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PubMed1999

The mat-r open reading frame is transcribed from a non-canonical promoter and contains an internal promoter to co-transcribe exons nad1e and nad5III in wheat mitochondria.

The expression of the mat-r locus (mat-r-nad1e-nad5III) was studied in wheat mitochondria. Transcription initiation sites were mapped by S1 protection, primer extension and capping experiments. Two different transcription initiation sites were found. One, non-canonical promoter of low expression level generates a transcript containing the complete mat-r open reading frame (orf), suggesting that this form is the maturase-reverse transcriptase mRNA. A second transcription initiation site, found within the coding region of the mat-r orf, directs the transcription of an abundant co-transcript containing the carboxy-terminal region of the mat-r orf, exon e of the nad1 gene, exon III of the nad5 gene and their respective trains-introns. The co-transcript promoter carries the consensus motif of plant mitochondrial promoters. Analysis of transcript sequences reveals the presence of editing sites in analogous positions in both nad1e and nad5III trans-introns, suggesting that RNA editing is necessary for the trans-splicing process.

Base Sequence↗
PubMed2004

RALEE--RNA ALignment editor in Emacs.

UNLABELLED: Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS. AVAILABILITY: The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples. CONTACT: sgj@sanger.ac.uk

Algorithms↗
PubMed2003

FeNO structure in distal pocket mutants of myoglobin based on resonance Raman spectroscopy.

FeNO vibrational frequencies were investigated for a series of myoglobin mutants using isotope-edited resonance Raman spectra of (15/14)NO adducts, which reveal the FeNO and NO stretching modes. The latter give rise to doublet bands, as a result of Fermi resonances with coincident porphyrin vibrations; these doublets were analyzed by curve-fitting to obtain the nuNO frequencies. Variations in nuNO among the mutants correlate with the reported nuCO variations for the CO adducts of the same mutants. The correlation has a slope near unity, indicating equal sensitivity of the NO and CO bonds to polar influences in the heme pocket. A few mutants deviate from the correlation, indicating that distal interactions differ for the NO and CO adducts, probably because of the differing distal residue geometries. In contrast to the strong and consistent nuFeC/nuCO correlation found for the CO adducts, nuFeN correlates only weakly with nuNO, and the slope of the correlation depends on which residue is being mutated. This variability is suggested to arise from steric interactions, which change the FeNO angle and therefore alter the Fe-NO and N-O bond orders. This effect is modeled with Density Functional Theory (DFT) and is rationalized on the basis of a valence isomer bonding model. The FeNO unit, which is naturally bent, is a more sensitive reporter of steric interactions than the FeCO unit, which is naturally linear. An important additional factor is the strength of the bond to the proximal ligand, which modulates the valence isomer equilibrium. The FeNO unit is bent more strongly in MbNO than in protein-free heme-NO complexes because of a combination of a strengthened proximal bond and distal interactions.

Animals↗
PubMed2003

[Guideline 'Treating asthma in children' for pediatric pulmonologists (2nd revised edition). II. Medical treatment].

The second revision of the guidelines for the treatment of asthma in children is largely based on the evidence of comparative studies. Short-acting beta 2-sympathicomimetics are the medication of choice for acute exacerbations and should therefore be prescribed to each patient. Inhaled corticosteroids (ICS) are the medication of choice for maintenance treatment. Starting with a high dose of ICS which is then reduced to a lower but effective level on the basis of the complaints (step-down approach) is no longer recommended, as this strategy is not more effective than a constant dosage schedule. If asthmatic symptoms persist despite ICS maintenance treatment then 3 therapeutic options are available in the following order: doubling the ICS dose, the addition of a long-acting beta 2-sympathicomimetic, and the addition of a leukotriene receptor antagonist.

Administration, Inhalation↗
PubMed2005

The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage.

Long perfect double-stranded RNA (dsRNA) molecules play a role in various cellular pathways. dsRNA may undergo extensive covalent modification (hyper-editing) by adenosine deaminases that act on RNA (ADARs), resulting in conversion of up to 50% of adenosine residues to inosine (I). Alternatively, dsRNA may trigger RNA interference (RNAi), resulting in silencing of the cognate mRNA. These two pathways have previously been shown to be antagonistic. We show a novel interaction between components of the ADAR and RNAi pathways. Tudor staphylococcal nuclease (Tudor-SN) is a subunit of the RNA-induced silencing complex, which is central to the mechanism of RNAi. Here we show that Tudor-SN specifically interacts with and promotes cleavage of model hyper-edited dsRNA substrates containing multiple I.U and U.I pairs. This interaction suggests a novel unsuspected interplay between the two pathways that is more complex than mutual antagonism.

Adenosine Deaminase↗
PubMed2005

A rapid new assay to detect RNA editing reveals antipsychotic-induced changes in serotonin-2C transcripts.

We report the development of a new assay as an alternative to direct DNA sequencing to measure RNA-edited variation in tissue. The new assay has been validated and is accurate, cheaper, more rapid, and less labor-intensive than DNA sequencing. We also outline the statistical modeling required for analyses of the hierarchical, clustered RNA-editing data generated in these studies. Using the new technique, we analyzed the effects of long-term antipsychotic medication on serotonin-2C receptor (5-HT2CR) RNA editing in rat brain. Our hypothesis that a drug with high affinity for 5-HT2CR, such as clozapine, would alter its RNA-editing profile was not confirmed. Whereas haloperidol, a typical antipsychotic drug that is primarily a dopamine receptor antagonist, reduced 5-HT2C VNV isoform frequency and the level of RNA editing at the D site, risperidone and not the prototype atypical antipsychotic drug clozapine increased the frequency of 5-HT2C VNV and D-site editing. Our data emphasize that caution is required in the interpretation of RNA-editing data in studies of psychiatric disorders, because these studies usually include subjects who received long-term exposure to medication. This newly established method will facilitate high-throughput investigations of RNA editing in disease pathology and in the pharmacological activity of drugs.

Animals↗
PubMed2002

Inhibition of hepatitis delta virus RNA editing by short inhibitory RNA-mediated knockdown of ADAR1 but not ADAR2 expression.

Hepatitis delta virus (HDV) requires host RNA editing at the viral RNA amber/W site. Of the two host genes responsible for RNA editing via deamination of adenosines in double-stranded RNAs, short inhibitory RNA-mediated knockdown of host ADAR1 expression but not that of ADAR2 led to decreased HDV amber/W editing and virus production. Despite substantial sequence and structural variation among the amber/W sites of the three HDV genotypes, ADAR1a was primarily responsible for editing all three. We conclude that ADAR1 is primarily responsible for editing HDV RNA at the amber/W site during HDV infection.

Adenosine Deaminase↗
PubMed2001

Conformational changes that occur during an RNA-editing adenosine deamination reaction.

ADARs are adenosine deaminases responsible for RNA-editing reactions that occur within duplex RNA. Currently little is known regarding the nature of the protein-RNA interactions that lead to site-selective adenosine deamination. We previously reported that ADAR2 induced changes in 2-aminopurine fluorescence of a modified substrate, consistent with a base-flipping mechanism. Additional data have been obtained using full-length ADAR2 and a protein comprising only the RNA binding domain (RBD) of ADAR2. The increase in 2-aminopurine fluorescence is specific to the editing site and dependent on the presence of the catalytic domain. Hydroxyl radical footprinting demonstrates that the RBD protects a region of the RNA duplex around the editing site, suggesting a significant role for the RBD in identifying potential ADAR2 editing sites. Nucleotides near the editing site on the non-edited strand become hypersensitive to hydrolytic cleavage upon binding of ADAR2 RBD. Therefore, the RBD may assist base flipping by increasing the conformational flexibility of nucleotides in the duplex adjacent to its binding site. In addition, an increase in tryptophan fluorescence is observed when ADAR2 binds duplex RNA, suggesting a conformational change in the catalytic domain of the enzyme. Furthermore, acrylamide quenching experiments indicate that RNA binding creates heterogeneity in the solvent accessibility of ADAR2 tryptophan residues, with one out of five tryptophans more solvent-accessible in the ADAR2.RNA complex.

2-Aminopurine↗
PubMed2000

Induction of cytidine to uridine editing on cytoplasmic apolipoprotein B mRNA by overexpressing APOBEC-1.

Post-transcriptional editing of apolipoprotein B (apoB) mRNA is regulated in hepatic cells to achieve a steady state proportion of edited and unedited RNA molecules. This activity is catalyzed by APOBEC-1 (apoB mRNA editing catalytic subunit 1) in what has been widely accepted as nuclear event occurring during or after mRNA splicing. Introns impair the efficiency of editing within an adjacent exon in a distance-dependent manner in reporter RNAs. We show here that this inhibition can be overcome by overexpressing APOBEC-1 and that the enhanced editing efficiency on these reporter RNAs occurred after splicing on cytoplasmic transcripts. Given the absolute requirement of auxiliary proteins in apoB mRNA editing, the data suggested that auxiliary proteins were distributed with APOBEC-1 in both the nucleus and cytoplasm of McArdle cells. In fact, immunolocalization of one such auxiliary protein, APOBEC-1 complementation factor (ACF) demonstrated a nuclear and cytoplasmic distribution. We also demonstrate that in the absence of alterations in APOBEC-1 expression, changes in edited apoB RNA induced by ethanol arise through the stimulation of nuclear editing activity. The finding that apoB mRNA editing can occur in the cytoplasm but normally does not suggests that under biological conditions, restricting editing activity to the nucleus must be an important step in regulating the proportion of the edited apoB mRNAs.

APOBEC-1 Deaminase↗
PubMed2004

TbDSS-1, an essential Trypanosoma brucei exoribonuclease homolog that has pleiotropic effects on mitochondrial RNA metabolism.

Mitochondrial gene expression in trypanosomes is controlled primarily at the levels of RNA processing and RNA stability. This regulation undoubtedly involves numerous ribonucleases. Here we characterize the Trypanosoma brucei homolog of the yeast DSS-1 mitochondrial exoribonuclease, which we term TbDSS-1. Biochemical fractionation indicates that TbDSS-1 is mitochondrially localized, as predicted by its N-terminal sequence. In contrast to its yeast homolog, TbDSS-1 does not appear to be associated with mitochondrial ribosomes. Targeted downregulation of TbDSS-1 by RNA interference in procyclic-form T. brucei results in a severe growth defect. In addition, TbDSS-1 depletion leads to a decrease in the levels of never edited cytochrome oxidase subunit I (COI) mRNA and both unedited and edited COIII mRNAs, indicating this enzyme functions in the control of mitochondrial RNA abundance. We also observe a considerable reduction in the level of edited apocytochrome b (CYb) mRNA and a corresponding increase in unedited CYb mRNA, suggesting that TbDSS-1 functions, either directly or indirectly, in the control of RNA editing. The abundance of both gCYb[560] and gA6[149] guide RNAs is reduced upon TbDSS-1 depletion, although the reduction in gCYb[560] is much more dramatic. The significant reduction in gCYb levels could potentially account for the observed decrease in CYb RNA editing. Western blot analyses of mitochondrial RNA editing and stability factors indicate that the perturbations of RNA levels observed in TbDSS-1 knock-downs do not result from secondary effects on other mitochondrial proteins. In all, these data demonstrate that TbDSS-1 is an essential protein that plays a role in mitochondrial RNA stability and RNA editing.

Amino Acid Sequence↗
PubMed1998

Three-dimensional computed tomographic reconstruction: planning tool for surgery of skull base pathologies.

Three-dimensional (3-D) computed tomographic (CT) reconstruction of the skull base region has added a different perspective to the data set usually presented in axial or coronal slices. It simultaneously demonstrates the spatial relationship of bones, tumors, vessels, and ventricles in a single illustration. Forty-nine patients with skull base lesions (44 with neoplastic and 5 with vascular pathologies) were examined with a spiral CT and 3-D reconstruction prior to surgery. A scanner and a maximum of 95 mL of iodized contrast media were used to enhance either tumor or vessels according to the specific pathology. Preoperative 3-D reconstruction was performed. It rendered a spatial representation of the pathology using data similar to that usually acquired in routine preoperative diagnostics. Complex anatomy can be visualized with only a handful of pictures. It was possible to easily compare various surgical approaches to the lesion on the basis of the 3-D computer model and to simulate the surgeon's view. The short time span (1 h average) necessary for reconstruction and editing allows the application of this method as a routine preoperative procedure for selected skull base pathologies.

Adult↗
PubMed1992

A single nuclear gene specifies the abundance and extent of RNA editing of a plant mitochondrial transcript.

A number of cytosines are altered to be recognized as uridines in transcripts of the NADH-dehydrogenase subunit 3 (nad3) gene in the mitochondria of the higher plant Petunia hybrida. Here we show that the extent of editing for three of the edit sites, all of which change the encoded amino acid, varies between different Petunia lines. Genetic analysis indicates that a single nuclear gene is responsible for this variation. Interestingly, according to RNA blot hybridization analysis, RNA editing extent and transcript abundance are correlated. This observation is consistent with the hypothesis that RNA editing is a post-transcriptional event.

Base Sequence↗
PubMed1993

A user-friendly Hypercard interface for human linkage analysis.

The availability of a large number of highly informative genetic markers has made human linkage analysis faster and easier to perform. However, current linkage analysis software does not provide an organizational database into which a large body of linkage data can be easily stored and manipulated. This manual entry and editing of linkage data is often time consuming and prone to typing errors. In addition, the large number of alleles in many of these markers must be reduced in order to perform linkage analysis with multiple loci across large genetic distances. This reduction in allele number is often difficult and confusing, especially in large pedigrees. We have taken advantage of the Macintosh-based Hypercard program to develop an interface with which linkage data can be easily stored, retrieved and edited. For each family, the components of the pedigree, including ID numbers, sex and affection status, only need to be entered once. The program (Linkage Interface) retrieves this information each time the data from a new polymorphic marker is entered. Linkage Interface has flexible editing capabilities that allow the user to change any portion of the pedigree, including the addition or deletion of family members, without affecting previously entered genotype data. Linkage Interface can also analyze both the pedigree and marker data and will detect any inconsistencies in inheritance patterns. In addition, the program can reduce the number of alleles for a polymorphic marker. Linkage Interface will then compare the 'reduced' data to the original marker data and assists in maintaining all informative meioses by pointing out which meioses have become non-informative.(ABSTRACT TRUNCATED AT 250 WORDS)

Female↗
PubMed2002

Editing site recognition and nucleotide insertion are separable processes in Physarum mitochondria.

Insertional RNA editing in Physarum polycephalum is a complex process involving the specific addition of non-templated nucleotides to nascent mitochondrial transcripts. Since all four ribonucleotides are substrates for the editing activity(s), both the site of insertion and the identity of the nucleotide to be added at a particular position must be specified, but the signals for these events have yet to be elucidated. Here we report the occurrence of sporadic errors in RNAs synthesized in vitro. These mistakes, which include omission of encoded nucleotides as well as misinsertions, occur only on templates that support editing. The pattern of these misediting events indicates that editing site recognition and nucleotide addition are separable events, and that the recognition step involves features of the mitochondrial template that are required for editing. The larger deletions lack all templated nucleotides between editing sites, suggesting that the transcription/editing apparatus can "jump" from one insertion site to another, perhaps mediated by interactions with editing determinants, while smaller omissions most likely reflect misalignment of the transcript upon resumption of templated RNA synthesis.

Animals↗
PubMed2001

Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: structure probing of an mRNA bound to its cognate gRNA.

Posttranscriptional editing of trypanosome mitochondrial messenger RNA is directed by small guide RNAs (gRNAs). Using crosslinking techniques, we have previously shown that the gRNA base pairs to the mRNA via a 5' anchor, whereas its 3' U-tail interacts with upstream purine-rich mRNA sequences. The incorporation of crosslinking data into RNA folding programs produced similar structure predictions for all gRNA/mRNA pairs examined. This suggests that gRNA/mRNA pairs can form common secondary structure motifs that may be important for recognition by the editing complex. In this study, the structure of CYb mRNA crosslinked to gCYb-558 was examined using solution-probing techniques. The mRNA/gRNA crosslinked molecules are efficient substrates for gRNA-directed cleavage. In addition, when the cleavage assay is performed in the presence or absence of additional UTP, the activities of both the U-specific exonuclease and terminal uridylyl transferase (tutase) can be detected. These results indicate that a partial editing complex can assemble and function on these substrates suggesting that the crosslink captured the molecules in a biologically relevant interaction. The structure probing data directly show that the U-tail protects several mRNA bases predicted to be involved in the U-tail-mRNA duplex. In combination with our previous studies, these new data provide additional support for the predicted secondary structure of interacting gRNA/mRNA pairs.

Animals↗
PubMed2007

The impact of partner alcohol problems on women's physical and mental health.

OBJECTIVE: The purpose of this study was to examine the association between partner alcohol problems and selected physical and mental health outcomes among married or cohabiting women, before and after adjusting for potential confounders, and to compare these associations with those reflecting the impact of the women's own alcohol-use disorders (AUDs). METHOD: This analysis is based on data from the Wave 1 2001-2002 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC), a cross-sectional, retrospective survey of a nationally representative sample of U.S. adults 18 years of age and older. The analytic sample consisted of 11,683 married or cohabiting women. Classification of their own AUDs was based on self-report of symptoms operationalizing the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV), criteria for alcohol abuse or dependence. Current partner alcohol problems were identified by the women after an explanation that recapitulated the essence of these criteria. Physical health measures included criminal victimization of any type, injury, emergency-department and hospital visits, self-reported fair or poor health, and Short Form-12 Health Survey Questionnaire, Version 2 (SF-12v2), -based physical quality of life. Mental health measures included DSM-IV mood and anxiety disorders, number of past-year stressors, and SF-12v2-based mental/psychological quality of life. All measures refer to the 12 months immediately preceding the interview. Associations were tested using bivariate and multivariate logistic and linear regression models. RESULTS: At the bivariate level, women whose partners had alcohol problems were more likely to experience victimization, injury, mood disorders, anxiety disorders, and being in fair or poor health than women whose partners did not have alcohol problems (odds ratio [OR]: 1.7-4.5). They also experienced more life stressors and had lower mental/psychological quality-of-life scores. All but one of these differences remained significant after adjusting for potential confounders, which included the significantly greater rates of substance use and AUDs among women whose partners had alcohol problems. Although the magnitudes of the ORs decreased after adjustment (adjusted OR [AOR]: 2.1-3.4), they generally exceeded the AORs associated with the women's own AUDs. CONCLUSIONS: Partner alcohol problems pose diverse health threats for women that go beyond their well-documented association with domestic violence. Mood, anxiety, stress, general health, and quality-of-life problems should be addressed by groups that provide couples' treatment or counseling to female partners of alcoholics.

Adolescent↗
PubMed1990

A model for RNA editing in kinetoplastid mitochondria: "guide" RNA molecules transcribed from maxicircle DNA provide the edited information.

A class of small RNA molecules possibly involved in RNA editing is present in the mitochondrion of Leishmania tarentolae. These "guide" RNA (gRNA) molecules are encoded in intergenic regions of the mitochondrial maxicircle DNA and contain sequences that represent precise complementary versions of the mature mRNAs within the edited regions. In addition, the 5' portions of several gRNAs can form hybrids with mRNAs just 3' of the preedited region. A model is presented in which a partial hybrid formed between the gRNA and preedited mRNA is substrate for multiple cycles of cleavage, addition or deletion of uridylates, and religation, eventually resulting in a complete hybrid between the gRNA and the mature edited mRNA.

Animals↗
PubMed1984

Analys. DNA: a computer program for nucleic acid sequence data processing.

A computer program written in BASIC language is described. The program allows processing and analysis of DNA data and has been designed to be used by persons with little or no computer experience. The operator using different options can search for direct homologies with varying degrees of matching, generate complementary strands, find restriction sites, invert the polarity of the sequence and edit a print-out.

Animals↗