Chironomus riparius proteome responses to spinosad exposure

The potential of proteome responses as early-warning indicators of insecticide exposure was evaluated using the non-biting midge Chironomus riparius (Meigen) as the model organism. Chironomus riparius larvae were exposed to environmentally relevant concentrations of the neurotoxic pesticide spinosad to uncover molecular events that may provide insights on the long-term individual and population level consequences. The iTRAQ labeling method was performed to quantify protein abundance changes between exposed and non-exposed organisms. Data analysis revealed a general dose-dependent decrease in the abundance of globin proteins as a result of spinosad exposure. Additionally, the downregulation of actin and a larval cuticle protein was also observed after spinosad exposure, which may be related to previously determined C. riparius life-history traits impairment and biochemical responses. Present results suggest that protein profile changes can be used as early warning biomarkers of pesticide exposure and may provide a better mechanistic interpretation of the toxic response of organisms, aiding in the assessment of the ecological effects of environmental contamination. This work also contributes to the understanding of the sublethal effects of insecticides in invertebrates and their molecular targets.info:eu-repo/semantics/publishedVersio

Pseudotyping retrovirus like particles vaccine candidates with Hepatitis C virus envelope protein E2 requires the cellular expression of CD81

Hepatitis C virus (HCV) infects 3% of world population being responsible for nearly half a million deaths annually urging the need for a prophylactic vaccine. Retrovirus like particles are commonly used scaffolds for antigens presentation being the core of diverse vaccine candidates. The immunogenicity of host proteins naturally incorporated in retrovirus was hypothesized to impact the performance of retrovirus based vaccines. In this work, the capacity of engineered retrovirus like particles devoided of host protein CD81 to display HCV envelope antigens was compared to non-engineered particles. A persistent inability of CD81 negative VLPs to incorporate HCV E2 protein as a result from the inefficient transport of HCV E2 to the plasma membrane, was observed. This work enabled the identification of a CD81-mediated transport of HCV E2 while stressing the importance of host proteins for the development of recombinant vaccines.publishe

Drivers of Insect Community Change along the Margins of Mountain Streams in Serra da Estrela Natural Park (Portugal)

Mountain ecosystems are important biodiversity hotspots and valuable natural laboratories to study community assembly processes. Here, we analyze the diversity patterns of butterflies and odonates in a mountainous area of high conservation value—Serra da Estrela Natural Park (Portugal)—and we assess the drivers of community change for each of the two insect groups. The butterflies and odonates were sampled along 150 m transects near the margins of three mountain streams, at three elevation levels (500, 1000, and 1500 m). We found no significant differences in odonate species richness between elevations, but marginal differences (p = 0.058) were found for butterflies due to the lower number of species at high altitudes. Both insect groups showed significant differences in beta diversity (βtotal) between elevations, with species richness differences being the most important component for odonates (βrich = 55.2%), while species replacement drove the changes between butterfly assemblages (βrepl = 60.3%). Climatic factors, particularly those depicting harsher conditions of temperature and precipitation, were the best predictors of total beta diversity (βtotal) and its components (βrich, βrepl) for the two study groups. The study of insect biodiversity patterns in mountain ecosystems and of the role played by different predictors contribute to further our understanding on the community assembly processes and may help to better predict environmental change impacts on mountain biodiversity.FUNDING: This work benefited the support from Energias de Portugal (EDP) Fund for Biodiversity 2011 and Fundação para a Ciência e a Tecnologia (FCT) through project PTDC/BIA-BIC/1013/2014 and contract DL57/2016/CP1375/CT0001 to MB. PAVB and MB are currently also funded by the project Azores DRCT Pluriannual Funding (M1.1.A/FUNC.UI&D/010/2021-2024). The APC was funded by FCT project UIDB/00329/2020–2024 (Thematic Line 1—integrated ecological assessment of environmental change on biodiversity).info:eu-repo/semantics/publishedVersio

Automatic 3D pulmonary nodule detection in CT images: a survey

This work presents a systematic review of techniques for the 3D automatic detection of pulmonary nodules in computerized-tomography (CT) images. Its main goals are to analyze the latest technology being used for the development of computational diagnostic tools to assist in the acquisition, storage and, mainly, processing and analysis of the biomedical data. Also, this work identifies the progress made, so far, evaluates the challenges to be overcome and provides an analysis of future prospects. As far as the authors know, this is the first time that a review is devoted exclusively to automated 3D techniques for the detection of pulmonary nodules from lung CT images, which makes this work of noteworthy value. The research covered the published works in the Web of Science, PubMed, Science Direct and IEEEXplore up to December 2014. Each work found that referred to automated 3D segmentation of the lungs was individually analyzed to identify its objective, methodology and results. Based on the analysis of the selected works, several studies were seen to be useful for the construction of medical diagnostic aid tools. However, there are certain aspects that still require attention such as increasing algorithm sensitivity, reducing the number of false positives, improving and optimizing the algorithm detection of different kinds of nodules with different sizes and shapes and, finally, the ability to integrate with the Electronic Medical Record Systems and Picture Archiving and Communication Systems. Based on this analysis, we can say that further research is needed to develop current techniques and that new algorithms are needed to overcome the identified drawbacks

MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development.

BACKGROUND: Microexons, exons that are ≤ 30 nucleotides, are a highly conserved and dynamically regulated set of cassette exons. They have key roles in nervous system development and function, as evidenced by recent results demonstrating the impact of microexons on behaviour and cognition. However, microexons are often overlooked due to the difficulty of detecting them using standard RNA-seq aligners. RESULTS: Here, we present MicroExonator, a novel pipeline for reproducible de novo discovery and quantification of microexons. We process 289 RNA-seq datasets from eighteen mouse tissues corresponding to nine embryonic and postnatal stages, providing the most comprehensive survey of microexons available for mice. We detect 2984 microexons, 332 of which are differentially spliced throughout mouse embryonic brain development, including 29 that are not present in mouse transcript annotation databases. Unsupervised clustering of microexons based on their inclusion patterns segregates brain tissues by developmental time, and further analysis suggests a key function for microexons in axon growth and synapse formation. Finally, we analyse single-cell RNA-seq data from the mouse visual cortex, and for the first time, we report differential inclusion between neuronal subpopulations, suggesting that some microexons could be cell type-specific. CONCLUSIONS: MicroExonator facilitates the investigation of microexons in transcriptome studies, particularly when analysing large volumes of data. As a proof of principle, we use MicroExonator to analyse a large collection of both mouse bulk and single-cell RNA-seq datasets. The analyses enabled the discovery of previously uncharacterized microexons, and our study provides a comprehensive microexon inclusion catalogue during mouse development

Standardised sampling of odonates (Odonata) in Serra da Estrela (Portugal) - 2013 and 2014

Mountain ecosystems are crucial for biodiversity conservation since they host high biodiversity. This study reports novel information on odonate species diversity, distribution and abundance from Serra da Estrela Natural Park (Portugal). Twenty six odonate species were sampled in this protected area, including the first finding of Macromia splendens (Pictet, 1843). New populations of Oxygastra curtisii (Dale, 1834), a protected species under the Habitats Directive, was found in this Natural Park and novel distribution and ecological data was collected for most species, including several rare species (e.g., Aeshna juncea (Linnaeus, 1758), Sympetrum flaveolum (Linnaeus, 1758)). All data were collected using standardised sampling allowing its use as baseline for long-term monitoring of Serra da Estrela mountain biodiversity.FUNDING: This work was financed by Energias de Portugal (EDP) Fund for Biodiversity 2011 through project "Biodiversidade, endemismos e espécies protegidas associadas às lagoas e cursos de água da Serra da Estrela: valorização de um século de aproveitamento hidroeléctrico". Fundação para a Ciência e a Tecnologia supported MB by contract DL 57/2016/CP1375/CT0001.info:eu-repo/semantics/publishedVersio

Standardised sampling of lepidopterans (Lepidoptera) in Serra da Estrela (Portugal) - 2013 and 2014. v1.2

Mountain ecosystems are crucial for biodiversity conservation since they host high biodiversity. This study reports novel information on lepidopteran species diversity, distribution and abundance from Serra da Estrela Natural Park (Portugal). Seventy two lepidopteran species were sampled in this protected area, including the first findings of Apatura ilia (Denis & Schiffermüller, 1775) and Vanessa virginiensis (Drury, 1773). New populations of Euphydrias aurinia (Rottemburg, 1775), a protected species under the Habitats Directive, was found in this Natural Park and novel distribution and ecological data was collected for most species, including several rare species [e.g., Coenonympha glycerion iphioides Staudinger, 1870, Cyaniris semiargus (Rottemburg, 1775)]. All data were collected using standardised sampling allowing its use as baseline for environmental changes long-term monitoring of Serra da Estrela mountain biodiversity.FUNDING: The study was financed by Energias de Portugal (EDP) under the Fundo EDP para a Biodioversidade 2011.info:eu-repo/semantics/publishedVersio

Evidence for lack of direct causality between pain and affective disturbances in a rat peripheral neuropathy model

[Epub ahead of print]Chronic pain is frequently accompanied by the manifestation of emotional disturbances and cognitive deficits. While a causality relation between pain and emotional/cognitive disturbances is generally assumed, several observations suggest a temporal dissociation and independent mechanisms. We therefore studied Sprague-Dawley rats that presented a natural resistance to pain manifestation in a neuropathy model (spared nerve injury [SNI]) and compared their performance in a battery of behavioral paradigms-anxiety, depression and fear memory-with animals that presented a pain phenotype. Afterward, we performed an extensive volumetric analysis across prefrontal, orbitofrontal and insular cortical areas. The majority of SNI animals manifested mechanical allodynia (low threshold [LT]), but 13% were similar to Sham controls (high threshold [HT]). Readouts of spontaneous hypersensivity (paw flinches) were also significantly reduced in HT and correlated with allodynia. To increase the specificity of our findings, we segregated the SNI animals in those with left (SNI-L) and right (SNI-R) lesions and the lack of association between pain and behavior still remains. Left-lesioned animals, independent of the LT or HT phenotype, presented increased anxiety-like behaviors and decreased well-being. In contrast, we found that the insular cortex (agranular division) was significantly smaller in HT than in LT. To conclude, pain and emotional disturbances observed following nerve injury are to some extent segregated phenomena. Also, HT and LT SNI presented differences in insular volumes, an area vastly implicated in pain perception, suggesting a supraspinal involvement in the manifestation of these phenotypes.This work has been funded by the European Regional Development Fund (FEDER), through the Competitiveness Factors Operational Programme (COMPETE) and the Northern Portugal Regional Operational Programme (NORTE 2020) under the Portugal 2020 Partnership Agreement (project NORTE-01-0145-FEDER-000023). It was also funded by National and International funds, through the Foundation for Science and Technology (FCT), under the scope of the projects POCI-01-0145- FEDER-007038 and PTDC/NEU-SCC/5301/2014 and by the IASP Early Career Research Grant 2015. Researchers were supported by FCT grant numbers PD/BD/114117/2015 (MRG via Inter-University Doctoral Programme in Ageing and Chronic Disease, PhDOC), SFRH/BD/109111/2015 (AMC via PhD Program in Health Sciences), SFRH/BD/52291/2013 (ME via PhDOC), SFRH/BD/89936/2012 (SB via PhD Program in Health Sciences (Applied)), PDE/BDE/113604/2015 (RM via PhD Program in Health Sciences (Applied)), PDE/BDE/113601/2015 (PSM via PhD Program in Health Sciences (Applied)) and SFRH/BPD/80118/2011 (HA). ARS integrated the Master Programme in Health Sciences of the School of Medicine, University of Minho.info:eu-repo/semantics/acceptedVersio

Biorecovery of Cr(VI) from wastewater and its catalytic reutilization

The performance of two zeolites with different structures and acidity properties was evaluated on the biosorption of Cr(VI) and catalytic oxidation of ethyl acetate. The starting zeolites, HY and HZSM5, were modified by ion exchange treatments in order to obtain zeolites with different acidity and sodium content. Arthrobacter viscosus supported on the different zeolites was used for Cr(VI) recovery from solution. The best removal efficiencies and uptake of chromium were achieved for the Y zeolites due to their higher ion exchange capacity. The Y and ZSM5 zeolites were characterized by ICP-AES, SEM, NH3 chemisorption, XRD and N2 adsorption. Y and ZSM5 zeolites obtained after biosorption of chromium were successfully reused as catalysts in the oxidation of ethyl acetate. The chromium-loaded ZSM5 zeolites were considerably more active and selective towards CO2 than chromium-loaded Y zeolites, essentially due to its different framework structure, textural and acidity properties

Conserved and highly expressed tRNA derived fragments in zebrafish

Background: Small non-coding RNAs (sncRNAs) are a class of transcripts implicated in several eukaryotic regulatory mechanisms, namely gene silencing and chromatin regulation. Despite significant progress in their identification by next generation sequencing (NGS) we are still far from understanding their full diversity and functional repertoire. Results: Here we report the identification of tRNA derived fragments (tRFs) by NGS of the sncRNA fraction of zebrafish. The tRFs identified are 18–30 nt long, are derived from specific 5′ and 3′ processing of mature tRNAs and are differentially expressed during development and in differentiated tissues, suggesting that they are likely produced by specific processing rather than random degradation of tRNAs. We further show that a highly expressed tRF (5′tRF-ProCGG) is cleaved in vitro by Dicer and has silencing ability, indicating that it can enter the RNAi pathway. A computational analysis of zebrafish tRFs shows that they are conserved among vertebrates and mining of publicly available datasets reveals that some 5′tRFs are differentially expressed in disease conditions, namely during infection and colorectal cancer. Conclusions: tRFs constitute a class of conserved regulatory RNAs in vertebrates and may be involved in mechanisms of genome regulation and in some diseases. Keywords: tRNA derived fragments, Zebrafish, Small non coding RNAs, tRNAspublishe