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Sökning: WFRF:(Corcoran Pádraic)

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1.
  • Binzer-Panchal, Amrei, et al. (författare)
  • Integrated molecular analysis of undifferentiated uterine sarcomas reveals clinically relevant molecular subtypes
  • 2019
  • Ingår i: Clinical Cancer Research. - American Association for Cancer Research. - 1078-0432. ; 25:7, s. 2155-2165
  • Tidskriftsartikel (refereegranskat)abstract
    • Purpose: Undifferentiated uterine sarcomas (UUS) are rare, extremely deadly, sarcomas with no effective treatment. The goal of this study was to identify novel intrinsic molecular UUS subtypes using integrated clinical, histopathologic, and molecular evaluation of a large, fully annotated, patient cohort. Experimental Design: Fifty cases of UUS with full clinicopathologic annotation were analyzed for gene expression (n ¼ 50), copy-number variation (CNV, n ¼ 40), cell morphometry (n ¼ 39), and protein expression (n ¼ 22). Gene ontology and network enrichment analysis were used to relate over- and underexpressed genes to pathways and further to clinicopathologic and phenotypic findings. Results: Gene expression identified four distinct groups of tumors, which varied in their clinicopathologic parameters. Gene ontology analysis revealed differential activation of pathways related to genital tract development, extracellular matrix (ECM), muscle function, and proliferation. A multi-variable, adjusted Cox proportional hazard model demonstrated that RNA group, mitotic index, and hormone receptor expression influence patient overall survival (OS). CNV arrays revealed characteristic chromosomal changes for each group. Morphometry demonstrated that the ECM group, the most aggressive, exhibited a decreased cell density and increased nuclear area. A cell density cutoff of 4,300 tumor cells per mm 2 could separate ECM tumors from the remaining cases with a sensitivity of 83% and a specificity of 94%. IHC staining of MMP-14, Collagens 1 and 6, and Fibronectin proteins revealed differential expression of these ECM-related proteins, identifying potential new biomarkers for this aggressive sarcoma subgroup. Conclusions: Molecular evaluation of UUS provides novel insights into the biology, prognosis, phenotype, and possible treatment of these tumors.
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2.
  • Binzer-Panchal, Amrei, et al. (författare)
  • Integrated Molecular Analysis of Undifferentiated Uterine Sarcomas Reveals Clinically Relevant Molecular Subtypes
  • 2019
  • Ingår i: Clinical Cancer Research. - AMER ASSOC CANCER RESEARCH. - 1078-0432 .- 1557-3265. ; 25:7, s. 2155-2165
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Purpose: Undifferentiated uterine sarcomas (UUS) are rare, extremely deadly, sarcomas with no effective treatment. The goal of this study was to identify novel intrinsic molecular UUS subtypes using integrated clinical, histopathologic, and molecular evaluation of a large, fully annotated, patient cohort.</p><p>Experimental Design: Fifty cases of UUS with full clinicopathologic annotation were analyzed for gene expression (n = 50), copy-number variation (CNV, n = 40), cell morphometry (n = 39), and protein expression (n = 22). Gene ontology and network enrichment analysis were used to relate over-and underexpressed genes to pathways and further to clinicopathologic and phenotypic findings.</p><p>Results: Gene expression identified four distinct groups of tumors, which varied in their clinicopathologic parameters. Gene ontology analysis revealed differential activation of pathways related to genital tract development, extracellular matrix (ECM), muscle function, and proliferation. A multivariable, adjusted Cox proportional hazard model demonstrated that RNA group, mitotic index, and hormone receptor expression influence patient overall survival (OS). CNV arrays revealed characteristic chromosomal changes for each group. Morphometry demonstrated that the ECM group, the most aggressive, exhibited a decreased cell density and increased nuclear area. A cell density cutoff of 4,300 tumor cells per mm(2) could separate ECM tumors from the remaining cases with a sensitivity of 83% and a specificity of 94%. IHC staining of MMP-14, Collagens 1 and 6, and Fibronectin proteins revealed differential expression of these ECM-related proteins, identifying potential new biomarkers for this aggressive sarcoma subgroup. Conclusions: Molecular evaluation of UUS provides novel insights into the biology, prognosis, phenotype, and possible treatment of these tumors.</p>
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3.
  • Corcoran, Pádraic, et al. (författare)
  • A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system
  • 2014
  • Ingår i: Molecular Phylogenetics and Evolution. - 1055-7903 .- 1095-9513. ; 78, s. 136-147
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>The large diversity of mating systems observed in the fungal kingdom underlines the importance of mating system change in fungal evolution. The selfing species <em>Neurospora tetrasperma</em> has evolved a novel method of achieving self-fertility by a mating system referred to as pseudohomothallism. However, little is known about the origin of <em>N. tetrasperma</em> and its relationship to the self-sterile, heterothallic, Neurospora species. In this study, we used a combination of phylogenetic and population genetic analyses to reconstruct the evolutionary history of <em>N. tetrasperma</em> and its heterothallic relatives. We sequenced 9 unlinked nuclear loci from 106 strains of <em>N. tetrasperma</em> sampled from across the globe, and a sample of 28 heterothallic strains of Neurospora. Our analyses provide strong support for monophyly of <em>N. tetrasperma</em>, but reject the monophyly of <em>N. crassa</em>. We estimate that <em>N. tetrasperma</em> is of a recent origin and that it diverged from the heterothallic species ~1 million years ago. We also extend previous findings on the diversification within the <em>N. tetrasperma</em> clade, with 10 lineages identified. Taken together, these findings indicate that <em>N. tetrasperma</em> is younger than has been previously reported and that a rapid diversification of lineages has occurred within the <em>N. tetrasperma</em> clade.</p>
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5.
  • Corcoran, Pádraic (författare)
  • <em>Neurospora tetrasperma</em> from Natural Populations Toward the Population Genomics of a Model Fungus
  • 2013
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • <p>The study of DNA sequence variation is a powerful approach to study genome evolution, and to reconstruct evolutionary histories of species. In this thesis, I have studied genetic variation in the fungus <em>Neurospora tetrasperma</em> and other closely related Neurospora species. I have focused on <em>N. tetrasperma</em> in my research because it has large regions of suppressed recombination on its mating-type chromosomes, had undergone a recent change in reproductive mode and is composed of multiple reproductively isolated lineages. Using DNA sequence data from a large sample set representing multiple species of Neurospora I estimated that <em>N. tetrasperma</em> evolved ~1 million years ago and that it is composed of at least 10 lineages. My analysis of the type of asexual spores produced using newly described <em>N. tetrasperma</em> populations in Britain revealed that lineages differ considerably in life history characteristics that may have consequences for their evolution. A comparative genomic analysis using three genomes of <em>N. tetrasperma</em> and the genome of <em>N. crassa</em> revealed that the <em>mat a</em> chromosomes in the lineages examine have been introgressed from other Neurospora species and that this introgression has reduced levels of molecular degeneration on the mating-type chromosomes. Finally, I generated a population genomic dataset composed of 92 <em>N. tetrasperma</em> genomes and two genomes of other Neurospora species<em>.</em> Analysis of these genomes revealed that all strains of <em>N. tetrasperma</em> have large regions of suppressed recombination on their mating-type chromosomes ranging from 69-84% of the chromosome and that the extent of divergence between mating-type chromosomes within lineages varies greatly (from 1.3 to 3.2%). I concluded that the source of this great divergence mating-type chromosome is large-scale introgression from other Neurospora species, and that these introgressed tracts have become fixed within <em>N. tetrasperma</em> lineages. I also discovered that genes within non-recombining introgressed regions of the mating-type chromosome have severely reduced levels of genetic variation as compared to the autosomes, and exhibit signatures of reduced molecular degeneration. My analysis of variation in coding regions revealed that positive selection on the introgressed regions has resulted in the removal of deleterious mutations and is responsible for the reductions in molecular degeneration observed.</p>
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6.
  • Corcoran, Padraic, et al. (författare)
  • Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma.
  • 2016
  • Ingår i: Genome Research. - 1088-9051 .- 1549-5469. ; 26:4, s. 486-498
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of nondegenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes. We found that suppressed recombination extends across at least 6 Mbp (similar to 63%) of the mating-type (mat) chromosome in N. tetrasperma and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six of eight lineages show introgression into one of their mat chromosomes, with multiple Neurospora species acting as donors. The introgressed tracts have been fixed within lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one lineage. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.</p>
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7.
  • Corcoran, Padraic, et al. (författare)
  • Quantifying functional heterothallism in the pseudohomothallic ascomycete Neurospora tetrasperma
  • 2012
  • Ingår i: Fungal Biology. - 1878-6146 .- 1878-6162. ; 116:9, s. 962-975
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Neurospora tetrasperma is a pseudohomothallic filamentous ascomycete that has evolved from heterothallic ancestors. Throughout its life cycle, it is predominantly heterokaryotic for mating type, and thereby self-fertile. However, studies of N. tetrasperma have revealed the occasional production of self-sterile asexual and sexual spores of a single-mating type, indicating that it can be functionally heterothallic. Here, we report the extensive sampling and isolation of natural, heterokaryotic, strains of N. tetrasperma from the United Kingdom (UK): 99 strains were collected from Surrey, England, and four from Edinburgh, Scotland. We verified by phylogenetic analyses that these strains belong to N. tetrasperma. We isolated cultures from single germinated asexual spores (conidia) from 17 of these newly sampled UK strains from Surrey, and 16 previously sampled strains of N. tetrasperma from New Zealand (NZ). Our results show that the N. tetrasperrna strains from the UK population produced a significantly greater proportion of self-sterile, homokaryotic conidia than the NZ population: the proportion of homokaryotic conidia was 42.6 % (133/312 spores) and 15.3 % (59/386) from the UK and the NZ populations, respectively. Although homokaryons recovered from several strains show a bias for one of the mating types, the total ratio of mat A to mat a mating type in homokaryons (UK: 72/61, NZ 28/31) did not deviate significantly from the expected 1:1 ratio for either of these populations. These results indicate that different populations exhibit differences in their life cycle characteristics, and that a higher degree of outcrossing might be expected from the UK population. This study points to the importance of studying multiple strains and populations when investigating life history traits of an organism with a complex life cycle, as previously undetected differences between populations may be revealed.</p>
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8.
  • Danesi, Claudia, et al. (författare)
  • Increased Calcium Influx through L-type Calcium Channels in Human and Mouse Neural Progenitors Lacking Fragile X Mental Retardation Protein
  • 2018
  • Ingår i: Stem Cell Reports. - 2213-6711. ; 11:6, s. 1449-1461
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>The absence of FMR1 protein (FMRP) causes fragile X syndrome (FXS) and disturbed FMRP function is implicated in several forms of human psychopathology. We show that intracellular calcium responses to depolarization are augmented in neural progenitors derived from human induced pluripotent stem cells and mouse brain with FXS. Increased calcium influx via nifedipine-sensitive voltage-gated calcium (Ca-v) channels contributes to the exaggerated responses to depolarization and type 1 metabotropic glutamate receptor activation. The ratio of L-type/T-type Ca-v channel expression is increased in FXS progenitors and correlates with enhanced progenitor differentiation to glutamate-responsive cells. Genetic reduction of brain-derived neurotrophic factor in FXS mouse progenitors diminishes the expression of Ca-v channels and activity-dependent responses, which are associated with increased phosphorylation of the phospholipase C-gamma 1 site within TrkB receptors and changes of differentiating progenitor subpopulations. Our results show developmental effects of increased calcium influx via L-type Ca-v channels in FXS neural progenitors.</p>
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9.
  • Jahan, Sultana N., et al. (författare)
  • Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans
  • 2015
  • Ingår i: Journal of Experimental Botany. - 0022-0957 .- 1460-2431. ; 66:9, s. 2785-2794
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>A host-induced gene-silencing strategy for controlling potato late blight is presented, a plant disease that conventionally requires regular application of fungicides at high rates.Phytophthora infestans is an oomycete that causes severe damage to potato, and is well known for its ability to evolve rapidly in order to overcome resistant potato varieties. An RNA silencing strategy was evaluated here to clarify if small interfering RNA homologous to selected genes in P. infestans could be targeted from the plant host to reduce the magnitude of the infection. As a proof-of-concept, a hairpin RNA (hp-RNA) construct using the GFP marker gene was designed and introduced in potato. At 72 hpi, a 55-fold reduction of the signal intensity of a corresponding GFP expressing P. infestans strain on leaf samples of transgenic plants, compared with wild-type potato, was detected. This suggests that an RNA interference construct in the potato host could be processed and target a transcript of the pathogen. Three genes important in the infection process of P. infestans, PiGPB1, PiCESA2, and PiPEC, together with PiGAPDH taking part in basic cell maintenance were subsequently tested using an analogous transgenic strategy. Out of these gene candidates, the hp-PiGPB1 targeting the G protein beta-subunit (PiGPB1) important for pathogenicity resulted in most restricted disease progress. Further, Illumina sequencing of inoculated transgenic potato leaves revealed sRNAs of 24/25 nt size homologous to the PiGPB1 gene in the transgenic plants indicating post-transcriptional silencing of the target gene. The work demonstrates that a host-induced gene-silencing approach is functional against P. infestans but is highly dependent on target gene for a successful outcome. This finding broadens the arsenal of control strategies to this important plant disease.</p>
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10.
  • St Onge, Kate, 1982-, et al. (författare)
  • Coalescent-based analysis distinguishes between allo- and autopolyploid origin in shepherd’s purse<em> (Capsella bursa-pastoris)</em>
  • 2012
  • Ingår i: Molecular biology and evolution. - 0737-4038 .- 1537-1719. ; 29:7, s. 1721-1733
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Polyploidization plays an important role in plant speciation. The most recent estimates 36 report that up to 15% of angiosperm speciation events and 31% in ferns are accompanied 37 by changes in ploidy level. Polyploids can arise either through autopolyploidy, when the 38 sets of chromosomes originate from a single species, or through allopolyploidy, when 39 they originate from different species. In this study we used two different coalescent-based 40 methods to determine the date and mode of the polyploidization event that led to the 41 tetraploid cosmopolitan weed, <em>Capsella bursa-pastoris</em>. We sampled 78 <em>C. bursa-pastoris </em>42 accessions, and 53 and 43 accessions from the only two other members of this genus, <em>C. </em>43 <em>grandiflora </em>and <em>C. rubella, </em>respectively, and sequenced these accessions at 14 unlinked 44 nuclear loci with locus-specific primers in order to be able to distinguish the two 45 homeologues in the tetraploid. A large fraction of fixed differences between 46 homeologous genes in <em>C. bursa-pastoris </em>are segregating as polymorphisms in <em>C. </em>47 <em>grandiflora</em>, consistent with an autopolyploid origin followed by disomic inheritance. To 48 test this, we first estimated the demographic parameters of an isolation-with-migration 49 model in a pairwise fashion between <em>C. grandiflora </em>and both genomes of <em>C. bursa- </em>50 <em>pastoris </em>and used these parameters in coalescent simulations to test the mode of origin of 51 <em>C. bursa-pastoris</em>. Secondly we used Approximate Bayesian Computation to compare an 52 allopolyploid and an autopolyploid model. Both analyses led to the conclusion that <em>C. </em>53 <em>bursa-pastoris </em>originated less than one million years ago by doubling of the <em>C. </em>54 <em>grandiflora </em>genome.</p>
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