scholarly journals Argonaute-mediated system for supersensitive and multiplexed detection of rare mutations

2019 ◽  
Author(s):  
Qian Liu ◽  
Xiang Guo ◽  
Guanhua Xun ◽  
Zhonglei Li ◽  
Yuesheng Chong ◽  
...  
Keyword(s):  
Detection System ◽  
Cost Effective ◽  
Nucleic Acid Detection ◽  
Wild Type ◽  
High Coverage ◽  
Rare Mutation ◽  
Single Tube ◽  
Rare Mutations ◽  
Oncogenic Mutations ◽  
Single Tube Reaction

AbstractThe ability to detect rare mutations has revolutionized diagnosis and monitoring of tumors, but is limited by the shortage of sensitive, cost-effective and high coverage methods for identification of extremely low abundant mutations. Here, we establish a single-tube multiplex PCR system by employing thermophilic Argonaute-derived DNA-guided nuclease for highly efficient rare mutation detection, referred to as A-Star (Argonaute-directed specific target enrichment and detection), that combines the selective cleavage of the wild type DNA in the DNA denaturation step and the followed amplification of mutant DNA during PCR. A-Star enables easy detection and quantitation of rare mutations originally as low as 0.01% in allele frequency with a ⩾ 5500-fold efficiency. We also demonstrate the feasibility of A-Star for detecting oncogenic mutations in complex biological systems such as solid tumors tissues and blood samples. Remarkably, A-Star could achieve the detection of multiple oncogenic genes simultaneously through a simple single-tube reaction. Taken together, our work illustrates a supersensitive and rapid nucleic acid detection system, thereby extending the utility for both research and therapeutic applications.

scholarly journals Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 899
Author(s):  
Fotis Pappas ◽  
Christos Palaiokostas
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Cost Effective ◽  
Limiting Factors ◽  
Phenotypic Traits ◽  
Production Volume ◽  
High Coverage ◽  
Genomic Relationships ◽  
Low Coverage

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

scholarly journals Is an integrated model of school eye health delivery more cost-effective than a vertical model? An implementation research in Zanzibar

2021 ◽  
Vol 6 (1) ◽  
pp. e000561
Author(s):  
Ving Fai Chan ◽  
Fatma Omar ◽  
Elodie Yard ◽  
Eden Mashayo ◽  
Damaris Mulewa ◽  
...  
Keyword(s):  
Implementation Research ◽  
Cost Savings ◽  
Cost Effective ◽  
Integrated Model ◽  
Health Screening ◽  
High Coverage ◽  
Health Delivery ◽  
Screening Cost ◽  
Eye Health ◽  
The Cost

ObjectiveTo review and compare the cost-effectiveness of the integrated model (IM) and vertical model (VM) of school eye health programme in Zanzibar.Methods and analysisThis 6-month implementation research was conducted in four districts in Zanzibar. Nine and ten schools were recruited into the IM and VM, respectively. In the VM, teachers conducted eye health screening and education only while these eye health components were added to the existing school feeding programme (IM). The number of children aged 6–13 years old screened and identified was collected monthly. A review of project account records was conducted with 19 key informants. The actual costs were calculated for each cost categories, and costs per child screened and cost per child identified were compared between the two models.ResultsScreening coverage was 96% and 90% in the IM and VM with 297 children (69.5%) from the IM and 130 children (30.5%) from VM failed eye health screening. The 6-month eye health screening cost for VM and IM was US$6 728 and US$7 355. The cost per child screened for IM and VM was US$1.23 and US$1.31, and the cost per child identified was US$24.76 and US$51.75, respectively.ConclusionBoth models achieved high coverage of eye health screening with the IM being a more cost-effective school eye health delivery screening compared with VM with great opportunities for cost savings.

scholarly journals Overexpression of OsABCG48 Lowers Cadmium in Rice (Oryza sativa L.)

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 918
Author(s):  
Xingzhe Cai ◽  
Meng Wang ◽  
Yucong Jiang ◽  
Changhu Wang ◽  
David W. Ow
Keyword(s):  
Oryza Sativa L ◽  
Cost Effective ◽  
Health Issues ◽  
Rna Seq ◽  
Wild Type ◽  
Genetic Changes ◽  
Cd Accumulation ◽  
Lateral Root Development ◽  
Atp Binding Cassette Transporter ◽  
Cost Effective Approach

Cadmium pollution threatens food safety and security by causing health issues and reducing farmland availability. Engineering genetic changes in crop plants to lower Cd accumulation can be a cost-effective approach to address this problem. Previously, we reported that a rice line, 2B, which expresses a truncated version of OsO3L2 had reduced Cd accumulation throughout the plant, including in seed. However, downstream events caused by expression of this gene were not known. In this study, RNA-seq was used to identify differentially expressed genes between the wild type and 2B rice with or without Cd treatment, leading to the study of an ABC transporter gene, OsABCG48 (ATP-Binding Cassette transporter G family member 48). Heterologous expression of OsABCG48 conferred tolerance to Cd in Schizosaccharomyces pombe, Arabidopsis and rice. Moreover, overexpressing OsABCG48 in rice lowered root Cd accumulation that was associated with more extensive lateral root development. These data suggest that OsABCG48 might have applications for engineering low-Cd rice.

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 CRISPR/Cas12a-Based Ultrasensitive and Rapid Detection of JAK2 V617F Somatic Mutation in Myeloproliferative Neoplasms

Biosensors ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 247
Author(s):  
Miaomiao Chen ◽  
Chunhua Zhang ◽  
Zhiqing Hu ◽  
Zhuo Li ◽  
Menglin Li ◽  
...  
Keyword(s):  
Detection System ◽  
Myeloproliferative Neoplasms ◽  
Cost Effective ◽  
Jak2 V617f ◽  
Jak2 V617f Mutation ◽  
Minimum Detectable Concentration ◽  
Lateral Flow Strip ◽  
Whole Process ◽  
Detectable Concentration ◽  
V617f Mutation

The JAK2 V617F mutation is a major diagnostic, therapeutic, and monitoring molecular target of Philadelphia-negative myeloproliferative neoplasms (MPNs). To date, numerous methods of detecting the JAK2 V617F mutation have been reported, but there is no gold-standard diagnostic method for clinical applications. Here, we developed and validated an efficient Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated protein 12a (Cas12a)-based assay to detect the JAK2 V617F mutation. Our results showed that the sensitivity of the JAK2 V617F/Cas12a fluorescence detection system was as high as 0.01%, and the JAK2 V617F/Cas12a lateral flow strip assay could unambiguously detect as low as 0.5% of the JAK2 V617F mutation, which was much higher than the sensitivity required for clinical application. The minimum detectable concentration of genomic DNA achieved was 0.01 ng/μL (~5 aM, ~3 copies/μL). In addition, the whole process only took about 1.5 h, and the cost of an individual test was much lower than that of the current assays. Thus, our methods can be applied to detect the JAK2 V617F mutation, and they are highly sensitive, rapid, cost-effective, and convenient.

scholarly journals E46K Mutant α-Synuclein Is Degraded by Both Proteasome and Macroautophagy Pathway

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2839 ◽  
Author(s):  
Jia-qing Yan ◽  
Yu-he Yuan ◽  
Shi-feng Chu ◽  
Guo-hui Li ◽  
Nai-hong Chen
Keyword(s):  
Pc12 Cells ◽  
Degradation Kinetics ◽  
Wild Type ◽  
Genetic Studies ◽  
Protein Levels ◽  
Rare Mutations ◽  
Kinetics Of ◽  
Block Protein Synthesis ◽  
Synthesis And Degradation ◽  
Human Wild Type

Genetic studies have revealed that rare mutations and multiplications of the gene locus in α-synuclein (α-syn) are implicated in the pathogenesis of Parkinson’s disease (PD). However, the pathological effects of α-syn are still obscure. The neurotoxicity of α-syn is mainly determined by its protein levels, which depend on a balance between synthesis and degradation. Therefore, verifying the possible routes contributing to the clearance of α-syn is important for PD therapy. In this study, we established stable lines overexpressing human wild-type (WT) and E46K mutant α-syn in rat PC12 cells and investigated the degradation pathways of α-syn by using a panel of inhibitors and inducers of lysosome and proteasome function. We also monitored the degradation kinetics of α-syn by using cycloheximide to block protein synthesis. Our data showed that both proteasome and chaperon-mediated autophagy (CMA) are responsible for the degradation of the WT α-syn. Meanwhile, E46K mutant α-syn is mainly degraded by the proteasome and macroautophagy pathway. Compared with the WT protein, E46K mutant α-syn turned over more slowly in PC12 cells. In addition, overexpression of E46K mutant α-syn increased vulnerability of PC12 cells to apoptosis insults when compared with WT α-syn. Our findings may verify the possible routes contributing to the degradation of the E46K mutant α-syn.

scholarly journals Scanning single-molecule counting system for Eprobe with highly simple and effective approach

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243319
Author(s):  
Takeshi Hanami ◽  
Tetsuya Tanabe ◽  
Takuya Hanashi ◽  
Mitsushiro Yamaguchi ◽  
Hidetaka Nakata ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Detection System ◽  
Signal To Noise Ratio ◽  
High Sensitivity ◽  
Nucleic Acid Detection ◽  
Digital Measurement ◽  
Excitation Light ◽  
Target Nucleic Acid ◽  
Fluorescent Molecules

Here, we report a rapid and ultra-sensitive detection technique for fluorescent molecules called scanning single molecular counting (SSMC). The method uses a fluorescence-based digital measurement system to count single molecules in a solution. In this technique, noise is reduced by conforming the signal shape to the intensity distribution of the excitation light via a circular scan of the confocal region. This simple technique allows the fluorescent molecules to freely diffuse into the solution through the confocal region and be counted one by one and does not require statistical analysis. Using this technique, 28 to 62 aM fluorescent dye was detected through measurement for 600 s. Furthermore, we achieved a good signal-to-noise ratio (S/N = 2326) under the condition of 100 pM target nucleic acid by only mixing a hybridization-sensitive fluorescent probe, called Eprobe, into the target oligonucleotide solution. Combination of SSMC and Eprobe provides a simple, rapid, amplification-free, and high-sensitive target nucleic acid detection system. This method is promising for future applications to detect particularly difficult to design primers for amplification as miRNAs and other short oligo nucleotide biomarkers by only hybridization with high sensitivity.

scholarly journals Automated Quality Assessment of Crops Using CNN - Keras

2021 ◽  
pp. 641-645
Author(s):  
Meghashree ◽  
Alwyn Edison Mendonca ◽  
Ashika S Shetty
Keyword(s):  
Image Classification ◽  
Agricultural Production ◽  
Detection System ◽  
Cost Effective ◽  
Farming System ◽  
Modern Method ◽  
Innovative Technology ◽  
Disease Detection ◽  
Agricultural Field ◽  
Plant Leaf

Plant disease is an on-going challenge for the farmers and it has been one of the major threats to the income and the food security. This project is used to classify plant leaf into diseased and healthy leaf,to improve the quality and quantity of agricultural production in the country. The innovative technology that helps in improve the quality and quantity in the agricultural field is the smart farming system. It represented the modern method that provides cost-effective disease detection and deep learning with convolutional neural networks (CNNs) has achieved large successfulness in the categorisation of different plant leaf diseases. CNN reads a really very larger picture in a simple way. CNN nearly utilised to examine visual imagery and are frequently working behind the scenes in image classification. To extract the general features and then classify them under multiple based upon the features detected. This project will help the farmers financially in increasing the production of the crop yield as well as the overall agricultural production. The paper reviews the expected methods of plant leaf disease detection system that facilitates the advancement in agriculture. It includes various phases such as image preprocessing, image classification, feature extraction and detecting healthy or diseased.

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