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Article
Open AccessDetection of ribonucleotides embedded in DNA by Nanopore sequencing
Ribonucleotides represent the most common non-canonical nucleotides found in eukaryotic genomes. The sources of chromosome-embedded ribonucleotides and the mechanisms by which unrepaired rNMPs trigger genome i...
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Article
Open AccessMacroalgal microbiomes unveil a valuable genetic resource for halogen metabolism
Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these met...
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Article
Open AccessDysregulation of testis mRNA expression levels in hatchery-produced vs wild greater amberjack Seriola dumerili
Reproductive dysfunctions have been recently documented in male greater amberjack Seriola dumerili caught from the wild and reared in captivity. In the present study, we compared testis transcriptome in wild fish...
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Article
Open AccessHuman PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system
Polyribonucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. In Escherichia coli, PNPase controls complex phenotypic traits like biofilm formation and growt...
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Article
Open AccessNatural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome
To date several studies address the important role of gut microbiome and its interplay with the human host in the health and disease status. However, the selection of a universal sampling matrix representative...
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Article
Open AccessMetabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance
In nature, microbial communities undergo changes in composition that threaten their resiliency. Here, we interrogated sourdough, a natural cereal-fermenting metacommunity, as a dynamic ecosystem in which playe...
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Article
Open AccessAccurate detection and quantification of SARS-CoV-2 genomic and subgenomic mRNAs by ddPCR and meta-transcriptomics analysis
SARS-CoV-2 replication requires the synthesis of a set of structural proteins expressed through discontinuous transcription of ten subgenomic mRNAs (sgmRNAs). Here, we have fine-tuned droplet digital PCR (ddPC...
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Article
Different substrates within a lake harbour connected but specialised microbial communities
Natural water bodies contain physically interconnected habitats suitable for microbes, such as different water layers and substrates for biofilms. Yet, little is known on the extent to which microbial communit...
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Article
Open AccessNo metagenomic evidence of tumorigenic viruses in cancers from a selected cohort of immunosuppressed subjects
The possible existence of yet undiscovered human tumorigenic viruses is still under scrutiny. The development of large-scale sequencing technologies, coupled with bioinformatics techniques for the characteriza...
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Article
Open AccessManagement at the service of research: ReOmicS, a quality management system for omics sciences
Management and research represent a binomial almost unknown, whose potentialities and requirements have not yet been fully exploited even if, recently, the scientific and social communities have felt the burde...
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Article
Open AccessWhole transcriptome profiling of Late-Onset Alzheimer’s Disease patients provides insights into the molecular changes involved in the disease
Alzheimer’s Disease (AD) is the most common cause of dementia affecting the elderly population worldwide. We have performed a comprehensive transcriptome profiling of Late-Onset AD (LOAD) patients using second...
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Open AccessMassive transcriptome sequencing of human spinal cord tissues provides new insights into motor neuron degeneration in ALS
ALS is a devastating and debilitating human disease characterized by the progressive death of upper and lower motor neurons. Although much effort has been made to elucidate molecular determinants underlying th...
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Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing
Comprehensive studies of the biodiversity of the microbial epilithic community on monuments may provide critical insights for clarifying factors involved in the colonization processes. We carried out a high-th...
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Open AccessCorrection: Corrigendum: Profiling RNA editing in human tissues: towards the inosinome Atlas
Scientific Reports 5: Article number: 14941; published online: 09 October 2015; updated: 08 February 2016. The original version of this Article contained typographical errors in the inosinome database link ‘ h...
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Open AccessProfiling RNA editing in human tissues: towards the inosinome Atlas
Adenine to Inosine RNA editing is a widespread co- and post-transcriptional mechanism mediated by ADAR enzymes acting on double stranded RNA. It has a plethora of biological effects, appears to be particularly...
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Article
Open AccessThe influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy
The rapid expansion of multicellular native and alien species outbreaks in aquatic and terrestrial ecosystems (bioinvasions) may produce significant impacts on bacterial community dynamics and nutrient pathways w...
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Article
Open AccessA platform independent RNA-Seq protocol for the detection of transcriptome complexity
Recent studies have demonstrated an unexpected complexity of transcription in eukaryotes. The majority of the genome is transcribed and only a little fraction of these transcripts is annotated as protein codin...
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Article
Open AccessRespiratory complex I is essential to induce a Warburg profile in mitochondria-defective tumor cells
Aerobic glycolysis, namely the Warburg effect, is the main hallmark of cancer cells. Mitochondrial respiratory dysfunction has been proposed to be one of the major causes for such glycolytic shift. This hypoth...
