Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals

We focus on a case study along an English canal comparing environmental DNA (eDNA) metabarcoding with two types of electrofishing techniques (wade‐and‐reach and boom‐boat). In addition to corroborating data obtained by electrofishing, eDNA provided a wider snapshot of fish assemblages. Given the semi‐lotic nature of canals, we encourage the use of eDNA as a fast and cost‐effective tool to detect and monitor whole fish communities

Hidden Diversity Hampers Conservation Efforts in a Highly Impacted Neotropical River System.

Neotropical Rivers host a highly diverse ichthyofauna, but taxonomic uncertainty prevents appropriate conservation measures. The Doce River Basin (DRB), lying within two Brazilian threatened hotspots (Atlantic Forest and Brazilian Savanna) in south-east Brazil, faced the worst ever environmental accident reported for South American catchments, due to a dam collapse that spread toxic mining tailings along the course of its main river. Its ichthyofauna was known to comprise 71 native freshwater fish species, of which 13 endemic. Here, we build a DNA barcode library for the DRB ichthyofauna, using samples obtained before the 2015 mining disaster, in order to provide a more robust biodiversity record for this basin, as a baseline for future management actions. Throughout the whole DRB, we obtained a total of 306 barcodes, assigned to 69 putative species (with a mean of 4.54 barcodes per species), belonging to 45 genera, 18 families, and 5 orders. Average genetic distances within species, genus, and families were 2.59, 11.4, and 20.5%, respectively. The 69 species identified represent over 76% of the known DRB ichthyofauna, comprising 43 native (five endemic, of which three threatened by extinction), 13 already known introduced species, and 13 unknown species (such as Characidium sp., Neoplecostomus sp., and specimens identified only at the sub-family level Neoplecostominae, according to morphological identification provided by the museum collections). Over one fifth of all analyzed species (N = 16) had a mean intraspecific genetic divergence higher than 2%. An integrative approach, combining NND (nearest neighbor distance), BIN (barcode index number), ABGD (automatic barcode gap discovery), and bPTP (Bayesian Poisson Tree Processes model) analyses, suggested the occurrence of potential cryptic species, species complex, or historical errors in morphological identification. The evidence presented calls for a more robust, DNA-assisted cataloging of biodiversity-rich ecosystems, in order to enable effective monitoring and informed actions to preserve and restore these delicate habitats

Implementation strategies for web-based applications for screening: a scoping review

1. Chor Yau Ooi, Chirk Jenn Ng, Anne E. Sales, & Lim, H. M

Implementation Strategies for Web-Based Apps for Screening: Scoping Review

Background: Screening is an effective primary prevention strategy in health care, as it enables the early detection of diseases. However, the uptake of such screening remains low. Different delivery methods for screening have been developed and found to be effective in increasing the uptake of screening, including the use of web-based apps. Studies have shown that web-based apps for screening are effective in increasing the uptake of health screening among the general population. However, not much is known about the effective implementation of such web-based apps in the real-world setting. Implementation strategies are theory-based methods or techniques used to enhance the adoption, implementation, and sustainability of evidence-based interventions. Implementation strategies are important, as they allow us to understand how to implement an evidence-based intervention. Therefore, a scoping review to identify the various implementation strategies for web-based apps for screening is warranted. Objective: This scoping review aims to identify (1) strategies used to implement web-based apps for health screening, (2) frameworks used for implementing web-based apps for health screening, (3) outcome measures of implementation strategies, and (4) effective implementation strategies. Methods: This scoping review was conducted based on Arksey and O’Malley’s framework. After identifying the review question, two researchers independently screened and selected relevant literature from PubMed, Embase, Cochrane, Cumulative Index of Nursing and Allied Health Literature, PsycINFO, International Standard Randomised Controlled Trial Number Registry, OpenGrey, ClinicalTrials.gov, World Health Organization International Clinical Trials Registry Platform, and Web of Science. This was followed by charting the data using a standardized form. Finally, we collated, summarized, and reported the results quantitatively and qualitatively based on the review objectives. Results: A total of 16,476 studies were retrieved, of which 5669 were duplicates. From a total of 10,807 studies, 10,784 studies were excluded based on their titles and abstracts. There were 23 full-text articles reviewed, and 4 articles were included in the final analysis. Many studies were excluded because they focused on the effectiveness and not on the implementation of web-based apps. Facilitation was the most cited implementation strategy used, followed by reminders, clinical champions, and educational meetings and materials. Only 2 studies used implementation frameworks to guide the evaluation of their studies. Common outcome measures for implementation strategies were feasibility, fidelity, and penetration. Implementation strategies reported to be effective were quality improvement meetings, facilitation, educational meetings, and clinical champions. Conclusions: There is a dearth of literature on the implementation of web-based apps for health screening. Implementation strategies were developed without any reported use of implementation theories or frameworks in most studies. More research on the development and evaluation of web-based screening app implementations is needed

Implementation strategies for web-based applications for screening : a scoping review

Introduction: Screening is an effective primary prevention strategy in healthcare. However, uptake of screening remains low. Many strategies have been developed and found to be effective in increasing uptake of screening including using web-based applications (web-apps). However, not much is known about effective implementation of web-apps for screening in the real-world setting. Objectives: This scoping review aimed to identify (1) implementation strategies to implement web-apps for screening; (2) implementation frameworks used for implementing web-apps for screening; (3) outcome measures of implementation strategies and (4) implementation strategies that were effective. Method: This scoping review was conducted based on Arksey O’Malley’s framework. After identifying the review question, two researchers independently screened and selected relevant literature from PubMed, Embase, Cochrane, CINAHL, PsycINFO, ISRCTN registry, OpenGrey, ClinicalTrials.gov, World Health Organization International Clinical Trials Registry Platform and Web of Science. This was followed by charting of the data using a standardized form. Finally, a researcher collated, summarised, and reported the results quantitatively and qualitatively based on the review objectives. Results: 16476 studies were retrieved where 5669 were duplicates. From a total of 10807 studies, 10784 studies were excluded based on screening of title and abstract. Twenty-three full-text articles were reviewed and 4 articles were included in the final analysis. Many studies were excluded because they did not focus on implementation of web-apps. Facilitation was the most cited implementation strategy used followed by reminders, clinical champions, educational meetings and materials. Only 2 studies used implementation frameworks to guide the evaluation of their studies. Common outcome measures for implementation strategies were feasibility, fidelity and penetration. Implementation strategies reported to be effective were quality improvement meetings, facilitation, educational meetings and clinical champions. Discussion/ Conclusion: There is a dearth of literature on implementation of web-apps for screening and therefore there is a need to conduct more research in development and evaluation of implementation of web-apps screening interventions

Chaperones as integrators of cellular networks: Changes of cellular integrity in stress and diseases

Cellular networks undergo rearrangements during stress and diseases. In un-stressed state the yeast protein-protein interaction network (interactome) is highly compact, and the centrally organized modules have a large overlap. During stress several original modules became more separated, and a number of novel modules also appear. A few basic functions, such as the proteasome preserve their central position. However, several functions with high energy demand, such the cell-cycle regulation loose their original centrality during stress. A number of key stress-dependent protein complexes, such as the disaggregation-specific chaperone, Hsp104, gain centrality in the stressed yeast interactome. Molecular chaperones, heat shock, or stress proteins form complex interaction networks (the chaperome) with each other and their partners. Here we show that the human chaperome recovers the segregation of protein synthesis-coupled and stress-related chaperones observed in yeast recently. Examination of yeast and human interactomes shows that (1) chaperones are inter-modular integrators of protein-protein interaction networks, which (2) often bridge hubs and (3) are favorite candidates for extensive phosphorylation. Moreover, chaperones (4) become more central in the organization of the isolated modules of the stressed yeast protein-protein interaction network, which highlights their importance in the de-coupling and re-coupling of network modules during and after stress. Chaperone-mediated evolvability of cellular networks may play a key role in cellular adaptation during stress and various polygenic and chronic diseases, such as cancer, diabetes or neurodegeneration.Comment: 13 pages, 3 figures, 1 glossar

PGF2α-F-prostanoid receptor signalling via ADAMTS1 modulates epithelial cell invasion and endothelial cell function in endometrial cancer

<p>Abstract</p> <p>Background</p> <p>An increase in cancer cell invasion and microvascular density is associated with a poorer prognosis for patients with endometrial cancer. In endometrial adenocarcinoma F-prostanoid (FP) receptor expression is elevated, along with its ligand prostaglandin (PG)F_2α, where it regulates expression and secretion of a host of growth factors and chemokines involved in tumorigenesis. This study investigates the expression, regulation and role of a disintegrin and metalloproteinase with thrombospondin repeat 1 (ADAMTS1) in endometrial adenocarcinoma cells by PGF_2αvia the FP receptor.</p> <p>Methods</p> <p>Human endometrium and adenocarcinoma tissues were obtained in accordance with Lothian Research Ethics Committee guidance with informed patient consent. Expression of ADAMTS1 mRNA and protein in tissues was determined by quantitative RT-PCR analysis and immunohistochemistry. Signal transduction pathways regulating ADAMTS1 expression in Ishikawa cells stably expressing the FP receptor to levels seen in endometrial cancer (FPS cells) were determined by quantitative RT-PCR analysis. In vitro invasion and proliferation assays were performed with FPS cells and human umbilical vein endothelial cells (HUVECs) using conditioned medium (CM) from PGF_2α-treated FPS cells from which ADAMTS1 was immunoneutralised and/or recombinant ADAMTS1. The role of endothelial ADAMTS1 in endothelial cell proliferation was confirmed with RNA interference. The data in this study were analysed by T-test or ANOVA.</p> <p>Results</p> <p>ADAMTS1 mRNA and protein expression is elevated in endometrial adenocarcinoma tissues compared with normal proliferative phase endometrium and is localised to the glandular and vascular cells. Using FPS cells, we show that PGF2α-FP signalling upregulates ADAMTS1 expression via a calmodulin-NFAT-dependent pathway and this promotes epithelial cell invasion through ECM and inhibits endothelial cell proliferation. Furthermore, we show that CM from FPS cells regulates endothelial cell ADAMTS1 expression in a rapid biphasic manner. Using RNA interference we show that endothelial cell ADAMTS1 also negatively regulates cellular proliferation.</p> <p>Conclusions</p> <p>These data demonstrate elevated ADAMTS1 expression in endometrial adenocarcinoma. Furthermore we have highlighted a mechanism whereby FP receptor signalling regulates epithelial cell invasion and endothelial cell function via the PGF_2α-FP receptor mediated induction of ADAMTS1.</p

Shark-dust: Application of high-throughput DNA sequencing of processing residues for trade monitoring of threatened sharks and rays

Illegal fishing, unregulated bycatch, and market demand for certain products (e.g., fins) are largely responsible for the rapid global decline of shark and ray populations. Controlling trade of endangered species remains difficult due to product variety, taxonomic ambiguity, and trade complexity. The genetic tools traditionally used to identify traded species typically target individual tissue samples, and are time-consuming and/or species-specific. Here, we performed high-throughput sequencing of trace DNA fragments retrieved from dust and scraps left behind by trade activities. We metabarcoded “shark-dust” samples from seven processing plants in the world's biggest shark landing site (Java, Indonesia), and identified 61 shark and ray taxa (representing half of all chondrichthyan orders), more than half of which could not be recovered from tissue samples collected in parallel from the same sites. Importantly, over 80% of shark-dust sequences were found to belong to CITES-listed species. We argue that this approach is likely to become a powerful and cost-effective monitoring tool wherever wildlife is traded

Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding.

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing water and sediment from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-throughput sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of eDNA from fish assemblages was observed and species richness was nearly twice as high before the major rain event compared to afterwards. Yet, peaks of diversity were primarily associated with only four of the locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams might that these anthropogenic barriers may have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access