scholarly journals An ultra high-density Arabidopsis thaliana crossover map that refines the influences of structural variation and epigenetic features

2019 ◽  
Author(s):  
Beth A. Rowan ◽  
Darren Heavens ◽  
Tatiana R. Feuerborn ◽  
Andrew J. Tock ◽  
Ian R. Henderson ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Gene Clusters ◽  
High Density ◽  
Small Scale ◽  
Disease Resistance Gene ◽  
Narrow Region ◽  
Cost Effective Method ◽  
Flanking Regions

AbstractMany environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of over 17,000 COs between the Col-0 and Ler accessions of Arabidopsis thaliana. COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders, and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large and small-scale SVs, representing influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.

scholarly journals High throughput sequencing of multiple amplicons for barcoding and integrative taxonomy

2016 ◽  
Author(s):  
Perrine Cruaud ◽  
Jean-Yves Rasplus ◽  
Lillian Jennifer Rodriguez ◽  
Astrid Cruaud
Keyword(s):  
Quality Control ◽  
Sanger Sequencing ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Integrative Taxonomy ◽  
Miseq Sequencing ◽  
Dna Taxonomy ◽  
Cost Effective Method ◽  
Diversity Assessment ◽  
Pcr Conditions

ABSTRACTUntil now, the potential of NGS has been seldom realised for the construction of barcode reference libraries. Using a two-step PCR approach and MiSeq sequencing, we tested a cost-effective method and developed a custom workflow to simultaneously sequence multiple markers (COI, Cytb and EF, altogether 2kb) from hundreds of specimens. Interestingly, primers and PCR conditions used for Sanger sequencing did not require optimisation to construct MiSeq library. After completion of quality controls, 87% of the species and 76% of the specimens had valid sequences for the three markers. Nine specimens (3%) exhibited two divergent (up to 10%) sequence clusters. In 95% of the species, MiSeq and Sanger sequences obtained from the same samplings were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into two divergent groups (>7%) on the final trees (Sanger + MiSeq). These problematic cases are difficult to explain but may represent coding NUMTS or heteroplasms. These results highlight the importance of performing quality control steps, working with expert taxonomists and using more than one marker for DNA-taxonomy or species diversity assessment. The power and simplicity of this method appears promising to build on existing experience, tools and resources while taking advantage of NGS.

scholarly journals Algal Biofuels: A Credible Prospective?

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Bhavish Patel ◽  
Bojan Tamburic ◽  
Fessehaye W. Zemichael ◽  
Pongsathorn Dechatiwongse ◽  
Klaus Hellgardt
Keyword(s):  
Energy Use ◽  
Primary Source ◽  
Cost Effective ◽  
Small Scale ◽  
Algal Biofuels ◽  
Algae Cultivation ◽  
Cost Effective Method ◽  
Near Future ◽  
Technological Integration ◽  
By Products

Global energy use has reached unprecedented levels and increasing human population, technological integration, and improving lifestyle will further fuel this demand. Fossil fuel based energy is our primary source of energy and it will remain to be in the near future. The effects from the use of this finite resource on the fate of our planet are only now being understood and recognised in the form of climate change. Renewable energy systems may offer a credible alternative to help maintain our lifestyle sustainably and there are a range of options that can be pursued. Biofuels, especially algae based, have gained significant publicity recently. The concept of making biofuels, biochemicals, and by-products works well theoretically and at small scale, but when considering scaleup, many solutions can be dismissed on either economical or ecological grounds. Even if an (cost-) effective method for algae cultivation is developed, other input parameters, namely, fixed nitrogen and fresh water, remain to be addressed. Furthermore, current processing routes for harvesting, drying, and extraction for conversion to subsequent products are economically unattractive. The strategies employed for various algae-based fuels are identified and it is suggested that ultimately only an integrated algal biorefinery concept may be the way forward.

scholarly journals  Pesticide use in vegetable production: A survey of Vietnamese farmers’ knowledge

2018 ◽  
Vol 54 (No. 4) ◽  
pp. 203-214 ◽  
Author(s):  
Nguyen Thanh Mai ◽  
Le Nga Thi Thanh ◽  
Havukainen Jouni ◽  
Hannaway David B
Keyword(s):  
Food Safety ◽  
Agricultural Soils ◽  
Cost Effective ◽  
Small Scale ◽  
Vegetable Production ◽  
Training And Education ◽  
Attitudes And Practices ◽  
Application Rates ◽  
Cost Effective Method

Concerns about inappropriate storage, application rates, and disposal practices of pesticides prompted this case study of Vietnamese farmers’ knowledge, attitudes, and practices. 128 small-scale vegetable growers in Lam Dong Province were included in field surveys, questionnaires, and interviews. Farmers reported inappropriate mixing of pesticides and disposal methods. Many also reported ill-timed applications posing potential hazards to the human health and environment. Improved training and monitoring of pesticide residues on foodstuffs and in agricultural soils and community water supplies are needed to ensure safe farmer practices. Community-based training and education, jointly funded by local, national, and international agricultural production and food safety groups, would be a cost-effective method of minimising pesticide applications and improving food safety.

Methods for accurate measurements of small fixed wing UAV inertial properties

2016 ◽  
Vol 120 (1233) ◽  
pp. 1785-1811 ◽  
Author(s):  
K. Lehmkühler ◽  
K.C. Wong ◽  
D. Verstraete
Keyword(s):  
Degrees Of Freedom ◽  
Wind Tunnel Test ◽  
Cost Effective ◽  
Mass Effect ◽  
Small Scale ◽  
Pendulum Motion ◽  
Single Degree Of Freedom ◽  
Cost Effective Method ◽  
Aerial Vehicle

ABSTRACTTwo methods have been compared for the determination of the inertial properties of a small, fixed-wing un-manned aerial vehicle. The first method uses the standard single degree of freedom pendulum method and the second method implements a novel, potentially easier, 3 degrees of freedom pendulum method, which yields the entire inertia tensor from a single swing test. Both methods are using system identification of the pendulum motion to estimate the inertial properties. Substantial corrections (up to 25%) have to be applied to the experimental results. These corrections are caused by the acceleration of the pendulum being immersed in the surrounding air, also called the added mass effect. It has been found that the methods presented in literature to determine the corrections for full-scale aircraft do not give the correct results for the small-scale un-manned aerial vehicle under consideration. The only feasible, cost-effective method to generate these corrections utilise swing tests with a geometrically similar object of known inertial properties. It has also been found that the corrections are unique with respect to the experimental methods. Several benchmarking methods, including the innovative use of static and dynamic wind-tunnel test data, give high confidence in the results.

scholarly journals A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kimberly R. Andrews ◽  
Samuel S. Hunter ◽  
Brandi K. Torrevillas ◽  
Nora Céspedes ◽  
Sarah M. Garrison ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
High Density ◽  
Snp Genotyping ◽  
Mouse Strains ◽  
Bioinformatic Pipeline ◽  
Genotyping Assay ◽  
Sequencing Technologies ◽  
Diagnostic Snps

Abstract Background Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array technologies, and a different assay must be developed for each backcross strain combination. “Next generation” high throughput DNA sequencing technologies have the potential to decrease cost and increase flexibility and power of speed congenics, but thus far have not been utilized for this purpose. Results We took advantage of the power of high throughput sequencing technologies to develop a cost-effective, high-density SNP genotyping assay that can be used across many combinations of backcross strains. The assay surveys 1640 genome-wide SNPs known to be polymorphic across > 100 mouse strains, with an expected average of 549 ± 136 SD diagnostic SNPs between each pair of strains. We demonstrated that the assay has a high density of diagnostic SNPs for backcrossing the BALB/c strain into the C57BL/6J strain (807–819 SNPs), and a sufficient density of diagnostic SNPs for backcrossing the closely related substrains C57BL/6N and C57BL/6J (123–139 SNPs). Furthermore, the assay can easily be modified to include additional diagnostic SNPs for backcrossing other closely related substrains. We also developed a bioinformatic pipeline for SNP genotyping and calculating the percentage of alleles that match the backcross recipient strain for each sample; this information can be used to guide the selection of individuals for the next backcross, and to assess whether individuals have become congenic. We demonstrated the effectiveness of the assay and bioinformatic pipeline with a backcross experiment of BALB/c-IL4/IL13 into C57BL/6J; after six generations of backcrosses, offspring were up to 99.8% congenic. Conclusions The SNP genotyping assay and bioinformatic pipeline developed here present a valuable tool for increasing the power and decreasing the cost of many studies that depend on speed congenics. The assay is highly flexible and can be used for combinations of strains that are commonly used for speed congenics. The assay could also be used for other techniques including QTL mapping, standard F2 crosses, ancestry analysis, and forensics.

scholarly journals Some explorations of the life history ratios to describe length composition, spawning-per-recruit, and the spawning potential ratio

2014 ◽  
Vol 72 (1) ◽  
pp. 204-216 ◽  
Author(s):  
Adrian Hordyk ◽  
Kotaro Ono ◽  
Keith Sainsbury ◽  
Neil Loneragan ◽  
Jeremy Prince
Keyword(s):  
Life History ◽  
Growth Parameters ◽  
Estimation Method ◽  
Cost Effective ◽  
Analytical Models ◽  
Small Scale ◽  
Natural Mortality ◽  
Von Bertalanffy ◽  
Cost Effective Method ◽  
Spawning Potential Ratio

Abstract Evaluating the status of data-poor fish stocks is often limited by incomplete knowledge of the basic life history parameters: the natural mortality rate (M), the von Bertalanffy growth parameters (L∞ and k), and the length at maturity (Lm). A common approach to estimate these individual parameters has been to use the Beverton–Holt life history invariants, the ratios M/k and Lm/L∞, especially for estimating M. In this study, we assumed no knowledge of the individual parameters, and explored how the information on life history strategy contained in these ratios can be applied to assessing data-poor stocks. We developed analytical models to develop a relationship between M/k and the von Bertalanffy growth curve, and demonstrate the link between the life history ratios and yield- and spawning-per-recruit. We further developed the previously recognized relationship between M/k and yield- and spawning-per-recruit by using information on Lm/L∞, knife-edge selectivity (Lc/L∞), and the ratio of fishing to natural mortality (F/M), to demonstrate the link between an exploited stock's expected length composition, and its spawning potential ratio (SPR), an internationally recognized measurement of stock status. Variation in length-at-age and logistic selectivity patterns were incorporated in the model to demonstrate how SPR can be calculated from the observed size composition of the catch; an advance which has potential as a cost-effective method for assessing data-poor stocks. A companion paper investigates the effects of deviations in the main assumptions of the model on the application of the analytical models developed in this study as a cost-effective method for stock assessment [Hordyk, A. R., Ono, K., Valencia, S., Loneragan, N. R., and Prince, J. D. 2015. A novel length based empirical estimation method of spawning potential ratio (SPR), and tests of its performance, for small-scale, data-poor fisheries. ICES Journal of Marine Science, 72: 217–231].

Prediction of Liner Wrinkling During High Strain Bending of Mechanically Lined Pipe

2019 ◽  
Author(s):  
Aurélien Pépin ◽  
Tomasz Tkaczyk ◽  
Michael Martinez ◽  
Noel O’Dowd ◽  
Kamran Nikbin
Keyword(s):  
High Strain ◽  
Cost Effective ◽  
Elevated Pressure ◽  
Numerical Approach ◽  
Mechanical Tests ◽  
Tensile Behaviour ◽  
Small Scale ◽  
Cost Effective Method ◽  
Metal Pipes ◽  
Corrosion Resistant Alloy

Abstract A high demand for transport of corrosive fluids subsea has generated interest in solid corrosion resistant alloy (CRA) and bi-metal pipes. Bi-metal pipes, including hot-roll bonded (HRB) clad and mechanically lined pipes (MLP), are made of a carbon steel (CS) pipe lined with a CRA layer. Mechanically lined pipes, where the CRA liner is held inside the host pipe by means of an interference fit, offer shorter lead times and are considerably more economical than equivalent solid CRA and HRB clad pipes with a metallurgical bond between CS and CRA layers. Reel-lay is a cost-effective method for installing subsea pipelines up to 18” (457.2 mm) in diameter. However, plastic straining associated with reeling may trigger wrinkling of the CRA liner. Two approaches for safe installation of reeled MLPs have therefore been proposed: pressurised and non-pressurised reeling. This paper focuses on reel-lay installation at atmospheric pressure. Nevertheless, the numerical analysis framework presented is also applicable to MLPs installed at elevated pressure in a scenario where they are subjected to bending after being depressurised. Small-scale mechanical tests were carried out to assess the effect of manufacturing and cyclic plastic bending on the tensile behaviour of the CRA liner. After full-scale bending trials had been undertaken, they were simulated numerically to demonstrate the suitability of the proposed numerical approach for predicting liner separation from the host pipe and subsequent wrinkling during high strain bending. To improve ovality prediction, which governs liner separation and wrinkling, the authors developed an advanced metal plasticity model.

Sequence capture using PCR-generated probes: a cost-effective method of targeted high-throughput sequencing for nonmodel organisms

2014 ◽  
pp. n/a-n/a ◽  
Author(s):  
Joshua V. Peñalba ◽  
Lydia L. Smith ◽  
Maria A. Tonione ◽  
Chodon Sass ◽  
Sarah M. Hykin ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Sequence Capture ◽  
Cost Effective Method

scholarly journals CRISPR-finder: A high throughput and cost-effective method to identify successfully edited Arabidopsis thaliana individuals

2021 ◽  
Vol 2 ◽  
Author(s):  
Efthymia Symeonidi ◽  
Julian Regalado ◽  
Rebecca Schwab ◽  
Detlef Weigel
Keyword(s):  
Arabidopsis Thaliana ◽  
Salicylic Acid ◽  
High Throughput ◽  
Cost Effective ◽  
Repair Process ◽  
Wild Type ◽  
Isochorismate Synthase ◽  
Guide Rna ◽  
Cost Effective Method ◽  
Variable Efficiency

Abstract Genome editing with the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR associated protein) system allows mutagenesis of a targeted region of the genome using a Cas endonuclease and an artificial guide RNA. Both because of variable efficiency with which such mutations arise and because the repair process produces a spectrum of mutations, one needs to ascertain the genome sequence at the targeted locus for many individuals that have been subjected to mutagenesis. We provide a complete protocol for the generation of amplicons up until the identification of the exact mutations in the targeted region. CRISPR-finder can be used to process thousands of individuals in a single sequencing run. We successfully identified an ISOCHORISMATE SYNTHASE 1 mutant line in which the production of salicylic acid was impaired compared to the wild type, as expected. These features establish CRISPR-finder as a high-throughput, cost-effective and efficient genotyping method of individuals whose genomes have been targeted using the CRISPR/Cas9 system.

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