scholarly journals K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Peio Ziarsolo ◽  
Tomas Hasing ◽  
Rebeca Hilario ◽  
Victor Garcia-Carpintero ◽  
Jose Blanca ◽  
...  
Keyword(s):  
Cost Effective ◽  
Genetic Distances ◽  
Set Design ◽  
Special Equipment ◽  
Genetic Studies ◽  
Set Up ◽  
Genomic Regions ◽  
Biology Laboratory ◽  
Genotyping Technology ◽  
Genetic Results

Abstract Background K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. Conclusion K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.

scholarly journals K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology

2020 ◽  
Author(s):  
Peio Ziarsolo ◽  
Tomas Hasing ◽  
Rebeca Hilario ◽  
Victor Garcia-Carpintero ◽  
Jose Blanca ◽  
...  
Keyword(s):  
Cost Effective ◽  
Genetic Distances ◽  
Set Design ◽  
Special Equipment ◽  
Genetic Studies ◽  
Set Up ◽  
Genomic Regions ◽  
Biology Laboratory ◽  
Genotyping Technology ◽  
Genetic Results

AbstractK-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.

scholarly journals K-Seq, An Affordable, Reliable, and Open Klenow NGS-Based Genotyping Technology

2020 ◽  
Author(s):  
Peio Ziarsolo ◽  
Tomas Hasing ◽  
Rebeca Hilario ◽  
Victor Garcia-Carpintero ◽  
Jose Blanca ◽  
...  
Keyword(s):  
Cost Effective ◽  
Genetic Distances ◽  
Set Design ◽  
Special Equipment ◽  
Genetic Studies ◽  
Set Up ◽  
Genomic Regions ◽  
Biology Laboratory ◽  
Genotyping Technology ◽  
Genetic Results

Abstract Background K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design.Results As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%.Conclusion K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.

scholarly journals Environmental Engineering Techniques to Restore Degraded Posidonia oceanica Meadows

Water ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 661
Author(s):  
Luigi Piazzi ◽  
Stefano Acunto ◽  
Francesca Frau ◽  
Fabrizio Atzori ◽  
Maria Francesca Cinti ◽  
...  
Keyword(s):  
Large Scale ◽  
Natural Habitat ◽  
Cost Benefit ◽  
Cost Effective ◽  
Posidonia Oceanica ◽  
Environmental Engineering ◽  
Bottom Surface ◽  
Sessile Invertebrates ◽  
Set Up ◽  
Short Time

Seagrass planting techniques have shown to be an effective tool for restoring degraded meadows and ecosystem function. In the Mediterranean Sea, most restoration efforts have been addressed to the endemic seagrass Posidonia oceanica, but cost-benefit analyses have shown unpromising results. This study aimed at evaluating the effectiveness of environmental engineering techniques generally employed in terrestrial systems to restore the P. oceanica meadows: two different restoration efforts were considered, either exploring non-degradable mats or, for the first time, degradable mats. Both of them provided encouraging results, as the loss of transplanting plots was null or very low and the survival of cuttings stabilized to about 50%. Data collected are to be considered positive as the survived cuttings are enough to allow the future spread of the patches. The utilized techniques provided a cost-effective restoration tool likely affordable for large-scale projects, as the methods allowed to set up a wide bottom surface to restore in a relatively short time without any particular expensive device. Moreover, the mats, comparing with other anchoring methods, enhanced the colonization of other organisms such as macroalgae and sessile invertebrates, contributing to generate a natural habitat.

scholarly journals Sustainable Ventilation Strategies for a Medium-Sized Space with Regional Effect

2021 ◽  
Vol 13 (9) ◽  
pp. 4651
Author(s):  
Ming-Lun Alan Fong
Keyword(s):  
Life Cycle ◽  
Life Cycle Cost ◽  
Co2 Emission ◽  
High Efficiency ◽  
Regional Climate ◽  
Cost Effective ◽  
Regional Effect ◽  
Climate Conditions ◽  
Ventilation Strategies ◽  
Set Up

The analysis of ventilation strategies is fundamentally affected by regional climate conditions and local cost databases, in terms of energy consumption, CO2 emission and cost-effective analysis. A systematic approach is covered in this paper to estimate a local economic and environmental impact on a medium-sized space located in two regions during supply-and-installation and operation phases. Three ventilation strategies, including mixing ventilation (MV), displacement ventilation (DV) and stratum ventilation (SV) were applied to medium-sized air-conditioned space with this approach. The trend of the results for three ventilation systems in the life cycle assessment (LCA) and life cycle cost (LCC) analysis is SV < DV < MV. The result of CO2 emission and regional LCC shows that SV is the lowest one in both regional studies. In comparison with the Hong Kong Special Administrative Region (HKSAR) during 20 Service years, the case analysis demonstrates that the percentage differences in LCC analysis of MV, DV & SV in Guangdong are less than 20.5%, 19.4% and 18.82% respectively. Their CO2 emission of MV, DV and SV in Guangdong are more than HKSAR in 10.69%, 11.22% and 12.05%, respectively. The present study could provide information about regional effects in the LCA and LCC analysis of three ventilation strategies emissions, and thereby help set up models for decision-making on high efficiency and cost-effective ventilation strategy plans.

Cost Effective Swath Bathymetry

2001 ◽  
Vol 35 (4) ◽  
pp. 33-45 ◽  
Author(s):  
Peter Hogarth
Keyword(s):  
Processing Time ◽  
Cost Effective ◽  
High Accuracy ◽  
High Coverage ◽  
Swath Bathymetry ◽  
World Survey ◽  
Set Up ◽  
Very High ◽  
Harbor Area ◽  
Wide Swath

Between 23rd and 25th July 2001 GeoSwath, a high specification shallow water wide swath bathymetry system, was used to survey the entire Portsmouth NH Harbor area. This paper deals with the results of this survey, illustrating the potential for significant reductions in the high costs, which have prevented widespread proliferation of Swath Bathymetry systems to date. Data, including a complete DTM gridded to 1 m resolution, will be presented and discussed in detail. These results show that the system is very easy to set up and use, requires greatly reduced boat and processing time, whilst offering high accuracy and very high coverage and resolution when used in a real-world survey of a dynamic harbor environment.

scholarly journals Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Guang Yao Fan ◽  
Yi Ye ◽  
Yi Ping Hou
Keyword(s):  
Population Structure ◽  
X Chromosome ◽  
Cost Effective ◽  
Genetic Distances ◽  
Ancestry Informative Marker ◽  
Genetic Population ◽  
Single Nucleotide ◽  
Chinese Populations ◽  
Population Structures ◽  
Biogeographical Ancestry

Abstract Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification.

scholarly journals Innovation Pathways in the NHS: An Introductory Review

2021 ◽  
Author(s):  
Anmol Arora ◽  
Andrew Wright ◽  
Mark Cheng ◽  
Zahra Khwaja ◽  
Matthew Seah
Keyword(s):  
Health Care ◽  
National Health ◽  
Health Care Professionals ◽  
New Technologies ◽  
Care Delivery ◽  
Cost Effective ◽  
Care Models ◽  
Set Up ◽  
The Uk ◽  
Introductory Review

AbstractHealthcare as an industry is recognised as one of the most innovative. Despite heavy regulation, there is substantial scope for new technologies and care models to not only boost patient outcomes but to do so at reduced cost to healthcare systems and consumers. Promoting innovation within national health systems such as the National Health Service (NHS) in the United Kingdom (UK) has been set as a key target for health care professionals and policy makers. However, while the UK has a world-class biomedical research industry, several reports in the last twenty years have highlighted the difficulties faced by the NHS in encouraging and adopting innovations, with the journey from idea to implementation of health technology often taking years and being very expensive, with a high failure rate. This has led to the establishment of several innovation pathways within and around the NHS, to encourage the invention, development and implementation of cost-effective technologies that improve health care delivery. These pathways span local, regional and national health infrastructure. They operate at different stages of the innovation pipeline, with their scope and work defined by location, technology area or industry sector, based on the specific problem identified when they were set up. In this introductory review, we outline each of the major innovation pathways operating at local, regional and national levels across the NHS, including their history, governance, operating procedures and areas of expertise. The extent to which innovation pathways address current challenges faced by innovators is discussed, as well as areas for improvement and future study.

scholarly journals How to Implement Safe, Efficient and Cost-Effective SARS-CoV-2 Testing in Urban and Rural Schools within One Month

COVID ◽  
2021 ◽  
Vol 1 (4) ◽  
pp. 717-727
Author(s):  
Parastoo Kheiroddin ◽  
Magdalena Gründl ◽  
Michael Althammer ◽  
Patricia Schöberl ◽  
Linda Plail ◽  
...  
Keyword(s):  
Data Transfer ◽  
Cost Effective ◽  
Testing System ◽  
Successful Implementation ◽  
Rural And Urban ◽  
Local Involvement ◽  
Working Day ◽  
Set Up ◽  
The Individual ◽  
Time Required

(1) Background: With vaccination and new variants of SARS-CoV-2 on the horizon, efficient testing in schools may enable prevention of mass infection outbreaks, keeping schools safe places and buying time until decisions on feasibility and the necessity of vaccination in children and youth are made. We established, in the course of the WICOVIR (Where Is the COrona VIRus) study, that gargle-based pool-PCR testing offers a feasible, efficient, and safe testing system for schools in Germany when applied by central university laboratories. (2) Objectives: We evaluated whether this approach can be implemented in different rural and urban settings. (3) Methods: We assessed the arrangements required for successful implementation of the WICOVIR approach in a variety of settings in terms of transport logistics, data transfer and pre-existing laboratory set-up, as well as the time required to establish the set-up. (4) Results: We found that once regulatory issues have been overcome, all challenges pertaining to logistics, data transfer, and laboratory testing on different platforms can be solved within one month. Pooling and depooling of samples down to the individual test result were achievable within one working day in all settings. Local involvement of the community and decentralized set-ups were keys for success. (5) Conclusion: The WICOVIR gargle-based pool-PCR system is so robust and simple that it can be implemented within one month in all settings now or in future pandemics.

scholarly journals Divergência genética entre acessos de mentrasto do Estado do Tocantins através de marcadores RAPD

2013 ◽  
Vol 4 (4) ◽  
pp. 290-298
Author(s):  
Elainy Martins Oliveira ◽  
Waldesse Oliveira Junior ◽  
Jaqueline Oliveira ◽  
Henrique Guilhon De Castro
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Geographic Location ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Ageratum Conyzoides ◽  
Genetic Studies ◽  
Low Degree ◽  
Medicinal Properties ◽  
Degree Of Association

Ageratum conyzoides (Asteraceae) is known in Brazil for its medicinal properties being mainly used as painkiller and anti-inflammatory. Due to the existence of few genetic studies for this species, this work aimed to characterize the genetic diversity among nine accessions from different sites at Tocantins state, to provide information about its genetic resources. Similarity coefficients obtained varied from 48% to 80%, result of amplification of 102 fragments, of which 72 (70.5%) were polymorphic. Groupment analysis allowed the differentiation in three groups. One of them was distinguished because it presented the highest similarity among all, being composed by ANA and NAT (80% similarity). In general, these data showed there is low degree of association between the geographic location of the accessions and the genetic distances. So, the collected accession ns in Tocantins state presented considerable genetic variability and the efficiency of RAPD markers for such characterization was here proven.

scholarly journals Energy Efficient Opportunistic Sensing Management in Fog Cloud Environment

2021 ◽  
Vol 10 (10) ◽  
pp. 20-26
Author(s):  
Anju Gupta ◽  
R K Bathla
Keyword(s):  
Energy Efficient ◽  
Cost Effective ◽  
Sensory Data ◽  
Computing Platform ◽  
Opportunistic Sensing ◽  
Battery Power ◽  
Wide Range ◽  
Sensor Cloud ◽  
Set Up ◽  
Potential Challenge

With so many people now wearing mobile devices with sensors (such as smartphones), utilizing the immense capabilities of these business mobility goods has become a prospective skill to significant behavioural and ecological sensors. A potential challenge for pervasive context assessment is opportunistic sensing, has been effectively used to a wide range of applications. The sensor cloud combines cloud technology with a wireless sensor, resulting in a scalable and cost-effective computing platform for real-time applications. Because the sensor's battery power is limited and the data centre’s servers consume a significant amount of energy to supply storage, a sensor cloud must be energy efficient. This study provides a Fog-based semantic for enabling these kinds of technologies quickly and successfully. The suggested structure is comprised of fundamental algorithms to help set up and coordinate the fog sensing jobs. It creates effective multihop routes for coordinating relevant devices and transporting acquired sensory data to fog sinks. It was claimed that energy-efficient sensor cloud approaches were categorized into different groups and that each technology was examined using numerous characteristics. The outcomes of a series of thorough test simulation in NS3 to define the practicality of the created console, as well as the proportion of each parameter utilized for each technology, are computed.

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