Demographic study of a wild house sparrow population by DNA fingerprinting

Over the past twenty years, several techniques from biochemical and molecular genetics, such as enzyme electrophoresis and isoelectric focusing, have been widely and successfully applied to the study of population differentiation and evolution. However, they have been less applicable to demographic problems such as assigning parentage to individuals within a population. This stems from a general weakness of data derived from enzyme loci: allele frequencies at polymorphic loci are sufficiently skewed that the majority of individuals are of one or two genotypes. Many enzyme systems can only be examined post mortem, so that the loci are of little use if the animals are to be studied in the wild. The search for new and more sensitive techniques for detecting genetic variation has continued, and recently a major discovery has come from molecular biology. Jeffreys et al. have reported the detection of a type of hypervariable 'minisatellite' DNA that is extraordinarily polymorphic in human populations. We have applied their technique to several bird species and particularly to a population of house sparrows (Passer domesticus) near Nottingham. We report here that one of the human minisatellite clones is a suitable probe for sparrow DNA and that it reveals variation as extensive as that found in man. These results suggest that analysis of minisatellite DNA will be a powerful tool in the study of demographic population genetics.     

Melanoma genome sequencing reveals frequent PREX2 mutations

Melanoma is notable for its metastatic propensity, lethality in the advanced setting and association with ultraviolet exposure early in life. To obtain a comprehensive genomic view of melanoma in humans, we sequenced the genomes of 25 metastatic melanomas and matched germline DNA. A wide range of point mutation rates was observed: lowest in melanomas whose primaries arose on non-ultraviolet-exposed hairless skin of the extremities (3 and 14 per megabase (Mb) of genome), intermediate in those originating from hair-bearing skin of the trunk (5-55 per Mb), and highest in a patient with a documented history of chronic sun exposure (111 per Mb). Analysis of whole-genome sequence data identified PREX2 (phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2)--a PTEN-interacting protein and negative regulator of PTEN in breast cancer--as a significantly mutated gene with a mutation frequency of approximately 14% in an independent extension cohort of 107 human melanomas. PREX2 mutations are biologically relevant, as ectopic expression of mutant PREX2 accelerated tumour formation of immortalized human melanocytes in vivo. Thus, whole-genome sequencing of human melanoma tumours revealed genomic evidence of ultraviolet pathogenesis and discovered a new recurrently mutated gene in melanoma.     

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion

Prior studies have identified recurrent oncogenic mutations in colorectal adenocarcinoma and have surveyed exons of protein-coding genes for mutations in 11 affected individuals. Here we report whole-genome sequencing from nine individuals with colorectal cancer, including primary colorectal tumors and matched adjacent non-tumor tissues, at an average of 30.7× and 31.9× coverage, respectively. We identify an average of 75 somatic rearrangements per tumor, including complex networks of translocations between pairs of chromosomes. Eleven rearrangements encode predicted in-frame fusion proteins, including a fusion of VTI1A and TCF7L2 found in 3 out of 97 colorectal cancers. Although TCF7L2 encodes TCF4, which cooperates with β-catenin in colorectal carcinogenesis, the fusion lacks the TCF4 β-catenin-binding domain. We found a colorectal carcinoma cell line harboring the fusion gene to be dependent on VTI1A-TCF7L2 for anchorage-independent growth using RNA interference-mediated knockdown. This study shows previously unidentified levels of genomic rearrangements in colorectal carcinoma that can lead to essential gene fusions and other oncogenic events.     

Integrated detection and population-genetic analysis of SNPs and copy number variation

Dissecting the genetic basis of disease risk requires measuring all forms of genetic variation, including SNPs and copy number variants (CNVs), and is enabled by accurate maps of their locations, frequencies and population-genetic properties. We designed a hybrid genotyping array (Affymetrix SNP 6.0) to simultaneously measure 906,600 SNPs and copy number at 1.8 million genomic locations. By characterizing 270 HapMap samples, we developed a map of human CNV (at 2-kb breakpoint resolution) informed by integer genotypes for 1,320 copy number polymorphisms (CNPs) that segregate at an allele frequency >1%. More than 80% of the sequence in previously reported CNV regions fell outside our estimated CNV boundaries, indicating that large (>100 kb) CNVs affect much less of the genome than initially reported. Approximately 80% of observed copy number differences between pairs of individuals were due to common CNPs with an allele frequency >5%, and more than 99% derived from inheritance rather than new mutation. Most common, diallelic CNPs were in strong linkage disequilibrium with SNPs, and most low-frequency CNVs segregated on specific SNP haplotypes.     

Oscillatory dependence of current-driven magnetic domain wall motion on current pulse length

Magnetic domain walls, in which the magnetization direction varies continuously from one direction to another, have long been objects of considerable interest. New concepts for devices based on such domain walls are made possible by the direct manipulation of the walls using spin-polarized electrical current through the phenomenon of spin momentum transfer. Most experiments to date have considered the current-driven motion of domain walls under quasi-static conditions, whereas for technological applications, the walls must be moved on much shorter timescales. Here we show that the motion of domain walls under nanosecond-long current pulses is surprisingly sensitive to the pulse length. In particular, we find that the probability of dislodging a domain wall, confined to a pinning site in a permalloy nanowire, oscillates with the length of the current pulse, with a period of just a few nanoseconds. Using an analytical model and micromagnetic simulations, we show that this behaviour is connected to a current-induced oscillatory motion of the domain wall. The period is determined by the wall's mass and the slope of the confining potential. When the current is turned off during phases of the domain wall motion when it has enough momentum, the domain wall is driven out of the confining potential in the opposite direction to the flow of spin angular momentum. This dynamic amplification effect could be exploited in magnetic nanodevices based on domain wall motion.     

Sustainable water resources management: River basin modelling and decision support framework

Sustainability is a key objective of water resources management and this paper describes a modelling and decision support framework that achieves this, illustrated by applications on the UK Thames and Mekong river basins. The decision support framework contains several modules, including an interactive user’s interface linked to a GIS, a geo-database, knowledge base, simulation models and optimization procedures. Based on the analysis of scenarios and proposed interventions, efficient modelling and optimization tools form a comprehensive integrated decision support framework for the analysis and operational management of water resources in the river basin, our emphasis has been on a practical implementation through careful screening of alternatives, consideration of the institutional framework and direct involvement of stakeholders in the decision making process. Operating in this environment is transparent, reproducible and auditable, securing the trust of all interested parties. This paper discusses its applications to water utilisation on the Mekong river basin and drought management of the Lower Thames stored reservoir system.     

Lower-crustal intrusion on the North Atlantic continental margin

When continents break apart, the rifting is sometimes accompanied by the production of large volumes of molten rock. The total melt volume, however, is uncertain, because only part of it has erupted at the surface. Furthermore, the cause of the magmatism is still disputed-specifically, whether or not it is due to increased mantle temperatures. We recorded deep-penetration normal-incidence and wide-angle seismic profiles across the Faroe and Hatton Bank volcanic margins in the northeast Atlantic. Here we show that near the Faroe Islands, for every 1 km along strike, 360-400 km(3) of basalt is extruded, while 540-600 km(3) is intruded into the continent-ocean transition. We find that lower-crustal intrusions are focused mainly into a narrow zone approximately 50 km wide on the transition, although extruded basalts flow more than 100 km from the rift. Seismic profiles show that the melt is intruded into the lower crust as sills, which cross-cut the continental fabric, rather than as an 'underplate' of 100 per cent melt, as has often been assumed. Evidence from the measured seismic velocities and from igneous thicknesses are consistent with the dominant control on melt production being increased mantle temperatures, with no requirement for either significant active small-scale mantle convection under the rift or the presence of fertile mantle at the time of continental break-up, as has previously been suggested for the North Atlantic Ocean.     

Two independent alleles at 6q23 associated with risk of rheumatoid arthritis

To identify susceptibility alleles associated with rheumatoid arthritis, we genotyped 397 individuals with rheumatoid arthritis for 116,204 SNPs and carried out an association analysis in comparison to publicly available genotype data for 1,211 related individuals from the Framingham Heart Study. After evaluating and adjusting for technical and population biases, we identified a SNP at 6q23 (rs10499194, approximately 150 kb from TNFAIP3 and OLIG3) that was reproducibly associated with rheumatoid arthritis both in the genome-wide association (GWA) scan and in 5,541 additional case-control samples (P = 10(-3), GWA scan; P < 10(-6), replication; P = 10(-9), combined). In a concurrent study, the Wellcome Trust Case Control Consortium (WTCCC) has reported strong association of rheumatoid arthritis susceptibility to a different SNP located 3.8 kb from rs10499194 (rs6920220; P = 5 x 10(-6) in WTCCC). We show that these two SNP associations are statistically independent, are each reproducible in the comparison of our data and WTCCC data, and define risk and protective haplotypes for rheumatoid arthritis at 6q23.