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*  Woese and Fox: Life, rearranged | PNAS
"Carl's deep understanding of the universality of ribosomal RNA and the pragmatic ease of getting abundant RNA for analysis were ... Ribosomal RNA: Life's Timekeeper. By then, Woese had accepted a faculty position in microbiology at the University of Illinois ... Soon, Woese set out to catalog ribosomal RNA sequences in a range of microbes. One form of rRNA-named 16S for the rate at which ... 1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955-6959. ...
https://www.pnas.org/content/109/4/1019
*  Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses | PNAS
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin ... Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin ... Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin ... Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses Message Subject (Your Name) has sent you a message ...
https://www.pnas.org/content/82/20/6955?ijkey=10b172a046d0f9f83fdca98e9e1b82e53ea61fe6&keytype2=tf_ipsecsha
*  The universal ancestor | PNAS
Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of ... The unrooted universal phylogenetic tree that emerged from ribosomal RNA (rRNA) sequence comparisons provided the first glimpse ... The fact that translation is an RNA-based mechanism suggests antiquity. The fact that it is complex and its key components tend ... and these histories coincided with those of the ribosomal components and the like-but only after the point of their ...
https://www.pnas.org/content/95/12/6854
*  Phylogenetic structure of the prokaryotic domain: The primary kingdoms | PNAS
However, ribosomal RNA does. It is a component of all self-replicating systems; it is readily isolated; and its sequence ... A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three ... ribosomal RNA has been characterized in a moderately large and varied collection of organisms and organelles, and the general ... It has been argued elsewhere that features such as RNA base modification generally represent the final stage in the evolution ...
http://www.pnas.org/content/74/11/5088
*  Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast | PNAS
Abbreviations: POM, projected orthologous module; RP, ribosomal protein; RRPE, ribosomal RNA processing element; TA, ... For example, RP module genes in C. albicans, D. hansenii, and Y. lipolytica are also enriched for the ribosomal RNA processing ... We show how a cis-element emerged concurrently in dozens of promoters of ribosomal protein genes, followed by the loss of a ... These cases include modules for key molecular functions, such as ribosomal protein synthesis (Fig. 1d ) and stress response ( ...
https://www.pnas.org/content/102/20/7203?ijkey=794db9c0b75326719bb8a7428d12a948ad96ae7b&keytype2=tf_ipsecsha
*  Is junk DNA bunk? A critique of ENCODE | PNAS
Conversely, some conserved functions, such as the complementary base-pairings that maintain ribosomal RNA secondary structures ... binding to proteins and other RNAs is something that RNAs do. It is inevitable that some such interactions, initially ... 2010) RNA dust: Where are the genes? DNA Res 17(2):51-59. ... Secondary structure of 16S ribosomal RNA. Science 212(4493):403 ... Initially, the RNA secondary structure is sufficient to catalyze self-removal, but fortuitously bound proteins that stabilize ...
https://www.pnas.org/content/110/14/5294.full
*  The RNA code: Nature's Rosetta Stone | PNAS
tRNA required the ribosomal peptidyl transferase (10).. Using these biochemical in vitro approaches, Nirenberg deciphered the ... 1967) Fine structure of RNA codewords recognized by bacterial, amphibian, and mammalian transfer RNA. Science 155(3764):820-826 ... The discovery of fragmented genes, RNA splicing, RNA editing, and viral (HIV) concatenated proteins followed because the coding ... which measured the binding of radioactive aminoacyl transfer RNA (tRNA) to ribosomes by a triplet (not doublet) synthetic RNA ...
https://www.pnas.org/content/111/16/5758.full
*  Parallel genomic evolution and metabolic interdependence in an ancient symbiosis | PNAS
RNA polymerase, β subunit; and ribosomal proteins L2, S5, and S11. The GenBank accession numbers for the genomes are: ... In RNA transcription, only the RNA polymerase core enzyme (rpoA, the α subunit; rpoB, the β subunit; and rpoC, the β′ subunit) ... It has genes to replicate its genome, transcribe RNA, and translate this mRNA into protein, although it is missing many genes ... Sulcia does have a minimal set of genes to transcribe RNA, translate protein, and replicate its genome, although its set of ...
https://www.pnas.org/content/104/49/19392.long
*  Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals | PNAS
Primers validated in previous studies (45⇓⇓-48) were used to amplify the 16S ribosomal RNA and GroEL. The taxonomic groups ... Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17(19):7843-7853. ...
https://www.pnas.org/content/114/3/E367
*  Cytoglobin modulates myogenic progenitor cell viability and muscle regeneration | PNAS
The transcript levels were normalized to 18s-ribosomal RNA. *P , 0.05 postinjury vs. baseline level; n = 3-5 in each group. (F ... Western Blot Analysis, RNA Isolation, and qRT-PCR.. Proteins from cell lysates, cellular fractions (i.e., nuclear and cytosolic ... Western blot analysis was performed as previously described (24, 28, 68). Total RNA, RT-PCR, and qRT-PCR were performed as ... Cygb was knocked down efficiently in C2C12 myoblasts using small, interfering RNA (siRNA) directed against Cygb (siCygb) (Fig. ...
http://www.pnas.org/content/111/1/E129
*  Evolution of the ribosome at atomic resolution | PNAS
Regions of variable size that interrupt the universal core secondary structure of ribosomal RNA. Ribosomal RNA-Structure, ... Here we describe an atomic level model of the evolution of ribosomal RNA (rRNA) from the large ribosomal subunit (LSU). Our ... 2008) The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit. RNA 14( ... Ribosomal RNA of eukaryotes contains expansion segments accreted onto the surface of the core, which is nearly identical in ...
http://www.pnas.org/content/111/28/10251
*  Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis | PNAS
Reverse transcription reactions were performed with (+) and without (−) 30S ribosomal subunit. The signals corresponding to the ... The RNA structure is critical for RNA function in all domains of life. We determined the transcriptome-wide RNA structurome of ... RNA structures play a pivotal role in the function of noncoding RNAs (ncRNAs) comprised of rRNAs, tRNAs, and small regulatory ... A) 5′-end-labeled in vitro transcribed RNA was treated with nucleases S1 and T1 at 25 °C, 37 °C, and 42 °C. RNA fragments were ...
https://www.pnas.org/content/113/26/7237
*  Somatic mtDNA mutations cause aging phenotypes without affecting reactive oxygen species production | PNAS
The levels of 18S ribosomal RNA was used as loading control. (B) Western blot analysis showing SOD2 protein levels in total ... RNA Isolation and Northern Blot Analysis. Total RNA was isolated from heart by using Trizol Reagent (Invitrogen) following the ... The RNA loading was normalized to 18S rRNA. ...
http://www.pnas.org/content/102/50/17993
*  A null model for microbial diversification | PNAS
2012) SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823-1829. ... delimited by regions of 16S ribosomal RNA (rRNA) genes showing at least 97% sequence identity, have been used for ... Gene family annotations are as follows: (A) ribosomal protein S14, (B) gutQ, (C) fliC, (D) glycerate kinase, (E) pilX, (F) pilS ... Functional categories are assigned one-letter abbreviations as defined by the COG database: J, Translation, ribosomal structure ...
https://www.pnas.org/content/114/27/E5414.long
*  Extreme polyploidy in a large bacterium | PNAS
The ribosomal RNA operon is preferentially amplified in some eukaryotes (26-28). Ribosomal RNA synthesis is the rate-limiting ...
https://www.pnas.org/content/105/18/6730
*  Wolbachia induces reactive oxygen species (ROS)-dependent activation of the Toll pathway to control dengue virus in the...
RNA Extraction, cDNA Synthesis, and Real-Time PCR Assays.. Total RNA was extracted from mosquito tissues using the RNeasy Mini ... The ribosomal protein S6 (RPS6) gene was used for normalization of cDNA templates. All primers used for real-time PCR are ... Two-day-old Waco females were fed with a sugar solution containing 1% H2O2 (vol/vol) for 5 d. The total RNA of midguts was ... Total RNA was extracted using RNeasy Mini Kit (QIAGEN), according to the manufacturer's instruction. A 4 × 44K microarray ( ...
http://www.pnas.org/content/109/1/E23
*  Antagonistic roles for the ubiquitin ligase Asr1 and the ubiquitin-specific protease Ubp3 in subtelomeric gene silencing | PNAS
RNA Sequencing and Analysis.. RNA from strains BY4742 and YTM27 was isolated by hot acidic phenol extraction. Ribosomal RNA ... RNA Sequencing and Analysis.. RNA from strains BY4742 and YTM27 was isolated by hot acidic phenol extraction. Ribosomal RNA ... RNA Isolation and RT-QPCR.. RNA was isolated from overnight 25-mL cultures of yeast by extraction with hot acidic phenol. After ... We performed comparative transcriptomic analysis (RNA-seq) on RNA isolated from yeast expressing either WT Asr1 or a RING ...
http://www.pnas.org/content/113/5/1309
*  Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection | PNAS
1). The genome contains six ribosomal RNA operons and 60 tRNAs for all amino acids. Its chromosomal origin and terminus ...
http://www.pnas.org/content/102/37/13272.long
*  Ghrelin octanoylation mediated by an orphan lipid transferase | PNAS
Ribosomal RNA (rRNA) levels were with the assay from Applied Biosystems (catalog no. 4310893E). PCR conditions for GOAT and 18s ... GOAT mRNA levels were determined with total RNA by using the RNeasy kit from Qiagen. One microgram of total RNA was converted ... Silencing RNAs were generated and used for determination of ghrelin acylation in TT cells. Fig. 2 shows the effects of ... The following five double-stranded RNA-silencing sequences were used to target GOAT transcript: siRNA7-1, 5′-UGU UGC AGA CAU ...
http://www.pnas.org/content/105/17/6320?ijkey=a7fe1932c50284dac29fd7cd6b4c67e71185f179&keytype2=tf_ipsecsha
*  Synthesis of phylogeny and taxonomy into a comprehensive tree of life | PNAS
2013) The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res 41( ...
http://www.pnas.org/content/112/41/12764
*  Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe | PNAS
2013) The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res 41( ... structure were characterized by using barcoded Illumina sequencing of the internal transcribed spacer region of the ribosomal ...
http://www.pnas.org/content/112/35/10967?ijkey=686b4ee4766343a6c646889978c72d28652f734f&keytype2=tf_ipsecsha
*  Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: Functional implications | PNAS
The RRF residues making direct contact with rRNA are shown with side chains (red). Ribosomal RNA residues making direct ... Number, position, and significance of the pseudouridines in the large subunit ribosomal RNA of Haloarcula marismortui and ... Evidence That Antibiotics Bind to Human Mitochondrial Ribosomal RNA Has Implications for Aminoglycoside Toxicity ... pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA ...
https://www.pnas.org/content/101/24/8900.long
*  Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice | PNAS
2013) The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res 41( ... The RNA pellet was air-dried at room temperature and dissolved in DEPC-treated water for 10 min at 55 °C. The quantity of RNA ... RNA Extraction, cDNA Synthesis, and qRT-PCR.. RNA was extracted with the TRIZOL Reagent (Life Technologies) following ... RNA Extraction, cDNA Synthesis, and qRT-PCR.. RNA was extracted with the TRIZOL Reagent (Life Technologies) following ...
http://www.pnas.org/content/113/9/E1306
*  Dispersal limitation promotes the diversification of the mammalian gut microbiota | PNAS
2013) The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acid Res 41:D590- ...
https://www.pnas.org/content/114/52/13768
*  dCas9-targeted locus-specific protein isolation method identifies histone gene regulators | PNAS
2015) End-targeting proteomics of isolated chromatin segments of a mammalian ribosomal RNA gene promoter. Nat Commun 6:6674. ... By isolating the RNAs enriched from each protein IP, we can test whether certain RNAs specifically interact with the proteins ... RNA Isolation, Reverse Transcription, and Real-Time PCR Analysis.. Total RNA was extracted and purified using TRIzol reagent ( ... 1997) The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding ...
http://www.pnas.org/content/115/12/E2734