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At least 1,117 records · Page 62Linked to original sources
PubMed1996

Genetic stability of a porcine rotavirus RNA segment during repeated plaque isolation.

The porcine group A rotavirus CC86 was characterized to explore its utility as a tool for mutation analysis. It has a semiduplication of the gene 11 RNA segment. Nucleotide sequence determination of cDNA confirmed that the NSP5 coding sequence and the conserved nontranslated termini of the RNA segment were retained. A comparison of the NSP5 genes of CC86 and CN86 that were isolated from the same fecal specimen showed eight base pair changes, suggesting that CN86 was not the immediate progenitor of CC86. Synthesis of NSP5 in monkey MA104 cells infected with CC86, CN86, or simian rotavirus SA11 was compared by one- and two-dimensional polyacrylamide gel electrophoresis. NSP5 from all three viruses had similar posttranslational modifications, and no difference in the expression levels was observed. To experimentally address the genetic stability of CC86 segment 11, the virus was passaged by serial plaque to plaque transfer. The repeated genetic bottlenecking led to a gradual loss of fitness. This effect is not observed when virus is passaged by the standard method of moderate dilution. Nucleotide sequence analysis of cDNA clones isolated from viral segment 11 RNA of virus from plaque-to-plaque passage numbers 0, 1, 4, and 8 showed occasional base substitutions, mostly in the NSP5 coding sequence. Two mutations, leading to His-to-Arg and Lys-to-Arg replacements, respectively, in NSP5 were established in the virus population. Forward and reverse base pair changes (A-U<-->G-C) at the two sites appeared to be concerted and take place at a very high frequency, suggesting that a mechanism equivalent to RNA editing might operate. The overall mutation rate of segment 11 was much lower, having a calculated maximal value of 5 x 10(-5) per replicated base.

Animals↗
PubMed2002

Genetic code ambiguity. Cell viability related to the severity of editing defects in mutant tRNA synthetases.

The rules of the genetic code are established in reactions that aminoacylate tRNAs with specific amino acids. Ambiguity in the code is prevented by editing activities whereby incorrect aminoacylations are cleared by specialized hydrolytic reactions of aminoacyl tRNA synthetases. Whereas editing reactions have long been known, their significance for cell viability is still poorly understood. Here we investigated in vitro and in vivo four different mutations in the center for editing that diminish the proofreading activity of valyl-tRNA synthetase (ValRS). The four mutant enzymes were shown to differ quantitatively in the severity of the defect in their ability to clear mischarged tRNA in vitro. Strikingly, in the presence of excess concentrations of alpha-aminobutyrate, one of the amino acids that is misactivated by ValRS, growth of bacterial strains bearing these mutant alleles is arrested. The concentration of misactivated amino acid required for growth arrest correlates inversely in a rank order with the degree of the editing defect seen in vitro. Thus, cell viability depends directly on the suppression of genetic code ambiguity by these specific editing reactions and is finely tuned to any perturbation of these reactions.

Amino Acid Sequence↗
PubMed2000

PSG-EXPERT. An expert system for the diagnosis of sleep disorders.

This paper describes PSG-EXPERT, an expert system in the domain of sleep disorders exploring polysomnographic data. The developed software tool is addressed from two points of view: (1)--as an integrated environment for the development of diagnosis-oriented expert systems; (2)--as an auxiliary diagnosis tool in the particular domain of sleep disorders. Developed over a Windows platform, this software tool extends one of the most popular shells--CLIPS (C Language Integrated Production System) with the following features: backward chaining engine; graph-based explanation facilities; knowledge editor including a fuzzy fact editor and a rules editor, with facts-rules integrity checking; belief revision mechanism; built-in case generator and validation module. It therefore provides graphical support for knowledge acquisition, edition, explanation and validation. From an application domain point of view, PSG-Expert is an auxiliary diagnosis system for sleep disorders based on polysomnographic data, that aims at assisting the medical expert in his diagnosis task by providing automatic analysis of polysomnographic data, summarising the results of this analysis in terms of a report of major findings and possible diagnosis consistent with the polysomnographic data. Sleep disorders classification follows the International Classification of Sleep Disorders. Major features of the system include: browsing on patients data records; structured navigation on Sleep Disorders descriptions according to ASDA definitions; internet links to related pages; diagnosis consistent with polysomnographic data; graphical user-interface including graph-based explanatory facilities; uncertainty modelling and belief revision; production of reports; connection to remote databases.

Computer Systems↗
PubMed1997

Polyadenylation creates the discriminator nucleotide of chicken mitochondrial tRNA(Tyr).

In the chicken mitochondrial genome, the gene for tRNA(Tyr) overlaps by one nucleotide with the downstream tRNA(Cys) gene, which is located on the same strand. The overlapping nucleotide, a guanosine residue, thus encodes both the discriminator base of the tRNA(Tyr) and the 5'base of the tRNA(Cys). When cDNA clones of circularized forms of the tRNA(Tyr) are analyzed, the discriminator nucleotide is an adenosine residue rather than the genomically encoded guanosine. Thus, the tRNA(Tyr) is subjected to an RNA editing activity similar to that shown to exist in the mitochondria of two other animal species. Interestingly, some cDNA clones have several adenosine residues at their 3'-ends instead of the expected CCA-sequence. Furthermore, a review of sequence data from animal mitochondrial genomes suggests that only tRNAs whose discriminator bases are adenosines tend to have genes that overlap with downstream genes. Thus, polyadenylation seems to be a major component of the RNA editing machinery that affects overlapping genes in animal mitochondria.

Animals↗
PubMed1995

Editing status at the Q/R site of glutamate receptor-A, -B, -5 and -6 subunit mRNA in the hippocampal kindling model of epilepsy.

The editing status of mRNA at the Q/R site of the glutamate receptor subtypes -A, -B, -5 and -6 modulates channel conductivity and ion selectivity of glutamate operated ion channels [4,15,26,30]. In order to investigate whether a modification of this editing process may be involved in kindling epileptogenesis, the percentage of edited variant was determined in the hippocampus of kindled rats and compared to the percentage in control animals. In the latter, GluR-A mRNA was detected only in the unedited form (with detection threshold for edited form < 0.7%), whereas GluR-B was completely edited (> 99%). For percentages were not significantly changed in Schaffer collateral/commissural pathway kindled animals that were sacrificed 24 h after the last generalized seizure. It is concluded that the increased sensitivity for the induction of seizures characteristic for Schaffer collateral kindled animals is not related to a less selective or less efficient mRNA editing process of the different glutamate receptor subunits in the hippocampus.

Animals↗
PubMed1998

Insertional editing of mitochondrial tRNAs of Physarum polycephalum and Didymium nigripes.

tRNAs encoded on the mitochondrial DNA of Physarum polycephalum and Didymium nigripes require insertional editing for their maturation. Editing consists of the specific insertion of a single cytidine or uridine relative to the mitochondrial DNA sequence encoding the tRNA. Editing sites are at 14 different locations in nine tRNAs. Cytidine insertion sites can be located in any of the four stems of the tRNA cloverleaf and usually create a G. C base pair. Uridine insertions have been identified in the T loop of tRNALys from Didymium and tRNAGlu from Physarum. In both tRNAs, the insertion creates the GUUC sequence, which is converted to GTPsiC (Psi = pseudouridine) in most tRNAs. This type of tRNA editing is different from other, previously described types of tRNA editing and resembles the mRNA and rRNA editing in Physarum and Didymium. Analogous tRNAs in Physarum and Didymium have editing sites at different locations, indicating that editing sites have been lost, gained, or both since the divergence of Physarum and Didymium. Although cDNAs derived from single tRNAs are generally fully edited, cDNAs derived from unprocessed polycistronic tRNA precursors often lack some of the editing site insertions. This enrichment of partially edited sequences in unprocessed tRNAs may indicate that editing is required for tRNA processing or at least that RNA editing occurs as an early event in tRNA synthesis.

Animals↗
PubMed2005

Is there any sense in antisense editing?

Several recent studies have hypothesized that sense-antisense RNA-transcript pairs create dsRNA duplexes that undergo extensive A-to-I RNA editing. We studied human and mouse genomic antisense regions and found that the editing level in these areas is negligible. This observation questions the scope of sense-antisense duplexes formation in-vivo, which is the basis for several proposed regulatory mechanisms.

Alu Elements↗
PubMed2005

PREP-Mt: predictive RNA editor for plant mitochondrial genes.

BACKGROUND: In plants, RNA editing is a process that converts specific cytidines to uridines and uridines to cytidines in transcripts from virtually all mitochondrial protein-coding genes. There are thousands of plant mitochondrial genes in the sequence databases, but sites of RNA editing have not been determined for most. Accurate methods of RNA editing site prediction will be important in filling in this information gap and could reduce or even eliminate the need for experimental determination of editing sites for many sequences. Because RNA editing tends to increase protein conservation across species by "correcting" codons that specify unconserved amino acids, this principle can be used to predict editing sites by identifying positions where an RNA editing event would increase the conservation of a protein to homologues from other plants. PREP-Mt takes this approach to predict editing sites for any protein-coding gene in plant mitochondria. RESULTS: To test the general applicability of the PREP-Mt methodology, RNA editing sites were predicted for 370 full-length or nearly full-length DNA sequences and then compared to the known sites of RNA editing for these sequences. Of 60,263 cytidines in this test set, PREP-Mt correctly classified 58,994 as either an edited or unedited site (accuracy = 97.9%). PREP-Mt properly identified 3,038 of the 3,698 known sites of RNA editing (sensitivity = 82.2%) and 55,956 of the 56,565 known unedited sites (specificity = 98.9%). Accuracy and sensitivity increased to 98.7% and 94.7%, respectively, after excluding the 489 silent editing sites (which have no effect on protein sequence or function) from the test set. CONCLUSION: These results indicate that PREP-Mt is effective at identifying C to U RNA editing sites in plant mitochondrial protein-coding genes. Thus, PREP-Mt should be useful in predicting protein sequences for use in molecular, biochemical, and phylogenetic analyses. In addition, PREP-Mt could be used to determine functionality of a mitochondrial gene or to identify particular sequences with unusual editing properties. The PREP-Mt methodology should be applicable to any system where RNA editing increases protein conservation across species.

Amino Acid Sequence↗
PubMed1994

Effect of fat feeding on human intestinal apolipoprotein B mRNA levels and editing.

Our purpose was to assess the effect of a fat-rich meal on intestinal apolipoprotein B (apoB) mRNA levels and editing. We obtained jejunal biopsies from eight healthy adults in the fasting state and 3 h after a meal containing 1 g/kg of fat. In the fasting state, 93% of the apoB mRNA contained the editing sequence resulting in apoB-48 production. Feeding induced no significant changes in apoB mRNA levels or editing. Our data are consistent with the concept that the significant increase in apoB-48 within triglyceride-rich lipoproteins in postprandial plasma is not due to alterations in apoB gene expression or editing.

Apolipoproteins B↗
PubMed1995

In vivo testing of a tobacco plastid DNA segment for guide RNA function in psbL editing.

A C-to-U RNA editing event creates a functional initiation codon for translation of the psbL mRNA in tobacco plastids. Small trans-acting guide RNAs (gRNAs) have been shown to be involved in editing site selection in kinetoplastid mitochondria. A computer search of the tobacco plastid genome (ptDNA) identified such a putative gRNA, a 14-nucleotide sequence motif that is complementary to the psbL mRNA, including the A nucleotide required to direct the C-to-U change. The critical A nucleotide of the putative gRNA gene was changed to G by plastid transformation. We report here that the introduced mutation did not abolish psbL editing. Since no other region of the plastid genome contains significant complementarity to the psbL editing site we suggest that, if gRNAs serve as trans-acting factors for plastid psbL mRNA editing, they either have only a limited complementarity to the editing site, or are encoded in the nuclear genome.

Base Sequence↗
PubMedDate not supplied

Mitochondrial cytochrome b mRNA editing in dinoflagellates: possible ecological and evolutionary associations?

To verify the hypothesis that mt mRNA editing is widespread in dinoflagellates, we analyzed cytochrome b (cob) mRNA editing for six species representing distinct ecotypes and taxonomic classes of Dinophyceae. Editing is detected in all, which is similar to the three other species studied previously in that edited sites appear to aggregate in four clusters and occur predominantly at first and second positions of codons (93%), overwhelmingly involving A --> G, U --> C, or C --> U substitutions with a smaller number of G --> C, G --> A changes. Comparative analyses on editing characteristics reveal interesting trends related to phylogenetic relatedness and ecological features. Editing density (percentage of nucleotide that is affected by editing) increases from early to derived lineages. Higher editing densities also map to red tide-forming lineages. Furthermore, similarity of location of edited codons (LOE) and the type of nucleotide changes (TOE) in different lineages mirror the taxonomic affinity of the lineages. Phylogenetic trees constructed from LOE and TOE resemble those inferred from cob sequences. The results bolster our earlier hypothesis that cob editing is widespread in dinoflagellates and suggest that density, location, and type of editing may bear yet-to-be-defined evolutionary and ecological significance.

Animals↗
PubMed2000

Database for a hearing conservation program.

We have developed a database and an analysis program (NoiseScan) for noise-induced hearing loss (NIHL). The exposure data are based on the evaluation of the noise immission level, which includes duration, frequency content, and the use of, and the attenuation performance of, hearing protectors. The input data can handle an unlimited number of exposure periods. If the noise exposure level is not known, the program lists noise levels of comparable work places, and thus provides an estimate of exposure. Confounding medical factors that may contribute to NIHL, such as elevated serum cholesterol level, hypertension, and extensive use of pain killers, are collected. Combined exposure to agents that clearly contribute to NIHL, such as hand-arm vibration, tobacco smoking, use of aminoglycosides and exposure to solvents are also assessed. An unlimited number of audiograms can be stored, and all the data can be completed and edited following collection. The program gives the predicted hearing loss according to the ISO 1999 model based on total exposure. At present, our NoiseScan program (under continuous development in an EU research program) is suitable for the data collection of various risk factors. It can be used to determine whether the hearing loss is occupational in origin and to estimate the efficiency of hearing conservation measures. NoiseScan also predicts the development of hearing loss in individuals in 5-year periods. The goal is to improve and validate the rules by which single and combined risk factors contribute to HIHL, thus leading to more precise prediction of individual hearing loss, and for the evaluation of success of the hearing conservation programs.

Audiometry↗
PubMed1997

Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases.

Double-stranded (ds) RNA-specific adenosine deaminase converts adenosine residues into inosines in dsRNA and edits transcripts of certain cellular and viral genes such as glutamate receptor (GluR) subunits and hepatitis delta antigen. The first member of this type of deaminase, DRADA1, has been recently cloned based on the amino acid sequence information derived from biochemically purified proteins. Our search for DRADA1-like genes through expressed sequence tag databases led to the cloning of the second member of this class of enzyme, DRADA2, which has a high degree of sequence homology to DRADA1 yet exhibits a distinctive RNA editing site selectivity. There are four differentially spliced isoforms of human DRADA2. These different isoforms of recombinant DRADA2 proteins, including one which is a human homolog of the recently reported rat RED1, were analyzed in vitro for their GluR B subunit (GluR-B) RNA editing site selectivity. As originally reported for rat RED1, the DRADA2a and -2b isoforms edit GluR-B RNA efficiently at the so-called Q/R site, whereas DRADA1 barely edits this site. In contrast, the R/G site of GluR-B RNA was edited efficiently by the DRADA2a and -2b isoforms as well as DRADA1. Isoforms DRADA2c and -2d, which have a distinctive truncated shorter C-terminal structure, displayed weak adenosine-to-inosine conversion activity but no editing activity tested at three known sites of GluR-B RNA. The possible role of these DRADA2c and -2d isoforms in the regulatory mechanism of RNA editing is discussed.

Adenosine Deaminase↗
PubMed2004

In vitro assays for kinetoplastid U insertion-deletion editing and associated activities.

This chapter describes biochemical assays that have been used in analyzing RNA editing in kinetoplastid mitochondria and to characterize the general mechanism of editing by the editosome. Studies using these assays have shown that the characteristics of each activity contribute to editing site selection, U addition and removal, and RNA ligation resulting in accurately edited mRNAs.

Animals↗
PubMed1999

Uridine insertion/deletion RNA editing in trypanosome mitochondria--a review.

The uridine insertion/deletion RNA editing in trypanosome mitochondria is a unique posttranscriptional RNA maturation process that involves the addition or removal of uridine residues at precise sites usually within the coding regions of mitochondrial transcripts. This process creates initiation and termination codons, corrects frameshifts and even builds entire open-reading frames from nonsense sequences. The development of several in-vitro editing assays has provided much insight into the molecular mechanism of RNA editing, which appears to involve cleavage, U addition, exonuclease trimming and ligation, essentially as proposed in the original 'enzyme cascade' model (Blum, B., Bakalara, N., Simpson, L., 1990. A model for RNA editing in kinetoplastid mitochondria: 'Guide' RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 60, 189-198). However, little is known about the biochemical properties of the proteins involved and the significance and role of this process. This article is a review of recent findings on uridine-insertion/deletion editing in trypanosome mitochondria, with an emphasis on the proteins isolated and characterized that may have a role in this process.

Animals↗
PubMed1999

C-->U editing of apolipoprotein B mRNA in marsupials: identification and characterisation of APOBEC-1 from the American opossum Monodelphus domestica.

The C->U editing of RNA is widely found in plant and animal species. In mammals it is a discrete process confined to the editing of apolipoprotein B (apoB) mRNA in eutherians and the editing of the mitochondrial tRNA for glycine in marsupials. Here we have identified and characterised apoB mRNA editing in the American opossum Monodelphus domestica. The apoB mRNA editing site is highly conserved in the opossum and undergoes complete editing in the small intestine, but not in the liver or other tissues. Opossum APOBEC-1 cDNA was cloned, sequenced and expressed. The encoded protein is similar to APOBEC-1 of eutherians. Motifs previously identified as involved in zinc binding, RNA binding and catalysis, nuclear localisation and a C-terminal leucine-rich domain are all conserved. Opossum APOBEC-1 contains a seven amino acid C-terminal extension also found in humans and rabbits, but not present in rodents. The opossum APOBEC-1 gene has the same intron/exon organisation in the coding sequence as the eutherian gene. Northern blot and RT-PCR analyses and an editing assay indicate that no APOBEC-1 was expressed in the liver. Thus the far upstream promoter responsible for hepatic expression in rodents does not operate in the opossum. An APOBEC-1-like enzyme such as might be involved in C->U RNA editing of tRNA in marsupial mitochondria was not demonstrated. The activity of opossum APOBEC-1 in the presence of both chicken and rodent auxiliary editing proteins was comparable to that of other mammals. These studies extend the origins of APOBEC-1 back 170 000 000 years to marsupials and help bridge the gap in the origins of this RNA editing process between birds and eutherian mammals.

APOBEC-1 Deaminase↗
PubMed1977

Development of food tables and use with computers. Review of nutrient data bases.

Numerous tables of food composition have been compiled since the 1890s to meet the needs for nutrient data by nutritionists, researchers, and consumers. Early tables included values for protein, fat, carbohydrate, and calories. By 1945, values for several vitamins and minerals were listed in tables of food composition. The contents of food composition tables have been updated and expanded as laboratory procedures for analyzing nutrients have been improved. A trend toward increased specificity for most nutrient classifications has resulted in consideration of up to one hundred nutritional components in the development of nutrient data bases. Tables of food composition have varied in number of food items, number of nutrients, and classification schemes. Food-group designations have been used in some tables as a technique to categorize data for similar food items. Computer-stored nutrient data bases tend to vary in much the same manner as printed tables of food composition. Computer-assisted diagnostic procedures for editing input data for validity and verifying reasonable relationships among nutrient data have been developed to detect data inconsistencies. As data for new food products are included and the effects of food processing methods are determined, food composition tables and computer-stored nutrient data bases are expected to become more comprehensive, reliable, and suitable for various uses.

Calorimetry↗