scholarly journals Linking the state of environmental DNA to its application for biomonitoring and stock assessment: Targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes

2021 ◽  
Author(s):  
Toshiaki Jo ◽  
Kenta Takao ◽  
Toshifumi Minamoto
Keyword(s):  
Stock Assessment ◽  
Environmental Dna ◽  
The State ◽  
Nuclear Genes ◽  
Particle Sizes ◽  
Dna Fragment

scholarly journals Assessing the Potential of Catch-Only Models to Inform on the State of Global Fisheries and the UN’s SDGs

2021 ◽  
Vol 13 (11) ◽  
pp. 6101
Author(s):  
Rishi Sharma ◽  
Henning Winker ◽  
Polina Levontin ◽  
Laurence Kell ◽  
Dan Ovando ◽  
...  
Keyword(s):  
Stock Assessment ◽  
Fishing Effort ◽  
The State ◽  
Sources Of Information ◽  
Ongoing Research ◽  
Traditional Assessment ◽  
Stock Status ◽  
Stock Assessments ◽  
Recent Developments ◽  
Measure Of Performance

Catch-only models (COMs) have been the focus of ongoing research into data-poor stock assessment methods. Two of the most recent models that are especially promising are (i) CMSY+, the latest refined version of CMSY that has progressed from Catch-MSY, and (ii) SRA+ (Stock Reduction Analysis Plus) a recent developments in field. Comparing COMs and evaluating their relative performance is essential for determining the state of regional and global fisheries that may be lacking necessary data that would be required to run traditional assessment models. In this paper we interrogate how performance of COMs can be improved by incorporating additional sources of information. We evaluate the performance of COMs on a dataset of 48 data-rich ICES (International Council for the Exploration of Seas) stock assessments. As one measure of performance, we consider the ability of the model to correctly classify stock status using FAO’s 3-tier classification that is also used for reporting on sustainable development goals to the UN. Both COMs showed notable bias when run with their inbuilt default heuristics, but as the quality of prior information increased, classification rates for the terminal year improved substantially. We conclude that although further COM refinements show some potential, most promising is the ongoing research into developing biomass or fishing effort priors for COMs in order to be able to reliably track stock status for the majority of the world’s fisheries currently lacking stock assessments.

scholarly journals A pilot for implementing environmental DNA (eDNA) based methods into environmental and biomonitoring

2021 ◽  
Vol 4 ◽  
Author(s):  
Tiina Laamanen ◽  
Veera Norros ◽  
Sanna Suikkanen ◽  
Mikko Tolkkinen ◽  
Kristiina Vuorio ◽  
...  
Keyword(s):  
Best Practices ◽  
Information Exchange ◽  
State Of The Art ◽  
Environmental Dna ◽  
Bulk Sample ◽  
The State ◽  
Molecular Techniques ◽  
Future Research ◽  
Dna Metabarcoding

Environmental DNA (eDNA) and other molecular based approaches are revolutionizing the field of biomonitoring. These approaches undergo rapid modifications, and it is crucial to develop the best practices by sharing the newest information and knowledge. In our ongoing project we: assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE; identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring; promote information exchange on eDNA methods and advance future research efforts both within SYKE and with our national and international partners. assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE; identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring; promote information exchange on eDNA methods and advance future research efforts both within SYKE and with our national and international partners. Scientific background Well-functioning and intact natural ecosystems are essential for human well-being, provide a variety of ecosystem services and contain a high diversity of organisms. However, human activities such as eutrophication, pollution, land-use or invasive species, are threatening the state and functioning of ecosystems from local to global scale (e.g. Benateau et al. 2019; Reid et al. 2018; Vörösmarty et al. 2010). New molecular techniques in the field and in the laboratory have enabled sampling and identification of much of terrestrial, marine and freshwater biodiversity. These include environmental DNA (eDNA, e.g. Valentini et al. 2016) and bulk-sample DNA metabarcoding approaches (e.g. Elbrecht et al. 2017) and targeted RNA-based methods (e.g. Mäki and Tiirola 2018). The eDNA technique uses DNA that is released from organisms into their environment, from which a signal of organisms’ presence in the system can be obtained. For example, in aquatic ecosystems, eDNA is typically extracted from sediment or filtered water samples (e.g. Deiner et al. 2016), and this approach is distinguished from bulk DNA metabarcoding, where organisms are directly identified from e.g. complete biological monitoring samples (e.g. Elbrecht et al. 2017). Despite the demonstrated potential of environmental and bulk-sample DNA metabarcoding approaches in recent years, there are still significant bottlenecks to their routine use that need to be addressed (e.g. Pawlowski et al. 2020). Methods and implementati on The project is divided into three work packages: WP1 Gathering existing knowledge, identifying knowledge gaps and proposing best practices, WP2 Roadmap to implementation and WP3 eDNA monitoring pilot. Please see more details in the Fig. 1

scholarly journals Publisher Correction: Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Babett Günther ◽  
Thomas Knebelsberger ◽  
Hermann Neumann ◽  
Silke Laakmann ◽  
Pedro Martínez Arbizu
Keyword(s):  
Environmental Dna ◽  
Nuclear Genes ◽  
Marine Environmental

scholarly journals Parameter estimation in stock assessment modelling: caveats with gradient-based algorithms

2018 ◽  
Vol 75 (5) ◽  
pp. 1553-1559 ◽  
Author(s):  
Sam Subbey
Keyword(s):  
Parameter Estimation ◽  
State Of The Art ◽  
Stock Assessment ◽  
The State ◽  
Cautionary Note ◽  
Machine Precision ◽  
Fisheries Science ◽  
Increasing Trend ◽  
Gradient Based ◽  
Blind Faith

Abstract Using simple illustrative examples, this note highlights some of the caveats with gradient-based algorithms. This class of algorithms underpins the state-of-the-art modelling platform in fisheries science. The goal is to sound a cautionary note about an increasing trend in fisheries science, where blind faith is being invested in results obtained from algorithms that are fast, and proven to have machine precision.

scholarly journals Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Babett Günther ◽  
Thomas Knebelsberger ◽  
Hermann Neumann ◽  
Silke Laakmann ◽  
Pedro Martínez Arbizu
Keyword(s):  
Environmental Dna ◽  
Nuclear Genes ◽  
Marine Environmental

scholarly journals Environmental DNA Fragment Conferring Early and Increased Sporulation and Antibiotic Production in Streptomyces Species

2005 ◽  
Vol 71 (3) ◽  
pp. 1638-1641 ◽  
Author(s):  
Asuncion Martinez ◽  
Steven J. Kolvek ◽  
Joern Hopke ◽  
Choi Lai Tiong Yip ◽  
Marcia S. Osburne
Keyword(s):  
Secondary Metabolites ◽  
Antibiotic Production ◽  
Environmental Dna ◽  
Streptomyces Lividans ◽  
Streptomyces Species ◽  
Dna Library ◽  
Dna Fragment

ABSTRACT Here we describe the rep gene, isolated from an environmental DNA library, which when transformed into Streptomyces species resulted in increased production of secondary metabolites and accelerated sporulation. We show that Streptomyces lividans strains bearing rep are particularly useful as expression hosts for heterologous antibiotic production.

scholarly journals Environmental DNA size sorting and degradation experiment indicates the state of Daphnia magna mitochondrial and nuclear eDNA is subcellular

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rashnat Moushomi ◽  
Gregory Wilgar ◽  
Gary Carvalho ◽  
Simon Creer ◽  
Mathew Seymour
Keyword(s):  
Daphnia Magna ◽  
Environmental Dna ◽  
The State ◽  
Size Sorting ◽  
Dna Size

scholarly journals Presence of atypical genotypes of Toxoplasma gondii isolated from cats in the state of Bahia, Northeast of Brazil

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0253630
Author(s):  
Ana Graziela de Jesus Deiró ◽  
Danielle Paschoal do Prado ◽  
Iuri Prates Sousa ◽  
Daniele de Santana Rocha ◽  
Rodrigo Alves Bezerra ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Microsatellite Markers ◽  
The State ◽  
Chain Reaction ◽  
Study Region ◽  
Pcr Rflp ◽  
Indirect Hemagglutination ◽  
Indirect Hemagglutination Test ◽  
Dna Fragment ◽  
Polymerase Chain

In this study, 20 blood, heart, and brain samples were collected from euthanized cats at the Zoonosis Control Centers and Veterinary Clinics in the state of Bahia, Brazil. The sera were examined for anti-T. gondii antibodies using the indirect hemagglutination test. The brains and hearts of seven seropositive cats were ground, and peptide digestion was performed for bioassay in mice. Toxoplasma gondii was isolated in 5/7 (71.42%) of seropositive cats. In these isolates, the parasite was genotyped using the Polymerase chain reaction, associated with the DNA fragment polymorphism obtained by restriction enzyme PCR-RFLP technique with 11 markers (SAG1, 5’-SAG2, 3’-SAG2, alt. SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, Apico, and CS3) and 15 microsatellite markers (TUB-2, W35, TgM-A, B18, B17, M33, IV.1, XI.1, M48, M102, N60, N82, AA, N61, N83). The analysis of the isolates by PCR-RFLP revealed five distinct genotypes. Three of these genotypes have never been reported before; one corresponded to the TgDgCo13 genotype, and one incomplete genotype. In genotyping analysis using microsatellite markers, it was observed that the isolates showed atypical alleles in the typing and fingerprint markers. This revealed five atypical genotypes. The typing marker B17 showed the highest degree of atypia. This study is the first to report the genotyping of T. gondii obtained from naturally infected cats in Bahia, Northeast Brazil. The genotypes found in this study were different from those found in other studies conducted in Bahia, which included different species of animals. None of the clonal lineages I, II, or III were found. This study demonstrates the diversity of T. gondii in the study region, with the presence of unusual genotypes, reaffirming the genetic variability of the parasite in Brazil.

scholarly journals Author Correction: Environmental DNA size sorting and degradation experiment indicates the state of Daphnia magna mitochondrial and nuclear eDNA is subcellular

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rashnat Moushomi ◽  
Gregory Wilgar ◽  
Gary Carvalho ◽  
Simon Creer ◽  
Mathew Seymour
Keyword(s):  
Daphnia Magna ◽  
Environmental Dna ◽  
The State ◽  
Size Sorting ◽  
Dna Size

scholarly journals The state of the art in stock assessment: where we are and where we are going

2003 ◽  
Vol 67 (S1) ◽  
pp. 15-20 ◽  
Author(s):  
Ray Hilborn
Keyword(s):  
State Of The Art ◽  
Stock Assessment ◽  
The State
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