Tools4miRs – one place to gather all the tools for miRNA analysis

MiRNAs are short, non-coding molecules that negatively regulate gene expression and thereby play several important roles in living organisms. Dozens of computational methods for miRNA-related research have been developed, which greatly differ in various aspects. The substantial availability of difficult-to-compare approaches makes it challenging for the user to select a proper tool and prompts the need for a solution that will collect and categorize all the methods. Here, we present tools4miRs, the first platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can additionally filter the available methods according to their specific research needs, capabilities and preferences. Tools4miRs is also a web-based target prediction meta-server that incorporates user-designated target prediction methods into the analysis of user-provided data

The Relationship of Anxiety and Stress With Working Memory Performance in a Large Non-depressed Sample

Clinical anxiety and acute stress caused by major life events have well-documented detrimental effects on cognitive processes, such as working memory (WM). However, less is known about the relationships of state anxiety or everyday stress with WM performance in non-clinical populations. We investigated the associations between these two factors and three WM composites (verbal WM, visuospatial WM, and n-back updating performance) in a large online sample of non-depressed US American adults. We found a trend for a negative association between WM performance and anxiety, but not with stress. Thus, WM performance appears rather robust against normal variation in anxiety and everyday stress.Peer reviewe

The Relationship of Anxiety and Stress With Working Memory Performance in a Large Non-depressed Sample

Clinical anxiety and acute stress caused by major life events have well-documented detrimental effects on cognitive processes, such as working memory (WM). However, less is known about the relationships of state anxiety or everyday stress with WM performance in non-clinical populations. We investigated the associations between these two factors and three WM composites (verbal WM, visuospatial WM, and n-back updating performance) in a large online sample of non-depressed US American adults. We found a trend for a negative association between WM performance and anxiety, but not with stress. Thus, WM performance appears rather robust against normal variation in anxiety and everyday stress

The inhibitory effect of noscapine on the in vitro cathepsin G-induced collagen expression in equine endometrium

Research Areas: Life Sciences & Biomedicine ; MicrobiologyABSTRACT - Cathepsin G (CAT) is a protease released by neutrophils when forming neutrophil extracellular traps that was already associated with inducing type I collagen (COL1) in equine endometrium in vitro. Endometrosis is a fibrotic condition mainly characterized by COL1 deposition in the equine endometrium. The objective was to evaluate if noscapine (an alkaloid for cough treatment with anti-neoplastic and anti-fibrotic properties) would reduce COL1A2 transcription (evaluated by qPCR) and COL1 protein relative abundance (evaluated by western blot) induced by CAT in equine endometrial explants from follicular and mid-luteal phases treated for 24 or 48 h. The explants treated with CAT increased COL1 expression. Noscapine decreased COL1A2 transcription at both estrous cycle phases, but COL1 relative protein only at the follicular phase, both induced by CAT. Additionally, the noscapine anti-fibrotic action was found to be more effective in the follicular phase. The CAT treatment caused more fibrosis at the longest period of treatment, while noscapine acted better at the shortest time of treatment. Our results showed that noscapine could act as an anti-fibrotic drug in equine endometrosis by inhibiting CAT in vitro. Noscapine offers a new promising therapeutic tool for treating fibrosis as a single non-selective agent to be considered in the future.info:eu-repo/semantics/publishedVersio

The In vitro inhibitory effect of sivelestat on elastase induced collagen and metallopeptidase expression in equine endometrium

Research Areas: Agriculture ; Veterinary Sciences ; ZoologyAbstract: Neutrophil extracellular traps (NETs) fight endometritis, and elastase (ELA), a protease found in NETs, might induce collagen type I (COL1) accumulation in equine endometrium. Metallopeptidases (MMPs) are involved in extracellular matrix balance. The aim was to evaluate the e ects of ELA and sivelestat (selective elastase inhibitor) on MMP-2 and MMP-9 expression and gelatinolytic activity, as well as the potential inhibitory e ect of sivelestat on ELA-induced COL1 in equine endometrium. Endometrial explants from follicular (FP) and mid-luteal (MLP) phases were treated for 24 or 48 h with ELA, sivelestat, and their combination. Transcripts of COL1A2, MMP2, and MMP9 were evaluated by qPCR; COL1 protein relative abundance by Western blot, and MMP-2 and MMP-9 gelatinolytic activity by zymography. In response to ELA treatment, there was an increase in MMP2 mRNA transcription (24 h) in active MMP-2 (48 h), both in FP, and in MMP9 transcripts in FP (48 h) and MLP (24 h) (p < 0.05). Sivelestat inhibited ELA-induced COL1A2 transcripts in FP (24 h) and MLP (24 h, 48 h) (p < 0.05). The sivelestat inhibitory e ect was detected in MMP9 transcripts in FP at 48 h (p < 0.05), but proteases activity was unchanged. Thus, MMP-2 and MMP-9 might be implicated in endometrium fibrotic response to ELA. In mare endometrium, sivelestat may decrease ELA-induced COL1 deposition and hinder endometrosis development.info:eu-repo/semantics/publishedVersio

Myeloperoxidase inhibition decreases the expression of collagen and metallopeptidase in mare endometria under in vitro conditions

Research Areas: Agriculture ; Veterinary Sciences ; ZoologyABSTRACT - Neutrophils can originate neutrophil extracellular traps (NETs). Myeloperoxidase (MPO) is a peroxidase found in NETs associated to equine endometrosis and can be inhibited by 4-aminobenzoic acid hydrazide (ABAH). Metallopeptidases (MMPs) participate in extracellular matrix stability and fibrosis development. The objectives of this in vitro work were to investigate, in explants of mare’s endometrium, (i) the ABAH capacity to inhibit MPO-induced collagen type I (COL1) expression; and (ii) the action of MPO and ABAH on the expression and gelatinolytic activity of MMP-2/-9. Explants retrieved from the endometrium of mares in follicular or mid-luteal phases were treated with MPO, ABAH, or their combination, for 24 or 48 h. The qPCR analysis measured the transcription of COL1A2, MMP2, and MMP9. Western blot and zymography were performed to evaluate COL1 protein relative abundance and gelatinolytic activity of MMP-2/-9, respectively. Myeloperoxidase elevated COL1 relative protein abundance at both treatment times in follicular phase (p < 0.05). The capacity of ABAH to inhibit MPO-induced COL1 was detected in follicular phase at 48 h (p < 0.05). The gelatinolytic activity of activated MMP-2 augmented in mid-luteal phase at 24 h after MPO treatment, but it was reduced with MPO+ABAH treatment. The activity of MMP-9 active form augmented in MPO-treated explants. However, this effect was inhibited by ABAH in the follicular phase at 48 h (p < 0.05). By inhibiting the pro-fibrotic effects of MPO, it might be possible to reduce the development of endometrosis. Metallopeptidase-2 might be involved in an acute response to MPO in the mid-luteal phase, while MMP-9 might be implicated in a prolonged exposition to MPO in the follicular phase.info:eu-repo/semantics/publishedVersio

Bilingualism and working memory performance: Evidence from a large-scale online study

The bilingual executive advantage (BEA) hypothesis has attracted considerable research interest, but the findings are inconclusive. We addressed this issue in the domain of working memory (WM), as more complex WM tasks have been underrepresented in the previous literature. First, we compared early and late bilingual vs. monolingual WM performance. Second, we examined whether certain aspects of bilingual experience, such as language switching frequency, are related to bilinguals' WM scores. Our online sample included 485 participants. They filled in an extensive questionnaire including background factors such as bilingualism and second language (L2) use, and performed 10 isomorphic verbal and visuospatial WM tasks that yielded three WM composite scores (visuospatial WM, verbal WM, n-back). For verbal and visuospatial WM composites, the group comparisons did not support the BEA hypothesis. N-back analysis showed an advantage of late bilinguals over monolinguals and early bilinguals, while the latter two groups did not differ. This between-groups analysis was followed by a regression analysis relating features of bilingual experience to n-back performance, but the results were non-significant in both bilingual groups. In sum, group differences supporting the BEA hypothesis were limited only to the n-back composite, and this composite was not predicted by bilingualism-related features. Moreover, Bayesian analyses did not give consistent support for the BEA hypothesis. Possible reasons for the failure to find support for the BEA hypothesis are discussed

Enzymes present in neutrophil extracellular traps may stimulate the fibrogenic PGF(2 alpha) pathway in the mare endometrium

Research Areas: AgricultureVeterinary SciencesEndometrosis is a fibrotic disease in mare endometrium whose pathological mechanisms remain obscure. Prostaglandin (PG)F2α, despite modulating reproductive physiological processes, may also provoke local pathological collagen deposition (fibrogenesis). Neutrophil extracellular traps (NETs) released during inflammation have been linked to fibrogenesis in several tissues. We have previously shown that enzymes found in NETs increase in vitro collagen production in mare endometrium. In this study, activation of PGF2α-pathway in equine endometrial explants challenged in vitro by enzymes found in NETs is shown. Our results indicate that both endocrine microenvironment (estrous cycle phase) and healthy or pathological conditions of endometrial tissues play an important role in PGF2α-pathway activation. In the endometrium of the follicular phase, we have observed both high production of PGF2α and/or PGF2α receptor gene transcription under the action of enzymes found in NETs, both conditions associated with fibrogenesis in other tissues. Nevertheless, transcription of the PGF2α receptor gene does not appear to be hormone-dependent, albeit their levels seem to be dependent on endometrial category in the mid-luteal phase. This study suggests that enzymes existing in NETs may instigate changes on PGF2α mediators, which may become an additional mechanism of fibrogenesis in mare endometrium.info:eu-repo/semantics/publishedVersio

The inhibition of Cathepsin G on endometrial explants with endometrosis in the mare

Research Areas: Veterinary SciencesAlthough proteases found in neutrophil extracellular traps (NETs) have antimicrobial properties, they also stimulate collagen type 1 (COL1) production by the mare endometrium, contributing for the development of endometrosis. Cathepsin G (CAT), a protease present in NETs, is inhibited by specific inhibitors, such as cathepsin G inhibitor I (INH; beta-keto-phosphonic acid). Matrix metallopeptidases (MMPs) are proteases involved in the equilibrium of the extracellular matrix. The objective of this study was to investigate the effect of CAT and INH (a selective CAT inhibitor) on the expression of MMP-2 and MMP-9 and on gelatinolytic activity. In addition, the putative inhibitory effect of INH on CAT-induced COL1 production in mare endometrium was assessed. Endometrial explants retrieved from mares in follicular phase or midluteal phase were treated for 24 or 48 h with CAT, inhibitor alone, or both treatments. In explants, transcripts (quantitative polymerase chain reaction) of COL1A2, MMP2, and MMP9, as well as the relative abundance of COL1 protein (Western blot), and activity of MMP-2 and MMP-9 (zymography) were evaluated. The protease CAT induced COL1 expression in explants, at both estrous cycle phases and treatment times. The inhibitory effect of INH was observed on COL1A2 transcripts in follicular phase at 24-h treatment, and in midluteal phase at 48 h (P < 0.05), and on the relative abundance of COL protein in follicular phase and midluteal phase explants, at 48 h (P < 0.001). Our study suggests that MMP-2 might also be involved in an earlier response to CAT, and MMP-9 in a later response, mainly in the follicular phase. While the use of INH reduced CAT-induced COL1 endometrial expression, MMPs might be involved in the fibrogenic response to CAT. Therefore, in mare endometrium, the use of INH may be a future potential therapeutic means to reduce CAT-induced COL1 formation and to hamper endometrosis establishment.info:eu-repo/semantics/publishedVersio

One hundred mitochondrial genomes of cicadas

Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.Fil: Lukasik, Piotr. University of Montana; Estados UnidosFil: Chong, Rebecca. University of Hawaii at Manoa; Estados UnidosFil: Nazario, Katherine. University of Connecticut; Estados UnidosFil: Matsuura, Yu. University of the Ryukyus; JapónFil: Bublitz, De Anna. University of Montana; Estados UnidosFil: Campbell, Matthew. University of Montana; Estados UnidosFil: Meyer, Mariah. University of Montana; Estados UnidosFil: Van Leuven, James. University of Montana; Estados UnidosFil: Pessacq, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Centro de Investigación Esquel de Montaña y Estepa Patagóica. Universidad Nacional de la Patagonia "San Juan Bosco". Facultad de Ciencias Naturales - Sede Esquel. Centro de Investigación Esquel de Montaña y Estepa Patagónica; ArgentinaFil: Veloso, Claudio. Universidad de Chile; ChileFil: Simon, Chris. University of Connecticut; Estados UnidosFil: McCutcheon, John. University of Montana; Estados Unido