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Search Results: 1 - 10 of 5958 matches for " Alfredo Ciccodicola "
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Uncovering the Complexity of Transcriptomes with RNA-Seq
Valerio Costa,Claudia Angelini,Italia De Feis,Alfredo Ciccodicola
Journal of Biomedicine and Biotechnology , 2010, DOI: 10.1155/2010/853916
Abstract: In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. Among them RNA-Seq is perhaps the most complex NGS application. Expression levels of specific genes, differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread hybridization-based or tag sequence-based approaches. However, the unprecedented level of sensitivity and the large amount of available data produced by NGS platforms provide clear advantages as well as new challenges and issues. This technology brings the great power to make several new biological observations and discoveries, it also requires a considerable effort in the development of new bioinformatics tools to deal with these massive data files. The paper aims to give a survey of the RNA-Seq methodology, particularly focusing on the challenges that this application presents both from a biological and a bioinformatics point of view.
Non-coding RNA and pseudogenes in neurodegenerative diseases: “The (un)Usual Suspects”
Valerio Costa,Roberta Esposito,Marianna Aprile,Alfredo Ciccodicola
Frontiers in Genetics , 2012, DOI: 10.3389/fgene.2012.00231
Abstract: Neurodegenerative disorders and cancer are severe diseases threatening human health. The glaring differences between neurons and cancer cells mask the processes involved in their pathogenesis. Defects in cell cycle, DNA repair, and cell differentiation can determine unlimited proliferation in cancer, or conversely, compromise neuronal plasticity, leading to cell death and neurodegeneration. Alteration in regulatory networks affecting gene expression contribute to human diseases onset, including neurodegenerative disorders, and deregulation of non-coding RNAs – particularly microRNAs (miRNAs) – is supposed to have a significant impact. Recently, competitive endogenous RNAs (ceRNAs) – acting as sponges – have been identified in cancer, indicating a new and intricate regulatory network. Given that neurodegenerative disorders and cancer share altered genes and pathways, and considering the emerging role of miRNAs in neurogenesis, we hypothesize ceRNAs may be implicated in neurodegenerative diseases. Here we propose, and computationally predict, such regulatory mechanism may be shared between the diseases. It is predictable that similar regulation occurs in other complex diseases, and further investigation is needed.
PPARG: Gene Expression Regulation and Next-Generation Sequencing for Unsolved Issues
Valerio Costa,Maria Assunta Gallo,Francesca Letizia,Marianna Aprile,Amelia Casamassimi,Alfredo Ciccodicola
PPAR Research , 2010, DOI: 10.1155/2010/409168
Abstract: Peroxisome proliferator-activated receptor gamma (PPAR ) is one of the most extensively studied ligand-inducible transcription factors (TFs), able to modulate its transcriptional activity through conformational changes. It is of particular interest because of its pleiotropic functions: it plays a crucial role in the expression of key genes involved in adipogenesis, lipid and glucid metabolism, atherosclerosis, inflammation, and cancer. Its protein isoforms, the wide number of PPAR target genes, ligands, and coregulators contribute to determine the complexity of its function. In addition, the presence of genetic variants is likely to affect expression levels of target genes although the impact of PPARG gene variations on the expression of target genes is not fully understood. The introduction of massively parallel sequencing platforms—in the Next Generation Sequencing (NGS) era—has revolutionized the way of investigating the genetic causes of inherited diseases. In this context, DNA-Seq for identifying—within both coding and regulatory regions of PPARG gene—novel nucleotide variations and haplotypes associated to human diseases, ChIP-Seq for defining a PPAR binding map, and RNA-Seq for unraveling the wide and intricate gene pathways regulated by PPARG, represent incredible steps toward the understanding of PPAR in health and disease. 1. Introduction Gene transcription requires an elaborate network of intra- and extracellular signals, such as hormones, xenobiotics, micro- and macronutrients (lipid metabolites, vitamins, ions, etc.) and drugs, that converge to the nucleus following different pathways, resulting in the expression of each gene in each tissue. It is a current assumption that transcription is mostly shaped by environmental factors, acting both via direct and indirect mechanisms. Translating exogenous and endogenous signals which affect gene transcription, into a cellular physiological response requires the coordinated action and the fine tuning of transcription factors (TFs) acting at DNA level, including those belonging to the nuclear receptor (NR) superfamily [1, 2]. The human NR superfamily comprises 48 ligand-inducible transcription factors that respond to a variety of stimuli and are able to modulate their transcriptional activity through conformational changes [3]. The most extensively studied members of this TF superfamily are the Peroxisome proliferator-activated receptors (PPARs, also known as nuclear receptor family 1C, NR1C). Crystallographic studies have shown that all NRs superfamily members, and among them PPARs, share common
Investigation of Gamma-aminobutyric acid (GABA) A receptors genes and migraine susceptibility
Francesca Fernandez, Teresa Esposito, Rod A Lea, Natalie J Colson, Alfredo Ciccodicola, Fernando Gianfrancesco, Lyn R Griffiths
BMC Medical Genetics , 2008, DOI: 10.1186/1471-2350-9-109
Abstract: We have performed an association analysis in a large population of case-controls (275 unrelated Caucasian migraineurs versus 275 controls) examining a set of 3 single nucleotide polymorphisms (SNPs) in the coding region (exons 3, 5 and 9) of the GABRE gene and also the I478F coding variant of the GABRQ gene.Our study did not show any association between the examined SNPs in our test population (P > 0.05).Although these particular GABA receptor genes did not show positive association, further studies are necessary to consider the role of other GABA receptor genes in migraine susceptibility.Migraine is a common neurological disorder with variable expression, affecting more than 12% of the general population [1]. The exact cause is unknown and there are no recognizable diagnostic pathological changes. Migraine is a neurological disorder, characterised by recurrent headache that is associated with nausea and/or vomiting, photophobia and phonophobia. The International Headache Society (IHS) has formally classified migraine into two main subtypes: migraine with aura (MA) and migraine without aura (MO) [2]. These two subtypes have substantial symptomatic overlap, but MA sufferers experience distinguishing neurological disturbances (the aura) that usually precede the headache phase of an attack.The pathogenesis and pathophysiology of migraine are poorly understood. A diverse group of variables have been implicated in the pathophysiology of migraine, in particular, the serotoninergic system, with drugs that release serotonin shown to precipitate migraine attacks [3], while drugs that interact with serotonin receptors have beneficial prophylactic and abortive effects [4]. Glutamate, which is a major excitatory neurotransmitter in the central nervous system, has also been broadly involved in migraine pathophysiology. Altered glutamate levels have been measured in migraine patients [5] and glutamate has been implicated in trigeminal activation and cortical spreading depression
Characterization of a Novel Polymorphism in PPARG Regulatory Region Associated with Type 2 Diabetes and Diabetic Retinopathy in Italy
Valerio Costa,Amelia Casamassimi,Katherine Esposito,Angela Villani,Mariaelena Capone,Rosa Iannella,Bruno Schisano,Miryam Ciotola,Carmen Di Palo,Feliciantonia Capone Corrado,Franco Santangelo,Dario Giugliano,Alfredo Ciccodicola
Journal of Biomedicine and Biotechnology , 2009, DOI: 10.1155/2009/126917
Abstract: Peroxisome proliferator-activated receptor gamma polymorphisms have been widely associated with type 2 diabetes, although their role in the pathogenesis of vascular complications is not yet demonstrated. In this study, a cohort of 211 type 2 diabetes, 205 obese, and 254 control individuals was genotyped for Pro12Ala, C1431T, C-2821T polymorphisms, and for a newly identified polymorphism (A-2819G). The above-mentioned polymorphisms were analyzed by gene-specific PCR and direct sequencing of all samples. A significant difference was found for -2819G frequency when patients with type 2 diabetes—particularly diabetic women with the proliferative retinopathy—were compared with healthy control individuals. In conclusion, we identified a novel polymorphism, A-2819G, in PPARG gene, and we found it to be associated with type 2 diabetes and proliferative retinopathy in diabetic females. In the analyzed population, this variant represents a genetic risk factor for developing the diabetic retinopathy, whereas Pro12Ala and C1431T do not.
DDX11L: a novel transcript family emerging from human subtelomeric regions
Valerio Costa, Amelia Casamassimi, Roberta Roberto, Fernando Gianfrancesco, Maria R Matarazzo, Michele D'Urso, Maurizio D'Esposito, Mariano Rocchi, Alfredo Ciccodicola
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-250
Abstract: During a project aimed to analyze genes located in the telomeric region of the long arm of the human X chromosome, we have identified a novel transcript family, DDX11L, members of which map to 1pter, 2q13/14.1, 2qter, 3qter, 6pter, 9pter/9qter, 11pter, 12pter, 15qter, 16pter, 17pter, 19pter, 20pter/20qter, Xpter/Xqter and Yqter. Furthermore, we partially sequenced the underrepresented subtelomeres of human chromosomes showing a common evolutionary origin.Our data indicate that an ancestral gene, originated as a rearranged portion of the primate DDX11 gene, and propagated along many subtelomeric locations, is emerging within subtelomeres of human chromosomes, defining a novel gene family. These findings support the possibility that the high plasticity of these regions, sites of DNA exchange among different chromosomes, could trigger the emergence of new genes.Human subtelomeric sequences are extraordinarily dynamic and variable regions near the ends of chromosomes, and represent the transition sites between chromosomes-specific sequences and telomeric repeats capping each chromosomal end [1]. The unusual nucleotide composition of human subtelomeres was first evident from fluorescence in situ hybridization (FISH) analysis of cloned segments of subtelomeric regions [2].However, to date, the large variability of subtelomeric sequences is underrepresented in the complete human genome database, because of the low representation of clones covering the proximity of these regions in the libraries used in the Human Genome Project. Moreover, the high level of polymorphism found in the human subtelomeres, makes assembling multiple different alleles of the same chromosome more challenging than most of the regions of human genome.The comparative analysis of fully sequenced subtelomeres of human 4p, 16p, 22q, Xq and Yq, has revealed a common structure, in which the proximal and distal subtelomeric domains are separated by a stretch of degenerate TTAGGG repeats [3-6]. The subtelome
Evidence of Bacteroides fragilis Protection from Bartonella henselae-Induced Damage
Linda Sommese, Chiara Pagliuca, Bice Avallone, Rossana Ippolito, Amelia Casamassimi, Valerio Costa, Roberta Colicchio, Raimondo Cerciello, Maria D'Armiento, Margherita Scarpato, Alfonso Giovane, Gabiria Pastore, Teresa Infante, Alfredo Ciccodicola, Carmela Fiorito, Francesco Paolo D'Armiento, Paola Salvatore, Claudio Napoli
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049653
Abstract: Bartonella henselae is able to internalize endothelial progenitor cells (EPCs), which are resistant to the infection of other common pathogens. Bacteroides fragilis is a gram-negative anaerobe belonging to the gut microflora. It protects from experimental colitis induced by Helicobacter hepaticus through the polysaccharide A (PSA). The aim of our study was to establish: 1) whether B. fragilis colonization could protect from B. henselae infection; if this event may have beneficial effects on EPCs, vascular system and tissues. Our in vitro results establish for the first time that B. fragilis can internalize EPCs and competes with B. henselae during coinfection. We observed a marked activation of the inflammatory response by Real-time PCR and ELISA in coinfected cells compared to B. henselae-infected cells (63 vs 23 up-regulated genes), and after EPCs infection with mutant B. fragilis ΔPSA (?90% up-regulated genes) compared to B. fragilis. Interestingly, in a mouse model of coinfection, morphological and ultrastructural analyses by hematoxylin-eosin staining and electron microscopy on murine tissues revealed that damages induced by B. henselae can be prevented in the coinfection with B. fragilis but not with its mutant B. fragilis ΔPSA. Moreover, immunohistochemistry analysis with anti-Bartonella showed that the number of positive cells per field decreased of at least 50% in the liver (20±4 vs 50±8), aorta (5±1 vs 10±2) and spleen (25±3 vs 40±6) sections of mice coinfected compared to mice infected only with B. henselae. This decrease was less evident in the coinfection with ΔPSA strain (35±6 in the liver, 5±1 in the aorta and 30±5 in the spleen). Finally, B. fragilis colonization was also able to restore the EPC decrease observed in mice infected with B. henselae (0.65 vs 0.06 media). Thus, our data establish that B. fragilis colonization is able to prevent B. henselae damages through PSA.
Impairment of circulating endothelial progenitors in Down syndrome
Valerio Costa, Linda Sommese, Amelia Casamassimi, Roberta Colicchio, Claudia Angelini, Valentina Marchesano, Lara Milone, Bartolomeo Farzati, Alfonso Giovane, Carmela Fiorito, Monica Rienzo, Marco Picardi, Bice Avallone, Massimiliano Marco Corsi, Berardo Sarubbi, Raffaele Calabrò, Paola Salvatore, Alfredo Ciccodicola, Claudio Napoli
BMC Medical Genomics , 2010, DOI: 10.1186/1755-8794-3-40
Abstract: Circulating endothelial progenitors of Down syndrome affected individuals were isolated, in vitro cultured and analyzed by confocal and transmission electron microscopy. ELISA was performed to measure SDF-1α plasma levels in Down syndrome and euploid individuals. Moreover, qRT-PCR was used to quantify expression levels of CXCL12 gene and of its receptor in progenitor cells. The functional impairment of Down progenitors was evaluated through their susceptibility to hydroperoxide-induced oxidative stress with BODIPY assay and the major vulnerability to the infection with human pathogens. The differential expression of crucial genes in Down progenitor cells was evaluated by microarray analysis.We detected a marked decrease of progenitors' number in young Down individuals compared to euploid, cell size increase and some major detrimental morphological changes. Moreover, Down syndrome patients also exhibited decreased SDF-1α plasma levels and their progenitors had a reduced expression of SDF-1α encoding gene and of its membrane receptor. We further demonstrated that their progenitor cells are more susceptible to hydroperoxide-induced oxidative stress and infection with Bartonella henselae. Further, we observed that most of the differentially expressed genes belong to angiogenesis, immune response and inflammation pathways, and that infected progenitors with trisomy 21 have a more pronounced perturbation of immune response genes than infected euploid cells.Our data provide evidences for a reduced number and altered morphology of endothelial progenitor cells in Down syndrome, also showing the higher susceptibility to oxidative stress and to pathogen infection compared to euploid cells, thereby confirming the angiogenesis and immune response deficit observed in Down syndrome individuals.Down syndrome (DS) is a complex disorder caused by trisomy of the entire or a critical portion of chromosome 21 (HSA21); it represents the most frequent genetic cause of mental retardation,
Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21
Valerio Costa,Claudia Angelini,Luciana D'Apice,Margherita Mutarelli,Amelia Casamassimi,Linda Sommese,Maria Assunta Gallo,Marianna Aprile,Roberta Esposito,Luigi Leone,Aldo Donizetti,Stefania Crispi,Monica Rienzo,Berardo Sarubbi,Raffaele Calabrò,Marco Picardi,Paola Salvatore,Teresa Infante,Piergiuseppe De Berardinis,Claudio Napoli,Alfredo Ciccodicola
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0018493
Abstract: Hybridization- and tag-based technologies have been successfully used in Down syndrome to identify genes involved in various aspects of the pathogenesis. However, these technologies suffer from several limits and drawbacks and, to date, information about rare, even though relevant, RNA species such as long and small non-coding RNAs, is completely missing. Indeed, none of published works has still described the whole transcriptional landscape of Down syndrome. Although the recent advances in high-throughput RNA sequencing have revealed the complexity of transcriptomes, most of them rely on polyA enrichment protocols, able to detect only a small fraction of total RNA content. On the opposite end, massive-scale RNA sequencing on rRNA-depleted samples allows the survey of the complete set of coding and non-coding RNA species, now emerging as novel contributors to pathogenic mechanisms. Hence, in this work we analysed for the first time the complete transcriptome of human trisomic endothelial progenitor cells to an unprecedented level of resolution and sensitivity by RNA-sequencing. Our analysis allowed us to detect differential expression of even low expressed genes crucial for the pathogenesis, to disclose novel regions of active transcription outside yet annotated loci, and to investigate a plethora of non-polyadenilated long as well as short non coding RNAs. Novel splice isoforms for a large subset of crucial genes, and novel extended untranslated regions for known genes—possibly novel miRNA targets or regulatory sites for gene transcription—were also identified in this study. Coupling the rRNA depletion of samples, followed by high-throughput RNA-sequencing, to the easy availability of these cells renders this approach very feasible for transcriptome studies, offering the possibility of investigating in-depth blood-related pathological features of Down syndrome, as well as other genetic disorders.
There are Two Different Language Systems in the Brain  [PDF]
Alfredo Ardila
Journal of Behavioral and Brain Science (JBBS) , 2011, DOI: 10.4236/jbbs.2011.12005
Abstract: In this paper it is emphasized that human language has two rather different dimensions corresponding to two different language systems: lexical/semantic and grammatical. These two language systems are supported by different brain structures (temporal and frontal), and based in different learning strategies (declarative and procedural). In cases of brain pathology, each one can be independently impaired (Wernicke aphasia and Broca aphasia). While the lexical/semantic language system may have appeared during human evolution long before the contemporary man, the grammatical language system probably represents a relatively recent acquisition. Language grammar may be the departing ability for the development of the metacognitive executive functions and is probably based in the ability to internally represent actions.
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