On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations.

A critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e.

Context dependence, ancestral misidentification, and spurious signatures of natural selection.

Population genetic analyses often use polymorphism data from one species, and orthologous genomic sequences from closely related outgroup species. These outgroup sequences are frequently used to identify ancestral alleles at segregating sites and to compare the patterns of polymorphism and divergence. Inherent in such studies is the assumption of parsimony, which posits that the ancestral state of each single nucleotide polymorphism (SNP) is the allele that matches the orthologous site in the outgroup sequence, and that all nucleotide substitutions between species have been observed.

Localizing recent adaptive evolution in the human genome.

Identifying genomic locations that have experienced selective sweeps is an important first step toward understanding the molecular basis of adaptive evolution. Using statistical methods that account for the confounding effects of population demography, recombination rate variation, and single-nucleotide polymorphism ascertainment, while also providing fine-scale estimates of the position of the selected site, we analyzed a genomic dataset of 1.2 million human single-nucleotide polymorphisms genotyped in African-American, European-American, and Chinese samples.

A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs.

Double muscling is a trait previously described in several mammalian species including cattle and sheep and is caused by mutations in the myostatin (MSTN) gene (previously referred to as GDF8). Here we describe a new mutation in MSTN found in the whippet dog breed that results in a double-muscled phenotype known as the "bully" whippet. Individuals with this phenotype carry two copies of a two-base-pair deletion in the third exon of MSTN leading to a premature stop codon at amino acid 313.

A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data.

Nonrandom mating induces correlations in allelic states within and among loci that can be exploited to understand the genetic structure of natural populations (Wright 1965). For many species, it is of considerable interest to quantify the contribution of two forms of nonrandom mating to patterns of standing genetic variation: inbreeding (mating among relatives) and population substructure (limited dispersal of gametes). Here, we extend the popular Bayesian clustering approach STRUCTURE (Pritchard et al.

Differential force microscope for long time-scale biophysical measurements.

Force microscopy techniques including optical trapping, magnetic tweezers, and atomic force microscopy (AFM) have facilitated quantification of forces and distances on the molecular scale. However, sensitivity and stability limitations have prevented the application of these techniques to biophysical systems that generate large forces over long times, such as actin filament networks. Growth of actin networks drives cellular shape change and generates nano-Newtons of force over time scales of minutes to hours, and consequently network growth properties have been difficult to study.

Real-time control of the energy landscape by force directs the folding of RNA molecules.

The rugged folding-energy landscapes of RNAs often display many competing minima. How do RNAs discriminate among competing conformations in their search for the native state? By using optical tweezers, we show that the folding-energy landscape can be manipulated to control the fate of an RNA: individual RNA molecules can be induced into either native or misfolding pathways by modulating the relaxation rate of applied force and even be redirected during the folding process to switch from misfolding to native folding pathways. Controlling folding pathways at the single-molecule level provides a way to survey the manifold of folding trajectories and intermediates, a capability that previously was available only to theoretical studies.

Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.

To understand the demographic history of rhesus macaques (Macaca mulatta) and document the extent of linkage disequilibrium (LD) in the genome, we partially resequenced five Encyclopedia of DNA Elements regions in 9 Chinese and 38 captive-born Indian rhesus macaques. Population genetic analyses of the 1467 single-nucleotide polymorphisms discovered suggest that the two populations separated about 162,000 years ago, with the Chinese population tripling in size since then and the Indian population eventually shrinking by a factor of four. Using coalescent simulations, we confirmed that these inferred demographic events explain a much faster decay of LD in Chinese (r(2) approximately 0.

Evolutionary and biomedical insights from the rhesus macaque genome.

The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families.

A single IGF1 allele is a major determinant of small size in dogs.

The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed.

Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner.

RNA polymerase II (RNAP II) is responsible for transcribing all messenger RNAs in eukaryotic cells during a highly regulated process that is conserved from yeast to human, and that serves as a central control point for cellular function. Here we investigate the transcription dynamics of single RNAP II molecules from Saccharomyces cerevisiae against force and in the presence and absence of TFIIS, a transcription elongation factor known to increase transcription through nucleosomal barriers. Using a single-molecule dual-trap optical-tweezers assay combined with a novel method to enrich for active complexes, we found that the response of RNAP II to a hindering force is entirely determined by enzyme backtracking.

Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method.

Chromatin remodeling complexes (remodelers) are large, multisubunit macromolecular assemblies that use ATP hydrolysis to alter the structure and positioning of nucleosomes. The mechanisms proposed for remodeler action on nucleosomes are diverse, and require structural evaluation and insights. Previous reconstructions of remodelers using electron microscopy revealed interesting features, but also significant discrepancies, prompting new approaches.

Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque.

E. coli DNA gyrase uses the energy of ATP hydrolysis to introduce essential negative supercoils into the genome, thereby working against the mechanical stresses that accumulate in supercoiled DNA. Using a magnetic-tweezers assay, we demonstrate that small changes in force and torque can switch gyrase among three distinct modes of activity.

Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids.

The bacteriophage phi29 generates large forces to compact its double-stranded DNA genome into a protein capsid by means of a portal motor complex. Several mechanical models for the generation of these high forces by the motor complex predict coupling of DNA translocation to rotation of the head-tail connector dodecamer. Putative connector rotation is investigated here by combining the methods of single-molecule force spectroscopy with polarization-sensitive single-molecule fluorescence.

Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results.

Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette. Several experimental variables were changed while measuring the unfolding/refolding kinetics, including handle lengths, trap stiffness, and modes of force applied to the molecule.

Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments.

By exerting mechanical force, it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hairpins in an optical tweezers setup.

Light-powering Escherichia coli with proteorhodopsin.

Proteorhodopsin (PR) is a light-powered proton pump identified by community sequencing of ocean samples. Previous studies have established the ecological distribution and enzymatic activity of PR, but its role in powering cells and participation in ocean energy fluxes remains unclear. Here, we show that when cellular respiration is inhibited by depleting oxygen or by the respiratory poison azide, Escherichia coli cells expressing PR become light-powered.

Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysis.

The eighth annual Human Genome Variation Meeting was held in September 2006 in the Hong Kong Special Administrative Region, China. The meeting highlighted recent advances in characterization of genetic variation, including genome-wide association studies and structural variation.

DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC.

ATP-dependent chromatin-remodeling complexes (remodelers) modulate gene transcription by regulating the accessibility of highly packaged genomic DNA. However, the molecular mechanisms involved at the nucleosomal level in this process remain controversial. Here, we monitor the real-time activity of single ySWI/SNF or RSC complexes on single, stretched nucleosomal templates under tensions above 1 pN forces.

Use of telephone care in a cardiovascular disease management programme for type 2 diabetes patients in Santiago, Chile.

Objectives: In 2004, the Chilean National Ministry of Health instituted a cardiovascular disease (CVD) management programme aimed at improving diabetes care among patients treated in the public healthcare system. We sought to identify the characteristics of patients participating in the CVD programme and the feasibility of extending its reach through structured nurse telephone contacts between outpatient encounters.

Methods: We surveyed 569 low-income adults with type 2 diabetes treated in public clinics of Santiago, to assess patients' participation in the CVD programme and willingness to use telephone care services.

Unusual mechanical stability of a minimal RNA kissing complex.

By using optical tweezers, we have investigated the mechanical unfolding of a minimal kissing complex with only two G.C base pairs. The loop-loop interaction is exceptionally stable; it is disrupted at forces ranging from 7 to 30 pN, as compared with 14-20 pN for unfolding hairpins of 7 and 11 bp.

Effect of force on mononucleosomal dynamics.

Using single-molecule optical-trapping techniques, we examined the force-induced dynamic behavior of a single nucleosome core particle. Our experiments using the DNA construct containing the 601 nucleosome-positioning sequence revealed that the nucleosome unravels in at least two major stages. The first stage, which we attributed to the unraveling of the first DNA wrap around the histone octamer, could be mechanically induced in a reversible manner, and when kept at constant force within a critical force range, exhibited two-state hopping behavior.

Identification of the FtsK sequence-recognition domain.

FtsK is a prokaryotic multidomain DNA translocase that coordinates chromosome segregation and cell division. FtsK is membrane anchored at the division septum and, guided by highly skewed DNA sequences, translocates the chromosome to bring the terminus of replication to the septum. Here, we use in vitro single-molecule and ensemble methods to unveil a mechanism of action in which the translocation and sequence-recognition activities are performed by different domains in FtsK.

Determination of thermodynamics and kinetics of RNA reactions by force.

Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured.