'Big Bang' tomography as a new route to atomic-resolution electron tomography

Until now it has not been possible to image at atomic resolution using classical electron tomographic methods, except when the target is a perfectly crystalline nano-object imaged along a few zone axes. The main reasons are that mechanical tilting in an electron microscope with sub-?ngstr?m precision over a very large angular range is difficult, that many real-life objects such as dielectric layers in microelectronic devices impose geometrical constraints and that many radiation-sensitive objects such as proteins limit the total electron dose. Hence, there is a need for a new tomographic scheme that is able to deduce three-dimensional information from only one or a few projections. Here we present an electron tomographic method that can be used to determine, from only one viewing direction and with sub-?ngstr?m precision, both the position of individual atoms in the plane of observation and their vertical position. The concept is based on the fact that an experimentally reconstructed exit wave consists of the superposition of the spherical waves that have been scattered by the individual atoms of the object. Furthermore, the phase of a Fourier component of a spherical wave increases with the distance of propagation at a known 'phase speed'. If we assume that an atom is a point-like object, the relationship between the phase and the phase speed of each Fourier component is linear, and the distance between the atom and the plane of observation can therefore be determined by linear fitting. This picture has similarities with Big Bang cosmology, in which the Universe expands from a point-like origin such that the distance of any galaxy from the origin is linearly proportional to the speed at which it moves away from the origin (Hubble expansion). The proof of concept of the method has been demonstrated experimentally for graphene with a two-layer structure and it will work optimally for similar layered materials, such as boron nitride and molybdenum disulphide.     

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.     

Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells

Cytosine methylation is required for mammalian development and is often perturbed in human cancer. To determine how this epigenetic modification is distributed in the genomes of primary and transformed cells, we used an immunocapturing approach followed by DNA microarray analysis to generate methylation profiles of all human chromosomes at 80-kb resolution and for a large set of CpG islands. In primary cells we identified broad genomic regions of differential methylation with higher levels in gene-rich neighborhoods. Female and male cells had indistinguishable profiles for autosomes but differences on the X chromosome. The inactive X chromosome (Xi) was hypermethylated at only a subset of gene-rich regions and, unexpectedly, overall hypomethylated relative to its active counterpart. The chromosomal methylation profile of transformed cells was similar to that of primary cells. Nevertheless, we detected large genomic segments with hypomethylation in the transformed cell residing in gene-poor areas. Furthermore, analysis of 6,000 CpG islands showed that only a small set of promoters was methylated differentially, suggesting that aberrant methylation of CpG island promoters in malignancy might be less frequent than previously hypothesized.     

Mutations in SEPT9 cause hereditary neuralgic amyotrophy

Hereditary neuralgic amyotrophy (HNA) is an autosomal dominant recurrent neuropathy affecting the brachial plexus. HNA is triggered by environmental factors such as infection or parturition. We report three mutations in the gene septin 9 (SEPT9) in six families with HNA linked to chromosome 17q25. HNA is the first monogenetic disease caused by mutations in a gene of the septin family. Septins are implicated in formation of the cytoskeleton, cell division and tumorigenesis.     

Volunteering leads to rock-paper-scissors dynamics in a public goods game

Collective efforts are a trademark of both insect and human societies. They are achieved through relatedness in the former and unknown mechanisms in the latter. The problem of achieving cooperation among non-kin has been described as the 'tragedy of the commons', prophesying the inescapable collapse of many human enterprises. In public goods experiments, initial cooperation usually drops quickly to almost zero. It can be maintained by the opportunity to punish defectors or the need to maintain good reputation. Both schemes require that defectors are identified. Theorists propose that a simple but effective mechanism operates under full anonymity. With optional participation in the public goods game, 'loners' (players who do not join the group), defectors and cooperators will coexist through rock-paper-scissors dynamics. Here we show experimentally that volunteering generates these dynamics in public goods games and that manipulating initial conditions can produce each predicted direction. If, by manipulating displayed decisions, it is pretended that defectors have the highest frequency, loners soon become most frequent, as do cooperators after loners and defectors after cooperators. On average, cooperation is perpetuated at a substantial level.     

Pluripotency of mesenchymal stem cells derived from adult marrow

We report here that cells co-purifying with mesenchymal stem cells--termed here multipotent adult progenitor cells or MAPCs--differentiate, at the single cell level, not only into mesenchymal cells, but also cells with visceral mesoderm, neuroectoderm and endoderm characteristics in vitro. When injected into an early blastocyst, single MAPCs contribute to most, if not all, somatic cell types. On transplantation into a non-irradiated host, MAPCs engraft and differentiate to the haematopoietic lineage, in addition to the epithelium of liver, lung and gut. Engraftment in the haematopoietic system as well as the gastrointestinal tract is increased when MAPCs are transplanted in a minimally irradiated host. As MAPCs proliferate extensively without obvious senescence or loss of differentiation potential, they may be an ideal cell source for therapy of inherited or degenerative diseases.     

A proteomic view of the Plasmodium falciparum life cycle

The completion of the Plasmodium falciparum clone 3D7 genome provides a basis on which to conduct comparative proteomics studies of this human pathogen. Here, we applied a high-throughput proteomics approach to identify new potential drug and vaccine targets and to better understand the biology of this complex protozoan parasite. We characterized four stages of the parasite life cycle (sporozoites, merozoites, trophozoites and gametocytes) by multidimensional protein identification technology. Functional profiling of over 2,400 proteins agreed with the physiology of each stage. Unexpectedly, the antigenically variant proteins of var and rif genes, defined as molecules on the surface of infected erythrocytes, were also largely expressed in sporozoites. The detection of chromosomal clusters encoding co-expressed proteins suggested a potential mechanism for controlling gene expression.     

Investigation of functional, physical, mechanical and thermal properties of TiO2 embedded polyester hybrid composites: A design of experiment (DoE) study

This paper presents a study on the Design of Experiments(Do E) approach to optimize the fabrication parameters of titania(TiO_2) embedded glass fiber reinforced polyester hybrid composites(HCs). HCs of unsaturated polyester resin(UPR) were fabricated using methyl ethyl ketone peroxide(MEKP) as the curing agent by hand lay-up process(HLUP) and compression molding technique(CMT). The fabrication parameters were optimized by Taguchi Do E(an orthogonal array of L25) using 3 control factors(concentration of TiO_2, concentration of MEKP and curing temperature) having 5 levels each. Statistical tools were employed to identify significant factors affecting tensile strengths and its reproducibility during HLUP. It was found that the concentration of TiO_2 in HCs significantly influenced the tensile strength(TS) followed by MEKP concentration and curing temperature. The highest value of TS was obtained at 3 wt% TiO_2, 2 wt% MEKP and 80 °C. Nevertheless, the sensitivity of TiO_2 concentration was basis for fabrication of polyester titania glass fiber hybrids(PTGFHs), which were further investigated for density and void fractions, linear shrinkage, flexural strength, impact strength, hardness and thermal behaviors. Moreover, cross-linking and hydrogen-bonding between polymeric chains, styrene, silica content of glass fiber and TiO_2 particles in PTGFHs were confirmed by Fourier transform infrared spectroscopy.