Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease

Using variants from the 1000 Genomes Project pilot European CEU dataset and data from additional resequencing studies, we densely genotyped 183 non-HLA risk loci previously associated with immune-mediated diseases in 12,041 individuals with celiac disease (cases) and 12,228 controls. We identified 13 new celiac disease risk loci reaching genome-wide significance, bringing the number of known loci (including the HLA locus) to 40. We found multiple independent association signals at over one-third of these loci, a finding that is attributable to a combination of common, low-frequency and rare genetic variants. Compared to previously available data such as those from HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions. In particular, 29 of the 54 fine-mapped signals seemed to be localized to single genes and, in some instances, to gene regulatory elements. Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease.     

Theory (In-)Equivalence and conventionalism in f(R) gravity

f(R) Gravity is the most natural extension of General Relativity within Riemannian Geometry. Due to (inter alia) its potential capacity for a unified treatment of early and late-time cosmic expansion, it has enjoyed recent attention in astrophysics and cosmology. I critically examine three inter-related claims found in the pertinent physics literature, of general interest to the philosopher of science. 1. f(R) Gravity is equivalent to a particular Brans-Dicke Theory. 2. The spacetime geometry underpinning f(R) Gravity has substantial conventional elements. 3. f(R) Gravity is an instance of a theory in which the distinction between matter and spacetime is conventional. Whilst the first claim can be vindicated in precise terms, the remaining two claims, I submit, are unwarranted – at least for the reasons usually adduced. On different grounds, though, the case for conventionalism about spacetime geometry in f(R) Gravity (as well as General Relativity) turns out to be considerably stronger.     

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

Several risk factors for Crohn's disease have been identified in recent genome-wide association studies. To advance gene discovery further, we combined data from three studies on Crohn's disease (a total of 3,230 cases and 4,829 controls) and carried out replication in 3,664 independent cases with a mixture of population-based and family-based controls. The results strongly confirm 11 previously reported loci and provide genome-wide significant evidence for 21 additional loci, including the regions containing STAT3, JAK2, ICOSLG, CDKAL1 and ITLN1. The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development.     

人类乙型肝炎样病毒核心蛋白中第7位疏水性氨基酸重复肚段区域的突变可以抑制病毒核衣壳的组装

人类乙型肝炎病毒的核衣壳由核心蛋白的二聚体所组成．但是,核心蛋白亚单位与亚单位之间相互作用的机制至今尚不清楚．研究发现,在人类乙型肝炎样病毒──土拨鼠肝炎病毒（WHV）核心蛋白的氨基端,存在着4个保守的疏水氨基酸残基（氨基酸位置101～102）．它们分别是亮氨酸101,亮氨酸108,缬氨酸115和苯丙氨酸122．这4个疏水氨基酸残基以每隔6个氨基酸残基而重复出现1次．它们被称为“第7位疏水性氨基酸重复肽段（hhr）”．由于蛋白质中的疏水键往往在蛋白质的相互作用中起重要作用,因此就在培养细胞系统中研究WHV核心蛋白的hhr区域在…     

The physics and metaphysics of Tychistic Bohmian Mechanics

The paper takes up Bell's (1987) “Everett (?) theory” and develops it further. The resulting theory is about the system of all particles in the universe, each located in ordinary, 3-dimensional space. This many-particle system as a whole performs random jumps through 3N-dimensional configuration space – hence “Tychistic Bohmian Mechanics” (TBM). The distribution of its spontaneous localisations in configuration space is given by the Born Rule probability measure for the universal wavefunction. Contra Bell, the theory is argued to satisfy the minimal desiderata for a Bohmian theory within the Primitive Ontology framework (for which we offer a metaphysically more perspicuous formulation than is customary). TBM's formalism is that of ordinary Bohmian Mechanics (BM), without the postulate of continuous particle trajectories and their deterministic dynamics. This “rump formalism” receives, however, a different interpretation. We defend TBM as an empirically adequate and coherent quantum theory. Objections voiced by Bell and Maudlin are rebutted. The “for all practical purposes”-classical, Everettian worlds (i.e. quasi-classical histories) exist sequentially in TBM (rather than simultaneously, as in the Everett interpretation). In a temporally coarse-grained sense, they quasi-persist. By contrast, the individual particles themselves cease to persist.     

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis

We present a genome-wide association study of ileal Crohn disease and two independent replication studies that identify several new regions of association to Crohn disease. Specifically, in addition to the previously established CARD15 and IL23R associations, we identified strong and significantly replicated associations (combined P < 10(-10)) with an intergenic region on 10q21.1 and a coding variant in ATG16L1, the latter of which was also recently reported by another group. We also report strong associations with independent replication to variation in the genomic regions encoding PHOX2B, NCF4 and a predicted gene on 16q24.1 (FAM92B). Finally, we demonstrate that ATG16L1 is expressed in intestinal epithelial cell lines and that functional knockdown of this gene abrogates autophagy of Salmonella typhimurium. Together, these findings suggest that autophagy and host cell responses to intracellular microbes are involved in the pathogenesis of Crohn disease.     

A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease

Crohn's disease is a chronic inflammatory disorder of the gastrointestinal tract, which is thought to result from the effect of environmental factors in a genetically predisposed host. A gene location in the pericentromeric region of chromosome 16, IBD1, that contributes to susceptibility to Crohn's disease has been established through multiple linkage studies, but the specific gene(s) has not been identified. NOD2, a gene that encodes a protein with homology to plant disease resistance gene products is located in the peak region of linkage on chromosome 16 (ref. 7). Here we show, by using the transmission disequilibium test and case-control analysis, that a frameshift mutation caused by a cytosine insertion, 3020insC, which is expected to encode a truncated NOD2 protein, is associated with Crohn's disease. Wild-type NOD2 activates nuclear factor NF-kappaB, making it responsive to bacterial lipopolysaccharides; however, this induction was deficient in mutant NOD2. These results implicate NOD2 in susceptibility to Crohn's disease, and suggest a link between an innate immune response to bacterial components and development of disease.     

人类乙型肝炎样病毒Pre—S1包膜蛋白的一个特定区域为乙肝病毒形成所必需

土拨鼠肝炎病毒（WHV）是一种哺乳类动物的肝炎病毒．这种病毒在结构和抗原怕与人类乙型肝炎病毒（HBV）非常相似．以往的研究报告指出,在一种称为鸭乙型肝炎病毒（DHBV）的Pre－S包膜蛋白中,含有一个特定区域．这一区域由天冬氨酸－天冬氨酸－脯氨酸－亮氨酸－亮氨酸（DDPLL）5个氨基酸残基所组成．已发现,这一区域在像DHBV这一类禽类乙肝病毒的病毒装配和分泌时所必需的（LenhoffR,SummersJ．JVirol,1994,68：4565～4571）．在WHV的Pre－S包胰蛋白中第201个氨基酸到第205个氨基酸所包含的顺序,甘氨酸－天冬氨酸－脯氨…