scholarly journals A Simple Technique for the Identification of Environmental DNA (eDNA ) in the Water Samples

2021 ◽  
pp. 77-80
Author(s):  
Chitra K. Y.
Keyword(s):  
Water Samples ◽  
Large Scale ◽  
Dna Isolation ◽  
Simple Technique ◽  
Environmental Dna ◽  
Water Bodies ◽  
Easy Method ◽  
Selective Staining ◽  
Generation Sequencing ◽  
Dark Pink

The environmental DNA(eDNA) is the DNA that is shed by the organisms in their environment by different ways viz. , mucous, faeces, skin, eggs, sperms and also when these organisms die due to natural death or disease. The eDNA will persist for several days. Identification of eDNA is a useful method of determining the organisms present in an aquatic environment like amphibians, reptiles, fishes , insects and larval forms of some of these organisms. By analysing the e-DNA it is possible to monitor the species distribution in water bodies like lakes and ponds simply by collecting a sample of water. The technique can be applied for the survey of the water bodies on a large scale for the genomic, taxonomic as well as pollutional studies. The DNA isolation procedures that are available are laborious and time consuming. Therefore, during the present study, a simplified method was devised i. e. , isolation of eDNA with ethanol after which Feulgen stain was applied to identify and confirm it, as it is an easy method before proceeding to work with the isolated eDNA using other techniqnies for further studies. The Feulgen method is used for the selective staining and the localisation of the DNA in the tissues but is adopted during the present study for the water samples for quick identification of eDNA. The smear of eDNA stained with Feulgen showed dark pink or magenta colour under the microscope where it was concentrated but stained lightly when dispersed and fragmented as observed in the present study. Further studies of the isolated eDNA are in progress in our laboratory for quantifying and sequencing eDNA using latest techniques like next generation sequencing for the identification of fish species in the lakes.

scholarly journals Determination of Potentially Harmful Element (PHE) Distribution in Water Bodies in Krugersdorp, a Mining City in the West Rand, Gauteng Province, South Africa

Minerals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1133
Author(s):  
Michael Shapi ◽  
Maryam Amra Jordaan ◽  
Andile Truelove Mbambo ◽  
Theophilus Clavell Davies ◽  
Emmanuel Chirenje ◽  
...  
Keyword(s):  
South Africa ◽  
Dissolved Oxygen ◽  
Water Samples ◽  
Large Scale ◽  
Water Bodies ◽  
Mitigation Measures ◽  
Potentially Harmful Elements ◽  
Game Reserve ◽  
The Town ◽  
Concentration Levels

The town of Krugersdorp in South Africa is the locus of an important wildlife game reserve, the Krugersdorp Game Reserve (KGR), which is juxtaposed by the (<1000 m) down-gradient of the large-scale gold mining outfits of Mintails Mogale Gold (MMG) and Rand Uranium (RU). The aim of the study was to determine the concentration levels of potentially harmful elements (PHEs) that have accumulated due to post-mining activities in the local water bodies in Krugersdorp and to use these data as a prerequisite and basis for formulation of the most appropriate remediation measures. Thirty water samples were collected and analysed in situ for: water temperature, pH, dissolved oxygen (mgl−1), dissolved oxygen (%), total dissolved solids (TDS), oxidation/reduction potential (ORP), and electrical conductivity (EC). This was later followed by laboratory analyses of aliquots of the water samples by ICP-MS for twelve PHEs whose concentration ranges were: As (0.70–32.20), Ag (0.16–105.00), Al (1.00–41.00), Co (0.07–6.16), Cr (1.60–5.00), Cu (0.80–8.00), Fe (23.00–117.00), Mn (0.14–12 255.00), Ni (0.20–7.00), Pb (0.80–6.30), V (1.90–55.20), and Zn (2.20–783.00). Areas of the town where excessive concentration levels of these elements have negatively impacted the health of its wildlife population and surrounding ecosystems are identified, and credible mitigation measures proffered.

scholarly journals Comparison of Methods for Genomic Deoxyribonucleic Acid (DNA) Extraction Suitable for Whole-Genome Genotyping in Traditional Varieties of Rice

2019 ◽  
Vol 39 (03) ◽  
Author(s):  
B Priyadharshini ◽  
M Vignesh ◽  
M Prakash ◽  
R Anandan
Keyword(s):  
Genomic Dna ◽  
Large Scale ◽  
Dna Isolation ◽  
High Throughput Analysis ◽  
Ctab Method ◽  
Maximum Quantity ◽  
Rice Genotypes ◽  
Step Over ◽  
Generation Sequencing

The utilization and conservation traditional rice genotypes have attracted global attention. Optimization of DNA isolation protocol for genetic characterization of plants is a necessary and primary step. Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research, with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated DNA is prerequisite for successful and reliable large-scale genotyping analysis. Therefore, standardization of DNA isolation is a basic requirement. Here we employed three methods of DNA isolation namely, Dellaporta, Hi-purA and modified CTAB techniques for isolation of genomic DNA from 25 indigenous rice genotypes. From the results, it was found that genomic DNA isolated by modified CTAB method to be the most appropriate for extracting high quality and maximum quantity DNA suitable for genotyping. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements and gel electrophoresis.

scholarly journals Towards Understanding the Liver Fluke Transmission Dynamics on Farms: Detection of Liver Fluke Transmitting Snail and Liver Fluke-Specific Environmental DNA in Water Samples from an Irrigated Dairy Farm in Southeast Australia

2020 ◽  
Author(s):  
Vignesh Rathinasamy ◽  
Jaclyn Swan ◽  
Lily Tran ◽  
Jane Kelley ◽  
Chris Hosking ◽  
...  
Keyword(s):  
Water Samples ◽  
Liver Fluke ◽  
Dairy Farm ◽  
Environmental Dna ◽  
Snail Host ◽  
Control Measures ◽  
Water Bodies ◽  
Proof Of Concept ◽  
Fluke Infection ◽  
Liver Fluke Infection

Abstract Background Livestock production around the world is impacted by liver fluke (Fasciola spp.) infection resulting in serious economic losses to the beef, dairy and sheep industries with significant losses of about $90 million per annum in Australia. Liver fluke infection is predominantly controlled by anthelmintic treatment and Triclabendazole (TCBZ) is usually the drug of choice due its superior efficacy against early immature, immature and adult liver fluke stages; however, the widespread emergence of TCBZ resistance in livestock threatens liver fluke control. We are in the urgent need for alternative control measures to lower the exposure of livestock to liver fluke infection which would help to preserve the usefulness of current anthelmintic treatments. Our ability to understand the prevalence of intermediate snail hosts and infective liver fluke stages in the environment is crucial to implement alternative control measures for liver fluke control. However, identification of liver fluke and snails in the environment is hampered by lack of efficient diagnostic methods. Environmental DNA (eDNA) based identification of liver fluke and the intermediate snail host in the water bodies is a promising method to identify liver fluke and snail prevalence on farms. Our aim is to provide a proof of concept to use a molecular tool (quantitative PCR) to detect and quantify eDNA of liver fluke and snail in water bodies on Victorian farming properties for potential large-scale analysis of liver fluke and snail ecology in water bodies. Methods To demonstrate the identification of liver fluke and snail in water bodies, we used a multiplex quantitative PCR assay for the independent but simultaneous detection of eDNA released from snail (Austropeplea tomentosa) a crucial intermediate snail host for liver fluke transmission in South-east Australia and free-living liver fluke stages (Fasciola hepatica). We have collected water samples from an irrigation channel over a period of 11 months in 2016 at a dairy farm located at Maffra, Victoria, South-east Australia and used water samples from selected months (February, March, May, September, October, November and December) for eDNA assay. Results The multiplex qPCR assay effectively allows for the detection and quantification of eDNA released from liver fluke life stages and snails and we observed differential levels of liver fluke and snail specific eDNA in water at the time points analysed in this study. This assay was able to detect 14 fg and 50 pg of liver fluke and snail DNA in the presence of potential inhibitors from field collected water samples. Conclusion The successful detection of eDNA specific to liver fluke and snails from the field collected water samples provides a proof of concept for the use of this method as a monitoring tool to determine the prevalence of liver fluke and liver fluke-transmitting snails in irrigation regions to allow for understanding the liver fluke transmission zones on farms to implement effective control strategies.

scholarly journals A workflow for the relative quantification of multiple fish species from oceanic water samples using environmental DNA (eDNA) to support large-scale fishery surveys

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257773
Author(s):  
Ana Ramón-Laca ◽  
Abigail Wells ◽  
Linda Park
Keyword(s):  
Dna Extraction ◽  
Marine Fish ◽  
Fish Species ◽  
Water Samples ◽  
Large Scale ◽  
Simultaneous Detection ◽  
Environmental Dna ◽  
The United States ◽  
Qpcr Assay ◽  
Multiplex Qpcr

While the number of published marine studies using environmental DNA (eDNA) has increased substantially in recent years, marine fish surveys are still scarce. To examine the potential for eDNA to support marine fisheries monitoring surveys, we optimized an eDNA isolation method, developed a multispecies assay and tested it on eDNA samples collected along the Pacific coast of the United States. Four commercial DNA extraction kits that exploit the capability of the nucleic acids binding a solid phase (two using a silica matrix and two magnetic beads) as well an organic separation method were tested. A species-specific multiplex qPCR assay was developed and tested to simultaneously target Pacific hake (Merluccius productus), Pacific lamprey (Entosphenus tridentatus) and eulachon (Thaleichthys pacificus). The specificity of the assay was tested in silico, in vitro and in natura. Environmental DNA isolation using phenol:chloroform:isoamyl purification with a phase lock was optimized and yielded the highest amount of total and target DNA and was used to extract 46 marine water samples for the detection of the three species of interest. The multiplex qPCR assay used in the quantification process was also optimized to provide convenience and accuracy. Pacific hake was present in 44% of the eDNA samples while the other two species were absent. Here, we present a complete workflow for the simultaneous detection and quantification of multiple marine fish species using eDNA. This workflow supports large-scale at-sea sampling efforts with preservation at ambient temperatures and has demonstrated DNA extraction efficiency and reliability. The multiplex qPCR assay is shown to be sensitive and specific for the purposes of simultaneously monitoring the relative abundance of multiple targeted fish species.

SITE-SPECIFIC EQUATIONS OF STATE FOR COASTAL SEA AREAS AND INLAND WATER BODIES

2017 ◽  
Author(s):  
Natalia Andrulionis ◽  
Natalia Andrulionis ◽  
Ivan Zavialov ◽  
Ivan Zavialov ◽  
Elena Kovaleva ◽  
...  
Keyword(s):  
Equation Of State ◽  
Black Sea ◽  
Water Samples ◽  
Equations Of State ◽  
Sea Water ◽  
Ionic Composition ◽  
Water Bodies ◽  
Aral Sea ◽  
The Black Sea ◽  
Coastal Sea

This article presents a new method of laboratory density determination and construction equations of state for marine waters with various ionic compositions and salinities was developed. The validation of the method was performed using the Ocean Standard Seawater and the UNESCO thermodynamic equation of state (EOS-80). Density measurements of water samples from the Aral Sea, the Black Sea and the Issyk-Kul Lake were performed using a high-precision laboratory density meter. The obtained results were compared with the density values calculated for the considered water samples by the EOS-80 equation. It was shown that difference in ionic composition between Standard Seawater and the considered water bodies results in significant inaccuracies in determination of water density using the EOS-80 equation. Basing on the laboratory measurements of density under various salinity and temperature values we constructed a new equation of state for the Aral Sea and the Black Sea water samples and estimated errors for their coefficients.

Next-Generation Sequencing: An Emerging Tool for Drug Designing

2019 ◽  
Vol 25 (31) ◽  
pp. 3350-3357 ◽  
Author(s):  
Pooja Tripathi ◽  
Jyotsna Singh ◽  
Jonathan A. Lal ◽  
Vijay Tripathi
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Massively Parallel Sequencing ◽  
Genomic Research ◽  
Biological Research ◽  
Next Generation ◽  
Human Welfare ◽  
Drug Designing ◽  
Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

scholarly journals Cyanobacterial Mats in Calcite-Precipitating Serpentinite-Hosted Alkaline Springs of the Voltri Massif, Italy

2020 ◽  
Vol 9 (1) ◽  
pp. 62
Author(s):  
Aysha Kamran ◽  
Kathrin Sauter ◽  
Andreas Reimer ◽  
Theresa Wacker ◽  
Joachim Reitner ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbial Mats ◽  
Environmental Dna ◽  
Cyanobacterial Mats ◽  
Cyanobacterial Community ◽  
Mineral Precipitation ◽  
Community Based ◽  
Specific Adaptation ◽  
Carbonate Buildups ◽  
Generation Sequencing

(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10–12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3–4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments.

scholarly journals A Short Review on Recent Advances of Hydrogel-Based Adsorbents for Heavy Metal Ions

Metals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 864
Author(s):  
Suguna Perumal ◽  
Raji Atchudan ◽  
Thomas Nesakumar Jebakumar Immanuel Edison ◽  
Rajendran Suresh Babu ◽  
Petchimuthu Karpagavinayagam ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Metal Ions ◽  
Heavy Metal Ions ◽  
Large Scale ◽  
Water Bodies ◽  
Dimensional Structure ◽  
High Porosity ◽  
Adsorption Method ◽  
Toxic Heavy Metal ◽  
Practical Applications

The growth of industry fulfills our necessity and promotes economic development. However, pollutants from such industries pollute water bodies which pose a high risk for living organisms. Thus, researchers have been urged to develop an efficient method to remove toxic heavy metal ions from water bodies. The adsorption method shows promising results for the removal of heavy metal ions and is easy to operate on a large scale, thus can be applied to practical applications. Numerous adsorbents were developed and reported, among them hydrogels, which attract great attention because of the reusability, ease of preparation, and handling. Hydrogels are generally prepared by the cross-linking of polymers that result in a three-dimensional structure, showing high porosity and high functionality. They are hydrophilic in nature because of the functional groups, and are non-toxic. Thus, this review provides various methods of hydrogel adsorbents preparation and summarizes recent progress in the use of hydrogel adsorbents for the removal of heavy metal ions. Further, the mechanism involved in the removal of heavy metal ions is briefly discussed. The most recent studies about the adsorption method for the treatment of heavy metal ions contaminated water are presented.

EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences

2021 ◽  
Author(s):  
Ting-Hsuan Wang ◽  
Cheng-Ching Huang ◽  
Jui-Hung Hung
Keyword(s):  
Open Source Software ◽  
Large Scale ◽  
A Priori ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Comparable Accuracy ◽  
Meta Analyses ◽  
Next Generation Sequencing Ngs ◽  
Adapter Trimming ◽  
Generation Sequencing

Abstract Motivation Cross-sample comparisons or large-scale meta-analyses based on the next generation sequencing (NGS) involve replicable and universal data preprocessing, including removing adapter fragments in contaminated reads (i.e. adapter trimming). While modern adapter trimmers require users to provide candidate adapter sequences for each sample, which are sometimes unavailable or falsely documented in the repositories (such as GEO or SRA), large-scale meta-analyses are therefore jeopardized by suboptimal adapter trimming. Results Here we introduce a set of fast and accurate adapter detection and trimming algorithms that entail no a priori adapter sequences. These algorithms were implemented in modern C++ with SIMD and multithreading to accelerate its speed. Our experiments and benchmarks show that the implementation (i.e. EARRINGS), without being given any hint of adapter sequences, can reach comparable accuracy and higher throughput than that of existing adapter trimmers. EARRINGS is particularly useful in meta-analyses of a large batch of datasets and can be incorporated in any sequence analysis pipelines in all scales. Availability and implementation EARRINGS is open-source software and is available at https://github.com/jhhung/EARRINGS. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0139868 ◽  
Author(s):  
Mohan A. V. S. K. Katta ◽  
Aamir W. Khan ◽  
Dadakhalandar Doddamani ◽  
Mahendar Thudi ◽  
Rajeev K. Varshney
Keyword(s):  
Quality Control ◽  
Next Generation Sequencing ◽  
Large Scale ◽  
Control Analysis ◽  
Next Generation ◽  
Quality Control Analysis ◽  
Illumina Data ◽  
Generation Sequencing
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