Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma

Background:
The physical periphery of a biological cell is mainly described by signaling pathways which are triggered by transmembrane proteins and receptors that are sentinels to control the whole gene regulatory network of a cell. However, our current knowledge about the gene regulatory mechanisms that are governed by extracellular signals is severely limited.Results: The purpose of this paper is three fold. First, we infer a gene regulatory network from a large-scale B-cell lymphoma expression data set using the C3NET algorithm. Second, we provide a functional and structural analysis of the largest connected component of this network, revealing that this network component corresponds to the peripheral region of a cell. Third, we analyze the hierarchical organization of network components of the whole inferred B-cell gene regulatory network by introducing a new approach which exploits the variability within the data as well as the inferential characteristics of C3NET. As a result, we find a functional bisection of the network corresponding to different cellular components.

Conclusions:
Overall, our study allows to highlight the peripheral gene regulatory network of B-cells and shows that it is centered around hub transmembrane proteins located at the physical periphery of the cell. In addition, we identify a variety of novel pathological transmembrane proteins such as ion channel complexes and signaling receptors in B-cell lymphoma. © 2012 Simoes et al.; licensee BioMed Central Ltd.

Structure and interactions of ultracold Yb ions and Rb atoms

In order to study ultracold charge-transfer processes in hybrid atom-ion traps, we have mapped out the potential-energy curves and molecular parameters for several low-lying states of the Rb, Yb+ system. We employ both a multireference configuration interaction and a full configuration interaction (FCI) approach. Turning points, crossing points, potential minima, and spectroscopic molecular constants are obtained for the lowest five molecular states. Long-range parameters, including the dispersion coefficients, are estimated from our ab initio data. The separated-atom ionization potentials and atomic polarizability of the ytterbium atom (ad=128.4 atomic units) are in good agreement with experiment and previous calculations. We present some dynamical calculations for (adiabatic) scattering lengths for the two lowest (Yb, Rb+) channels that were carried out in our work. However, we find that the pseudopotential approximation is rather limited in validity and only applies to nK temperatures. The adiabatic scattering lengths for both the triplet and singlet channels indicate that both are large and negative in the FCI approximation.

The phylogeny, structure and function of trematode cysteine proteases, with particular emphasis on the Fasciola hepatica cathepsin L family

Helminth parasites (nematodes, flatworms and cestodes) infect over 1 billion of the world's population causing high morbidity and mortality. The large tissue-dwelling worms express papain-like cysteine peptidases, termed cathepsins that play important roles in virulence including host entry, tissue migration and the suppression of host immune responses. Much of our knowledge of helminth cathepsins comes from studies using flatworms or trematode (fluke) parasites. The developmentally-regulated expression of these proteases correlates with the passage of parasites through host tissues and their encounters with different host macromolecules. Recent phylogenetic, biochemical and structural studies indicate that trematode cathepsins exhibit overlapping but distinct substrate specificities due to divergence within the protease active site. Here we provide an overview of the evolution, biochemistry and structure of these important enzymes and highlight how recent advances in proteomics and gene silencing techniques are allowing researchers to probe their biological functions. We focus mainly on members of the cathepsin L gene family of the animal and human pathogen, Fasciola hepatica, because of our deep understanding of their function, biochemistry and structure.

A complete analytic theory for structure and dynamics of populations and communities spanning wide ranges in body size

The prediction and management of ecosystem responses to global environmental change would profit from a clearer understanding of the mechanisms determining the structure and dynamics of ecological communities. The analytic theory presented here develops a causally closed picture for the mechanisms controlling community and population size structure, in particular community size spectra, and their dynamic responses to perturbations, with emphasis on marine ecosystems. Important implications are summarised in non-technical form. These include the identification of three different responses of community size spectra to size-specific pressures (of which one is the classical trophic cascade), an explanation for the observed slow recovery of fish communities from exploitation, and clarification of the mechanism controlling predation mortality rates. The theory builds on a community model that describes trophic interactions among size-structured populations and explicitly represents the full life cycles of species. An approximate time-dependent analytic solution of the model is obtained by coarse graining over maturation body sizes to obtain a simple description of the model steady state, linearising near the steady state, and then eliminating intraspecific size structure by means of the quasi-neutral approximation. The result is a convolution equation for trophic interactions among species of different maturation body sizes, which is solved analytically using a novel technique based on a multiscale expansion.

Crystal structure and magnetic properties of the new phase Mn3IrSi

A new phase in the ternary Ir-Mn-Si system has been synthesised. From powder neutron diffraction data the crystal structure was determined to be of the AlAu4 type and to be described in the cubic space group P2(1)3 with the unit cell a = 6.4973(3) Angstrom. Susceptibility measurements using a SQUID-magnetometer showed a transition typical of anti ferromagnetism, with T-N = 210 K. Low temperature antiferromagnetic order is confirmed by extra peaks in neutron diffractograms recorded at 10 and 80 K. (C) 2004 Elsevier B.V. All rights reserved.

The Temporal Focus Scale:Factor structure and association with alcohol use in a sample of Northern Irish school children

The Temporal Focus Scale (TFS) is a 12-item self-report measure of cognitive engagement with the temporal domains of past, present and future. Developed in college student samples, a three-factor structure with adequate reliability and validity was documented in a series of independent studies. We tested the factor structure of the scale in a sample of Northern Irish adolescents and found that our data supported a three factor structure, although there were problems with item 10. Because time perspective measures have been found to relate differentially to various health behaviours, we tested the relations between scores on the TFS and self-reported alcohol use. Results showed that scores on the TFS were not consistent statistical predictors of drinking category in a logistic regression. Results are discussed in terms of scale development, future scale use and the assessment of health-compromising behaviours such as adolescent alcohol consumption. © 2012 The Foundation for Professionals in Services for Adolescents.

Are power laws that estimate fractal dimension a good descriptor of soil structure and its link to soil biological properties?

The study of interrelationships between soil structure and its functional properties is complicated by the fact that the quantitative description of soil structure is challenging. Soil scientists have tackled this challenge by taking advantage of approaches such as fractal geometry, which describes soil architectural complexity through a scaling exponent (D) relating mass and numbers of particles/aggregates to particle/aggregate size. Typically, soil biologists use empirical indices such as mean weight diameters (MWD) and percent of water stable aggregates (WSA), or the entire size distribution, and they have successfully related these indices to key soil features such as C and N dynamics and biological promoters of soil structure. Here, we focused on D, WSA and MWD and we tested whether: D estimated by the exponent of the power law of number-size distributions is a good and consistent correlate of MWD and WSA; D carries information that differs from MWD and WSA; the fraction of variation in D that is uncorrelated with MWD and WSA is related to soil chemical and biological properties that are thought to establish interdependence with soil structure (e.g., organic C, N, arbuscular mycorrhizal fungi). We analysed observational data from a broad scale field study and results from a greenhouse experiment where arbuscular mycorrhizal fungi (AMF) and collembola altered soil structure. We were able to develop empirical models that account for a highly significant and large portion of the correlation observed between WSA and MWD but we did not uncover the mechanisms that underlie this correlation. We conclude that most of the covariance between D and soil biotic (AMF, plant roots) and abiotic (C. N) properties can be accounted for by WSA and MWD. This result implies that the ecological effects of the fragmentation properties described by D and generally discussed under the framework of fractal models can be interpreted under the intuitive perspective of simpler indices and we suggest that the biotic components mostly impacted the largest size fractions, which dominate MWD, WSA and the scaling exponent ruling number-size distributions. (C) 2010 Elsevier Ltd. All rights reserved.

Structure and reactivity of the Ru(0 0 0 1) electrode towards fuel cell electrocatalysis

The reactivity of the Ru(0 0 0 1) electrode towards the adsorption and electrooxidation of CO and methanol has been studied by variable-temperature in situ FTIR spectroscopy in both perchloric acid and sodium hydroxide solution, and the results interpreted in terms of the surface chemistry of the Ru(0 0 0 1) electrode. Both linear (CO) and threefold hollow (CO) binding CO adsorbates (bands at 1970-2040 and 1770-1820 cm, respectively) were observed on the Ru(0 0 0 1) electrode in both 0.1 M HClO and 0.1 M NaOH solutions from the CO adsorption. In the acid solution, CO was detected as the main adsorbed species on Ru(0 0 0 1) surface over all the potential region studied. In contrast, in the alkaline solution, more CO than CO was detected at lower potentials, whilst increasing the potential resulted in the transformation of CO to CO. At higher potentials, the oxidation of the adsorbed CO took place via reaction with the active (1 × 1)-O oxide/hydroxide. It was found that no dissociative adsorption or electrooxidation of methanol took place at the Ru(0 0 0 1) at potentials below 900 mV vs Ag/AgCl in perchloric acid solution at both 20 and 55°C. However, in the alkaline solution, methanol did undergo dissociative adsorption, to form linearly adsorbed CO (CO) with little or no CO adsorbed at threefold hollow sites (CO) at both 20 and 55°C. Increasing the temperature from 20 to 55°C clearly facilitated the methanol dissociative adsorption to CO and also enhanced the electrooxidation of the CO. At the higher potentials, significant oxidation of methanol to CO and methyl formate in acid solution and to bicarbonate and formate in alkaline solution, was observed, which was attributed to the formation of an active RuO phase on the Ru(0 0 0 1) surface, in agreement with our previous studies. © 2003 Elsevier Ltd. All right reserved.

Methanol oxidation on PtRu electrodes. Influence of surface structure and Pt-Ru atom distribution

The activities of different types of PtRu catalysts for methanol oxidation are compared. Materials used were: UHV-cleaned PtRu alloys, UHV-evaporated Ru onto Pt(111) as well as adsorbed Ru on Pt(111) prepared with and without additional reduction by hydrogen. Differences in the catalytic activity are observed to depend on the preparation procedure of the catalysts. The dependence of the respective catalytic activities upon the surface composition is reported. UHV-STM data for Pt(111)/Ru show the formation of two- and three-dimensional structures depending on surface coverage. A molecular insight on the electrochemical reaction is given via in situ infrared spectroscopy. Analysis of the data indicates that the most probable rate-determining step is the reaction of adsorbed CO with Ru oxide.