scholarly journals Towards a simple way to collect eDNA using a 3D-printed passive sampler

2021 ◽  
Vol 4 ◽  
Author(s):  
Héloïse Verdier ◽  
Lara Konecny ◽  
Christophe Marquette ◽  
Tristan Lefebure
Keyword(s):  
Field Experiments ◽  
High Efficiency ◽  
Environmental Dna ◽  
Aquatic Biodiversity ◽  
Non Invasive ◽  
Physico Chemical ◽  
Wide Range ◽  
3D Printed ◽  
Promising Solution ◽  
High Binding Affinity

Environmental DNA has emerged as a revolutionary approach to monitor aquatic biodiversity. The study of the DNA released by macro-organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Despite its many advantages, methodological challenges limit the widespread use of eDNA. Among them, eDNA sampling represents one of the most challenging step. Often based on the filtration of a large volume of water, this process can be long and tedious, requiring human intervention and special care, and which is not applicable to a wide range of habitats. As an alternative to filtration, passive eDNA sampling using natural substrates appears to be a promising solution. This approach uses the natural properties of some minerals (eg. silica), organisms (eg. sponges) or even communities (e.g. biofilms) to collect and preserved eDNA. Yet, such approaches are difficult to standardize and may not be applicable in many habitats. To circumvent that problem, we have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape of the samplers has been designed to facilitate their handling in laboratory and field experiments. Here we describe and test the ability of HAp samplers to recover freshwater eDNA. We show that HAp samplers recover DNA with high efficiency and are effective even on small amounts of waterlouse eDNA. However, the eDNA recovery is also highly variable across experiments. We show that by understanding the physico-chemical interactions between DNA and the HAp sampler surface, we could improve the replicability of the process and provide a robust alternative to filtration.

scholarly journals Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers

2021 ◽  
Author(s):  
Heloise Verdier ◽  
Lara Konecny-Dupre ◽  
Christophe Marquette ◽  
Helen Reveron ◽  
Solene Tadier ◽  
...  
Keyword(s):  
Aquatic Organisms ◽  
Environmental Dna ◽  
Aquatic Environments ◽  
Non Invasive ◽  
Turbid Waters ◽  
Physico Chemical ◽  
Wide Range ◽  
Artificial Dna ◽  
3D Printed ◽  
High Binding Affinity

1. The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as filtration and precipitation are time consuming, require human intervention and are not applicable to a wide range of habitats such as turbid waters and poorly-accessible environments. To circumvent these limitations, we propose to use the binding properties of minerals to create a passive eDNA sampler. 2. We have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape and the geometry of the samplers have been designed to facilitate their handling in laboratory and field. Here we describe and test the ability of HAp samplers to recover artificial DNA and eDNA. 3. We show that HAp samplers efficiently recover DNA and are effective even on small amounts of eDNA (<1 ng). However, we also observed large variations in the amount of DNA recovered even under controlled conditions. 4. By better understanding the physico-chemical interactions between DNA and the HAp sampler surface, one could improve the repeatability of the sampling process and provide an easy-to-use eDNA sampling tool for aquatic environments.

scholarly journals Coiling-Up Space Metasurface for High-Efficient and Wide-angle Acoustic Wavefront Steering

2021 ◽  
Vol 8 ◽  
Author(s):  
Shuang Chen ◽  
Yuancheng Fan ◽  
Fan Yang ◽  
Kangyao Sun ◽  
Quanhong Fu ◽  
...  
Keyword(s):  
High Efficiency ◽  
Structural Parameters ◽  
Space Structures ◽  
Destructive Interference ◽  
Diffraction Mode ◽  
Anomalous Reflection ◽  
Wide Range ◽  
High Efficient ◽  
Scattering Field ◽  
3D Printed

The recent advent of acoustic metasurface displays tremendous potential with their unique and flexible capabilities of wavefront manipulations. In this paper, we propose an acoustic metagrating made of binary coiling-up space structures to coherently control the acoustic wavefront steering. The acoustic wave steering is based on the in-plane coherent modulation of waves in different diffraction channels. The acoustic metagrating structure with a subwavelength thickness is realized with 3D printed two coiling-up space metaunits. By adjusting structural parameters of the metaunits, the −1st-order diffraction mode can be retained, and the rest of the diffraction orders are eliminated as much as possible through destructive interference, forming a high-efficiency anomalous reflection in the scattering field. The anomalous reflection performance of the designed metagrating is achieved over a wide range of incident angles with high efficiency.

scholarly journals A validated protocol for fish farm monitoring using environmental DNA

2021 ◽  
Vol 4 ◽  
Author(s):  
Xavier Pochon ◽  
Susie Wood ◽  
Javier Atalah ◽  
Lauren Fletcher ◽  
Olivier Laroche ◽  
...  
Keyword(s):  
New Zealand ◽  
Assessment Tool ◽  
Environmental Dna ◽  
Fish Farming ◽  
Cost Effective ◽  
Low Flow ◽  
Biotic Index ◽  
Fish Farms ◽  
Physico Chemical ◽  
Wide Range

Sea-based fish farms are associated with strong benthic enrichment gradients and routine monitoring is usually required by regulation. Internationally a wide range of approaches exist for measuring the degree of benthic deterioration around fish farming activities, ranging from simple visual or odour assessments to the calculation of secondary indices that combine multiple biological and/or physico-chemical metrics (e.g., AZTI Marine Biotic Index; Invertebrate Species Index; Norwegian Quality Index; Infauna Trophic Index). In New Zealand, the health of marine benthic ecosystems around coastal salmon farms is currently measured using an Enrichment State (ES) index. This index incorporates physico-chemical (redox, organic matter, sulphates, etc.) and benthic macrofaunal measurements, which requires taxonomic expertise, is time consuming and expensive. Supported by a range of private/government agencies and industry partners, we have developed and tested the robustness of bacterial, eukaryotic, and multi-trophic Metabarcoding Biotic Indices (b-MBI, e-MBI, and mt-MBI, respectively) using a molecular Eco-Group approach. The indices were calculated via automatic computer pipelines using data collected over a period of nine years from a range of high- and low-flow salmon farms (12 farms and 60 stations) from three distinct regions in New Zealand. The MBIs were compared against the established ES index. All MBIs yielded strong and highly significant relationships with the ES index. The strongest relationships (R2 &gt; 0.9) were obtained with the b-MBI. A refinement of the b-MBI (2019-2020) was supported by highly prolific microbes throughout the ES spectrum, and in particular in the upper end of the organic enrichment scale where traditional benthic indices tend to fail. This resulted in ES values of both (molecular-based versus morphology-based) indices to follow a near one-to-one relationship, performing consistently across water flow environments and considered sub-regions. Station-averaged results were also used to compare regulated compliance outcomes between the two indices, based on the current key compliance criteria for farms within each flow regime. Of the 67 seabed monitoring stations that were subsequently classified as compliant or non‑compliant, 62 stations had identical compliance outcomes (i.e. 92% of instances). Furthermore, the b-MBI showed consistently narrower (~50%) confidence interval bands when compared to the traditional ES index. The b-MBI offers unprecedented precision for determining subtle changes along enrichment gradients, constituting a valuable asset for triggering timely management responses and improving compliance. The protocols developed in this project enable rapid, standardised, and cost-effective eDNA isolation and extraction, followed by automatic b-MBI calculation. The affordability and versatility of the b-MBI tool suggests that it could be immediately integrated into current monitoring strategies as the primary benthic assessment tool for assessing benthic impacts of salmon farms in New Zealand.

scholarly journals Evaluation of biodiversity in estuaries using environmental DNA metabarcoding

2020 ◽  
Author(s):  
Hyojin Ahn ◽  
Manabu Kume ◽  
Yuki Terashima ◽  
Feng Ye ◽  
Satoshi Kameyama ◽  
...  
Keyword(s):  
Fish Species ◽  
Environmental Conditions ◽  
Environmental Dna ◽  
Aquatic Biodiversity ◽  
Non Invasive ◽  
Dna Metabarcoding ◽  
And Migration ◽  
Low Degrees ◽  
River Mouths ◽  
Rare Fishes

AbstractBiodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river, suggesting the potential of eDNA for non-invasive assessment of aquatic biodiversity.

scholarly journals DNA metabarcoding potentially reveals multi-assemblage eutrophication responses in an eastern North American river

2017 ◽  
Author(s):  
Joseph M. Craine ◽  
Matthew V. Cannon ◽  
Andrew J. Elmore ◽  
Steven M. Guinn ◽  
Noah Fierer
Keyword(s):  
Water Quality ◽  
Environmental Dna ◽  
Nutrient Concentrations ◽  
Marker Genes ◽  
Full Potential ◽  
Aquatic Biodiversity ◽  
Main River ◽  
Wide Range ◽  
Relative Abundances ◽  
Taxonomic Groups

AbstractFreshwater aquatic ecosystems provide a wide range of ecosystem services, yet provision of these services is increasingly threatened by human activities. Directly quantifying freshwater biotic assemblages has long been a proxy for assessing changing environmental conditions, yet traditional aquatic biodiversity assessments are often time consuming, expensive, and limited to only certain habitats and certain taxa. Sequencing aquatic environmental DNA via metabarcoding has the potential to remedy these deficiencies. Such an approach could be used to quantify changes in the relative abundances of a broad suite of taxa along environmental gradients, providing data comparable to that obtained using more traditional bioassessment approaches. To determine the utility of metabarcoding for comprehensive aquatic biodiversity assessments, we sampled aquatic environmental DNA at 25 sites that spanned the full length of the Potomac River from its headwaters to the Potomac estuary. We measured dissolved nutrient concentrations and also sequenced amplified marker genes using primer pairs broadly targeting four taxonomic groups. The relative abundances of bacteria, phytoplankton, invertebrate, and vertebrate taxa were distinctly patterned along the river with significant differences in their abundances across headwaters, the main river, and the estuary. Within the main river, changes in the abundances of these broad taxonomic groups reflected either increasing river size or a higher degree of eutrophication. The larger and more eutrophic regions of the river were defined by high total dissolved phosphorus in the water, a unique suite of bacteria, phytoplankton such as species of the diatom Nitzschia, invertebrates like the freshwater snail Physella acuta, and high abundance of fish including the common carp (Cyprinus carpio). Taxonomic richness of phytoplankton and vertebrates increased downriver while it consistently decreased for bacteria. Given these results, multi-assemblage aquatic environmental DNA assessment of surface water quality is a viable tool for bioassessment. With minimal sampling effort, we were able to construct the equivalent of a freshwater water quality index, differentiate closely-related taxa, sample places where traditional monitoring would be difficult, quantify species that are difficult to detect with traditional techniques, and census taxa that are generally captured with more traditional bioassessment approaches. To realize the full potential of aquatic environmental DNA for bioassessment, research is still needed on primer development, a geographically broad set of reference sites need to be characterized, and reference libraries need to be further developed to improve taxonomic identification.

Increases in grain yield of wheat by breeding for an osmoregulation gene: relationship to water supply and evaporative demand

2000 ◽  
Vol 51 (8) ◽  
pp. 971 ◽  
Author(s):  
J. M. Morgan
Keyword(s):  
Water Supply ◽  
Field Experiments ◽  
High Efficiency ◽  
Free Water ◽  
Water Evaporation ◽  
Yield Response ◽  
Evaporative Demand ◽  
Potential Yield ◽  
Pollen Selection ◽  
Wide Range

The effect of water stress on yield increases produced by breeding for an osmoregulation gene (or) was examined using both backcross-bred lines (produced using allele identification in pollen grains) and inbred lines (produced using leaf tests). Yields were measured in 39 field experiments spanning 8 seasons. These included experiments where water was supplied through drip irrigators and rain excluded with a mobile shelter. Several approaches to the measurement of stress environment were examined. The commonly used site mean yield, although most accessible and so utilising the most data, was least effective in explaining variation in yield response. Comparatively high efficiency (84%) could be achieved using measurements of rainfall or evaporative demand for specific periods of crop ontogeny, but this suffered the limitation of being season or treatment specific. The results did, however, demonstrate the value of the pollen selection method in increasing yield under conditions of reduced water supply. In keeping with past climatic analyses, and with the theory underlying variations in leaf water potential to which osmoregulation responds, an index incorporating water supply and evaporative demand accounted well for the yield increase (85%) over the wide range of seasons and treatments examined. It requires inputs of available soil water at sowing, rainfall, and free-water evaporation during the growing period, together with sowing and anthesis dates. The index was used to assess potential yield responses in the various climates covered by the Australian wheatbelt. Greatest potential lay at the drier, inland, margins especially where soils are lighter and water-holding capacities lower.

scholarly journals Development of an environmental DNA method for monitoring fish communities: ground truthing in diverse lakes with characterised fish faunas

2018 ◽  
Author(s):  
Jianlong Li ◽  
Tristan W. Hatton-Ellis ◽  
Lori-Jayne Lawson Handley ◽  
Helen S. Kimbell ◽  
Marco Benucci ◽  
...  
Keyword(s):  
Water Samples ◽  
Fish Communities ◽  
Environmental Dna ◽  
Quantitative Information ◽  
12S Rrna ◽  
Similar Species ◽  
List Type ◽  
Large Lakes ◽  
Non Invasive ◽  
Wide Range

AbstractAccurate, cost-effective monitoring of fish is required to assess the quality of lakes under the European Water Framework Directive (WFD). Recent studies have shown that environmental DNA (eDNA) metabarcoding is an effective and non-invasive method, which can provide semi-quantitative information on fish communities in large lakes.This study further investigated the potential of eDNA metabarcoding as a tool for WFD status assessment by collecting and analysing water samples from eight Welsh lakes and six meres in Cheshire, England, with well described fish faunas. Water samples (N = 252) were assayed using two mitochondrial DNA regions (Cytb and 12S rRNA).eDNA sampling indicated the presence of very similar species in the lakes compared to those expected on the basis of existing and historical information. In total, 24 species were detected with a total of 111 species occurrences in the lakes studied using eDNA. Secondly, there was a significant positive correlation between expected faunas and eDNA data in terms of confidence of species occurrence (Spearman’s r = 0.74, df = 109, p <; 0.001). Thirdly, eDNA data can estimate relative abundance with the standard five-level classification scale (“DAFOR”). Lastly, four ecological fish communities were characterised using eDNA data which agrees with the pre-defined lake types according to environmental characteristics.Synthesis and applications. This study provides further evidence that eDNA metabarcoding could be a powerful and non-invasive monitoring tool for WFD purpose in a wide range of lake types, considerably outperforming other methods for community level analysis.

Role of Cardiac MRI in Detecting Familial Hypertrophic Cardiomyopathy: Review

2016 ◽  
Vol 1 (1) ◽  
pp. 4
Author(s):  
Marymol Koshy ◽  
Bushra Johari ◽  
Mohd Farhan Hamdan ◽  
Mohammad Hanafiah
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Magnetic Resonance ◽  
Genetic Disorder ◽  
Familial Hypertrophic Cardiomyopathy ◽  
Non Invasive ◽  
Wide Range ◽  
Proper Diagnosis ◽  
Magnetic Resonance Imaging Mri ◽  
Potential Use

Hypertrophic cardiomyopathy (HCM) is a global disease affecting people of various ethnic origins and both genders. HCM is a genetic disorder with a wide range of symptoms, including the catastrophic presentation of sudden cardiac death. Proper diagnosis and treatment of this disorder can relieve symptoms and prolong life. Non-invasive imaging is essential in diagnosing HCM. We present a review to deliberate the potential use of cardiac magnetic resonance (CMR) imaging in HCM assessment and also identify the risk factors entailed with risk stratification of HCM based on Magnetic Resonance Imaging (MRI).

Synthesis of Elaborate Benzofuran-2-Carboxamide Derivatives Through a Combination of 8-Aminoquinoline Directed C–H Arylations and Transamidations

2019 ◽  
Author(s):  
Michael Oschmann ◽  
Linus Johansson Holm ◽  
Oscar Verho
Keyword(s):  
Small Molecule ◽  
High Efficiency ◽  
Synthetic Strategy ◽  
Small Molecule Screening ◽  
Physiological Properties ◽  
Wide Range ◽  
Directing Group ◽  
Synthetic Sequence

Benzofurans are everywhere in nature and they have been extensively studied by medicinal chemists over the years because of their chemotherapeutic and physiological properties. Herein, we describe a strategy that can be used to access elaborate benzo-2-carboxamide derivatives, which involves a synthetic sequence of 8-aminoquinoline directed C–H arylations followed by transamidations. For the directed C–H arylations, Pd catalysis was used to install a wide range of aryl and heteroaryl substituents at the C3 position of the benzofuran scaffold in high efficiency. Directing group cleavage and further diversification of the C3-arylated benzofuran products were then achieved in a single synthetic operation through the utilization of a two-step transamidation protocol. By bocylating the 8-aminoquinoline amide moiety of these products, it proved possible to activate them towards aminolysis with different amine nucleophiles. Interestingly, this aminolysis reaction was found to proceed efficiently without the need of any additional catalyst or additive. Given the high efficiency and modularity of this synthetic strategy, it constitute a very attractive approach for generating structurally-diverse collections of benzofuran derivatives for small molecule screening.

To the 70th anniversary of World Meteorological Organization. Scientific and technical cooperation of Hydrometeorological Center of the USSR/Russia in the Programs of World Meteorological Organization

2020 ◽  
pp. 117-138
Author(s):  
S.V. Borshch ◽  
◽  
R.M. Vil’fand ◽  
D.B. Kiktev ◽  
V.M. Khan ◽  
...  
Keyword(s):  
Environmental Monitoring ◽  
High Efficiency ◽  
World Meteorological Organization ◽  
70Th Anniversary ◽  
Technical Level ◽  
Technical Cooperation ◽  
Wide Range

The paper presents the summary and results of long-term and multi-faceted experience of international scientific and technical cooperation of Hydrometeorological Center of Russia in the field of hydrometeorology and environmental monitoring within the framework of WMO programs, which indicates its high efficiency in performing a wide range of works at a high scientific and technical level. Keywords: World Meteorological Organization, major WMO programs, representatives of Hydrometeorological Center of Russia in WMO

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