23 Result(s)
within
Riccardo Aiese Cigliano
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Article
Open AccessExploring the gene expression network involved in the heat stress response of a thermotolerant tomato genotype
The increase in temperatures due to the current climate change dramatically affects crop cultivation, resulting in yield losses and altered fruit quality. Tomato is one of the most extensively grown and consum...
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Article
Open AccessDistinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina
Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in sha** the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our und...
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Article
Open AccessMitochondrial DNA is a target of HBV integration
Hepatitis B virus (HBV) may integrate into the genome of infected cells and contribute to hepatocarcinogenesis. However, the role of HBV integration in hepatocellular carcinoma (HCC) development remains unclea...
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Article
Open AccessTranscriptomic profiles of the ruminal wall in Italian Mediterranean dairy buffaloes fed green forage
Green feed diet in ruminants exerts a beneficial effect on rumen metabolism and enhances the content of milk nutraceutical quality. At present, a comprehensive analysis focused on the identification of genes, ...
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Article
Open AccessExploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation
Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desire...
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Article
Open AccessWhole-genome resequencing reveals genomic footprints of Italian sweet and hot pepper heirlooms giving insight into genes underlying key agronomic and qualitative traits
Pepper is a major crop species of the Solanaceae family, largely appreciated for its high nutritional and healthy contribution to human diets. In the Mediterranean basin, the favorable pedoclimatic conditions ...
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Article
Open AccessisoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data
Accurate copy number variant (CNV) detection is especially challenging for both targeted sequencing (TS) and whole‐exome sequencing (WES) data. To maximize the performance, the parameters of the CNV calling al...
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Article
Open AccessThe impact of chromosomal fusions on 3D genome folding and recombination in the germ line
The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear. Here, we take advantage of chromosome...
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Article
Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration
Following severe or chronic liver injury, adult ductal cells (cholangiocytes) contribute to regeneration by restoring both hepatocytes and cholangiocytes. We recently showed that ductal cells clonally expand a...
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Article
Whole-Genome Sequencing of an Uncommon Cryptococcus neoformans MLST43 Genotype Isolated in Nigeria
Cryptococcosis is a human infection caused mainly by two species of the Cryptococcus genus, Cryptococcus neoformans and Cryptococcus gattii, whose populations contain several phylogenetically related haploid (VN/...
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Article
Open AccessA de novo transcriptome assembly approach elucidates the dynamics of ovarian maturation in the swordfish (**phias gladius)
The Mediterranean swordfish (**phias gladius) has been recently classified as overfished and in 2016, the International Commission for the Conservation of the Atlantic Tunas (ICCAT) established a multi-annual man...
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Protocol
A Walkthrough to the Use of GreeNC: The Plant lncRNA Database
Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time, and interaction with symbiotic organisms, making them of gre...
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Article
Open AccessAn improved assembly and annotation of the melon (Cucumis melo L.) reference genome
We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical map** approach allowed correcting the order and the orientation of 21 previous scaff...
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Article
Open AccessAuthor Correction: The hypothesis that Helicobacter pylori predisposes to Alzheimer’s disease is biologically plausible
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
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Article
Open AccessMaize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription
RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosi...
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Article
Open AccessThe hypothesis that Helicobacter pylori predisposes to Alzheimer’s disease is biologically plausible
There is epidemiological evidence that H. pylori might predispose to Alzheimer’s disease. To understand the cellular processes potentially linking such unrelated events, we incubated the human gastric cells MNK-2...
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Article
Open AccessTranscriptomic response of durum wheat to nitrogen starvation
Nitrogen (N) is a key macronutrient representing a limiting factor for plant growth and development and affects productivity in wheat. In this study, durum wheat response to N chronic starvation during grain f...
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Article
Open AccessStress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis
Plant’s response and adaptation to abiotic stresses involve sophisticated genetic and epigenetic regulatory systems. To obtain a global view of molecular response to osmotic stresses, including the non-coding ...
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Article
Open AccessEffects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling
Mecp2 null mice model Rett syndrome (RTT) a human neurological disorder affecting females after apparent normal pre- and peri-natal developmental periods. Neuroanatomical studies in cerebral cortex of RTT mous...
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Article
Open AccessRapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius
In microorganisms, Ion Torrent sequencing technology has been proved to be useful in whole-genome sequencing of bacterial genomes (5 Mbp). In our study, for the first time we used this technology to perform a ...
