Genome sequence, comparative analysis and haplotype structure of the domestic dog

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.     

Light-induced shape-memory polymers

Materials are said to show a shape-memory effect if they can be deformed and fixed into a temporary shape, and recover their original, permanent shape only on exposure to an external stimulus. Shape-memory polymers have received increasing attention because of their scientific and technological significance. In principle, a thermally induced shape-memory effect can be activated by an increase in temperature (also obtained by heating on exposure to an electrical current or light illumination). Several papers have described light-induced changes in the shape of polymers and gels, such as contraction, bending or volume changes. Here we report that polymers containing cinnamic groups can be deformed and fixed into pre-determined shapes--such as (but not exclusively) elongated films and tubes, arches or spirals--by ultraviolet light illumination. These new shapes are stable for long time periods, even when heated to 50 degrees C, and they can recover their original shape at ambient temperatures when exposed to ultraviolet light of a different wavelength. The ability of polymers to form different pre-determined temporary shapes and subsequently recover their original shape at ambient temperatures by remote light activation could lead to a variety of potential medical and other applications.     

Partial quantum information

Information--be it classical or quantum--is measured by the amount of communication needed to convey it. In the classical case, if the receiver has some prior information about the messages being conveyed, less communication is needed. Here we explore the concept of prior quantum information: given an unknown quantum state distributed over two systems, we determine how much quantum communication is needed to transfer the full state to one system. This communication measures the partial information one system needs, conditioned on its prior information. We find that it is given by the conditional entropy--a quantity that was known previously, but lacked an operational meaning. In the classical case, partial information must always be positive, but we find that in the quantum world this physical quantity can be negative. If the partial information is positive, its sender needs to communicate this number of quantum bits to the receiver; if it is negative, then sender and receiver instead gain the corresponding potential for future quantum communication. We introduce a protocol that we term 'quantum state merging' which optimally transfers partial information. We show how it enables a systematic understanding of quantum network theory, and discuss several important applications including distributed compression, noiseless coding with side information, multiple access channels and assisted entanglement distillation.     

Complement factor 5 is a quantitative trait gene that modifies liver fibrogenesis in mice and humans

Fibrogenesis or scarring of the liver is a common consequence of all chronic liver diseases. Here we refine a quantitative trait locus that confers susceptibility to hepatic fibrosis by in silico mapping and show, using congenic mice and transgenesis with recombined artificial chromosomes, that the gene Hc (encoding complement factor C5) underlies this locus. Small molecule inhibitors of the C5a receptor had antifibrotic effects in vivo, and common haplotype-tagging polymorphisms of the human gene C5 were associated with advanced fibrosis in chronic hepatitis C virus infection. Thus, the mouse quantitative trait gene led to the identification of an unknown gene underlying human susceptibility to liver fibrosis, supporting the idea that C5 has a causal role in fibrogenesis across species.     

Inversin, the gene product mutated in nephronophthisis type II, functions as a molecular switch between Wnt signaling pathways

Cystic renal diseases are caused by mutations of proteins that share a unique subcellular localization: the primary cilium of tubular epithelial cells. Mutations of the ciliary protein inversin cause nephronophthisis type II, an autosomal recessive cystic kidney disease characterized by extensive renal cysts, situs inversus and renal failure. Here we report that inversin acts as a molecular switch between different Wnt signaling cascades. Inversin inhibits the canonical Wnt pathway by targeting cytoplasmic dishevelled (Dsh or Dvl1) for degradation; concomitantly, it is required for convergent extension movements in gastrulating Xenopus laevis embryos and elongation of animal cap explants, both regulated by noncanonical Wnt signaling. In zebrafish, the structurally related switch molecule diversin ameliorates renal cysts caused by the depletion of inversin, implying that an inhibition of canonical Wnt signaling is required for normal renal development. Fluid flow increases inversin levels in ciliated tubular epithelial cells and seems to regulate this crucial switch between Wnt signaling pathways during renal development.     

Superconductors: time-reversal symmetry breaking?

One of the mysteries of modern condensed-matter physics is the nature of the pseudogap state of the superconducting cuprates. Kaminski et al. claim to have observed signatures of time-reversal symmetry breaking in the pseudogap regime in underdoped Bi2Sr2CaCu2O8+delta (Bi2212). Here we argue that the observed circular dichroism is due to the 51 superstructure replica of the electronic bands and therefore cannot be considered as evidence for spontaneous time-reversal symmetry breaking in cuprates.     

Genetic variation in DLG5 is associated with inflammatory bowel disease

Crohn disease and ulcerative colitis are two subphenotypes of inflammatory bowel disease (IBD), a complex disorder resulting from gene-environment interaction. We refined our previously defined linkage region for IBD on chromosome 10q23 and used positional cloning to identify genetic variants in DLG5 associated with IBD. DLG5 encodes a scaffolding protein involved in the maintenance of epithelial integrity. We identified two distinct haplotypes with a replicable distortion in transmission (P = 0.000023 and P = 0.004 for association with IBD, P = 0.00012 and P = 0.04 for association with Crohn disease). One of the risk-associated DLG5 haplotypes is distinguished from the common haplotype by a nonsynonymous single-nucleotide polymorphism 113G-->A, resulting in the amino acid substitution R30Q in the DUF622 domain of DLG5. This mutation probably impedes scaffolding of DLG5. We stratified the study sample according to the presence of risk-associated CARD15 variants to study potential gene-gene interaction. We found a significant difference in association of the 113A DLG5 variant with Crohn disease in affected individuals carrying the risk-associated CARD15 alleles versus those carrying non-risk-associated CARD15 alleles. This is suggestive of a complex pattern of gene-gene interaction between DLG5 and CARD15, reflecting the complex nature of polygenic diseases. Further functional studies will evaluate the biological significance of DLG5 variants.     

甚大望远镜干涉仪——挑战未来

20世纪最后的25年里，光学干涉及综合技术日益成熟，主要成功体现在从直接检测恒星脉动到有测试台系统的光学成图，目前的进展已经到设备对天文团体开放。这一领域灵活的活动性和快速进展表明，地面和空间干涉仪将成为主要观测工具。     

选择实验的理论和应用——以中国退耕还林为例

选择实验的理论基础来自于要素价值理论和随机效用理论,既是一种对环境资源进行价值评估的重要方法,也是揭示研究对象政策偏好的重要手段.利用该方法不仅可以通过对支付意愿或接受赔偿意愿进行评估,进而对一项政策的各个要素的相对重要性进行排序,还可以得到因多个政策要素同时改变时导致的价值变化,从而有助于政策制订者对政策进行调整.本文在评述选择实验的基本理论和方法的基础上,以中国正在实施的退耕还林工程为例,利用选择实验方法对该政策进行了评估,并且基于研究结果对未来的政策改进提出了相关建议.