Validating maps from single particle electron cryomicroscopy

Progress in single particle cryo-EM, most recently due to the introduction of direct detector devices, has made the high-resolution structure determination of biological assemblies smaller than 500kDa more routine, but has also increased attention on the need for tools to demonstrate the validity of single particle maps. Although map validation is a continuing subject of research, some consensus has been reached on procedures that reduce model bias and over-fitting during map refinement as well as specific tests that demonstrate map validity. Tilt-pair analysis may be used as a method for demonstrating the consistency at low resolution of a map with image data. For higher-resolution maps, new procedures for more robust resolution assessment and for validating the refinement of atomic coordinate models into single particle maps have been developed

Ocean-atmosphere climate shift during the mid-to-late Holocene transition

Climate records of the mid-to-late Holocene transition, between 3–4 thousand years before present (ka), often exhibit a rapid change in response to the gradual change in orbital insolation. Here we investigate North Atlantic Central Water circulation as a possible mechanism regulating the latitudinal temperature gradient (LTG), which, in turn, amplifies climate sensitivity to small changes in solar irradiance. Through this mechanism, sharp climate events and transitions are the result of a positive feedback process that propagates and amplifies climate events in the North Atlantic region. We explore these linkages using an intermediate water temperature record reconstructed from Mg/Ca measurements of benthic foraminifera (Hyalinea balthica) from a sediment core off NW Africa (889 m depth) between 0 to 5.5 ka. Our results show that Eastern North Atlantic Central Waters (ENACW) cooled by ~1°±0.7 °C~1°±0.7 °C and densities decreased by σθ=0.4±0.2σθ=0.4±0.2 between 3.3 and 2.6 ka. This shift in ENACW hydrography illustrates a transition towards enhanced mid-latitude atmospheric circulation after 2.7 ka in particular during cold events of the late-Holocene. The presented records demonstrate the important role of ENACW circulation in propagating the climate signatures of the LTG by reducing the meridional heat transfer from high to low latitudes during the transition from the Holocene Thermal Maximum to the late-Holocene. In addition, the dynamic response of ENACW circulation to the gradual climate forcing of LTGs provides a prime example of an amplifying climate feedback mechanism

Global Slope Change Synopses for Measurement Maps

Quality control using scalar quality measures is standard practice in manufacturing. However, there are also quality measures that are determined at a large number of positions on a product, since the spatial distribution is important. We denote such a mapping of local coordinates on the product to values of a measure as a measurement map. In this paper, we examine how measurement maps can be clustered according to a novel notion of similarity - mapscape similarity - that considers the overall course of the measure on the map. We present a class of synopses called global slope change that uses the profile of the measure along several lines from a reference point to different points on the borders to represent a measurement map. We conduct an evaluation of global slope change using a real-world data set from manufacturing and demonstrate its superiority over other synopses

How to Control Clustering Results?

One of the most important and challenging questions in the area of clustering is how to choose the best-fitting algorithm and parameterization to obtain an optimal clustering for the considered data. The clustering aggregation concept tries to bypass this problem by generating a set of separate, heterogeneous partitionings of the same data set, from which an aggregate clustering is derived. As of now, almost every existing aggregation approach combines given crisp clusterings on the basis of pair-wise similarities. In this paper, we regard an input set of soft clusterings and show that it contains additional information that is efficiently useable for the aggregation. Our approach introduces an expansion of mentioned pair-wise similarities, allowing control and adjustment of the aggregation process and its result. Our experiments show that our flexible approach offers adaptive results, improved identification of structures and high useability

Cryomicroscopy reveals the structural basis for a flexible hinge motion in the immunoglobulin M pentamer

Immunoglobulin M (IgM) is the most ancient of the five isotypes of immunoglobulin (Ig) molecules and serves as the first line of defence against pathogens. Here, we use cryo-EM to image the structure of the human full-length IgM pentamer, revealing antigen binding domains flexibly attached to the asymmetric and rigid core formed by the Cμ4 and Cμ3 constant regions and the J-chain. A hinge is located at the Cμ3/Cμ2 domain interface, allowing Fabs and Cμ2 to pivot as a unit both in-plane and out-of-plane. This motion is different from that observed in IgG and IgA, where the two Fab arms are able to swing independently. A biased orientation of one pair of Fab arms results from asymmetry in the constant domain (Cμ3) at the IgM subunit interacting most extensively with the J-chain. This may influence the multi-valent binding to surface-associated antigens and complement pathway activation. By comparison, the structure of the Fc fragment in the IgM monomer is similar to that of the pentamer, but is more dynamic in the Cμ4 domain

Turning to God in the Face of Ostracism: Effects of Social Exclusion on Religiousness

The present research proposes that individuals who are socially excluded can turn to religion to cope with the experience. Empirical studies conducted to test this hypothesis consistently found that socially excluded persons reported (a) significantly higher levels of religious affiliation (Studies 1, 2, and 4) and (b) stronger intentions to engage in religious behaviors (Study 2) than comparable, nonexcluded individuals. Direct support for the stress-buffering function of religiousness was also found, with a religious prime reducing the aggression-eliciting effects of consequent social rejection (Study 5). These effects were observed in both Christian and Muslim samples, revealing that turning to religion can be a powerful coping response when dealing with social rejection. Theoretical and practical implications of these findings are discussed

Relationship between quantum decoherence times and solvation dynamics in condensed phase chemical systems

A relationship between the time scales of quantum coherence loss and short-time solvent response for a solute/bath system is derived for a Gaussian wave packet approximation for the bath. Decoherence and solvent response times are shown to be directly proportional to each other, with the proportionality coefficient given by the ratio of the thermal energy fluctuations to the fluctuations in the system-bath coupling. The relationship allows the prediction of decoherence times for condensed phase chemical systems from well developed experimental methods.Comment: 10 pages, no figures, late

Three-dimensional architecture of the human BRCA1-A histone deubiquitinase core complex

BRCA1 is a tumor suppressor found to be mutated in hereditary breast and ovarian cancer and plays key roles in the maintenance of genomic stability by homologous recombination repair. It is recruited to damaged chromatin as a component of the BRCA1-A deubiquitinase, which cleaves K63-linked ubiquitin chains attached to histone H2A and H2AX. BRCA1-A contributes to checkpoint regulation, repair pathway choice, and HR repair efficiency through molecular mechanisms that remain largely obscure. The structure of an active core complex comprising two Abraxas/BRCC36/BRCC45/MERIT40 tetramers determined by negative-stain electron microscopy (EM) reveals a distorted V-shape architecture in which a dimer of Abraxas/BRCC36 heterodimers sits at the base, with BRCC45/Merit40 pairs occupying each arm. The location and ubiquitin-binding activity of BRCC45 suggest that it may provide accessory interactions with nucleosome-linked ubiquitin chains that contribute to their efficient processing. Our data also suggest how ataxia telangiectasia mutated (ATM)-dependent BRCA1 dimerization may stabilize self-association of the entire BRCA1-A complex

Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis

SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2’-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes

CDK1 controls CHMP7-dependent nuclear envelope reformation

Through membrane sealing and disassembly of spindle microtubules, the Endosomal Sorting Complex Required for Transport-III (ESCRT-III) machinery has emerged as a key player in the regeneration of a sealed nuclear envelope (NE) during mitotic exit, and in the repair of this organelle during interphase rupture. ESCRT-III assembly at the NE occurs transiently during mitotic (M) exit and is initiated when CHMP7, an ER-localised ESCRT-II/ESCRT-III hybrid protein, interacts with the Inner Nuclear Membrane (INM) protein LEM2. Whilst classical nucleocytoplasmic transport mechanisms have been proposed to separate LEM2 and CHMP7 during interphase, it is unclear how CHMP7 assembly is suppressed in mitosis when NE and ER identities are mixed. Here, we use live cell imaging and protein biochemistry to examine the biology of these proteins during M-exit. Firstly, we show that CHMP7 plays an important role in the dissolution of LEM2 clusters that form at the NE during M-exit. Secondly, we show that CDK1 phosphorylates CHMP7 upon M-entry at Ser3 and Ser441 and that this phosphorylation reduces CHMP7’s interaction with LEM2, limiting its assembly during M-phase. We show that spatiotemporal differences in the dephosphorylation of CHMP7 license its assembly at the NE during telophase, but restrict its assembly on the ER at this time. Without CDK1 phosphorylation, CHMP7 undergoes inappropriate assembly in the peripheral ER during M-exit, capturing LEM2 and downstream ESCRT-III components. Lastly, we establish that a microtubule network is dispensable for ESCRT-III assembly at the reforming nuclear envelope. These data identify a key cell-cycle control programme allowing ESCRT-III-dependent nuclear regeneration