scholarly journals Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms

2020 ◽  
Author(s):  
R. Rebecca Love ◽  
Marco Pombi ◽  
Moussa W. Guelbeogo ◽  
Nathan R. Campbell ◽  
Melissa T. Stephens ◽  
...  
Keyword(s):  
Anopheles Gambiae ◽  
High Throughput ◽  
Low Cost ◽  
Natural Populations ◽  
Chromosome Analysis ◽  
Special Importance ◽  
Nucleotide Polymorphisms ◽  
Molecular Genotyping ◽  
Tag Snps ◽  
Molecular Approaches

ABSTRACTChromosomal inversion polymorphisms have special importance in the Anopheles gambiae complex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. The study of inversions in natural populations is reliant on polytene chromosome analysis by expert cytogeneticists, a process that is limited by the rarity of trained specialists, low throughput, and restrictive sampling requirements. To overcome this barrier, we ascertained tag single nucleotide polymorphisms (SNPs) that are highly correlated with inversion status (inverted or standard orientation). We compared the performance of the tag SNPs using two alternative high throughput molecular genotyping approaches versus traditional cytogenetic karyotyping of the same 960 individual An. gambiae and An. coluzzii mosquitoes sampled from Burkina Faso, West Africa. We show that both molecular approaches yield comparable results, and that either one performs as well or better than cytogenetics in terms of genotyping accuracy. Given the ability of molecular genotyping approaches to be conducted at scale and at relatively low cost without restriction on mosquito sex or developmental stage, molecular genotyping via tag SNPs has the potential to revitalize research into the role of chromosomal inversions in the behavior and ongoing adaptation of An. gambiae and An. coluzzii to environmental heterogeneities.

scholarly journals Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms

2020 ◽  
Vol 10 (9) ◽  
pp. 3299-3307 ◽  
Author(s):  
R Rebecca Love ◽  
Marco Pombi ◽  
Moussa W Guelbeogo ◽  
Nathan R Campbell ◽  
Melissa T Stephens ◽  
...  
Keyword(s):  
Anopheles Gambiae ◽  
High Throughput ◽  
Natural Populations ◽  
Chromosome Analysis ◽  
Special Importance ◽  
Nucleotide Polymorphisms ◽  
Molecular Genotyping ◽  
Gambiae Complex ◽  
Tag Snps ◽  
Anopheles Gambiae Complex

Abstract Chromosomal inversion polymorphisms have special importance in the Anopheles gambiae complex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. The study of inversions in natural populations is reliant on polytene chromosome analysis by expert cytogeneticists, a process that is limited by the rarity of trained specialists, low throughput, and restrictive sampling requirements. To overcome this barrier, we ascertained tag single nucleotide polymorphisms (SNPs) that are highly correlated with inversion status (inverted or standard orientation). We compared the performance of the tag SNPs using two alternative high throughput molecular genotyping approaches vs. traditional cytogenetic karyotyping of the same 960 individual An. gambiae and An. coluzzii mosquitoes sampled from Burkina Faso, West Africa. We show that both molecular approaches yield comparable results, and that either one performs as well or better than cytogenetics in terms of genotyping accuracy. Given the ability of molecular genotyping approaches to be conducted at scale and at relatively low cost without restriction on mosquito sex or developmental stage, molecular genotyping via tag SNPs has the potential to revitalize research into the role of chromosomal inversions in the behavior and ongoing adaptation of An. gambiae and An. coluzzii to environmental heterogeneities.

scholarly journals Natural diversity of the malaria vector Anopheles gambiae

2016 ◽  
Author(s):  
Keyword(s):  
Insecticide Resistance ◽  
Anopheles Gambiae ◽  
Malaria Control ◽  
Mosquito Control ◽  
Local Population ◽  
Natural Populations ◽  
Target Space ◽  
Anopheles Coluzzii ◽  
Nucleotide Polymorphisms ◽  
Gene Drive

The sustainability of malaria control in Africa is threatened by rising levels of insecticide resistance, and new tools to prevent malaria transmission are urgently needed. To gain a better understanding of the mosquito populations that transmit malaria, we sequenced the genomes of 765 wild specimens of Anopheles gambiae and Anopheles coluzzii sampled from 15 locations across Africa. The data reveal high levels of genetic diversity, with over 50 million single nucleotide polymorphisms across the 230 Mbp genome. We observe complex patterns of population structure and marked variations in local population size, some of which may be due at least in part to malaria control interventions. Insecticide resistance genes show strong signatures of recent selection associated with multiple independent mutations spreading over large geographical distances and between species. The genetic variability of natural populations substantially reduces the target space for novel gene-drive strategies for mosquito control. This large dataset provides a foundation for tracking the emergence and spread of insecticide resistance and developing new vector control tools.

Diagnostic KASP Markers of Wheat Broad-spectrum Powdery Mildew Resistance Genes Pm21, PmV and Pm12 Developed for High Throughput Marker-assisted Selection

Plant Disease ◽  
2021 ◽  
Author(s):  
Xu Zhang ◽  
Wenrui Wang ◽  
Cheng Liu ◽  
Shanying Zhu ◽  
Huiming Gao ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
High Throughput ◽  
Broad Spectrum ◽  
Marker Assisted Selection ◽  
Low Cost ◽  
Aegilops Speltoides ◽  
Nucleotide Polymorphisms ◽  
Wheat Powdery Mildew ◽  
Kasp Marker ◽  
Kasp Markers

Wheat powdery mildew is a devastating disease that seriously threatens yield worldwide. Utilization of host resistance is considered an effective strategy to minimize powdery mildew damage. Pm21, PmV, and Pm12 confer broad-spectrum resistance to wheat powdery mildew in China, of which Pm21 and PmV are allelic genes derived from the 6VS chromosome of Dasypyrum villosum, and Pm12 is derived from the 6SS chromosome of Aegilops speltoides and most likely orthologous to the former two genes. To accurately and efficiently transfer and pyramid these genes using marker-assisted selection (MAS), distinctive single nucleotide polymorphisms (SNPs) among the exon sequences of Pm21, PmV, and Pm12 and their homologous sequences in the common wheat genome were identified and used for developing diagnostic Kompetitive Allele-Specific PCR (KASP) markers. The markers were validated in different genotypes including transgenic vectors, transgenic lines, translocation lines, resistance stocks with documented Pm genes, and in multiple susceptible cultivars without Pm genes. As a result, we initially developed a KASP marker that can simultaneously diagnose Pm21, Pm12, and PmV. Subsequently, we obtained a highly diagnostic KASP marker for each of the three genes that could distinguish among the three genes and also accurately distinguish them from other resistant stocks with documented Pm genes and from multiple susceptible genotypes. Compared with previously reported markers, the highly diagnostic KASP markers developed in this study have the advantages of low cost, easy assay, accuracy, and potentially high throughput for MAS.

scholarly journals Organ-specific, multimodal, wireless optoelectronics for high-throughput phenotyping of peripheral neural pathways

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Woo Seok Kim ◽  
Sungcheol Hong ◽  
Milenka Gamero ◽  
Vivekanand Jeevakumar ◽  
Clay M. Smithhart ◽  
...  
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Optoelectronic Device ◽  
Antenna System ◽  
Neural Pathways ◽  
Organ Specific ◽  
Coil Antenna ◽  
Sensory Fibers

AbstractThe vagus nerve supports diverse autonomic functions and behaviors important for health and survival. To understand how specific components of the vagus contribute to behaviors and long-term physiological effects, it is critical to modulate their activity with anatomical specificity in awake, freely behaving conditions using reliable methods. Here, we introduce an organ-specific scalable, multimodal, wireless optoelectronic device for precise and chronic optogenetic manipulations in vivo. When combined with an advanced, coil-antenna system and a multiplexing strategy for powering 8 individual homecages using a single RF transmitter, the proposed wireless telemetry enables low cost, high-throughput, and precise functional mapping of peripheral neural circuits, including long-term behavioral and physiological measurements. Deployment of these technologies reveals an unexpected role for stomach, non-stretch vagal sensory fibers in suppressing appetite and demonstrates the durability of the miniature wireless device inside harsh gastric conditions.

scholarly journals Design of Low-Cost and High-Strength Titanium Alloys Using Pseudo-Spinodal Mechanism through Diffusion Couple Technology and CALPHAD

Materials ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 2910
Author(s):  
Chaoyi Ding ◽  
Chun Liu ◽  
Ligang Zhang ◽  
Di Wu ◽  
Libin Liu
Keyword(s):  
Diffusion Couple ◽  
Titanium Alloys ◽  
High Throughput ◽  
Volume Fraction ◽  
Raw Materials ◽  
Low Cost ◽  
High Strength ◽  
High Yield ◽  
Α Phase ◽  
Cr System

The high cost of development and raw materials have been obstacles to the widespread use of titanium alloys. In the present study, the high-throughput experimental method of diffusion couple combined with CALPHAD calculation was used to design and prepare the low-cost and high-strength Ti-Al-Cr system titanium alloy. The results showed that ultra-fine α phase was obtained in Ti-6Al-10.9Cr alloy designed through the pseudo-spinodal mechanism, and it has a high yield strength of 1437 ± 7 MPa. Furthermore, application of the 3D strength model of Ti-6Al-xCr alloy showed that the strength of the alloy depended on the volume fraction and thickness of the α phase. The large number of α/β interfaces produced by ultra-fine α phase greatly improved the strength of the alloy but limited its ductility. Thus, we have demonstrated that the pseudo-spinodal mechanism combined with high-throughput diffusion couple technology and CALPHAD was an efficient method to design low-cost and high-strength titanium alloys.

Efficient High-throughput Techniques for the Analysis of Disease-Resistant Plant Varieties and Detection of Food Adulteration

2021 ◽  
Vol 23 ◽  
Author(s):  
Romesh Kumar Salgotra ◽  
Rafiq Ahmad Bhat ◽  
Deyue Yu ◽  
Javaid Akhter Bhat
Keyword(s):  
Multiplex Pcr ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Low Cost ◽  
Crop Improvement ◽  
Small Sample ◽  
Food Crops ◽  
Genomic Resources ◽  
Breeding Programmes ◽  
Next Generation Sequencing Ngs

Abstract: Over the past two decades, the advances in the next generation sequencing (NGS) platforms have led to the identification of numerous genes/QTLs at high-resolution for their potential use in crop improvement. The genomic resources generated through these high-throughput sequencing techniques have been efficiently used in screening of particular gene of interest particularly for numerous types of plant stresses and quality traits. Subsequently, the identified-markers linked to a particular trait have been used in marker-assisted backcross breeding (MABB) activities. Besides, these markers are also being used to catalogue the food crops for detection of adulteration to improve the quality of food. With the advancement of technologies, the genomic resources are originating with new markers; however, to use these markers efficiently in crop breeding, high-throughput techniques (HTT) such as multiplex PCR and capillary electrophoresis (CE) can be exploited. Robustness, ease of operation, good reproducibility and low cost are the main advantages of multiplex PCR and CE. The CE is capable of separating and characterizing proteins with simplicity, speed and small sample requirements. Keeping in view the availability of vast data generated through NGS techniques and development of numerous markers, there is a need to use these resources efficiently in crop improvement programmes. In summary, this review describes the use of molecular markers in the screening of resistance genes in breeding programmes and detection of adulterations in food crops using high-throughput techniques.

Abstract 12905: Gene Expression and Expression Quantifying Trait Loci Analysis of Left Atrium of Patients With Post-operative Atrial Fibrillation

Circulation ◽  
2015 ◽  
Vol 132 (suppl_3) ◽  
Author(s):  
Martin I Sigurdsson ◽  
Mahyar Heydarpour ◽  
Louis Saddic ◽  
Tzuu-Wang Chang ◽  
Stanton K Shernan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Atrial Fibrillation ◽  
Left Atrium ◽  
High Throughput ◽  
Specific Gene ◽  
Eqtl Analysis ◽  
Gene Variants ◽  
Nucleotide Polymorphisms ◽  
Novel Genes ◽  
Trait Loci

Introduction: The majority of information on the genetic background of atrial fibrillation (AF) results from genomic DNA variant analysis without consideration of tissue expression. Hypothesis: Analysis of tissue-specific gene expression in left atrium (LA) can further understanding of the molecular mechanism of identified AF risk variants, and identify novel genes and gene variants associated with AF. Methods: We isolated mRNA from samples of the LA free wall taken during mitral valve surgery in 62 Caucasian individuals. Gene expression in the LA was compared between patients who did and did not have post-operative AF (poAF) using high-throughput RNA expression. Using genotypes of 1.4 million single nucleotide polymorphisms (SNP) we performed cis expression quantifying trait loci (eQTL) analysis, correlating gene expression of each gene with the genotypes of adjacent (<1Mbp) SNPs. Results: We identified 23 differentially expressed genes in the LA of patients with poAF, including three potassium channel genes (KCNA7, KCNH8 and KCNK17). The largest expression difference was in LOC645323, a long non-coding RNA. The expression of PITX2, ZFHX3 and KCNN3, previously shown to be associated with AF, did not differ between patients with and without poAF. We identified 12,476 cis eQTL relationships in the LA, several of those included genetic regions and genes previously associated with AF. We confirmed an eQTL relationship between rs3744029 genotype and the expression of MYOZ1. Furthermore we describe a novel eQTL relationship between rs6795970 genotype and the expression of the SCN10A gene. Conclusions: We have analysed the human LA expression via high-throughput RNA sequencing, and identified novel genes and gene variants likely involved in the molecular pathophysiology of AF.

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