Dynamics of GB-speckles with a small number of scatterers

2021 ◽  
Vol 19 (1) ◽  
pp. 015601
Author(s):  
Sergey Ulyanov ◽  
Onega Ulianova ◽  
Yury Saltykov ◽  
Sergey Zaytsev ◽  
Alexander Ulyanov ◽  
...  
Keyword(s):  
Rough Surfaces ◽  
Nucleotide Sequences ◽  
Chlamydia Psittaci ◽  
Statistical Characteristics ◽  
Gaussian Beams ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Individual Single Nucleotide Polymorphism ◽  
The Difference ◽  
A New Technique

Abstract A method for generating dynamic GB-speckles, formed during diffraction of focused Gaussian beams by moving virtual rough surfaces, obtained for two nucleotide sequences (the ompA genes of the Chlamydia psittaci GR9 and AMK-16 strains), is proposed. The statistical characteristics of the 1st- and 2nd-order statistics of GB-speckles, formed at a small number of scattering events, are studied. The difference in the manifestation of the Doppler effect in the dynamics of GB-speckles and for speckles, formed with a small number of scatterers, produced by light diffraction on physically-existing rough surfaces and in scattering micro-streams is revealed. The problems of interference of dynamic GB-speckles are considered. A new technique for detecting individual single nucleotide polymorphism in nucleotide sequences using the interference of dynamic GB-speckles is proposed.

scholarly journals Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Hongwei Li ◽  
Bo Zhu ◽  
Ling Xu ◽  
Zezhao Wang ◽  
Lei Xu ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genomic Prediction ◽  
Whole Genome Sequence ◽  
Data Sets ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Individual Single Nucleotide Polymorphism ◽  
Improve Accuracy ◽  
The Individual

A haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted as a unit. In this study, we used both the Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data to explore haploblocks and assess haplotype effects, and the haploblocks were defined based on the different LD thresholds. The accuracies of genomic prediction (GP) for dressing percentage (DP), meat percentage (MP), and rib eye roll weight (RERW) based on haplotype were investigated and compared for both data sets in Chinese Simmental beef cattle. The accuracies of GP using the entire imputed WGS data were lower than those using the HD chip data in all cases. For DP and MP, the accuracy of GP using haploblock approaches outperformed the individual single nucleotide polymorphism (SNP) approach (GBLUP_In_Block) at specific LD levels. Hotelling’s test confirmed that GP using LD-based haplotypes from WGS data can significantly increase the accuracies of GP for RERW, compared with the individual SNP approach (∼1.4 and 1.9% for GHBLUP and GHBLUP+GBLUP, respectively). We found that the accuracies using haploblock approach varied with different LD thresholds. The LD thresholds (r2 ≥ 0.5) were optimal for most scenarios. Our results suggested that LD-based haploblock approach can improve accuracy of genomic prediction for carcass traits using both HD chip and imputed WGS data under the optimal LD thresholds in Chinese Simmental beef cattle.

scholarly journals Genotype of an individual single nucleotide polymorphism regulates DNA methylation at theTRPC3alternative promoter

Epigenetics ◽  
2011 ◽  
Vol 6 (10) ◽  
pp. 1236-1241 ◽  
Author(s):  
Alex Martin-Trujillo ◽  
Isabel Iglesias-Platas ◽  
Eliecer Coto ◽  
Marc Corral-Juan ◽  
Hector San Nicolás ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Nucleotide Polymorphism ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Individual Single Nucleotide Polymorphism

Sex Differences in Childhood Associations between DNA Markers and General Cognitive Ability

2007 ◽  
Vol 28 (3) ◽  
pp. 161-164 ◽  
Author(s):  
Rosalind Arden ◽  
Nicole Harlaar ◽  
Robert Plomin
Keyword(s):  
Sex Differences ◽  
Single Nucleotide Polymorphisms ◽  
Cognitive Ability ◽  
Dna Markers ◽  
Community Sample ◽  
Nucleotide Polymorphisms ◽  
General Cognitive Ability ◽  
Single Nucleotide ◽  
The Difference

Abstract. An association between intelligence at age 7 and a set of five single-nucleotide polymorphisms (SNPs) has been identified and replicated. We used this composite SNP set to investigate whether the associations differ between boys and girls for general cognitive ability at ages 2, 3, 4, 7, 9, and 10 years. In a longitudinal community sample of British twins aged 2-10 (n > 4,000 individuals), we found that the SNP set is more strongly associated with intelligence in males than in females at ages 7, 9, and 10 and the difference is significant at 10. If this finding replicates in other studies, these results will constitute the first evidence of the same autosomal genes acting differently on intelligence in the two sexes.

UTILIZATION OF DNA MARKERS FOR EVALUATING AMYLOSE CONTENT OF GRAIN IN RICE

2013 ◽  
Vol 83 (5) ◽  
Author(s):  
Dương Thanh Thủy ◽  
Taiichiro Ookawa
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amylose Content ◽  
Waxy Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Branching Enzymes ◽  
Wx Gene ◽  
High Amylose ◽  
Suitable Marker ◽  
Granule Bound Starch Synthase

The sensory and functional properties of rice are predominantly associated with its amylose content. Granule-bound starch synthase (GBSS) encoded by the Waxy (Wx) gene determines the synthesis of amylose, while starch branching enzymes encoded by Sbe genes are involved in the formation of amylopectin. Some studies have demonstrated that Wx gene is the major controller of amylose content but there are one or more modifying genes affecting the amylose content. Three markers,  microsatellite, Single – nucleotide – polymorphism (G/T SNP) in Wx gene and Single – nucleotide – polymorphism (T/C SNP) in Sbe1 gene, were tested for their association with amylose content using sixty-nine  rice accessions from twenty countries. Of the three markers, two markers in Wx gene are significantly associated with amylose content. The combination of two markers in Wx gene (haplotypes) explained 83.8% of the variation in amylose content and discriminated the three market classes of glutinous, low, intermediate and high amylose content of rice from each other. And T/C SNP in Sbe1 locus was not a suitable marker for amylose content. Keywords: marker, amylose content, Waxy gene.

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