The changing landscape of membrane protein structural biology through developments in electron microscopy

Membrane proteins are ubiquitous in biology and are key targets for therapeutic development. Despite this, our structural understanding has lagged behind that of their soluble counterparts. This review provides an overview of this important field, focusing in particular on the recent resurgence of electron microscopy (EM) and the increasing role it has to play in the structural studies of membrane proteins, and illustrating this through several case studies. In addition we examine some of the challenges remaining in structural determination, and what steps are underway to enhance our knowledge of these enigmatic proteins

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants

A multi-wavelength survey of AGN in the XMM-LSS field: I. Quasar selection via the KX technique

AIMS: We present a sample of candidate quasars selected using the KX-technique. The data cover 0.68 deg^2 of the X-ray Multi-Mirror (XMM) Large-Scale Structure (LSS) survey area where overlapping multi-wavelength imaging data permits an investigation of the physical nature of selected sources. METHODS: The KX method identifies quasars on the basis of their optical (R and z') to near-infrared (Ks) photometry and point-like morphology. We combine these data with optical (u*,g'r',i',z') and mid-infrared (3.6-24 micron) wavebands to reconstruct the spectral energy distributions (SEDs) of candidate quasars. RESULTS: Of 93 sources selected as candidate quasars by the KX method, 25 are classified as quasars by the subsequent SED analysis. Spectroscopic observations are available for 12/25 of these sources and confirm the quasar hypothesis in each case. Even more, 90% of the SED-classified quasars show X-ray emission, a property not shared by any of the false candidates in the KX-selected sample. Applying a photometric redshift analysis to the sources without spectroscopy indicates that the 25 sources classified as quasars occupy the interval 0.7 < z < 2.5. The remaining 68/93 sources are classified as stars and unresolved galaxies.Comment: 13 pages, 9 figures, A&A 494, p. 579-589. Replaced with published version. Fig. 9 in first astro-ph submission has been update

Increased food availability raises eviction rate in a cooperative breeding mammal

In group-living mammals, the eviction of subordinate females from breeding groups by dominants may serve to reduce feeding competition or to reduce breeding competition. Here, we combined both correlational and experimental approaches to investigate whether increases in food intake by dominant females reduces their tendency to evict subordinate females in wild meerkats ($\textit{Suricata suricatta}$). We used 20 years of long-term data to examine the association between foraging success and eviction rate, and provisioned dominant females during the second half of their pregnancy, when they most commonly evict subordinates. We show that rather than reducing the tendency for dominants to evict subordinates, foraging success of dominant females is positively associated with the probability that pregnant dominant females will evict subordinate females and that experimental feeding increased their rates of eviction. Our results suggest that it is unlikely that the eviction of subordinate females serves to reduce feeding competition and that its principal function may be to reduce reproductive competition. The increase in eviction rates following experimental feeding also suggests that rather than feeding competition, energetic constraints may normally constrain eviction rates.The KMP is supported by the Universities of Cambridge, Zurich and Pretoria. Components of this research were supported by the Natural Environment Research Council (grant no. NE/G006822/1) and the European Research Council (grant no. 294494)

SSE: a nucleotide and amino acid sequence analysis platform

<p>Abstract</p> <p>Background</p> <p>There is an increasing need to develop bioinformatic tools to organise and analyse the rapidly growing amount of nucleotide and amino acid sequence data in organisms ranging from viruses to eukaryotes.</p> <p>Finding</p> <p>A simple sequence editor (SSE) was developed to create an integrated environment where sequences can be aligned, annotated, classified and directly analysed by a number of built-in bioinformatic programs. SSE incorporates a sequence editor for the creation of sequence alignments, a process assisted by integrated CLUSTAL/MUSCLE alignment programs and automated removal of indels. Sequences can be fully annotated and classified into groups and annotated of sequences and sequence groups and access to analytical programs that analyse diversity, recombination and RNA secondary structure. Methods for analysing sequence diversity include measures of divergence and evolutionary distances, identity plots to detect regions of nucleotide or amino acid homology, reconstruction of sequence changes, mono-, di- and higher order nucleotide compositional biases and codon usage.</p> <p>Association Index calculations, GroupScans, Bootscanning and TreeOrder scans perform phylogenetic analyses that reconcile group membership with tree branching orders and provide powerful methods for examining segregation of alleles and detection of recombination events. Phylogeny changes across alignments and scoring of branching order differences between trees using the Robinson-Fould algorithm allow effective visualisation of the sites of recombination events.</p> <p>RNA secondary and tertiary structures play important roles in gene expression and RNA virus replication. For the latter, persistence of infection is additionally associated with pervasive RNA secondary structure throughout viral genomic RNA that modulates interactions with innate cell defences. SSE provides several programs to scan alignments for RNA secondary structure through folding energy thermodynamic calculations and phylogenetic methods (detection of co-variant changes, and structure conservation between divergent sequences). These analyses complement methods based on detection of sequence constraints, such as suppression of synonymous site variability.</p> <p>For each program, results can be plotted in real time during analysis through an integrated graphics package, providing publication quality graphs. Results can be also directed to tabulated datafiles for import into spreadsheet or database programs for further analysis.</p> <p>Conclusions</p> <p>SSE combines sequence editor functions with analytical tools in a comprehensive and user-friendly package that assists considerably in bioinformatic and evolution research.</p

Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

Copyright: © 2015 Solà et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

Eliminating Malaria Vectors.

Malaria vectors which predominantly feed indoors upon humans have been locally eliminated from several settings with insecticide treated nets (ITNs), indoor residual spraying or larval source management. Recent dramatic declines of An. gambiae in east Africa with imperfect ITN coverage suggest mosquito populations can rapidly collapse when forced below realistically achievable, non-zero thresholds of density and supporting resource availability. Here we explain why insecticide-based mosquito elimination strategies are feasible, desirable and can be extended to a wider variety of species by expanding the vector control arsenal to cover a broader spectrum of the resources they need to survive. The greatest advantage of eliminating mosquitoes, rather than merely controlling them, is that this precludes local selection for behavioural or physiological resistance traits. The greatest challenges are therefore to achieve high biological coverage of targeted resources rapidly enough to prevent local emergence of resistance and to then continually exclude, monitor for and respond to re-invasion from external populations

Serum amyloid A primes microglia for ATP-dependent interleukin-1\u3b2 release

Acute-phase response is a systemic reaction to environmental/inflammatory insults and involves production of acute-phase proteins, including serum amyloid A (SAA). Interleukin-1\u3b2 (IL-1\u3b2), a master regulator of neuroinflammation produced by activated inflammatory cells of the myeloid lineage, in particular microglia, plays a key role in the pathogenesis of acute and chronic diseases of the peripheral nervous system and CNS. IL-1\u3b2 release is promoted by ATP acting at the purinergic P2X7 receptor (P2X7R) in cells primed with toll-like receptor (TLR) ligands

Testing density-functional approximations on a lattice and the applicability of the related Hohenberg-Kohn-like theorem

We present a metric-space approach to quantify the performance of approximations in lattice density-functional theory for interacting many-body systems and to explore the regimes where the Hohenberg-Kohn-type theorem on fermionic lattices is applicable. This theorem demonstrates the existence of one-to-one mappings between particle densities, wave functions and external potentials. We then focus on these quantities, and quantify how far apart in metric space the approximated and exact ones are. We apply our method to the one-dimensional Hubbard model for different types of external potentials, and assess the regimes where it is applicable to one of the most used approximations in density-functional theory, the local density approximation (LDA). We find that the potential distance may have a very different behaviour from the density and wave function distances, in some cases even providing the wrong assessments of the LDA performance trends. We attribute this to the systems reaching behaviours which are borderline for the applicability of the one-to-one correspondence between density and external potential. On the contrary the wave function and density distances behave similarly and are always sensitive to system variations. Our metric-based method correctly predicts the regimes where the LDA performs fairly well and the regimes where it fails. This suggests that our method could be a practical tool for testing the efficiency of density-functional approximations

Detailed maps of interstellar clouds in front of omega Centauri: Small-scale structures in the Galactic Disc-Halo interface

We used the multiplex capabilities of the AAOmega spectrograph at the Anglo-Australian Telescope to create a half-square-degree map of the neutral and low-ionized ISM in front of the nearby (~5 kpc), most massive Galactic globular cluster, omega Centauri. Its redshifted, metal-poor and hot horizontal branch stars probe the medium-strong Ca II K and Na I D2 line absorption, and weak absorption in the lambda5780 and lambda5797 Diffuse Interstellar Bands (DIBs), on scales around a parsec. The kinematical and thermodynamical picture emerging from these data is that we predominantly probe the warm neutral medium and weakly-ionized medium of the Galactic Disc-Halo interface, ~0.3-1 kpc above the mid-plane. A comparison with Spitzer Space Telescope 24-micron and DIRBE/IRAS maps of the warm and cold dust emission confirms that both Na I and Ca II trace the overall column density of the warm neutral and weakly-ionized medium. Clear signatures are seen of the depletion of calcium atoms from the gas phase into dust grains. Curiously, the coarse DIRBE/IRAS map is a more reliable representation of the relative reddening between sightlines than the Na I and Ca II absorption-line measurements, most likely because the latter are sensitive to fluctuations in the local ionization conditions. The behaviour of the DIBs is consistent with the lambda5780 band being stronger than the lambda5797 band in regions where the ultraviolet radiation level is relatively high, as in the Disc-Halo interface. This region corresponds to a sigma-type cloud. In all, our maps and simple analytical model calculations show in unprecedented detail that small-scale density and/or ionization structures exist in the extra-planar gas of a spiral galaxy. (abridged)Comment: Accepted for publication in MNRA