Arianna Consiglio

Italian National Research Council, Italy

In previous reports, we had shown in Camelus dromedarius that diversity in T cell receptor gamma (TRG) and delta (TRD) variable domains can be generated by somatic hypermutation (SHM). In the present paper, we further the previous finding by analyzing 85 unique spleen cDNA sequences encoding a total of 331 mutations from a single animal, and compar...

It is known from recent studies that more than 90% of human multi-exon genes are subject to Alternative Splicing (AS), a key molecular mechanism in which multiple transcripts may be generated from a single gene. It is widely recognized that a breakdown in AS mechanisms plays an important role in cellular differentiation and pathologies. Polymerase...

PlantPIs is a web querying system for a database collection of plant protease inhibitors data. Protease inhibitors in plants are naturally occurring proteins that inhibit the function of endogenous and exogenous proteases. In this paper the design and development of a web framework providing a clear and very flexible way of querying plant protease...

A system for Operational Risk management based on the computational paradigm of Bayesian Networks is presented. The algorithm allows the construction of a Bayesian Network targeted for each bank using only internal loss data, and takes into account in a simple and realistic way the correlations among different processes of the bank. The internal lo...

In this paper we present an approach for extracting interpretable information granules for classification. The approach, called DC^γ (double clustering with genetic algorithms) is based on two clustering steps. The first step uses LVQ1 to identify cluster prototypes in the multidimensional data space so as to represent hidden relationship...

Spinal muscular atrophy (SMA) is a rare degenerative disorder with loss of motor neurons caused by mutations in the SMN1 gene. Nusinersen, an antisense oligonucleotide, was approved for SMA treatment to compensate the deficit of the encoded protein SMN by modulating the pre–mRNA splicing of SMN2, the centromeric homologous of SMN1, thus inducing th...

Flow cytometry (FCM) can investigate dozens of parameters from millions of cells and hundreds of specimens in a short time and at a reasonable cost, but the amount of data that is generated is considerable. Computational approaches are useful to identify novel subpopulations and molecular biomarkers, but generally require deep expertize in bioinfor...

Microcephalic Osteodysplastic Primordial Dwarfism type II (MOPDII) represents the most common form of primordial dwarfism. MOPD clinical features include severe prenatal and postnatal growth retardation, postnatal severe microcephaly, hypotonia, and an increased risk for cerebrovascular disease and insulin resistance. Autosomal recessive biallelic...

Long non-coding RNAs (lncRNAs) have emerged as key regulators of cellular senescence by transcriptionally and post-transcriptionally modulating the expression of many important genes involved in senescence-associated pathways and processes. Among the different lncRNAs associated to senescence, Senescence Associated Long Non-coding RNA (SALNR) was f...

Long non-coding RNAs (lncRNAs) have emerged as key regulators of cellular senescence by transcriptionally and post-transcriptionally modulating the expression of many important genes involved in senescence-associated pathways and processes. Among the different lncRNAs associated to senescence, Senescence Associated Long Non-coding RNA ( SALNR ) was...

Background In previous investigations of combined miRNAs/mRNAs expressions in neurodegenerative diseases like Multiple Sclerosis (MS) and Amyotrophic Lateral Sclerosis (ALS) we have targeted some interesting genes and molecular pathways that needed further confirmation. Methods By nanofluidic qPCR analysis, we aimed to verify the expression of gen...

Intestinal microorganisms impact health by maintaining gut homeostasis and shaping the host immunity, while gut dysbiosis associates with many conditions, including autism, a complex neurodevelopmental disorder with multifactorial aetiology. In autism, gut dysbiosis correlates with symptom severity and is characterised by a reduced bacterial variab...

This work describes a non-invasive, automated software framework to discriminate between individuals with a genetic disorder, Pitt–Hopkins syndrome (PTHS), and healthy individuals through the identification of morphological facial features. The input data consist of frontal facial photographs in which faces are located using histograms of oriented...

Glioblastomas (GBM) are the most aggressive tumors originating in the brain. Histopathologic features include circuitous, disorganized and highly permeable blood vessels with intermittent blood flow. Permeable blood vessels may contribute to the inability to direct therapeutic agents to tumor cells. Current known targets for anti-angiogenic therapi...

Glioblastomas (GBM) are the most aggressive tumors originating in the brain. Histopathologic features include circuitous, disorganized, and highly permeable blood vessels with intermittent blood flow. These features contribute to the inability to direct therapeutic agents to tumor cells. Known targets for anti-angiogenic therapies provide minimal o...

Annual Meeting of the Bioinformatics Italian Society (BITS 2021)

MicroRNAs (miRNAs) are a set of short non-coding RNAs that play significant regulatory roles in cells. The study of miRNA data produced by Next-Generation Sequencing techniques can be of valid help for the analysis of multifactorial diseases, such as Multiple Sclerosis (MS). Although extensive studies have been conducted on young adults affected by...

The analysis of gene expression data is a complex task, and many tools and pipelines are available to handle big sequencing datasets for case-control (bivariate) studies. In some cases, such as pilot or exploratory studies, the researcher needs to compare more than two groups of samples consisting of a few replicates. Both standard statistical bioi...

MicroRNAs (miRNAs), a class of non-coding RNAs, seem to play a key role in complex diseases like multiple sclerosis (MS), as well as in many cognitive functions associated with the disease. In a previous cross-sectional evaluation on pediatric MS (PedMS) patients, the expression of some miRNAs and their target genes were found to be associated with...

Viral infections are accompanied by a massive production of small interfering RNAs (siRNAs) of plant origin, such as virus‐activated (va)siRNAs, which drive the widespread silencing of host gene expression, and whose effects in plant pathogen interactions remain unknown. By combining phenotyping and molecular analyses, we characterized vasiRNAs tha...

MicroRNAs (miRNAs) are ubiquitous regulators of gene expression, evolutionarily conserved in plants and mammals. In recent years, although a growing number of papers debate the role of plant miRNAs on human gene expression, the molecular mechanisms through which this effect is achieved are still not completely elucidated. Some evidence suggest that...

High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. Howe...

Multiple Sclerosis (MS) is a demyelinating autoimmune disease that usually affects young adults; however, recently some symptoms of cognitive impairment have been recognized as early signs of MS onset in pediatric patients (PedMS). The underlying relationships between these two conditions, as well as their molecular markers, have not been fully und...

Attention Deficit Hyperactivity Disorder (ADHD) is a childhood-onset neurodevelopmental disorder, whose etiology and pathogenesis are still largely unknown. In order to uncover novel regulatory networks and molecular pathways possibly related to ADHD, we performed an integrated miRNA and mRNA expression profiling analysis in peripheral blood sample...

MicroRNAs (miRNAs) are a set of short non coding RNAs that play significant regulatory roles in cells. The study of miRNA data can be of valuable support for the early diagnosis of multifactorial diseases such as pediatric Multiple Sclerosis. However the analysis of miRNA expressions poses several challenges due to high dimensionality and imbalance...

Introduction The Pediatric onset of Multiple Sclerosis (PedMS) occurs in up to 10% of all cases. Cognitive impairment is one of the frequent symptoms, exerting severe impact in patients’ quality of life and school performances. The underlying pathogenic mechanisms are not fully understood, and molecular markers predictive of cognitive dysfunctions...

[This corrects the article DOI: 10.3389/fnmol.2018.00288.].

MicroRNAs (miRNAs) and transcription factors (TFs) play key roles in complex multifactorial diseases like multiple sclerosis (MS). Starting from the miRNomic profile previously associated with a cohort of pediatric MS (PedMS) patients, we applied a combined molecular and computational approach in order to verify published data in patients with adul...

Folding reporters are proteins with easily identifiable phenotypes, such as antibiotic resistance, whose folding and function is compromised when fused to poorly folding proteins or random open reading frames. We have developed a strategy where, by using TEM-1 β-lactamase (the enzyme conferring ampicillin resistance) on a genomic scale, we can sele...

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease. While genetics and other factors contribute to ALS pathogenesis, critical knowledge is still missing and validated biomarkers for monitoring the disease activity have not yet been identified. To address those aspects we carried out this study with the primary...

A handheld laser-induced breakdown spectroscopy (LIBS) instrument is proposed as a novel tool able to provide information on the nature of meteorites and discriminate among iron, stone, stony-iron meteorites and meteor-wrongs. Further, a novel fuzzy logic –based inference algorithm is applied to LIBS broadband spectra for the identification of mete...

Multiple Sclerosis (MS) is a complex disease of the CNS that usually affects young adults, although 3-5% of cases are diagnosed in childhood and adolescence (hence called pediatric MS, PedMS). Genetic predisposition, among other factors, seems to contribute to the risk of the onset, in pediatric as in adult ages, but few studies have investigated t...

Extracellular vesicles (EVs), nanoparticles originated from different cell types, seem to be implicated in several cellular activities. In the Central Nervous System (CNS), glia and neurons secrete EVs and recent studies have demonstrated that the intercellular communication mediated by EVs has versatile functional impact in the cerebral homeostasi...

Background When the reads obtained from high-throughput RNA sequencing are mapped against a reference database, a significant proportion of them - known as multireads - can map to more than one reference sequence. These multireads originate from gene duplications, repetitive regions or overlapping genes. Removing the multireads from the mapping res...

Unfortunately in the original publication [1] the following text is missing from the Acknowledgments section: The funds of the Puglia Region are derived from the freed resources referred to P.O.R. Puglia for Scholarships for attendance of Ph.D courses activated by Apulian Universities for the XXVI Cycle.

Background The bottlenose dolphin (Tursiops truncatus) is a mammal that belongs to the Cetartiodactyla and have lived in marine ecosystems for nearly 60 millions years. Despite its popularity, our knowledge about its adaptive immunity and evolution is very limited. Furthermore, nothing is known about the genomics and evolution of dolphin antigen re...

High-performance Next-Generation Sequencing (NGS) has become a widely used technology to characterize case-control comparison studies for RNA transcripts, such as mRNAs and small non-coding RNAs. The first step in the analysis strategies is mapping NGS reads against a reference database and a critical issue emerges in this phase: the problem of mul...

NonCode aReNA Database is an integrated and non-redundant source of ncRNAs sequences. The database is freely available via an easy-to-use web interface that allows the user to search and retrieve non-redundant lists and sequences of ncRNAs also using their classification in Sequence Ontology (SO). ncRNA sequence annotations are from VEGA, ENSEMBL,...

Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flank...

Metagenomics is revolutionizing the study of environmental microbiology by means innovative protocols able to bypass the narrow bottleneck of single organisms isolation and culturing. The methodology includes the direct extraction of the entire genetic material from any biological sample which can be then analyzed by deep-sequencing thanks to the N...

Motivations Metagenomics is experiencing an explosive im-provement from the advent of high-throughput next-generation sequencing (NGS) technolo-gies which allows an unprecedented large-scale identification of microorganisms living in almost every environment. In particular, the use of amplicon-based metagenomic approach to explore the diversity of...

PDF file containing supplementary documentation about the data warehouse. In particular, we report a more detailed description of the repository and data marts, and four tables with a detailed description of fact tables, hierarchies and dimensional tables.

A system for Operational Risk management based on the computational paradigm of Bayesian Networks is presented. The algorithm allows the construction of a Bayesian Network targeted for each bank using only internal loss data, and takes into account in a simple and realistic way the correlations among different processes of the bank. The internal lo...

In this paper we describe an approach for mining interpretable diagnostic rules through a fuzzy information granulation process. Specifically, this process is performed by the DC* algorithm (Double Clustering with A*), which is aimed at mining from data a set of fuzzy information granules that satisfy a number of interpretability constraints. Such...

DC* (Double Clustering by A*) is an algorithm for interpretable fuzzy information granulation of data. It is mainly based on two clustering steps. The first step applies the LVQ1 algorithm to find a suitable representation of data relationships. The second clustering step is based on the A* search strategy and is aimed at finding an optimal number...