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At least 487 records · Page 27Linked to original sources
PubMed2001

RNA editing in higher plant plastids: oligoribonucleotide SSCP analysis allows the proof of base conversion directly at the RNA level.

Plastid RNA editing of a number of transcripts at specific sites changes genomically encoded cytidines to nucleosides, which act like uridines in RT-PCR analyses. To study plastid-editing directly at the RNA level, we established a single-strand conformational polymorphism assay for the discrimination of small RNA molecules. The electrophoretic mobility of a oligoribonucleotide resulting from a RNase T1-digested and edited plastid mRNA was shown to be identical with a control RNA molecule containing a uridine at the editing site, whereas the unedited RNA behaved like a RNA molecule containing a cytidine at the respective position.

Chromosome Mapping↗
PubMed2006

Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf.

The tomato microarray TOM1 offers the possibility to monitor the levels of several thousand transcripts in parallel. The microelements represented on this tomato microarray have been putatively assigned to unigenes, and organised in functional classes using the MapMan ontology (Thimm et al., 2004. Plant J. 37: 914-939). This ontology was initially developed for use with the Arabidopsis ATH1 array, has a low level of redundancy, and can be combined with the MapMan software to provide a biologically structured overview of changes of transcripts, metabolites and enzyme activities. Use of this application is illustrated using three case studies with published or novel TOM1 array data sets for Solanaceous species. Comparison of previously reported data on transcript levels in potato leaves in the middle of the day and the middle of the night identified coordinated changes in the levels of transcripts of genes involved in various metabolic pathways and cellular events. Comparison with diurnal changes of gene expression in Arabidopsis revealed common features, illustrating how MapMan can be used to compare responses in different organisms. Comparison of transcript levels in new experiments performed on the leaves of the cultivated tomato S. lycopersicum and the wild relative S. pennellii revealed a general decrease of levels of transcripts of genes involved in terpene and, phenylpropanoid metabolism as well as chorismate biosynthesis in the crop compared to the wild relative. This matches the recently reported decrease of the levels of secondary metabolites in the latter. In the third case study, new expression array data for two genotypes deficient in TCA cycle enzymes is analysed to show that these genotypes have elevated levels of transcripts associated with photosynthesis. This in part explains the previously documented enhanced rates of photosynthesis in these genotypes. Since the Solanaceous MapMan is intended to be a community resource it will be regularly updated on improvements in tomato gene annotation and transcript profiling resources.

Arabidopsis↗
PubMed1993

Two-dimensional J-resolved 13C solid-state NMR analysis of the products of ethylene conversion on zeolite H-ZSM-5.

Two-dimensional (2D) J-resolved 13C NMR spectroscopy has been used to analyze the products of ethylene conversion inside the channels of zeolite H-ZSM-5 at 373 K. The observed 13C signals of aliphatic hydrocarbon fragments have been attributed to various CHn (n = 1-3) groups. Multiplicities and positions of these signals suggest that a mixture of branched and linear ethylene oligomers is formed inside zeolite H-ZSM-5.

Ethylenes↗
PubMed1978

Kinetic analysis of the acid-alkaline conversion of horseradish peroxidases.

The nature of the acid-alkaline conversion of horseradish peroxidases was studied by measuring four rate constants in reactions, E + H+ (k1) in equilibrium (k2) EH+ and E + H2O (k3) in equilibrium (k4) EH+ + OH-, where EH+ and E denote the acid and alkaline forms of the enzymes. The values of k1, (k2 + k3), and k4 were obtained by measuring the relaxation rates of the acid leads to alkaline and alkaline leads to acid conversions by means of th pH jump method with a stopped-flow apparatus. The value of k3 could also be obtained by measuring the rate of reactions between hydrogen peroxide and peroxidases at alkaline pH. The measurements were conducted with four peroxidases having different pKa values: peroxidase A )pKa = 9.3), peroxidase C (pKa = 11.1), diacetyldeuteroperoxidase A (pKa = 7.7), and diacetyldeuteroperoxidase C (pKa = 9.1). The value of k1 was about 10(10) M-1 s-1 in the reaction of the four enzymes while k4 was quite different between the enzymes. The pKa was determined by k3 and k4 for the natural peroxidases and by k1 and k2 for the diacetyldeuteroperoxidases. The mechanism of the acid-alkaline conversion was discussed in comparison with that of metmyoglobin.

Acetylation↗
PubMed1970

Analysis of T4 phage proteins. I. Conversion of precursor proteins into lower molecular weight peptides during normal capsid formation.

Radioisotopically labeled T4-proteins extracted from purified capsids and phage and from infected cells were separated by gel electrophoresis in the presence of sodium dodecyl sulfate and a reducing reagent. They were identified by autoradiography and by counting of the fractionated gels. Four major protein bands (F, A, D, and E) were detected in capsid and phage. These accounted for more than 90% of the total capsid protein and 70% of the phage protein (60% of the total capsid protein was in A-band). Coelectrophoresis of [(14)C]proteins from capsids and [(3)H]proteins from phage-infected cells indicated that the protein coded by gene 23 (P23) was a peptide chain approximately 25% longer than A-protein. Pulse-chase experiments combined with differential extraction indicated that conversion of P23 into A-protein and alteration of the protein coded by gene 22 (P22) appeared to be vital steps in formation of normal capsids. Mutations in several other genes known to prevent normal capsid formation inhibited conversion of P23 to A-protein and alteration of P22.

Autoradiography↗
PubMed2002

Structural and conformational analysis of the oxidase to dehydrogenase conversion of xanthine oxidoreductase.

Xanthine oxidoreductase (XOR) is a 300-kDa homodimer that can exist as an NAD+-dependent dehydrogenase (XD) or as an O2-dependent oxidase (XO) depending on the oxidation state of its cysteine thiols. Both XD and XO undergo limited cleavage by chymotrypsin and trypsin. Trypsin selectively cleaved both enzyme forms at Lys184, while chymotrypsin cleaved XD primarily at Met181 but cleaved XO at Met181 and at Phe560. Chymotrypsin, but not trypsin, cleavage also prevented the reductive conversion of XO to XD; thus the region surrounding Phe560 appears to be important in the interconversion of the two forms. Size exclusion chromatography showed that disulfide bond formation reduced the hydrodynamic volume of the enzyme, and two-dimensional gel electrophoresis of chymotrypsin-digested XO showed significant, disulfide bond-mediated, conformational heterogeneity in the N-terminal third of the enzyme but no evidence of disulfide bonds between the N-terminal and C-terminal regions or between XOR subunits. These results indicate that intrasubunit disulfide bond formation leads to a global conformational change in XOR that results in the exposure of the region surrounding Phe560. Conformational changes within this region in turn appear to play a critical role in the interconversion between the XD and XO forms of the enzyme.

Animals↗
PubMed1994

Analysis of sequence transfers resembling gene conversion in a mouse antibody transgene.

The role of gene conversion in murine immunoglobulin gene diversification is unclear. An antibody gene construct designed to provide the homologous donor and acceptor sequences required for conversion mechanisms was produced and used to generate transgenic mice. When these transgenic mice were immunized, DNA sequence transfers between tandem transgene VDJ regions were detectable and resembled gene conversion events. There is a strong link between these conversion-like sequence transfers and transgene somatic hypermutation, suggesting that both processes might occur at the same stage of B cell differentiation.

Animals↗
PubMed2005

Gene conversion tracts associated with crossovers in Rhizobium etli.

Gene conversion has been defined as the nonreciprocal transfer of information between homologous sequences. Despite its broad interest for genome evolution, the occurrence of this mechanism in bacteria has been difficult to ascertain due to the possible occurrence of multiple crossover events that would mimic gene conversion. In this work, we employ a novel system, based on cointegrate formation, to isolate gene conversion events associated with crossovers in the nitrogen-fixing bacterium Rhizobium etli. In this system, selection is applied only for cointegrate formation, with gene conversions being detected as unselected events. This minimizes the likelihood of multiple crossovers. To track the extent and architecture of gene conversions, evenly spaced nucleotide changes were made in one of the nitrogenase structural genes (nifH), introducing unique sites for different restriction endonucleases. Our results show that (i) crossover events were almost invariably accompanied by a gene conversion event occurring nearby; (ii) gene conversion events ranged in size from 150 bp to 800 bp; (iii) gene conversion events displayed a strong bias, favoring the preservation of incoming sequences; (iv) even small amounts of sequence divergence had a strong effect on recombination frequency; and (v) the MutS mismatch repair system plays an important role in determining the length of gene conversion segments. A detailed analysis of the architecture of the conversion events suggests that multiple crossovers are an unlikely alternative for their generation. Our results are better explained as the product of true gene conversions occurring under the double-strand break repair model for recombination.

Bacterial Proteins↗
PubMedDate not supplied

[Laparoscopic cholecystectomy. An analysis of the reasons for a conversion to conventional surgery in an elective surgery department].

BACKGROUND: To assess which factors determined conversion to laparotomy in patients undergoing laparoscopic elective cholecystectomy. SETTING: department of General Surgery. University of Genoa. Italy. METHODS: Two hundred sixty-four consecutive laparoscopic cholecystectomies were performed in our Department. INTERVENTIONS: laparoscopic cholecystectomy was performed according to Dubois's technique. Duration of the procedure was not considered a reason for conversion. RESULTS: 121 patients showed "difficult intraoperative situations" with further conversion risk factor. Conversion to laparotomy was necessary in 11 patients (4.16%). Five patients underwent conversion in the first 50 cases (10%), while six in the last 214 (2.8%). We had to convert to open cholecystectomy only in eleven patients, despite the high rate of technical difficulties and anatomic anomalies even in cases which, in the past, represented a contraindication to this kind of technique. The use of new instruments and new surgical techniques has reduced to only factors of increased risk in those situations that in the past were considered as contraindications to laparoscopic cholecystectomy. CONCLUSIONS: Conversion to open cholecystectomy is based on the surgeon's decision and the safety should be the main consideration in performing laparoscopic cholecystectomy. The use of a careful dissection could avoid the conversion in many patients.

Adolescent↗
PubMed1998

Whale Hageman factor (factor XII): prevented production due to pseudogene conversion.

In Southern blot analysis of the Hind III-digested whale genomic DNA obtained from the livers of two individual whales, we detected a single band with a size of five kilobase pairs which hybridized to full length guinea pig Hageman factor cDNA. We amplified two successive segments of the whale Hageman factor gene by polymerase chain reaction (PCR), and sequenced the PCR products with a combined total of 1367 base pairs. Although all of the exon-intron assemblies predicted were identical to those of the human Hageman factor gene, there were two nonsense mutations making stop codons and a single nucleotide insertion causing a reading frame shift. We could not detect any message of the Hageman factor gene expression by northern blot analysis or by reverse transcription-polymerase chain reaction (RT-PCR) analysis. These results suggest that in the whale, production of the Hageman factor protein is prevented due to conversion of its gene to a pseudogene. The deduced amino acid sequence of whale Hageman factor showed the highest homology with the bovine molecule among the land mammals analyzed so far.

Amino Acid Sequence↗
PubMed1978

Communicative performance of mentally retarded adults in four conversational settings.

A sociolinguistic analysis of the communicative performances and social interactions of four mentally retarded adults was conducted. Role relationships were examined along dimensions of dominance-submission and control in various conversational settings. Audiotape recordings were made of each adult's conversation while engaged in discourse with his speech-language pathologist, peers, parents, and with a normal young child. Relational communication coding schemes involving the analysis of questions and subsequent responses were applied to the data. Results indicated that the retarded adults, though not always able to hold a dominant position in a conversation, were capable of expressing the same types of control as normal adults. The types of control expressed by each subject varied as a function of the conversational setting. Furthermore, differences existed in the types and frequencies of control expressed across subjects. These findings suggest that a sociolinguistic approach provides important information regarding the mentally retarded adult's communicative performance.

Adult↗
PubMed2005

Guidelines and challenges for estimating the economic costs and benefits of adolescent substance abuse treatments.

Many economic evaluations have been conducted for adult substance abuse treatments, but only a few have been conducted for adolescent-specific treatments. This is the first article to present rigorous methodological guidelines for estimating the economic costs and benefits of adolescent substance abuse treatments while also addressing the potential challenges associated with such research activities. A representative case study of two adolescent substance abuse treatment programs (one residential and one outpatient) is presented to show some of the initial steps of a comprehensive economic evaluation (e.g., cost analyses, selection of treatment outcome measures, and valuation of outcome measures via monetary conversion factors). Cost data were collected and analyzed using the Drug Abuse Treatment Cost Analysis Program. Monetary conversion factors were obtained and presented for a variety of treatment outcomes. The methodological guidelines, discussion of analytic challenges, and recommendations set forth in this article provide a foundation for future economic studies on adolescent substance abuse treatments.

Adolescent↗
PubMed2026

Positive conversion of latent tuberculosis screening in patients with inflammatory bowel disease on antitumor necrosis factor alpha drugs: a systematic review and meta-analysis.

Inflammatory bowel disease (IBD) patients undergoing antitumor necrosis factor-alpha (anti-TNF) therapy are at increased risk of developing tuberculosis (TB), making screening before anti-TNF initiation mandatory. Repeated screening during treatment is not yet recommended because of a lack of studies to support this practice. We aimed to determine the proportion of patients who develop latent TB during anti-TNF therapy. We systematically searched studies from MEDLINE, Embase, and Lilacs, and performed a single-arm meta-analysis investigating the positive conversion rate in IBD patients under anti-TNF therapy with previous negative TB screening. We calculated the combined proportion with 95% confidence interval, using the random-effects model. A P value less than 0.05 was considered statistically significant for subgroup differences. We included 13 studies from nine countries with 1153 patients. The overall positive conversion rate was 9.20%. Portugal had 18.01% of positive conversion, Spain 4.51%, and the USA 1.11%. Tests for subgroup differences were statistically significant for subgroup analysis by country and consistency of test used (performig same test as baseline). Subgroup analyses by continent, study design, or specific test (tuberculin skin test or interferon-gamma release assay) showed no statistical difference. Meta-regression analysis showed a significant positive association between positive conversion and TB incidence. In conclusion, IBD patients on anti-TNF therapy can have a positive conversion rate of 9.20%. Higher conversion rates were seen in European and Asian studies compared with those in the Americas (particularly the USA). TB prevention strategies should, therefore, be individualized and based on geographic location and risk factors.

Humans↗
PubMed2001

Acute cor pulmonale in massive pulmonary embolism: incidence, echocardiographic pattern, clinical implications and recovery rate.

OBJECTIVE: The indications for the use of thrombolytic agents in massive pulmonary embolism (MPE) remain controversial and it has been suggested that transthoracic echocardiographic (TTE) examination, which is able to detect an associated right ventricular dysfunction, may cast light on this question. The goal of this study was to examine the incidence of acute cor pulmonale (ACP) in MPE, diagnosed on the basis of TTE criteria, its clinical implications and its resolution rate. DESIGN: Ten-year retrospective clinical study. SETTING: A medical and a coronary intensive care unit, university hospital. PATIENTS: One hundred sixty-one patients with proven MPE. INTERVENTIONS: Acute cor pulmonale was defined as right ventricular end-diastolic area / left ventricular end-diastolic area (RVEDA/LVEDA) ratio in the long axis greater than 0.6 associated with septal dyskinesia in the short axis. ACP patients were divided into three groups according to circulatory status: 32 patients without circulatory failure constituted group 1, 32 patients with circulatory failure requiring inotropic support, but free of metabolic acidosis, constituted group 2 and 34 patients in whom circulatory failure was associated with metabolic acidosis (defined by a base deficit >5 mEq/l) constituted group 3. RESULTS: Acute cor pulmonale was present in 61% of patients with MPE and carried a 23% mortality, but this mortality was very different in stable patients (groups 1 and 2, 64 patients, 3% mortality) and in unstable patients (group 3, 34 patients, 59% mortality). A multivariate logistic regression analysis showed that the TTE results were not predictive of the risk of death. Conversely, the same analysis showed that the presence of metabolic acidosis was a powerful predictor of death. CONCLUSION: Because none of the TTE measurements in ACP could be used to stratify the severity of MPE, TTE was of no help in deciding on medical thrombolysis. However, depending on its severity, metabolic acidosis could justify a large cooperative study to assess the impact of thrombolytic therapy on mortality rate in this specific group.

Acidosis↗