抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

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Scalable molecular dynamics with NAMD

/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

https://cdr.lib.unc.edu/downloads/v692t8920

A global reference for human genetic variation.

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Local ancestry inference (LAI) allows identification of the ancestry of all chromosomal segments in admixed individuals, and it is a critical step in the analysis of human genomes with applications from pharmacogenomics and precision medicine to genome-wide association studies. In recent years, many LAI techniques have been developed in both industry and academic research. However, these methods require large training data sets of human genomic sequences from the ancestries of interest. Such reference data sets are usually limited, proprietary, protected by privacy restrictions, or otherwise not accessible to the public. Techniques to generate training samples that resemble real haploid sequences from ancestries of interest can be useful tools in such scenarios, since a generalized model can often be shared, but the unique human sample sequences cannot. In this work we present a class-conditional VAE-GAN to generate new human genomic sequences that can be used to train local ancestry inference (LAI) algorithms. We evaluate the quality of our generated data by comparing the performance of a state-of-the-art LAI method when trained with generated versus real data.

Class-Conditional VAE-GAN for Local-Ancestry Simulation.

The eastern Pacific black ghost shark, Hydrolagus melanophasma is reported from deep waters off Chile and is described from specimens collected off Valdivia at depths of 1150 to 1720 m. This species is distinguished from all other members of the genus by its large, curved dorsal fin spine, which extends beyond the dorsal fin apex; a second dorsal fin of uniform height along the caudal peduncle; large pectoral fins extending beyond the pelvic fin insertion; and a uniform black color of the body. Catch records of this species in Chile suggest a discontinuous distribution along the continental slope of the eastern Pacific Ocean, restricted to the Middle America and Atacama trenches. These observations elevate the number of chimaeroid fishes inhabiting Chile to five species.

https://espace.library.uq.edu.au/view/UQ:270254/Articulo_40_23.pdf

First record of Hydrolagus melanophasma James, Ebert, Long & Didier, 2009 (Chondrichthyes, Chimaeriformes, Holocephali) from the southeastern Pacific Ocean

An optical trap (and alignment device) having a light source for generating first and second light beams, and a pair of lenses for focusing the light beams to a trap region in a counter-propagating manner for trapping a particle in the trap region. A light source illuminates the trap region with a third beam of light, and a camera is positioned for capturing a portion of each of the first, second and third light beams. Actuators exert forces on generally rigid portions of optical fiber used to deliver the first and second light beams to the trap region, such that the generally rigid portions pivot about pivot points located at supported members from which the optical fibers extend. Position sensitive detectors measure the position of the beams leaving the optical fibers, and feed position signals back to the actuator drivers to ensure proper positioning of the beams.

Optical trap utilizing a pivoting optical fiber

A novel splice mutation within equine KIT and the W15 allele in the homozygous state lead to all white coat color phenotypes

The spinetail devilray Mobula japanica was recorded for the first time in the south-eastern Pacific Ocean, from a single beach-washed specimen examined at Bahia Inglesa, Chile. The presence of this temperate-tropical species at about 27° south of its previously recorded range in the eastern Pacific Ocean may be explained by the absence of rigorous species-specific landing reports along the coasts of Peru and Chile. Alternatively, a strong warm phase of El Nino Southern Oscillation may have facilitated conditions allowing this epipelagic species to travel towards higher latitudes. This record increases the known range of M. japanica and the occurrence of mobulids in Chilean waters to three species. Photographs and morphometrics of the specimen are provided.

Carlos Bustamante

Papers

Class-Conditional VAE-GAN for Local-Ancestry Simulation.

First record of Hydrolagus melanophasma James, Ebert, Long & Didier, 2009 (Chondrichthyes, Chimaeriformes, Holocephali) from the southeastern Pacific Ocean

Optical trap utilizing a pivoting optical fiber

A novel splice mutation within equine KIT and the W15 allele in the homozygous state lead to all white coat color phenotypes

First record of Mobula japanica (Rajiformes: Myliobatidae) from the south-eastern Pacific Ocean