1,721,112 research outputs found
Investigating the role of lncRNAs in CNS pathophysiology: LINC00520 as a potential biomarker for Parkinson’s disease in human in vitro models
No full textMETA-ANALYSIS OF SUBSTANTIA NIGRA TRANSCRIPTOME DATA: SEARCHING FOR NEW BIOMARKERS OF PD
No full textThe understanding of the genetic basis of the PD and the correlation between genotype and phenotype has revolutionized knowledge about the pathogenetic mechanisms of neurodegeneration, opening up exciting new therapeutic and neuroprotective perspectives. Genomic knowledge for PD is still very open and can provide a good start for studies of the molecular mechanisms that underlie the gene expression variations and the epigenetic mechanisms that may contribute to the complex and characteristic phenotype of PD. Here we use the software TRAM (Transcriptome Mapper), to analyse publicly available microarray data of PD patients and controls substantia nigra, to identify chromosomal segments (Map mode) and gene clusters (Cluster mode) which are biologically relevant in the two different conditions. TRAM integrates original methods for parsing, normalizing, mapping and statistically analyzing expression data; in addition, it is able to easily generate maps showing differential expression between two sample groups, relative to two different biological conditions. We performed a systematic meta-analysis of 143 samples from pool A (patients with PD) and 119 samples from pool B (healthy controls), for a total of respectively 4,128,764 data points (gene expression value) and 3,417,633 data points, relative to 37,580 distinct loci for wich A/B ratio value was determinable. Results obtained included 5 significantly over-expressed segments and 90 over/under-expressed clusters. A list of statistically significant over/under-expressed genes has been generated, including coding genes, ncRNAs and uncharacterized transcripts. This study offers a new approach for the regional analysis of gene expression in neurodegenerative diseases
Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson's Disease Data
Full text linkParkinson's disease (PD) is one of the most common progressive neurodegenerative diseases. Clinical and epidemiological studies indicate that sex differences, as well as genetic components and ageing, can influence the prevalence, age at onset and symptomatology of PD. This study undertook a systematic meta-analysis of substantia nigra microarray data using the Transcriptome Mapper (TRAM) software to integrate and normalize a total of 10 suitable datasets from multiple sources. Four different analyses were performed according to default parameters, to better define the segments differentially expressed between PD patients and healthy controls, when comparing men and women data sets. The results suggest a possible regulation of specific sex-biased systems in PD susceptibility. TRAM software allowed us to highlight the different activation of some genomic regions and loci involved in molecular pathways related to neurodegeneration and neuroinflammatory mechanisms
Exposure of Zebrafish Embryos to Urea Affects NOS1 Gene Expression in Neuronal Cells
Full text linkNitrogen-based fertilizers represent the most common fertilization tools, particularly used in crop food agriculture, despite the low cost-efficiency and the high negative environmental impact. At present, there is still inadequate information available about the effects of urea on human health; nevertheless, previous studies in animals observed that high urea concentration exposure can damage different tissues, including the brain. In several vertebrates, a crucial factor involved in neuronal cell formation is represented by the gas molecule, nitric oxide (NO), derived from the conversion of arginine to citrulline through the enzymatic activity of nitric oxide synthases (NOS). In zebrafish, three different isoforms of the NOS gene are known: nos1, nos2a, and nos2b. In the present study we show that nos1 represents the unique isoform with a stable high expression in the brain and spinal cord during all the embryonic stages of zebrafish development. Then, by using a specific transgenic zebrafish line, Tg(HuC:GFP), to mark neuronal cells, we observed nos1 to be specifically expressed in neurons. Interestingly, we observed that urea exposure at sub-lethal doses affected cell proliferation and the number of nos1-expressing cells, inducing apoptosis. Consistently, brain NO levels were observed to be reduced in urea-treated animals compared to untreated ones. This finding represents the first evidence that urea exposure affects the expression of a key gene involved in neuronal cell formation during embryonic development
Selection of suitable reference genes for gene expression studies in HMC3 cell line by quantitative real-time RT-PCR
Full text linkAbstract Microglia represent the primary immune defense system within the central nervous system and play a role in the inflammatory processes occurring in numerous disorders, such as Parkinson’s disease (PD). PD onset and progression are associated with factors considered possible causes of neuroinflammation, i.e. genetic mutations. In vitro models of microglial cells were established to identify specific molecular targets in PD through the analysis of gene expression data. Recently, the Human Microglial Clone 3 cell line (HMC3) has been characterized and a new human microglia model has emerged. Here we perform RT-qPCR analyses to evaluate the expression of ten reference genes in HMC3, untreated or stimulated to a pro-inflammatory status. The comparative ∆CT method, BestKeeper, Normfinder, geNorm and RefFinder algorithms were used to assess the stability of the candidate genes. The results showed that the most suitable internal controls are HPRT1, RPS18 and B2M genes. In addition, the most stable and unstable reference genes were used to normalize the expression of a gene of interest in HMC3, resulting in a difference in the statistical significance in cells treated with Rotenone. This is the first reference gene validation study in HMC3 cell line in pro-inflammatory status and can contribute to more reliable gene expression analysis in the field of neurodegenerative and neuroinflammatory research
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Role of the human CYYR1 gene: from the functional study of the Danio rerio ortholog to the potential implication in tumorigenic processes
Full text linkIl locus CYYR1 identificato e clonato sul cromosoma 21 umano è stato caratterizzato dal punto di vista molecolare come un sistema multitrascritto, esclusivo dei vertebrati che ad oggi è orfano di una funzione specifica. Dati presenti in lettura e rintracciati mostrano una possibile relazione tra il gene CYYR1 e il pathway di Sonic Hedgehog (SHH).
In questo progetto di tesi è stato utilizzato il modello animale Danio rerio per indagare il ruolo funzionale dell’ortologo (cyyr1), attraverso esperimenti di gain e loss of function che hanno permesso di dimostrare un suo coinvolgimento nello sviluppo del sistema nervoso centrale, del cuore e del tessuto muscolare. Lo studio dell’ortologo in zebrafish è stato associato all’utilizzo di linee cellulari di rabdomiosarcoma umano. I risultati ottenuti dall’induzione al differenziamento miogenico di queste linee, insieme ai dati ottenuti in Danio rerio, confermano il possibile coinvolgimento del gene CYYR1 nella miogenesi.
Lo studio delle relazione tra il pathway di SHH e l’espressione del gene CYYR1 è stato condotto in entrambi i modelli con l’utilizzo di differenti inibitori della via di segnalazione. I risultati ottenuti mostrano che sistemi inibitori agenti direttamente sul recettore SMO riducono l’espressione del gene. Un dato inaspettato in Danio rerio ottenuto durante questi esperimenti di inibizione, ha aperto una nuova linea di ricerca in collaborazione con l’Università di Warwick tesa a verificare la relazione tra il gene cyyr1 e il gene lefty1. Gli esperimenti condotti presso il laboratorio della Prof.ssa Sampath hanno dimostrato la localizzazione del prodotto proteico cyyr1 in Danio rerio e indagato co-localizzazioni con la proteina lefty1.
Infine, in collaborazione con Dr. Deflorian e della Prof.ssa Pistocchi, è stato generato un mutante di Danio rerio deleto per il gene cyyr1 con la tecnica CRISPR/Cas9. La caratterizzazione del mutante cyyr1 -/- ha confermato alcuni dei dati ottenuti attraverso esperimenti di loss of function.CYYR1 (Cysteine/tyrosine-rich 1) cloned on HC21 defines a new family of highly conserved vertebrate-specific genes. The human locus is characterized by a multitranscript-system including alternative spliced isoforms and one ncRNA gene overlapped in antisense orientation. To date, the function of the CYYR1 product is still unknown even if original results suggest the need of further investigations in order to verify a putative role of CYYR1 in the tumorigenic process of rhabdomyosarcoma, caused by dysfunction of cell differentiation.
We perform a full characterization of cyyr1 expression and function in zebrafish model; the gene is present in single copy and the predicted protein maintains almost 58% of identity with human protein. A broad expression in central nervous system (CNS), somites and muscles is demonstred by WISH approach during development up to 24-48 hpf.
The cyyr1 knock-down with two different MOs targetting the ATG and the first splice-site of the transcript, affected both CNS and muscle development with a significant rescue in embryo co-injected with cyyr1 mRNA. Defects were also evident in ciliated cells of neuromast of the lateral line.
Morphologically the cyyr1-MOs injected embryos display features of embryos inhibited for the Hh pathway through injection of the lefty mRNA, moreover cyyr1 expression was significantly inhibited following Hh inhibition. Interestingly, the injection of cyyr1 mRNA was able to partially rescue Hh-defective phenotype in embryos at 24 hpf. Results from immunofluorescent staining, qPCR and western blotting, support a role for cyyr1 in primary myogenesis probably downstream of Hh pathway. The analysis of CYYR1 expression in rhabdomyosarcoma cell lines seems to indicate an inverse correlation between CYYR1 expression and the range of differentiating capabilities of these cells.
These data have encouraged us to better investigate the possible interplay between cyyr1 and Hh-mediated myogenesis even in cyyr1 editing conditions and, as well in rhabdomyosarcoma cell model
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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