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Topic: Small subunit ribosomal RNA

	Untitled Document
		The small subunit ribosomal RNA gene, the large subunit robosomal RNA gene, the 5.8S ribosomal RNA gene and the internal transcribed spacer (ITS) of Gonyaulax polyedra were cloned, and their sequences were analyzed to better understand their evolutionary position.
		The small unit of ribosomal RNA gene was 1,794 nt long, the large subunit ribosomal gene was approximately 3,500 nt long, and the 5.8S ribosomal RNA gene was 159 nt long.
		The intergenic spacer of ribosomal RNA gene (IGS) was about 2,200 nt long, indicating that 5,800 nt of transcribed sequences were separated by roughly 2,200 nt of intergenic spacer.
	home.ewha.ac.kr /~ebk11/lee_cloning.htm (218 words)

	RNA Synthesis
		Messenger RNAs (mRNAs): This class of RNAs are the genetic coding templates used by the translational machinery to determine the order of amino acids incorporated into an elongating polypeptide in the process of translation.
		Ribosomal RNAs (rRNAs): This class of RNAs are assembled, together with numerous ribosomal proteins, to form the ribosomes.
		The resultant RNA is, therefore, complimentary to the template strand of the DNA duplex and identical to the non-template strand.
	www-isu.indstate.edu /thcme/mwking/rna.html (2011 words)

	Ribosomal RNA - Wikipedia, the free encyclopedia
		Ribosomal RNA (rRNA) is the central component of the ribosome, the protein manufacturing machinery of all living cells.
		The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids (at center of small ribosomal subunit) and to interact with the tRNAs during translation by providing petidyltransferase activity (large subunit).
		Ribosomal RNA characteristics are important in medicine and in evolution.
	en.wikipedia.org /wiki/Ribosomal_RNA (410 words)

	UMASS Amherst Yeast snoRNA Database References
		Consequences of mutations in the non-coding RMRP RNA in cartilage-hair hypoplasia.
		Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center.
		Rat nucleolar 7-2 RNA is homologous to mouse mitochondrial RNase mitochondrial RNA-processing RNA.
	people.biochem.umass.edu /fournierlab/snornadb/references.php (2822 words)

	PCR Amplification of a Gene for Ribosomal RNA from Different Organisms
		A ribosome is composed of a large subunit and a small subunit and each subunit contains specific RNAs that are associated with ribosomal proteins.
		Ribosomes play the same essential role in protein synthesis in all contemporary organisms and the genes for ribosomal RNAs in each subunit are highly conserved.
		The gene for the small-subunit ribosomal RNA (16 S-like) has been especially useful in evolutionary studies of distant phylogenetic relationships because it has remained quite stable during evolution of all organisms.
	www.modernbio.com /pcr_amplification_of_a_gene_for_ribosomal_rna.htm (410 words)

	`Well-determined' regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA
		Recent structural analyses of genomic RNAs from RNA coliphages suggest that both well-determined base paired helices and well-determined structural domains that are identified by `energy dot plot' analysis using the RNA folding package mfold, are likely to be predicted correctly.
		We have analyzed 15 small subunit rRNAs from bacteria (14) and chloroplasts (1).
		These RNAs have a large number of well-determined helices and their RNA secondary structures are predicted to be unusually stable.
	www.bioinfo.rpi.edu /~zukerm/ref/ZUKM95.html (4505 words)

	The Bay Paul Center Portal
		Elwood, H.J., G.J. Olsen and M.L. Sogin: The Small-Subunit Ribosomal RNA Gene Sequences from the Hypotrichous Ciliates Oxytricha nova and Stylonychia pustulata, Mol.
		Sogin, M.L., H.J. Elwood and J.H. Gunderson: Evolutionary diversity of eukaryotic small subunit rRNA genes, Proc.
		Sogin, M.L., M.T. Swanton, J.H. Gunderson and H.J. Elwood: Sequence of the Small Subunit Ribosomal RNA Gene from the Hypotrichous Ciliate Euplotes aediculatus, J.
	jbpc.mbl.edu /cv-sogin.html (5163 words)

	biblio (Site not responding. Last check: 2007-09-16)
		Phylogenetic analysis of the small subunit ribosomal RNA of Marteilia refringens validates the existence of phylum Paramyxea (Desportes and Perkins, 1990).
		The nucleotide sequence of the small subunit ribosomal RNA gene of Marteilia refringens is used to elucidate the phylogenetic position of the phylum Paramyxea.
		The small subunit ribosomal RNA gene sequence of M. refringens is very different from all known sequences of eukaryotic organisms, including those of myxosporeans and haplosporeans.
	biomserv.univ-lyon1.fr /sitelabo/bibmanager/abstract.php?id_art=52 (179 words)

	RNA
		With the goal of understanding which regions of B2 RNA are important for high-affinity binding to RNA polymerase II and repression of transcription, we performed a structural and deletion analysis of a 178 nucleotide (nt) B2 RNA.
		Deletion studies revealed that a 51-nt region of B2 RNA is sufficient for high-affinity binding to RNA polymerase II, association with preinitiation complexes, and repression of transcription in vitro, the latter of which involves a large predominately single-stranded region within the RNA.
		Heparin was successfully removed by precipitation of the RNA with lithium chloride, as demonstrated by the reversal of the inhibition on RT-PCR reactions.
	barf.jcowboy.org /rna.xml (5016 words)

	SSU rRNA Secondary Structure Prediction and Alignment Main (Site not responding. Last check: 2007-09-16)
		This server allows you to enter an RNA sequence and predict the secondary structure interactions interpreting the sequence as a bacterial small subunit ribosomal RNA.
		This grammar is a probabilistic model that has been trained to recognize bacterial small subunit ribosomal RNA.
		Modeling RNA with a stochastic context free grammar disallows the modeling of of pseudoknotted interactions.
	www.cse.ucsc.edu /research/compbio/ssurrna.html (423 words)

	Conserved primer sequences for PCR amplification and sequencing from nuclear ribosomal RNA
		The nuclear-encoded ribosomal RNA genes (rDNA) of fungi exist as a multiple-copy gene family comprised of highly similar DNA sequences (typically from 8-12 kb each) arranged in a head-to-toe manner.
		Depending on the orientation and position of the 5S RNA gene, the PCR may be used to sequentially amplify either aportion of the intergenic spacer region (IGS) beyond the large subunit RNA coding region.
		The small subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustula.
	www.biology.duke.edu /fungi/mycolab/primers.htm (1101 words)

	BioMed Central \| Full text \| How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys
		Over the past few years, cultivation-independent identification of microbial organisms by PCR amplification and sequencing of small-subunit ribosomal RNA (SSU rRNA) genes revealed a huge diversity of eubacterial and archaeal phylotypes in environmental samples, many of which are not represented by cultured organisms [1,2].
		Sequencing of 81 clones from an EES of the small river, the Seymaz (Geneva, Switzerland) yielded 58 distinct SSU rRNA phylotypes.
		This may be due to the extreme divergence of foraminiferan ribosomal genes, which cannot be directly amplified with most known universal primers [30], although other explanations, such as a low abundance of Foraminifera in the samples, cannot be discarded.
	www.biomedcentral.com /1741-7007/2/13 (5537 words)

	RNA (Site not responding. Last check: 2007-09-16)
		SMALL SUBUNIT DATABASE: Over 11 500 complete or nearly complete sequences are now available from the Antwerp database on small subunit ribosomal RNA.
		VIROID RNA (46) This is an online database to facilitate research on viroid, viroid-like RNAs and human hepatitis delta virus (vHDV) by presenting a large number of sequences and related data in a comprehensive and user-friendly format (e.g.
		A novel "map" format provides the edited RNA sequence aligned with the genomic DNA sequence and the translated amino acid sequence; both U-deletions and U-insertions are indicated by gaps in the edited sequence or the genomic sequence.
	www.rna.icmb.utexas.edu /linxs/databases/nucleic-acids/rna.html (885 words)

	BioMed Central \| Full text \| Evaluation of sequence alignments and oligonucleotide probes with respect to ...
		And with the availability of high-resolution RNA crystal structures for the 30S [11] and 50S [12] ribosomal subunits and the subsequent validation of comparative rRNA secondary structure models [10], the biologists are impelled to use three-dimensional structure of rRNA for evaluating sequence alignments of rRNA genes.
		In this regard, all-atom structure of ribosomal RNA of Escherichia coli [13] deduced from the crystal structure of 30S ribosomal subunit of Thermus thermophilus [11], can be used as a reference structure to evaluate individual rRNA sequences and the multiple alignments of rRNA genes.
		Although the native conformation of ribosomes is disturbed during the experimental procedures of FISH [25], a thorough in silico evaluation of oligonucleotide probes with respect to the higher-order structure and experimental accessibility data (Figure 4) may help the users to design more successful hybridization experiments.
	www.biomedcentral.com /1471-2105/7/240 (4905 words)

	RNAmods - related links (Site not responding. Last check: 2007-09-16)
		RNAs not directly involved in protein synthesis, in the 75-400 nucleotides range, synthesized by either RNA Polymerase I, II or III
		The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.
		Small Nucleolar RNAs (snoRNAs) from the Yeast Saccharomyces cerevisiae.
	www-medlib.med.utah.edu /RNAmods/rnadata.htm (372 words)

	Phylogeny of Lobose Amoebae Based on Actin and Small-Subunit Ribosomal RNA Genes -- Fahrni et al. 20 (11): 1881 -- ...
		RNA was extracted as described previously (Bolivar et al.
		Phylogeny of the genera Entamoeba and Endolimax as deduced from small-subunit ribosomal RNA sequences.
		Primary and secondary structure of the small-subunit ribosomal RNA of the naked, marine amoeba Vannella anglica: phylogenetic implications.
	mbe.oxfordjournals.org /cgi/content/full/20/11/1881 (3696 words)

	van de Peer, Yves (Site not responding. Last check: 2007-09-16)
		Capesius I. van de Peer Y. Secondary structure of the large ribosomal subunit RNA of the moss Funaria hygrometrica.- In: Journal of plant physiology, 151(1997), p.
		Chalwatzis N. Hauf J. van de Peer Y. Kinzelbach R. Zimmerman F.K. 18S ribosomal RNA genes of insects: primary structure of the genes and molecular phylogeny of the Holometabola.- In: Annals of the Entomological Society of America, 89(1996), p.
		Winnepenninckx B. Backeljau T. van de Peer Y. de Wachter R. Structure of the small subunit ribosomal RNA of the pulmonate snail Limicolaria kambeul, and phylogenetic analysis of the metazoa.- In: FEBS letters, 309(1992), p.
	anet.ua.ac.be /acadbib/ua/664 (2081 words)

	Transcription
		In eukaryotes, this requires — at least for protein-encoding genes — that the nucleosomes in front of the advancing RNA polymerase (RNAP II) be removed.
		Several types of RNA are synthesized in the nucleus of eukaryotic cells.
		serves as an assembly point for the proteins needed to recruit the small subunit of the ribosome to begin translation.
	users.rcn.com /jkimball.ma.ultranet/BiologyPages/T/Transcription.html (2193 words)

	Molecular phylogeny of nitrogen-fixing unicellular cyanobacteria
		Molecular phylogenetic study was conducted using maximum likelihood tree inference methods with small subunit ribosomal RNA sequence data to ascertain the evolutionary relationships among sheathless, single-cell cyanobacteria capable of nitrogen fixation.
		In this report, we present a phylogenetic analysis of small ribosomal subunit RNA (SSU rRNA) sequences to evaluate the phylogenetic relationships among sheathless, unicellular cyanobacteria with nitrogen-fixation abilities.
		A negative control, in which template was replaced by double distilled water, and an additional control, in which total RNA served as template in the absence of reverse transcriptase, were also run during all PCR amplifications.
	ejournal.sinica.edu.tw /bbas/content/2001/3/bot423-04.html (3281 words)

	[No title]
		The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata.
		We have determined the complete nucleotide sequence of the small-subunit ribosomal RNA genes for the ciliate protozoans Stylonychia pustulata and Oxytricha nova.
		In a phylogeny inferred from comparisons of several eukaryotic small-subunit ribosomal RNAs, the divergence of the ciliates from the eukaryotic line of descent is seen to coincide with the radiation of the plants, the animals, and the fungi.
	biol1.bio.nagoya-u.ac.jp:8001 /~hori/ElwoodHJ85.html (102 words)

	RNA Sequences
		Database on the Structure of Large Subunit Ribosomal RNA
		Database on the Structure of Small Subunit Ribosomal RNA
		RNA splicing and gene structure in Caenorhabditis elegans
	www.public.iastate.edu /~juncao/RNASequences.htm (34 words)

	Ibis Therapeutics - RNA Links (Site not responding. Last check: 2007-09-16)
		The example of 16s ribosomal RNA provides a subject that is particularly refractory and is therefore suited to the integration of material from many souces.
		Analysis is available on a subunit basis, for example, small subunit prokaryote, eukaryote or mitochondria, with a further selection of particular species due to be included.
		Large and small ribosomal subunit RNA databases (LSU and SSU rRNA) are available.
	www.ibisrna.com /public/rna_links.html (402 words)

	Mitochondrial DNA Restriction Fragment Length Polymorphism (RFLP) and 18S Small-Subunit Ribosomal DNA PCR-RFLP Analyses ...
		Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify and independent rhizopod lineage containing the Euglyphina and the Chlorarachniophyta.
		Ribosomal RNA genes of ‘pathogenic’ and ‘nonpathogenic’ Entamoeba histolytica are distinct.
		Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of Acanthamoeba from humans with keratitis and from sewage sludge.
	jcm.asm.org /cgi/content/full/40/4/1199 (3549 words)

	SCU \| Centre for Animal Conservation Genetics
		Bulletin 466, New York State Museum, albany, N.Y. Johnson, A.M. and Baverstock, P.R. Rapid ribosomal RNA sequencing and the phylogenetic analysis of protists.
		Baverstock, P.R. and Johnson, A.M. Ribosomal RNA nucleotide sequence: A comparison of newer methods used for its determination, and its use in phylogenetic analysis.
		Johnson, A.M., Fielke, R., Christy, P.E., Robinson, B. and Baverstock, P.R. Small subunit ribosomal RNA evolution in the genus Acanthamoeba.
	www.scu.edu.au /research/cacg/publications.html (2301 words)

	Search results for research title
		Ribosomal RNA sequencing, alignment of known sequences, study of secondary structure, and use for studying the phylogenetic relationship between living species
		12, 671-678 (1995) The phylogeny of Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides.
		USA 93, 7732-7736 (1996) Substitution rate calibration of small ribosomal subunit RNA identifies chlorarachniophyte endosymbionts as remnants of green algae.
	www.br.fgov.be /cgi-bin/BIODIV/research.pl?res_id=674 (1515 words)

	Profiles of microorganisms: the microbial world (Site not responding. Last check: 2007-09-16)
		The gene most commonly used for this codes for the RNA in the small subunit (SSU) of the ribosome.
		We should note a technical point about this tree: the comparison of ribosomal RNA gene sequences can show the possible relatedness of organisms, but other information is needed to provide the root of a tree.
		By using a primer from a highly conserved region of the gene for SSU rRNA, any ribosomal genes in the sample will be copied and their sequences can be compared with the sequences of known organisms.
	www.helios.bto.ed.ac.uk /bto/microbes/index.htm (3020 words)

	RNA SYNTHESIS
		Ribosomal RNAs (rRNAs): This class of RNAs are assembled, together with numerous ribosomal proteins, to form the
		The capacity of the various polymerases to synthesize different RNAs was shown with the toxin a-amanitin.
		subunit is only transiently associated with the holoenzyme.
	www.sierr.unina.it /biocell/rna_synthesis.htm (1861 words)

	Brown / Paper/Abstract ~ PMMB ~ Program in Mathematics and Molecular Biology (Site not responding. Last check: 2007-09-16)
		I was able to correct several small errors in the code that does secondary structure prediction.
		I now have secondary structure predictions for ALL bacterial small subunit ribosomal RNA sequences in the RDP database that have complete sequences.
		I hope to extend this work to use SCFG features of small subunit ribosomal RNA sequences in a SVM classifier that does phylogenetic classification.
	www.math.fsu.edu /~pmmb/papers/brown.htm (153 words)

	RNA Sequence Databases
		A comprehensive database for small nucleolar RNAs (SnoRNAs) from the yeast Saccharomyces cerevisae.
		Ribosomal Database Project, RDP is curated databse that offers ribosomal nucleotide sequences.
		It comprises 11,500 complete or nearly complete sequences of small subunit ribosomal RNA.
	members.rediff.com /ebioinfogen/rna.htm (182 words)

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