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At least 1,081 records · Page 60Linked to original sources
PubMed1996

Exploring phenotype space through neutral evolution.

RNA secondary-structure folding algorithms predict the existence of connected networks of RNA sequences with identical secondary structures. Fitness landscapes that are based on the mapping between RNA sequence and RNA secondary structure hence have many neutral paths. A neutral walk on these fitness landscapes gives access to a virtually unlimited number of secondary structures that are a single point mutation from the neutral path. This shows that neutral evolution explores phenotype space and can play a role in adaptation.

Algorithms↗
PubMed1991

The gene encoding rat liver glycogen phosphorylase contains multiple polyadenylation signal sequences.

RNA blot analysis of rat liver and adipose tissues detected two glycogen phosphorylase (GP)-encoding transcripts. The polymerase chain reaction was used to characterize the 3'-noncoding region of the gene (L-GP) encoding liver-GP (L-GP) from the lean Zucker rat (Fa/Fa). Three distinct classes of colinear cDNA clones were identified by nucleotide (nt) sequence analysis, demonstrating that the L-GP gene contains at least three functional polyadenylation sites. The predominant L-GP transcript was generated by polyadenylation 130 nt 3' from the end of the coding region. A previously uncharacterized L-GP transcript is generated by polyadenylation at 346 nt 3' of the first polyadenylation site. Polyadenylation site selection does not appear to be regulated in a tissue-specific fashion. The relative steady-state L-GP mRNA levels in the different types of adipose tissues were comparable to, or exceeded transcript levels in liver.

Adipose Tissue↗
PubMed2001

Optimization of experimental conditions for RNA-based sequencing of MLH1 and MSH2 genes.

The most sensitive technique for the detection of germline mutations is exon by exon sequencing of the gene under investigation using genomic DNA as a template for analysis. This approach, however, has cost and sensitivity limitations that can, at least in part, be overcome by RNA-based analysis. Germline mutations of MLH1 and MSH2 are the most frequent cause of the inherited susceptibility to colorectal and other epithelial cancers known as hereditary non-polyposis colorectal cancer (HNPCC). We compared the analysis of the MLH1 and MSH2 genes using mRNA and genomic DNA as starting material from 21 HNPCC patients. All samples were investigated by RT-PCR, sequencing of cDNA and simultaneous sequencing of genomic DNA. The cDNA was generated using specific primers complementary to the ends of MLH1 and MSH2 genes, respectively. Mutations in MLH1 and MSH2 were detected in 11 out of 21 unrelated patients. In 10 out of 11 cases, mutations were detected independently of the type of primers used for reverse transcription (RT). One novel missense mutation (K751R) in MLH1 was detected using this method. One nonsense mutation (E205X) in MSH2 was only detectable when RT was performed using MSH2 gene-specific primers. Shorter PCR products indicative of alternatively spliced transcripts were not observed when MLH1 or MSH2 specific cDNA RT primers were employed to generate template, except in one case where exon skipping was observed for exons 9 and 10. In this report we demonstrate that primers specific for RT of MLH1 and MSH2 are crucial for increasing the sensitivity of cDNA analysis. DNA sequencing using RNA as a basis for template construction may be a valuable and economical alternative to genomic DNA sequencing.

Adaptor Proteins, Signal Transducing↗
PubMed2001

Identification of Arcobacter cryaerophilus isolated from a traffic accident victim with bacteremia by 16S ribosomal RNA gene sequencing.

Traditional ways of identifying slow growing bacteria is slow and often difficult. In this study, a small, Gram-negative, facultative anaerobic, slow growing bacillus was isolated from the blood culture of a 7-year old traffic accident victim. The bacterium was non-hemolytic, catalase and oxidase positive. An attempt to use the Vitek system (GNI+) and the API system (20NE) to identify the strain was unsuccessful as the growth controls showed negative results. 16S ribosomal RNA gene sequencing showed that there was 1 base difference between the isolate and Arcobacter cryaerophilus (GenBank Accession no. U25805), 1 base difference between the isolate and A. cryaerophilus (GenBank Accession no. U34387), 10 base differences between the isolate and A. cryaerophilus (GenBank Accession no. L14624), 34 base differences between the isolate and A. butzleri (GenBank Accession no. U34386), 34 base differences between the isolate and A. butzleri (GenBank Accession no. U34387), and 38 base differences between the isolate and A. butzleri (GenBank Accession no. L14626), indicating that the isolate most closely resembled a strain of A. cryaerophilus. Identification of the isolate in our case by conventional methods was difficult, as the absence of a curved morphology has made it confused with other Gram-negative non-fermentative bacteria, and the slow growth rate has made it unidentifiable by both the Vitek and API systems. Although the exact source of infection and route of transmission in our case remains elusive, we speculate that the bacteria were transmitted through the respiratory tract while the boy was suffocated in the mud. The present report represents an example of showing the usefulness of 16S rRNA gene sequencing for identification of slow growing bacteria.

Accidents, Traffic↗
PubMed1981

A sequence from Drosophila melanogaster 18S rRNA bearing the conserved hypermodified nucleoside am psi: analysis by reverse transcription and high-performance liquid chromatography.

The naturally occurring modified nucleoside 3-[3-amino-3-carboxypropyl]-1-methylpseudouridine (abbreviated am psi) is found in eukaryotic 18S rRNA. We localized am psi to sequence resolution in D. melanogaster 18S rRNA. This hypermodified base causes an absolute stop in cDNA elongation. The RNA sequence bearing am psi was determined by dideoxy-sequencing with reverse transcriptase. The rDNA coding for this part of the 18S rRNA was sequenced by the Maxam-Gilbert method. Together these two sequencing methods can be used to position the cDNA stop (am psi) in the rRNA sequence. Chemical evidence for the existence of am psi in this RNA sequence was obtained by high-performance liquid chromatography (HPLC) of 18S rRNA nucleosides from radioactive-labeled cells. L-[2-14C] methionine will selectively label am psi in eukaryotic 18S rRNA. Using HPLC, we found a single 14C-labeled nucleotide in digests of 18S rRNA. This nucleotide is in the RNA sequence bearing the cDNA stop since a restriction fragment which hybridizes to this sequence protects the modified base from RNase T1 digestion.

Animals↗
PubMed1999

Cryptosporidium is more closely related to the gregarines than to coccidia as shown by phylogenetic analysis of apicomplexan parasites inferred using small-subunit ribosomal RNA gene sequences.

The phylogenetic placement of gregarine parasites (Apicomplexa: Gregarinasina) within the Apicomplexa was derived by comparison of small-subunit ribosomal RNA gene sequences. Gregarine sequences were obtained from Gregarina niphandrodes Clopton, Percival, and Janovy, 1991, and Monocystis agilis Stein, 1848 (Eugregarinorida Léger 1900), as well as from Ophriocystis elektroscirrha McLaughlin and Myers, 1970 (Neogregarinorida Grassé 1953). The sequences were aligned with several other gregarine and apicomplexan sequences from GenBank and the resulting data matrix analyzed by parsimony and maximum-likelihood methods. The gregarines form a monophyletic clade that is a sister group to Cryptosporidium spp. The gregarine/ Cryptosporidium clade is separate from the other major apicomplexan clade containing the coccidia, adeleids, piroplasms, and haemosporinids. The trees indicate that the genus Cryptosporidium has a closer phylogenetic affinity with the gregarines than with the coccidia. These results do not support the present classification of the Cryptosporidiidae in the suborder Eimerioirina Léger, 1911.

Animals↗
PubMed1995

Synthesis and conformational investigation of tandem repeat sequence in RNA polymerase II.

The largest subunit of RNA polymerase II has a very interesting sequence in the C-terminus; that is, a tandem repeat sequence of Ser-Pro-Thr-Ser-Pro-Ser-Tyr consisted of proline residues and three kinds of residues having side-chain hydroxyl groups. Although lack of this tandem repeat is a lethal event in vivo, its functional role is unclear. The sequential polypeptide corresponding to this tandem repeat, poly(Ser-Pro-Thr-Ser-Pro-Ser-Tyr), was synthesized and its conformation was investigated by circular dichroism comparing to the monomeric heptapeptide. In addition, the theoretical conformational analysis based on the molecular mechanics was tried for the heptapeptide in the repeating unit and the periodic polyheptapeptide corresponding to the tandem repeat sequence. These results suggested the possibility that the tandem repeat contains a kind of super conformation composed of the repetitive turn structure in the native state. The characteristic repetitive turn structure would be the key of its function mechanism.

Amino Acid Sequence↗
PubMed1996

A fluorescence-labeling method for sequencing small RNA on polyacrylamide gel.

A practical fluorescence-labeling method for sequencing small RNAs by the traditional 'direct read out' on polyacrylamide gel electrophoresis was established. The 3' terminus of RNA was oxidized into dialdehyde by sodium periodate and then labeled with fluorescein-5-thiosemicarbazide through the condensation reaction between carbazide and aldehyde. The fluorescence-labeled RNA was partially degraded enzymatically and fractionated by polyacrylamide gel electrophoresis. The fluorescent bands were visualised by ultraviolet photography. A partial sequence of yeast 5S rRNA was determined. The result indicates that this method can be used in sequencing small RNAs rapidly, conveniently and safely.

Electrophoresis, Polyacrylamide Gel↗
PubMed1999

Rapid and specific detection of RNA base sequence using fluorescence polarization.

Rapid and specific determination of the RNA gene of hepatitis C virus (HCV), which had been multiplied by NASBA, was performed using a fluorescence polarization assay. The polarization of the probe DNA in the presence of HCV positive sample, amplified by NASBA, was obviously different from those in the presence of negative control samples. The total time for the gene amplification and detection was about 90 min, while the polarization detection was completed within 10 min. The slight increase of polarization was also confirmed with the hybridization between probe oligo-DNA 25-mers and the synthesized complementary oligo-RNA 25-mers. The polarization of positive and negative samples showed excellent agreement with the results obtained from electrophoresis and dot-blot hybridization.

Base Sequence↗
PubMed2005

RNA-mediated control of metal nanoparticle shape.

RNA sequences previously isolated by in vitro selection were further characterized for their ability to control palladium particle growth. Five pyridyl-modified RNA sequences (Pdases) representing each of the different evolved families were found to form hexagonal plates with a high degree of shape specificity. However, a sixth nonrelated pyridyl-modified RNA sequence was found to form exclusively cubic particles under identical conditions. Replacing pyridyl-modified RNA with native RNA resulted in a complete loss of RNA function. Removing the 3'-fixed sequence region from the Pdase had little effect on particle growth; however, further truncations into the variable region resulted in a significant loss of activity and particle shape control. These Pdases were selected using the organometallic precursor complex tris(dibenzylideneacetone) dipalladium(0) ([Pd2(DBA)3]). Changing the metal center and ligand of the group VIII organometallic precursor complex revealed a strong dependence of particle growth and shape on the DBA ligands. Changing the metal center from Pd to Pt while retaining the DBA ligands gave predominantly hexagonal Pt, but with a decrease in shape control. Taken together, the results of this study suggest that the full-length Pdases contain active sites capable of highly specific molecular recognition of organometallic complexes as particle formation reagents.

Base Sequence↗
PubMed1985

Post-transcriptional regulation of rat liver gene expression by glucocorticoids.

We have investigated the mechanisms whereby glucocorticoids control the expression of specific genes in the livers of adult male rats. Construction and differential screening of a cDNA library representing normal rat liver polysomal poly(A)+ RNAs allowed selection of probes for hormonally regulated genes. The mechanism of this regulation was analysed by studying the changes in relative abundance of the RNA sequences homologous to four selected recombinants in RNA from subcellular fractions of liver, and comparing them with that of albumin mRNA. The relative abundance of these four RNA sequences increased to varying degrees in the nucleus, whilst that of three of them was concomitantly depleted in polysomal RNA when circulating levels of glucocorticoids were negligible, i.e. 14 days after adrenalectomy. One of the sequences was identified as alpha 2U-globulin mRNA. Within 2 hours of injecting Dexamethasone (a synthetic glucocorticoid) into rats that had been adrenalectomised 14 days previously, the relative abundances of alpha 2U-globulin RNA in nuclear and polysomal RNA returned to those found in normal rat liver. The data indicate that reduced glucocorticoid levels lead to sequence specific retention of RNA in the nucleus and that the RNA retained is released to the cytoplasm following glucocorticoid injection. Our results provide an example, for the first time, of glucocorticoid regulation of gene expression at the post-transcriptional level of nucleo-cytoplasmic transport.

Adrenalectomy↗
PubMed2005

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.

Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of foldalign. The server can be used to scan two sequences for a common structural RNA motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. The web server can be accessed at http://foldalign.kvl.dk.

Algorithms↗
PubMed1998

The Signal Recognition Particle Database (SRPDB).

This release of the SRPDB (signal recognition particle database, http://pegasus.uthct.edu/SRPDB/SRPDB . html ) adds four SRP RNA sequences (a total of 99 SRP RNA sequences), 23 SRP protein sequences (a total of 63 protein sequences from SRP9, SRP14, SRP19, SRP21, SRP54, SRP68 or SRP72), and, for the first time, sequences of the alpha subunit of the eukaryotic SRP receptor and its homologous bacterial proteins (a total of 21 sequences). Sequences are offered phylogenetically ordered, annotated with links to the primary databases, and in aligned form. Also downloadable are sample SRP RNA secondary structure diagrams, three-dimensional models of representative SRP RNAs, and search motifs.

Amino Acid Sequence↗
PubMed1996

Human papillomavirus deoxyribonucleic acid and ribonucleic acid in seminal plasma and sperm cells.

OBJECTIVE: To investigate the possible presence and expression of human papillomavirus viruses (HPV) in human plasma and sperm cells. DESIGN: Controlled clinical study. SETTING: A major medical center affiliated with a medical college. PATIENTS: Twenty-four randomly selected patients who attended Fertility Clinics at the Chang Gung Memorial Hospital. INTERVENTIONS: Specimens of semen were collected from volunteered patients MAIN OUTCOME MEASURE: The presence of HPV types 16 and 18 DNA and RNA sequences were examined by polymerase chain reaction. RESULTS: Human papillomavirus type 16 E6 and E7 DNA and RNA sequences were found in two and zero seminal plasma specimens, respectively, and in six and two sperm cells specimens, respectively. Deoxyribonucleic acid and RNA sequences of HPV type 18 were found in eight and two seminal specimens and in 11 and 5 sperm cells specimens, respectively. CONCLUSION: These results seem to suggest that HPV cannot only infect human sperm cells, certain HPV genes are expressed actively in infected sperm cells. The virus-infected sperm cells conceivably can behave as vectors or carriers for the transmission of HPV, to sexual partner during sexual contact, to fetuses through fertilized eggs, or both.

Base Sequence↗
PubMed2025

LungGENIE: the lung gene-expression and network imputation engine.

BACKGROUND: Few cohorts have study populations large enough to conduct molecular analysis of ex vivo lung tissue for genomic analyses. Transcriptome imputation is a non-invasive alternative with many potential applications. We present a novel transcriptome-imputation method called the Lung Gene Expression and Network Imputation Engine (LungGENIE) that uses principal components from blood gene-expression levels in a linear regression model to predict lung tissue-specific gene-expression. METHODS: We use paired blood and lung RNA sequencing data from the Genotype-Tissue Expression (GTEx) project to train LungGENIE models. We replicate model performance in a unique dataset, where we generated RNA sequencing data from paired lung and blood samples available through the SUNY Upstate Biorepository (SUBR). We further demonstrate proof-of-concept application of LungGENIE models in an independent blood RNA sequencing data from the Genetic Epidemiology of COPD (COPDGene) study. RESULTS: We show that LungGENIE prediction accuracies have higher correlation to measured lung tissue expression compared to existing cis-expression quantitative trait loci-based methods (median Pearson's r = 0.25, IQR 0.19-0.32), with close to half of the reliably predicted transcripts being replicated in the testing dataset. Finally, we demonstrate significant correlation of differential expression results in chronic obstructive pulmonary disease (COPD) from imputed lung tissue gene-expression and differential expression results experimentally determined from lung tissue. CONCLUSION: Our results demonstrate that LungGENIE provides complementary results to existing expression quantitative trait loci-based methods and outperforms direct blood to lung results across internal cross-validation, external replication, and proof-of-concept in an independent dataset. Taken together, we establish LungGENIE as a tool with many potential applications in the study of lung diseases.

Humans↗
PubMed1997

Small RNA database.

The small RNA database is a compilation of all the small size RNA sequences available to date, including nuclear, nucleolar, cytoplasmic and mitochondrial small RNAs from eukaryotic organisms and small RNAs from prokaryotic cells as well as viruses. Currently, about 600 small RNA sequences are in our database. It also gives the sources of individual RNAs and their GenBank accession numbers. The small RNA database can be accessed through WWW(World Wide Web). Our WWW URL address is: http://mbcr.bcm.tmc.edu/smallRNA/smallrna. html . The new small RNA sequences published since our last compilation are listed in this paper.

Animals↗
PubMed2001

RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension.

The RNA world hypothesis regarding the early evolution of life relies on the premise that some RNA sequences can catalyze RNA replication. In support of this conjecture, we describe here an RNA molecule that catalyzes the type of polymerization needed for RNA replication. The ribozyme uses nucleoside triphosphates and the coding information of an RNA template to extend an RNA primer by the successive addition of up to 14 nucleotides-more than a complete turn of an RNA helix. Its polymerization activity is general in terms of the sequence and the length of the primer and template RNAs, provided that the 3' terminus of the primer pairs with the template. Its polymerization is also quite accurate: when primers extended by 11 nucleotides were cloned and sequenced, 1088 of 1100 sequenced nucleotides matched the template.

Base Sequence↗