A5033073054- RNA Research and Splicing
- Herpesvirus Infections and Treatments
- Animal Virus Infections Studies
- Muscle Physiology and Disorders
- RNA and protein synthesis mechanisms
- Cytomegalovirus and herpesvirus research
- Poxvirus research and outbreaks
- SARS-CoV-2 and COVID-19 Research
- Immune Cell Function and Interaction
- interferon and immune responses
- HIV Research and Treatment
- Viral gastroenteritis research and epidemiology
- Plant Virus Research Studies
- Viral Infections and Immunology Research
- RNA modifications and cancer
- Hepatitis C virus research
- RNA regulation and disease
- vaccines and immunoinformatics approaches
- Viral Infections and Vectors
- Zoonotic diseases and public health
- Animal Disease Management and Epidemiology
- Genetics and Neurodevelopmental Disorders
- T-cell and B-cell Immunology
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
IRCCS Eugenio Medea
2016-2025
Institute of Bioinformatics
2015
Zero to Three
2013
Istituti di Ricovero e Cura a Carattere Scientifico
2001-2010
Ospedale Maggiore
2001-2003
Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico
2001-2003
University of Milan
2001-2003
Ferrari (Italy)
2003
MRC Human Nutrition Research
2003
San Raffaele University of Rome
2000
The novel coronavirus severe acute respiratory syndrome 2 (SARS-CoV-2) that recently emerged in China is thought to have a bat origin, as its closest known relative (BatCoV RaTG13) was described previously horseshoe bats. We analyzed the selective events accompanied divergence of SARS-CoV-2 from BatCoV RaTG13. To this end, we applied population genetics-phylogenetics approach, which leverages within-population variation and an outgroup. Results indicated most sites viral open reading frames...
Many human genes have adapted to the constant threat of exposure infectious agents; according "hygiene hypothesis," lack parasites in modern settings results immune imbalances, augmenting susceptibility development autoimmune and allergic conditions. Here, by estimating number pathogen species/genera a specific geographic location (pathogen richness) for 52 populations analyzing 91 interleukin (IL)/IL receptor (IL genes), we show that helminths been major selective force on subset these...
Limb girdle muscular dystrophies (LGMD) are characterized by genetic and clinical heterogeneity: seven autosomal dominant 12 recessive loci have so far been identified. Aims of this study were to evaluate the relative proportion different types LGMD in 181 predominantly Italian patients (representing 155 independent families), describe pattern forms, identify possible correlations between genotype, phenotype, protein expression levels, as prognostic factors. Based on data, majority probands...
Historically, allelic variations in blood group antigen (BGA) genes have been regarded as possible susceptibility factors for infectious diseases. Since host–pathogen interactions are major determinants evolution, BGAs can be thought of selection targets. In order to verify this hypothesis, we obtained an estimate pathogen richness geographic locations corresponding 52 populations distributed worldwide; after correction multiple tests and variables different from selective forces,...
Abstract TLR3 recognizes dsRNA and activates antiviral immune responses through the production of inflammatory cytokines type I IFNs. Genetic association studies have provided evidence concerning role a polymorphism in (rs3775291, Leu412Phe) viral infection susceptibility. We genotyped rs3775291 population Spanish HIV-1–exposed seronegative (HESN) individuals who remain HIV despite repeated exposure i.v. injection drug use (IDU-HESN individuals) as witnessed by their hepatitis C virus...
The ongoing worldwide monkeypox outbreak is caused by viral lineages (globally referred to as hMPXV1) that are related but distinct from clade IIb MPXV viruses transmitted within Nigeria. Analysis of the genetic differences has indicated APOBEC-mediated editing might be responsible for unexpectedly high number mutations observed in hMPXV1 genomes. Here, using 1,624 publicly available sequences, we analyzed accrued between 2017 and emergence current predominant variant (B.1), well those have...
Human pre‐mRNAs contain a definite number of exons and several pseudoexons which are located within intronic regions. We applied computational approach to address the question how neglected in favor possibly identify sequence elements preventing pseudoexon splicing. A search for possible splicing silencers was carried out on selection that resembled terms splice site strength exon enhancer (ESE) representation; three motifs were retrieved through hexamer composition comparisons. One these...
Human ERAP1 and ERAP2 encode two endoplasmic reticulum aminopeptidases. These enzymes trim peptides to optimal size for loading onto major histocompatibility complex class I molecules shape the antigenic repertoire presented CD8+ T cells. Therefore, may be considered potential selection targets modulators of infection susceptibility. We resequenced genic regions in three HapMap populations. In both cases, we observed high levels nucleotide variation, an excess intermediate-frequency alleles,...
Middle East respiratory syndrome-related coronavirus (MERS-CoV) spreads to humans via zoonotic transmission from camels. MERS-CoV belongs lineage C of betacoronaviruses (betaCoVs), which also includes viruses isolated bats and hedgehogs. A large portion the betaCoV genome consists two open reading frames (ORF1a ORF1b) that are translated into polyproteins. These cleaved by viral proteases generate 16 nonstructural proteins (nsp1 nsp16) compose replication-transcription complex. We...
Middle East respiratory syndrome coronavirus (MERS-CoV) originated in bats and spread to humans via zoonotic transmission from camels. We analyzed the evolution of spike (S) gene betacoronaviruses (betaCoVs) isolated different mammals, bat populations, as well MERS-CoV strains current outbreak. Results indicated several positively selected sites located region comprising two heptad repeats (HR1 HR2) their linker. Two (R652 V1060) were betaCoVs phylogeny correspond mutations associated with...
Humans possess a communication system based on spoken and written language. Other animals can learn vocalization by imitation, but this is not equivalent to human Many genes were described be implicated in language impairment (LI) developmental dyslexia (DD), their evolutionary history has been thoroughly analyzed. Herein we analyzed the evolution of ten involved DD LI. Results show that LI for mammals aves was comparable vocal-learner species non-learners. For lineage, several sites showing...
Monkeypox is an emerging zoonosis endemic to Central and West Africa. virus (MPXV) genetically structured in 2 major clades (clades 1 2/3), but its evolution poorly explored.We retrieved MPXV genomes from public repositories we analyzed geographic patterns using STRUCTURE. Molecular dating was performed a Bayesian approach.We show that the population transmitted Africa 2/3) experienced limited drift. Conversely, clade (transmitted Congo Basin) possibly underwent bottleneck or founder effect....
Coronaviruses encode a variable number of accessory proteins that are involved in host-virus interaction, suppression immune responses, or evasion. SARS-CoV-2 encodes at least twelve proteins, whose roles during infection have been studied. Nevertheless, the role ORF3c protein, an alternative open reading frame ORF3a, has remained elusive. Herein, we show protein mitochondrial localization and alters metabolism, inducing shift from glucose to fatty acids oxidation enhanced oxidative...
The Flavivirus genus comprises several human pathogens such as dengue virus (DENV), Japanese encephalitis (JEV), and Zika (ZIKV). Although ZIKV usually causes mild symptoms, growing evidence is linking it to congenital birth defects increased risk of Guillain-Barré syndrome. encodes a polyprotein that processed produce three structural seven nonstructural (NS) proteins. We investigated the evolution viral in related flaviviruses (DENV, Spondweni virus, Kedougou virus). After accounting for...
Defects in genes of the Toll-like receptor 3 (TLR3) pathway are associated with susceptibility to herpes simplex virus type 1 encephalitis (HSE). We analyzed a cohort 11 adult Italian patients whom viral developed. detected 2 rare missense mutations TLR3: patient HSE (p.Leu297Val) and varicella-zoster (p.Leu199Phe). Both extremely human populations have pathogenicity scores highly suggestive functional effect. Data herein expand phenotypic spectrum TLR3 support role genetic defects as risk...
Hepatitis E virus (HEV, genus Orthohepevirus) is a common cause of hepatitis worldwide. Human-infecting HEV strains (Orthohepevirus A) include human-restricted and enzootic genotypes. Viruses in the Orthohepevirus A species also infect rabbits (HEV-3ra), camels, swine. Using selection-informed method, we dated origin at least 21 million years ago, whereas originated Asia, most likely from human-infecting ancestor that existed ~4500 to 6800 ago. In this period, appearance large human...
<b><i>Background:</i></b> Caveolin-3 is the muscle-specific protein product of caveolin gene family and an integral membrane component caveolae. Mutations in encoding caveolin-3 (<i>CAV3</i>) underlie four distinct disorders skeletal muscle: autosomal dominant form limb–girdle muscular dystrophy type 1C (LGMD-1C), rippling muscle disease (RMD), sporadic familial forms hyperCKemia, distal myopathy. <b><i>Objective:</i></b> To characterize a multigenerational Italian affected by myopathic...
Mutations in the DYSF gene underlie two main muscle diseases: Limb Girdle Muscular Dystrophy (LGMD) 2B and Miyoshi myopathy (MM). Dysferlin is involved membrane-repair thought to interact with other dysferlin molecules annexins A1 A2 at sarcolemma. We performed genotype/phenotype correlations a large cohort of dysferlinopathic patients explored possible role as modifier factors LGMD-2B MM. In particular, clinical examination, expression sarcolemmal proteins genetic analysis were on 27...
The non-coding portion of human genome is punctuated by a large number multispecies conserved sequence (MCS) elements with largely unknown function. We demonstrate that MCSs are unevenly distributed in introns the majority relatively short (< 9 kb long) displaying no or few and MCS density reaching up to 10% total size longer introns. After correction for intron length, were found be enriched within genes involved development transcription, whereas depleted immune response loci. Moreover,...
Mammalian genomes consist of regions differing in GC content, referred to as isochores or GC-content domains. The scientific debate is still open whether such compositional heterogeneity a selected neutral trait.Here we analyze SNP allele frequencies, retrotransposon insertion polymorphisms (RIPs), well fixed substitutions accumulated the human lineage since its divergence from chimpanzee indicate that biased gene conversion (BGC) has been playing role within-genome content variation. Yet,...
Abstract Background More than 2 billion individuals worldwide suffer from helminth infections. The highest parasite burdens occur in children and infection during pregnancy is a risk factor for preterm delivery reduced birth weight. Therefore, infections can be regarded as strong selective pressure. Results Here we propose that candidate susceptibility genes parasitic worm identified by searching SNPs display correlation with the diversity of species/genera transmitted different geographic...