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.

Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.

/pdf/levels-and-patterns-of-nucleotide-variation-in-domestication-55qsqxh97a.pdf

Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection

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 reflecting mirror for alignment

During its life-cycle the bacteriophage φ29 actively packages its dsDNA genome into a proteinacious capsid, compressing its genome to near crystalline densities against large electrostatic, elastic, and entropic forces This remarkable process is accomplished by a nano-scale, molecular DNA pump – a complex assembly of three protein and nucleic acid rings which utilizes the free energy released in ATP hydrolysis to perform the mechanical work necessary to overcome these large energetic barriers We have developed a single molecule optical tweezers assay which has allowed us to probe the detailed mechanism of this packaging motor By following the rate of packaging of a single bacteriophage as the capsid is filled with genome and as a function of optically applied load, we find that the compression of the genome results in the build-up of an internal force, on the order of ∼ 55 pN, due to the compressed genome The ability to work against such large forces makes the packaging motor one of the strongest known molecular motors By titrating the concentration of ATP, ADP, and inorganic phosphate at different opposing load, we are able to determine features of the mechanochemistry of this motor – the coupling between the mechanical and chemical cycles We find that force is generated not upon binding of ATP, but rather upon release of hydrolysis products Finally, by improving the resolution of the optical tweezers assay, we are able to observe the discrete increments of DNA encapsidated each cycle of the packaging motor We find that DNA is packaged in 10-bp increments preceded by the binding of multiple ATPs The application of large external forces slows the packaging rate of the motor, revealing that the 10-bp steps are actually composed of four 25-bp steps which occur in rapid succession These data show that the individual subunits of the pentameric ring-ATPase at the core of the packaging motor are highly coordinated, with the binding of ATP and the translocation of DNA temporally segregated into two distinct phases of the mechanochemical cycle of the entire ring Because this ring-ATPase is a member of the ASCE superfamily of ATPases, these results may have implications for a broad and diverse family of cellular motors

Viral DNA Packaging: One Step at a Time

sebastia’n herna’ndez, rodolfo vo¤gler, carlos bustamante and julio lamilla Departamento de Biologia Marina, Facultad de Ciencias del Mar, Universidad Catolica del Norte, Casilla 117, Coquimbo, Chile, Present address: School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand, Centro Interdisciplinario de Ciencias Marinas, Avenida Instituto Politecnico Nacional s/n, Col. Playa Palo de Santa Rita, CP 952 La Paz, BCS, Mexico, Laboratorio de Elasmobranquios (ELASMOLAB), Instituto de Zoologia, Universidad Austral de Chile, Casilla 567, Valdivia, Chile

Review of the occurrence and distribution of the basking shark ( Cetorhinus maximus ) in Chilean waters

Se informa sobre el registro mas austral del marrajo de aleta larga Isurus paucus Gitart Manday, 1966 en el Pacifico suroriental. El ejemplar correspondio a una hembra de 310 cm de longitud total, capturada por un pesquero artesanal frente a la costa de Valparaiso, Chile, por un pesquero artesanal cuya especie objetivo era el marrajo de aleta corta, I. oxyrinchus. Los principales caracteres taxonomicos utilizados en la identificacion del marrajo de aleta larga que permitieron distinguirlo de la otra especie del genero Isurus (marrajo de aleta corta), fueron la forma de la cabeza y hocico, la longitud de las aletas pectorales, la posicion relativa de la primera aleta dorsal con respecto al margen posterior de las aletas pectorales y la posicion relativa de la segunda aleta dorsal con respecto de la anal. Los antecedentes recopilados indican que la presencia de Isurus paucus no se restringiria a zonas de aguas calidas, sino que tambien se distribuye en aguas templadas-frias

/pdf/southernmost-record-of-isurus-paucus-gitart-manday-1966-14i1naqhqy.pdf

Carlos Bustamante

Papers

Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection

Optical trap utilizing a reflecting mirror for alignment

Viral DNA Packaging: One Step at a Time

Review of the occurrence and distribution of the basking shark ( Cetorhinus maximus ) in Chilean waters

Southernmost record of Isurus paucus Gitart Manday, 1966 (Elasmobranchii: Lamnidae) in the southeast Pacific Ocean