Search results for "Sequencing"
showing 10 items of 1087 documents
Hundreds of nuclear and plastid loci yield insights into orchid relationships
2020
ABSTRACTPremise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test…
Characterization of p20 and p23 genes in Corsican isolates of Citrus tristeza virus.
2011
Tristeza disease, caused by the Citrus tristeza virus (CTV), is the most important viral disease for almost all the citrus species. Main syndromes are quick decline, stem pitting, vein clearing and seedlings yellows but expression and intensity of symptomatology depends on the interactions of the factors involved in the pathosystem such as host-strain-rootstock-climate-vector. Several isolates of CTV have been studied all over the world. Two Corsican isolates have been previously characterized, the K strain from Marumi kumquat, known to be symptomless on Mexican lime, and the CaL -1 from calamondin inducing stem pitting, but no sequences of p20 gene are published or available in GenBank. Tw…
Mixed infection of Pectobacterium carotovorum subsp. Carotovorum and P. carotovorum subsp. Brasiliensis in tomato stem rot in Italy
2016
Grafted tomato plants grown in a soilless culture system in heated greenhouses in Sicily were affected by stem rot disease. Symptoms consisted of dark brown longitudinal discoloration of the basal part of the stem and petioles. Longitudinal sections of the stem revealed brown watersoaked or soft-rotted pith tissue and internal vascular discoloration. Bacterial isolates with two different colony morphologies were obtained from symptomatic tissues. Isolates were identified as Pectobacterium spp. on the basis of biochemical and molecular analyses. The analysis of the 16S rRNA gene sequence and of the concatenated sequences of the housekeeping genes rpoS and pgi revealed that the isolates of th…
Pancreatic undifferentiated carcinoma with osteoclast-like giant cells is genetically similar to, but clinically distinct from, conventional ductal a…
2017
Undifferentiated carcinoma of the pancreas with osteoclast-like giant cells (UCOGC) is currently considered a morphologically and clinically distinct variant of pancreatic ductal adenocarcinoma (PDAC). In this study, we report clinical and pathological features of a series of 22 UCOGCs, including the whole exome sequencing of eight UCOGCs. We observed that 60% of the UCOGCs contained a well-defined epithelial component and that patients with pure UCOGC had a significantly better prognosis than did those with an UCOGC with an associated epithelial neoplasm. The genetic alterations in UCOGC are strikingly similar to those known to drive conventional PDAC, including activating mutations in the…
Comparing the Ecotoxicological Effects of Perfluorooctanoic Acid (PFOA) and Perfluorohexanoic Acid (PFHxA) on Freshwater Microbial Community
2022
The ubiquitous presence of perfluorinated carboxylic acids (PFCAs) around the globe has attracted increasing attention, due to their persistency, bioaccumulation, and toxicity. Nevertheless, the ecotoxicological effects of the compounds on aquatic microorganisms has remained understudied. Hence, the present study focused on determining, and comparing, the effects of regulated long-chain PFCA, perfluorooctanoic acid (PFOA), and nonregulated short-chain PFCA, perfluorohexanoic acid (PFHxA), on the diversity, structure, microbial growth, and activity of a freshwater microbial community. In the experiment, lake water was incubated for a period of four weeks at three different concentrations of …
An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes
2015
Item does not contain fulltext Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequen…
The Global Soil Mycobiome consortium dataset for boosting fungal diversity research
2021
This version of the article has been accepted for publication, after peer review and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at https://doi.org/10.1007/s13225-021-00493-7. Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The dataset comprises 722,682 fu…
Parallel and scalable short-read alignment on multi-core clusters using UPC++
2016
[Abstract]: The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the …
Acquired IFNγ resistance impairs anti-tumor immunity and gives rise to T-cell-resistant melanoma lesions
2016
Melanoma treatment has been revolutionized by antibody-based immunotherapies. IFNγ secretion by CD8+ T cells is critical for therapy efficacy having anti-proliferative and pro-apoptotic effects on tumour cells. Our study demonstrates a genetic evolution of IFNγ resistance in different melanoma patient models. Chromosomal alterations and subsequent inactivating mutations in genes of the IFNγ signalling cascade, most often JAK1 or JAK2, protect melanoma cells from anti-tumour IFNγ activity. JAK1/2 mutants further evolve into T-cell-resistant HLA class I-negative lesions with genes involved in antigen presentation silenced and no longer inducible by IFNγ. Allelic JAK1/2 losses predisposing to …
Exploring the mechanisms by which reindeer droppings induce fen peat methane production
2021
Abstract Peatlands, especially fens, are known to emit methane. Reindeer (Rangifer tarandus) use mires mainly as spring and summer pastures. In this work we observed that adding reindeer droppings to fen peat increased the potential methane production by 40%. This became apparent when droppings originating from reindeer kept in pen or pasture in winter were added to methanogenic fen peat samples. The droppings introduced Methanobacteriaceae (Methanobrevibacter; > 90% of the mcrA MiSeq reads) to the peat, which was originally populated by Methanosarcinaceae, Methanosaetaceae, Methanoregulaceae, Methanobacteriaceae, Methanomassiliicoccaceae, Methanocellaceae and Methanomicrobiaceae. The origi…