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Search Results: 1 - 10 of 12 matches for " Klio Maratou "
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Alternative Splicing and Transcriptome Profiling of Experimental Autoimmune Encephalomyelitis Using Genome-Wide Exon Arrays
Alan Gillett,Klio Maratou,Chris Fewings,Robert A. Harris,Maja Jagodic,Tim Aitman,Tomas Olsson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007773
Abstract: Multiple Sclerosis (MS) is a chronic inflammatory disease causing demyelination and nerve loss in the central nervous system. Experimental autoimmune encephalomyelitis (EAE) is an animal model of MS that is widely used to investigate complex pathogenic mechanisms. Transcriptional control through isoform selection and mRNA levels determines pathway activation and ultimately susceptibility to disease.
Triple-target microarray experiments: a novel experimental strategy
Thorsten Forster, Yael Costa, Douglas Roy, Howard J Cooke, Klio Maratou
BMC Genomics , 2004, DOI: 10.1186/1471-2164-5-13
Abstract: The addition of Alexa 594 as a dye-label for an additional – third – target sample works within the framework of more commonplace Cy5/Cy3 labelled target sample combinations. Standard normalisation methods are still applicable, and the resulting data can be expected to allow identification of expression differences in a biological experiment, given sufficient levels of biological replication (as is necessary for most microarray experiments).The use of three dye-labelled target samples can be a valuable addition to the standard repertoire of microarray experiment designs. The method enables direct comparison between two experimental populations as well as measuring these two populations in relation to a third reference sample, allowing comparisons within the slide and across slides. These benefits are only offset by the added level of consideration required in the experimental design and data processing of a triple-target study design. Common methods for data processing and analysis are still applicable, but there is scope for the development of custom models for triple-target data. In summary, we do not consider the triple-target approach to be a new standard, but a valuable addition to the existing microarray study toolkit.Microarray technology is a high-throughput and parallel platform that enables research on whole genomes, thereby helping to increase our understanding of the regulation of biological systems. All variations of this technique involve the deposition of a large number of probe sequences (e.g. oligonucleotides, cDNA) – representing a whole genome or subsets thereof – in a regular grid-like array on a physical substrate, usually a glass slide for custom spotted arrays. Microarray studies are costly in terms of equipment, consumables and time, therefore careful design and replication are particularly important if the resulting experiment is to be maximally informative. As opposed to high-density arrays like Affymetrix (probes produced in-situ in a proc
MiMiR – an integrated platform for microarray data sharing, mining and analysis
Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Tim Aitman, Laurence Game
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-379
Abstract: A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.Microarray technologies have matured rapidly over the past few years and present major challenges in managing, sharing, analysing and re-using the large amount of data generated [1] despite the considerable international efforts in standardising data format, content an
Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat
Jonatan Tuncel ,Sabrina Haag,Anthony C. Y. Yau,Ulrika Norin,Amelie Baud,Erik L?nnblom,Klio Maratou,A. Jimmy Ytterberg,Diana Ekman,Soley Thordardottir,Martina Johannesson,Alan Gillett,EURATRANS Consortium,Pernilla Stridh,Maja Jagodic,Tomas Olsson,Alberto Fernández-Teruel,Roman A. Zubarev,Richard Mott,Timothy J. Aitman,Jonathan Flint,Rikard Holmdahl
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004151
Abstract: Genetic variation in the major histocompatibility complex (MHC) affects CD4:CD8 lineage commitment and MHC expression. However, the contribution of specific genes in this gene-dense region has not yet been resolved. Nor has it been established whether the same genes regulate MHC expression and T cell selection. Here, we assessed the impact of natural genetic variation on MHC expression and CD4:CD8 lineage commitment using two genetic models in the rat. First, we mapped Quantitative Trait Loci (QTLs) associated with variation in MHC class I and II protein expression and the CD4:CD8 T cell ratio in outbred Heterogeneous Stock rats. We identified 10 QTLs across the genome and found that QTLs for the individual traits colocalized within a region spanning the MHC. To identify the genes underlying these overlapping QTLs, we generated a large panel of MHC-recombinant congenic strains, and refined the QTLs to two adjacent intervals of ~0.25 Mb in the MHC-I and II regions, respectively. An interaction between these intervals affected MHC class I expression as well as negative selection and lineage commitment of CD8 single-positive (SP) thymocytes. We mapped this effect to the transporter associated with antigen processing 2 (Tap2) in the MHC-II region and the classical MHC class I gene(s) (RT1-A) in the MHC-I region. This interaction was revealed by a recombination between RT1-A and Tap2, which occurred in 0.2% of the rats. Variants of Tap2 have previously been shown to influence the antigenicity of MHC class I molecules by altering the MHC class I ligandome. Our results show that a restricted peptide repertoire on MHC class I molecules leads to reduced negative selection of CD8SP cells. To our knowledge, this is the first study showing how a recombination between natural alleles of genes in the MHC influences lineage commitment of T cells.
Genetic Analysis of the Cardiac Methylome at Single Nucleotide Resolution in a Model of Human Cardiovascular Disease
Michelle D. Johnson equal contributor,Michael Mueller equal contributor,Martyna Adamowicz-Brice,Melissa J. Collins,Pascal Gellert,Klio Maratou,Prashant K. Srivastava,Maxime Rotival,Shahena Butt,Laurence Game,Santosh S. Atanur,Nicholas Silver,Penny J. Norsworthy,Sarah R. Langley,Enrico Petretto,Michal Pravenec,Timothy J. Aitman
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004813
Abstract: Epigenetic marks such as cytosine methylation are important determinants of cellular and whole-body phenotypes. However, the extent of, and reasons for inter-individual differences in cytosine methylation, and their association with phenotypic variation are poorly characterised. Here we present the first genome-wide study of cytosine methylation at single-nucleotide resolution in an animal model of human disease. We used whole-genome bisulfite sequencing in the spontaneously hypertensive rat (SHR), a model of cardiovascular disease, and the Brown Norway (BN) control strain, to define the genetic architecture of cytosine methylation in the mammalian heart and to test for association between methylation and pathophysiological phenotypes. Analysis of 10.6 million CpG dinucleotides identified 77,088 CpGs that were differentially methylated between the strains. In F1 hybrids we found 38,152 CpGs showing allele-specific methylation and 145 regions with parent-of-origin effects on methylation. Cis-linkage explained almost 60% of inter-strain variation in methylation at a subset of loci tested for linkage in a panel of recombinant inbred (RI) strains. Methylation analysis in isolated cardiomyocytes showed that in the majority of cases methylation differences in cardiomyocytes and non-cardiomyocytes were strain-dependent, confirming a strong genetic component for cytosine methylation. We observed preferential nucleotide usage associated with increased and decreased methylation that is remarkably conserved across species, suggesting a common mechanism for germline control of inter-individual variation in CpG methylation. In the RI strain panel, we found significant correlation of CpG methylation and levels of serum chromogranin B (CgB), a proposed biomarker of heart failure, which is evidence for a link between germline DNA sequence variation, CpG methylation differences and pathophysiological phenotypes in the SHR strain. Together, these results will stimulate further investigation of the molecular basis of locally regulated variation in CpG methylation and provide a starting point for understanding the relationship between the genetic control of CpG methylation and disease phenotypes.
Dialog tipai Piero Paolo Pasolinio romane “Teorema” | Tipi di dialogo nel romanzo “Teorema” di Pier Paolo Pasolini
Rasa Klio?toraityt?
Literatura , 2006,
Abstract: Nella vita e nell’opera di P. P. Pasolini i concetti di dialogo e di dialogicità sono fondamentali. Si può considerare tutta l’opera pasoliniana come ricerca di un dialogo nell’apertura al mondo, al tempo, alla storia, alla tradizione culturale e letteraria. Finora non sono stati ancora studiati i rapporti tra il pensiero pasoliniano e la filosofia del dialogo. In questo articolo, adottando il metodo del dialogo e della comunicazione letteraria, si vuole dimostrare che l’autore del “Teorema” attraverso i concetti di dialogo, di rapporti dialogici e d’incontro cerca di esprimere come l’avvento di una divinità misteriosa possa rivelare il significato dell’essere dell’uomo, l’assenza dell’autenticità e il trionfo dell’inautenticità nel mondo contemporaneo.
Piero Paolo Pasolini poetika. Kūryba kaip veiksmas | Poetica di Pier Paolo Pasolini. Parola come azione
Rasa Klio?toraityt?
Literatura , 2004,
Abstract: In questo articolo si vuole dimostrare che tutta l’opera pasoliniana, pur essendo molteplice e multiforme, ha un tratto unificante: la parola si presenta come azione. A tale affermazione si è giunti utilizzando il metodo di dialogo e di comunicazione letteraria. La ricerca del dialogo è presente in tutta l’opera di Pier Paolo Pasolini. L’idea, che la parola si presenta come azione, è rintracciabile fin dagli esordi dell’attività artistica e rimane durante tutto il corso della sua opera. Tale poetica, che è in stretto legame con l’esistenza stessa dell’autore, rende attuale la tradizione classica del testo e costringe ad un ripensamento dell’istituzione letteraria e dell’istanza dell’autore.
Estimating the Effectiveness and Feasibility of a Game-based Project for Early Foreign Language Learning
Eleni Griva,Klio Semoglou
English Language Teaching , 2012, DOI: 10.5539/elt.v5n9p33
Abstract: This paper outlines the rationale for and the purpose of designing and implementing a project aiming to make very young EFL learners develop their language skills through their involvement in interactive psychomotor activities. The project, which is a part of a broader longitudinal project having introduced EFL in the first primary school grade, was implemented in two 2nd grade Greek classrooms with a total of 44 seven year old children. Multisensory teaching was followed through the use of a combination of activities: classroom creative activities included memory and word games, drawings, constructions, role-play games, pantomime as well as songs. In the gym, children participated in physical activities such as races, chases and hopscotch as well as dance and music activities, with the aim to improve their oral communicative skills and creativity. In order to examine the effectiveness and feasibility of the project, an evaluation study was conducted by using a pre- and post- language test and journals kept by the teachers. It was evident that the project had a positive effect on developing very young learners’ language skills, and on enhancing their motivation to participate in psychomotor activities.
Reading Preferences and Strategies Employed by Primary School Students: Gender, Socio-Cognitive and Citizenship Issues
Eleni Griva,Anastasia Alevriadou,Klio Semoglou
International Education Studies , 2012, DOI: 10.5539/ies.v5n2p24
Abstract: The purpose of the present study was to identify the correlation between gender and reading preferences and reading strategies employed by 5th and 6th Grade students of primary school in Greece. The main objectives of the present study were (1) to identify possible differences between male and female students in employing cognitive and metacognitive strategies, (2) to record the difficulties encountered by males and females when reading and (3) to highlight possible differences between male and female students in reading preferences. 405 Greek students (206 boys and 199 girls, M=11.21 years old, SD.=0.47) participated in the study and were asked to fill in a questionnaire including questions related to reading preferences and attitudes. In addition, 32 students from the total sample were asked to choose their favourite text to read and think aloud about the processes they followed and the strategies they used. The questionnaire results indicated significant differences between male and female students in reading preferences, since the female students showed a greater preference for ‘human-interest’ stories and male ones preferred to read comics and action-stories. The verbal data revealed the female students’ flexibility in strategy use and their higher metacognitive awareness compared to male students. Reading, gender and social factors are discussed in the light of citizenship education.
Molecular Vibration-Sensing Component in Human Olfaction
Simon Gane, Dimitris Georganakis, Klio Maniati, Manolis Vamvakias, Nikitas Ragoussis, Efthimios M. C. Skoulakis, Luca Turin
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0055780
Abstract: Whether olfaction recognizes odorants by their shape, their molecular vibrations, or both remains an open and controversial question. A convenient way to address it is to test for odor character differences between deuterated and undeuterated odorant isotopomers, since these have identical ground-state conformations but different vibrational modes. In a previous paper (Franco et al. (2011) Proc Natl Acad Sci USA 108:9, 3797-802) we showed that fruit flies can recognize the presence of deuterium in odorants by a vibrational mechanism. Here we address the question of whether humans too can distinguish deuterated and undeuterated odorants. A previous report (Keller and Vosshall (2004) Nat Neurosci 7:4, 337-8) indicated that naive subjects are incapable of distinguishing acetophenone and d-8 acetophenone. Here we confirm and extend those results to trained subjects and gas-chromatography [GC]-pure odorants. However, we also show that subjects easily distinguish deuterated and undeuterated musk odorants purified to GC-pure standard. These results are consistent with a vibrational component in human olfaction.
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