Artificial molecular and nanostructures for advanced nanomachinery

Artificial nanomachines can be broadly defined as manmade molecular and nanosystems that are capable of performing useful tasks, very often, by means of doing mechanical work at the nanoscale. Recent advances in nanoscience allow these tiny machines to be designed and made with unprecedented sophistication and complexity, showing promise in novel applications, including molecular assemblers, self-propelling nanocarriers and in vivo molecular computation. This Feature Article overviews and compares major types of nanoscale machines, including molecular machines, self-assembled nanomachines and hybrid inorganic nanomachines, to reveal common structural features and operating principles across different length scales and material systems. We will focus on systems with feature size between 1 and 100 nm, where classical laws of physics meet those of quantum mechanics, giving rise to a spectrum of exotic physiochemical properties. Concepts of nanomachines will be illustrated by selected seminal work along with state-of-the-art progress, including our own contribution, across the fields. The Article will conclude with a brief outlook of this exciting research area

The 2dF Galaxy Redshift Survey: correlation functions, peculiar velocities and the matter density of the Universe

We present a detailed analysis of the two-point correlation function, ξ(σ, π), from the 2dF Galaxy Redshift Survey (2dFGRS). The large size of the catalogue, which contains ∼220 000 redshifts, allows us to make high-precision measurements of various properties of the galaxy clustering pattern. The effective redshift at which our estimates are made is zs≈ 0.15, and similarly the effective luminosity, Ls≈ 1.4L*. We estimate the redshift-space correlation function, ξ(s), from which we measure the redshift-space clustering length, s0= 6.82 ± 0.28 h−1 Mpc. We also estimate the projected correlation function, Ξ(σ), and the real-space correlation function, ξ(r), which can be fit by a power law (r/r0), with r0= 5.05 ± 0.26 h−1 Mpc, γr= 1.67 ± 0.03. For r≳ 20 h−1 Mpc, ξ drops below a power law as, for instance, is expected in the popular Λ cold dark matter model. The ratio of amplitudes of the real- and redshift-space correlation functions on scales of 8–30 h−1 Mpc gives an estimate of the redshift-space distortion parameter β. The quadrupole moment of ξ(σ, π) on scales 30–40 h−1 Mpc provides another estimate of β. We also estimate the distribution function of pairwise peculiar velocities, ƒ(v), including rigorously the significant effect due to the infall velocities, and we find that the distribution is well fit by an exponential form. The accuracy of our ξ(σ, π) measurement is sufficient to constrain a model, which simultaneously fits the shape and amplitude of ξ(r) and the two redshift-space distortion effects parametrized by β and velocity dispersion, a. We find β= 0.49 ± 0.09 and a= 506 ± 52 km s−1, although the best-fitting values are strongly correlated. We measure the variation of the peculiar velocity dispersion with projected separation, a(σ), and find that the shape is consistent with models and simulations. This is the first time that β and ƒ(v) have been estimated from a self-consistent model of galaxy velocities. Using the constraints on bias from recent estimates, and taking account of redshift evolution, we conclude that β (L=L*, z= 0) = 0.47 ± 0.08, and that the present-day matter density of the Universe, Ωm≈ 0.3, consistent with other 2dFGRS estimates and independent analyses

tropiTree:an NGS-based EST-SSR resource for 24 tropical tree species

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data

A review of elliptical and disc galaxy structure, and modern scaling laws

A century ago, in 1911 and 1913, Plummer and then Reynolds introduced their models to describe the radial distribution of stars in `nebulae'. This article reviews the progress since then, providing both an historical perspective and a contemporary review of the stellar structure of bulges, discs and elliptical galaxies. The quantification of galaxy nuclei, such as central mass deficits and excess nuclear light, plus the structure of dark matter halos and cD galaxy envelopes, are discussed. Issues pertaining to spiral galaxies including dust, bulge-to-disc ratios, bulgeless galaxies, bars and the identification of pseudobulges are also reviewed. An array of modern scaling relations involving sizes, luminosities, surface brightnesses and stellar concentrations are presented, many of which are shown to be curved. These 'redshift zero' relations not only quantify the behavior and nature of galaxies in the Universe today, but are the modern benchmark for evolutionary studies of galaxies, whether based on observations, N-body-simulations or semi-analytical modelling. For example, it is shown that some of the recently discovered compact elliptical galaxies at 1.5 < z < 2.5 may be the bulges of modern disc galaxies.Comment: Condensed version (due to Contract) of an invited review article to appear in "Planets, Stars and Stellar Systems"(www.springer.com/astronomy/book/978-90-481-8818-5). 500+ references incl. many somewhat forgotten, pioneer papers. Original submission to Springer: 07-June-201

Complement Activity in the Egg Cytosol of Zebrafish Danio rerio: Evidence for the Defense Role of Maternal Complement Components

Most fish embryos that develop externally are exposed to an environment full of microbes. How they survive microbial attacks are not understood to date. Here we demonstrated that the egg cytosol prepared from the newly fertilized eggs of zebrafish Danio rerio is capable of killing the Gram-negative bacterium Escherichia coli, via in vitro assay system of the complement activity established. All findings indicate that it is the complement system operating via the alternative pathway that is attributable to the bacteriolytic activity. This is the first report providing the evidence for the functional role of the maternal complement components in fish eggs, paving the way for study of maternal immunity in other organisms whose eggs are fertilized in vitro

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Investigation of Atomic Level Patterns in Protein—Small Ligand Interactions

BACKGROUND: Shape complementarity and non-covalent interactions are believed to drive protein-ligand interaction. To date protein-protein, protein-DNA, and protein-RNA interactions were systematically investigated, which is in contrast to interactions with small ligands. We investigate the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset of 2,320 complexes. METHODOLOGY AND PRINCIPAL FINDINGS: We show that protein-ligand interactions are governed by different forces for different ligand types, i.e., protein-organic compound interactions are governed by hydrogen bonds, van der Waals contacts, and covalent bonds; protein-metal ion interactions are dominated by electrostatic force and coordination bonds; protein-anion interactions are established with electrostatic force, hydrogen bonds, and van der Waals contacts; and protein-inorganic cluster interactions are driven by coordination bonds. We extracted several frequently occurring atomic-level patterns concerning these interactions. For instance, 73% of investigated covalent bonds were summarized with just three patterns in which bonds are formed between thiol of Cys and carbon or sulfur atoms of ligands, and nitrogen of Lys and carbon of ligands. Similar patterns were found for the coordination bonds. Hydrogen bonds occur in 67% of protein-organic compound complexes and 66% of them are formed between NH- group of protein residues and oxygen atom of ligands. We quantify relative abundance of specific interaction types and discuss their characteristic features. The extracted protein-organic compound patterns are shown to complement and improve a geometric approach for prediction of binding sites. CONCLUSIONS AND SIGNIFICANCE: We show that for a given type (group) of ligands and type of the interaction force, majority of protein-ligand interactions are repetitive and could be summarized with several simple atomic-level patterns. We summarize and analyze 10 frequently occurring interaction patterns that cover 56% of all considered complexes and we show a practical application for the patterns that concerns interactions with organic compounds

The utility of pathway selective estrogen receptor ligands that inhibit nuclear factor-κB transcriptional activity in models of rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic inflammatory disease that produces synovial proliferation and joint erosions. The pathologic lesions of RA are driven through the production of inflammatory mediators in the synovium mediated, in part, by the transcription factor NF-κB. We have identified a non-steroidal estrogen receptor ligand, WAY-169916, that selectively inhibits NF-κB transcriptional activity but is devoid of conventional estrogenic activity. The activity of WAY-169916 was monitored in two models of arthritis, the HLA-B27 transgenic rat and the Lewis rat adjuvant-induced model, after daily oral administration. In both models, a near complete reversal in hindpaw scores was observed as well as marked improvements in the histological scores. In the Lewis rat adjuvant model, WAY-169916 markedly suppresses the adjuvant induction of three serum acute phase proteins: haptoglobin, α1-acid glycoprotein (α1-AGP), and C-reactive protein (CRP). Gene expression experiments also demonstrate a global suppression of adjuvant-induced gene expression in the spleen, liver, and popliteal lymph nodes. Finally, WAY-169916 was effective in suppressing tumor necrosis factor-α-mediated inflammatory gene expression in fibroblast-like synoviocytes isolated from patients with RA. Together, these data suggest the utility of WAY-169916, and other compounds in its class, in treating RA through global suppression of inflammation via selective blockade of NF-κB transcriptional activity

Prevalence and risk factors of helminths and intestinal protozoa infections among children from primary schools in western Tajikistan

BACKGROUND: Intestinal parasitic infections represent a public health problem in Tajikistan, but epidemiological evidence is scarce. The present study aimed at assessing the extent of helminths and intestinal protozoa infections among children of 10 schools in four districts of Tajikistan, and to make recommendations for control. METHODS: A cross-sectional survey was carried out in early 2009. All children attending grades 2 and 3 (aged 7-11 years) from 10 randomly selected schools were invited to provide a stool sample and interviewed about sanitary situation and hygiene behaviour. A questionnaire pertaining to demographic and socioeconomic characteristics was addressed to the heads of households. On the spot, stool samples were subjected to duplicate Kato-Katz thick smear examination for helminth diagnosis. Additionally, 1-2 g of stool was fixed in sodium acetate-acetic acid formalin, transferred to a specialized laboratory in Europe and examined for helminths and intestinal protozoa. The results from both methods combined served as diagnostic 'gold' standard. RESULTS: Out of 623 registered children, 602 participated in our survey. The overall prevalence of infection with helminths and pathogenic intestinal protozoa was 32.0% and 47.1%, respectively. There was pronounced spatial heterogeneity. The most common helminth species was Hymenolepis nana (25.8%), whereas the prevalences of Ascaris lumbricoides, hookworm and Enterobius vermicularis were below 5%. The prevalence of pathogenic intestinal protozoa, namely Giardia intestinalis and Entamoeba histolytica/E. dispar was 26.4% and 25.9%, respectively. Almost half of the households draw drinking water from unimproved sources, such as irrigation canals, rivers and unprotected wells. Sanitary facilities were pit latrines, mostly private, and a few shared with neighbours. The use of public tap/standpipe as a source of drinking water emerged as a protective factor for G. intestinalis infection. Protecte spring water reduced the risk of infection with E. histolytica/E. dispar and H. nana. CONCLUSIONS: Our data obtained from the ecological 'lowland' areas in western Tajikistan call for school-based deworming (recommended drugs: albendazole and metronidazole), combined with hygiene promotion and improved sanitation. Further investigations are needed to determine whether H. nana represents a public health problem

Natural Variation in Grain Selenium Concentration of Wild Barley, Hordeum spontaneum, Populations from Israel

Wild barley (Hordeum spontaneum), the progenitor of cultivated barley, is an important genetic resource for cereal improvement. Selenium (Se) is an essential trace mineral for humans and animals with antioxidant, anticancer, antiarthropathy, and antiviral effects. In the current study, the grain Se concentration (GSeC) of 92 H. spontaneum genotypes collected from nine populations representing different habitats in Israel was investigated in the central area of Guizhou Province, China. Remarkable variations in GSeC were found between and within populations, ranging from 0 to 0.387 mg kg−1 among the 92 genotypes with an average of 0.047 mg kg−1. Genotype 20_C from the Sede Boqer population had the highest GSeC, while genotype 25_1 from the Atlit population had the lowest. The mean value of GSeC in each population varied from 0.010 to 0.105 mg kg−1. The coefficient of variation for each population ranged from 12% to 163%. Significant correlations were found between GSeC and 12 ecogeographical factors out of 14 studied. Habitat soil type also significantly affected GSeC. The wild barley exhibited wider GSeC ranges and greater diversity than its cultivated counterparts. The higher Se grain concentrations found in H. spontaneum populations suggest that wild barley germplasm confer higher abilities for Se uptake and accumulation, which can be used for genetic studies of barley nutritional value and for further improvement of domesticated cereals