Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Mode-locked diode-pumped vanadate lasers operated with PbS quantum dots

The use of glasses doped with PbS nanocrystals as intracavity saturable absorbers for passive Q-switching and mode locking of c-cut Nd:Gd0.7Y0.3VO4, Nd:YVO4, and Nd:GdVO4 lasers is investigated. Q-switching yields pulses as short as 35 ns with an average output power of 435 mW at a repetition rate of 6–12 kHz at a pump power of 5–6 W. Mode locking through a combination of PbS nanocrystals and a Kerr lens results in 1.4 ps long pulses with an average output power of 255 mW at a repetition rate of 100 MHz

Binding studies of crocin to β-Lactoglobulin and its impacts on both components

© 2020 Elsevier Ltd Light susceptibility of crocin and high degree of unsaturation limit its application in food systems. This study aimed to investigate the impact of molecular binding of crocin to β-lactoglobulin (β-LG) on crocin stability as well as the conformational stability of β-LG. The overall binding affinity was estimated about 1.74 × 103 M−1 through following UV spectral changes of β-LG at different concentrations of crocin. A 1:1 binding stoichiometry for the complex of crocin and β-LG was recognized using Job's method. The results of molecular docking and molecular dynamic simulation indicated that in addition to a single hydrogen bond with an oxygen linker attached to polyene chain, hydrophobic interactions play the major role in binding of crocin's polyene chain to β-LG surface. Three-dimensional emission and CD spectra showed conformational alterations in both tertiary and secondary structure of β-LG varying with crocin concentration. Depending on the temperature, crocin showed a dual effect on the thermodynamic stability of β-LG. Crocin destabilized β-LG up to room temperature, but stabilized at higher temperatures. The CD spectra of crocin in the Soret region and simulation results proved the bending of polyene chain and changes in the angle between sugar groups and polyene chain in combination with the protein. β-LG complexation enhanced the chemical stability of crocin by 20% during a 30-day storage, while its degradation was accelerated under UV irradiation. According to the results, it is predicted crocin functionalities to be affected by β-LG association and vice versa