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.

/pdf/scalable-molecular-dynamics-with-namd-51o1z7rwp8.pdf

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.

We present a procedure for imaging metal-coated biomolecules with the scanning tunneling microscope. This procedure is simple, easy to implement and gives reproducible results. The biomolecules are adsorbed on glow discharged mica, then coated with a thin film of platinum- carbon. We have applied this method for visualizing two different kind of biomolecules: planar membranes and DNA molecules. The contrast and lateral resolution of the images are comparable to electron micrographs of the same molecules. The lateral resolution is limited by the grain size of the coating film while the vertical resolution seems to be unaffected for very small coating thickness (less than 3 nm).© (1992) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Scanning tunneling microscopy of metal-coated biomolecules

A Mechanochemical Model of a Viral DNA Packaging Motor

A general method to describe the spectroscopy of large, internally inhomogeneous particles is presented. The theory utilizes an approach similar to the one used by De Voe in the treatment of the optical properties of polymers. It is found that if the particle is dense the intermediate and radiation coupling mechanisms must be included in addition to the dipole-dipole coupling. Through these coupling mechanisms it is found that the excitation generated at each group in the chromophore can delocalize over regions comparable to the size of the wavelength of light. The spatially averaged equations of the absorbance for a collection of large inhomogeneous arbitrarily shaped aggregates will be presented. This theory is then applied to the polymer and salt induced Psi-type circular dichroism observed in DNA aggregates. Using the formalism developed, it is shown that the anomalously large signals observed in the circular dichroism of certain molecular aggregates result from: (a) the presence of a long-range chiral structure in the aggregate; (b) delocalization throughout the entire particle of the light-induced excitations in the chromophores. This is the first successful attempt to explain the physical origin of the psi-type CD effect. Useful information regarding the chiral structure of the aggregates can be inferred from the theory.

Theory of Absorption and Circular Dichroism of Large Inhomogeneous Molecular Aggregates

Limited sample sizes are often a problem for species of conservation concern when using genetic tools to make population assessments. Lack of analytical power from small sample sizes can be compensated for by use of a large marker set. Here we report on development and characterization of 17 novel microsatellite markers for the reef manta ray (Mobula alfredi). Loci were screened on 60 reef manta rays (M. alfredi) sampled from the east coast of Australia. The number of alleles per locus varied from 2 to 13 with observed heterozygosities ranging between 0.300 and 0.917. The development of these 17 additional markers increases the total number of microsatellite markers available for this species to 27.

/pdf/development-and-characterization-of-17-polymorphic-3j2m9iu48b.pdf

Development and characterization of 17 polymorphic microsatellite markers for the reef manta ray (Mobula alfredi).

https://www.biorxiv.org/content/biorxiv/early/2014/09/16/009191.full.pdf

Carlos Bustamante

Papers

Scanning tunneling microscopy of metal-coated biomolecules

A Mechanochemical Model of a Viral DNA Packaging Motor

Theory of Absorption and Circular Dichroism of Large Inhomogeneous Molecular Aggregates

Development and characterization of 17 polymorphic microsatellite markers for the reef manta ray (Mobula alfredi).

Article/Discovery Inference of Gorilla demographic and selective history from whole genome sequence data