scholarly journals Determination of complete chromosomal haplotypes by bulk DNA sequencing

2019 ◽  
Author(s):  
Richard W. Tourdot ◽  
Cheng-Zhong Zhang
Keyword(s):  
Genetic Variation ◽  
Long Range ◽  
Essential Feature ◽  
Individual Genome ◽  
Homologous Chromosomes ◽  
Human Genomes ◽  
Computational Strategy ◽  
Haplotype Phase ◽  
Chromosome Haplotype

AbstractHaplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Determining the haplotype phase requires knowledge of both the genotypes at variant sites and their linkage across each chromosome. Haplotype linkage can be either inferred statistically from a genotyped population, or determined by long-range sequencing of an individual genome. However, extending haplotype inference to the whole-chromosome scale remains challenging and usually requires special experimental techniques. Here we describe a general computational strategy to determine complete chromosomal haplotypes using a combination of bulk long-range sequencing and Hi-C sequencing. We demonstrate that this strategy can resolve the haplotypes of parental chromosomes in diploid human genomes at high precision (99%) and completeness (98%), and is further able to assemble the syntenic organization of aneuploid genomes (“digital karyotype”).

A new computational strategy to calculate the surface energy of a dipolar crystal surface

CrystEngComm ◽  
2021 ◽  
Author(s):  
Marco Bruno ◽  
Stefano Ghignone
Keyword(s):  
Dipole Moment ◽  
Surface Energy ◽  
Energy Surface ◽  
Crystal Surface ◽  
Computational Strategy

Determination of the energy surface, γ_((hkl)) (J/m2), of crystal polar faces is a very difficult task, for the presence of a dipole moment perpendicular to these surfaces that prevents the...

Determination of the Number of Conserved Chromosomal Segments Between Species

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1387-1395 ◽  
Author(s):  
Sudhir Kumar ◽  
Sudhindra R Gadagkar ◽  
Alan Filipski ◽  
Xun Gu
Keyword(s):  
Statistical Approach ◽  
Common Ancestor ◽  
Chromosomal Rearrangements ◽  
Structural Similarity ◽  
The Other ◽  
Segment Length ◽  
Human Genomes ◽  
Genomic Divergence ◽  
Human And Mouse

AbstractGenomic divergence between species can be quantified in terms of the number of chromosomal rearrangements that have occurred in the respective genomes following their divergence from a common ancestor. These rearrangements disrupt the structural similarity between genomes, with each rearrangement producing additional, albeit shorter, conserved segments. Here we propose a simple statistical approach on the basis of the distribution of the number of markers in contiguous sets of autosomal markers (CSAMs) to estimate the number of conserved segments. CSAM identification requires information on the relative locations of orthologous markers in one genome and only the chromosome number on which each marker resides in the other genome. We propose a simple mathematical model that can account for the effect of the nonuniformity of the breakpoints and markers on the observed distribution of the number of markers in different conserved segments. Computer simulations show that the number of CSAMs increases linearly with the number of chromosomal rearrangements under a variety of conditions. Using the CSAM approach, the estimate of the number of conserved segments between human and mouse genomes is 529 ± 84, with a mean conserved segment length of 2.8 cM. This length is <40% of that currently accepted for human and mouse genomes. This means that the mouse and human genomes have diverged at a rate of ∼1.15 rearrangements per million years. By contrast, mouse and rat are diverging at a rate of only ∼0.74 rearrangements per million years.

scholarly journals Bichromatic Photoassociation Spectroscopy for the Determination of Rotational Constants of Cs2 0 u + Long-Range State below the 6S1/2 + 6P1/2 Asymptote

Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 3963
Author(s):  
Jizhou Wu ◽  
Jie Ma ◽  
Yuqing Li ◽  
Wenliang Liu ◽  
Peng Li ◽  
...  
Keyword(s):  
Long Range ◽  
Spectroscopic Technique ◽  
Rigid Rotor ◽  
Simple Analysis ◽  
Rotational Constants ◽  
Vibrational Levels ◽  
Photoassociation Spectroscopy ◽  
Rotor Model ◽  
Good Agreement

This article demonstrates new observation of the high-resolution ro-vibrational bichromatic photoassociation spectra (BPAS) of Cs2 in the 0u+ long-range state below the asymptotes 6S1/2 + 6P1/2. By combining with a modulation spectroscopic technique, precise references of the frequency differences have been engineered through the BPAS, with which the rotational constants of low-lying vibrational levels of the Cs20u+ long-range state have been accurately determined by fitting the frequency differences to the non-rigid-rotor model. The rotational constants for the newly observed seven ro-vibrational levels are summarized and disagreement for the level ῦ = 498 is clarified. The rotational constants of different vibrational levels demonstrate strong perturbations of the related energy structures. A simple analysis is performed and shows good agreement with experimental results.

Parentage determination of black sea bream (Acanthopagrus schlegelii) for stock enhancement: effectiveness and loss of genetic variation

2021 ◽  
Vol 40 (6) ◽  
pp. 41-49
Author(s):  
Binbin Shan ◽  
Yan Liu ◽  
Na Song ◽  
Changping Yang ◽  
Shengnan Liu ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Black Sea ◽  
Stock Enhancement ◽  
Sea Bream ◽  
Acanthopagrus Schlegelii

scholarly journals Determination of morphometric, biochemical and genetic variation in Sclerotium delphinii isolates

2014 ◽  
Vol 8 (16) ◽  
pp. 1696-1703
Author(s):  
P. Gawande S. ◽  
G. Borkar S. ◽  
T. Nagrale D. ◽  
K. Sharma A.
Keyword(s):  
Genetic Variation ◽  
Sclerotium Delphinii
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