A second generation human haplotype map of over 3.1 million SNPs

We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.     

Mutations in SEC63 cause autosomal dominant polycystic liver disease

Mutations in PRKCSH, encoding the beta-subunit of glucosidase II, an N-linked glycan-processing enzyme in the endoplasmic reticulum (ER), cause autosomal dominant polycystic liver disease. We found that mutations in SEC63, encoding a component of the protein translocation machinery in the ER, also cause this disease. These findings are suggestive of a role for cotranslational protein-processing pathways in maintaining epithelial luminal structure and implicate noncilial ER proteins in human polycystic disease.     

Active genes are tri-methylated at K4 of histone H3

Lysine methylation of histones in vivo occurs in three states: mono-, di- and tri-methyl. Histone H3 has been found to be di-methylated at lysine 4 (K4) in active euchromatic regions but not in silent heterochromatic sites. Here we show that the Saccharomyces cerevisiae Set1 protein can catalyse di- and tri-methylation of K4 and stimulate the activity of many genes. Using antibodies that discriminate between the di- and tri-methylated state of K4 we show that di-methylation occurs at both inactive and active euchromatic genes, whereas tri-methylation is present exclusively at active genes. It is therefore the presence of a tri-methylated K4 that defines an active state of gene expression. These findings establish the concept of methyl status as a determinant for gene activity and thus extend considerably the complexity of histone modifications.     

Technology and the Myth of ‘Natural Man’

The main suggestions and objections raised by Don Ihde and Charles Lenay to my ‘Technology and the body: the (im)possibilities of re-embodiment’ are summarized and discussed. On the one hand, I agree that we should pay more attention to whole body experience and to further resisting Cartesian assumptions in the field of cognitive neuroscience and philosophy of cognition. On the other hand, I explain that my account in no way presupposes the myth of ‘natural man’ or of a natural, delineated body from before the fall into technology.     

Common variants at 12q14 and 12q24 are associated with hippocampal volume

Aging is associated with reductions in hippocampal volume that are accelerated by Alzheimer's disease and vascular risk factors. Our genome-wide association study (GWAS) of dementia-free persons (n = 9,232) identified 46 SNPs at four loci with P values of <4.0 × 10(-7). In two additional samples (n = 2,318), associations were replicated at 12q14 within MSRB3-WIF1 (discovery and replication; rs17178006; P = 5.3 × 10(-11)) and at 12q24 near HRK-FBXW8 (rs7294919; P = 2.9 × 10(-11)). Remaining associations included one SNP at 2q24 within DPP4 (rs6741949; P = 2.9 × 10(-7)) and nine SNPs at 9p33 within ASTN2 (rs7852872; P = 1.0 × 10(-7)); along with the chromosome 12 associations, these loci were also associated with hippocampal volume (P < 0.05) in a third younger, more heterogeneous sample (n = 7,794). The SNP in ASTN2 also showed suggestive association with decline in cognition in a largely independent sample (n = 1,563). These associations implicate genes related to apoptosis (HRK), development (WIF1), oxidative stress (MSR3B), ubiquitination (FBXW8) and neuronal migration (ASTN2), as well as enzymes targeted by new diabetes medications (DPP4), indicating new genetic influences on hippocampal size and possibly the risk of cognitive decline and dementia.     

Growth mechanisms of Ag and Cu nanodendrites via Galvanic replacement reactions

Dendritic silver and copper crystals were produced via Galvanic replacement reactions on zinc and aluminum plates, respectively. The growth orientations of these metals were determined using electron microscopy. The results showed that a fast crystal growth associated with a high concentration of metal cations led to kinetically controlled growth along the <112> axes of the cubic close-packed structures. However, a slow growth rate resulted in thermodynamically controlled growth along the [111] axis. The crystal growth was not found to rely upon the direct deposition of metal cations at crystallographic sites on crystal facets, but instead, hydrated metal cations deposited on the crystal surface to form an amorphous coating layer, followed by the reduction of metal cations and crystallization at the crystal/coating interface. Twin defects and stacking faults were often observed across the whole particle and commonly observed ?{422} diffraction spots were explained by stacking faults rather than by the possible presence of any superstructures. The present work offers evidences to claim that both the crystal growth rate and Coulomb interaction between negatively charged crystal surface and metal cations play an important role in the formation of metal dendrites in replacement reactions.     

Ultrastructure of a mucous gland cell found in the tube feet of the starfishAsterina stellifera

Resumen Es describida la ultraestrutura de un segundo tipo de célula glandular mucosa que es encontrada en el pié ambulacrario de la estrella del marAsterina stellifera. Los gránulos secretores de esta célula tienen en su interior una ultraestrutura en forma de pequeños puntos densos y delicadas fibrillas, mas faltando una organizatión, principalmente comparada con la organizatión del otro tipo de granulo mucoso, también encontrado en el mismo pié ambulacrario.     

Electron diffraction and electron microscopy studies on the crystalline component of enamel of theOdontaspis (selachii)

Résumé L'auteur constate que dans la dent du Requin du genreOdontaspis l'ultrastucture de la substance qui recouvre la dentine est morphologiquement très semblable à celle de l'émail de la dent humaine. Par diffraction électronique le composant cristallin de l'émail du Requin a été déterminé comme étant del'apatite. Ces résultats montrent que le revêtement externe de la dent d'Odontaspis peut être considéré comme un véritable émail.     

Endogenous neurosteroids regulate GABAA receptors through two discrete transmembrane sites

Inhibitory neurotransmission mediated by GABA(A) receptors can be modulated by the endogenous neurosteroids, allopregnanolone and tetrahydro-deoxycorticosterone. Neurosteroids are synthesized de novo in the brain during stress, pregnancyand after ethanol consumption, and disrupted steroid regulation of GABAergic transmission is strongly implicated in several debilitating conditions such as panic disorder, major depression, schizophrenia, alcohol dependence and catamenial epilepsy. Determining how neurosteroids interact with the GABA(A) receptor is a prerequisite for understanding their physiological and pathophysiological roles in the brain. Here we identify two discrete binding sites in the receptor's transmembrane domains that mediate the potentiating and direct activation effects of neurosteroids. They potentiate GABA responses from a cavity formed by the alpha-subunit transmembrane domains, whereas direct receptor activation is initiated by interfacial residues between alpha and beta subunits and is enhanced by steroid binding to the potentiation site. Thus, significant receptor activation by neurosteroids relies on occupancy of both the activation and potentiation sites. These sites are highly conserved throughout the GABA(A )receptor family, and their identification provides a unique opportunity for the development of new therapeutic, neurosteroid-based ligands and transgenic disease models of neurosteroid dysfunction.