scholarly journals Development of eDNA tools for the detection of marine invasive non-native species to support European flat oyster (Ostrea edulis) restoration projects.

2021 ◽  
Vol 4 ◽  
Author(s):  
Sean Markus ◽  
Iveta Matejusova ◽  
Alex Douglas ◽  
William Sanderson
Keyword(s):  
Real Time ◽  
Native Species ◽  
Large Scale ◽  
Keystone Species ◽  
Environmental Dna ◽  
Ostrea Edulis ◽  
Anthropogenic Pressures ◽  
Didemnum Vexillum ◽  
Sea Squirt ◽  
Flat Oyster

The European flat oyster (Ostrea edulis) is an important keystone species in Scottish coastal waters. However due to anthropogenic pressures, significant reductions to oyster beds have been observed across Europe. In Scotland, several projects are currently aiming to restore European flat oyster habitats through the translocation of juvenile oysters from various sources including hatcheries and aquaculture. However, translocation of shellfish is not risk free and can increase the risk of accidental translocation of invasive non-native species (INNS). If INNS become established outside of their native range they can cause irreversible harm to native organisms and habitats. This study aims to develop molecular tools to detect environmental DNA of INNS which can be potentially associated with the translocation of live shellfish stocks. We have developed a species-specific real-time PCR assay for detection of Pacific oyster (Crassostrea gigas) and tested its sensitivity in a large-scale replicated mesocosm based experiment with varying densities of C.gigas. A secondary objective of the experiment was to assess the detection of another invasive species, the carpet sea squirt Didemnum vexillum which was cohabited with C. gigas. We aim to quantify the detection probability of increasing densities of C. gigas from repeat water samples and qPCR replicates. This project also aims to investigate the feasibility of using portable, real-time sequencing technologies such as the Oxford Nanopore MinION to develop robust tools to support native oyster restoration programmes.

scholarly journals Sustainable large‐scale production of European flat oyster ( Ostrea edulis ) seed for ecological restoration and aquaculture: a review

2021 ◽  
Author(s):  
Bérenger Colsoul ◽  
Pierre Boudry ◽  
María Luz Pérez‐Parallé ◽  
Ana Bratoš Cetinić ◽  
Tristan Hugh‐Jones ◽  
...  
Keyword(s):  
Ecological Restoration ◽  
Large Scale ◽  
Scale Production ◽  
Ostrea Edulis ◽  
Large Scale Production ◽  
Flat Oyster

scholarly journals A non-lethal method for detection of Bonamia ostreae in flat oyster (Ostrea edulis) using environmental DNA

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Louise von Gersdorff Jørgensen ◽  
Johan Wedel Nielsen ◽  
Mikkel Kehler Villadsen ◽  
Bent Vismann ◽  
Sussie Dalvin ◽  
...  
Keyword(s):  
Water Samples ◽  
Sea Water ◽  
Diagnostic Technique ◽  
Environmental Dna ◽  
Detection Methods ◽  
Ostrea Edulis ◽  
Breeding Programs ◽  
Bonamia Ostreae ◽  
Flat Oyster ◽  
Selection Of

Abstract Surveillance and diagnosis of parasitic Bonamia ostreae infections in flat oysters (Ostrea edulis) are prerequisites for protection and management of wild populations. In addition, reliable and non-lethal detection methods are required for selection of healthy brood oysters in aquaculture productions. Here we present a non-lethal diagnostic technique based on environmental DNA (eDNA) from water samples and demonstrate applications in laboratory trials. Forty oysters originating from Limfjorden, Denmark were kept in 30 ppt sea water in individual tanks. Water was sampled 6 days later, after which all oysters were euthanized and examined for infection, applying PCR. Four oysters (10%) were found to be infected with B. ostreae in gill and mantle tissue. eDNA purified from the water surrounding these oysters contained parasite DNA. A subsequent sampling from the field encompassed 20 oysters and 15 water samples from 5 different locations. Only one oyster turned out positive and all water samples proved negative for B. ostreae eDNA. With this new method B. ostreae may be detected by only sampling water from the environment of isolated oysters or isolated oyster populations. This non-lethal diagnostic eDNA method could have potential for future surveys and oyster breeding programs aiming at producing disease-free oysters.

scholarly journals Environmental DNA Based Surveillance for the Highly Invasive Carpet Sea Squirt Didemnum vexillum: A Targeted Single-Species Approach

2021 ◽  
Vol 8 ◽  
Author(s):  
Iveta Matejusova ◽  
Jennifer Graham ◽  
Fiona Bland ◽  
Jean-Pierre Lacaze ◽  
Guillaume Herman ◽  
...  
Keyword(s):  
Water Samples ◽  
Native Species ◽  
Limit Of Detection ◽  
Sampling Site ◽  
Monitoring Program ◽  
Environmental Dna ◽  
Qpcr Assay ◽  
Didemnum Vexillum ◽  
Sampling Points ◽  
The Impact

The presence and diversity of marine non-native species, the number of new invasions, and the impact on native communities and habitats are important metrics used to assess the health of marine ecosystems. Monitoring for marine non-native species, using traditional approaches such as rapid assessment surveys (RASs), requires taxonomic expertise and may still fail to detect rare or inconspicuous species. This study reports a validation process for a quantitative PCR (qPCR) assay based on the cytochrome oxidase 1 gene, designed to detect highly invasive tunicate Didemnum vexillum by targeting environmental DNA (eDNA) present in water samples. The D. vexillum qPCR assay showed high sensitivity, with the threshold limit of detection (LOD) and modeled LOD3 (based on triplicate qPCR reactions) estimated as 9.187 and 1.117 copies reaction–1, respectively and the limit of quantification (LOQ) was calculated as 18 copies reaction–1. Analyses of water samples collected from selected Pacific oyster farms and recreational marinas in Scotland showed 100% concordance between the historical data on presence of D. vexillum from RASs and detection of D. vexillum eDNA. Consistency of detection of D. vexillum eDNA among different sampling points within each infected sampling site varied, ranging between 100% positive throughout the site to some sampling points testing “negative” or only as “suspected” for D. vexillum. Sites with lower within-site detection consistency included sites with a low density of D. vexillum as reported by RASs or were sites undergoing D. vexillum management. The present pilot monitoring program demonstrates the potential to generate important data on presence of D. vexillum. This program will be scaled up across large geographic regions and used in the first instance to focus and target the traditional RASs to D. vexillum eDNA-positive sites in a cost-effective way, with an aim to verify the species presence by visual observation and direct Sanger sequencing of positive qPCR products.

scholarly journals Identification of genes from flat oyster Ostrea edulis as suitable housekeeping genes for quantitative real time PCR

2010 ◽  
Vol 29 (6) ◽  
pp. 937-945 ◽  
Author(s):  
Benjamin Morga ◽  
Isabelle Arzul ◽  
Nicole Faury ◽  
Tristan Renault
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Housekeeping Genes ◽  
Ostrea Edulis ◽  
Quantitative Real Time Pcr ◽  
Flat Oyster

scholarly journals Mapping biodiversity hotspots of fish communities in subtropical streams through environmental DNA

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rosetta C. Blackman ◽  
Maslin Osathanunkul ◽  
Jeanine Brantschen ◽  
Cristina Di Muri ◽  
Lynsey R. Harper ◽  
...  
Keyword(s):  
Large Scale ◽  
Fish Communities ◽  
Environmental Dna ◽  
River Network ◽  
Fish Diversity ◽  
Conservation Areas ◽  
Anthropogenic Pressures ◽  
Sampling Campaign ◽  
Chao Phraya River ◽  
River Catchments

AbstractLarge tropical and subtropical rivers are among the most biodiverse ecosystems worldwide, but also suffer from high anthropogenic pressures. These rivers are hitherto subject to little or no routine biomonitoring, which would be essential for identification of conservation areas of high importance. Here, we use a single environmental DNA multi-site sampling campaign across the 200,000 km2 Chao Phraya river basin, Thailand, to provide key information on fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network. By using hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. The clusters not only accurately matched the topology of the river network, but also revealed distinct groups of sites enabling informed conservation measures. Our study reveals novel opportunities of large-scale monitoring via eDNA to identify relevant areas within whole river catchments for conservation and habitat protection.

Species-specific diagnostic assays for Bonamia ostreae and B. exitiosa in European flat oyster Ostrea edulis: conventional, real-time and multiplex PCR

2013 ◽  
Vol 104 (2) ◽  
pp. 149-161 ◽  
Author(s):  
A Ramilo ◽  
JI Navas ◽  
A Villalba ◽  
E Abollo
Keyword(s):  
Multiplex Pcr ◽  
Real Time ◽  
Ostrea Edulis ◽  
Diagnostic Assays ◽  
Bonamia Ostreae ◽  
Flat Oyster ◽  
Species Specific

scholarly journals Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis)

2019 ◽  
Vol 10 ◽  
Author(s):  
Luke E. Holman ◽  
Christopher M. Hollenbeck ◽  
Thomas J. Ashton ◽  
Ian A. Johnston
Keyword(s):  
Environmental Dna ◽  
Bivalve Mollusk ◽  
Ostrea Edulis ◽  
Non Invasive ◽  
Flat Oyster

Methods for the Quantification of Salivary Cortisol and of a-amylase in Biosensors and Portable Devices

2018 ◽  
Vol 68 (12) ◽  
pp. 2857-2859
Author(s):  
Cristina Mihaela Ghiciuc ◽  
Andreea Silvana Szalontay ◽  
Luminita Radulescu ◽  
Sebastian Cozma ◽  
Catalina Elena Lupusoru ◽  
...  
Keyword(s):  
Real Time ◽  
Medical Practice ◽  
Salivary Cortisol ◽  
Clinical Studies ◽  
Large Scale ◽  
Psychological Research ◽  
Portable Devices ◽  
Salivary Amylase ◽  
Specificity And Sensitivity

There is an increasing interest in the analysis of salivary biomarkers for medical practice. The objective of this article was to identify the specificity and sensitivity of quantification methods used in biosensors or portable devices for the determination of salivary cortisol and salivary a-amylase. There are no biosensors and portable devices for salivary amylase and cortisol that are used on a large scale in clinical studies. These devices would be useful in assessing more real-time psychological research in the future.

scholarly journals BattleNet: Capturing Advantageous Battlefield in RTS Games (Student Abstract)

2020 ◽  
Vol 34 (10) ◽  
pp. 13849-13850
Author(s):  
Donghyeon Lee ◽  
Man-Je Kim ◽  
Chang Wook Ahn
Keyword(s):  
Artificial Intelligence ◽  
Decision Making ◽  
Real Time ◽  
Large Scale ◽  
Outcome Predictor ◽  
Short Term ◽  
Rts Game

In a real-time strategy (RTS) game, StarCraft II, players need to know the consequences before making a decision in combat. We propose a combat outcome predictor which utilizes terrain information as well as squad information. For training the model, we generated a StarCraft II combat dataset by simulating diverse and large-scale combat situations. The overall accuracy of our model was 89.7%. Our predictor can be integrated into the artificial intelligence agent for RTS games as a short-term decision-making module.

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