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Search Results: 1 - 10 of 407654 matches for " Jim M Dunwell "
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Detection of Oxidation Products of 5-Methyl-2′-Deoxycytidine in Arabidopsis DNA
Shuo Liu, Thomas L. Dunwell, Gerd P. Pfeifer, Jim M. Dunwell, Ihsan Ullah, Yinsheng Wang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0084620
Abstract: Epigenetic regulations play important roles in plant development and adaptation to environmental stress. Recent studies from mammalian systems have demonstrated the involvement of ten-eleven translocation (Tet) family of dioxygenases in the generation of a series of oxidized derivatives of 5-methylcytosine (5-mC) in mammalian DNA. In addition, these oxidized 5-mC nucleobases have important roles in epigenetic remodeling and aberrant levels of 5-hydroxymethyl-2′-deoxycytidine (5-HmdC) were found to be associated with different types of human cancers. However, there is a lack of evidence supporting the presence of these modified bases in plant DNA. Here we reported the use of a reversed-phase HPLC coupled with tandem mass spectrometry method and stable isotope-labeled standards for assessing the levels of the oxidized 5-mC nucleosides along with two other oxidatively induced DNA modifications in genomic DNA of Arabidopsis. These included 5-HmdC, 5-formyl-2′-deoxycytidine (5-FodC), 5-carboxyl-2′-deoxycytidine (5-CadC), 5-hydroxymethyl-2′-deoxyuridine (5-HmdU), and the (5′S) diastereomer of 8,5′-cyclo-2′-deoxyguanosine (S-cdG). We found that, in Arabidopsis DNA, the levels of 5-HmdC, 5-FodC, and 5-CadC are approximately 0.8 modifications per 106 nucleosides, with the frequency of 5-HmdC (per 5-mdC) being comparable to that of 5-HmdU (per thymidine). The relatively low levels of the 5-mdC oxidation products suggest that they arise likely from reactive oxygen species present in cells, which is in line with the lack of homologous Tet-family dioxygenase enzymes in Arabidopsis.
Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots
Chun Li, Meng Li, Jim M Dunwell, Yuan-Ming Zhang
BMC Evolutionary Biology , 2012, DOI: 10.1186/1471-2148-12-15
Abstract: Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes), were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots.Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots.The plant seed is not only an organ of propagation and dispersal but also the major plant tissue harvested and used either directly as part of the human diet or as feed for animals. At the present time there is concern over long term food security and the impact of the move towards meat-based diets that will lead to a significant increase in the demand for plant protein for animal feed [1]. The amount of protein present in plant seeds varies from ~10% of the dry weight in most monocot (e.g. O. sativa, S. bicolor, S. italica, Z. mays and B. distachyon) to more than 30% in most dicots (e.g. G. max, R. communis, C. sativus and A. thaliana), and forms a major source of dietary protein [2-7]. To determine whether differences in evolutionary patterns may explain the phenotypic differences observed, a comparative investigation of evolutionary divergence in genes underlying protein synthesis in these two groups of plants is thus warranted.Seed storage proteins can be classified into four groups: albumins, globulins, prolamins and glutelins [8]. Albumins and globulins comprise the storage proteins of dicots, whereas prolamins and glutelins are the major proteins in monocots [4,9,10]. 2S albumins, a major class of dicot seed storage proteins, have been most widely studied in the Cruciferae, notably B. napus and A. thaliana [9,10]. Prolamins, the major endosperm storage proteins of all cereal grai
Transcriptome analysis and crop improvement: (A review)
DUNWELL,JIM M; MOYA-LEóN,MARIA A; HERRERA,RAUL;
Biological Research , 2001, DOI: 10.4067/S0716-97602001000300003
Abstract: the identification and characterization of differential gene expression from tissues subjected to stress has gained much attention in plant research. the recognition of elements involved in the response to a particular stress enhances the possibility of promoting crop improvement through direct genetic modification. however, the performance of some of the `first generation' of transgenic plants with the incorporation of a single gene has not always been as expected. these results have stimulated the development of new transgenic constructions introducing more than one gene and capable of modifying complex pathways. several techniques are available to conduct the analysis of gene regulation, with such information providing the basis for novel constructs specifically designed to modify metabolism. this review deals with techniques that allow the identification and characterization of differentially-expressed genes and the use of molecular pathway information to produce transgenic plants. (biol res 2001; 34 3-4: 153-164)
Transcriptome analysis and crop improvement: (A review)
JIM M DUNWELL,MARIA A MOYA-LEóN,RAUL HERRERA
Biological Research , 2001,
Abstract: The identification and characterization of differential gene expression from tissues subjected to stress has gained much attention in plant research. The recognition of elements involved in the response to a particular stress enhances the possibility of promoting crop improvement through direct genetic modification. However, the performance of some of the `first generation' of transgenic plants with the incorporation of a single gene has not always been as expected. These results have stimulated the development of new transgenic constructions introducing more than one gene and capable of modifying complex pathways. Several techniques are available to conduct the analysis of gene regulation, with such information providing the basis for novel constructs specifically designed to modify metabolism. This review deals with techniques that allow the identification and characterization of differentially-expressed genes and the use of molecular pathway information to produce transgenic plants. (Biol Res 2001; 34 3-4: 153-164)
Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array
Laima Antanaviciute, Felicidad Fernandez Fernandez, Johannes Jansen, Elisa Banchi, Katherine M Evans, Roberto Viola, Riccardo Velasco, Jim M Dunwell, Michela Troggio, Daniel J Sargent
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-203
Abstract: Of the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2?cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7?cM with the addition of the SNP markers, whilst marker density increased from 3.8?cM/marker to 0.5?cM/marker. Just three regions in excess of 10?cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence.We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.
Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription
Rebecca L Poole, Gary LA Barker, Kay Werner, Gaia F Biggi, Jane Coghill, J George Gibbings, Simon Berry, Jim M Dunwell, Keith J Edwards
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-475
Abstract: Examination of 71,930 Long SAGE tags generated from six libraries derived from two wheat genotypes grown under two different conditions suggested that SAGE is a reliable and reproducible technique for use in studying the hexaploid wheat transcriptome. However, our results also showed that in poorly annotated and/or poorly sequenced genomes, such as hexaploid wheat, considerably more information can be extracted from SAGE data by carrying out a systematic analysis of both perfect and "fuzzy" (partially matched) tags. This detailed analysis of the SAGE data shows first that while there is evidence of alternative polyadenylation this appears to occur exclusively within the 3' untranslated regions. Secondly, we found no strong evidence for widespread alternative splicing in the developing wheat grain transcriptome. However, analysis of our SAGE data shows that antisense transcripts are probably widespread within the transcriptome and appear to be derived from numerous locations within the genome. Examination of antisense transcripts showing sequence similarity to the Puroindoline a and Puroindoline b genes suggests that such antisense transcripts might have a role in the regulation of gene expression.Our results indicate that the detailed analysis of transcriptome data, such as SAGE tags, is essential to understand fully the factors that regulate gene expression and that such analysis of the wheat grain transcriptome reveals that antisense transcripts maybe widespread and hence probably play a significant role in the regulation of gene expression during grain development.With cereals constituting more than 60% of the world's dietary intake, the bread wheat Triticum aestivum is one of the most important crops in world agriculture [1,2]. Despite the high yields achieved in Europe there is still a real need to generate improved cultivars, as yield and flour quality can be dramatically affected by the environment. This need has become even greater in recent years with tight
Production of haploids and doubled haploids in oil palm
Jim M Dunwell, Mike J Wilkinson, Stephen Nelson, Sri Wening, Andrew C Sitorus, Devi Mienanti, Yuzer Alfiko, Adam E Croxford, Caroline S Ford, Brian P Forster, Peter DS Caligari
BMC Plant Biology , 2010, DOI: 10.1186/1471-2229-10-218
Abstract: Here we present the first high-throughput screen to identify spontaneously-formed haploid (H) and doubled haploid (DH) palms. We secured over 1,000 Hs and one DH from genetically diverse material and derived further DH/mixoploid palms from Hs using colchicine. We demonstrated viability of pollen from H plants and expect to generate 100% homogeneous F1 seed from intercrosses between DH/mixoploids once they develop female inflorescences.This study has generated genetically diverse H/DH palms from which parental clones can be selected in sufficient numbers to enable the commercial-scale breeding of F1 varieties. The anticipated step increase in productivity may help to relieve pressure to extend palm cultivation, and limit further expansion into biodiverse rainforest.Success of early F1 hybrid maize varieties exemplifies the advantages of heterosis [1]. The use of doubled haploids as parents for F1 variety production fully exploits this phenomenon and has enabled substantial yield improvements in several crops [2,3]. This strategy was outlined with the first DH crop variety [4] and has led to H/DH production systems being described for > 250 species [5]. However, few of these protocols generate the large numbers of Hs/DHs needed for commercial breeding, with just three methods (androgenesis, wide crossing, gynogenesis [6]) routinely adopted for H/DH production in only 30 species [5]. The most important of these methods in widespread use in commercial breeding is the generation of haploids in maize via pollination with a haploid inducing line such as a 'Stock 6' derivative. Desire for a more generic H/DH production system to improve agricultural yields is increasing as population growth, climate change, biofuel demand and other land-use pressures intensify. Clearly, in any species the production of F1 varieties depends not only on the production of homozygous lines to act as parents, but also it requires an efficient method to intercross the parents. This latter procedu
Treatment of irritable bowel syndrome with probiotics: An etiopathogenic approach at last?
Bixquert Jiménez,M.;
Revista Espa?ola de Enfermedades Digestivas , 2009, DOI: 10.4321/S1130-01082009000800006
Abstract: irritable bowel syndrome (ibs) is the most common functional digestive disorder, and may affect 11-20% of the adult population in industrialized countries. in accordance with rome iii criteria (2006) ibs involves abdominal pain and bowel habit disturbance, which are not explained by structural or biochemical abnormalities. several hypotheses attempt to account for the pathophysiology of ibs, but the etiology still remains uncertain or obscure, perhaps multifactorial. abnormalities in colonic microflora have recently been suggested in such patients, as has abnormal small-intestine bacterial overgrowth (sibo), or in particular a significant reduction in the amount of intraluminal bifidobacteria or lactobacilli, with consequences like the production of colonic gas, and motility or sensitivity disturbances of the intestinal tract. the disorder is difficult to treat, and the wide spectrum of non-drug and drug treatments shows our ignorance about the cause of the condition. newer drugs, both pro- and anti-serotonin, have failed to show long-term efficacy or have been withdrawn due to concerns about harmful effects. recent research has provided increasing support for the idea that disturbances of intestinal microbiota occur in patients with ibs, and that such abnormalities may contribute to ibs symptoms. studies in scandinavian countries in the last ten years emphasize the role of probiotics in the modulation of intestinal microbiota, and as a consequence in the regulation of the motility and hypersensitivity of the digestive tract. although results between studies are difficult to compare because of differences in study design, probiotic dose, strain, and duration of therapy, some studies show symptom improvement. lactobacilli are found among the normal bacterial flora of the gastrointestinal tract, and lactobacillus plantarum (lp) is one of the species frequently isolated from the human mucosa, which is capable of surviving the low ph of the stomach and duodenum, resisti
UNA PROPUESTA PARA LA MAXIMIZACIóN DE LA ESTADíSTICA Q_k
Jiménez M. José
Revista Colombiana de Estadística , 2001,
Abstract: En este artículo mediante el método de los multiplicadores de Lagrange se presenta una forma de maximizar la Estadística Q_k, y de esta manera cuantificar el impacto que ejerce en la suma de cuadrados de los residuales un grupo de observaciones previamente seleccionadas si son corregidas o modificadas.
UNA GENERALIZACIóN DE LA ESTADíSTICA DE COOK UNA GENERALIZACIóN DE LA ESTADíSTICA DE COOK
Jiménez M. José
Revista Colombiana de Estadística , 2001,
Abstract: This paper presents a generalization of the Cook's statistics useful in the identification of influential observations in the least squares estimation of the multiple regression parameters. En este artículo se presenta una generalización de la estadística de Cook la cual permite identificar las observaciones más influyentes en la estimación vía mínimos cuadrados de los parámetros del modelo de regresión lineal múltiple.
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