1,721,010 research outputs found
Progerin expression induces a significant downregulation of transcription from human repetitive sequences in iPSC-derived dopaminergic neurons
No full textRepetitive DNA sequences represent about half of the human genome. They have a central role in human biology, especially neurobiology, but are notoriously difficult to study. The purpose of this study was to quantify the transcription from repetitive sequences in a progerin-expressing cellular model of neuronal aging. Progerin is a nuclear protein causative of the Hutchinson–Gilford progeria syndrome that is also incrementally expressed during the normal aging process. A dedicated pipeline of analysis allowed to quantify transcripts containing repetitive sequences from RNAseq datasets oblivious of their genomic localization, tolerating a sufficient degree of mutational noise, all with low computational requirements. The pipeline has been applied to a published panel of RNAseq datasets derived from a well-established and well-described cellular model of aging of dopaminergic neurons. Progerin expression strongly downregulated the transcription from all the classes of repetitive sequences: satellites, long and short interspersed nuclear elements, human endogenous retroviruses, and DNA transposon. The Alu element represented by far the principal source of transcript originating either from repetitive sequences or from canonical coding genes; it was expressed on average at 192,493.5 reads per kilobase million (RPKM) (SE = 21,081.3) in the control neurons and dropped to 43,760.1 RPKM (SE = 5315.0) in the progerin-expressing neurons, being significant downregulated (p = 0.0005). The results highlighted a global perturbation of transcripts derived from repetitive sequences in a cellular model of aging and provided a direct link between progerin expression and alteration of transcription from human repetitive elements
Gene, Protein, and in Silico Analyses of FoxO, an Evolutionary Conserved Transcription Factor in the Sea Urchin Paracentrotus lividus
Full text linkFoxO is a member of the evolutionary conserved family of transcription factors containing a Forkhead box, involved in many signaling pathways of physiological and pathological processes. In mammals, mutations or dysfunctions of the FoxO gene have been implicated in diverse diseases. FoxO homologs have been found in some invertebrates, including echinoderms. We have isolated the FoxO cDNA from the sea urchin Paracentrotus lividus (Pl-foxo) and characterized the corresponding gene and mRNA. In silico studies showed that secondary and tertiary structures of Pl-foxo protein corresponded to the vertebrate FoxO3 isoform, with highly conserved regions, especially in the DNA-binding domain. A phylogenetic analysis compared the Pl-foxo deduced protein with proteins from different animal species and confirmed its evolutionary conservation between vertebrates and invertebrates. The increased expression of Pl-foxo mRNA following the inhibition of the PI3K signaling pathway paralleled the upregulation of Pl-foxo target genes involved in apoptosis or cell-cycle arrest events (BI-1, Bax, MnSod). In silico studies comparing molecular data from sea urchins and other organisms predicted a network of Pl-foxo protein–protein interactions, as well as identified potential miRNAs involved in Pl-foxo gene regulation. Our data may provide new perspectives on the knowledge of the signaling pathways underlying sea urchin development
Microbial biotechnology for wastewater treatment into circular economy
No full textIn wastewater treatment plants (WWTPs), biotechnological processes imply the activities of microbial consortia to obtain clean water, by transforming organic and inorganic pollutants into environmental-friendly products considered valuable resources. Thus, microbial biotechnology drives the development of circular economy systems integrating environment preservation into bioenergy production and resource recovery. A crucial aspect to optimize bioenergy production and resource recovery is the study of microbial communities operating in WWTPs to be characterized for their structure (types, relationships, and relative amounts of microorganisms) and functions (metabolic and biochemical capabilities). Genome-based analyses, like metagenomics, metatranscriptomics, and metaproteomics (collectively termed omics technologies), are powerful tools to characterize microbial communities.
This chapter describes and discusses technological aspects of omics approaches and examples of their applications in WWTP investigations. Particularly, biotechnological aspects and issues that can affect the transition to a circular economy system, where WWTPs play a key role feeding biorefinery systems, are highlighted and commented
A multivariate statistical test for differential expression analysis
Full text linkStatistical tests of differential expression usually suffer from two problems. Firstly, their statistical power is often limited when applied to small and skewed data sets. Secondly, gene expression data are usually discretized by applying arbitrary criteria to limit the number of false positives. In this work, a new statistical test obtained from a convolution of multivariate hypergeometric distributions, the Hy-test, is proposed to address these issues. Hy-test has been carried out on transcriptomic data from breast and kidney cancer tissues, and it has been compared with other differential expression analysis methods. Hy-test allows implicit discretization of the expression profiles and is more selective in retrieving both differential expressed genes and terms of Gene Ontology. Hy-test can be adopted together with other tests to retrieve information that would remain hidden otherwise, e.g., terms of (1) cell cycle deregulation for breast cancer and (2) “programmed cell death” for kidney cancer
An extended catalogue of ncRNAs in Streptomyces coelicolor reporting abundant tmRNA, RNase-P RNA and RNA fragments derived from pre-ribosomal RNA leader sequences
No full textStreptomyces coelicolor is a model organism for studying streptomycetes. This genus possesses relevant medical and economical roles, because it produces many biologically active metabolites of pharmaceutical interest, including the majority of commercialized antibiotics. In this bioinformatic study, the transcriptome of S. coelicolor has been analyzed to identify novel RNA species and quantify the expression of both annotated and novel transcripts in solid and liquid growth medium cultures at different times. The major characteristics disclosed in this study are: (i) the diffuse antisense transcription; (ii) the great abundance of transfer-messenger RNAs (tmRNA); (iii) the abundance of rnpB transcripts, paramount for the RNase-P complex; and (iv) the presence of abundant fragments derived from pre-ribosomal RNA leader sequences of unknown biological function. Overall, this study extends the catalogue of ncRNAs in S. coelicolor and suggests an important role of non-coding transcription in the regulation of biologically active molecule production
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
Reactivation of aerobic granular sludge for the treatment of industrial shipboard slop wastewater: Effects of long-term storage on granules structure, biofilm activity and microbial community
No full textThis work reports on reactivation of aerobic granular sludge (AGS) for the treatment of industrial recalcitrant wastewater (slop wastewater) characterized by high salinity and hydrocarbons. AGS were reactivated in two reactors, R1 and R2, to treat industrial slop wastewater after a long-term storage for 12-months at 4 °C. In R1, salt-adapted mature aerobic granules were previously subjected to a step-wise increase of hydrocarbons, whereas in R2 aerobic granules were previously cultivated in presence of salinity and hydrocarbons. After a short-term reactivation period, the slop dosage caused a simultaneous decrease of granules dimensions and proteins/polysaccharides (PN/PS) ratio down to 1.76 (R1) and 2.35 (R2). Then, the increase of granules dimensions and of the PN/PS ratio up to 5.63 (R1) and 4.22 (R2), suggested a new granulation process. The difference in total petroleum hydrocarbons (TPHs) removal efficiencies (≈87 % R1, and ≈97 % R2) was mainly due to a biodegradation effect in R2 where granules were previously cultivated with slop. This was confirmed by a simultaneous decrease of TPHs concentration in the bulk and adsorbed into granules. Based on Next Generation Sequencing of metagenomic 16S encoding genes, in R2 typical oil-polluted seawater-associated bacteria were detected, which probably played key roles in TPHs biodegradation
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