scholarly journals Genome-wide markers reveal differentiation between and within the cryptic sister species, sunset and vermilion rockfish

2021 ◽  
Author(s):  
Gary C. Longo ◽  
John Harms ◽  
John R. Hyde ◽  
Matthew T. Craig ◽  
Ana Ramón-Laca ◽  
...  
Keyword(s):  
Management Strategies ◽  
Cost Effective ◽  
Sister Species ◽  
Nucleotide Polymorphisms ◽  
Relative Contribution ◽  
Genetic Groups ◽  
Cost Effective Method ◽  
Species Population ◽  
Single Complex ◽  
Species Specific

AbstractThe vermilion rockfish complex, which consists of the cryptic sister species vermilion and sunset rockfish, is one of the most valuable recreational fisheries on the U.S. West Coast. These species are currently managed as a single complex, and because of uncertainty surrounding the relative contribution of each species within existing data sources, the stock status of each species is not fully known. A reliable and cost-effective method is needed to disentangle these species that will allow for the development of abundance indices, life history profiles, and catch histories that may potentially support species-specific stock assessments. Using restriction-site associated DNA sequence (RADseq) markers we generated 10,003 polymorphic loci to characterize the vermilion rockfish complex. PCA and Bayesian clustering approaches based on these loci clearly distinguished between sunset and vermilion rockfishes and identified hybrid individuals. These loci included 203 highly differentiated (FST ≥ 0.99) single nucleotide polymorphisms, which we consider candidates in the planned development of a diagnostic assay capable of distinguishing between these cryptic species. In addition to clearly delineating to species, subsets of the interspecific markers allowed for insight into intraspecific differentiation in both species. Population genetic analyses for sunset rockfish identified two weakly divergent genetic groups with similar levels of genetic diversity. Vermilion rockfish, however, were characterized by three distinct genetic groups with much stronger signals of differentiation and significantly different genetic diversities. Collectively, these data will contribute to well-informed, species-specific management strategies to protect this valuable species complex.

scholarly journals MassARRAY-based single nucleotide polymorphism analysis in breast cancer of north Indian population

BMC Cancer ◽  
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Divya Bakshi ◽  
Ashna Nagpal ◽  
Varun Sharma ◽  
Indu Sharma ◽  
Ruchi Shah ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Mutations ◽  
Cost Effective ◽  
P Value ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cost Effective Method ◽  
Common Genetic Variants ◽  
Underlying Causes

Abstract Background Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis. Methods SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study. Results The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08–2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136–5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123–0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46–0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings. Conclusion It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.

Performance of bycatch reduction devices varies for chondrichthyan, reptile, and cetacean mitigation in demersal fish trawls: assimilating subsurface interactions and unaccounted mortality

2016 ◽  
Vol 74 (1) ◽  
pp. 343-358 ◽  
Author(s):  
Corey B. Wakefield ◽  
Julia Santana-Garcon ◽  
Stacey R. Dorman ◽  
Stuart Blight ◽  
Ainslie Denham ◽  
...  
Keyword(s):  
Electronic Monitoring ◽  
Bottlenose Dolphins ◽  
Cost Effective ◽  
Demersal Fish ◽  
Mitigation Strategies ◽  
Trawl Fishery ◽  
Bycatch Reduction ◽  
Cost Effective Method ◽  
Species Specific

To improve bycatch mitigation of chondrichthyans, reptiles and cetaceans for a tropical demersal fish-trawl fishery, species-specific responses to bycatch reduction devices (BRDs) were investigated using both in situ subsurface and onboard observations. There are few, if any, studies that have determined mitigation performances of BRDs from subsurface interactions for these species, as most are rarely encountered and thus require substantial levels of observer coverage for robust assessments. This study combined in-net and onboard (774 day trawls and 1320 day trawl hours of subsurface observer coverage) electronic monitoring on all fish-trawl vessels (n = 3) to compare bycatch mitigation performances among nine megafauna groups, based on escape rates and interaction durations for three BRDs over 6 months (June to December 2012). Overall, 26.9% of day trawls had no megafauna interactions and 38.3% of the 1826 interactions escaped, with most in rapid time (91.4% in ≤ 5 min). The upward inclined exclusion grid significantly improved the escape proportions for most chondrichthyans by 20–30%. All BRDs were highly effective in reducing reptile (turtles and seasnakes) bycatch, but irrelevant for the few sawfish (n = 13) that readily entangled in the anterior of the net. Cetacean (bottlenose dolphins only) interactions with BRDs were very rare (n = 7) despite high levels of attendance and depredation during trawling. Loss of targeted teleosts through the BRD hatch was rare (1.3% of day trawls). This relatively cost-effective method of electronic monitoring achieved very high levels of subsurface observer coverage (60% of day trawls or 56% of day trawl hours), and provided evidence that the subsurface expulsion of megafauna in poor condition is negligible. Furthermore, this study provides species-specific improvements toward bycatch mitigation strategies for demersal fish trawling.

Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 394-403 ◽  
Author(s):  
A Selvi ◽  
N V Nair ◽  
N Balasundaram ◽  
T Mohapatra
Keyword(s):  
Microsatellite Markers ◽  
Cost Effective ◽  
Diversity Analysis ◽  
Phenetic Analysis ◽  
Potential Cost ◽  
Banding Patterns ◽  
Genomic Libraries ◽  
Cost Effective Method ◽  
Low Diversity ◽  
Species Specific

The use of maize microsatellite markers as a potential cost-effective method for molecular analysis of sugarcane was evaluated. Of the 34 primer pairs obtained from maize genomic libraries, 14 showed repeatable amplifications in Saccharum species clones, commercial hybrids, and the related genera Erianthus, accounting for 41.17% cross transferability. Complex banding patterns were encountered in sugarcane with the number of amplified fragments ranging from 7 to 14 with an average of 10 per primer, indicating the high polyploidy and heterozygosity existing in sugarcane. Phenetic analysis of the SSR polymorphisms produced by nine primers could clearly differentiate the different species of Saccharum and Erianthus and revealed the relationships that existed between them. Genetic similarity co-efficient indicated low diversity existing among the S. officinarum clones (82%) and a relatively higher level of diversity in the S. spontaneum clones (69.7%). Higher level of divergence of Erianthus from Saccharum was also clearly estabilished. Five primers produced genus- and species-specific fragments for Erianthus, S. spontaneum, S. officinarum, and S. barberi. The polymorphic primers, when tested on a panel of 30 commercial sugarcane cultivars, revealed a broad range (32.4–83.3%) of pair-wise similarity values, indicating their ability to detect high levels of polymorphism. A combination of two primers could differentiate all the varieties, further emphasizing their potential in fingerprinting and varietal identification.Key words: maize microsatellites, Saccharum, Erianthus, diversity analysis, fingerprinting.

scholarly journals A simple genetic identification method for Northeast Atlantic smoothhound sharks (Mustelus spp.)

2009 ◽  
Vol 66 (3) ◽  
pp. 561-565 ◽  
Author(s):  
Edward D. Farrell ◽  
Maurice W. Clarke ◽  
Stefano Mariani
Keyword(s):  
Management Strategies ◽  
Cost Effective ◽  
Accurate Method ◽  
Genetic Identification ◽  
Ne Atlantic ◽  
Northeast Atlantic ◽  
Identification Method ◽  
Distribution Ranges ◽  
Galeorhinus Galeus ◽  
Species Specific

Abstract Farrell, E. D., Clarke, M. W., and Mariani, S. 2009. A simple genetic identification method for Northeast Atlantic smoothhound sharks (Mustelus spp.). – ICES Journal of Marine Science, 66: 561–565. Considerable ambiguity exists in the identification of the commercially valuable smoothhound sharks (Mustelus spp.) in the Northeast (NE) Atlantic. The lack of a clear and accurate method of identification prevents the collation of reliable species-specific landings and survey data for these fish and hinders the accurate delineation of the distribution ranges of species and stock boundaries, making it impossible to apply sound species-specific conservation and management strategies. This paper reports on the development of a multiplex PCR reaction that utilizes a set of mtDNA primers for the identification of Mustelus asterias, Mustelus mustelus, and Galeorhinus galeus. The high throughput method allows for the rapid and cost-effective identification of large numbers of samples; its application to 431 fish collected between 2006 and 2008 also raises important questions regarding the biogeography of the genus Mustelus in the NE Atlantic.

scholarly journals Phylogenetic Placement of Isolates Within the Trans-Eurasian Clade A.Br.008/009 of Bacillus anthracis

2019 ◽  
Vol 7 (12) ◽  
pp. 689
Author(s):  
Markus Antwerpen ◽  
Wolfgang Beyer ◽  
Olga Bassy ◽  
María Victoria Ortega-García ◽  
Juan Carlos Cabria-Ramos ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Cost Effective ◽  
Variable Number ◽  
Pcr Analysis ◽  
Nucleotide Polymorphisms ◽  
Additional Information ◽  
Cost Effective Method ◽  
Amplification Assay ◽  
Human Infections ◽  
Chromosomal Sequences

The largest phylogenetic lineage known to date of the anthrax pathogen Bacillus anthracis is the wide-spread, so-called Trans-Eurasian clade systematically categorized as the A.Br.008/009 group sharing two defining canonical single-nucleotide polymorphisms (canSNP). In this study, we genome-sequenced a collection of 35 B. anthracis strains of this clade, derived from human infections, animal outbreaks or soil, mostly from European countries isolated between 1936 and 2008. The new data were subjected to comparative chromosomal analysis, together with 75 B. anthracis genomes available in public databases, and the relative placements of these isolates were determined within the global phylogeny of the A.Br.008/009 canSNP group. From this analysis, we have detected 3754 chromosomal SNPs, allowing the assignation of the new chromosomal sequences to established sub-clades, to define new sub-clades, such as two new Spanish, one Bulgarian or one German group(s), or to introduce orphan lineages. SNP-based results were compared with that of a multilocus variable number of tandem repeat analysis (MLVA). This analysis indicated that MLVA typing might provide additional information in cases when genomics yields identical genotypes or shows only minor differences. Introducing the delayed mismatch amplification assay (DMAA) PCR-analysis, we developed a cost-effective method to interrogate for a set of ten phylogenetically informative SNPs within genomes of A.Br.008/009 canSNP clade strains of B. anthracis. By this approach, additional 32 strains could be assigned to five of ten defined clades.

PLATELET COUNT: A PROGNOSTIC INDICATOR IN PREECLAMPSIA AND ECLAMPSIA

2021 ◽  
pp. 73-75
Author(s):  
Naveed Tamboli ◽  
Hemant Murdeshwar ◽  
Gulafroz Sk Samad
Keyword(s):  
Platelet Count ◽  
Bleeding Time ◽  
Management Strategies ◽  
Cost Effective ◽  
Prognostic Indicator ◽  
Fetal Outcome ◽  
Clotting Time ◽  
Cost Effective Method ◽  
Induced Hypertension ◽  
A Prospective Study

Introduction: Hypertensive disorders of pregnancy is one of the major complications of pregnancy. It forms the fatal triad along with the haemorrhage and infection that contributes greatly to fetal and maternal morbidity and mortality.Of the various parameters used, platelet count is the most simple and cost effective method for prediction of PIH(Pregnancy induced hypertension).This study soughts the importance of platelet count as the most consistent and reliable method in early detection of PIH cases. Materials and methods: A prospective study was conducted on 164 cases and 70 controls over a period of 2 years. The bleeding time, clotting time, hemoglobin estimation and platelet count were performed.The patients were classied into mild preeclamptic, severe preeclamptic and eclamptic based on the clinical and haematological parameters. Observations: The platelet count in severe preeclampsia and eclampsia was signicantly lower than in mild pre eclampsia and controls. Thrombocytopenia was seen in total 35 cases of severe pre-eclampsia and eclampsia combined,out of which 30 (85.7%) had poor maternal outcome and 34 (97.1%) poor fetal outcome. Conclusion:The frequency of thrombocytopenia is found to be directly related with the severity of disease. So routine test like platelet count can be used as a simple and cost effective tool to monitor the progression of preeclampsia and and plan preemptive management strategies that has been proven to have a crucial role in reducing the morbidity and mortality of both mother and fetus

Genotyping-by-Sequencing (GBS) of large amphibian genomes: a comparative study of two non-model species endemic to Italy

2019 ◽  
Vol 69 (3) ◽  
pp. 307-326 ◽  
Author(s):  
Valentina Rovelli ◽  
Aritz Ruiz-González ◽  
Leonardo Vignoli ◽  
Daniele Macale ◽  
Vincenzo Buono ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Nucleotide Polymorphisms ◽  
Model Species ◽  
Amphibian Species ◽  
High Coverage ◽  
Snp Data ◽  
Cost Effective Method ◽  
Conservation Concern ◽  
Large Genomes

Abstract Next Generation Sequencing (NGS) and related technologies have revolutionized the field of conservation and population genetics, providing novel tools and the capacity to discover thousands of new Single Nucleotide Polymorphisms (SNPs) for the analysis of population parameters. However, gathering NGS data for organisms with very large genomes, such as amphibians, remains challenging because it is still unclear how the current methods perform. Here, we use the Genotyping-by-Sequencing (GBS) approach to generate SNP data for the genotyping of two amphibian species that are of conservation concern, the Sardinian brook salamander (Euproctus platycephalus) and the Italian stream frog (Rana italica). Both E. platycephalus and R. italica have very large genomes (5.53 Gb and >20 Gb, respectively) so genomic data are not available for either of them. We used 95 individual samples and one Illumina lane for each species, with an additional lane for E. platycephalus. After filtering, we obtained 961 and 854 high-coverage SNPs for E. platycephalus and R. italica, respectively. Our results suggest that GBS can serve as a reliable and cost-effective method for genotyping large amphibian genomes, including non-model species.

scholarly journals MassARRAY-based single nucleotide polymorphism analysis in breast cancer of North Indian Population.

2020 ◽  
Author(s):  
Divya Bakshi ◽  
Ashna Nagpal ◽  
Varun Sharma ◽  
Indu Sharma ◽  
Ruchi Shah ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Mutations ◽  
Cost Effective ◽  
P Value ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cost Effective Method ◽  
Common Genetic Variants ◽  
Underlying Causes

Abstract Background Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis. Methods SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study. Results The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08-2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136-5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123 -0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46-0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings. Conclusion It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.

Satellite remote sensing and the management of protected areas

2019 ◽  
pp. 79-94
Author(s):  
Nathalie Pettorelli
Keyword(s):  
Remote Sensing ◽  
Protected Areas ◽  
Satellite Data ◽  
Satellite Remote Sensing ◽  
Management Strategies ◽  
Cost Effective ◽  
Global Scale ◽  
Climatic Conditions ◽  
The Third ◽  
Cost Effective Method

This chapter explores how satellite-based approaches can be used as a cost-effective method to support monitoring efforts of protected areas, offering a cheap, verifiable way to identify areas of concern at a global scale, and to support managers in their effort to design and apply adaptive management strategies. Because protected areas can differ in terms of management needs and landscape/seascape access, the chapter starts with a quick introduction to categories of protected areas. Where to set new protected areas is one of the key questions faced by decision makers in need of meeting current biodiversity targets, and the second part of this work explores how satellite remote sensing can inform such a choice. Climatic conditions can significantly impact protected areas’ biodiversity, and the third section of this chapter briefly assesses common ways to derive information about local climatic anomalies from satellite data. The last sections of this chapter discuss the use of satellite data to assess effectiveness, and introduce the Digital Observatory of Protected Areas.

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