Moving I`iwi (Vestiaria coccinea) as a Surrogate for Future Translocations of Endangered `Akohekohe (Palmeria dolei)

Translocations often play an important role in the recovery of endangered species. To assess feasibility for translocation of endangered `Akohekohe (Palmeria dolei), we conducted an experimental translocation of I`iwi (Vestiaria coccinea) from east to west Maui. Mist-netting, veterinary screening of candidate birds, and helicopter transport of healthy I`iwi were successful, resulting in no injuries or mortalities. Translocated birds were assigned to two types of release. Hard release birds were radio tagged and released on the day of translocation. In contrast, soft release birds were held in large cages for 7 days and fed artificial nectar. During holding soft release I`iwi feeding rates, fecal production, and mass were monitored. Soft release birds suffered 33% mortality during the holding period. At the end of the holding period, soft release survivors were outfitted with a radio transmitter and released. All translocated I`iwi were followed by radio telemetry for an average of 21 days. Once released, soft release birds showed higher rates of movement, possibly reflecting conflict with established hard released I`iwi. Our results suggest that translocation efforts for wild `Akohekohe will be successful if hard release protocols are followed

A baseline assessment of migratory and resident bird use of a prairie restoration site in eastern Washington

Prairies, and other types of grassland ecosystems, have suffered some of the most profound losses worldwide, due to anthropogenic factors such as fossil fuel extraction, agriculture, and climate change. Likewise, organisms inhabiting grassland ecosystems have become extirpated across much of their historical range, not the least of which has been a 50% decline in grassland birds since the 1960s. In response to losses of intact prairie in eastern Washington, a 120-ac site has been established on the EWU campus to regenerate native prairie and monitor changes in the ecosystem as native plants recolonize and replace non-natives. Because birds are an important indicator species of ecosystem health, the goal of our research was to estimate baseline abundance and diversity of birds at the prairie restoration site before restoration takes place. We also assessed bird abundance and diversity at a small, intact prairie remnant 20 mi north of the EWU campus to compare current bird use of the restoration site with that of an intact prairie system. We assessed bird abundance and bird diversity using the line-transect method. We established one transect at each site, and counted all birds seen or heard within 50 meters of the transects. Our findings will provide a baseline of knowledge about how and when birds will begin to reinhabit the EWU restoration site and inform future restoration efforts on the benefits and outcomes of restoring native grasslands locally, and worldwide

Cluster randomised control trial protocol for estimating the effectiveness and cost-effectiveness of a complex intervention to increase care home staff influenza vaccination rates compared to usual practice (FLUCARE)

The care home staff influenza vaccination rate in England is significantly lower than the 75% World Health Organisation recommendation. This represents a substantial potential for resident harm. Barriers to staff vaccination stem from individual and organisational levels. Existing interventions address some but not all barriers and are not underpinned by behavioural science theory. This study aims to estimate the effectiveness and cost-effectiveness of a theory-informed intervention to improve care home staff vaccination rates compared to routine practice. Set in care homes with both nursing and residential focus, and a range of ownership status, only homes providing long stay care to older people with a staff vaccination rate below 40% are eligible to participate. Participation expressions of interest will be sought using a variety of approaches prior to seeking consent. The primary outcome measure is the proportion of staff vaccinated at 6 months, with secondary outcome measures being proportion vaccinated at 3 months, numbers of staff sick days, general practitioner and nurse visits to care home, care home resident hospitalisations and mortality. Based on the assumptions that the mean cluster (care home) size is 54 staff, a coefficient of variation of 0.48, control vaccination rate is 55%, intervention 75%, intra-cluster correlation coefficient of 0.2 and with 90% power, and 20% attrition, we require 39 care homes per arm. Blocked randomisation will be at the level of care home, stratified by the proportion of non-white care home staff, and implemented by Norwich Clinical Trials Unit. The intervention comprises co-designed information videos and posters, provision of in-house staff vaccination clinics, and incentive scheme and monthly data collection on trial outcomes. Beyond usual practice, the control arm will additionally contribute monthly data. Data will be collected at the start, monthly and at 6 months, and analysis will be blind to allocation. Statistical analysis will use the intention-to-treat principle with the difference in vaccination rates between groups compared using a random effect logistic regression model at the staff-level. This will be the first study to use a theory-informed intervention designed to comprehensively address identified barriers to care home staff influenza vaccination

A miRNA-Target Prediction Case Study

Giansanti, V., Castelli, M., Beretta, S., & Merelli, I. (2019). Comparing Deep and Machine Learning Approaches in Bioinformatics: A miRNA-Target Prediction Case Study. In V. V. Krzhizhanovskaya, M. H. Lees, P. M. A. Sloot, J. J. Dongarra, J. M. F. Rodrigues, P. J. S. Cardoso, J. Monteiro, ... R. Lam (Eds.), Computational Science – ICCS 2019: 19th International Conference, Faro, Portugal, June 12–14, 2019, Proceedings, Part III (pp. 31-44). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11538 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-030-22744-9_3MicroRNAs (miRNAs) are small non-coding RNAs with a key role in the post-transcriptional gene expression regularization, thanks to their ability to link with the target mRNA through the complementary base pairing mechanism. Given their role, it is important to identify their targets and, to this purpose, different tools were proposed to solve this problem. However, their results can be very different, so the community is now moving toward the deployment of integration tools, which should be able to perform better than the single ones. As Machine and Deep Learning algorithms are now in their popular years, we developed different classifiers from both areas to verify their ability to recognize possible miRNA-mRNA interactions and evaluated their performance, showing the potentialities and the limits that those algorithms have in this field. Here, we apply two deep learning classifiers and three different machine learning models to two different miRNA-mRNA datasets, of predictions from 3 different tools: TargetScan, miRanda, and RNAhybrid. Although an experimental validation of the results is needed to better confirm the predictions, deep learning techniques achieved the best performance when the evaluation scores are taken into account.authorsversionpublishe

MicroRNA in lung cancer

MicroRNAs (miRNAs) are small non-protein-coding RNAs that function as endogenous negative gene regulators. Dysfunctions of miRNAs are frequently found in malignancies, including lung cancer. In this review, we summarise the current understanding of miRNAs in lung cancer tumourigenesis, and highlight their potential in overcoming drug resistance, abetting histological sub-classification techniques, and serving as biomarkers for lung cancer risk stratification and outcome prediction

Regulation of Heterochromatin Assembly on Unpaired Chromosomes during Caenorhabditis elegans Meiosis by Components of a Small RNA-Mediated Pathway

Many organisms have a mechanism for down regulating the expression of non-synapsed chromosomes and chromosomal regions during meiosis. This phenomenon is thought to function in genome defense. During early meiosis in Caenorhabditis elegans, unpaired chromosomes (e.g., the male X chromosome) become enriched for a modification associated with heterochromatin and transcriptional repression, dimethylation of histone H3 on lysine 9 (H3K9me2). This enrichment requires activity of the cellular RNA-directed RNA polymerase, EGO-1. Here we use genetic mutation, RNA interference, immunofluorescence microscopy, fluorescence in situ hybridization, and molecular cloning methods to identify and analyze three additional regulators of meiotic H3K9me2 distribution: CSR-1 (a Piwi/PAZ/Argonaute protein), EKL-1 (a Tudor domain protein), and DRH-3 (a DEAH/D-box helicase). In csr-1, ekl-1, and drh-3 mutant males, we observed a reduction in H3K9me2 accumulation on the unpaired X chromosome and an increase in H3K9me2 accumulation on paired autosomes relative to controls. We observed a similar shift in H3K9me2 pattern in hermaphrodites that carry unpaired chromosomes. Based on several assays, we conclude that ectopic H3K9me2 accumulates on paired and synapsed chromosomes in these mutants. We propose alternative models for how a small RNA-mediated pathway may regulate H3K9me2 accumulation during meiosis. We also describe the germline phenotypes of csr-1, ekl-1, and drh-3 mutants. Our genetic data suggest that these factors, together with EGO-1, participate in a regulatory network to promote diverse aspects of development

MicroRNA networks direct neuronal development and plasticity

MicroRNAs (miRNAs) constitute a class of small, non-coding RNAs that act as post-transcriptional regulators of gene expression. In neurons, the functions of individual miRNAs are just beginning to emerge, and recent studies have elucidated roles for neural miRNAs at various stages of neuronal development and maturation, including neurite outgrowth, dendritogenesis, and spine formation. Notably, miRNAs regulate mRNA translation locally in the axosomal and synaptodendritic compartments, and thereby contribute to the dynamic spatial organization of axonal and dendritic structures and their function. Given the critical role for miRNAs in regulating early brain development and in mediating synaptic plasticity later in life, it is tempting to speculate that the pathology of neurological disorders is affected by altered expression or functioning of miRNAs. Here we provide an overview of recently identified mechanisms of neuronal development and plasticity involving miRNAs, and the consequences of miRNA dysregulation

Regulation of microRNA biogenesis and turnover by animals and their viruses

Item does not contain fulltextMicroRNAs (miRNAs) are a ubiquitous component of gene regulatory networks that modulate the precise amounts of proteins expressed in a cell. Despite their small size, miRNA genes contain various recognition elements that enable specificity in when, where and to what extent they are expressed. The importance of precise control of miRNA expression is underscored by functional studies in model organisms and by the association between miRNA mis-expression and disease. In the last decade, identification of the pathways by which miRNAs are produced, matured and turned-over has revealed many aspects of their biogenesis that are subject to regulation. Studies in viral systems have revealed a range of mechanisms by which viruses target these pathways through viral proteins or non-coding RNAs in order to regulate cellular gene expression. In parallel, a field of study has evolved around the activation and suppression of antiviral RNA interference (RNAi) by viruses. Virus encoded suppressors of RNAi can impact miRNA biogenesis in cases where miRNA and small interfering RNA pathways converge. Here we review the literature on the mechanisms by which miRNA biogenesis and turnover are regulated in animals and the diverse strategies that viruses use to subvert or inhibit these processes

Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials.

Funder: laura and john arnold foundationBACKGROUND: Convalescent plasma has been widely used to treat COVID-19 and is under investigation in numerous randomized clinical trials, but results are publicly available only for a small number of trials. The objective of this study was to assess the benefits of convalescent plasma treatment compared to placebo or no treatment and all-cause mortality in patients with COVID-19, using data from all available randomized clinical trials, including unpublished and ongoing trials (Open Science Framework, https://doi.org/10.17605/OSF.IO/GEHFX ). METHODS: In this collaborative systematic review and meta-analysis, clinical trial registries (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform), the Cochrane COVID-19 register, the LOVE database, and PubMed were searched until April 8, 2021. Investigators of trials registered by March 1, 2021, without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID-19 patients, regardless of setting or treatment schedule. Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung-Knapp-Sidik-Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. RESULTS: A total of 16,477 patients were included in 33 trials (20 unpublished with 3190 patients, 13 published with 13,287 patients). 32 trials enrolled only hospitalized patients (including 3 with only intensive care unit patients). Risk of bias was low for 29/33 trials. Of 8495 patients who received convalescent plasma, 1997 died (23%), and of 7982 control patients, 1952 died (24%). The combined risk ratio for all-cause mortality was 0.97 (95% confidence interval: 0.92; 1.02) with between-study heterogeneity not beyond chance (I2 = 0%). The RECOVERY trial had 69.8% and the unpublished evidence 25.3% of the weight in the meta-analysis. CONCLUSIONS: Convalescent plasma treatment of patients with COVID-19 did not reduce all-cause mortality. These results provide strong evidence that convalescent plasma treatment for patients with COVID-19 should not be used outside of randomized trials. Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead