scholarly journals Genetic Mapping in Autohexaploid Sweet Potato with Low-coverage NGS-based Genotyping Data

2019 ◽  
Author(s):  
Eiji Yamamoto ◽  
Kenta Shirasawa ◽  
Takumi Kimura ◽  
Yuki Monden ◽  
Masaru Tanaka ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Sweet Potato ◽  
Genetic Markers ◽  
Cost Effective ◽  
Read Depth ◽  
Sequencing Data ◽  
Single Experiment ◽  
Association Analyses ◽  
Effective Manner ◽  
Allele Dosage

AbstractNext-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, the benefits of NGS-based methods are limited in autopolyploids as their genetic segregation mode is complex. Moreover, autopolyploids have large genomes and require abundant sequencing data to obtain sufficient genetic markers. There are several methods for genetic mapping in autopolyploids. These approaches may be impractical for plant genetic studies as they require large amounts of data and are not cost-effective. In the present study, we propose a simple strategy for genetic mapping of polyploids in a cost-effective manner. The allele dosage probabilities calculated from NGS read counts were used in association analyses to detect loci associated with specific phenotypes. This approach is superior to conventional methods of determining allele dosage, which usually result in the filtering of many genetic markers with low read depth. The validity of the strategy was demonstrated using real phenotype data from autohexaploid sweet potato populations to detect genetic loci for both qualitative and quantitative traits, the latter of which required the use of allele dosage probabilities for the detection of loci. We demonstrate that this proposed method is useful with reasonable NGS read counts.

scholarly journals Dual indexed design of in-Drop single-cell RNA-seq libraries improves sequencing quality and throughput

2019 ◽  
Author(s):  
Austin N. Southard Smith ◽  
Alan J. Simmons ◽  
Bob Chen ◽  
Angela L. Jones ◽  
Marisol A. Ramirez Solano ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Cost Effective ◽  
Quality Data ◽  
Sequencing Data ◽  
High Quality ◽  
High Data ◽  
Sequencing Technologies ◽  
Effective Manner ◽  
Sequencing Quality

AbstractThe increasing demand of single-cell RNA-sequencing (scRNA-seq) experiments, such as the number of experiments and cells queried per experiment, necessitates higher sequencing depth coupled to high data quality. New high-throughput sequencers, such as the Illumina NovaSeq 6000, enables this demand to be filled in a cost-effective manner. However, current scRNA-seq library designs present compatibility challenges with newer sequencing technologies, such as index-hopping, and their ability to generate high quality data has yet to be systematically evaluated. Here, we engineered a new dual-indexed library structure, called TruDrop, on top of the inDrop scRNA-seq platform to solve these compatibility challenges, such that TruDrop libraries and standard Illumina libraries can be sequenced alongside each other on the NovaSeq. We overcame the index-hopping issue, demonstrated significant improvements in base-calling accuracy, and provided an example of multiplexing twenty-four scRNA-seq libraries simultaneously. We showed favorable comparisons in transcriptional diversity of TruDrop compared with prior library structures. Our approach enables cost-effective, high throughput generation of sequencing data with high quality, which should enable more routine use of scRNA-seq technologies.

scholarly journals Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data

2020 ◽  
Vol 10 (8) ◽  
pp. 2661-2670 ◽  
Author(s):  
Eiji Yamamoto ◽  
Kenta Shirasawa ◽  
Takumi Kimura ◽  
Yuki Monden ◽  
Masaru Tanaka ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Sweet Potato ◽  
Ipomoea Batatas ◽  
Large Scale ◽  
Agronomic Traits ◽  
Estimation Accuracy ◽  
Detection Power ◽  
Allele Dosage ◽  
Low Coverage ◽  
Ngs Data

Next-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, for high precision genetic analysis, the complicated genetic segregation mode in polyploid organisms requires high-coverage NGS data and elaborate analytical algorithms. In the present study, we propose a simple strategy for the genetic mapping of polyploids using low-coverage NGS data. The validity of the strategy was investigated using simulated data. Previous studies indicated that accurate allele dosage estimation from low-coverage NGS data (read depth < 40) is difficult. Therefore, we used allele dosage probabilities calculated from read counts in association analyses to detect loci associated with phenotypic variations. The allele dosage probabilities showed significant detection power, although higher allele dosage estimation accuracy resulted in higher detection power. On the contrary, differences in the segregation patterns between the marker and causal genes resulted in a drastic decrease in detection power even if the marker and casual genes were in complete linkage and the allele dosage estimation was accurate. These results indicated that the use of a larger number of markers is advantageous, even if the accuracy of allele dosage estimation is low. Finally, we applied the strategy for the genetic mapping of autohexaploid sweet potato (Ipomoea batatas) populations to detect loci associated with agronomic traits. Our strategy could constitute a cost-effective approach for preliminary experiments done performed to large-scale studies.

Strategic planning in grassland farming: Principles andapplications

1997 ◽  
pp. 191-197
Author(s):  
W.J. Parker ◽  
N.M. Shadbolt ◽  
D.I. Gray
Keyword(s):  
Strategic Planning ◽  
Performance Indicators ◽  
Cost Effective ◽  
Key Performance Indicators ◽  
Strategic Plans ◽  
Effective Manner ◽  
Farm Business ◽  
Pastoral Farming ◽  
Financial Environment

Three levels of planning can be distinguished in grassland farming: strategic, tactical and operational. The purpose of strategic planning is to achieve a sustainable long-term fit of the farm business with its physical, social and financial environment. In pastoral farming, this essentially means developing plans that maximise and best match pasture growth with animal demand, while generating sufficient income to maintain or enhance farm resources and improvements, and attain personal and financial goals. Strategic plans relate to the whole farm business and are focused on the means to achieve future needs. They should be routinely (at least annually) reviewed and monitored for effectiveness through key performance indicators (e.g., Economic Farm Surplus) that enable progress toward goals to be measured in a timely and cost-effective manner. Failure to link strategy with control is likely to result in unfulfilled plans. Keywords: management, performance

scholarly journals Novel Regeneration Approach for Creating Reusable FO-SPR Probes with NTA Surface Chemistry

Nanomaterials ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 186
Author(s):  
Jia-Huan Qu ◽  
Karen Leirs ◽  
Remei Escudero ◽  
Žiga Strmšek ◽  
Roman Jerala ◽  
...  
Keyword(s):  
Surface Chemistry ◽  
Fluorescent Protein ◽  
Cost Effective ◽  
Nitrilotriacetic Acid ◽  
Antibody Fragments ◽  
Rapid Screening ◽  
Red Fluorescent Protein ◽  
Effective Manner ◽  
Surface Regeneration ◽  
Sensitivity Specificity

To date, surface plasmon resonance (SPR) biosensors have been exploited in numerous different contexts while continuously pushing boundaries in terms of improved sensitivity, specificity, portability and reusability. The latter has attracted attention as a viable alternative to disposable biosensors, also offering prospects for rapid screening of biomolecules or biomolecular interactions. In this context here, we developed an approach to successfully regenerate a fiber-optic (FO)-SPR surface when utilizing cobalt (II)-nitrilotriacetic acid (NTA) surface chemistry. To achieve this, we tested multiple regeneration conditions that can disrupt the NTA chelate on a surface fully saturated with His6-tagged antibody fragments (scFv-33H1F7) over ten regeneration cycles. The best surface regeneration was obtained when combining 100 mM EDTA, 500 mM imidazole and 0.5% SDS at pH 8.0 for 1 min with shaking at 150 rpm followed by washing with 0.5 M NaOH for 3 min. The true versatility of the established approach was proven by regenerating the NTA surface for ten cycles with three other model system bioreceptors, different in their size and structure: His6-tagged SARS-CoV-2 spike fragment (receptor binding domain, RBD), a red fluorescent protein (RFP) and protein origami carrying 4 RFPs (Tet12SN-RRRR). Enabling the removal of His6-tagged bioreceptors from NTA surfaces in a fast and cost-effective manner can have broad applications, spanning from the development of biosensors and various biopharmaceutical analyses to the synthesis of novel biomaterials.

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals Postnatal management of children with antenatal hydronephrosis

2020 ◽  
Vol 26 (1) ◽  
Author(s):  
Mohammed S. ElSheemy
Keyword(s):  
Renal Function ◽  
Urinary Tract Obstruction ◽  
Cost Effective ◽  
Voiding Cystourethrography ◽  
Main Body ◽  
Antenatal Hydronephrosis ◽  
Postnatal Management ◽  
Effective Manner ◽  
Lower Urinary Tract Obstruction

Abstract Background Postnatal management of infants with antenatal hydronephrosis (ANH) is still one of the most controversial issues. The majority of infants with ANH are asymptomatic with only few children who develop renal insufficiency. Thus, the biggest challenge for pediatric urologists is to distinguish children who will require further investigations and possible intervention prior to the development of symptoms, complications or renal damage in a cost effective manner without exposing them to the hazards of unnecessary investigations. Main body In this review article, literature on ANH were reviewed to present the current suggestions, recommendations, guidelines and their rational for postnatal management of ANH. It is agreed that a large portion of infants with ANH will improve; thus, the protocol of management is based mainly on observation and follow-up by ultrasound to detect either resolution, stabilization or worsening of hydronephrosis. The first 2 years of life are critical for this follow-up as the final picture is mostly reached during that period. Advanced imaging using voiding cystourethrography or renal scintigraphy are required for children at risk. Then, surgical intervention is selected only for a subgroup of these infants who showed worsening of hydronephrosis or renal function. Conclusions The protocol of management is based mainly on observation and follow-up by US to detect either resolution, stabilization or worsening of hydronephrosis. Postnatal evaluation should be performed for any neonate with a history ANH at any stage during pregnancy even if it was resolved during third trimester. Exclusion of UTI should be performed by urinalysis for all cases followed by urine culture if indicated. Serum creatinine should be performed especially in patients with bilateral ANH. US is the initial standard diagnostic imaging technique. Other imaging modalities like VCUG and nuclear renal scans may be required according to the results of the US evaluation. The most important items in decision making are the presence of bilateral or unilateral hydronephrosis, presence or absence of hydroureter, presence of lower urinary tract obstruction and degree of hydronephrosis on the initial postnatal US. Then an intervention is selected only for a subgroup of these patients who showed deterioration in renal function or degree of hydronephrosis or were complicated by UTIs. All these recommendations are based on the available literature. However, management of ANH is still a controversial issue due to lack of high evidence-based recommendations. Randomised controlled studies are still needed to provide a high level evidence for different aspects of management.

scholarly journals An Artificial-Intelligence-Discovered Functional Ingredient, NRT_N0G5IJ, Derived from Pisum sativum, Decreases HbA1c in a Prediabetic Population

Nutrients ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1635
Author(s):  
Sweeny Chauhan ◽  
Alish Kerr ◽  
Brian Keogh ◽  
Stephanie Nolan ◽  
Rory Casey ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Pisum Sativum ◽  
Cost Effective ◽  
Glycated Haemoglobin ◽  
Glucose Regulation ◽  
Functional Ingredient ◽  
Effective Manner ◽  
Human Skeletal Muscle Cells ◽  
Increased Risk

The prevalence of prediabetes is rapidly increasing, and this can lead to an increased risk for individuals to develop type 2 diabetes and associated diseases. Therefore, it is necessary to develop nutritional strategies to maintain healthy glucose levels and prevent glucose metabolism dysregulation in the general population. Functional ingredients offer great potential for the prevention of various health conditions, including blood glucose regulation, in a cost-effective manner. Using an artificial intelligence (AI) approach, a functional ingredient, NRT_N0G5IJ, was predicted and produced from Pisum sativum (pea) protein by hydrolysis and then validated. Treatment of human skeletal muscle cells with NRT_N0G5IJ significantly increased glucose uptake, indicating efficacy of this ingredient in vitro. When db/db diabetic mice were treated with NRT_N0G5IJ, we observed a significant reduction in glycated haemoglobin (HbA1c) levels and a concomitant benefit on fasting glucose. A pilot double-blinded, placebo controlled human trial in a population of healthy individuals with elevated HbA1c (5.6% to 6.4%) showed that HbA1c percentage was significantly reduced when NRT_N0G5IJ was supplemented in the diet over a 12-week period. Here, we provide evidence of an AI approach to discovery and demonstrate that a functional ingredient identified using this technology could be used as a supplement to maintain healthy glucose regulation.

scholarly journals Spectroscopic detection of forest diseases: a review (1970–2020)

2021 ◽  
Author(s):  
Lorenzo Cotrozzi
Keyword(s):  
Early Detection ◽  
Optical Sensors ◽  
Near Infrared ◽  
Sustainable Forest Management ◽  
Visible Spectrum ◽  
Cost Effective ◽  
Infrared Region ◽  
Forest Disturbances ◽  
Effective Manner ◽  
Forest Diseases

AbstractSustainable forest management is essential to confront the detrimental impacts of diseases on forest ecosystems. This review highlights the potential of vegetation spectroscopy in improving the feasibility of assessing forest disturbances induced by diseases in a timely and cost-effective manner. The basic concepts of vegetation spectroscopy and its application in phytopathology are first outlined then the literature on the topic is discussed. Using several optical sensors from leaf to landscape-level, a number of forest diseases characterized by variable pathogenic processes have been detected, identified and quantified in many country sites worldwide. Overall, these reviewed studies have pointed out the green and red regions of the visible spectrum, the red-edge and the early near-infrared as the spectral regions most sensitive to the disease development as they are mostly related to chlorophyll changes and symptom development. Late disease conditions particularly affect the shortwave-infrared region, mostly related to water content. This review also highlights some major issues to be addressed such as the need to explore other major forest diseases and geographic areas, to further develop hyperspectral sensors for early detection and discrimination of forest disturbances, to improve devices for remote sensing, to implement long-term monitoring, and to advance algorithms for exploitation of spectral data. Achieving of these goals will enhance the capability of vegetation spectroscopy in early detection of forest stress and in managing forest diseases.

scholarly journals To Trade or Not To Trade? Criteria for Applying Cap and Trade

2001 ◽  
Vol 1 ◽  
pp. 953-957 ◽  
Author(s):  
Stephanie Benkovic ◽  
Joseph Kruger
Keyword(s):  
Emissions Trading ◽  
Environmental Problem ◽  
Cost Effective ◽  
Cap And Trade ◽  
Policy Tool ◽  
Effective Manner ◽  
Effective Policy ◽  
Foreign Governments ◽  
Trading Program ◽  
The U.S

The use of emissions trading (cap and trade) is gaining worldwide recognition as an extremely effective policy tool. The U.S. Sulfur Dioxide (SO2) Emissions Trading Program has achieved an unprecedented level of environmental protection in a cost-effective manner. The successful results of the program have led domestic and foreign governments to consider the application of cap and trade to address other air quality issues. Certain analyses are particularly important in determining whether or not cap and trade is an appropriate policy tool. This paper offers a set of questions that can be used as criteria for determining whether or not cap and trade is the preferred policy approach to an environmental problem.

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