1,721,013 research outputs found
Digital differential expression analysis of early embryonic de novo assembled sexed transcriptomes of Ceratitis capitata, a world-wide agricultural pest, to identify new sex-specific and sex-biased genes.
No full textThe agricultural pest Ceratitis capitata, also known as the Mediterranean fruit fly or Medfly, belongs to the Tephritidae family, which includes a large number of damaging pest species. The knowledge of the life-cycle and of the biology of pest species opens new chances to develop eco-sustainable control strategies, alternative to pesticides. Reproduction and sex determination are at the same time crucial aspects to understand insect biology and optimal targets to limit their population growth and diffusion. In the Medfly, where XY (males) and XX (females) sexual chromosomes are present, the primary signal of sex determination, constituted by a dominant factor linked to the Y-chromosome, is still uknown. To identify this factor and to search for new early sex-biased genes we applied Illumina sequencing to RNA from 8-10 hours and 23-25 hours after egg laying (AEL) embryos of C. capitata, leading to define about 20,000 novel unique reconstructed transcripts. We utilized short reads mapping and counting, using BOWTIE and SAMTOOLS software, and the EdgeR software to evaluate and compare the expression levels of the reconstructed transcripts between sexed embryonic samples and stages. We identified about 3000 male-biased and about 1000 female-biased transcripts at 8-10h AEL. Selected candidate transcripts are under validation by qPCR expression analyses and RNAi functional analyses
Annocript: a flexible pipeline for transcriptome annotation also capable to identify non-coding transcripts.
No full textImpact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data
Full text linkBackground: Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of primate genomes, especially from a regulatory perspective. Due to their recent activity they are also one of the primary sources of structural variants (SVs) in the human genome. By taking advantage of sequencing technologies and bioinformatics tools, recent surveys uncovered specific TE structural variants (TEVs) that gave rise to polymorphisms in human populations. When combined with RNA-seq data this information provides the opportunity to study the potential impact of TEs on gene expression in human. Results: In this work, we assessed the effects of the presence of specific TEs in cis on the expression of flanking genes by producing associations between polymorphic TEs and flanking gene expression levels in human lymphoblastoid cell lines. By using public data from the 1000 Genome Project and the Geuvadis consortium, we exploited an expression quantitative trait loci (eQTL) approach integrated with additional bioinformatics data mining analyses. We uncovered human loci enriched for common, less common and rare TEVs and identified 323 significant TEV-cis-eQTL associations. SINE-R/VNTR/Alus (SVAs) resulted the TE class with the strongest effects on gene expression. We also unveiled differential functional enrichments on genes associated to TEVs, genes associated to TEV-cis-eQTLs and genes associated to the genomic regions mostly enriched in TEV-cis-eQTLs highlighting, at multiple levels, the impact of TEVs on the host genome. Finally, we also identified polymorphic TEs putatively embedded in transcriptional units, proposing a novel mechanism in which TEVs may mediate individual-specific traits. Conclusion: We contributed to unveiling the effect of polymorphic TEs on transcription in lymphoblastoid cell lines
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
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
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Exploratory analysis of transposable elements expression in the C. elegans early embryo
Full text linkBackground: Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is becoming evident that TE have a role in several physiological and pathological processes. In particular, it has been shown that TE transcription is necessary for the correct development of mice embryos and that their expression is able to finely modulate transcription of coding and non-coding genes. Moreover, their activity in the central nervous system (CNS) and other tissues has been correlated with the creation of somatic mosaicisms and with pathologies such as neurodevelopmental and neurodegenerative diseases as well as cancers. Results: We analyzed TE expression among different cell types of the Caenorhabditis elegans (C. elegans) early embryo asking if, where and when TE are expressed and whether their expression is correlated with genes playing a role in early embryo development. To answer these questions, we took advantage of a public C. elegans embryonic single-cell RNA-seq (sc-RNAseq) dataset and developed a bioinformatics pipeline able to quantify reads mapping specifically against TE, avoiding counting reads mapping on TE fragments embedded in coding/non-coding transcripts. Our results suggest that i) canonical TE expression analysis tools, which do not discard reads mapping on TE fragments embedded in annotated transcripts, may over-estimate TE expression levels, ii) Long Terminal Repeats (LTR) elements are mostly expressed in undifferentiated cells and might play a role in pluripotency maintenance and activation of the innate immune response, iii) non-LTR are expressed in differentiated cells, in particular in neurons and nervous system-Associated tissues, and iv) DNA TE are homogenously expressed throughout the C. elegans early embryo development. Conclusions: TE expression appears finely modulated in the C. elegans early embryo and different TE classes are expressed in different cell types and stages, suggesting that TE might play diverse functions during early embryo development
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Gene discovery in the Old World Leishmania vector Phlebotomus perniciosus (Diptera, Psychodidae): de novo assembly and digital gene expression analysis of sexed transcriptomes from a laboratory strain and Ischia island natural populations.
No full textIn the Old World, the sand fly Phlebotomus perniciosus is the main vector of Leishmania infantum, the parasitic protozoan that causes visceral and cutaneous leishmaniases in humans and canine reservoir host, as well as, of known and emerging arboviruses considered relevant from an European public health perspective. P. perniciosus is widely distributed in the western Mediterranean Basin with the most important endemic focus of canine and human visceral leishmaniases of this area located in Italy, in the Campania region. We are applying RNA-seq and digital gene expression analysis to identify genes with sex-specific or sex-biased expression at a genome-wide level and to isolate genes involved in the sex determination pathway of the P. perniciosus. We defined a de novo reference transcriptome of about 50k transcripts which includes well conserved alternatively spliced transcripts of the doublesex (dsx) and fruitless (fru) ortholog genes, which are responsible in Drosophila of somatic sexual differentition and genetic control of courtship behaviour, respectively. Interestingly, an ortholog of the key switch gene of insect female sex determination, the transformer (tra) gene, is apparently absent in P. perniciosus transcriptome and the tra auxiliary factor transformer-2 (tra-2) is highly divergent respect to other dipteran tra-2 orthologs. These preliminary data suggest only a partial conservation of the sex determination cascade in this species. Our data could contribute to the study of the evolution of sex determination pathway in the under-studied Nematocera dipteran suborder, the comparative and genome-wide analysis of haematofagy in Nematocera species and to develop new control methods for the sand fly vector species
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