) were 28% less than the growth yields of the control. While the levels of acids were not affected in ATCC 824(pRD1) fermentations, the acetone and butanol concentrations were 96 and 75% lower, respectively, than the concentrations in the control fermentations. The lower level of solvent production by ATCC 824(pRD1) was compensated for by approximately 100-fold higher levels of lactate production. The lack of any significant impact on butyrate formation fluxes by the lower PTB and BK levels suggests that butyrate formation fluxes are not controlled by the levels of the butyrate formation enzymes. (+info)
In situ identification of cyanobacteria with horseradish peroxidase-labeled, rRNA-targeted oligonucleotide probes. (6/10063)Individual cyanobacterial cells are normally identified in environmental samples only on the basis of their pigmentation and morphology. However, these criteria are often insufficient for the differentiation of species. Here, a whole-cell hybridization technique is presented that uses horseradish peroxidase (HRP)-labeled, rRNA-targeted oligonucleotides for in situ identification of cyanobacteria. This indirect method, in which the probe-conferred enzyme has to be visualized in an additional step, was necessary since fluorescently monolabeled oligonucleotides were insufficient to overstain the autofluorescence of the target cells. Initially, a nonfluorescent detection assay was developed and successfully applied to cyanobacterial mats. Later, it was demonstrated that tyramide signal amplification (TSA) resulted in fluorescent signals far above the level of autofluorescence. Furthermore, TSA-based detection of HRP was more sensitive than that based on nonfluorescent substrates. Critical points of the assay, such as cell fixation and permeabilization, specificity, and sensitivity, were systematically investigated by using four oligonucleotides newly designed to target groups of cyanobacteria. (+info)
The use of terminal blocking groups for the specific joining of oligonucleotides in RNA ligase reactions containing equimolar concentrations of acceptor and donor molecules. (7/10063)Under the conditions that RNA ligase converts the tetranucleotide, pA-A2-A, to larger polynucleotides, no such polymerization can be detected with the derivative, pA-A2-A(MeOEt), that possesses a terminal 2'-0-(alpha-methoxyethyl) group. The protection against self condensation offered by the methoxyethyl group in this system allows the specific joining of donor and acceptor oligonucleotides in reaction mixtures containing equimolar concentrations of the two species. Thus, the enzyme, together with ATP, converts equimolar quantities of A-A2-A and pA-A2-A(MeOEt) to A-A6-A(MeOEt) in 55% yield, while a similar reaction with A-A2-A and pU-U2-U(MeOEt) results in a 40% yield of A-A3-U3-U(MeOEt). The intermediate in these ligations is a disubstituted pyrophosphate composed of the donor molecule and the adenylate moiety deriving from ATP. In the case of the intermediate arising from the blocked adenosine tetranucleotide, the assigned structure, A5'pp5'A-A2-A(MeOEt), has been confirmed by chemical synthesis. The pyrophosphate derivative is able to participate in joining reactions in the absence of ATP. These observations constitute an efficient approach to the synthesis of larger polynucleotides from a specific series of oligonucleotide blocks since (i), the methoxyethyl group can be easily introduced into each oligonucleotide using the single addition reaction catalyzed by polynucleotide phosphorylase in the presence of a 2'-0-(alpha-methoxyethyl)nucleoside 5'-diphosphate, and (ii), the blocking group may be readily removed under mild conditions after each successive ligation reaction. Two other octanucleotides, I-I2-A-U3-U and U-U2-C-I3-A, have also been synthesized by this method, and these molecules correspond (with I substituting for G) to sequences appearing near the 3' terminus of the 6S RNA transcribed from phage lambda DNA. The terminal 3'-phosphate group serves equally well as a blocking group for specific ligation reactions in that the ligase converts equimolar amounts of A-A2-A and pA-A2-Ap to A-A6-Ap in 50% yield. (+info)
An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. (8/10063)Current global phylogenies are built predominantly on rRNA sequences. However, an experimental system for studying the evolution of rRNA is not readily available, mainly because the rRNA genes are highly repeated in most experimental organisms. We have constructed an Escherichia coli strain in which all seven chromosomal rRNA operons are inactivated by deletions spanning the 16S and 23S coding regions. A single E. coli rRNA operon carried by a multicopy plasmid supplies 16S and 23S rRNA to the cell. By using this strain we have succeeded in creating microorganisms that contain only a foreign rRNA operon derived from either Salmonella typhimurium or Proteus vulgaris, microorganisms that have diverged from E. coli about 120-350 million years ago. We also were able to replace the E. coli rRNA operon with an E. coli/yeast hybrid one in which the GTPase center of E. coli 23S rRNA had been substituted by the corresponding domain from Saccharomyces cerevisiae. These results suggest that, contrary to common belief, coevolution of rRNA with many other components in the translational machinery may not completely preclude the horizontal transfer of rRNA genes. (+info)
Transfer-messenger RNA - Wikipedia
Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1. In trans-translation, tmRNA and its associated proteins bind to bacterial ribosomes which have stalled in the middle of protein biosynthesis, for example when reaching the end of a messenger RNA which has lost its stop codon. The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. In the majority of bacteria these functions are carried out by standard one-piece tmRNAs. In other bacterial species, a permuted ssrA gene produces a two-piece tmRNA in which two separate RNA chains are joined by base-pairing. tmRNA was first designated 10Sa RNA ...
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences - Murdoch Research Repository
A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the green algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.. ...
Systems biology of bacterial small RNAs | Stavans Lab
Small RNAs (sRNAs) are post-transcriptional regulators of gene expression that play fundamental roles in the response of bacterial cells to environmental cues. We study the response of genetic networks and architectural motifs that include sRNAs, as well as the cell-to-cell variability in the expression of genes controlled by sRNAs. To do so, we use fluorescence microscopy and microfluidic techniques that allow us to measure directly the concentrations of fluorescently-tagged target proteins in individual cells as they respond to controlled stimuli, as well as single-molecule fluorescence in-situ hybridization to monitor the response at the target transcript level.. ...
MACROMOLECULAR KETOALDEHYDES - BAXTER INTERNATIONAL INC.
Methods of producing macromolecular compositions and using same are provided. The method includes preparing a resin material; forming an acetyl group on the resin material; and oxidizing the acetyl group via a one-step reaction including reacting a sulfoxide and an acid with the acetyl group to form a ketoaldehyde group. The macromolecular compositions are capable of removing an effective amount of one or more constituents from a physiological solution, such as urea during dialysis therapy.
BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. MOLECULAR EVOLUTION. ...
The rates of macromolecular chain elongation modulate the initiation frequencies for transcription and translation in...
Here we show that most macromolecular biosynthesis reactions in growing bacteria are sub-saturated with substrate. The experiments should in part test predictions from a previously proposed model (Jen
Systematic probing of the bacterial RNA structurome to reveal new functions.
Systematic probing of the bacterial RNA structurome to reveal new functions. Curr Opin Microbiol. 2017 Feb 01;36:14-19 Authors: Ignatova Z, Narberhaus F Abstract RNA folds into intricate structures. Recent discoveries using next-generation sequencing (NGS) approaches have revealed unprecedented structural complexity with a pivotal role in regulating RNA function and stability...
Zymo research august 2013.xls
ZR-96 Quick-RNA™ Kit (4 x 96 Preps) [[Includes E1009 x 8: DNase I Set (250 U) w/ 10X Reaction Buffer (1 ml)] Quick-RNA™ MiniPrep Kit (50 Preps) w/Zymo-Spin™ IIICG Columns (Capped) & Spin-Away™ Filters [Includes E1009 x 1: DNase I Se Sample: Quick-RNA™ MiniPrep Kit (10 Preps) Quick-RNA™ MiniPrep Kit (200 Preps) w/Zymo-Spin™ IIICG Columns (Capped) & Spin-Away™ Filters [Includes E1009 x 4: DNase I Set (250 U) w/ 10X Reaction Buffer (1 ml)] ZR small-RNA™ PAGE Recovery Kit (20 Preps) ZR-96 RNA Clean & Concentrator™ Kit (2 x 96 Preps) RNA Shield Purification Kit (50 prep) supplied w/ 50 ml RNA Shield RNA Shield Purification Kit (50 prep) Without RNA Shield ZR Fungal/Bacterial RNA MicroPrep™ Kit (50 Preps) ZR Fungal/Bacterial RNA MiniPrep™ Kit (50 Preps) ZR Tissue & Insect RNA MicroPrep™ Kit (50 Preps) ZR Soil/Fecal RNA MicroPrep™ Kit (50 Preps) Direct-zol™ RNA MiniPrep (50 Preps) w/ Zymo-Spin™ IIC Columns (Capped) [Includes E1009 x 1: DNase I Set (250 U) w/ 10X Reaction ...
CopraRNA - Results
CopraRNA is a tool for sRNA target prediction. It computes whole genome predictions by combination of whole genome IntaRNA predictions using homologous sRNA sequences from distinct organisms.
Synthesis and Applications of a Two-Step Reagent Forming Cross-links between Ribonucleic Acid and Protein | Biochemical Society...
GERALD FINK, RICHARD BRIMACOMBE; Synthesis and Applications of a Two-Step Reagent Forming Cross-links between Ribonucleic Acid and Protein. Biochem Soc Trans 1 December 1975; 3 (6): 1014-1015. doi: https://doi.org/10.1042/bst0031014. Download citation file:. ...
A Blood-based Test for the Detection of ROS1 and RET Fusion Transcripts from Circulating Ribonucleic Acid Using Digital...
Detection of circulating ribonucleic acid (cRNA) from blood is an unmet need in clinical diagnostics. Here we describe methods that...
இரைபோ கருவமிலம் - தமிழ் விக்கிப்பீடியா
இரைபோ கருவமிலம் அல்லது ஆர்.என்.ஏ. (RNA - Ribonucleic acid) என்பது ஒரு கருவமிலம் ஆகும். இதனை இரைபோக் கருக்காடி, ஐங்கரிமவினியக் கருக்காடி, ஐவினியக் கருக்காடி, ஐங்கரிமவினியக் கருவமிலம், ஐவினியக் கருவமிலம் என்ற பெயர்கள் கொண்டும் அழைக்கலாம். இது அனைத்து உயிரினங்களுக்கும் தேவையான நான்கு பெரிய பிரிவுகளில் அடங்கும் பருமூலக்கூறுகளில் ஒன்றான கருவமிலங்களில் ஒன்றாகும். இவையும் டி.என்.ஏ யைப் ...
Heterogeneous macromolecular composition of renal basement membranes in health, diabetes and glomerulonephritis :: MEDICA, MUSC...
Although basement membranes are ubiquitous structures throughout the body, basement membranes have distinct compositions that are specific to their location. This basement membrane heterogeneity may, in part, reflect functional differences among various basement membranes. We examined basement membrane heterogeneity in normal, healthy mouse kidneys to assess the similarities and differences between glomerular and tubular basement membrane composition. It was demonstrated that mouse glomerular and tubular basement membrane share similar compositions but differ with respect to specific amounts of some components. In diabetes mellitus and passive Heymann nephritis (PHN) , damage to the glomerular barrier occurs and is accompanied by an increase in penneability to proteins the size of albumin and larger: Presumably, the biochemical nature of the filter is not maintained. The acute effects of streptozotocin diabetes and PHN on the macromolecular composition of rat GBM was investigated to determine if ...
Heterogeneous macromolecular composition of renal basement membranes in health, diabetes and glomerulonephritis :: MEDICA, MUSC...
Although basement membranes are ubiquitous structures throughout the body, basement membranes have distinct compositions that are specific to their location. This basement membrane heterogeneity may, in part, reflect functional differences among various basement membranes. We examined basement membrane heterogeneity in normal, healthy mouse kidneys to assess the similarities and differences between glomerular and tubular basement membrane composition. It was demonstrated that mouse glomerular and tubular basement membrane share similar compositions but differ with respect to specific amounts of some components. In diabetes mellitus and passive Heymann nephritis (PHN) , damage to the glomerular barrier occurs and is accompanied by an increase in penneability to proteins the size of albumin and larger: Presumably, the biochemical nature of the filter is not maintained. The acute effects of streptozotocin diabetes and PHN on the macromolecular composition of rat GBM was investigated to determine if ...
Q03AJ7 | smpB | SsrA-binding protein | Druggability | Cancer
casSAR Dugability of Q03AJ7 | smpB | SsrA-binding protein - Also known as SSRP_LACP3, smpB. Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a tag peptide, a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the tag peptide encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation.
B7MYQ8 | smpB | SsrA-binding protein | Druggability | Cancer
casSAR Dugability of B7MYQ8 | smpB | SsrA-binding protein - Also known as SSRP_ECO81, smpB. Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a tag peptide, a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the tag peptide encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation.
The Role of SmpB in Licensing tmRNA Entry into Stalled Ribosomes by Mickey R. Miller
Ribosomes translate the genetic information contained in mRNAs into protein by linking together amino acids with the help of aminoacyl-tRNAs. In bacteria, protein synthesis stalls when the ribosome reaches the 3-end of truncated mRNA transcripts lacking a stop codon. Trans-translation is a conserved bacterial quality control process that rescues stalled ribosomes. Transfer-messenger RNA (tmRNA) and its protein partner SmpB mimic a tRNA by entering the A site of the ribosome and accepting the growing peptide chain. The ribosome releases the truncated mRNA and resumes translation on the tmRNA template. The open reading frame found on tmRNA encodes a peptide tag that marks the defective nascent peptide for proteolysis. A stop codon at the end of the open reading frame allows the ribosome to be recycled and engage in future rounds of translation.The entry of tmRNA into stalled ribosomes presents a challenge to our understanding of ribosome function because during the canonical decoding process, the
CN09 28935 protein (Agrobacterium rhizogenes) - STRING interaction network
SsrA-binding protein; Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a tag peptide, a short internal open reading frame. During trans-translation Ala- aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to ...
KKL-35 | Ribosome rescue inhibitor | KKL35 | KKL 35 | CAS [865285-29-6] | Axon 2997 | Axon Ligand™ with |99% purity available...
KKL-35 | Ribosome rescue inhibitor | KKL35 | KKL 35 | CAS [865285-29-6] | Axon 2997 | Axon Ligand™ with >99% purity available from supplier Axon Medchem, prime source of life science reagents for your research
tmRNA and associated ligands: a puzzling relationship. - Inserm
Translation is an efficient and accurate mechanism, needing thorough systems of control-quality to ensure the correspondence between the information carried by the messenger RNA (mRNA) and the newly synthesized protein. Among them, trans-translation ensures delivering of stalled ribosomes when translation occurs on truncated mRNAs in bacteria, followed by the degradation of the incomplete nascent proteins. This process requires transfer-messenger RNA (tmRNA), an original molecule acting as both a tRNA and an mRNA. tmRNA first enters the decoding site of stuck ribosomes and, despite the lack of any codon-anticodon interaction, acts as a tRNA by transferring its alanine to the incomplete protein. Translation then switches to a small internal coding sequence (mRNA domain), which encodes a tag directing the incomplete protein towards degradation. Although playing a central role during trans-translation, tmRNA function depends on associated proteins. Genetic, biochemical and recent structural data are
Global snapshots of bacterial RNA networks | The EMBO Journal
Waters et al (2017) build on previous work from the Tollervey group who originally developed cross‐linking, ligation, and sequencing of hybrids (CLASH) to discover new snoRNA-rRNA interactions on snoRNA‐related yeast proteins (Kudla et al, 2011). An earlier attempt to apply this proximity ligation method to Hfq in enterohemorrhagic E. coli (EHEC) yielded few RNA hybrids (Tree et al, 2014); however, encouraged by the observation that RNase E recognizes the short seed helix formed between an sRNA and its target (Bandyra et al, 2012), the authors now focused on ligation to RNase E, which much elevated the proportion of RNA hybrids (Waters et al, 2017). Since these hybrids are significantly enriched in pairs of known sRNA seed regions and co‐regulated targets, they likely represent bona fide sRNA-mRNA interactions. What recruits RNase E to these many duplexes cannot be directly concluded from the data. However, plenty of coincidences with Hfq sites suggest a model whereby RNase E is recruited ...
MK-8776 ic50 | Safety, pharmacokinetics, and pharmacodynamic properties of oral DEBIO1143 (AT-406)
Supplementary MaterialsSupplementary Information srep11880-s1. model of interacting individual cells. By heading beyond the cell-autonomous explanation, we present that primary physico-chemical constraints certainly favour the establishment of such a coupling under Srebf1 extremely broad circumstances. The MK-8776 ic50 characterization we attained by tuning the aberrant cells demand for ATP, amino-acids and MK-8776 ic50 essential fatty acids and/or the imbalance in nutritional partitioning provides quantitative support to the theory that synergistic multi-cell results enjoy a central function in tumor sustainment. In mind, a cells lively problem is composed in selecting how exactly to process nutrition (say, glucose molecules) into chemical energy (adenosine 5-triphosphate, ATP) that will then be transduced into useful forms of mechanical or chemical work. Rapid cellular growth, in specific, requires high rates of macromolecular biosynthesis and MK-8776 ic50 of energy production, which ...
CAS CH 421 » Academics | Boston University
Introductory biochemistry. Protein structure and folding, enzyme mechanisms, kinetics, and allostery; nucleic acid structure; macromolecular biosynthesis with emphasis on specificity and fidelity; lipids and membrane structure; vitamins and coenzymes; introduction to intermediary metabolism. Three hours lecture, one hour discussion, four hours lab.. ...
This model describes the SsrA-binding protein, also called tmRNA binding protein, small protein B, and SmpB. The small, stable RNA SsrA (also called tmRNA or 10Sa RNA) recognizes stalled ribosomes such as occur during translation from message that lacks a stop codon. It becomes charged with Ala like a tRNA, then acts as mRNA to resume translation started with the defective mRNA. The short C-terminal peptide tag added by the SsrA system marks the abortively translated protein for degradation. SmpB binds SsrA after its aminoacylation but before the coupling of the Ala to the nascent polypeptide chain and is an essential part of the SsrA peptide tagging system. SmpB has been associated with the survival of bacterial pathogens in conditions of stress. It is universal in the first 100 sequenced bacterial genomes ...
RCSB PDB - 5U9F: 3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure II)
As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
Regulatory RNA qPCR Profiler | System Biosciences
Using the Regulatory RNA qPCR Profiler. First, get your regulatory RNA ready for qPCR by converting to cDNA While some lncRNAs have endogenouse polyA tails, other lncRNAs do not. To enhance qPCR assay performance, the cDNA synthesis workflow includes steps and reagents to polyadenylate all lncRNAs before cDNA conversion using the tagged oligo dT adaptor and random primers. This combined RNA tailing and oligo dT plus random primers boosts cDNA yield significantly and enables strand-specific lncRNA qPCR profiling.. ...
Making the jump: new insights into the mechanism of trans -translation | Journal of Biology | Full Text
The transfer-messenger ribonucleoprotein (tmRNP), which is composed of RNA and a small protein, small protein B (SmpB), recycles ribosomes that are stalled on broken mRNAs lacking stop codons and tags the partially translated proteins for degradation. Although it is not yet understood how the ribosome gets from the 3 end of the truncated message onto the messenger portion of the tmRNA to add the tag, a recent study in BMC Biology has shed some light on this astonishing feat.
Activation of GCN2 kinase by ribosome stalling links translation elong by Ryuta Ishimura, Gabor Nagy et al.
Ribosome stalling during translation has recently been shown to cause neurodegeneration, yet the signaling pathways triggered by stalled elongation complexes are unknown. To investigate these pathways we analyzed the brain of C57BL/6J-Gtpbp2(nmf205)(-/-) mice in which neuronal elongation complexes are stalled at AGA codons due to deficiencies in a tRNA(Arg)UCU tRNA and GTPBP2, a mammalian ribosome rescue factor. Increased levels of phosphorylation of eIF2α (Ser51) were detected prior to neurodegeneration in these mice and transcriptome analysis demonstrated activation of ATF4, a key transcription factor in the integrated stress response (ISR) pathway. Genetic experiments showed that this pathway was activated by the eIF2α kinase, GCN2, in an apparent deacylated tRNA-independent fashion. Further we found that the ISR attenuates neurodegeneration in C57BL/6J-Gtpbp2(nmf205)(-/-) mice, underscoring the importance of cellular and stress context on the outcome of activation of this pathway. These results
Demo, G, Svidritskiy E, Madireddy R, Diaz-Avalos R, Grant T, Grigorieff N, Sousa D, Korostelev AA. 2017. Mechanism of ribosome rescue by ArfA and RF2. eLife. 6(e23687):1-18. Abstract ...
Sandwalk: Ribonucleic Acid (RNA)
Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as plan of creation, unity of design, etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory. ...
KAKEN - Researchers | TAKAHASHI Hidehisa (30423544)
Affiliation：北海道大学,医学研究院,講師, Research Field：General medical chemistry,Pathological medical chemistry,Tumor biology and related fields,Tumor biology, Keywords：転写,RNAポリメラーゼII,発現制御,腫瘍,転写制御,がん,転写因子,ユビキチン,転写伸長因子,腫瘍性疾患, # of Research Projects：9, # of Research Products：70, Ongoing Project：新規の転写伸長制御因子Med26を標的とした腫瘍治療シーズ開発基盤の確立
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trans-translation in mycobacteria: expression, regulation, and the effects of ribosome inhibitors :: University of Southern...
Unique bacterial process, trans-translation, has been studied to be an important process in many bacteria. However, there was nothing known about the significance of this process in mycobacteria, especially in relation to drug susceptibility. Consistent with findings in Escherichia coli, Salmonella typhimurium, and Synechocystis sp., we found that interfering with the expression of tmRNA and the smpB gene (critical components of trans-translation) in Mycobacterium smegmatis caused increased bactericidal activity of antimicrobial agents that target the ribosomes. Moreover, exposure to ribosome inhibitors increased the expression of tmRNA. This increase was driven by the tmRNA gene promoter which activity seemed to utilize a de-repression mechanism. Not only is trans-translation important to the bacterial response to ribosome inhibitors, evidence from this laboratory suggests that trans-translation is essential in mycobacteria. Thus, we believe that trans-translation may represent a new important ...
Small molecule inhibition of trans-translation impairs Staphylococcus aureus viability [electronic resource] /
Staphylococcus aureus quickly develops resistance to antibiotics and poses a significant health threat to humans. New antibiotic targets are needed for the development of new antibiotics. Trans-translation has important roles in maintaining bacterial viability. Small molecules, KKL-35 and KKL-40, were recently identified as specific inhibitors of trans-translation. We have investigated the roles of trans-translation on S. aureus viability and the potential of KKL-35 and KKL-40 as antibiotics. We find that KKLs show bactericidal activity against multiple S. aureus strains at relatively low concentration. We also find that sub-lethal doses of KKLs make S. aureus more susceptible to antimicrobials. Neither KKL-35 nor KKL-40 are cytotoxic to human HeLa cells. Unfortunately, KKL-40 is inactivated by human serum. Therefore, new inhibitors will need to be identified in future studies. Notably, the development of resistance by S.aureus against KKLs remains at a low level. Therefore trans-translation is ...
Dual-acting riboswitch control of translation initiation and mRNA decay | PNAS
In contrast to btuB and thiM, our results show that the lysC riboswitch employs a different regulation mechanism, by directly modulating the cleavage of RNase E (Fig. 6B). Our data indicate that, in the absence of ligand, the riboswitch folds into the ON state that not only allows ribosome binding but also sequesters RNase E cleavage sites, thus ensuring efficient mRNA translation. However, in its ligand-bound form, the lysC riboswitch adopts the OFF state that concomitantly sequesters the RBS and exposes RNase E cleavage sites, thus effectively inhibiting translation and initiating mRNA decay. The location of RNase E cleavage sites in the riboswitch expression platform, and not in the ORF, strongly suggests that the lysC riboswitch directly controls the cleavage of the mRNA as a function of ligand binding. In such cases, the transcript stability and concomitant translation are reduced directly through endoribonucleolytic action, a situation referred to as nucleolytic repression (Fig. 6B) ...
Hok/sok system - Wikipedia
The hok/sok system is a postsegregational killing mechanism employed by the R1 plasmid in Escherichia coli. It was the first type I toxin-antitoxin pair to be identified through characterisation of a plasmid-stabilising locus. It is a type I system because the toxin is neutralised by a complementary RNA, rather than a partnered protein (type II toxin-antitoxin). The hok/sok system involves three genes: hok, host killing - a long lived (half-life 20 minutes) toxin sok, suppression of killing - a short lived (half-life 30 seconds) RNA antitoxin mok, modulation of killing - required for hok translation When E. coli undergoes cell division, the two daughter cells inherit the long-lived hok toxin from the parent cell. Due to the short half-life of the sok antitoxin, daughter cells inherit only small amounts and it quickly degrades. If a daughter cell has inherited the R1 plasmid, it has inherited the sok gene and a strong promoter which brings about high levels of transcription. So much so that in an ...
Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic...
In this paper, the Escherichia coli cell is considered as a system designed for rapid growth, but limited by the medium. We propose that this very design causes the cell to become subsaturated with precursors and catalytic components at all levels of macromolecular biosynthesis and leads to a molecular sharing economy at a high level of competition inside the cell. Thus, the promoters compete with each other in the binding of a limited amount of free RNA polymerase and the ribosome binding sites on the mRNA chains compete with each other for the free ribosomes. The macromolecular chain elongation reactions sequester a considerable proportion of the total amount of RNA polymerase and ribosomes in the cells. We propose that the degree of subsaturation of the macromolecular biosynthetic apparatus renders a variable fraction of RNA polymerase and ribosomes unavailable for the initiation of new chain synthesis and that this, at least in part, determines the composition of the cell as a function of ...
Therapeutics for Drug-Resistant Bacterial Infections: Inhibitors of Bacterial RNA Polymerase<...
TY - PAT. T1 - Therapeutics for Drug-Resistant Bacterial Infections: Inhibitors of Bacterial RNA Polymerase. AU - Ebright, Richard. AU - Feng, Yu. AU - Zhang, Yu. PY - 2017/1. Y1 - 2017/1. N2 - Invention Summary: Bacterial infectious diseases kill 100,000 persons each year in the US and 11 million persons each year worldwide, representing nearly a fifth of deaths each year worldwide. For six decades, antibiotics have been our bulwark against bacterial infectious diseases. However, now this bulwark is collapsing. For all major bacterial pathogens, strains resistant to at least one current antibiotic have arisen, and, for several bacterial pathogens, strains resistant to all current antibiotics have arisen. There is an urgent national and international need for new classes of antibacterial agents effective against bacterial pathogens resistant to current antibacterial agents. Rutgers researchers have identified five new drug targets within the structure of bacterial RNA polymerase, the enzyme ...
Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in...
In 1995, the release of the first fully sequenced bacterial genome heralded a new era of bacterial genomic research (21). Over the past 20 years, the number of sequenced bacterial genomes has risen exponentially, and new research strategies, techniques, and applications have emerged to exploit the opportunities that these resources provide. While raw genomic sequence data are valuable, the availability of fully annotated genome sequences, outlining the positions of known genes and genomic features, dramatically increases their utility. Global expression analysis techniques such as microarrays and RNA-seq depend heavily on annotated genome sequences as a reference source for genes in the bacterial cell. These techniques have proved extremely useful; however, recently, certain limitations to their application are becoming apparent. A major concern in this regard is that they do not provide expression data for genes that are not included in genome annotation files. Bacterial sRNAs represent a class ...
Riboregulation in |i|Neisseria meningitidis|/i
In this thesis, we first investigated the regulon of the alternative sigma factor E by employing next-generation sequencing of both the genome and the transcriptome of N. meningitidis wildtype and an overexpression mutant. Its small regulatory repertoire compared to E. coli and its lack of regulating proteins involved in the outer membrane stress response is a prime example of divergent evolution of superficially similar regulatory systems in these two gram-negative bacteria. Second, the chaperon protein Hfq and its role in riboregulation by facilitating RNA-RNA interactions between a sRNA and its mRNA target(s) was investigated by studying its regulatory proteome in depth. Finally, the regulatory roles of two sRNAs, NmsRs and NrrF are described; showing their extensive involvement in the related cell biological processes of carbohydrate metabolism and oxidative phosphorylation by simultaneously downregulating multiple enzymes involved in these pathways ...
Need Input on Northern With Bacterial RNA
Christine Ward (mjward at vt.edu) wrote: : Greetings Netters: : I could really use some input from those of you with experience doing : Northerns on bacterial RNA. I have been using the Chomczynski (sp?) : and Sacchi procedure (AGPC procedure, Analytical Biochem.) to isolate : total RNA from a Gram negative organism. I have upscaling the original : procedure by a factor of 10 to isolate RNA from about 1 x 10e9 organisms. : When I do my Northerns, all I see is one really good smear. : When I stain the total RNA on the membrane with methylene blue, my markers : look OK, and I can clearly see the 23S and 16S rRNA bands in my RNA prep. : I believe my technique is quite good--using clean pipettors, DEPCd solutions, : storing RNA in formamide etc. OD260/OD280 is about 1.8, which supposedly : indicates pure RNA. My gut instinct is that I have some residual : protein (and therefore RNAse carryover), OR that the particular RNA I am : trying to detect has a very rapid turnover rate (even though the ...
Biomiga Bacterial RNA Kit - R6616-01 [R6616-01] - £128.00 : Interlink Scientific Services Limited, Sales and Maintenance Of...
Interlink Scientific Services Limited Biomiga Bacterial RNA Kit - R6616-01 [R6616-01] - Description : Introduction The EZgeneTM total RNA kit provides an easy and fast method for isolating total RNA from Gram-positive (B. subtilis) Or Gram-negative (E. coli) Bacteria within 30 min. Only trace genomic DNA exists in the purified RNA, which can be eliminated by DNase I treatment (See detail in the protocol) when it is necessary. Storage and StabilityDNase I (optional) and lysozyme should be stored at -20℃. All other components can be stored at room temperature. All kit components are guaranteed for 12 monthsr from the date of purchasing.Kit ContentsCatalog#R6616-00R6616-01R6616-02Preps450250Buffer LY 2.4 mL28 mL135 mLBuffer RB3 mL30 mL135 mLRNA Wash Buffer *2 mL20 mL3 x 24 mLDEPC-Treated dH2O 500 µL10 mL30 mLDNase Stop Buffer 200 µL2.4 mL12 mLezBind Columns450250Collection Tubes8100500Lysozyme 1.2 mg15 mg75 mgUser Menu111Note４DNase I are not supplied. They could be purchased from Biomiga. Before
DiVA - Search result
It is nowadays widely accepted that non-coding RNAs play important roles in post-transcriptional regulation of genes in all kingdoms of life. In bacteria, the largest group of RNA regulators are the small RNAs (sRNAs). Almost all sRNAs act through anti-sense base-pairing with target mRNAs, and by doing so regulate their translation and/or stability. As important modulators of gene expression, sRNAs are involved in all aspects of bacterial physiology. My studies aimed to deepen our understanding of the mechanisms behind sRNA-mediated gene regulation. We have shown that translation of the di-guanylate-cyclase YdaM, a major player in the biofilm regulatory cascade, is repressed by the sRNAs OmrA and OmrB. OmrAB require the RNA chaperone protein Hfq for efficient regulation. Interestingly, our results suggest a non-canonical mechanism for Hfq-mediated ydaM-OmrA/B base-pairing. Instead of serving as RNA interaction platform, Hfq restructures the ydaM mRNA to enable sRNA binding. We also addressed the ...
Difference between revisions of User:Jarle Pahr/Degradation tags - OpenWetWare
Turnover of Endogenous SsrA-tagged Proteins Mediated by ATP-dependent Proteases in Escherichia coli*[S with combining enclosing square]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516991 ...
Structure and Interactions of Escherichia coli Ribosomal Ribonucleic Acid | Biochemical Society Transactions
Thank you for your interest in spreading the word about Biochemical Society Transactions.. NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.. ...
Transfer RNA molecule - Stock Image G110/0742 - Science Photo Library
Transfer RNA molecule. Computer artwork of the double helix of tRNA (transfer ribonucleic acid), formed by spiralling paired strands of sugar phosphates, linked by nucleotide base pairs. Transfer RNA carries amino acid groups to ribosomes for protein synthesis. Protein synthesis is controlled by DNA (deoxyribonucleic acid, not seen) in the nucleus of a cell. - Stock Image G110/0742
Transfer RNA molecule - Stock Image G110/0740 - Science Photo Library
Transfer RNA molecule. Computer artwork of the double helix of tRNA (transfer ribonucleic acid), formed by spiralling paired strands of sugar phosphates, linked by nucleotide base pairs. Transfer RNA carries amino acid groups to ribosomes for protein synthesis. Protein synthesis is controlled by DNA (deoxyribonucleic acid, not seen) in the nucleus of a cell. - Stock Image G110/0740
Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA | The EMBO Journal
The vast majority of currently known ProQ‐binding sRNAs are of unknown function (Smirnov et al, 2016). We have previously observed that asRNAs are enriched in the ProQ interactome, suggesting that this protein may be involved in gene expression regulation via perfect base pairing with cis‐encoded mRNA targets. Some of these asRNAs and their regulatory mechanisms have been characterized, including members of the Sib, Rdl, and IstR families of type I antitoxins, the transposon‐associated art200 and the intergenic cis‐acting SraG sRNAs (Darfeuille et al, 2007; Ellis et al, 2015; Fontaine et al, 2016; Han et al, 2010; Kawano, 2012; Mok et al, 2010). Some other ProQ‐associated sRNAs are derived from transcriptional attenuators (SraF, rimP leader) or have been proposed to function as trans‐encoded base‐pairing sRNAs (SraL) (Argaman et al, 2001; Naville & Gautheret, 2010; Nechooshtan et al, 2009; Plumbridge et al, 1985; Silva et al, 2013; Sittka et al, 2008). Recently, one of the ...
Scleraxis messenger ribonucleic acid is expressed in C2C12 myoblasts and its level is down-regulated by bone morphogenetic...
Fingerprint Dive into the research topics of Scleraxis messenger ribonucleic acid is expressed in C2C12 myoblasts and its level is down-regulated by bone morphogenetic protein-2 (BMP2). Together they form a unique fingerprint. ...
Go to a Shamen for Tinnitus?
The first two times we went, he didn´t show up. I stared to wonder if it was a sign that I shouldn´t go. But my friend said, that he was just super busy and sometimes just forgets, as he is Peruvian.. Well, the third time we went he was there. No, let me rephrase that. The third time we went, he came to „his office after an hour of waiting. „His office because it is basically his house, where he reserved a room to welcome his patients. It is a big door on the street, you go in and set foot into a backyard. Here are several buildings, the house of his family, some small stables and a house for visitors. The room I went into to talk to him looked like it had been a stable and he decorated it differently, it was dark and had no windows, oh wait, it had one tiny window, but it didn´t really let the sunlight in.. I had exected a very spiritual person, you know the ones you see on pictures. They have long hair and wear these special clothes, but he was just a normal person. A farmer, comming ...
Rn28s1 28S ribosomal RNA [ Mus musculus] annotation in GTF file
Hi,. I looked at the GTF file M13 from the GENCODE (https://www.gencodegenes.org/mouse_releases/13.html) and I found the gene name for the 18S ribosomal RNA (Rn18s), but I couldnt find the 28S ribosomal RNA (Rn28s). Does anyone know about it? Does it call in other name?. Thanks. ...
The ribonucleic acid content of chromosomes - CSHL Scientific Digital Repository
Kaufmann, Berwind Petersen, McDonald, Margaret R., Gay, Helen (November 1948) The ribonucleic acid content of chromosomes. Genetics, 33 (6). p. 615. ...
Discover Whats New With The Latest Anti-Aging Treatments… One thing we can be certain about is that there are many new and exciting treatments, devices, techniques and products coming out all the time. The overall trend is that the latest anti-ageing treatments are kinder, gentler and more effective on our skin than ever before. Which…. Read More ...
Altered expression of mitochondrial 16S ribosomal RNA in p53-de¢cientmouse embryos revealed by
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Everyone* knows that DNA codes for proteins. In between the DNA and the protein though, there is an intermediate molecule called RNA - ribonucleic acid (DNA is deoxyribonucleic acid). RNA is similar to DNA in many respects - long chain of bases that we can consider letters, which form a code - but its less…
Shutting down genes in cancer, bacteria, and viruses
Ribonucleic acid (RNA) interference is a relatively new technique in which small molecules called short interfering RNA (siRNA) can be inserted into cells to turn off a chosen gene.
DNA and RNA codon tables
Bacterial, archaeal and plant plastid 11 See translation table 1. Alternative yeast nuclear 12 CTG CUG Ser (S) Leu (L) ... In RNA, it is replaced with uracil (U). This is the only difference between the standard RNA codon table and the standard ... Standard RNA codon table. Amino-acid biochemical properties Nonpolar Polar Basic Acidic ↓ Termination: stop codon * ... RNA codon involved Translation with this code Standard translation Notes Standard 1 Includes translation table 8 (plant ...
"Large variations in bacterial ribosomal RNA genes". Molecular Biology and Evolution. 29 (10): 2937-48. doi:10.1093/molbev/ ... The two RNA polymerases may recognize and bind to different kinds of promoters within the chloroplast genome. The ribosomes ... Chloroplasts make all of a cell's purines and pyrimidines-the nitrogenous bases found in DNA and RNA. They also convert ... Protein synthesis within chloroplasts relies on two RNA polymerases. One is coded by the chloroplast DNA, the other is of ...
Mehta, Preeti; Woo, Perry; Venkataraman, Krithika; Karzai, A. Wali (2012). Bacterial Regulatory RNA. Methods in Molecular ...
She has also played a major role in the discovery and characterization of bacterial small RNAs. Gottesman was born on May 19, ... Small RNA are short RNA sequences that have a wide variety of functions within cells. They have been shown to be vital in cell ... The small RNAs have also been shown to be a factor in certain diseases such as cancer, diabetes, and liver disease. The ATP- ... The DsrA small RNA helps to translate the RpoS factor by binding to the RpoS leader sequence. Elected to the National Academy ...
List of recombinant proteins
Bacterial Regulatory RNA. Methods in Molecular Biology. 905. pp. 273-89. doi:10.1007/978-1-61779-949-5_18. ISBN 978-1-61779-948 ... Dirks-Hofmeister ME, Kolkenbrock S, Moerschbacher BM (2013). "Parameters that enhance the bacterial expression of active plant ... "Ribosome purification approaches for studying interactions of regulatory proteins and RNAs with the ribosome". ...
Small RNA. Bacterial small RNAs play important roles in many cellular processes; 11 small RNAs have been experimentally ... Type strain of Enterococcus faecalis at BacDive - the Bacterial Diversity Metadatabase ... "Small RNAs in vancomycin-resistant Enterococcus faecium involved in daptomycin response and resistance". Scientific Reports. 7 ... "Genome-Wide Identification of Small RNAs in the Opportunistic Pathogen Enterococcus faecalis V583". PLOS ONE. 6 (9): e23948. ...
5 prime ureB sRNA
Bacterial small RNA Wen, Y; Feng, J; Scott, DR; Marcus, EA; Sachs, G (January 2011). "A cis-encoded antisense small RNA ... In molecular biology, 5' ureB sRNA is a small RNA. It is located at the 5' end of the ureB gene in the urease gene cluster, and ... Wen, Y; Feng, J; Sachs, G (February 2013). "Helicobacter pylori 5'ureB-sRNA, a cis-encoded antisense small RNA, negatively ...
Proline-Rich Coiled Coil 1
No evidence of RNA alternate splicing was determined. Kagachi, Chihiro (2007). "A Comparison of Bacterial Genomes". Seikagaku- ...
"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity". Science. 337 (6096): 816-21. Bibcode:2012Sci ... Chen I, Dubnau D (March 2004). "DNA uptake during bacterial transformation". Nature Reviews. Microbiology. 2 (3): 241-9. doi: ... In 2010, scientists at the J. Craig Venter Institute created the first synthetic genome and inserted it into an empty bacterial ... July 2010). "Creation of a bacterial cell controlled by a chemically synthesized genome". Science. 329 (5987): 52-6. Bibcode: ...
Ames TD, Breaker RR (January 2011). "Bacterial aptamers that selectively bind glutamine". RNA Biol. 8 (1): 82-89. doi:10.4161/ ... functions as an RNA structure. A distinct predicted non-coding RNA called yfr14 overlaps both yfr6 and Downstream-peptide RNAs ... Downstream-peptide RNAs overlap a predicted non-coding RNA called yfr6 that is over 200 nucleotides in length, but it was ... The Downstream-peptide motif has a structural resemblance to a different candidate RNA structure called the glnA RNA motif ...
For RNA-based phages, RNA replicase is synthesized early in the process. Proteins modify the bacterial RNA polymerase so it ... ICTV classification of prokaryotic (bacterial and archaeal) viruses Order. Family. Morphology. Nucleic acid. Examples ... RNA phage such as MS2 have the smallest genomes of only a few kilobases. However, some DNA phages such as T4 may have large ... "Novel Phage Therapy Saves Patient with Multidrug-Resistant Bacterial Infection". UC Health - UC San Diego. Retrieved 2018-05-13 ...
Bacterial small RNAs play critical roles in virulence and stress/adaptation responses. Although their specific functions have ... "Bacterial small RNAs in the Genus Rickettsia". BMC Genomics. 16: 1075. doi:10.1186/s12864-015-2293-7. ISSN 1471-2164. PMC ... 1989). Approved Lists of Bacterial Names (amended ed.). Washington, DC: American Society for Microbiology. Truper H.G.; De' ... the bacterial genus Rickettsia was named after Howard Taylor Ricketts, in honor of his pioneering work on tick-borne spotted ...
Peter G. Schultz
"Bacterial Genome Containing Chimeric DNA-RNA Sequences". Journal of the American Chemical Society. 140 (36): 11464-11473. doi: ... One goal of this work is to culture the yeast-bacteria hybrids and see whether the bacterial genome evolves to increase the ... A bacterial organism has been generated which biosynthesizes a novel, previously unnatural amino acid (p-aminophenylalanine) ... and bacteria whose chromosomes are hybrids which include both RNA and DNA. In order to probe details of the traditionally ...
Kortmann J, Narberhaus F (March 2012). "Bacterial RNA thermometers: molecular zippers and switches". Nature Reviews. ... Upstream activation sequence RNA List of cis-regulatory RNA elements Polyadenylation signals, mRNA AU-rich element, mRNA Other ... Only once this region has been bound with the appropriate set of TFs, and in the proper order, can RNA polymerase bind and ... The term "silencer" can also refer to a region in the 3' untranslated region of messenger RNA, that binds proteins which ...
The genome has one open reading frame which encodes the RNA-dependent RNA polymerase (RdRp). The genome is associated with the ... 2020). "Narnaviruses: Novel players in fungal-bacterial symbioses". The ISME Journal. doi:10.1038/s41396-020-0638-y.CS1 maint: ... Replication follows the positive-strand RNA virus replication model. Positive-strand RNA virus transcription is the method of ... The genus has two species: Narnaviridae Narnavirus Saccharomyces 20S RNA narnavirus Saccharomyces 23S RNA narnavirus ICTV. " ...
Lim K, Furuta Y, Kobayashi I (October 2012). "Large variations in bacterial ribosomal RNA genes". Molecular Biology and ... tRNA replication origin regions tRNA small RNA ribosomal protein replication origin regions ribosomal RNA tRNAs ribosomal RNA ... The two RNA polymerases may recognize and bind to different kinds of promoters within the chloroplast genome. The ribosomes in ... While similar to bacterial ribosomes, chloroplast translation is more complex than in bacteria, so chloroplast ribosomes ...
Mobile genetic elements
Hausner, Georg; Hafez, Mohamed; Edgell, David R. (2014-03-10). "Bacterial group I introns: mobile RNA catalysts". Mobile DNA. 5 ... Viruses: They are viral agents composed of a molecule of genetic material (DNA or RNA) and with the ability to form complex ... Satellite nucleic acids: they are DNA or RNA molecules, which are encapsidated as a stowaway in the virions of certain helper ... Retroposons: they are exclusive transposons of mammals that move in the genome, being transcribed into DNA and then into RNA, ...
Heat shock protein
Some bacterial heat shock proteins are upregulated via a mechanism involving RNA thermometers such as the FourU thermometer, ... Narberhaus F (2010). "Translational control of bacterial heat shock and virulence genes by temperature-sensing mRNAs". RNA ... 7 (1): 84-9. doi:10.4161/rna.7.1.10501. PMID 20009504.. *^ Walter S, Buchner J (April 2002). "Molecular chaperones--cellular ... HSF1 inhibition by a potent RNA aptamer attenuates mitogenic (MAPK) signaling and induces cancer cell apoptosis. ...
Advances in confocal microscopy at the end of the 20th century identified proteins, RNA or carbohydrates localising to many non ... Muthunayake, Nisansala S.; Tomares, D.T; Childers, W. Seth; Schrader, Jared M. (May 2020). "Phase‐separated bacterial ... Bacteria Ribonucleoprotein Bodies (BR-bodies)- In recent studies it has been shown that bacteria RNA degradosomes can assemble ... RNA and other biopolymers into either colloidal emulsions, liquid crystals, solid crystals or aggregates within cells. The ...
Bechhofer DH, Deutscher MP (June 2019). "Bacterial ribonucleases and their roles in RNA metabolism". Critical Reviews in ... Hsiao YY, Yang CC, Lin CL, Lin JL, Duh Y, Yuan HS (April 2011). "Structural basis for RNA trimming by RNase T in stable RNA 3'- ... It is inhibited by both double stranded DNA and RNA, as well as cytosine residues on the 3' end of RNA. Two cytosines at the 3 ... Li Z, Pandit S, Deutscher MP (January 1999). "Maturation of 23S ribosomal RNA requires the exoribonuclease RNase T". RNA. 5 (1 ...
Molecular models of DNA
Molecular modeling of RNA polymerase. Molecular modeling of a bacterial DNA primase template. Molecular modeling of DNA ... These include computer molecular models of molecules as varied as RNA polymerase, an E. coli, bacterial DNA primase template ...
Mycobacterium tuberculosis sRNA
Bacillus subtilis sRNAs Bacterial small RNA Brucella sRNA Caenorhabditis elegans sRNA Escherichia coli sRNA Pseudomonaa sRNA ... Livny J, Waldor MK (April 2007). "Identification of small RNAs in diverse bacterial species". Current Opinion in Microbiology. ... The small RNA (sRNA) families were identified through RNomics - the direct analysis of RNA molecules isolated from cultures of ... "A screen for non-coding RNA in Mycobacterium tuberculosis reveals a cAMP-responsive RNA that is expressed during infection". ...
Peters, JM; Vangeloff, AD; Landick, R (7 October 2011). "Bacterial transcription terminators: the RNA 3'-end chronicles". ... In intrinsic termination, the RNA transcript doubles back and base pairs with itself, creating an RNA stem-loop, or hairpin, ... This bacteriophage protein 7 stops transcription termination by blocking the RNA polymerase (RNAP) RNA-exit channel and ... allowing it to unwind and dissociate from the RNA polymerase. Overall, the modified RNA structure is what terminates ...
Richard H. Ebright
"Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex". Cell. 108 (5): ... the demonstration that bacterial transcription-translation coupling involves direct physical bridging of RNA polymerase and a ... and the identification of novel antibacterial drug targets in bacterial RNA polymerase. In 1994, Ebright was awarded the ... "Opening and closing of the bacterial RNA polymerase clamp". Science. 337 (6094): 591-595. Bibcode:2012Sci...337..591C. doi: ...
Qian Z, Macvanin M, Dimitriadis EK, He X, Zhurkin V, Adhya S (August 2015). "A New Noncoding RNA Arranges Bacterial Chromosome ... Several of them are non-coding RNAs, and one such RNA named naRNA4 (nucleoid-associated RNA 4), is encoded in a repetitive ... Moreover, HU preferentially binds to RNA containing secondary structures and an RNA-DNA hybrid in which the RNA contains a nick ... which cleaves RNA in an RNA-DNA hybrid and the complex binds to an antibody specific to RNA-DNA hybrids. Because of its helical ...
... causing the dissociation of the RNA polymerase from the template and the release of the new RNA strand. In RNA polymerase II, ... Rho factor is widely present in different bacterial sequences and is responsible for the genetic polarity in E. coli. It works ... In RNA polymerase I, Transcription termination factor, RNA polymerase I binds downstream of the pre-rRNA coding regions, ... When the Rho protein reaches the RNA polymerase complex, transcription is terminated by dissociation of the RNA polymerase from ...
... Bacterial small RNA. (Lister 1873). Schleifer et al. 1986. Subspecies. ... "RNA Biology. 13 (3): 353-366. doi:10.1080/15476286.2016.1146855. ISSN 1547-6286. PMC 4829306 . PMID 26950529.. ... "Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon ... Hundreds of novel small RNAs were identified by Meulen et al. in the genome of L. lactis MG1363. One of them: LLnc147 was shown ...
Human gene is no longer transcribed into RNA. Alasdair J Edgar (2005) Mice have a transcribed L-threonine aldolase/GLY1 gene, ... pdf Bell SC; Turner JM (1973). "Bacterial threonine aldolase and serine hydroxymethyltransferase enzyme". Biochem. Soc. Trans. ...
Single cell sequencing
"Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells". Nature Communications ... To target larger non-poly(A) RNAs, such as long non-coding mRNA, histone mRNA, circular RNA, and enhancer RNA, size selection ... Standard methods such as microarrays and bulk RNA-seq analysis analyze the expression of RNAs from large populations of cells. ... Current scRNA-seq protocols involve isolating single cells and their RNA, and then following the same steps as bulk RNA-seq: ...
Bacterial small RNAs (sRNA) are an important class of regulatory molecules. Many Brucella sRNAs have been identified. Infection ...
Finding the virus, viral RNA, or antibodies in blood. Differential diagnosis. Malaria, cholera, typhoid fever, meningitis, ... balance as well as treating any bacterial infections that may develop. Dialysis may be needed for kidney failure, and ... Ebolaviruses contain single-stranded, non-infectious RNA genomes. Ebolavirus genomes contain seven genes including 3'-UTR- ... The specific diagnosis of EVD is confirmed by isolating the virus, detecting its RNA or proteins, or detecting antibodies ...
RNA editing in plastidsEdit. RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior ... Because it is similar to bacterial amino acid transporters and the mitochondrial import protein Tim17 (translocase on the i ... Chloroplasts also contain a mysterious second RNA polymerase that is encoded by the plant's nuclear genome. The two RNA ... Among land plants, the contents of the chloroplast genome are fairly similar-they code for four ribosomal RNAs, 30-31 tRNAs ...
Evolution of biological complexity
1993). "On the evolution of RNA editing". Trends in Genetics. 9 (8): 265-268. doi:10.1016/0168-9525(93)90011-6.. ... "Being Pathogenic, Plastic, and Sexual while Living with a Nearly Minimal Bacterial Genome". PLoS Genet. 3 (5): e75. doi ... Daniel, Chammiran; Behm, Mikaela; Öhman, Marie (2015). "The role of Alu elements in the cis-regulation of RNA processing". ... RNA editing may have arisen in Trypanosoma brucei. ...
Fluorescence in situ hybridization
Single-molecule RNA FISH. Single-molecule RNA FISH, also known as Stellaris® RNA FISH, is a method of detecting and ... Bacterial FISH probes are often primers for the 16s rRNA region. FISH is widely used in the field of microbial ecology, to ... doi:10.1261/rna.2701111. PMC 3096040. PMID 21518807.. *^ a b c Bernasconi, B.; Karamitopolou-Diamantiis, E.; Tornillo, L.; ... RNA Fluorescent In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent ...
Abel-Santos, E (editor) (2012). Bacterial Spores: Current Research and Applications. Caister Academic Press. ISBN 978-1-908230- ... and the sigma factor subunits of RNA polymerase. ... Gram-negative bacteria only: Bacterial outer membrane *Porin. * ... Further information: Bacterial morphological plasticity. Under conditions of starvation, especially the lack of carbon and ... While the rest of a bacterial cell may stain, the endospore is left colourless. To combat this, a special stain technique ...
David W. Deamer
Loman, N.J.; Quick, J.; Simpson, J.T. (2015). "A complete bacterial genome assembled de novo using only nanopore sequencing ... and polyuridylic acid as homopolymers or as segments within single RNA molecules". Biophysical Journal. 77 (6): 3227-3233. doi: ... could distinguish between purine and pyrimidine bases in single RNA molecules. In 2007, Oxford Nanopore Technologies (ONT) ...
RNA polymerase - Simple English Wikipedia, the free encyclopedia
All are similar and related to each other and to bacterial RNAP:. *RNA polymerase I synthesizes a pre-rRNA which will form the ... Non-coding RNA or "RNA genes". These are a broad class of genes that encode RNA which is not translated into protein. The most ... RNA polymerase IV synthesizes siRNA in plants.. *RNA polymerase V synthesizes RNAs involved in siRNA-directed ... RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol. ...
... family members are homologous to the bacterial RecA, Archaeal RadA and yeast Rad51. The protein is highly conserved ... messenger RNA. . Breast cancer (progesteron receptor negative). Over-expression. -. messenger RNA. . ...
Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal RNA polymerase being ... Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular RNA ... although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein- ... while archaeal flagella appear to have evolved from bacterial type IV pili. In contrast to the bacterial flagellum, which ...
bacterial RNA polymerase: rpoB. *eukaryotic RNA polymerase: RNA polymerase II. Termination. (bacterial,. eukaryotic). * ... the TATA box is found at RNA polymerase II promoter regions, although some in vitro studies have demonstrated that RNA ... "RNA polymerase III accurately initiates transcription from RNA polymerase II promoters in vitro". The Journal of Biological ... TATA-binding protein (TBP) can be recruited in two ways, by SAGA, a cofactor for RNA polymerase II, or by TFIID. When ...
Single particle analysis
This bacterial protein complex is a machine for folding other proteins, which get trapped within the shell. Fatty acid synthase ... Important information on protein synthesis, ligand binding and RNA interaction can be obtained using this novel technique at ...
A fundamental building block of RNA structure crucial to RNA function in diverse biological systems". EMBO Rep. 1 (1): 18-23. ...
cellular response to molecule of bacterial origin. • positive regulation of interferon-gamma production. • embryonic axis ... positive regulation of transcription from RNA polymerase II promoter. • negative regulation of cell proliferation. • signal ...
Bacteria - Simple English Wikipedia, the free encyclopedia
Bacterial evolution. Microbiological reviews 51 (2): 221-71. . *↑ Holland L. (1990). "Woese, Carl in the forefront of ... All modern ideas start with the sequence analysis of DNA and RNA. In 1987, Carl Woese, the forerunner of the molecular ... Bacterial cells do not have a nucleus, and most have no organelles with membranes around them. Most have a cell wall. They do ... The complete DNA sequence is known for many bacterial strains.. Shape[change , change source]. Bacteria vary widely in size and ...
ARNr 16S, a enciclopedia libre
"Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes". FEMS Microbiology ... "The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses". PLoS One 8 (2 ... "Comparative RNA function analysis reveals high functional similarity between distantly related bacterial 16 S rRNAs". ... Schmidt TM, Relman DA (1994). Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods in ...
... and use of endonuclease digestion of PCR-amplified RNA to demonstrate lack of mRNA expression from the second allele". American ...
Arqueas, a enciclopedia libre
Werner F (2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395-404. PMID 17697097. doi: ... 1994). "Evolutionary relationships of bacterial and archaeal glutamine synthetase genes". J Mol Evol. (38(6)): 566-576.. ... Ng SY, Chaban B, Jarrell KF (2006). "Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and ... Cavalier-Smith T. (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial ...
ವಂಶವಾಹಿ - ವಿಕಿಪೀಡಿಯ
೪೧.೦ ೪೧.೧ Eddy SR (December 2001). "Non-coding RNA genes and the modern RNA world". Nat. Rev. Genet. 2 (12): 919-29. doi: ... Ochman, H; Lawrence, JG; Groisman, EA (18 May 2000). "Lateral gene transfer and the nature of bacterial innovation.". Nature ... ೯೦.೦ ೯೦.೧ Claverie JM (September 2005). "Fewer genes, more noncoding RNA". Science 309 (5740): 1529-30. Bibcode:2005Sci... ... Domingo, E; Escarmís, C; Sevilla, N; Moya, A; Elena, SF; Quer, J; Novella, IS; Holland, JJ (June 1996). "Basic concepts in RNA ...
Nudler E, Mironov AS (Jan 2004). "The riboswitch control of bacterial metabolism". Trends in Biochemical Sciences. 29 (1): 11-7 ... Atkins JF, Gesteland RF, Cech T (2006). The RNA world: the nature of modern RNA suggests a prebiotic RNA world. Plainview, N.Y ... of RNAs with molecular properties predicted for RNAs of the RNA World constitutes an additional argument supporting the RNA ... Properties of RNA. The properties of RNA make the idea of the RNA world hypothesis conceptually plausible, though its ...
Innate immune system
RNA silencing mechanisms are also important in the plant systemic response, as they can block virus replication. The ... When host cells die, either by programmed cell death (also called apoptosis) or by cell injury due to a bacterial or viral ... Baulcombe D (September 2004). "RNA silencing in plants". Nature. 431 (7006): 356-63. Bibcode:2004Natur.431..356B. doi:10.1038/ ... For example, the Influenza A virus produces NS1 protein, which can bind to host and viral RNA, interact with immune signaling ...
효소 - 위키백과, 우리 모두의 백과사전
효소는 5,000가지 이상의 생화학 반응 유형들을 촉매하는 것으로 알려져 있다. 대부분의 효소들은 단백질이지만, 일부 효소들은 촉매 기능을 가지고 있는 RNA 분자이다. 촉매 기능을 가지고 있는 RNA를 리보자임이라고 한다 ... Fisher JF, Meroueh SO, Mobashery S (February 2005). "Bacterial resistance to beta-lactam antibiotics: compelling opportunism, ... 리보자임이라고 불리는 소수의 RNA 기반 생물학적 촉매가 존재하며, 리보자임은 단독으로 또는 단백질과 복합체를 형성하여 작용할 수 있다. 리보자임들 중 가장 일반적인 것은 촉매 기능을 가진 RNA와 단백질의 복합체인 리보솜이다. ... 이와 유사한 교정 기작은 RNA 중합효소, 아미노아실 tRNA 합성효소, 리보솜에서도 발견된다. ...
... it recruits autophagy adaptor such as NDP52 leading to the formation of an autophagosome and bacterial degradation. ... detecting single stranded RNA. Following activation of the toll-like receptor, intracellular signaling cascades are initiated, ... "Subversion of cellular autophagosomal machinery by RNA viruses". PLoS Biol. 3 (5): e156. doi:10.1371/journal.pbio.0030156. PMC ... "Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion". Nature. 482 (7385): 414-8. doi ...
An autoantigen is usually a normal protein or protein complex (and sometimes DNA or RNA) that is recognized by the immune ... or because of viral or intracellular bacterial infection. The fragments are then presented on the cell surface in the complex ... named the hypothetical substances halfway between bacterial constituents and antibodies "substances immunogenes ou antigenes" ( ...
Rekayasa genetika bahasa Indonesia, ensiklopedia bebas
"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity". Science. 337 (6096): 816-21. Bibcode:2012Sci ... July 2010). "Creation of a bacterial cell controlled by a chemically synthesized genome". Science. 329 (5987): 52-6. Bibcode: ...
Euzeby, JP (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int. J. Syst. ... Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics". Syst. Appl. Microbiol. 14 (4): 305-310. doi: ... Palys, T; Nakamura LK; Cohan FM (1997). "Discovery and classification of ecological diversity in the bacterial world: the role ... Gurtler, V; Mayall BC (2001). "Genomic approaches to typing, taxonomy and evolution of bacterial isolates". Int. J. Syst. Evol ...
Tumor necrosis factor alpha
negative regulation of transcription from RNA polymerase II promoter. • positive regulation of NF-kappaB transcription factor ... other bacterial products, and Interleukin-1 (IL-1). In the skin, mast cells appear to be the predominant source of pre-formed ... positive regulation of transcription from RNA polymerase II promoter. • positive regulation of leukocyte adhesion to arterial ...
Type strain of Enterococcus faecium at BacDive - the Bacterial Diversity Metadatabase ... "Small RNAs in vancomycin-resistant Enterococcus faecium involved in daptomycin response and resistance". Scientific Reports. 7 ...
Instead, the naked viral RNA may alter the function of the cells through a mechanism similar to RNA interference, in which the ... Circulative viruses are protected inside aphids by the chaperone protein symbionin, produced by bacterial symbionts. Many plant ... The RNA carries genetic information to code for the production of new infectious particles. More recently virus research has ... Some viruses (e.g. tobacco mosaic virus (TMV)) have RNA sequences that contain a "leaky" stop codon. In TMV 95% of the time the ...
Common cold - Simple English Wikipedia, the free encyclopedia
A rhinovirus is an RNA-containing virus of the family Picornaviridae. There are 99 known types of viruses in this family of ... Secondary bacterial infections may occur resulting in sinusitis, pharyngitis, or an ear infection. It is estimated that ...
After her participation in the landmark research reporting the first synthesis of mammalian insulin in bacterial cells, Villa- ... focused on how proteins are produced from RNA in poliovirus. She dedicated her thesis to her colleagues David Rekosh and David ... when she was part of a team that discovered how bacterial cells could be used to generate insulin. ... "A bacterial clone synthesizing proinsulin". Proc Natl Acad Sci USA. 75 (8): 3727-31. Bibcode:1978PNAS...75.3727V. doi:10.1073/ ...
Need Input on Northern With Bacterial RNA
... Shahram Mori smori at nmsu.edu Mon Mar 13 02:39:14 EST 1995 *Previous message: Need ... RNA. : Does anyone know of any compounds I could add to my growing culture : to slow the RNA turnover rate without killing my ... Northerns on bacterial RNA. I have been using the Chomczynski (sp?) : and Sacchi procedure (AGPC procedure, Analytical Biochem ... When I stain the total RNA on the membrane with methylene blue, my markers : look OK, and I can clearly see the 23S and 16S ...
Systems-Level Analysis of Bacterial Regulatory Small RNA Networks | SpringerLink
The RNA landscape of all sequenced bacteria is littered with regulatory noncoding small RNAs (sRNA). Understanding the ... Nguyen TC, Cao X, Yu P et al (2016) Mapping RNA-RNA interactome and RNA structure in vivo by MARIO. Nat Commun 7:12023CrossRef ... Han K, Tjaden B, Lory S (2016) GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by ... Wong J., Pang I., Wilkins M., Tree J.J. (2018) Systems-Level Analysis of Bacterial Regulatory Small RNA Networks. In: Rajewsky ...
DNA/RNA tunnel of bacterial DNA dependent RNA polymerase (IPR021975) | InterPro | EMBL-EBI
DNA/RNA tunnel of bacterial DNA dependent RNA polymerase (IPR021975). Short name: RNApol_Rpb2_rif ... This domain is part of the beta subunit of bacterial DNA dependent RNA polymerase. This domain is the binding site for the ... antibacterial drug rifampin (and its analogues) which blocks the DNA/RNA tunnel and prevents initiation of transcription. ...
JCI - Bacterial control of host gene expression through RNA polymerase II
Bacterial control of host gene expression through RNA polymerase II. Nataliya Lutay,1 Ines Ambite,1 Jenny Grönberg Hernandez,1 ... Here, we identify a new mechanism of bacterial adaptation through broad suppression of RNA polymerase II-dependent (Pol II- ... Effects on RNA Pol II-dependent transcription. RNA Pol II controls eukaryotic gene expression through mRNA precursors, most ... Such bacterial modulation of host gene expression may be essential to sustain asymptomatic bacterial carriage by ensuring that ...
Comparative genomics boosts target prediction for bacterial small RNAs | PNAS
2012) Accessibility and conservation: General features of bacterial small RNA-mRNA interactions? RNA Biol 9(7):954-965. ... RNA-RNA interaction. Small RNAs (sRNAs) are ubiquitous and important regulators of gene expression in bacteria. The most common ... 2011) Bacterial small RNA regulators: Versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 3(12): ... 2011) Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc Natl Acad Sci USA 108(30): ...
Systems biology of bacterial small RNAs | Stavans Lab
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression | Nature
RNA can also serve in these capacities. For example, RNA has sufficient structural plasticity to form ribozyme1,2 and receptor3 ... It has also been proposed7,8,9,10,11,12 that certain messenger RNAs might use allosteric mechanisms to mediate regulatory ... Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. *Wade Winkler1. , ... Winkler, W., Nahvi, A. & Breaker, R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. ...
Computational analysis of bacterial RNA-Seq data
RNA-seq) have enabled tremendous leaps forward in our understanding of bacterial transcriptomes. However, computational methods ... for analysis of bacterial transcriptome data have not kept pace with the large and growing data sets generated by RNA-seq … ... Computational analysis of bacterial RNA-Seq data Nucleic Acids Res. 2013 Aug;41(14):e140. doi: 10.1093/nar/gkt444. Epub 2013 ... Our results suggest that Rockhopper can be used for efficient and accurate analysis of bacterial RNA-seq data, and that it can ...
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity | Science
RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945 (2009). doi:10.1016/j.cell.2009.07.040 pmid:19945378 ... Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477, 486 (2011). doi:10.1038/ ... A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity Message Subject. (Your Name) has forwarded a ... A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. By Martin Jinek, Krzysztof Chylinski, Ines ...
DNA & RNA Purification Bacterial Genomic Miniprep Kit | China-Mainland | Sigma-Aldrich
The GenElute Bacterial Genomic Kit provides a simple and convenient technique to isolate high quality DNA from both Gram(-) and ... Figure 3. Purified genomic DNA was isolated from various bacterial species using the GenElute Bacterial Genomic DNA kit. A 1 µg ... Typical DNA Yields with the GenElute Bacterial Genomic DNA Kit.. Source. Type of Media. Amount of Overnight Culture. OD600 per ... The GenElute Bacterial Genomic DNA Kit contains all of the reagents needed to purify genomic DNA from Gram negative bacteria ( ...
Bacterial RNA Isolation From Infected Eukaryotic Hosts ( Remove 90% of mamma...)
Bacterial,RNA,Isolation,From,Infected,Eukaryotic,Hosts,biological,advanced biology technology,biology laboratory technology, ... Works with any bacterial species ... Seamless integration with MICROB Express ... Enables microarray expression analysis with ... Remove 90% of mammalian RNA from ... Simple procedure takes less than 2 hours ... ... Mammalian and Bacterial Expression in One Vector. 3. Bacterial mRNA Isolation, Fast and Easy. 4. Bacterial RNA Isolation From ...
The bacterial Sm-like protein Hfq: a key player in RNA transactions. - PubMed - NCBI
The bacterial Sm-like protein Hfq: a key player in RNA transactions.. Valentin-Hansen P1, Eriksen M, Udesen C. ... The recent findings that Hfq assists in bimolecular RNA-RNA interactions and is similar structurally and functionally to ... The conserved RNA-binding protein Hfq, originally discovered in Escherichia coli as a host factor for Qbeta replicase, has ... control has been an area of increasing focus because the protein has been linked to the action of many versatile RNA-based ...
Microbial Transcriptomics | Bacterial and viral RNA-Seq
RNA-Seq) offers an unbiased approach for analyzing and quantifying bacterial, viral, and other microbial transcripts. ... RNA-Seq for Microbial Transcript Analysis. Bacterial, viral, and other microbial RNA-Seq experiments enable annotation and ... Note: If using the TruSeq RNA library prep kit, you will NOT need to extract RNA and transcribe to cDNA. If you use an RNA ... Next-generation RNA sequencing (RNA-Seq) of bacteria, viruses, and other microbes has become a standard method for analyzing ...
Bacterial small RNA - Wikipedia
Bacterial small RNAs (sRNA) are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, ... How ribonucleases dictate the rules in the control of small non-coding RNAs". RNA Biol. 5 (4): 230-243. doi:10.4161/rna.6915. ... a Staphylococcus regulatory RNA database". RNA. 21 (5): 1005-1017. doi:10.1261/rna.049346.114. ISSN 1469-9001. PMC 4408781. ... Vogel J, Papenfort K (December 2006). "Small non-coding RNAs and the bacterial outer membrane". Curr. Opin. Microbiol. 9 (6): ...
Bacterial RNA Isolation From Infected Eukaryotic Hosts | Thermo Fisher Scientific - AU
... is the only kit available for bacterial RNA enrichment from mixed host-bacterial RNA populations. A robust yet simple procedure ... MICROBEnrich depletes mammalian (host cell) RNA selectively, leaving behind highly enriched bacterial RNA. ... is the only kit available for bacterial RNA enrichment from mixed host-bacterial RNA populations. A robust yet simple procedure ... because no method has existed to isolate bacterial RNA away from host cell RNA, the corresponding analyses of bacterial ...
Systematic probing of the bacterial RNA structurome to reveal new functions.
2017 Feb 01;36:14-19 Authors: Ignatova Z, Narberhaus F Abstract RNA folds into intricate structures. Recent discoveries using ... approaches have revealed unprecedented structural complexity with a pivotal role in regulating RNA function and stability... ... Systematic probing of the bacterial RNA structurome to reveal new functions. Curr Opin Microbiol. ... Systematic probing of the bacterial RNA structurome to reveal new functions. Curr Opin Microbiol. 2017 Feb 01;36:14-19 Authors ...
Eukaryotic-type plastid nucleoid protein pTAC3 is essential for transcription by the bacterial-type plastid RNA polymerase |...
Eukaryotic-type plastid nucleoid protein pTAC3 is essential for transcription by the bacterial-type plastid RNA polymerase. ... Plastid transcription is mediated by two distinct types of RNA polymerases (RNAPs), bacterial-type RNAP (PEP) and phage-type ... Eukaryotic-type plastid nucleoid protein pTAC3 is essential for transcription by the bacterial-type plastid RNA polymerase ... Details for RNA extraction, RNA gel blotting analysis, and construction and analysis of plastid DNA tiling macroarrays are ...
Addgene: A bacterial Argonaute with noncanonical guide RNA specificity.
Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries. - PubMed -...
Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among ... Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries.. Lamichhane ... Selection of Peptides Targeting Helix 31 of Bacterial 16S Ribosomal RNA by Screening M13 Phage-Display Libraries ... Selection of Peptides Targeting Helix 31 of Bacterial 16S Ribosomal RNA by Screening M13 Phage-Display Libraries ...
Molecules | Free Full-Text | A Search for Dual Action HIV-1 Reverse Transcriptase, Bacterial RNA Polymerase Inhibitors | HTML
In turn, bacterial RNA polymerase (RNAP), a proven target for broad-spectrum antibacterial therapy [7,8,9], is structurally and ... Figure 2. Docking scores for previously reported triazole NNRTIs (1-11) , known bacterial RNA polymerase inhibitor (12) [14 ... Figure 2. Docking scores for previously reported triazole NNRTIs (1-11) , known bacterial RNA polymerase inhibitor (12) [14 ... Chopra, I. Bacterial RNA polymerase: A promising target for the discovery of new antimicrobial agents. Curr. Opin. Investig. ...
RNase E: at the interface of bacterial RNA processing and decay
It functions as part of a large macromolecular complex known as the RNA degradosome. Recent evidence suggests that this complex ... RNase E is an essential endonuclease that is abundant in many bacteria and plays an important part in all aspects of RNA ... RNase E: at the interface of bacterial RNA processing and decay Nat Rev Microbiol. 2013 Jan;11(1):45-57. doi: 10.1038/ ... I also propose a new model to rationalize the mechanism of RNase E action in the context of its localization in the bacterial ...
Beta-Prime Subunit of Bacterial RNA Polymerase - Proteopedia, life in 3D
Bacterial RNA Polymerase: New Insights on a Fundamental Molecular Machine. Introduction to RNAP. RNA polymerase (RNAP) is a ... 1 Bacterial RNA Polymerase: New Insights on a Fundamental Molecular Machine *1.1 Introduction to RNAP ... DNA Translocation and the RNA/DNA Hybrid in the active site channel provides the genetic information for RNA transcription. The ... RNA polymerase (RNAP) is an information-processing molecular machine that copies DNA into RNA. It is a multi-subunit complex ...
Perform Microarray Analysis with Limited Bacterial RNA | Thermo Fisher Scientific
Bacterial RNA from Infected Host RNA * An easy method of removing ,90% of host RNA from complex mixtures of host-bacterial ... input RNA amount, RNA quality, the bacterial species from which the RNA was isolated, and incubation time of the in vitro ... Enrich for Bacterial RNA- Even from Mixed Host-Pathogen Samples MICROBExpress™ to Purify Bacterial mRNA * The only system ... Linear Bacterial RNA Amplification MessageAmp II-Bacteria is based on a linear amplification method (Figure 1) in which the RNA ...
RCSB PDB - 4A8Q: Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo...
Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation ... Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation ... Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation ... RNA-dependent RNA polymerases (RdRps) are key to the replication of RNA viruses. A common divalent cation binding site, ...
RCSB PDB - 1MJI: DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIAL RIBOSOMAL PROTEIN L5/5S RRNA...
Molecules | Free Full-Text | Selection of Peptides Targeting Helix 31 of Bacterial 16S Ribosomal RNA by Screening M13 Phage...
Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m2G966 and m5C967, that are highly conserved among ... Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. ... naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, ... Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. ...
Sequence specific detection of bacterial 23S ribosomal RNA by TLR13 | eLife
IL-1β induction by bacterial RNA depends on MyD88 and UNC93b1, but not MAVS, TLR2, TLR4 or TLR7.. (A) L. salivarius total RNA ( ... Extraction of bacterial RNA from native and denatured agarose gel. Request a detailed protocol Total RNA isolated from either ... Isolation of bacterial RNA. Request a detailed protocol Lactobacillus salivarius (LAB) (ATCC 11741) and DH5α were grown in ... Bacterial RNA induces IL-1β through a MyD88- and Unc93b1-dependent pathway. Our previous studies showed that transfection of ...
Imaging bacterial protein expression using genetically encoded sensors composed of RNA
... Wenjiao Song,1,* Rita L. Strack,1,* and ... An RNA mutation that increases the affinity of an RNA-protein interaction. Nucleic Acids Res. 1987;15:10483-10493. [PMC free ... We tested the ability of each RNA to induce DFHBI fluorescence in a streptavidin-dependent manner (Fig. 1b). Several RNAs were ... This method involves fusing RNA aptamers that bind metabolites to Spinach2, a 98-nt RNA that switches on the fluorescence of 3, ...
PLOS Computational Biology: A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
Despite extensive experimental studies, the kinetic mechanism of the PPi release in bacterial RNA polymerases (RNAP) still ... which sharply contrasts with the more complex four-state hopping model in the yeast RNA polymerase (Pol II). We also observe a ... consistent with the faster transcription rate in the bacterial systems. Our results greatly improve our understanding of the ...
Bacterial small RNAs in the Genus Rickettsia | BMC Genomics | Full Text
Pain A, Ott A, Amine H, Rochat T, Bouloc P, Gautheret D. An assessment of bacterial small RNA target prediction programs. RNA ... Comparison of sRNA predictions and five well-known bacterial sRNAs (6S RNA, α-tmRNA, rpsL_ricks, 4.5S RNA, RNaseP_bact_a) ... Out of approximately 5 % bacterial total RNA, 95 % is composed of ribosomal and transfer RNA, while the remaining 5 % of the ... Liu JM, Camilli A. A broadening world of bacterial small RNAs. Current Opinion in Microbiology. 2010;13(1):18-23.PubMed Central ...
BacteriaSRNAsPathogensGeneMRNAProteinsMoleculesRibosomalAbstractPathogenRegulatorySpeciesGenomeEukaryoticInfectionsInfectionGenomesMechanismsRRNATranscriptionEscherichiaGenesRegulateSubunit2016SynthesisPost-transcriptional regulatorsPurificationViralVivoRegulationRegulatorsMolecularVirulenceQuantitation of bacterialTranscriptomesPredictionTranscriptome analysisVirusesCDNADiverse bacterialHigh-throughput2017ColiProtein-RNA complexSequencingBiologyDetectionFingerprintRibonucleaseSpecific bacterialGenomicHybridizationSRNA targetResistance to antibioticsAnalysesStabilityAnalysisTranscriptsTargetsApproachesMRNAsPolymerasesTranscriptomics
- to slow the RNA turnover rate without killing my bacteria? (bio.net)
- regarding RNA isolation from bacteria would post some suggestions. (bio.net)
- The RNA landscape of all sequenced bacteria is littered with regulatory noncoding small RNAs (sRNA). (springer.com)
- Miranda-Rios, J., Navarro, M. & Soberón, M. A conserved RNA structure ( thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. (nature.com)
- Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. (sciencemag.org)
- Bacteria and archaea have evolved RNA-mediated adaptive defense systems called clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) that protect organisms from invading viruses and plasmids ( 1 - 3 ). (sciencemag.org)
- Here we review recent findings and offer a perspective on how the major variant RNA polymerase of bacteria, which contains the sigma54 factor, functions for regulated gene expression. (mdpi.com)
- Sigma's GenElute Bacterial Genomic Kit provides a simple and convenient technique to isolate high quality DNA from both Gram negative ( Figure 1 ) and Gram positive bacteria ( Figure 2 ). (sigmaaldrich.com)
- The GenElute Bacterial Genomic DNA Kit contains all of the reagents needed to purify genomic DNA from Gram negative bacteria ( Figure 3 ). (sigmaaldrich.com)
- Agarose gel analysis of genomic DNA isolated from the indicated Gram negative bacteria prepared using the GenElute Bacterial Genomic DNA Kit versus kits from other suppliers. (sigmaaldrich.com)
- This host-bacterial cell total RNA mixture can be obtained by a variety of RNA isolation methods, ideally by Ambion's new RiboPure-Bacteria Kit . (bio-medicine.org)
- Here, we present new discoveries from the transcriptome-wide determination of RNA structuromes in bacteria and discuss emerging concepts in the role of mRNA structures in regulating transcription, translation and degradation. (medworm.com)
- Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. (nih.gov)
- RNase E is an essential endonuclease that is abundant in many bacteria and plays an important part in all aspects of RNA metabolism. (nih.gov)
- Recent evidence suggests that this complex associates with the inner membrane of bacteria, an observation that challenges traditional models in which soluble RNases are proposed to randomly interact with RNAs in the cytosol. (nih.gov)
- MessageAmp II-Bacteria (patent pending) is based on a linear RNA amplification technology that enables whole genome expression analysis from limited bacterial samples. (thermofisher.com)
- MessageAmp II-Bacteria can be used with any bacterial species and is compatible with purified total RNA, bacterial mRNA enriched using Ambion's MICROB Express ™ Kit (see sidebar), or bacterial RNA enriched from host cell mixtures with the MICROB Enrich ™ Kit (see sidebar). (thermofisher.com)
- MessageAmp II-Bacteria is based on a linear amplification method (Figure 1) in which the RNA sample is first polyadenylated with Poly(A) Polymerase, then reverse transcribed using oligo(dT) primers containing a T7 RNA polymerase promoter. (thermofisher.com)
- It is important to understand that the amplified RNA yields obtained with the MessageAmp II-Bacteria Kit or any amplification system will vary based on factors such as RNA isolation method, input RNA amount, RNA quality, the bacterial species from which the RNA was isolated, and incubation time of the in vitro transcription reaction. (thermofisher.com)
- Total RNA isolation methods that include a glass fiber filter based purification step, such as Ambion's RiboPure™-Bacteria Kit , give higher aRNA yields than organic extraction methods. (thermofisher.com)
- Figure 2 shows typical aRNA yields for 5 bacterial species using 100 ng of total RNA isolated with the RiboPure-Bacteria Kit and amplified using MessageAmp II-Bacteria and a 6 hour IVT reaction. (thermofisher.com)
- Affymetrix E. coli Antisense Whole Genome Arrays were used to compare biotinylated MessageAmp II-Bacteria aRNA derived from E. coli total RNA and MICROBExpress enriched mRNA, as well as the recommended Affymetrix labeling protocol using 10 µg E. coli total RNA. (thermofisher.com)
- Here we show that TLR13 detects the 23S ribosomal RNA of both gram-positive and gram-negative bacteria. (elifesciences.org)
- Li and Chen have now discovered that TLR13 is responsible for detecting a certain type of ribosomal RNA called 23S ribosomal RNA that are present in bacteria but not in eukaryotic cells. (elifesciences.org)
- Total RNA was extracted from HBMEC and associated bacteria a using RiboPure-Bacteria kit (Ambion) that includes zirconia-silica beads for bead beating with a special vortex adapter (Ambion). (asm.org)
- Intact bacteria were separated from HBMEC quickly to avoid any alteration of bacterial gene expression. (asm.org)
- IMPORTANCE Small RNAs (sRNAs) in bacteria are abundant and play important roles in posttranscriptional regulation of gene expression, particularly under stress conditions. (asm.org)
- Bacteria and other microorganisms use small RNA molecules to help them respond to stress conditions and to changes in their environment, such as fluctuations in temperature or the availability of nutrients. (elifesciences.org)
- In bacteria, the control of gene expression post-transcription is mediated in part by small RNAs (sRNAs), and their contributions enrich the computational complexity and repertoire of regulatory circuits ( Beisel and Storz, 2011 ). (elifesciences.org)
- The Toll pathway mediates most defenses against Gram-positive bacteria and fungi, whereas the Imd pathway is required to resist Gram-negative bacterial infection. (epfl.ch)
- GNBP1 double-stranded RNA expression renders flies susceptible to Gram-positive bacterial infection and reduces the induction of the antifungal peptide encoding gene Drosomycin after infection by Gram-positive bacteria but not after fungal infection. (epfl.ch)
- This is suggested to be due to higher HIV RNA levels in cervicovaginal fluids in women living with HIV (WLWH) with BV, as bacteria associated with BV may induce viral replication and shedding in the genital tract despite undetectable HIV RNA plasma viral load. (biomedcentral.com)
- Bacterial vaginosis (BV) is characterized by an overgrowth of anaerobic bacteria and a relative loss of lactobacillus species. (biomedcentral.com)
- We have optimized a method for isolating RNA of Listeria monocytogenes ( L. monocytogenes ) bacteria infecting bone marrow derived macrophage cells (BMDM). (bio-protocol.org)
- Next, we resuspend the bacteria and extract RNA following DNase treatment. (bio-protocol.org)
- While bacteria were long thought to rely primarily on transcriptional control, it is now well established that they also use numerous small RNA s to regulate mRNA translation and stability. (embopress.org)
- A major recent shift in our view of gene expression is that even the simplest organisms-bacteria-extensively control their genes post‐transcriptionally using small noncoding RNAs (sRNAs). (embopress.org)
- they constitute major leaps forward in imaging RNA networks in bacteria. (embopress.org)
- In bacteria, RapA is an RNA polymerase (RNAP)-associated Swi2/Snf2 protein that mediates RNAP recycling during transcription. (nih.gov)
- Many of the current bacterial 16S primers have been designed from sequence data obtained from in vitro cultured species, even though environmental microbiologists estimate that less than 2% of bacteria can be cultured in the laboratory. (biomedcentral.com)
- How to find small non-coding RNAs in bacteria. (openrepository.com)
- However, our ever-increasing understanding of the roles played by RNA regulators has revealed far greater complexity to regulation of metabolism in bacteria. (illinois.edu)
- In bacteria, small non-coding RNAs (sRNAs), which are relatively short transcripts (~50-300 nucleotides), regulate a wide range of physiological functions in response to external signals ( Wassarman, 2002 ). (frontiersin.org)
- The pathogenic bacteria were specifically detected by DNA-RNA hybridization in an hour. (elsevier.com)
- As far as bacteria are concerned, other living creatures are just another niche to exploit, which means that pretty much every animal and plant has a set of bacterial pathogens that come along with it. (scientificamerican.com)
- These bacteria infect insects and other arthropods and are much beloved of journalists (well, compared to other insect bacteria at least) because one of their effects is to stop insects producing male offspring (so only female survive to pass on the bacterial genome), which gives journalists the opportunity to write silly headlines. (scientificamerican.com)
- However when the bacterial infection was closely examined, it was found that infected individuals of both species contained the same number of bacteria. (scientificamerican.com)
- The temperature sensitivity of RNA secondary and tertiary structures is exploited by bacteria to fabricate RNA thermosensing systems that allow a rapid adaptive response to temperature change. (biologists.org)
- RNA thermometers (RNATs) present in non-coding regions of certain mRNAs of pathogenic bacteria enable rapid upregulation of translation of virulence proteins when the temperature of the bacterium rises after entering a mammalian host. (biologists.org)
- Whereas the roles of temperature-sensitive RNA structures similar to RNATs in Eukarya and Archaea are largely unknown, there would appear to be a potential for all taxa to adaptively regulate their thermal physiology through exploitation of RNA-based thermosensory responses akin to those of bacteria. (biologists.org)
- Elucidating whether animals too have exploited the types of RNA thermosensing tools that are used so effectively by bacteria seems likely to provide exciting new insights into the mechanisms of evolutionary adaptation and acclimatization to temperature. (biologists.org)
- Because almost all work on the thermosensory roles of RNA has been performed with bacteria, animal physiologists may be unfamiliar with the potentials of these mechanisms for fostering evolutionary adaptation and acclimatization to temperature. (biologists.org)
- Also, models for noncoding RNAs in eukaryotes are generally inappropriate for the small regulatory RNAs common in bacteria. (beds.ac.uk)
- Culture-based analyses correlated qualitatively with relative abundance data on bacterial and fungal taxa obtained by NanoString, and the analysis of serial samples demonstrated the use of this method to simultaneously detect bacteria and fungi and to detect microbes at low abundance without an amplification step. (asm.org)
- IMPORTANCE Here we demonstrate the use of an RNA-based analysis of specific taxa of interest, including bacteria and fungi, within microbial communities. (asm.org)
- IMPORTANCE Small RNAs (sRNAs) regulate gene expression in diverse bacteria by interacting with mRNAs to change their structure, stability, or translation. (asm.org)
- This tool will facilitate elucidation of sRNA regulons in bacteria, allowing new discoveries regarding the roles of sRNAs in bacterial stress responses and metabolic regulation. (asm.org)
- While 16S hypervariable regions can vary dramatically between bacteria, the 16S gene as a whole maintains greater length homogeneity than its eukaryotic counterpart (18S ribosomal RNA), which can make alignments easier. (wikipedia.org)
- This study presents a unique approach (CopraRNA, for Comparative Prediction Algorithm for sRNA Targets) towards reliably predicting the targets of bacterial small regulatory RNAs (sRNAs). (pnas.org)
- Small RNAs (sRNAs) constitute a large and heterogeneous class of bacterial gene expression regulators. (pnas.org)
- Small RNAs (sRNAs) are post-transcriptional regulators of gene expression that play fundamental roles in the response of bacterial cells to environmental cues. (weizmann.ac.il)
- Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis (the causative agent of tularaemia), Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. (wikipedia.org)
- Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure. (wikipedia.org)
- It is now known that most bacterial sRNAs are encoded by free-standing genes located in the intergenic regions (IGR) between two known genes. (wikipedia.org)
- Since these initial discoveries, over six thousand bacterial sRNAs have been identified, largely through RNA-sequencing experiments. (wikipedia.org)
- RNA-sequencing, or RNA-seq, is used to analyze expression levels of all transcripts in a genome, including sRNAs. (wikipedia.org)
- Bacterial sRNAs have a wide variety of regulatory mechanisms. (wikipedia.org)
- We hypothesize that intergenic regions in rickettsial species encode for small, non-coding RNAs (sRNAs) involved in the regulation of its transcriptome, leading to altered virulence and adaptation depending on the host niche. (biomedcentral.com)
- We further characterized novel sRNAs from typhus ( R. prowazekii and R. typhi ) and spotted fever ( R. rickettsii and R. conorii ) groups for their promoters and Rho-independent terminators using Bacterial Promoter Prediction Program (BPROM) and TransTermHP prediction algorithms, respectively. (biomedcentral.com)
- Many bacterial small RNAs (sRNAs) control membrane protein production, but sRNA-mediated regulation of membrane fatty acid composition is less well understood. (asm.org)
- Bacterial small RNAs (sRNAs) are key elements of regulatory networks that modulate gene expression. (elifesciences.org)
- Like many other sRNAs, RydC bears a 'seed' region that recognises specific transcripts through base-pairing, and its activities are facilitated by the RNA chaperone Hfq. (elifesciences.org)
- Small RNA molecules (sRNAs) are now recognized as key regulators controlling bacterial gene expression, as sRNAs provide a quick and efficient means of positively or negatively altering the expression of specific genes. (frontiersin.org)
- To date, numerous sRNAs have been identified and characterized in a myriad of bacterial species, but more recently, a theme in bacterial sRNAs has emerged: the presence of more than one highly related sRNAs produced by a given bacterium, here termed sibling sRNAs. (frontiersin.org)
- Indeed, there are several examples of bacterial sibling sRNAs with non-redundant regulatory functions, but there are also instances of apparent regulatory redundancy between sibling sRNAs. (frontiersin.org)
- This review provides a comprehensive overview of the current knowledge of bacterial sibling sRNAs, and also discusses important questions about the significance and evolutionary implications of this emerging class of regulators. (frontiersin.org)
- The recent implication of regulatory RNAs (small RNAs [sRNAs]) in antibiotic response and resistance in several bacterial pathogens suggests that they should be considered innovative drug targets. (asm.org)
- Of interest is the lack of knowledge about sRNAs implicated in Gram-positive compared to Gram-negative bacterial resistance. (asm.org)
- Small non-coding RNAs (sRNAs) that act as regulators of gene expression have been identified in all kingdoms of life, including microRNA (miRNA) and small interfering RNA (siRNA) in eukaryotic cells. (prolekare.cz)
- Our results also suggest that sRNAs may represent a distinct class of virulence factors that are important for bacterial infection in vivo . (prolekare.cz)
- Other recent work used RNA‐seq to capture the target suites of individual sRNAs. (embopress.org)
- Thus, there is still a need for accurate in silico prediction methods to identify sRNAs within a given bacterial species. (pasteur.fr)
- Bacterial small RNAs (sRNAs) act as key elements in regulatory networks to control gene expression at the post-transcriptional level. (uni-jena.de)
- While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. (openrepository.com)
- Small RNAs (sRNAs) posttranscriptionally regulate mRNA targets, typically under conditions of environmental stress. (asm.org)
- Although hundreds of sRNAs have been discovered in diverse bacterial genomes, most sRNAs remain uncharacterized, even in model organisms. (asm.org)
- Our results suggest that SPOT can facilitate elucidation of sRNA target regulons to expand our understanding of the many regulatory roles played by bacterial sRNAs. (asm.org)
- Bacterial small RNAs (sRNAs) range in size from 50 to 530 nucleotides (nt). (asm.org)
- Is the Subject Area "Bacterial pathogens" applicable to this article? (plos.org)
- Genital infections can increase HIV-1 RNA shedding in semen, but shedding also occurs in the absence of typical pathogens. (iavi.org)
- This minireview discusses sRNA-mediated mechanisms exploited by bacterial pathogens to fight against antibiotics. (asm.org)
- As a consequence of natural selection, bacterial pathogens evolve to survive and evade drugs designed to eliminate them, as they have done for millions of years against natural antibiotics produced by competing organisms in their environment ( 5 ). (asm.org)
- Studying the transcriptome of bacterial pathogens during infection is a very informative and effective tool for discovering genes that contribute to successful infection. (bio-protocol.org)
- Additional validation was undertaken in separate studies of children with meningococcal disease (n = 24) and inflammatory diseases (n = 48) and on published gene expression datasets.A 2-transcript RNA expression signature distinguishing bacterial infection from viral infection was evaluated against clinical and microbiological diagnosis.Definite bacterial and viral infection was confirmed by culture or molecular detection of the pathogens. (ox.ac.uk)
- While RNA-seq is now a routine method for gene expression analysis in bacterial pathogens, the past years have also witnessed a surge of novel RNA-seq based approaches going beyond standard mRNA profiling. (rna-seqblog.com)
- Saliba AE, C Santos S, Vogel J. (2017) New RNA-seq approaches for the study of bacterial pathogens . (rna-seqblog.com)
- Understanding the factors that determine the cost of antibiotic resistance is therefore key to our overall understanding of the evolution of antibiotic resistance in bacterial pathogens. (genetics.org)
- Fröhlich KS , Papenfort K (2016) Interplay of regulatory RNAs and mobile genetic elements in enteric pathogens. (uni-jena.de)
- In order to identify these novel proteins, we established a Large-Scale Transcriptomic Analysis Pipeline in Crowd (LSTrAP-Crowd), where 285 individuals processed 26 terabytes of RNA-sequencing data of the 17 most notorious bacterial pathogens. (biomedcentral.com)
- We identified genes related to protein synthesis in common bacterial pathogens and thus provide a resource of potential antibiotic development targets for experimental validation. (biomedcentral.com)
- Stress-induced host membrane remodeling protects from infection by non-motile bacterial pathogens. (openrepository.com)
- Overall, our findings reveal host membrane remodeling as a novel stress-responsive cell-autonomous defense mechanism that protects epithelial cells from infection by non-motile bacterial pathogens. (openrepository.com)
- These membranes often encounter two types of bacterial pathogens. (phys.org)
- Ribosomal RNA is naturally amplified in bacterial cells, which makes it a promising target for sensitive detection without the necessity for prior in vitro amplification.Using fluorescent microarray methods with rRNA targets from a range of pathogens, an optimal probe was selected from a pool of probe candidates identified in silico. (ed.ac.uk)
- Here, we present new algorithms, specific to bacterial gene structures and transcriptomes, for analysis of RNA-seq data. (nih.gov)
- The algorithms are implemented in an open source software system called Rockhopper that supports various stages of bacterial RNA-seq data analysis, including aligning sequencing reads to a genome, constructing transcriptome maps, quantifying transcript abundance, testing for differential gene expression, determining operon structures and visualizing results. (nih.gov)
- Gene expression analysis following host-bacterial interactions is revolutionizing our understanding of the host response to bacterial infection. (bio-medicine.org)
- Unfortunately, the benefits of RNA amplification have not been easily accessible to researchers analyzing bacterial gene expression profiles. (thermofisher.com)
- More importantly, microarray analysis demonstrated that no bias was introduced in the gene expression pattern during the RNA isolation procedure. (asm.org)
- It is possible to analyze the whole gene expression of a bacterial pathogen during its interaction with the host. (asm.org)
- The feasibility of this approach, however, depends upon the ability to recover biologically relevant bacterial RNA, and serious consideration should be given to prevent gene expression changes associated with preparative procedures ( 6 , 10 ). (asm.org)
- This approach did not require time-consuming steps that can affect bacterial gene expression but creates other technical issues for microarray analysis, as human RNA can compete with bacterial RNA during cDNA synthesis and labeling, limit the amount of bacterial RNA that can be used, and impede accurate quantitation of bacterial RNA. (asm.org)
- We have conducted a systematic examination of how changes in the number of RNA-Seq reads per sample influences both profiling of a single bacterial transcriptome and the comparison of gene expression among samples. (biomedcentral.com)
- The extracted RNA is suitable for gene expression analysis by real-time PCR or microarray. (bio-protocol.org)
- Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. (biomedcentral.com)
- Dual RNA-seq analyzing pathogen and host simultaneously has revealed roles of noncoding RNAs during infection and enabled the correlation of bacterial gene activity with specific host responses. (rna-seqblog.com)
- In our group, we use Caulobacter crescentus as a model organism to study the principles of RNA-mediated processes in alpha-proteobacteria, and to uncover novel mechanisms of bacterial gene regulation. (uni-jena.de)
- Fröhlich KS *, Förstner KU, Gitai Z* (2018) Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus . (uni-jena.de)
- Fröhlich KS , Vogel J (2009) Activation of gene expression by small RNA. (uni-jena.de)
- We review such approaches with a focus on RNA-seq as a versatile tool to investigate the different layers of gene expression in which RNA is made, processed, regulated, modified, translated, and turned over. (openrepository.com)
- To dissect relative contributions of both mechanisms and elucidate gene-specific host transcriptional responses throughout the first 8h of lytic HSV-1 infection, we employed RNA-seq of total, newly transcribed (4sU-labelled) and chromatin-associated RNA in wild-type (WT) and Δvhs infection of primary human fibroblasts. (helmholtz-hzi.de)
- While the combined effects of both phenomena dominated infection-induced changes in total RNA, extensive gene-specific transcriptional regulation was observable in chromatin-associated RNA and was surprisingly concordant between WT and Δvhs infection. (helmholtz-hzi.de)
- Scientists discover transcripts from the same gene that can express both proteins and noncoding RNA. (the-scientist.com)
- Vitamin A had the greatest effect on the structure of the bacterial community and gene expression. (sciencemag.org)
- In total, the crowd processed 26,269 RNA-seq experiments and used the data to construct gene co-expression networks, which were used to identify more than a hundred uncharacterized genes that were transcriptionally associated with protein synthesis. (biomedcentral.com)
- In addition, we performed a range of analyses-Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing-that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. (openrepository.com)
- The secondary and tertiary orders of RNA structure are crucial for a suite of RNA-related functions, including regulation of translation, gene expression and RNA turnover. (biologists.org)
- This webinar, Part 1 of the "Advances in RNA-based Biomarker Development for Precision Oncology" webinar series sponsored by GeneCentric Therapeutics, will discuss how gene expression signatures can accelerate (and rehabilitate) drug programs, define targeted patient populations, expand drug indications, and improve clinical success. (genomeweb.com)
- Compared at the genus level, the relative abundances of bacterial taxa detected by analysis of RNA correlated with the relative abundances of the same taxa as measured by sequencing of the V4V5 region of the 16S rRNA gene amplified from community DNA from the same sample. (asm.org)
- The RNA-Seq experiment also revealed cross-regulation of AIL gene expression at the transcriptional level. (plantphysiol.org)
- We have determined the solution structure of a complex formed between the RsmE protein, a member of this family from Pseudomonas fluorescens, and a target RNA encompassing the ribosome-binding site of the hcnA gene. (unil.ch)
- A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. (google.com)
- Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA and of a portion of the target gene are identical. (google.com)
- c) introducing the RNA into the target cell, thereby inhibiting expression of the target gene. (google.com)
- It is suggested that 16S rRNA gene can be used as a reliable molecular clock because 16S rRNA sequences from distantly related bacterial lineages are shown to have similar functionalities. (wikipedia.org)
- As a result, 16S rRNA gene sequencing has become prevalent in medical microbiology as a rapid and cheap alternative to phenotypic methods of bacterial identification. (wikipedia.org)
- The bacterial 16S gene contains nine hypervariable regions (V1-V9), ranging from about 30 to 100 base pairs long, that are involved in the secondary structure of the small ribosomal subunit. (wikipedia.org)
- Bouvier M, Sharma CM, Mika F et al (2008) Small RNA binding to 5′ mRNA coding region inhibits translational initiation. (springer.com)
- 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)
- Based on the structure and other data, we propose a model for a dynamic effector complex comprising Hfq, small RNA, and the cognate mRNA target. (elifesciences.org)
- 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)
- It is similar to MAPS, but additionally ligates short sRNA-mRNA duplexes in vivo by co-expressing T4 RNA ligase before capturing candidate target mRNAs with a sRNA-specific oligonucleotide. (rna-seqblog.com)
- A transcription unit (TU) consists of K ≥ 1consecutive genes on the same strand of a bacterial genome that are transcribed into a single mRNA molecule under certain conditions. (rna-seqblog.com)
- Fröhlich KS , Papenfort K, Fekete A, Vogel J (2013) A small RNA activates CFA synthase by isoform-specific mRNA stabilization. (uni-jena.de)
- TargetRNA2 uses several features to identify message targets of sRNA regulation, including conservation of regions of the sRNA, structural accessibility of regions of the sRNA, structural accessibility of regions of the mRNA and energy of hybridization between the two RNAs. (omictools.com)
- Turnover of mRNA may be regulated by temperature-sensitive RNA structures. (biologists.org)
- In animals, these responses might include regulation of translation of stress-induced proteins, alternative splicing of messenger RNA precursors, differential expression of allelic proteins, modulation of activities of small non-coding RNAs, regulation of mRNA turnover and control of RNA editing. (biologists.org)
- Small RNA-dependent translational repression often occurs via interactions that directly interfere with ribosome binding to the mRNA. (asm.org)
- The RsmE homodimer with its two RNA-binding sites makes optimal contact with an 5'-A/UCANGGANGU/A-3' sequence in the mRNA. (unil.ch)
- Although proteins fulfil most of the requirements that biology has for structural and functional components such as enzymes and receptors, RNA can also serve in these capacities. (nature.com)
- The recent findings that Hfq assists in bimolecular RNA-RNA interactions and is similar structurally and functionally to eukaryotic Sm proteins have further fueled interest in this important post-transcriptional regulator. (nih.gov)
- The 6S RNA binds to RNA polymerase and regulates transcription, tmRNA has functions in protein synthesis, including the recycling of stalled ribosomes, 4.5S RNA regulates signal recognition particle (SRP), which is required for the secretion of proteins and RNase P is involved in maturing tRNAs. (wikipedia.org)
- However, in vivo dynamics of chloroplast RNA polymerases and eukaryotic-type plastid nucleoid proteins have not been directly characterized experimentally. (pnas.org)
- These RNAs selectively bind target proteins, and exhibit fluorescence increases that enable protein expression to be imaged in living cells. (pubmedcentralcanada.ca)
- A crucial step in the production of proteins is the translation of messenger RNA molecules. (elifesciences.org)
- Other RNA molecules called small RNAs are also involved in this process: these small RNAs bind to the messenger RNA molecules to either increase or decrease the production of proteins. (elifesciences.org)
- The key to understanding these fundamental processes of sRNA-based regulation is to determine how RNAs are bound and presented by Hfq and other effector proteins. (elifesciences.org)
- RNA chaperones are ubiquitous and abundant proteins found in all living organisms and viruses. (plantphysiol.org)
- RNA tends to be kinetically trapped in misfolded forms, and RNA binding proteins, acting as chaperones, can resolve these structures, ensuring accessibility for its biological function. (plantphysiol.org)
- After infection, we lyse the cells and filter the lysates through 0.45 µm filters to discard most of the host proteins and RNA. (bio-protocol.org)
- IsrM targets the mRNAs coding for SopA, a SPI-1 effector, and HilE, a global regulator of the expression of SPI-1 proteins, which are major virulence factors essential for bacterial invasion. (prolekare.cz)
- Understanding the components of such RNA regulons is not only important to dissect the regulatory circuits underlying bacterial physiology and virulence, but also to fathom where and why organisms favor regulatory RNA over proteins. (embopress.org)
- These include variations of the technique to capture post-transcriptional networks controlled by small RNAs and to discover associated RNA-binding proteins in the pathogen itself. (rna-seqblog.com)
- Grad-seq guides the discovery of RNA-binding proteins. (rna-seqblog.com)
- in vivo UV treatment covalently cross-links RNA to proteins before co-purification and RNA-seq. (rna-seqblog.com)
- To do this we measured the fitness of resistant mutants in the presence of other antibiotics (ciprofloxacin and carbenicillin) that have similar effects on bacterial growth rate but bind to different target enzymes (DNA gyrase and penicillin-binding proteins, respectively) and in 41 single-carbon source environments of varying quality. (genetics.org)
- Rapid upregulation of translation of bacterial heat-shock proteins likewise is governed in part by RNATs. (biologists.org)
- The higher-order structures of proteins and RNA are readily perturbed by changes in temperature, threatening the 'balancing act' so critical for function. (biologists.org)
- Noncoding RNA molecules generally interact with RNA -binding proteins (RBPs) to become functional in the cellular environment. (helmholtz-hzi.de)
- Proteins of the RsmA/CsrA family are global translational regulators in many bacterial species. (unil.ch)
- It has several functions: Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteins. (wikipedia.org)
- In the expression and interference phases, transcription of the repeat-spacer element into precursor CRISPR RNA (pre-crRNA) molecules followed by enzymatic cleavage yields the short crRNAs that can pair with complementary protospacer sequences of invading viral or plasmid targets ( 4 - 11 ). (sciencemag.org)
- they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. (wikipedia.org)
- The cycle starts with exposure of the phage-display peptide library to the target RNA molecules, which are immobilized on a streptavidin surface. (nih.gov)
- Many small RNA molecules use a protein called Hfq to help them interact with their target messenger RNAs. (elifesciences.org)
- In some cases this protein protects the small RNA molecules when they are not bound to their targets. (elifesciences.org)
- Hfq also helps the small RNA to bind to the messenger RNA, and then recruits other enzymes that eventually degrade the complex formed by the different RNA molecules. (elifesciences.org)
- CLASH (crosslinking, ligation, and sequencing of hybrids): RNA molecules are UV-crosslinked to a flagged RBP in vivo . (rna-seqblog.com)
- Next, the bound RNA is trimmed using an RNase and RNA linkers are ligated to the immobilized RNA molecules in the RNA-RBP complexes. (rna-seqblog.com)
- Finally, coupled RNA molecules are ligated into one single molecule of two different types, either single or chimeric fragments. (rna-seqblog.com)
- These molecular helpers remove the protective cap at the start of ribonucleic acid (RNA) molecules. (xonl.de)
- Scientists from the Schepens Eye Research Institute, a subsidiary of Mass. Eye and Ear and affiliate of Harvard Medical School, have found for the first time that a bacterial pathogen can literally mow down protective molecules, known as mucins, on mucus membranes to enter and infect a part of the body. (phys.org)
- Onconase from Rana pipiens selectively destroyed the RNA of type-I human immunodeficiency virus (HIV-I) without degrading host RNA molecules [ 11 ] and RNase from Rana catesbeiana inhibited the replication of Japanese encephalitis virus [ 12 ]. (biomedcentral.com)
- 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)
- The most frequently encountered acquired resistance mechanism involves the methylation of the ribosomal RNA (e.g., by Erm family methyltransferases), which results in decreased drug-binding efficiency and increased viability in the presence of antibiotics [ 7 , 8 ]. (biomedcentral.com)
- Ribosomal RNA is naturally amplified in bacterial cells, which makes it a promising target for sensitive detection without the necessity for prior in vitro amplification. (ed.ac.uk)
- 16S ribosomal RNA (or 16S rRNA) is the RNA component of the 30S small subunit of a prokaryotic ribosome (SSU rRNA). (wikipedia.org)
- 2017 Feb 01;36:14-19 Authors: Ignatova Z, Narberhaus F Abstract RNA folds into intricate structures. (medworm.com)
- Moreover, RNA must be obtained from biologically relevant models of infection that reflect the complexity of pathogen-host interaction. (asm.org)
- Moreover, the ratio between host and pathogen RNA may vary among samples, making normalization of microarray data difficult. (asm.org)
- Dual RNA-seq for simultaneous transcriptomics in host-pathogen interactions. (rna-seqblog.com)
- Bacterial resistance to antibiotics usually incurs a fitness cost in the absence of selecting drugs, and this cost of resistance plays a key role in the spread of antibiotic resistance in pathogen populations. (genetics.org)
- Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function. (openrepository.com)
- Furthermore, we found that ant ail6 plants have elevated levels of two defense hormones: salicylic acid and jasmonic acid, and show increased resistance to the bacterial pathogen Pseudomonas syringae . (plantphysiol.org)
- Plant defense responses against viral and bacterial pathogen infections. (degruyter.com)
- SprD is a small regulatory RNA required for S. aureus pathogenicity with an identified function, although the mechanism of virulence control by the RNA is yet to be elucidated. (inserm.fr)
- Dimastrogiovanni D, Fröhlich KS , Bandyra KJ, Bruce HA, Hohensee S, Vogel J, Luisi BF (2014) Recognition of the small regulatory RNA RydC by the bacterial Hfq protein. (uni-jena.de)
- Fröhlich KS *, Gottesman S* (2018) Small Regulatory RNAs in the Enterobacterial Response to Envelope Damage and Oxidative Stress. (uni-jena.de)
- RNA thermosensors: how might animals exploit their regulatory potential? (biologists.org)
- Purified genomic DNA was isolated from various bacterial species using the GenElute Bacterial Genomic DNA kit. (sigmaaldrich.com)
- However, the kit should perform well with RNA from any bacterial species. (bio-medicine.org)
- Using the sRNA Identification Protocol using High-throughput Technology (SIPHT) web interface, we predicted over 1,700 small RNAs present in the intergenic regions of 16 different strains representing 13 rickettsial species. (biomedcentral.com)
- This is the first description of novel small RNAs for a highly pathogenic species of Rickettsia , which should lead to new insights into rickettsial virulence and adaptation mechanisms. (biomedcentral.com)
- Our analysis provides a guide for the many researchers seeking to determine the appropriate sequencing depth for RNA-Seq-based studies of diverse bacterial species. (biomedcentral.com)
- We also experimentally validated three of the primer pairs identified by our method on multiple bacterial species, belonging to different genera and phyla. (biomedcentral.com)
- Moreover, increasing interest in members of the human microbiota and environmental microbial communities has highlighted the importance of understudied bacterial species with largely unknown transcriptome structures and RNA-based control mechanisms. (openrepository.com)
- Even the smallest subpopulation that rides out a catastrophe can ensure continuity of the bacterial species as such. (paperity.org)
- Bacteroides vulgatus , a bacterial species positively correlated with host growth in gnotobiotic mouse models of postnatal human microbiota development, had the biggest response to vitamin A deficiency, exhibiting an increase in its abundance. (sciencemag.org)
- Therefore, we established a community of cultured, sequenced human gut-derived bacterial species in gnotobiotic mice and fed the animals a defined micronutrient-sufficient diet, followed by a derivative diet devoid of vitamin A, folate, iron, or zinc, followed by return to the sufficient diet. (sciencemag.org)
- The major classes of bacterial noncoding RNA are known only for a few species, meaning that the RNA biology of the vast majority of microbes that are important for human health remains unexplored. (helmholtz-hzi.de)
- Exploiting RNA as a programmable antibiotic to treat bacterial infections and dysbiosis requires that we comprehensively understand the major RNA -based pathways and mechanisms in these species. (helmholtz-hzi.de)
- We designed rRNA-targeting probe sets to detect 42 bacterial and fungal genera or species common in cystic fibrosis (CF) sputum and demonstrated the taxon specificity of these probes, as well as a linear response over more than 3 logs of input RNA. (asm.org)
- It also establishes how this research can make a difference in the survival and propagation of various bacterial species as (p)ppGpp has the ability to instantaneously modify global cellular metabolism in response to the environmental changes to optimize growth which increases the survival rate. (brightkite.com)
- We show that (i) binase does not to attack IAV particle-protected viral RNA, (ii) internalized binase could be detected within the cytosol of MDCK-II cells and that (iii) binase impairs IAV replication by specifically degrading viral RNA species within the infected MDCK-II cells without obvious effect on cellular mRNAs. (biomedcentral.com)
- Hundreds of small RNAs have been identified in numerous bacterial species such as Bacillus subtilis ( 5 ), Listeria monocytogenes ( 6 ), and Salmonella enterica ( 7 , 8 ). (asm.org)
- Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing. (sciencemag.org)
- Ambion now introduces a new technology, MICROB Enrich , that enables whole genome microarray expression analyses of bacterial RNA after host-bacterial interactions. (bio-medicine.org)
- Bacterial genome plasticity is mandatory to adapt and respond to environmental threats, including antibiotic stress. (asm.org)
- We present a new model for in silico identification of sRNA and asRNA candidates within an entire bacterial genome. (pasteur.fr)
- Hi I am sequencing a bacterial genome and have assembled my Illumina reads (40 bp single) using b. (usegalaxy.org)
- Bacterial RNA Biology on a Genome Scale. (openrepository.com)
- Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti. (openrepository.com)
- We use the infection of E. coli cells by bacteriophage lambda, whose DNA integrates at a unique site into the bacterial genome, when following the lysogenic pathway. (weizmann.ac.il)
- By primer extension we examined the effect of binase on the integrity of viral RNAs within the cells and using a mini-genome system we explored the effect of binase on the viral expression. (biomedcentral.com)
- Aw JGA, Shen Y, Wilm A et al (2016) In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation. (springer.com)
- Bacterial RNA Isolation From Infected Eukaryotic Hosts ( Remove 90% of mamma. (bio-medicine.org)
- Although the mass of eukaryotic RNA isolated from host-bacterial cell mixtures is often far greater than the mass of bacterial RNA isolated, this complex mixture of total RNAs is the starting material for the MICROB Enrich proced ure. (bio-medicine.org)
- I do mostly eukaryotic RNA-seq using Tophat2 and then cufflinks, DEseq, edgeR, etc. (biostars.org)
- Bacterial transcriptome assembly faces different challenges than eukaryotic transcriptome assembly. (beds.ac.uk)
- For example, bacterial genomes are generally denser than eukaryotic genomes and neighboring bacterial transcripts frequently overlap, making it challenging to distinguish the boundaries of neighboring bacterial transcripts. (beds.ac.uk)
- Owing to its bacterial origin, binase evades mammalian RNase inhibitors and retains its catalytic activity inside eukaryotic organisms [ 15 ]. (biomedcentral.com)
- Such conditions, commonly referred to as acquired immunodeficiency syndrome (AIDS), or AIDS related complex (ARC), make HIV patients vulnerable to opportunistic infections such as bacterial, fungal, viral, protozoal, and neoplastic diseases, which ultimately lead to death. (mdpi.com)
- These mice can be used to investigate the role of TLR13 in immune responses to bacterial infections in vivo. (elifesciences.org)
- The balancing role of TTP comes at the cost of an increased risk of bacterial infections. (ovid.com)
- Yet, due to serious side effects, they are often considered to be the last resort treatment in case of severe bacterial infections. (jbsdonline.com)
- Single-cell RNA-seq addresses heterogeneity in infections. (rna-seqblog.com)
- The test aids in the differential diagnosis of other vaginal infections that clinically present with the same signs and symptoms as bacterial vaginosis, Coriell said. (genomeweb.com)
- In this work, we assess the use of the NanoString nCounter technology ( 15 ) to detect specific bacterial and fungal taxa in sputum samples from individuals with CF-related respiratory infections. (asm.org)
- Our discovery may ultimately lead to new ways of diagnosing, treating and preventing bacterial infections originating not only in the eye but in other parts of the body as well. (phys.org)
- 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)
- Here we show that one of the small pathogenicity island RNAs, named SprD, contributes significantly to causing disease in an animal model of infection. (inserm.fr)
- Single-cell RNA-seq studies have addressed how heterogeneity among individual host cells may determine infection outcomes. (rna-seqblog.com)
- In summary, our study provides a comprehensive picture of the molecular mechanisms that govern cellular RNA metabolism during the first 8h of lytic HSV-1 infection.IMPORTANCE The HSV-1 virion host shut-off (vhs) protein efficiently cleaves both host and viral mRNAs in a translation-dependent manner. (helmholtz-hzi.de)
- 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)
- Addgene: RNA-guided editing of bacterial genomes using CRISPR-Cas systems. (addgene.org)
- A two plasmid system for editing bacterial genomes using an RNA-guided Cas9 nuclease. (addgene.org)
- For organisms whose genomes have not been sequenced and annotated, transcriptomes must be assembled de novo from the RNA-seq data. (beds.ac.uk)
- In this Review, I summarize the major roles of RNase E in RNA processing and decay and discuss the various mechanisms that regulate its activity. (nih.gov)
- Here, we review the mechanisms and functions of selected bacterial RNA regulators and discuss their importance in modulating nutrient uptake as well as primary and secondary metabolic pathways. (illinois.edu)
- Bobrovskyy, M & Vanderpool, CK 2013, ' Regulation of bacterial metabolism by small RNAs using diverse mechanisms ', Annual Review of Genetics , vol. 47, pp. 209-232. (illinois.edu)
- 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)
- look OK, and I can clearly see the 23S and 16S rRNA bands in my RNA prep. (bio.net)
- This domain is the binding site for the antibacterial drug rifampin (and its analogues) which blocks the DNA/RNA tunnel and prevents initiation of transcription. (ebi.ac.uk)
- We find that the transcriptome maps generated by our algorithms are highly accurate when compared with focused experimental data from E. coli and N. gonorrhoeae, and we validate our system's ability to identify novel small RNAs, operons and transcription start sites. (nih.gov)
- Plastid transcription is mediated by two distinct types of RNA polymerases (RNAPs), bacterial-type RNAP (PEP) and phage-type RNAP (NEP). (pnas.org)
- in the active site channel provides the genetic information for RNA transcription. (proteopedia.org)
- Chen X, Chou WC, Ma Q, Xu Y. (2017) SeqTU: A Web Server for Identification of Bacterial Transcription Units . (rna-seqblog.com)
- In this article, we show that the average cost of rifampicin resistance in the pathogenic bacterium Pseudomonas aeruginosa is reduced by the addition of ribosome inhibitors (chloramphenicol or streptomycin) that indirectly constrain transcription rate and therefore reduce demand for RNA polymerase activity. (genetics.org)
- Long Noncoding RNA SSR42 Controls Staphylococcus aureus Alpha-Toxin Transcription in Response to Environmental Stimuli. (openrepository.com)
- To better understand the biological processes regulated by these two transcription factors, we performed RNA sequencing ( RNA-Seq ) on ant ail6 double mutants. (plantphysiol.org)
- The research article I will be analyzing is, "Control of bacterial transcription, translation and replication by (p)ppGpp" written by Anjana Srivatsan and Jue D Wang, published in 2008 Current Opinion in Microbiology 11: 100-105. (brightkite.com)
- The main research area of the paper is to control and regulate bacterial transcription, translation and replication with the use of the small nucleotides, pppGpp and ppGpp (also known as, (p)ppGpp). (brightkite.com)
- The introduction makes a convincing case of importance and value of the study by presenting the experiments performed already as well as showing success in generating the nucleotides ppGpp and pppGpp, which retained their capacity to control bacterial transcription, translation and replication. (brightkite.com)
- Argaman L, Argaman L, Hershberg R et al (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli . (springer.com)
- We demonstrate the performance of Rockhopper using 2.1 billion sequenced reads from 75 RNA-seq experiments conducted with Escherichia coli, Neisseria gonorrhoeae, Salmonella enterica, Streptococcus pyogenes and Xenorhabdus nematophila. (nih.gov)
- The conserved RNA-binding protein Hfq, originally discovered in Escherichia coli as a host factor for Qbeta replicase, has emerged as a pleiotropic regulator that modulates the stability or the translation of an increasing number of mRNAs. (nih.gov)
- We established a protocol for isolation of microarray-grade bacterial RNA from Escherichia coli K1 interacting with human brain microvascular endothelial cells. (asm.org)
- We developed a protocol for RNA extraction from Escherichia coli K1 interacting with human brain microvascular endothelial cells (HBMEC). (asm.org)
- Where can i find some bacterial RNA-Seq data, e.g. of Escherichia Coli? (biostars.org)
- Coleman J, Green PJ, Inouye M (1984) The use of RNAs complementary to specific mRNAs to regulate the expression of individual bacterial genes. (springer.com)
- RNA genes located on the DNA strand complementary to that which encodes the protein. (pasteur.fr)
- Most interestingly, analysis of chromatin-associated RNA revealed vhs-nuclease-activity-dependent transcriptional down-regulation of at least 150 cellular genes, in particular of many integrin adhesome and extracellular matrix components. (helmholtz-hzi.de)
- 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)
- 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)
- Fröhlich KS , Papenfort K, Berger AA, Vogel J (2012) A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. (uni-jena.de)
- Here, we review recent insights concerning RNA-based control of toxin synthesis, and discuss possible implications for persister generation. (paperity.org)
- Since more than half of the available antibiotics target the structurally conserved bacterial ribosomes, factors involved in protein synthesis are thus prime targets for the development of novel antibiotics. (biomedcentral.com)
- More than half of the antibiotics currently in use target the bacterial ribosome, typically at the elongation step of protein synthesis [ 3 ], through direct or proximal binding of the peptidyl transferase center (PTC) which catalyzes peptide bond formation [ 4 ]. (biomedcentral.com)
- Bacterial small RNAs, whose biogenesis is predominantly attributed to either the intergenic regions (trans-acting) or to the antisense strand of an open reading frame (cis-acting), are now appreciated to be among the most important post-transcriptional regulators of bacterial virulence and growth. (biomedcentral.com)
- Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo. (openrepository.com)
- Figure 1 shows an Agilent 2100 bioanalyzer electropherogram of a complex host-bacterial RNA population before and after bacterial RNA purification with MICROB Enrich . (bio-medicine.org)
- MAPS (MS2-affinity purification coupled with RNA-seq): an MS2 affinity tag is fused to a sRNA of interest and co-purified with its interacting RNA and sequenced. (rna-seqblog.com)
- Even in insects, the immune system is vital to defend animals from bacterial, fungal, and viral attacks. (scientificamerican.com)
- To analyze whether binase impairs virus replication by direct interaction with the viral particle we applied a hemagglutination inhibition assay and monitored the integrity of the viral RNA within the virus particle by RT-PCR. (biomedcentral.com)
- 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)
- Santiago-Frangos A*, Fröhlich KS *, Jeliazkov JR, Małecka-Grajek EM, Marino G, Gray JJ, Luisi BF, Woodson SA, Hardwick SW (2019) Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation. (uni-jena.de)
- 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)
- This work reveals yet another aspect of bacterial physiology controlled at the posttranscriptional level by sRNA regulators. (asm.org)
- Soukup, G. A. & Breaker, R. R. Engineering precision RNA molecular switches. (nature.com)
- RNA polymerase (RNAP) is a molecular machine that copies DNA into RNA and is found in every living organism. (proteopedia.org)
- Here, we use explicit solvent molecular dynamics (MD) simulations to map ions (NH 4 + , K + ) and water binding sites of a free bacterial A-site and their aminoglycoside complexes. (jbsdonline.com)
- Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. (unil.ch)
- This book is a valuable resource for molecular biologists and other investigators collecting the large number of reported DNA and RNA sequences and making them available in computer-readable form. (elsevier.com)
- A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule. (inserm.fr)
Quantitation of bacterial1
- Automated detection and quantitation of bacterial RNA by using electrical microarrays. (semanticscholar.org)
- Recent advances in high-throughput RNA sequencing (RNA-seq) have enabled tremendous leaps forward in our understanding of bacterial transcriptomes. (nih.gov)
- Our results suggest that Rockhopper can be used for efficient and accurate analysis of bacterial RNA-seq data, and that it can aid with elucidation of bacterial transcriptomes. (nih.gov)
- However, because no method has existed to isolate bacterial RNA away from host cell RNA, the corresponding analyses of bacterial transcriptomes has been impossible. (bio-medicine.org)
- How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? (biomedcentral.com)
- High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. (biomedcentral.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)
- In an attempt to address the paucity of computational methods for assembling bacterial transcriptomes from RNA-seq data, we previously developed Rockhopper [ 12 ], a system that supports reference-based assembly of bacterial transcriptomes. (beds.ac.uk)
- In the current study, we have developed novel algorithms for de novo assembly of bacterial transcriptomes, which we have implemented in the system Rockhopper 2. (beds.ac.uk)
- We show that our algorithms for de novo assembly of bacterial transcriptomes outperform other leading approaches, in terms of both sensitivity and specificity. (beds.ac.uk)
- Busch A, Richter AS, Backofen R (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. (springer.com)
- SeqTU provides a user-friendly interface and automated prediction of TUs from given RNA-seq data. (rna-seqblog.com)
- Here, we describe our s mall RNA target p rediction o rganizing t ool (SPOT), which streamlines the process of sRNA target prediction by providing a single pipeline that combines available computational prediction tools with customizable results filtering based on experimental data. (asm.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)
- 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)
- Should Rna-Seq Reads Map To One Strand Of Cdna Reference? (biostars.org)
- long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. (rna-seqblog.com)
- Here, we report an approach to detect diverse bacterial and fungal taxa in complex samples by direct analysis of community RNA in one step using NanoString probe sets. (asm.org)
- While the entire 16S sequence allows for comparison of all hypervariable regions, at approximately 1,500 base pairs long it can be prohibitively expensive for studies seeking to identify or characterize diverse bacterial communities. (wikipedia.org)
- Characterization of small non-coding ribonucleic acids (sRNA) among the large volume of data generated by high-throughput RNA-seq or tiling microarray analyses remains a challenge. (pasteur.fr)
- Transcriptome assays are increasingly being performed by high-throughput RNA sequencing (RNA-seq). (beds.ac.uk)
- High-throughput RNA sequencing (RNA-seq) is being used increasingly for transcriptome assays [ 1 ]. (beds.ac.uk)
- 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)
- 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)
- Brownlee GG (1971) Sequence of 6S RNA of E. coli . (springer.com)
- 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)
- MICROB Enrich was optimized using E. coli RNA in a background of human, mouse and rat RNA. (bio-medicine.org)
- We initially attempted to coextract bacterial and human RNA from a mixed sample of E. coli K1 and HBMEC. (asm.org)
- RNA extracted from a pure culture of E. coli K1 (data not shown) produced high quality RNA as expected (23S/16S = 1.8). (asm.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)
- 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)
- 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)
- Bottom middle: Sequencing of RNA hybrids reveals global sRNA interactomes. (embopress.org)
- 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)
- In particular, assembling transcripts is often a core stage of RNA-seq data analysis, yet efficient and accurate transcriptome assembly remains a challenging problem owing to a variety of factors, including artifacts from library construction, errors in sequencing, variable intra-read and inter-read error rates, repeat sequences, and transcript expression ranges that span several orders of magnitude [ 3 ]. (beds.ac.uk)
- From October 2019, Dr Kathrin Fröhlich is Junior Research Group Leader of the Group Bacterial RNA Biology at the Friedrich Schiller University Jena. (uni-jena.de)
- 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)
- Подробные сведения о темах исследования «Modified Oligonucleotides for Guiding RNA Cleavage Using Bacterial RNase P». Вместе они формируют уникальный семантический отпечаток (fingerprint). (nsu.ru)
- The bacterial extra-cellular ribonuclease binase is a well-studied RNase from Bacillus pumilus . (biomedcentral.com)
- Dear all I am working on 12 samples of strand specific bacterial RNA-seq data(4 reps for 3 treat. (biostars.org)
- Typical DNA Yields with the GenElute Bacterial Genomic DNA Kit. (sigmaaldrich.com)
- 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)
- A team led by researchers at the University of Georgia have recently developed a machine-learning method to accurately identify TUs from RNA-seq data, based on two features of the assembled RNA reads: the continuity and stability of RNA-seq coverage across a genomic region. (rna-seqblog.com)
Resistance to antibiotics2
- By amplifying RNA, microarray analyses can now be performed with up to 500-fold less starting material. (thermofisher.com)
- Qualitative and quantitative DNA- and RNA-based taxonomic microbiota analyses were combined to study the relationship of relative and absolute bacterial abundances and transcriptionally active bacterial microbiota components in the stomach of humans and mice. (asm.org)
- Genetic, multi-omic, and pharmacologic analyses indicated that retinol treatment affected B. vulgatus fitness through the activity of the bacterial AcrAB-TolC efflux system. (sciencemag.org)
- Soukup, G. A. & Breaker, R. R. Relationship between internucleotide linkage geometry and the stability of RNA. (nature.com)
- We have found patterns of the oligonucleotide sugar-phosphate backbone modi-fications that enhance oligonucleotide stability in the biological environment and do not violate the ability to interact with the enzyme and induce the RNA hydrolysis. (nsu.ru)
- Barquist L, Vogel J (2015) Accelerating discovery and functional analysis of small RNAs with new technologies. (springer.com)
- However, computational methods for analysis of bacterial transcriptome data have not kept pace with the large and growing data sets generated by RNA-seq technology. (nih.gov)
- Bacterial Transcriptional Start Site Analysis By Using Rna-Seq Data. (biostars.org)
- Hi community, I have just discovered a wonderful Galaxy server for RNA-Seq analysis: Oqtans http://galaxy.raetschlab.org/ . (usegalaxy.org)
- RNA samples are now been sequenced and I am designing a pipeline for data analysis. (usegalaxy.org)
- Hello, I am new to galaxy as well as RNA seq analysis. (usegalaxy.org)
- Hi, I am having a fastq file for my RNA data analysis in my computer. (usegalaxy.org)
- Hello, I am doing RNA-seq analysis using use galaxy.org, I want to run htseq but I do not know. (usegalaxy.org)
- HI, I am new to the RNA-seq, and the only available sources for me to do analysis is the Galaxy s. (usegalaxy.org)
- RNA-Seq analysis indicated that the ryhB -knockout mutant had a hyperactive metabolic state compared with the parent strain. (frontiersin.org)
- We find that Rockhopper 2 outperforms other de novo transcriptome assemblers and offers accurate and efficient analysis of bacterial RNA-seq data. (beds.ac.uk)
- Analysis of the data can be a bottleneck in RNA-seq studies owing to the size of the data, the complexity of the analysis, and a lack of user-friendly software tools. (beds.ac.uk)
- In addition to de novo transcriptome assembly, Rockhopper 2 is a comprehensive system that supports the various stages of RNA-seq data analysis, including normalizing data from different experiments, quantifying transcript abundance, and testing for differential transcript expression. (beds.ac.uk)
- SPARTA is a reference-based bacterial RNA-seq analysis workflow application for single-end Illumina reads. (rna-seqblog.com)
- SPARTA is turnkey software that simplifies the process of analyzing RNA-seq data sets, making bacterial RNA-seq analysis a routine process that can be undertaken on a personal computer or in the classroom. (rna-seqblog.com)
- 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)
- 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)
- RIP-seq (native RNA immunoprecipitation followed by RNA-seq): target transcripts are immunoprecipated with a protein of interest in cell lysates and analysed by RNA-seq. (rna-seqblog.com)
- A) RNA targets for phage display. (nih.gov)
- and those that act via the global RNA‐binding protein Hfq typically target multiple mRNAs. (embopress.org)
- Vascular plants have evolved a complex transcriptional network that is mediated by two types of RNA polymerases (RNAPs): cyanobacterium-derived plastid-encoded plastid RNA polymerase (PEP) and nuclear-encoded phage-type RNA polymerase (NEP). (pnas.org)
- RNA polymerases beta chain signature. (pdbj.org)
- Was wondering which would be the best mapper for strand-specific RNA-seq mapping for bacterial transcriptomics? (biostars.org)