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Sample records for cryoem density maps

  1. Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps.

    PubMed

    Si, Dong; He, Jing

    2017-01-01

    Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although α-helices can be detected from density maps at 5-8 Å resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 Å-8.25 Å resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands with an overall 2.05 Å 2-way distance between the detected β-traces and the observed ones, if the best of the fifteen detection cases is considered.

  2. Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps

    PubMed Central

    Si, Dong

    2017-01-01

    Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although α-helices can be detected from density maps at 5–8 Å resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 Å–8.25 Å resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands with an overall 2.05 Å 2-way distance between the detected β-traces and the observed ones, if the best of the fifteen detection cases is considered. PMID:28164115

  3. Refinement of Atomic Structures Against cryo-EM Maps.

    PubMed

    Murshudov, G N

    2016-01-01

    This review describes some of the methods for atomic structure refinement (fitting) against medium/high-resolution single-particle cryo-EM reconstructed maps. Some of the tools developed for macromolecular X-ray crystal structure analysis, especially those encapsulating prior chemical and structural information can be transferred directly for fitting into cryo-EM maps. However, despite the similarities, there are significant differences between data produced by these two techniques; therefore, different likelihood functions linking the data and model must be used in cryo-EM and crystallographic refinement. Although tools described in this review are mostly designed for medium/high-resolution maps, if maps have sufficiently good quality, then these tools can also be used at moderately low resolution, as shown in one example. In addition, the use of several popular crystallographic methods is strongly discouraged in cryo-EM refinement, such as 2Fo-Fc maps, solvent flattening, and feature-enhanced maps (FEMs) for visualization and model (re)building. Two problems in the cryo-EM field are overclaiming resolution and severe map oversharpening. Both of these should be avoided; if data of higher resolution than the signal are used, then overfitting of model parameters into the noise is unavoidable, and if maps are oversharpened, then at least parts of the maps might become very noisy and ultimately uninterpretable. Both of these may result in suboptimal and even misleading atomic models.

  4. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

    PubMed Central

    Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

    2016-01-01

    Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3–4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids – typical in a macromolecular assembly – is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps. DOI: http://dx.doi.org/10.7554/eLife.17219.001 PMID:27669148

  5. Bayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps

    PubMed Central

    Habeck, Michael

    2017-01-01

    A growing array of experimental techniques allows us to characterize the three-dimensional structure of large biological assemblies at increasingly higher resolution. In addition to X-ray crystallography and nuclear magnetic resonance in solution, new structure determination methods such cryo-electron microscopy (cryo-EM), crosslinking/mass spectrometry and solid-state NMR have emerged. Often it is not sufficient to use a single experimental method, but complementary data need to be collected by using multiple techniques. The integration of all datasets can only be achieved by computational means. This article describes Inferential structure determination, a Bayesian approach to integrative modeling of biomolecular complexes with hybrid structural data. I will introduce probabilistic models for cryo-EM maps and outline Markov chain Monte Carlo algorithms for sampling model structures from the posterior distribution. I will focus on rigid and flexible modeling with cryo-EM data and discuss some of the computational challenges of Bayesian inference in the context of biomolecular modeling. PMID:28382301

  6. Accurate model annotation of a near-atomic resolution cryo-EM map

    PubMed Central

    Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D.; King, Jonathan A.; Schmid, Michael F.; Chiu, Wah

    2017-01-01

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages. PMID:28270620

  7. Accurate model annotation of a near-atomic resolution cryo-EM map.

    PubMed

    Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D; King, Jonathan A; Schmid, Michael F; Chiu, Wah

    2017-03-21

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

  8. ATTRACT-EM: A New Method for the Computational Assembly of Large Molecular Machines Using Cryo-EM Maps

    PubMed Central

    de Vries, Sjoerd J.; Zacharias, Martin

    2012-01-01

    Many of the most important functions in the cell are carried out by proteins organized in large molecular machines. Cryo-electron microscopy (cryo-EM) is increasingly being used to obtain low resolution density maps of these large assemblies. A new method, ATTRACT-EM, for the computational assembly of molecular assemblies from their components has been developed. Based on concepts from the protein-protein docking field, it utilizes cryo-EM density maps to assemble molecular subunits at near atomic detail, starting from millions of initial subunit configurations. The search efficiency was further enhanced by recombining partial solutions, the inclusion of symmetry information, and refinement using a molecular force field. The approach was tested on the GroES-GroEL system, using an experimental cryo-EM map at 23.5 Å resolution, and on several smaller complexes. Inclusion of experimental information on the symmetry of the systems and the application of a new gradient vector matching algorithm allowed the efficient identification of docked assemblies in close agreement with experiment. Application to the GroES-GroEL complex resulted in a top ranked model with a deviation of 4.6 Å (and a 2.8 Å model within the top 10) from the GroES-GroEL crystal structure, a significant improvement over existing methods. PMID:23251350

  9. Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

    PubMed

    DiMaio, F; Chiu, W

    2016-01-01

    Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data.

  10. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

    SciTech Connect

    Dror, Oranit Lasker, Keren; Nussinov, Ruth; Wolfson, Haim

    2007-01-01

    A method for detecting structural homologs of components in an intermediate resolution cryo-EM map and their spatial configuration is presented. Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6–10 Å resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 Å resolution.

  11. Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix.

    PubMed

    He, Jing; Zeil, Stephanie; Hallak, Hussam; McKaig, Kele; Kovacs, Julio; Wriggers, Willy

    2015-11-01

    Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices.

  12. Principles of cryo-EM single-particle image processing

    PubMed Central

    Sigworth, Fred J.

    2016-01-01

    Single-particle reconstruction is the process by which 3D density maps are obtained from a set of low-dose cryo-EM images of individual macromolecules. This review considers the fundamental principles of this process and the steps in the overall workflow for single-particle image processing. Also considered are the limits that image signal-to-noise ratio places on resolution and the distinguishing of heterogeneous particle populations. PMID:26705325

  13. Direct Measurement of the Structure of Reconstituted High-Density Lipoproteins by Cryo-EM

    PubMed Central

    Murray, Stephen C.; Gillard, Baiba K.; Ludtke, Steven J.; Pownall, Henry J.

    2016-01-01

    Early forms of high-density lipoproteins (HDL), nascent HDL, are formed by the interaction of apolipoprotein AI with macrophage and hepatic ATP-binding cassette transporter member 1. Various plasma activities convert nascent to mature HDL, comprising phosphatidylcholine (PC) and cholesterol, which are selectively removed by hepatic receptors. This process is important in reducing the cholesterol burden of arterial wall macrophages, an important cell type in all stages of atherosclerosis. Interaction of apolipoprotein AI with dimyristoyl (DM)PC forms reconstituted (r)HDL, which is a good model of nascent HDL. rHDL have been used as an antiathersclerosis therapy that enhances reverse cholesterol transport in humans and animal models. Thus, identification of the structure of rHDL would inform about that of nascent HDL and how rHDL improves reverse cholesterol transport in an atheroprotective way. Early studies of rHDL suggested a discoidal structure, which included pairs of antiparallel helices of apolipoprotein AI circumscribing a phospholipid bilayer. Another rHDL model based on small angle neutron scattering supported a double superhelical structure. Herein, we report a cryo-electron microscopy-based model of a large rHDL formed spontaneously from apolipoprotein AI, cholesterol, and excess DMPC and isolated to near homogeneity. After reconstruction we obtained an rHDL structure comprising DMPC, cholesterol, and apolipoprotein AI (423:74:1 mol/mol) forming a discoidal particle 360 Å in diameter and 45 Å thick; these dimensions are consistent with the stoichiometry of the particles. Given that cryo-electron microscopy directly observes projections of individual rHDL particles in different orientations, we can unambiguously state that rHDL particles are protein bounded discoidal bilayers. PMID:26743047

  14. Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly

    PubMed Central

    Lasker, Keren; Topf, Maya; Sali, Andrej; Wolfson, Haim J.

    2009-01-01

    Summary Models of macromolecular assemblies are essential for a mechanistic description of cellular processes. Such models are increasingly obtained by fitting atomic-resolution structures of components into a density map of the whole assembly. Yet, current density-fitting techniques are frequently insufficient for an unambiguous determination of the positions and orientations of all components. Here, we describe MultiFit, a method for simultaneously fitting atomic structures of components into their assembly density map at resolutions as low as 25 Å. The component positions and orientations are optimized with respect to a scoring function that includes the quality-of-fit of components in the map, the protrusion of components from the map envelope, as well as the shape complementarity between pairs of components. The scoring function is optimized by our exact inference optimizer DOMINO that efficiently finds the global minimum in a discrete sampling space. MultiFit was benchmarked on 7 assemblies of known structure, consisting of up to 7 proteins each. The input atomic structures of the components were obtained from the Protein Data Bank as well as by comparative modeling based on 16 – 99% sequence identity to a template structure. A near-native configuration was usually found as the top-scoring model. Therefore, MultiFit can provide initial configurations for further refinement of many multi-component assembly structures described by electron microscopy. PMID:19233204

  15. Perceived density of road maps.

    PubMed

    Schwartz-Chassidim, Hadas; Meyer, Joachim; Parmet, Yisrael; Rogatka, Efrat; Amzaleg, Ohad

    2014-11-01

    Maps should be designed so that users can comprehend and use the information. Display decisions, such as choosing the scale at which an area is shown, depend on properties of the displayed information such as the perceived density (PD) of the information. Taking a psychophysical approach we suggest that the PD of information in a road map is related to the scale and properties of the mapped area. 54 participants rated the PD of 60 maps from different regions. We provide a simple model that predicts the PD of electronic road map displays, using the logarithm of the number of roads, the logarithm of the number of junctions and the length of the shown roads. The PD model was cross-validated using a different set of 60 maps (n = 44). The model can be used for automatically adjusting display scales and for evaluating map designs, considering the required PD to perform a map-related task.

  16. Gorgon and Pathwalking: Macromolecular Modeling Tools for Subnanometer Resolution Density Maps

    PubMed Central

    Baker, Matthew L.; Baker, Mariah R.; Hryc, Corey F.; Ju, Tao; Chiu, Wah

    2013-01-01

    The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions. PMID:22696403

  17. Near-atomic-resolution cryo-EM for molecular virology.

    PubMed

    Hryc, Corey F; Chen, Dong-Hua; Chiu, Wah

    2011-08-01

    Electron cryo-microscopy (cryo-EM) is a technique in structural biology that is widely used to solve the three-dimensional structures of macromolecular assemblies, close to their biological and solution conditions. Recent improvements in cryo-EM and single-particle reconstruction methodologies have led to the determination of several virus structures at near-atomic resolution (3.3 - 4.6 Å). These cryo-EM structures not only resolve the Cα backbones and side-chain densities of viral capsid proteins, but also suggest functional roles that the protein domains and some key amino acid residues play. This paper reviews the recent advances in near-atomic-resolution cryo-EM for probing the mechanisms of virus assembly and morphogenesis.

  18. Building and Refining Protein Models within Cryo-electron Microscopy Density Maps Based on Homology Modeling and Multi-scale Structure Refinement

    PubMed Central

    Zhu, Jiang; Cheng, Lingpeng; Fang, Qin; Hong Zhou, Z.; Honig, Barry

    2010-01-01

    Summary Automatic modeling methods using cryo-electron microscopy (cryoEM) density maps as constrains are promising approaches to building atomic models of individual proteins or protein domains. However, their application to large macromolecular assemblies has not been possible largely due to computational limitations inherent to such unsupervised methods. Here we describe a new method, EM-IMO, for building, modifying and refining local structures of protein models using cryoEM maps as a constraint. As a supervised refinement method, EM-IMO allows users to specify parameters derived from inspections, so as to guide, and as a consequence, significantly speed up the refinement. An EM-IMO-based refinement protocol is first benchmarked on a data set of 50 homology models using simulated density maps. A multi-scale refinement strategy that combines EM-IMO-based and molecular dynamics (MD)-based refinement is then applied to build backbone models for the seven conformers of the five capsid proteins in our near-atomic resolution cryoEM map of the grass carp reovirus (GCRV) virion, a member of the aquareovirus genus of the Reoviridae family. The refined models allow us to reconstruct a backbone model of the entire GCRV capsid and provide valuable functional insights that are described in the accompanying publication. Our study demonstrates that the integrated use of homology modeling and a multi-scale refinement protocol that combines supervised and automated structure refinement offers a practical strategy for building atomic models based on medium- to high-resolution cryoEM density maps. PMID:20109465

  19. Active Free Surface Density Maps

    NASA Astrophysics Data System (ADS)

    Çelen, S.

    2016-10-01

    Percolation problems were occupied to many physical problems after their establishment in 1957 by Broadbent and Hammersley. They can be used to solve complex systems such as bone remodeling. Volume fraction method was adopted to set some algorithms in the literature. However, different rate of osteoporosis could be observed for different microstructures which have the same mass density, mechanical stimuli, hormonal stimuli and nutrition. Thus it was emphasized that the bone might have identical porosity with different specific surfaces. Active free surface density of bone refers the used total area for its effective free surface. The purpose of this manuscript is to consolidate a mathematical approach which can be called as “active free surface density maps” for different surface patterns and derive their formulations. Active free surface density ratios were calculated for different Archimedean lattice models according to Helmholtz free energy and they were compared with their site and bond percolation thresholds from the background studies to derive their potential probability for bone remodeling.

  20. Density Altitude Maps of Iran and Iraq

    DTIC Science & Technology

    1991-05-01

    standard, DA is lower than PA. DA can also be expressed as the altitude in the ICAO standard atmosphere at which a given density occurs. The maps...produced in this study show the altitude in the ICAO standard atmosphere at which surface density occurs.

  1. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.

    PubMed

    Punjani, Ali; Rubinstein, John L; Fleet, David J; Brubaker, Marcus A

    2017-03-01

    Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a few days. However, processing cryo-EM image data to reveal heterogeneity in the protein structure and to refine 3D maps to high resolution frequently becomes a severe bottleneck, requiring expert intervention, prior structural knowledge, and weeks of calculations on expensive computer clusters. Here we show that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer. Furthermore, SGD with Bayesian marginalization allows ab initio 3D classification, enabling automated analysis and discovery of unexpected structures without bias from a reference map. These algorithms are combined in a user-friendly computer program named cryoSPARC (http://www.cryosparc.com).

  2. Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids.

    PubMed

    van Zundert, G C P; Bonvin, A M J J

    2016-08-01

    Cryo-electron microscopy provides fascinating structural insight into large macromolecular machines at increasing detail. Despite significant advances in the field, the resolution of the resulting three-dimensional images is still typically insufficient for de novo model building. To bridge the resolution gap and give an atomic interpretation to the data, high-resolution models are typically placed into the density as rigid bodies. Unfortunately, this is often done manually using graphics software, a subjective method that can lead to over-interpretation of the data. A more objective approach is to perform an exhaustive cross-correlation-based search to fit subunits into the density. Here we show, using five experimental ribosome maps ranging in resolution from 5.5 to 6.9Å, that cross-correlation-based fitting is capable of successfully fitting subunits correctly in the density for over 90% of the cases. Importantly, we provide indicators for the reliability and ambiguity of a fit, using the Fisher z-transformation and its associated confidence intervals, giving a formal approach to identify over-interpreted regions in the density. In addition, we quantify the resolution requirement for a successful fit as a function of the subunit size. For larger subunits the resolution of the data can be down-filtered to 20Å while still retaining an unambiguous fit. We leverage this information through the use of multi-scale image pyramids to accelerate the search up to 30-fold on CPUs and 40-fold on GPUs at a negligible loss in success rate. We implemented this approach in our rigid-body fitting software PowerFit, which can be freely downloaded from https://github.com/haddocking/powerfit.

  3. FOLD-EM: automated fold recognition in medium- and low-resolution (4–15 Å) electron density maps

    PubMed Central

    Saha, Mitul; Morais, Marc C.

    2012-01-01

    Motivation: Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a ‘mosaic’ backbone model of the assembly that could aid map interpretation and illuminate biological function. Result: Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM—a computational tool that can identify folded macromolecular domains in medium to low resolution (4–15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies. Availability and implementation: FOLD-EM is available at: http

  4. Biometric recognition via fixation density maps

    NASA Astrophysics Data System (ADS)

    Rigas, Ioannis; Komogortsev, Oleg V.

    2014-05-01

    This work introduces and evaluates a novel eye movement-driven biometric approach that employs eye fixation density maps for person identification. The proposed feature offers a dynamic representation of the biometric identity, storing rich information regarding the behavioral and physical eye movement characteristics of the individuals. The innate ability of fixation density maps to capture the spatial layout of the eye movements in conjunction with their probabilistic nature makes them a particularly suitable option as an eye movement biometrical trait in cases when free-viewing stimuli is presented. In order to demonstrate the effectiveness of the proposed approach, the method is evaluated on three different datasets containing a wide gamut of stimuli types, such as static images, video and text segments. The obtained results indicate a minimum EER (Equal Error Rate) of 18.3 %, revealing the perspectives on the utilization of fixation density maps as an enhancing biometrical cue during identification scenarios in dynamic visual environments.

  5. Mapping tree density at a global scale.

    PubMed

    Crowther, T W; Glick, H B; Covey, K R; Bettigole, C; Maynard, D S; Thomas, S M; Smith, J R; Hintler, G; Duguid, M C; Amatulli, G; Tuanmu, M-N; Jetz, W; Salas, C; Stam, C; Piotto, D; Tavani, R; Green, S; Bruce, G; Williams, S J; Wiser, S K; Huber, M O; Hengeveld, G M; Nabuurs, G-J; Tikhonova, E; Borchardt, P; Li, C-F; Powrie, L W; Fischer, M; Hemp, A; Homeier, J; Cho, P; Vibrans, A C; Umunay, P M; Piao, S L; Rowe, C W; Ashton, M S; Crane, P R; Bradford, M A

    2015-09-10

    The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

  6. Maps of current density using density-functional methods

    NASA Astrophysics Data System (ADS)

    Soncini, A.; Teale, A. M.; Helgaker, T.; de Proft, F.; Tozer, D. J.

    2008-08-01

    The performance of several density-functional theory (DFT) methods for the calculation of current densities induced by a uniform magnetic field is examined. Calculations are performed using the BLYP and KT3 generalized-gradient approximations, together with the B3LYP hybrid functional. For the latter, both conventional and optimized effective potential (OEP) approaches are used. Results are also determined from coupled-cluster singles-and-doubles (CCSD) electron densities by a DFT constrained search procedure using the approach of Wu and Yang (WY). The current densities are calculated within the CTOCD-DZ2 distributed origin approach. Comparisons are made with results from Hartree-Fock (HF) theory. Several small molecules for which correlation is known to be especially important in the calculation of magnetic response properties are considered-namely, O3, CO, PN, and H2CO. As examples of aromatic and antiaromatic systems, benzene and planarized cyclooctatetraene molecules are considered, with specific attention paid to the ring current phenomenon and its Kohn-Sham orbital origin. Finally, the o-benzyne molecule is considered as a computationally challenging case. The HF and DFT induced current maps show qualitative differences, while among the DFT methods the maps show a similar qualitative structure. To assess quantitative differences in the calculated current densities with different methods, the maximal moduli of the induced current densities are compared and integration of the current densities to yield shielding constants is performed. In general, the maximal modulus is reduced in moving from HF to B3LYP and BLYP, and further reduced in moving to KT3, OEP(B3LYP), and WY(CCSD). The latter three methods offer the most accurate shielding constants in comparison with both experimental and ab initio data and hence the more reliable route to DFT calculation of induced current density in molecules.

  7. Spatial Density Maps from a Debris Cloud

    NASA Astrophysics Data System (ADS)

    Healy, L.; Kindl, S.; Binz, C.

    2016-09-01

    A debris cloud from a fragmentation on orbit may be modeled by transformation of variables from the instantaneous velocity distribution at the fragmentation time to the spatial distribution at some elapsed time later. There are no Gaussian distributions assumed and the evolution map is quite nonlinear, being derived from the solution of the Lambert, two-point boundary value, problem and the state transition matrix for unperturbed propagation, so the traditional tools of analysis that assume these qualities fail dramatically. The transformation of variables technique does not suffer from any such assumptions, and unlike the Monte Carlo method, is not subject to sampling errors or approximations. Structures and features are evident in the density maps, and these structures show promise for simplified approximation of the density map. Most prominent of the structures is the well-known pinch point at the fragmentation location in inertial space. The anti-pinch line, or wedge, is also observed. Bands on the opposite side of the fragmentation are very noticeable, and their existence may be motivated from simple orbit dynamics. These bands make the anti-pinch line actually more of a set of anti-pinch line segments. By computing these density maps over time, the evolution may be studied. There is a density generator, a density band at roughly the same altitude as the pinch point, that cycles around the earth and appears a source of the bands, with newly created bands moving radially outward and diminishing in density. Although the initial velocity distribution affects the final spatial distribution, the Lambert solutions, which are the most time consuming to compute, need only be computed once. Therefore, different initial distributions may be changed and the results recomputed with relative speed. A comparison of the effects of initial distributions is shown in this paper.

  8. Cryo-EM reveals the steric zipper structure of a light chain-derived amyloid fibril

    PubMed Central

    Schmidt, Andreas; Annamalai, Karthikeyan; Schmidt, Matthias; Grigorieff, Nikolaus; Fändrich, Marcus

    2016-01-01

    Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but it has so far remained difficult to reveal the assembly of the peptide subunits in a full-scale fibril. Using electron cryomicroscopy (cryo-EM), we present a reconstruction of a fibril formed from the pathogenic core of an amyloidogenic immunoglobulin (Ig) light chain. The fibril density shows a lattice-like assembly of face-to-face packed peptide dimers that corresponds to the structure of steric zippers in peptide crystals. Interpretation of the density map with a molecular model enabled us to identify the intermolecular interactions between the peptides and rationalize the hierarchical structure of the fibril based on simple chemical principles. PMID:27185936

  9. 3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM

    PubMed Central

    Chua, Eugene Y.D.; Vogirala, Vinod K.; Inian, Oviya; Wong, Andrew S.W.; Nordenskiöld, Lars; Plitzko, Juergen M.; Danev, Radostin; Sandin, Sara

    2016-01-01

    The Volta phase plate is a recently developed electron cryo-microscopy (cryo-EM) device that enables contrast enhancement of biological samples. Here we have evaluated the potential of combining phase-plate imaging and single particle analysis to determine the structure of a small protein–DNA complex. To test the method, we made use of a 200 kDa Nucleosome Core Particle (NCP) reconstituted with 601 DNA for which a high-resolution X-ray crystal structure is known. We find that the phase plate provides a significant contrast enhancement that permits individual NCPs and DNA to be clearly identified in amorphous ice. The refined structure from 26,060 particles has an overall resolution of 3.9 Å and the density map exhibits structural features consistent with the estimated resolution, including clear density for amino acid side chains and DNA features such as the phosphate backbone. Our results demonstrate that phase-plate cryo-EM promises to become an important method to determine novel near-atomic resolution structures of small and challenging samples, such as nucleosomes in complex with nucleosome-binding factors. PMID:27563056

  10. Functional conformations of the L11–ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations

    PubMed Central

    Li, Wen; Sengupta, Jayati; Rath, Bimal K.; Frank, Joachim

    2006-01-01

    The interaction between the GTPase-associated center (GAC) and the aminoacyl-tRNA·EF-Tu·GTP ternary complex is of crucial importance in the dynamic process of decoding and tRNA accommodation. The GAC includes protein L11 and helices 43–44 of 23S rRNA (referred to as L11–rRNA complex). In this study, a method of fitting based on a systematic comparison between cryo-electron microscopy (cryo-EM) density maps and structures obtained by molecular dynamics simulations has been developed. This method has led to the finding of atomic models of the GAC that fit the EM maps with much improved cross-correlation coefficients compared with the fitting of the X-ray structure. Two types of conformations of the L11–rRNA complex, produced by the simulations, match the cryo-EM maps representing the states either bound or unbound to the aa-tRNA·EF-Tu·GTP ternary complex. In the bound state, the N-terminal domain of L11 is extended from its position in the crystal structure, and the base of nucleotide A1067 in the 23S ribosomal RNA is flipped out. This position of the base allows the RNA to reach the elbow region of the aminoacyl-tRNA when the latter is bound in the A/T site. In the unbound state, the N-terminal domain of L11 is rotated only slightly, and A1067 of the RNA is flipped back into the less-solvent-exposed position, as in the crystal structure. By matching our experimental cryo-EM maps with much improved cross-correlation coefficients compared to the crystal structure, these two conformations prove to be strong candidates of the two functional states. PMID:16682558

  11. Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem.

    PubMed

    Katsevich, E; Katsevich, A; Singer, A

    2015-01-22

    In cryo-electron microscopy (cryo-EM), a microscope generates a top view of a sample of randomly oriented copies of a molecule. The problem of single particle reconstruction (SPR) from cryo-EM is to use the resulting set of noisy two-dimensional projection images taken at unknown directions to reconstruct the three-dimensional (3D) structure of the molecule. In some situations, the molecule under examination exhibits structural variability, which poses a fundamental challenge in SPR. The heterogeneity problem is the task of mapping the space of conformational states of a molecule. It has been previously suggested that the leading eigenvectors of the covariance matrix of the 3D molecules can be used to solve the heterogeneity problem. Estimating the covariance matrix is challenging, since only projections of the molecules are observed, but not the molecules themselves. In this paper, we formulate a general problem of covariance estimation from noisy projections of samples. This problem has intimate connections with matrix completion problems and high-dimensional principal component analysis. We propose an estimator and prove its consistency. When there are finitely many heterogeneity classes, the spectrum of the estimated covariance matrix reveals the number of classes. The estimator can be found as the solution to a certain linear system. In the cryo-EM case, the linear operator to be inverted, which we term the projection covariance transform, is an important object in covariance estimation for tomographic problems involving structural variation. Inverting it involves applying a filter akin to the ramp filter in tomography. We design a basis in which this linear operator is sparse and thus can be tractably inverted despite its large size. We demonstrate via numerical experiments on synthetic datasets the robustness of our algorithm to high levels of noise.

  12. Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem*

    PubMed Central

    Katsevich, E.; Katsevich, A.; Singer, A.

    2015-01-01

    In cryo-electron microscopy (cryo-EM), a microscope generates a top view of a sample of randomly oriented copies of a molecule. The problem of single particle reconstruction (SPR) from cryo-EM is to use the resulting set of noisy two-dimensional projection images taken at unknown directions to reconstruct the three-dimensional (3D) structure of the molecule. In some situations, the molecule under examination exhibits structural variability, which poses a fundamental challenge in SPR. The heterogeneity problem is the task of mapping the space of conformational states of a molecule. It has been previously suggested that the leading eigenvectors of the covariance matrix of the 3D molecules can be used to solve the heterogeneity problem. Estimating the covariance matrix is challenging, since only projections of the molecules are observed, but not the molecules themselves. In this paper, we formulate a general problem of covariance estimation from noisy projections of samples. This problem has intimate connections with matrix completion problems and high-dimensional principal component analysis. We propose an estimator and prove its consistency. When there are finitely many heterogeneity classes, the spectrum of the estimated covariance matrix reveals the number of classes. The estimator can be found as the solution to a certain linear system. In the cryo-EM case, the linear operator to be inverted, which we term the projection covariance transform, is an important object in covariance estimation for tomographic problems involving structural variation. Inverting it involves applying a filter akin to the ramp filter in tomography. We design a basis in which this linear operator is sparse and thus can be tractably inverted despite its large size. We demonstrate via numerical experiments on synthetic datasets the robustness of our algorithm to high levels of noise. PMID:25699132

  13. Cryo-EM structure of respiratory complex I reveals a link to mitochondrial sulfur metabolism.

    PubMed

    D'Imprima, Edoardo; Mills, Deryck J; Parey, Kristian; Brandt, Ulrich; Kühlbrandt, Werner; Zickermann, Volker; Vonck, Janet

    2016-12-01

    Mitochondrial complex I is a 1MDa membrane protein complex with a central role in aerobic energy metabolism. The bioenergetic core functions are executed by 14 central subunits that are conserved from bacteria to man. Despite recent progress in structure determination, our understanding of the function of the ~30 accessory subunits associated with the mitochondrial complex is still limited. We have investigated the structure of complex I from the aerobic yeast Yarrowia lipolytica by cryo-electron microscopy. Our density map at 7.9Å resolution closely matches the 3.6-3.9Å X-ray structure of the Yarrowia lipolytica complex. However, the cryo-EM map indicated an additional subunit on the side of the matrix arm above the membrane surface, pointing away from the membrane arm. The density, which is not present in any previously described complex I structure and occurs in about 20 % of the particles, was identified as the accessory sulfur transferase subunit ST1. The Yarrowia lipolytica complex I preparation is active in generating H2S from the cysteine derivative 3-mercaptopyruvate, catalyzed by ST1. We thus provide evidence for a link between respiratory complex I and mitochondrial sulfur metabolism.

  14. Solving protein nanocrystals by cryo-EM diffraction: multiple scattering artifacts.

    PubMed

    Subramanian, Ganesh; Basu, Shibom; Liu, Haiguang; Zuo, Jian-Min; Spence, John C H

    2015-01-01

    The maximum thickness permissible within the single-scattering approximation for the determination of the structure of perfectly ordered protein microcrystals by transmission electron diffraction is estimated for tetragonal hen-egg lysozyme protein crystals using several approaches. Multislice simulations are performed for many diffraction conditions and beam energies to determine the validity domain of the required single-scattering approximation and hence the limit on crystal thickness. The effects of erroneous experimental structure factor amplitudes on the charge density map for lysozyme are noted and their threshold limits calculated. The maximum thickness of lysozyme permissible under the single-scattering approximation is also estimated using R-factor analysis. Successful reconstruction of density maps is found to result mainly from the use of the phase information provided by modeling based on the protein data base through molecular replacement (MR), which dominates the effect of poor quality electron diffraction data at thicknesses larger than about 200 Å. For perfectly ordered protein nanocrystals, a maximum thickness of about 1000 Å is predicted at 200 keV if MR can be used, using R-factor analysis performed over a subset of the simulated diffracted beams. The effects of crystal bending, mosaicity (which has recently been directly imaged by cryo-EM) and secondary scattering are discussed. Structure-independent tests for single-scattering and new microfluidic methods for growing and sorting nanocrystals by size are reviewed.

  15. Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling

    PubMed Central

    de Vries, Sjoerd J.; Chauvot de Beauchêne, Isaure; Schindler, Christina E.M.; Zacharias, Martin

    2016-01-01

    Protein-protein interactions carry out a large variety of essential cellular processes. Cryo-electron microscopy (cryo-EM) is a powerful technique for the modeling of protein-protein interactions at a wide range of resolutions, and recent developments have caused a revolution in the field. At low resolution, cryo-EM maps can drive integrative modeling of the interaction, assembling existing structures into the map. Other experimental techniques can provide information on the interface or on the contacts between the monomers in the complex. This inevitably raises the question regarding which type of data is best suited to drive integrative modeling approaches. Systematic comparison of the prediction accuracy and specificity of the different integrative modeling paradigms is unavailable to date. Here, we compare EM-driven, interface-driven, and contact-driven integrative modeling paradigms. Models were generated for the protein docking benchmark using the ATTRACT docking engine and evaluated using the CAPRI two-star criterion. At 20 Å resolution, EM-driven modeling achieved a success rate of 100%, outperforming the other paradigms even with perfect interface and contact information. Therefore, even very low resolution cryo-EM data is superior in predicting heterodimeric and heterotrimeric protein assemblies. Our study demonstrates that a force field is not necessary, cryo-EM data alone is sufficient to accurately guide the monomers into place. The resulting rigid models successfully identify regions of conformational change, opening up perspectives for targeted flexible remodeling. PMID:26846888

  16. Validation of cryo-EM structure of IP₃R1 channel.

    PubMed

    Murray, Stephen C; Flanagan, John; Popova, Olga B; Chiu, Wah; Ludtke, Steven J; Serysheva, Irina I

    2013-06-04

    About a decade ago, three electron cryomicroscopy (cryo-EM) single-particle reconstructions of IP3R1 were reported at low resolution. It was disturbing that these structures bore little similarity to one another, even at the level of quaternary structure. Recently, we published an improved structure of IP3R1 at ∼1 nm resolution. However, this structure did not bear any resemblance to any of the three previously published structures, leading to the question of why the structure should be considered more reliable than the original three. Here, we apply several methods, including class-average/map comparisons, tilt-pair validation, and use of multiple refinement software packages, to give strong evidence for the reliability of our recent structure. The map resolution and feature resolvability are assessed with the gold standard criterion. This approach is generally applicable to assessing the validity of cryo-EM maps of other molecular machines.

  17. Cryo-EM: Spinning the Micelles Away.

    PubMed

    Singh, Satinder K; Sigworth, Fred J

    2015-09-01

    Structural characterization of integral membrane proteins (MPs) demands that the samples be pure, monodisperse, and stable. Detergents are required to extract MPs from the lipid bilayer in which they reside and to stabilize them for downstream biophysical analyses. Some of the best MP-stabilizing detergents pose problems for cryo-EM studies, but in this issue of Structure, Hauer et al. (2015) now offer a solution called GraDeR.

  18. Fingerprint recognition using model-based density map.

    PubMed

    Wan, Dingrui; Zhou, Jie

    2006-06-01

    Utilizing more information other than minutiae is much helpful for large-scale fingerprint recognition applications. In this paper, we proposed a polynomial model to approximate the density map of fingerprints and used the model's parameters as a novel kind of feature for fingerprint representation. Thus, the density information can be utilized into the matching stage with a low additional storage cost. A decision-level fusion scheme is further used to combine the density map matching with conventional minutiae-based matching and experimental results showed a much better performance than using single minutiae-based matching.

  19. Evolution of probability densities in stochastic coupled map lattices

    NASA Astrophysics Data System (ADS)

    Losson, Jérôme; Mackey, Michael C.

    1995-08-01

    This paper describes the statistical properties of coupled map lattices subjected to the influence of stochastic perturbations. The stochastic analog of the Perron-Frobenius operator is derived for various types of noise. When the local dynamics satisfy rather mild conditions, this equation is shown to possess either stable, steady state solutions (i.e., a stable invariant density) or density limit cycles. Convergence of the phase space densities to these limit cycle solutions explains the nonstationary behavior of statistical quantifiers at equilibrium. Numerical experiments performed on various lattices of tent, logistic, and shift maps with diffusivelike interelement couplings are examined in light of these theoretical results.

  20. SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley

    PubMed Central

    Ren, Xifeng; Wang, Jibin; Liu, Lipan; Sun, Genlou; Li, Chengdao; Luo, Hong; Sun, Dongfa

    2016-01-01

    A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley. PMID:27530597

  1. CryoEM at IUCrJ: a new era

    PubMed Central

    Subramaniam, Sriram; Kühlbrandt, Werner; Henderson, Richard

    2016-01-01

    In this overview, we briefly outline recent advances in electron cryomicroscopy (cryoEM) and explain why the journal IUCrJ, published by the International Union of Crystallography, could provide a natural home for publications covering many present and future developments in the cryoEM field. PMID:26870375

  2. ESammon: A Computationaly Enhanced Sammon Mapping based on Data Density.

    PubMed

    Wang, Chanpaul Jin; Fang, Hua; Wang, Honggang

    2016-02-01

    Sammon mapping is a widely used visualization technique to display complex data from high- to low-dimensional space. However, its extensive computational cost may pose potential computational challenges to big data visualization. This paper proposes a computationally-enhanced Sammon mapping (ESammon) by leveraging the characteristics of spatial data density. Unlike the conventional Sammon, ESammon preserves critical pairwise distances between data points in the process of projection, instead of all distances. Specifically, we integrated the Directed-Acyclic-Graph (DAG) based data density characterization method to select the critical distances. The numerical results demonstrated that our ESammon can achieve comparable projection results as the conventional Sammon mapping while reducing the computational cost from O(N(2)) toO(N).

  3. An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images.

    PubMed

    Biswas, Abhishek; Ranjan, Desh; Zubair, Mohammad; Zeil, Stephanie; Al Nasr, Kamal; He, Jing

    2016-03-17

    A key idea in de novo modeling of a medium-resolution density image obtained from cryo-electron microscopy is to calculate the optimal mapping between the secondary structure traces observed in the density image and those predicted on the protein sequence. When secondary structures are not determined precisely, either from the image or from the amino acid sequence of the protein, this results in additional computational overhead. We present an efficient method that addresses the secondary structure placement problem dealing with multiple secondary structure predictions and calculates the optimal mapping. The method was tested using 12 simulated images from α-proteins and two Cryo-EM images of α-β proteins. We observed that the rank of the true topologies is consistently improved by using multiple secondary structure predictions instead of the single prediction method. The results show that the algorithm is robust and works well even when errors/misses in the predicted secondary structures are present in the image or the sequence. The results also show that the algorithm is efficient and is able to handle proteins with as many as 33 helices.

  4. Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ${\\Phi}$6 Major Capsid Protein

    SciTech Connect

    Nemecek, Daniel; Plevka, Pavel; Boura, Evzen

    2013-11-29

    Bacteriophage ${\\Phi}$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of ${\\Phi}$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the ${\\Phi}$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.

  5. Streptavidin crystals as nanostructured supports and image-calibration references for cryo-EM data collection.

    PubMed

    Wang, Liguo; Ounjai, Puey; Sigworth, Fred J

    2008-11-01

    For cryo-EM structural studies, we seek to image membrane proteins as single particles embedded in proteoliposomes. One technical difficulty has been the low density of liposomes that can be trapped in the approximately 100nm ice layer that spans holes in the perforated carbon support film of EM grids. Inspired by the use of two-dimensional (2D) streptavidin crystals as an affinity surface for biotinylated DNA (Crucifix et al., 2004), we propose to use the crystals to tether liposomes doped with biotinylated lipids. The 2D crystal image also serves as a calibration of the image formation process, providing an absolute conversion from electrostatic potentials in the specimen to the EM image intensity, and serving as a quality control of acquired cryo-EM images. We were able to grow streptavidin crystals covering more than 90% of the holes in an EM grid, and which remained stable even under negative stain. The liposome density in the resulting cryo-EM sample was uniform and high due to the high-affinity binding of biotin to streptavidin. Using computational methods, the 2D crystal background can be removed from images without noticeable effect on image properties.

  6. Heat map visualization of high-density clinical chemistry data.

    PubMed

    Auman, J Todd; Boorman, Gary A; Wilson, Ralph E; Travlos, Gregory S; Paules, Richard S

    2007-10-22

    Clinical chemistry data are routinely generated as part of preclinical animal toxicity studies and human clinical studies. With large-scale studies involving hundreds or even thousands of samples in multiple treatment groups, it is currently difficult to interpret the resulting complex, high-density clinical chemistry data. Accordingly, we conducted this study to investigate methods for easy visualization of complex, high-density data. Clinical chemistry data were obtained from male rats each treated with one of eight different acute hepatotoxicants from a large-scale toxicogenomics study. The raw data underwent a Z-score transformation comparing each individual animal's clinical chemistry values to that of reference controls from all eight studies and then were visualized in a single graphic using a heat map. The utility of using a heat map to visualize high-density clinical chemistry data was explored by clustering changes in clinical chemistry values for >400 animals. A clear distinction was observed in animals displaying hepatotoxicity from those that did not. Additionally, while animals experiencing hepatotoxicity showed many similarities in the observed clinical chemistry alterations, distinct differences were noted in the heat map profile for the different compounds. Using a heat map to visualize complex, high-density clinical chemistry data in a single graphic facilitates the identification of previously unrecognized trends. This method is simple to implement and maintains the biological integrity of the data. The value of this clinical chemistry data transformation and visualization will manifest itself through integration with other high-density data, such as genomics data, to study physiology at the systems level.

  7. A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis)

    PubMed Central

    Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou

    2016-01-01

    Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016

  8. Selective mapping: a strategy for optimizing the construction of high-density linkage maps.

    PubMed Central

    Vision, T J; Brown, D G; Shmoys, D B; Durrett, R T; Tanksley, S D

    2000-01-01

    Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps. PMID:10790413

  9. Density equalizing map projections (cartograms) in public health applications

    SciTech Connect

    Merrill, D.W.

    1998-05-01

    In studying geographic disease distributions, one normally compares rates among arbitrarily defined geographic subareas (e.g. census tracts), thereby sacrificing some of the geographic detail of the original data. The sparser the data, the larger the subareas must be in order to calculate stable rates. This dilemma is avoided with the technique of Density Equalizing Map Projections (DEMP){copyright}. Boundaries of geographic subregions are adjusted to equalize population density over the entire study area. Case locations plotted on the transformed map should have a uniform distribution if the underlying disease risk is constant. On the transformed map, the statistical analysis of the observed distribution is greatly simplified. Even for sparse distributions, the statistical significance of a supposed disease cluster can be calculated with validity. The DEMP algorithm was applied to a data set previously analyzed with conventional techniques; namely, 401 childhood cancer cases in four counties of California. The distribution of cases on the transformed map was analyzed visually and statistically. To check the validity of the method, the identical analysis was performed on 401 artificial cases randomly generated under the assumption of uniform risk. No statistically significant evidence for geographic non-uniformity of rates was found, in agreement with the original analysis performed by the California Department of Health Services.

  10. FINDMOL: automated identification of macromolecules in electron-density maps.

    PubMed

    McKee, E W; Kanbi, L D; Childs, K L; Grosse-Kunstleve, R W; Adams, P D; Sacchettini, J C; Ioerger, T R

    2005-11-01

    Automating the determination of novel macromolecular structures via X-ray crystallographic methods involves building a model into an electron-density map. Unfortunately, the conventional crystallographic asymmetric unit volumes are usually not well matched to the biological molecular units. In most cases, the facets of the asymmetric unit cut the molecules into a number of disconnected fragments, rendering interpretation by the crystallographer significantly more difficult. The FINDMOL algorithm is designed to quickly parse the arrangement of trace points (pseudo-atoms) derived from a skeletonized electron-density map without requiring higher level prior information such as sequence information or number of molecules in the asymmetric unit. The algorithm was tested with a variety of density-modified maps computed with medium- to low-resolution data. Typically, the resulting volume resembles the biological unit. In the remaining cases the number of disconnected fragments is very small. In all examples, secondary-structural elements such as alpha-helices or beta-sheets are easily identifiable in the defragmented arrangement. FINDMOL can greatly assist a crystallographer during manual model building or in cases where automatic model building can only build partial models owing to limitations of the data such as low resolution and/or poor phases.

  11. Mapping of an approximate neutral density surface with Ungridded data

    NASA Astrophysics Data System (ADS)

    You, Yuzhu

    2008-02-01

    A neutral density surface is a logical study frame for water-mass mixing since water parcels spread along such a surface without doing work against buoyancy restoring force. Mesoscale eddies are believed to stir and subsequently mix predominantly along such surfaces. Because of the nonlinear nature of the equation of state of seawater, the process of accurately mapping a neutral density surface necessarily involves lateral computation from one conductivity, temperature and depth (CTD) cast to the next in a logical sequence. By contrast, the depth of a potential density surface on any CTD cast is found solely from the data on this cast. The lateral calculation procedure causes a significant inconvenience. In a previous paper by present author published in this journal (You, 2006), the mapping of neutral density surfaces with regularly gridded data such as Levitus data has been introduced. In this note, I present a new method to find the depth of a neutral density surface from a cast without having to specify an integration path in space. An appropriate reference point is required that is on the neutral density surface and thereafter the neutral density surface can be determined by using the CTD casts in any order. This method is only approximate and the likely errors can be estimated by plotting a scatter diagram of all the pressures and potential temperatures on the neutral density surfaces. The method assumes that the variations of potential temperature and pressure (with respect to the values at the reference point) on the neutral density surface are proportional. It is important to select the most appropriate reference point in order to approximately satisfy this assumption, and in practice this is found by inspecting the θ-p plot of data on the surface. This may require that the algorithm be used twice. When the straight lines on the θ-p plot, drawn from the reference point to other points on the neutral density surface, enclose an area that is external to

  12. Statistical quality indicators for electron-density maps

    SciTech Connect

    Tickle, Ian J.

    2012-04-01

    A likelihood-based metric for scoring the local agreement of a structure model with the observed electron density is described. The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ{sup 2} significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

  13. Intercalibration of neutral density measurements for mapping the thermosphere

    NASA Astrophysics Data System (ADS)

    Weimer, D. R.; Sutton, E. K.; Mlynczak, M. G.; Hunt, L. A.

    2016-06-01

    This paper describes a technique for mapping exospheric temperatures, derived from neutral density measurements from the Challenging Mini-satellite Payload (CHAMP) and Gravity Recovery and Climate Experiment (GRACE) satellites. The Naval Reasearch Laboratory Mass Spectrometer, Incoherent Scatter Radar Extended Model (NRLMSISE-00) thermosphere model is used for the conversion. Adjustments for each satellite were needed in order for the time-averaged densities to agree with the model. It was necessary to correct for inexact modeling of the annual and semiannual oscillations in the density, as well as the declining densities during the solar minimum. It was found that a time-varying perturbation in the atomic oxygen in the model could produce a good agreement at both altitudes. The time series of this oxygen variation was found to have a very high correlation with independent measurements of CO2 emissions measured with the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument. The temperature data are averaged on a spherical grid having equal areas in each pixel, avoiding functional fits that would blur finer details. The use of solar magnetic rather than geographic coordinates enhances the auroral ovals. There are strong elevations in the exospheric temperatures in the polar regions, particularly near the dayside cusp. Spatial filtering with spherical wavelets is used to remove statistical fluctuations, although some details are lost. The exospheric temperature maps are well ordered by the nitric oxide emission measurements from SABER. The technique that is described here could be applied to future improvements of empirical density models, having an accuracy and spatial resolution that is not presently available.

  14. Statistical quality indicators for electron-density maps.

    PubMed

    Tickle, Ian J

    2012-04-01

    The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ(2) significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

  15. Mapping Densities in Analogue Laboratory Turbulent Plumes Using Dye Concentration

    NASA Astrophysics Data System (ADS)

    Fisher, M. A.; Kobs-Nawotniak, S. E.

    2014-12-01

    Changing tephra concentration in volcanic eruption columns is difficult to measure in the field due to fluid opacity. The bulk fluid erupted may be higher density than the surrounding atmosphere at the vent and then transition to positive buoyancy through the ingestion and heating of ambient air; thus, the concentration of the plume fluid as it rises is critical to determining whether the material rises in a sustained plume or collapses into a pyroclastic density current. We evaluate the changing concentration of an analogue plume via tracer dye intensity and relate it to plume radius expansion and vent distance. To calibrate our concentration metric, we calculated the density and dye concentration of pre-determined tracer-water mixtures. The density of the solution was directly measured using a micropipette and high precision balance. The calculated density falls within the standard error of the measured density for each step. Five photographs were taken of each concentration using a mounted Ex-FH100 digital camera with identical lighting. Using a MATLAB script, the RGB (Red-Green-Blue) color value was extracted from five pixels located at the same coordinates in each image, confirming that there was no inherent error caused by the camera and that the RGB value was the same across an entire image. We created a color map to convert from the RGB color value of a pixel in an image to its corresponding concentration. This method algorithm can then be applied to an analogue volcanic tank model, using the color variations in the plume eddies to determine the tracer concentration, and thereby density distribution, in the plume.

  16. Databases and archiving for cryoEM

    PubMed Central

    Patwardhan, Ardan; Lawson, Catherine L.

    2017-01-01

    Cryo-EM in structural biology is currently served by three public archives – EMDB for 3DEM reconstructions, PDB for models built from 3DEM reconstructions and EMPIAR for the raw 2D image data used to obtain the 3DEM reconstructions. These archives play a vital role for both the structural community and the wider biological community in making the data accessible so that results may be reused, reassessed and integrated with other structural and bioinformatics resources. The important role of the archives is underpinned by the fact that many journals mandate the deposition of data to PDB and EMDB on publication. The field is currently undergoing transformative changes where on the one hand high-resolution structures are becoming a routine occurrence while on the other hand electron tomography is enabling the study of macromolecules in the cellular context. Concomitantly the archives are evolving to best serve their stakeholder communities. In this chapter we describe the current state of the archives, resources available for depositing, accessing, searching, visualising and validating data, on-going community-wide initiatives and opportunities and challenges for the future. PMID:27572735

  17. Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.

    PubMed

    Merk, Alan; Bartesaghi, Alberto; Banerjee, Soojay; Falconieri, Veronica; Rao, Prashant; Davis, Mindy I; Pragani, Rajan; Boxer, Matthew B; Earl, Lesley A; Milne, Jacqueline L S; Subramaniam, Sriram

    2016-06-16

    Recent advances in single-particle cryoelecton microscopy (cryo-EM) are enabling generation of numerous near-atomic resolution structures for well-ordered protein complexes with sizes ≥ ∼200 kDa. Whether cryo-EM methods are equally useful for high-resolution structural analysis of smaller, dynamic protein complexes such as those involved in cellular metabolism remains an important question. Here, we present 3.8 Å resolution cryo-EM structures of the cancer target isocitrate dehydrogenase (93 kDa) and identify the nature of conformational changes induced by binding of the allosteric small-molecule inhibitor ML309. We also report 2.8-Å- and 1.8-Å-resolution structures of lactate dehydrogenase (145 kDa) and glutamate dehydrogenase (334 kDa), respectively. With these results, two perceived barriers in single-particle cryo-EM are overcome: (1) crossing 2 Å resolution and (2) obtaining structures of proteins with sizes < 100 kDa, demonstrating that cryo-EM can be used to investigate a broad spectrum of drug-target interactions and dynamic conformational states.

  18. Recent technical advancements enabled atomic resolution CryoEM

    NASA Astrophysics Data System (ADS)

    Xueming, Li

    2016-01-01

    With recent breakthroughs in camera and image processing technologies single-particle electron cryo-microscopy (CryoEM) has suddenly gained the attention of structural biologists as a powerful tool able to solve the atomic structures of biological complexes and assemblies. Compared with x-ray crystallography, CryoEM can be applied to partially flexible structures in solution and without the necessity of crystallization, which is especially important for large complexes and assemblies. This review briefly explains several key bottlenecks for atomic resolution CryoEM, and describes the corresponding solutions for these bottlenecks based on the recent technical advancements. The review also aims to provide an overview about the technical differences between its applications in biology and those in material science. Project supported by Tsinghua-Peking Joint Center for Life Sciences, China.

  19. Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core

    NASA Astrophysics Data System (ADS)

    da Fonseca, Paula C. A.; Morris, Edward P.

    2015-07-01

    The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3.5 Å. Our map allows the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results open new prospects to tackle the proteasome functional mechanisms. Moreover, they also further demonstrate that cryo-EM is emerging as a realistic approach for general structural studies of protein-ligand interactions.

  20. Portable cosmic particle detectors for subsurface density mapping

    NASA Astrophysics Data System (ADS)

    Oláh, László; Gábor Barnaföldi, Gergely; Hamar, Gergö; Surányi, Gergely; Varga, Dezsö

    2016-04-01

    Muography deduces the density length in the interior of the investigated geological object, such as a mountain or volcano by the measurement of the cosmic muon absorption along different paths through the object. If path lengths (average densities) are measured, the average density (path length) can be deduced along the muon paths. A portable, low power consumption cosmic particle tracking detector based on Close Cathode multi-wire proportional chambers [1,2] has been developed for muography based on our earlier developments and experiences at the Wigner RCP of the HAS in Budapest [3,4,5]. The newly developed tracking system consists of six layers with the sensitive area of 0.25 m2 [6]. The spatial resolution of 2 mm provides an angular resolution of 15 mrad. This instrument has been optimized for underground and outdoor measurements: it has a Raspberry pi controlled data acquisition system which includes a custom designed board with a coincidence unit and allows high level remote control, data management and analysis. The individual trigger signals, number of missed triggers, analogue signals from chambers and the temperature are recorded. The duration of data readout (dead time) is 100 microsec. The DAQ software runs on the Raspberry Pi. For standard operation, a graphical user interface has been developed, running on any remote computer with Internet connection (both of wired and wireless) to the Raspberry Pi. A temperature-controlled high-voltage power supply provides a stable and reasonable (> 95 %) tracking performance for the measurements. With total power consumption of 5W, a portable tracking detector can operate for 5 days with a standard 50 Ah battery and with gas (non flammable Ar-CO2 mixture) consumption of 0.5 liter per hour, a 10 l bottle at pressure of 150 bar is enough for four month. The portability (total weight of less than 30 kg) allowed that our tracking detectors have been applied in underground caverns for subsurface density mapping. The

  1. Pulmonary Hypertension: Scientometric Analysis and Density-Equalizing Mapping.

    PubMed

    Götting, Michael; Schwarzer, Mario; Gerber, Alexander; Klingelhöfer, Doris; Groneberg, David A

    2017-01-01

    Pulmonary hypertension (PH) is characterized by the increase of the mean pulmonary arterial pressure in the lung circulation. Despite the large number of experimental and clinical studies conducted on pulmonary hypertension, there is no comprehensive work that analyzed the global research activity on PH so far. We retrieved the bibliometric data of the publications on pulmonary hypertension for two periods from the Web of science database. Here, we set the first investigation period from 1900 to 2007 (t1) due to the cited half life of articles and the relating difficulties to interpret the citation parameters. The second evaluation period (t2) covers the time interval from 2008 onwards including the year 2015. The data were analyzed and processed to density-equalizing maps using the NewQIS platform. A total number of 18,986 publications were identified in t1 that come from 85 countries. The US published the highest number of publications (n = 7,290), followed by the UK, Germany, Japan and France. In t2 19,676 items could be found worked out by 130 countries. The raking started just the same with the USA as most publishing nation with 7,127 publications on PH, followed by the UK and Germany. Japan fell back on 6th place, whereas China came into view on the 5th position. Analyzing the average citation rate as a parameter for research quality, Mexico reached the highest value in t1 and Ireland in t2. While, the country specific h-index underlined the leading position of the US research in both evaluation periods again. The average number of international collaboration items was expanding from none in 1978 to 530 items in 2015 with the USA as the country with the highest number of collaboration articles. The present study is the first large scale density-equalizing mapping and scientometric analysis of global PH research activity. Our data draw a sketch of the global research architecture in this field, indicating a need for specific research programs in countries with

  2. Pulmonary Hypertension: Scientometric Analysis and Density-Equalizing Mapping

    PubMed Central

    Götting, Michael; Schwarzer, Mario; Gerber, Alexander; Groneberg, David A.

    2017-01-01

    Pulmonary hypertension (PH) is characterized by the increase of the mean pulmonary arterial pressure in the lung circulation. Despite the large number of experimental and clinical studies conducted on pulmonary hypertension, there is no comprehensive work that analyzed the global research activity on PH so far. We retrieved the bibliometric data of the publications on pulmonary hypertension for two periods from the Web of science database. Here, we set the first investigation period from 1900 to 2007 (t1) due to the cited half life of articles and the relating difficulties to interpret the citation parameters. The second evaluation period (t2) covers the time interval from 2008 onwards including the year 2015. The data were analyzed and processed to density-equalizing maps using the NewQIS platform. A total number of 18,986 publications were identified in t1 that come from 85 countries. The US published the highest number of publications (n = 7,290), followed by the UK, Germany, Japan and France. In t2 19,676 items could be found worked out by 130 countries. The raking started just the same with the USA as most publishing nation with 7,127 publications on PH, followed by the UK and Germany. Japan fell back on 6th place, whereas China came into view on the 5th position. Analyzing the average citation rate as a parameter for research quality, Mexico reached the highest value in t1 and Ireland in t2. While, the country specific h-index underlined the leading position of the US research in both evaluation periods again. The average number of international collaboration items was expanding from none in 1978 to 530 items in 2015 with the USA as the country with the highest number of collaboration articles. The present study is the first large scale density-equalizing mapping and scientometric analysis of global PH research activity. Our data draw a sketch of the global research architecture in this field, indicating a need for specific research programs in countries with

  3. Land use, forest density, soil mapping, erosion, drainage, salinity limitations

    NASA Technical Reports Server (NTRS)

    Yassoglou, N. J. (Principal Investigator)

    1973-01-01

    The author has identified the following significant results. The results of analyses show that it is possible to obtain information of practical significance as follows: (1) A quick and accurate estimate of the proper use of the valuable land can be made on the basis of temporal and spectral characteristics of the land features. (2) A rather accurate delineation of the major forest formations in the test areas was achieved on the basis of spatial and spectral characteristics of the studied areas. The forest stands were separated into two density classes; dense forest, and broken forest. On the basis of ERTS-1 data and the existing ground truth information a rather accurate mapping of the major vegetational forms of the mountain ranges can be made. (3) Major soil formations are mapable from ERTS-1 data: recent alluvial soils; soil on quarternary deposits; severely eroded soil and lithosol; and wet soils. (4) An estimation of cost benefits cannot be made accurately at this stage of the investigation. However, a rough estimate of the ratio of the cost for obtaining the same amount information from ERTS-1 data and from conventional operations would be approximately 1:6 to 1:10, in favor of the ERTS-1.

  4. Cryo-EM structure of the large subunit of the spinach chloroplast ribosome

    PubMed Central

    Ahmed, Tofayel; Yin, Zhan; Bhushan, Shashi

    2016-01-01

    Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 Å. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features. PMID:27762343

  5. Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study

    PubMed Central

    Huang, Rui; Ripstein, Zev A.; Augustyniak, Rafal; Lazniewski, Michal; Ginalski, Krzysztof; Kay, Lewis E.; Rubinstein, John L.

    2016-01-01

    The AAA+ (ATPases associated with a variety of cellular activities) enzymes play critical roles in a variety of homeostatic processes in all kingdoms of life. Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), the archaeal homolog of the ubiquitous AAA+ protein Cdc48/p97, functions in concert with the 20S proteasome by unfolding substrates and passing them on for degradation. Here, we present electron cryomicroscopy (cryo-EM) maps showing that VAT undergoes large conformational rearrangements during its ATP hydrolysis cycle that differ dramatically from the conformational states observed for Cdc48/p97. We validate key features of the model with biochemical and solution methyl-transverse relaxation optimized spectroscopY (TROSY) NMR experiments and suggest a mechanism for coupling the energy of nucleotide hydrolysis to substrate unfolding. These findings illustrate the unique complementarity between cryo-EM and solution NMR for studies of molecular machines, showing that the structural properties of VAT, as well as the population distributions of conformers, are similar in the frozen specimens used for cryo-EM and in the solution phase where NMR spectra are recorded. PMID:27402735

  6. Existence, uniqueness, and construction of the density-potential mapping in time-dependent density-functional theory.

    PubMed

    Ruggenthaler, Michael; Penz, Markus; van Leeuwen, Robert

    2015-05-27

    In this work we review the mapping from densities to potentials in quantum mechanics, which is the basic building block of time-dependent density-functional theory and the Kohn-Sham construction. We first present detailed conditions such that a mapping from potentials to densities is defined by solving the time-dependent Schrödinger equation. We specifically discuss intricacies connected with the unboundedness of the Hamiltonian and derive the local-force equation. This equation is then used to set up an iterative sequence that determines a potential that generates a specified density via time propagation of an initial state. This fixed-point procedure needs the invertibility of a certain Sturm-Liouville problem, which we discuss for different situations. Based on these considerations we then present a discussion of the famous Runge-Gross theorem which provides a density-potential mapping for time-analytic potentials. Further we give conditions such that the general fixed-point approach is well-defined and converges under certain assumptions. Then the application of such a fixed-point procedure to lattice Hamiltonians is discussed and the numerical realization of the density-potential mapping is shown. We conclude by presenting an extension of the density-potential mapping to include vector-potentials and photons.

  7. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An ultra-dense consensus (UDC) genetic map of tetraploid cotton was constructed using six high-density component maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cut...

  8. A high density genetic linkage map for rainbow trout (Onchorynchus mykiss) containing 47,839 SNPS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High-density SNP arrays have become the tool of choice for QTL mapping, genome-wide association studies and genomic selection. More recently, high-density linkage maps generated by SNP array data have proven to be crucial for the accurate assembly of scaffolds and contigs in whole-genome sequencing ...

  9. A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check

    PubMed Central

    Blenda, Anna; Fang, David D.; Rami, Jean-François; Garsmeur, Olivier; Luo, Feng; Lacape, Jean-Marc

    2012-01-01

    A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton. PMID:23029214

  10. Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

    PubMed Central

    Ishida, Hisashi; Matsumoto, Atsushi

    2014-01-01

    To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA. PMID:24999999

  11. Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus

    PubMed Central

    Tian, Meilin; Li, Yangping; Jing, Jing; Mu, Chuang; Du, Huixia; Dou, Jinzhuang; Mao, Junxia; Li, Xue; Jiao, Wenqian; Wang, Yangfan; Hu, Xiaoli; Wang, Shi; Wang, Ruijia; Bao, Zhenmin

    2015-01-01

    Genetic linkage maps are critical and indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density and high-resolution linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as echinoderms. In this study, high-density, high-resolution genetic map was constructed for a sea cucumber species, Apostichopus japonicus, utilizing the 2b-restriction site-associated DNA (2b-RAD) method. A total of 7839 markers were anchored to the linkage map with the map coverage of 99.57%, to our knowledge, this is the highest marker density among echinoderm species. QTL mapping and association analysis consistently captured one growth-related QTL located in a 5 cM region of linkage group (LG) 5. An annotated candidate gene, retinoblastoma-binding protein 5 (RbBP5), which has been reported to be an important regulator of cell proliferation, was recognized in the QTL region. This linkage map represents a powerful tool for research involving both fine-scale QTL mapping and marker assisted selection (MAS), and will facilitate chromosome assignment and improve the whole-genome assembly of sea cucumber in the future. PMID:26439740

  12. RELION: Implementation of a Bayesian approach to cryo-EM structure determination

    PubMed Central

    Scheres, Sjors H.W.

    2012-01-01

    RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs. PMID:23000701

  13. Volta phase plate cryo-EM of the small protein complex Prx3

    NASA Astrophysics Data System (ADS)

    Khoshouei, Maryam; Radjainia, Mazdak; Phillips, Amy J.; Gerrard, Juliet A.; Mitra, Alok K.; Plitzko, Jürgen M.; Baumeister, Wolfgang; Danev, Radostin

    2016-01-01

    Cryo-EM of large, macromolecular assemblies has seen a significant increase in the numbers of high-resolution structures since the arrival of direct electron detectors. However, sub-nanometre resolution cryo-EM structures are rare compared with crystal structure depositions, particularly for relatively small particles (<400 kDa). Here we demonstrate the benefits of Volta phase plates for single-particle analysis by time-efficient cryo-EM structure determination of 257 kDa human peroxiredoxin-3 dodecamers at 4.4 Å resolution. The Volta phase plate improves the applicability of cryo-EM for small molecules and accelerates structure determination.

  14. The 3.8Å resolution cryo-EM structure of Zika Virus#

    PubMed Central

    Sirohi, Devika; Chen, Zhenguo; Sun, Lei; Klose, Thomas; Pierson, Theodore C.; Rossmann, Michael G.; Kuhn, Richard J.

    2016-01-01

    The recent rapid spread of Zika virus and its unexpected linkage to birth defects and an autoimmune-neurological syndrome has generated worldwide concern. Zika virus is a flavivirus like dengue, yellow fever and West Nile viruses. We present the 3.8Å resolution structure of mature Zika virus determined by cryo-electron microscopy. The structure of Zika virus is similar to other known flavivirus structures except for the ~10 amino acids that surround the Asn154 glycosylation site found in each of the 180 envelope glycoproteins that make up the icosahedral shell. The carbohydrate moiety associated with this residue, recognizable in the cryo-EM electron density, may function as an attachment site of the virus to host cells. This region varies not only among Zika virus strains but also in other flaviviruses and suggests that changes in this region influence virus transmission and disease. PMID:27033547

  15. Methods for High-Density Admixture Mapping of Disease Genes

    PubMed Central

    Patterson, Nick; Hattangadi, Neil; Lane, Barton; Lohmueller, Kirk E.; Hafler, David A.; Oksenberg, Jorge R.; Hauser, Stephen L.; Smith, Michael W.; O’Brien, Stephen J.; Altshuler, David; Daly, Mark J.; Reich, David

    2004-01-01

    Admixture mapping (also known as “mapping by admixture linkage disequilibrium,” or MALD) has been proposed as an efficient approach to localizing disease-causing variants that differ in frequency (because of either drift or selection) between two historically separated populations. Near a disease gene, patient populations descended from the recent mixing of two or more ethnic groups should have an increased probability of inheriting the alleles derived from the ethnic group that carries more disease-susceptibility alleles. The central attraction of admixture mapping is that, since gene flow has occurred recently in modern populations (e.g., in African and Hispanic Americans in the past 20 generations), it is expected that admixture-generated linkage disequilibrium should extend for many centimorgans. High-resolution marker sets are now becoming available to test this approach, but progress will require (a) computational methods to infer ancestral origin at each point in the genome and (b) empirical characterization of the general properties of linkage disequilibrium due to admixture. Here we describe statistical methods to estimate the ancestral origin of a locus on the basis of the composite genotypes of linked markers, and we show that this approach accurately estimates states of ancestral origin along the genome. We apply this approach to show that strong admixture linkage disequilibrium extends, on average, for 17 cM in African Americans. Finally, we present power calculations under varying models of disease risk, sample size, and proportions of ancestry. Studying ∼2,500 markers in ∼2,500 patients should provide power to detect many regions contributing to common disease. A particularly important result is that the power of an admixture mapping study to detect a locus will be nearly the same for a wide range of mixture scenarios: the mixture proportion should be 10%–90% from both ancestral populations. PMID:15088269

  16. Comparative hi-density intraspecific linkage mapping using three elite populations from common parents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High-density linkage maps are fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, e.g., Upland cotton (Gossypium hirsutum L., 2n=52). Using 3 full-sib intra-specific mapping populations fr...

  17. A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The availability of a high-density SNP chip and a reference genome sequence of the pig have enabled the construction of a high-density linkage map. A high density linkage map is an essential tool for the further fine-mapping of QTL for a variety of traits in the pig and for a better und...

  18. Alignment of cryo-EM movies of individual particles by optimization of image translations.

    PubMed

    Rubinstein, John L; Brubaker, Marcus A

    2015-11-01

    Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due to both instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for >1 MDa protein particles. Another algorithm allows individual <1 MDa protein particle trajectories to be estimated, but requires rolling averages to be calculated from frames and fits linear trajectories for particles. Here we describe an algorithm that allows for individual <1 MDa particle images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM.

  19. Low-density geochemical mapping and the robustness of geochemical patterns

    USGS Publications Warehouse

    Smith, D.B.; Reimann, C.

    2008-01-01

    Geochemical mapping of entire continents and, ultimately, the world is still a challenge for applied geochemists. At sample densities traditionally used for geochemical exploration (1 site per 1-25 km2), geochemical mapping of whole continents is logistically extremely demanding and tremendously expensive. The first low-density geochemical surveys (1 site per 200 km2) were carried out during the late 1960s in Africa. Later surveys conducted in various parts of the world had sample densities ranging from 1 site per 300 km2 to 1 site per 18 000 km2. Although these surveys were deemed successful by the investigators in defining variations in background element content on a regional scale, the scientific community was sceptical that low-density geochemical mapping was possible and would provide useful information. The main area of criticism centred around the concern that at such low sample densities the resulting maps would not be robust, i.e. if the same area were resampled and remapped, different geochemical patterns would emerge. Different examples from the USA, Europe, China and Africa demonstrate that low-density geochemical mapping will result in stable and robust geochemical patterns at the continental scale. Such maps are urgently needed for a wide variety of applications. ?? 2008 AAG/ Geological Society of London.

  20. Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea)

    PubMed Central

    Ao, Jingqun; Li, Jia; You, Xinxin; Mu, Yinnan; Ding, Yang; Mao, Kaiqiong; Bian, Chao; Mu, Pengfei; Shi, Qiong; Chen, Xinhua

    2015-01-01

    High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs) evenly distributed across the large yellow croaker (Larimichthys crocea) genome were identified using restriction-site associated DNA sequencing (RAD-seq). Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04%) of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker. PMID:26540048

  1. Unravelling the structures of biological macromolecules by cryo-EM

    PubMed Central

    Fernandez-Leiro, Rafael; Scheres, Sjors H.W.

    2016-01-01

    Preface Understanding how proteins and other biological macromolecules perform their complicated tasks in the living cell is often aided by knowledge of their three-dimensional structures. Because many tasks involve the cleavage or formation of chemical bonds, structural characterisation at the atomic level is most useful. Recent developments in electron microscopy of frozen hydrated samples (cryo-EM) have provided unprecedented opportunities for the structural characterization of biological macromolecules. This is resulting in a wave of new information about biological processes that were impossible to characterize with previously existing techniques in structural biology. PMID:27629640

  2. Single-particle cryo-EM at crystallographic resolution

    PubMed Central

    Cheng, Yifan

    2015-01-01

    Until only a few years ago, single-particle electron cryo-microscopy (cryo-EM) was usually not the first choice for many structural biologists due to its limited resolution in the range of nanometer to subnanometer. Now, this method rivals X-ray crystallography in terms of resolution and can be used to determine atomic structures of macromolecules that are either refractory to crystallization or difficult to crystallize in specific functional states. In this review, I discuss the recent breakthroughs in both hardware and software that transformed cryo-microscopy, enabling understanding of complex biomolecules and their functions at atomic level. PMID:25910205

  3. GIS for mapping waterfowl density and distribution from aerial surveys

    USGS Publications Warehouse

    Butler, W.I.; Stehn, R.A.; Balogh, G.R.

    1995-01-01

    We modified standard aerial survey data collection to obtain the geographic location for each waterfowl observation on surveys in Alaska during 1987-1993. Using transect navigation with CPS (global positioning system), data recording on continuously running tapes, and a computer data input program, we located observations with an average deviation along transects of 214 m. The method provided flexibility in survey design and data analysis. Although developed for geese nesting near the coast of the Yukon-Kuskokwim Delta, the methods are widely applicable and were used on other waterfowl surveys in Alaska to map distribution and relative abundance of waterfowl. Accurate location data with GIS analysis and display may improve precision and usefulness of data from any aerial transect survey.

  4. A novel three-dimensional variant of the watershed transform for segmentation of electron density maps.

    PubMed

    Volkmann, Niels

    2002-01-01

    Electron density maps at moderate resolution are often difficult to interpret due to the lack of recognizable features. This is especially true for electron tomograms that suffer in addition to the resolution limitation from low signal-to-noise ratios. Reliable segmentation of such maps into smaller, manageable units can greatly facilitate interpretation. Here, we present a segmentation approach targeting three-dimensional electron density maps derived by electron microscopy. The approach consists of a novel three-dimensional variant of the immersion-based watershed algorithm. We tested the algorithm on calculated data and applied it to a wide variety of electron density maps ranging from reconstructions of single macromolecules to tomograms of subcellular structures. The results indicate that the algorithm is reliable, efficient, accurate, and applicable to a wide variety of biological problems.

  5. Breast density mapping based upon system calibration, x-ray techniques, and FFDM images

    NASA Astrophysics Data System (ADS)

    Chen, Biao; Smith, Andrew P.; Jing, Zhenxue; Wu, Tao

    2007-03-01

    Clinical studies have correlated a high breast density to a women's risk of breast cancer. A breast density measurement that can quantitatively depict the volume distribution and percentage of dense tissues in breasts would be very useful for risk factor assessment of breast cancer, and might be more predictive of risks than the common but subjective and coarse 4-point BIRADS scale. This paper proposes to use a neural-network mapping to compute the breast density information based upon system calibration data, x-ray techniques, and Full Field Digital Mammography (FFDM) images. The mapping consists of four modules, namely, system calibration, generator of beam quality, generator of normalized absorption, and a multi-layer feed-forward neural network. As the core of breast density mapping, the network accepts x-ray target/filter combination, normalized x-ray absorption, pixel-wise breast thickness map, and x-ray beam quality during image acquisition as input elements, and exports a pixel-wise breast density distribution and a single breast density percentage for the imaged breast. Training and testing data sets for the design and verification of the network were formulated from calibrated x-ray beam quality, imaging data with a step wedge phantom under a variety x-ray imaging techniques, and nominal breast densities of tissue equivalent materials. The network was trained using a Levenberg-Marquardt algorithm based back-propagation learning method. Various thickness and glandular density phantom studies were performed with clinical x-ray techniques. Preliminary results showed that the neural network mapping is promising in accurately computing glandular density distribution and breast density percentage.

  6. Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

    NASA Astrophysics Data System (ADS)

    Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

    2016-08-01

    Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

  7. Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

    PubMed Central

    Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

    2016-01-01

    Local surface charge density of lipid membranes influences membrane–protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values. PMID:27561322

  8. Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii

    PubMed Central

    Bai, Zhi-Yi; Han, Xue-Kai; Liu, Xiao-Jun; Li, Qing-Qing; Li, Jia-Le

    2016-01-01

    A high-density genetic map is essential for quantitative trait locus (QTL) fine mapping. In this study, 4,508 effective single nucleotide polymorphism markers (detected using specific-locus amplified fragment sequencing) and 475 microsatellites were mapped to 19 linkage groups (LGs) using a family with 157 individuals. The map spanned 2,713 cM, with an average of 259 markers and 79 loci per LG and an average inter-marker distance of 1.81 cM. To identify QTLs for pearl quality traits, 26 putatively significant QTLs were detected for 10 traits, including, three for shell width, seven for body weight, two for shell weight, two for margin mantle weight, five for inner mantle weight, and seven for shell nacre colour. Among them, five QTLs associated with shell nacre colour were mapped to LG17 and explained 19.7% to 22.8% of the trait variation; this suggests that some important genes or loci determine shell nacre colour in LG17. The linkage map and mapped QTLs for shell nacre colour would be useful for improving the quality of Hyriopsis cumingii via marker-assisted selection. PMID:27587236

  9. Estimation of high-resolution dust column density maps. Empirical model fits

    NASA Astrophysics Data System (ADS)

    Juvela, M.; Montillaud, J.

    2013-09-01

    Context. Sub-millimetre dust emission is an important tracer of column density N of dense interstellar clouds. One has to combine surface brightness information at different spatial resolutions, and specific methods are needed to derive N at a resolution higher than the lowest resolution of the observations. Some methods have been discussed in the literature, including a method (in the following, method B) that constructs the N estimate in stages, where the smallest spatial scales being derived only use the shortest wavelength maps. Aims: We propose simple model fitting as a flexible way to estimate high-resolution column density maps. Our goal is to evaluate the accuracy of this procedure and to determine whether it is a viable alternative for making these maps. Methods: The new method consists of model maps of column density (or intensity at a reference wavelength) and colour temperature. The model is fitted using Markov chain Monte Carlo methods, comparing model predictions with observations at their native resolution. We analyse simulated surface brightness maps and compare its accuracy with method B and the results that would be obtained using high-resolution observations without noise. Results: The new method is able to produce reliable column density estimates at a resolution significantly higher than the lowest resolution of the input maps. Compared to method B, it is relatively resilient against the effects of noise. The method is computationally more demanding, but is feasible even in the analysis of large Herschel maps. Conclusions: The proposed empirical modelling method E is demonstrated to be a good alternative for calculating high-resolution column density maps, even with considerable super-resolution. Both methods E and B include the potential for further improvements, e.g., in the form of better a priori constraints.

  10. Identification of irrigated crop types from ERTS-1 density contour maps and color infrared aerial photography. [Wyoming

    NASA Technical Reports Server (NTRS)

    Marrs, R. W.; Evans, M. A.

    1974-01-01

    The author has identified the following significant results. The crop types of a Great Plains study area were mapped from color infrared aerial photography. Each field was positively identified from field checks in the area. Enlarged (50x) density contour maps were constructed from three ERTS-1 images taken in the summer of 1973. The map interpreted from the aerial photography was compared to the density contour maps and the accuracy of the ERTS-1 density contour map interpretations were determined. Changes in the vegetation during the growing season and harvest periods were detectable on the ERTS-1 imagery. Density contouring aids in the detection of such charges.

  11. Likelihood-based modification of experimental crystal structure electron density maps

    DOEpatents

    Terwilliger, Thomas C.

    2005-04-16

    A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

  12. A Comparison of Spatial Analysis Methods for the Construction of Topographic Maps of Retinal Cell Density

    PubMed Central

    Garza-Gisholt, Eduardo; Hemmi, Jan M.; Hart, Nathan S.; Collin, Shaun P.

    2014-01-01

    Topographic maps that illustrate variations in the density of different neuronal sub-types across the retina are valuable tools for understanding the adaptive significance of retinal specialisations in different species of vertebrates. To date, such maps have been created from raw count data that have been subjected to only limited analysis (linear interpolation) and, in many cases, have been presented as iso-density contour maps with contour lines that have been smoothed ‘by eye’. With the use of stereological approach to count neuronal distribution, a more rigorous approach to analysing the count data is warranted and potentially provides a more accurate representation of the neuron distribution pattern. Moreover, a formal spatial analysis of retinal topography permits a more robust comparison of topographic maps within and between species. In this paper, we present a new R-script for analysing the topography of retinal neurons and compare methods of interpolating and smoothing count data for the construction of topographic maps. We compare four methods for spatial analysis of cell count data: Akima interpolation, thin plate spline interpolation, thin plate spline smoothing and Gaussian kernel smoothing. The use of interpolation ‘respects’ the observed data and simply calculates the intermediate values required to create iso-density contour maps. Interpolation preserves more of the data but, consequently includes outliers, sampling errors and/or other experimental artefacts. In contrast, smoothing the data reduces the ‘noise’ caused by artefacts and permits a clearer representation of the dominant, ‘real’ distribution. This is particularly useful where cell density gradients are shallow and small variations in local density may dramatically influence the perceived spatial pattern of neuronal topography. The thin plate spline and the Gaussian kernel methods both produce similar retinal topography maps but the smoothing parameters used may affect

  13. A comparison of spatial analysis methods for the construction of topographic maps of retinal cell density.

    PubMed

    Garza-Gisholt, Eduardo; Hemmi, Jan M; Hart, Nathan S; Collin, Shaun P

    2014-01-01

    Topographic maps that illustrate variations in the density of different neuronal sub-types across the retina are valuable tools for understanding the adaptive significance of retinal specialisations in different species of vertebrates. To date, such maps have been created from raw count data that have been subjected to only limited analysis (linear interpolation) and, in many cases, have been presented as iso-density contour maps with contour lines that have been smoothed 'by eye'. With the use of stereological approach to count neuronal distribution, a more rigorous approach to analysing the count data is warranted and potentially provides a more accurate representation of the neuron distribution pattern. Moreover, a formal spatial analysis of retinal topography permits a more robust comparison of topographic maps within and between species. In this paper, we present a new R-script for analysing the topography of retinal neurons and compare methods of interpolating and smoothing count data for the construction of topographic maps. We compare four methods for spatial analysis of cell count data: Akima interpolation, thin plate spline interpolation, thin plate spline smoothing and Gaussian kernel smoothing. The use of interpolation 'respects' the observed data and simply calculates the intermediate values required to create iso-density contour maps. Interpolation preserves more of the data but, consequently includes outliers, sampling errors and/or other experimental artefacts. In contrast, smoothing the data reduces the 'noise' caused by artefacts and permits a clearer representation of the dominant, 'real' distribution. This is particularly useful where cell density gradients are shallow and small variations in local density may dramatically influence the perceived spatial pattern of neuronal topography. The thin plate spline and the Gaussian kernel methods both produce similar retinal topography maps but the smoothing parameters used may affect the outcome.

  14. Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution

    NASA Astrophysics Data System (ADS)

    Sun, Lei; Zhang, Xinzheng; Gao, Song; Rao, Prashant A.; Padilla-Sanchez, Victor; Chen, Zhenguo; Sun, Siyang; Xiang, Ye; Subramaniam, Sriram; Rao, Venigalla B.; Rossmann, Michael G.

    2015-07-01

    The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.

  15. Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution.

    PubMed

    Sun, Lei; Zhang, Xinzheng; Gao, Song; Rao, Prashant A; Padilla-Sanchez, Victor; Chen, Zhenguo; Sun, Siyang; Xiang, Ye; Subramaniam, Sriram; Rao, Venigalla B; Rossmann, Michael G

    2015-07-06

    The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.

  16. Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution

    PubMed Central

    Sun, Lei; Zhang, Xinzheng; Gao, Song; Rao, Prashant A.; Padilla-Sanchez, Victor; Chen, Zhenguo; Sun, Siyang; Xiang, Ye; Subramaniam, Sriram; Rao, Venigalla B.; Rossmann, Michael G.

    2015-01-01

    The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth. PMID:26144253

  17. Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM

    PubMed Central

    Li, Wen; Agirrezabala, Xabier; Lei, Jianlin; Bouakaz, Lamine; Brunelle, Julie L; Ortiz-Meoz, Rodrigo F; Green, Rachel; Sanyal, Suparna; Ehrenberg, Måns; Frank, Joachim

    2008-01-01

    The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes of different aa-tRNAs, we compared cryo-EM maps of the kirromycin-stalled ribosome bound with ternary complexes containing Phe-tRNAPhe, Trp-tRNATrp, or Leu-tRNALeuI. The three maps suggest a common binding manner of cognate aa-tRNAs in their specific binding with both the ribosome and EF-Tu. All three aa-tRNAs have the same ‘loaded spring' conformation with a kink and twist between the D-stem and anticodon stem. The three complexes are similarly integrated in an interaction network, extending from the anticodon loop through h44 and protein S12 to the EF-Tu-binding CCA end of aa-tRNA, proposed to signal cognate codon–anticodon interaction to the GTPase centre and tune the accuracy of aa-tRNA selection. PMID:19020518

  18. Maps of the little bangs through energy density and temperature fluctuations

    SciTech Connect

    Basu, Sumit Chatterjee, Rupa; Nayak, Tapan K.

    2016-01-22

    Heavy-ion collisions at ultra-relativistic energies are often referred to as little bangs. We propose for the first time to map the heavy-ion collisions at ultra-relativistic energies, similar to the maps of the cosmic microwave background radiation, using fluctuations of energy density and temperature in small phase space bins. We study the evolution of fluctuations at each stage of the collision using an event-by-event hydrodynamic framework. We demonstrate the feasibility of making fluctuation maps from experimental data and its usefulness in extracting considerable information regarding the early stages of the collision and its evolution.

  19. Eulerian Mapping Closure Approach for Probability Density Function of Concentration in Shear Flows

    NASA Technical Reports Server (NTRS)

    He, Guowei; Bushnell, Dennis M. (Technical Monitor)

    2002-01-01

    The Eulerian mapping closure approach is developed for uncertainty propagation in computational fluid mechanics. The approach is used to study the Probability Density Function (PDF) for the concentration of species advected by a random shear flow. An analytical argument shows that fluctuation of the concentration field at one point in space is non-Gaussian and exhibits stretched exponential form. An Eulerian mapping approach provides an appropriate approximation to both convection and diffusion terms and leads to a closed mapping equation. The results obtained describe the evolution of the initial Gaussian field, which is in agreement with direct numerical simulations.

  20. ConfMatch: automating electron-density map interpretation by matching conformations.

    PubMed

    Wang, C E

    2000-12-01

    Building a protein model from the initial three-dimensional electron-density distribution (density map) is an important task in X-ray crystallography. This problem is computationally challenging because proteins are extremely flexible. The algorithm ConfMatch is a global real-space fitting procedure in torsion-angle space. It solves this 'map-interpretation' problem by matching a detailed conformation of the molecule to the density map (conformational matching). This 'best-match' structure is defined as one which maximizes the sum of the density at atom positions. ConfMatch is a practical systematic algorithm based on a branch-and-bound search. The most important idea of ConfMatch is an efficient method for computing accurate bounds. ConfMatch relaxes the conformational matching problem, a problem which can only be solved in exponential time, into one which can be solved in polynomial time. The solution to the relaxed problem is a guaranteed upper bound for the conformational matching problem. In most empirical cases, these bounds are accurate enough to prune the search space dramatically, enabling ConfMatch to solve structures with more than 100 free dihedral angles. Experiments have shown that ConfMatch may be able to automate the interpretation of density maps of small proteins.

  1. Factors that Influence the Formation and Stability of Thin, Cryo-EM Specimens

    PubMed Central

    Glaeser, Robert M.; Han, Bong-Gyoon; Csencsits, Roseann; Killilea, Alison; Pulk, Arto; Cate, Jamie H.D.

    2016-01-01

    Poor consistency of the ice thickness from one area of a cryo-electron microscope (cryo-EM) specimen grid to another, from one grid to the next, and from one type of specimen to another, motivates a reconsideration of how to best prepare suitably thin specimens. Here we first review the three related topics of wetting, thinning, and stability against dewetting of aqueous films spread over a hydrophilic substrate. We then suggest that the importance of there being a surfactant monolayer at the air-water interface of thin, cryo-EM specimens has been largely underappreciated. In fact, a surfactant layer (of uncontrolled composition and surface pressure) can hardly be avoided during standard cryo-EM specimen preparation. We thus suggest that better control over the composition and properties of the surfactant layer may result in more reliable production of cryo-EM specimens with the desired thickness. PMID:26386606

  2. 1.0 Mm Maps and Radial Density Distributions of Southern Hii/molecular Cloud Complexes

    NASA Technical Reports Server (NTRS)

    Cheung, L. H.; Frogel, J. A.; Gezar, D. Y.; Hauser, M. G.

    1980-01-01

    Several 1.0 continuum mapping observations were made of seven southern hemisphere h12/molecular cloud complexes with 65 arcsec resolution. The radial density distribution of the clouds with central luminosity sources was determined observationally. Strong similarities in morphology and general physical conditions were found to exist among all of the southern clouds in the sample.

  3. An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

    PubMed Central

    Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

    2013-01-01

    We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

  4. The development of cryo-EM into a mainstream structural biology technique

    PubMed Central

    Nogales, Eva

    2016-01-01

    Single-particle cryo-electron microscopy (cryo-EM) has emerged over the last two decades as a technique capable of studying challenging systems that otherwise defy structural characterization. Recent technical advances have resulted in a ‘quantum leap’ in applicability, throughput and achievable resolution that has gained this technique worldwide attention. Here I discuss some of the major historical landmarks in the development of the cryo-EM field, ultimately leading to its present success. PMID:27110629

  5. Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports

    PubMed Central

    Meyerson, Joel R.; Rao, Prashant; Kumar, Janesh; Chittori, Sagar; Banerjee, Soojay; Pierson, Jason; Mayer, Mark L.; Subramaniam, Sriram

    2014-01-01

    Poor partitioning of macromolecules into the holes of holey carbon support grids frequently limits structural determination by single particle cryo-electron microscopy (cryo-EM). Here, we present a method to deposit, on gold-coated carbon grids, a self-assembled monolayer whose surface properties can be controlled by chemical modification. We demonstrate the utility of this approach to drive partitioning of ionotropic glutamate receptors into the holes, thereby enabling 3D structural analysis using cryo-EM methods. PMID:25403871

  6. Particle visualization in high-power impulse magnetron sputtering. I. 2D density mapping

    SciTech Connect

    Britun, Nikolay Palmucci, Maria; Konstantinidis, Stephanos; Snyders, Rony

    2015-04-28

    Time-resolved characterization of an Ar-Ti high-power impulse magnetron sputtering discharge has been performed. This paper deals with two-dimensional density mapping in the discharge volume obtained by laser-induced fluorescence imaging. The time-resolved density evolution of Ti neutrals, singly ionized Ti atoms (Ti{sup +}), and Ar metastable atoms (Ar{sup met}) in the area above the sputtered cathode is mapped for the first time in this type of discharges. The energetic characteristics of the discharge species are additionally studied by Doppler-shift laser-induced fluorescence imaging. The questions related to the propagation of both the neutral and ionized discharge particles, as well as to their spatial density distributions, are discussed.

  7. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process

    PubMed Central

    Valle, Mikel; Sengupta, Jayati; Swami, Neil K.; Grassucci, Robert A.; Burkhardt, Nils; Nierhaus, Knud H.; Agrawal, Rajendra K.; Frank, Joachim

    2002-01-01

    During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, the anticodon end of the tRNA reaches the decoding center in the 30S subunit. Here we present the cryo- electron microscopy (EM) study of an Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic, kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new conformation that appears to facilitate the initial codon–anticodon interaction. Furthermore, the elbow region of the tRNA is seen to contact the GTPase-associated center on the 50S subunit of the ribosome, suggesting an active role of the tRNA in the transmission of the signal prompting the GTP hydrolysis upon codon recognition. PMID:12093756

  8. Muographic mapping of the subsurface density structures in Miura, Boso and Izu peninsulas, Japan.

    PubMed

    Tanaka, Hiroyuki K M

    2015-02-09

    While the benefits of determining the bulk density distribution of a landmass are evident, established experimental techniques reliant on gravity measurements cannot uniquely determine the underground density distribution. We address this problem by taking advantage of traffic tunnels densely distributed throughout the country. Cosmic ray muon flux is measured in the tunnels to determine the average density of each rock overburden. After analyzing the data collected from 146 observation points in Miura, South-Boso and South-Izu Peninsula, Japan as an example, we mapped out the shallow density distribution of an area of 1340 km(2). We find a good agreement between muographically determined density distribution and geologic features as described in existing geological studies. The average shallow density distribution below each peninsula was determined with a great accuracy (less than ±0.8%). We also observed a significant reduction in density along fault lines and interpreted that as due to the presence of multiple cracks caused by mechanical stress during recurrent seismic events. We show that this new type of muography technique can be applied to estimate the terrain density and porosity distribution, thus determining more precise Bouguer reduction densities.

  9. Muographic mapping of the subsurface density structures in Miura, Boso and Izu peninsulas, Japan

    PubMed Central

    Tanaka, Hiroyuki K. M.

    2015-01-01

    While the benefits of determining the bulk density distribution of a landmass are evident, established experimental techniques reliant on gravity measurements cannot uniquely determine the underground density distribution. We address this problem by taking advantage of traffic tunnels densely distributed throughout the country. Cosmic ray muon flux is measured in the tunnels to determine the average density of each rock overburden. After analyzing the data collected from 146 observation points in Miura, South-Boso and South-Izu Peninsula, Japan as an example, we mapped out the shallow density distribution of an area of 1340 km2. We find a good agreement between muographically determined density distribution and geologic features as described in existing geological studies. The average shallow density distribution below each peninsula was determined with a great accuracy (less than ±0.8%). We also observed a significant reduction in density along fault lines and interpreted that as due to the presence of multiple cracks caused by mechanical stress during recurrent seismic events. We show that this new type of muography technique can be applied to estimate the terrain density and porosity distribution, thus determining more precise Bouguer reduction densities. PMID:25660352

  10. Muographic mapping of the subsurface density structures in Miura, Boso and Izu peninsulas, Japan

    NASA Astrophysics Data System (ADS)

    Tanaka, Hiroyuki K. M.

    2015-02-01

    While the benefits of determining the bulk density distribution of a landmass are evident, established experimental techniques reliant on gravity measurements cannot uniquely determine the underground density distribution. We address this problem by taking advantage of traffic tunnels densely distributed throughout the country. Cosmic ray muon flux is measured in the tunnels to determine the average density of each rock overburden. After analyzing the data collected from 146 observation points in Miura, South-Boso and South-Izu Peninsula, Japan as an example, we mapped out the shallow density distribution of an area of 1340 km2. We find a good agreement between muographically determined density distribution and geologic features as described in existing geological studies. The average shallow density distribution below each peninsula was determined with a great accuracy (less than +/-0.8%). We also observed a significant reduction in density along fault lines and interpreted that as due to the presence of multiple cracks caused by mechanical stress during recurrent seismic events. We show that this new type of muography technique can be applied to estimate the terrain density and porosity distribution, thus determining more precise Bouguer reduction densities.

  11. MRSA: a density-equalizing mapping analysis of the global research architecture.

    PubMed

    Addicks, Johann P; Uibel, Stefanie; Jensen, Anna-Maria; Bundschuh, Matthias; Klingelhoefer, Doris; Groneberg, David A

    2014-09-30

    Methicillin-resistant Staphylococcus aureus (MRSA) has evolved as an alarming public health thread due to its global spread as hospital and community pathogen. Despite this role, a scientometric analysis has not been performed yet. Therefore, the NewQIS platform was used to conduct a combined density-equalizing mapping and scientometric study. As database, the Web of Science was used, and all entries between 1961 and 2007 were analyzed. In total, 7671 entries were identified. Density equalizing mapping demonstrated a distortion of the world map for the benefit of the USA as leading country with a total output of 2374 publications, followed by the UK (1030) and Japan (862). Citation rate analysis revealed Portugal as leading country with a rate of 35.47 citations per article, followed by New Zealand and Denmark. Country cooperation network analyses showed 743 collaborations with US-UK being most frequent. Network citation analyses indicated the publications that arose from the cooperation of USA and France as well as USA and Japan as the most cited (75.36 and 74.55 citations per collaboration article, respectively). The present study provides the first combined density-equalizing mapping and scientometric analysis of MRSA research. It illustrates the global MRSA research architecture. It can be assumed that this highly relevant topic for public health will achieve even greater dimensions in the future.

  12. StreamMap: Smooth Dynamic Visualization of High-Density Streaming Points.

    PubMed

    Li, Chenhui; Baciu, George; Yu, Han

    2017-02-13

    Interactive visualization of streaming points for real-time scatterplots and linear blending of correlation patterns is increasingly becoming the dominant mode of visual analytics for both big data and streaming data from active sensors and broadcasting media. To better visualize and interact with inter-stream patterns, it is generally necessary to smooth out gaps or distortions in the streaming data. Previous approaches either animate the points directly or present a sampled static heatmap. We propose a new approach, called StreamMap, to smoothly blend high-density streaming points and create a visual flow that emphasizes the density pattern distributions. In essence, we present three new contributions for the visualization of high-density streaming points. The first contribution is a density-based method called super kernel density estimation that aggregates streaming points using an adaptive kernel to solve the overlapping problem. The second contribution is a robust density morphing algorithm that generates several smooth intermediate frames for a given pair of frames. The third contribution is a trend representation design that can help convey the flow directions of the streaming points. The experimental results on three datasets demonstrate the effectiveness of StreamMap when dynamic visualization and visual analysis of trend patterns on streaming points are required.

  13. High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya.

    PubMed Central

    Ma, Hao; Moore, Paul H; Liu, Zhiyong; Kim, Minna S; Yu, Qingyi; Fitch, Maureen M M; Sekioka, Terry; Paterson, Andrew H; Ming, Ray

    2004-01-01

    A high-density genetic map of papaya (Carica papaya L.) was constructed using 54 F(2) plants derived from cultivars Kapoho and SunUp with 1501 markers, including 1498 amplified fragment length polymorphism (AFLP) markers, the papaya ringspot virus coat protein marker, morphological sex type, and fruit flesh color. These markers were mapped into 12 linkage groups at a LOD score of 5.0 and recombination frequency of 0.25. The 12 major linkage groups covered a total length of 3294.2 cM, with an average distance of 2.2 cM between adjacent markers. This map revealed severe suppression of recombination around the sex determination locus with a total of 225 markers cosegregating with sex types. The cytosine bases were highly methylated in this region on the basis of the distribution of methylation-sensitive and -insensitive markers. This high-density genetic map is essential for cloning of specific genes of interest such as the sex determination gene and for the integration of genetic and physical maps of papaya. PMID:15020433

  14. A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

    PubMed Central

    2012-01-01

    Background Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed

  15. Multispectral x-ray imaging for core temperature and density maps retrieval in direct drive implosions

    SciTech Connect

    Tommasini, Riccardo; Koch, Jeffrey A.; Izumi, Nobuhiko; Welser, Leslie A.; Mancini, Roberto C.; Delettrez, Jacques; Regan, Sean; Smalyuk, Vladimir

    2006-10-15

    We report on the experiments aimed at obtaining core temperature and density maps in direct drive implosions at the Omega laser facility using multimonochromatic x-ray imagers. These instruments use an array of pinholes and a flat multilayer mirror to provide unique multispectral images distributed over a wide spectral range. Using argon as a dopant in the direct-drive filled plastic shells produces emission images in the Ar He-{beta} and Ly-{beta} spectral regions. These images allow the retrieval of temperature and density maps of the plasma. We deployed three identical multimonochromatic x-ray imagers in a quasiorthogonal line-of-sight configuration to allow tomographic reconstruction of the structure of the imploding core.

  16. Multispectral X-ray Imagaing for Core Temperature and Density Maps Retrieval in Direct Drive Implosions

    SciTech Connect

    Tommasini, R; Koch, J A; Izumi, N; Welser, L A; Mancini, R C; Delettrez, J; Regan, S; Smalyuk, V

    2006-04-26

    We report on the experiments aimed at obtaining core temperature and density maps in direct drive implosions at the OMEGA Laser Facility using multi-monochromatic X-ray imagers. These instruments use an array of pinholes and a flat multilayer mirror to provide unique multi-spectral images distributed over a wide spectral range. Using Argon as a dopant in the DD-filled plastic shells produces emission images in the Ar He-b and Ly-b spectral regions. These images allow the retrieval of temperature and density maps of the plasma. We deployed three identical multi-monochromatic X-ray imagers in a quasi-orthogonal line-of-sight configuration to allow tomographic reconstruction of the structure of the imploding core.

  17. Maritime Dynamic Traffic Generator. Volume III: Density Data on World Maps

    DTIC Science & Technology

    1975-06-01

    AD-A012 498 MARITIME DYNAMIC TR/\\FFIC GENERATOR. VOLUME III: DENSITY DATA ON WORLD MAPS Franklin D. MacKenzie Transportation Systems Center Cambridqe... Transportation Systems Center i]. ContractorGrant No. Kendall Square (Camhridge MA 02142 13. Type of Report and Period Covered 12. Sponsorini"Agency Name and... Transportation • Systems Center to define and analyze requirements for navigation and communica .. ..... .. tion services throtgh a satellite for commercial

  18. An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

    PubMed Central

    Peng, Wenzhu; Xu, Jian; Zhang, Yan; Feng, Jianxin; Dong, Chuanju; Jiang, Likun; Feng, Jingyan; Chen, Baohua; Gong, Yiwen; Chen, Lin; Xu, Peng

    2016-01-01

    High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly. PMID:27225429

  19. CryoEM structure of the spliceosome immediately after branching

    PubMed Central

    Galej, Wojciech P.; Wilkinson, Max E.; Fica, Sebastian M.; Oubridge, Chris; Newman, Andrew J.; Nagai, Kiyoshi

    2016-01-01

    Pre-mRNA splicing proceeds by two consecutive trans-esterification reactions via a lariat-intron intermediate. We present the 3.8Å cryoEM structure of the spliceosome immediately after lariat formation. The 5’-splice site is cleaved but remains close to the catalytic Mg2+ site in the U2/U6 snRNA triplex, and the 5’-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2’OH. The 5’-exon is held between the Prp8 N-terminal and Linker domains, and base-pairs with U5 snRNA loop 1. Non-Watson-Crick interactions between the branch helix and 5’-splice site dock the branch adenosine into the active site, while intron nucleotides +3 to +6 base-pair with the U6 snRNA ACAGAGA sequence. Isy1 and the step one factors Yju2 and Cwc25 stabilise docking of the branch helix. The intron downstream of the branch site emerges between the Prp8 RT and Linker domains and extends towards Prp16 helicase, suggesting a plausible mechanism of remodelling before exon ligation. PMID:27459055

  20. Specimen preparation for high-resolution cryo-EM

    PubMed Central

    Passmore, Lori A.; Russo, Christopher J.

    2016-01-01

    Imaging a material with electrons at near-atomic resolution requires a thin specimen that is stable in the vacuum of the transmission electron microscope. For biological samples, this comprises a thin layer of frozen aqueous solution containing the biomolecular complex of interest. The process of preparing a high-quality specimen is often the limiting step in the determination of structures by single-particle electron cryomicroscopy (cryo-EM). Here we describe a systematic approach for going from a purified biomolecular complex in aqueous solution to high-resolution electron micrographs that are suitable for 3D structure determination. This includes a series of protocols for the preparation of vitrified specimens on various specimen supports, including all-gold and graphene. We also describe techniques for troubleshooting when a preparation fails to yield suitable specimens, and common mistakes to avoid during each part of the process. Finally, we include recommendations for obtaining the highest quality micrographs from prepared specimens with current microscope, detector and support technology. PMID:27572723

  1. gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration.

    PubMed

    Hoang, Thai V; Cavin, Xavier; Ritchie, David W

    2013-11-01

    Fitting high resolution protein structures into low resolution cryo-electron microscopy (cryo-EM) density maps is an important technique for modeling the atomic structures of very large macromolecular assemblies. This article presents "gEMfitter", a highly parallel fast Fourier transform (FFT) EM density fitting program which can exploit the special hardware properties of modern graphics processor units (GPUs) to accelerate both the translational and rotational parts of the correlation search. In particular, by using the GPU's special texture memory hardware to rotate 3D voxel grids, the cost of rotating large 3D density maps is almost completely eliminated. Compared to performing 3D correlations on one core of a contemporary central processor unit (CPU), running gEMfitter on a modern GPU gives up to 26-fold speed-up. Furthermore, using our parallel processing framework, this speed-up increases linearly with the number of CPUs or GPUs used. Thus, it is now possible to use routinely more robust but more expensive 3D correlation techniques. When tested on low resolution experimental cryo-EM data for the GroEL-GroES complex, we demonstrate the satisfactory fitting results that may be achieved by using a locally normalised cross-correlation with a Laplacian pre-filter, while still being up to three orders of magnitude faster than the well-known COLORES program.

  2. Fusion to a homo-oligomeric scaffold allows cryo-EM analysis of a small protein

    PubMed Central

    Coscia, Francesca; Estrozi, Leandro F.; Hans, Fabienne; Malet, Hélène; Noirclerc-Savoye, Marjolaine; Schoehn, Guy; Petosa, Carlo

    2016-01-01

    Recent technical advances have revolutionized the field of cryo-electron microscopy (cryo-EM). However, most monomeric proteins remain too small (<100 kDa) for cryo-EM analysis. To overcome this limitation, we explored a strategy whereby a monomeric target protein is genetically fused to a homo-oligomeric scaffold protein and the junction optimized to allow the target to adopt the scaffold symmetry, thereby generating a chimeric particle suitable for cryo-EM. To demonstrate the concept, we fused maltose-binding protein (MBP), a 40 kDa monomer, to glutamine synthetase, a dodecamer formed by two hexameric rings. Chimeric constructs with different junction lengths were screened by biophysical analysis and negative-stain EM. The optimal construct yielded a cryo-EM reconstruction that revealed the MBP structure at sub-nanometre resolution. These findings illustrate the feasibility of using homo-oligomeric scaffolds to enable cryo-EM analysis of monomeric proteins, paving the way for applying this strategy to challenging structures resistant to crystallographic and NMR analysis. PMID:27485862

  3. Single-Particle Cryo-EM of the Ryanodine Receptor Channel in an Aqueous Environment

    PubMed Central

    Baker, Mariah R.; Fan, Guizhen

    2015-01-01

    Ryanodine receptors (RyRs) are tetrameric ligand-gated Ca2+ release channels that are responsible for the increase of cytosolic Ca2+ concentration leading to muscle contraction. Our current understanding of RyR channel gating and regulation is greatly limited due to the lack of a high-resolution structure of the channel protein. The enormous size and unwieldy shape of Ca2+ release channels make X-ray or NMR methods difficult to apply for high-resolution structural analysis of the full-length functional channel. Single-particle electron cryo-microscopy (cryo-EM) is one of the only effective techniques for the study of such a large integral membrane protein and its molecular interactions. Despite recent developments in cryo-EM technologies and break-through single-particle cryo-EM studies of ion channels, cryospecimen preparation, particularly the presence of detergent in the buffer, remains the main impediment to obtaining atomic-resolution structures of ion channels and a multitude of other integral membrane protein complexes. In this review we will discuss properties of several detergents that have been successfully utilized in cryo-EM studies of ion channels and the emergence of the detergent alternative amphipol to stabilize ion channels for structure-function characterization. Future structural studies of challenging specimen like ion channels are likely to be facilitated by cryo-EM amenable detergents or alternative surfactants. PMID:26913144

  4. Single-particle cryo-EM of the ryanodine receptor channel in an aqueous environment

    PubMed Central

    Baker, Mariah R.; Fan, Guizhen; Serysheva, Irina I.

    2015-01-01

    Ryanodine receptors (RyRs) are tetrameric ligand-gated Ca2+ release channels that are responsible for the increase of cytosolic Ca2+ concentration leading to muscle contraction. Our current understanding of RyR channel gating and regulation is greatly limited due to the lack of a high-resolution structure of the channel protein. The enormous size and unwieldy shape of Ca2+ release channels make X-ray or NMR methods difficult to apply for high-resolution structural analysis of the full-length functional channel. Single-particle electron cryo-microscopy (cryo-EM) is one of the only effective techniques for the study of such a large integral membrane protein and its molecular interactions. Despite recent developments in cryo-EM technologies and break-through single-particle cryo-EM studies of ion channels, cryospecimen preparation, particularly the presence of detergent in the buffer, remains the main impediment to obtaining atomic-resolution structures of ion channels and a multitude of other integral membrane protein complexes. In this review we will discuss properties of several detergents that have been successfully utilized in cryo-EM studies of ion channels and the emergence of the detergent alternative amphipol to stabilize ion channels for structure-function characterization. Future structural studies of challenging specimen like ion channels are likely to be facilitated by cryo-EM amenable detergents or alternative surfactants. PMID:25844145

  5. Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases

    PubMed Central

    Mazhab-Jafari, Mohammad T.; Rubinstein, John L.

    2016-01-01

    Electron cryomicroscopy (cryo-EM) has significantly advanced our understanding of molecular structure in biology. Recent innovations in both hardware and software have made cryo-EM a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Cryo-EM has even become the method of choice in some situations where x-ray crystallography and NMR spectroscopy are possible but where cryo-EM can determine structures at higher resolution or with less time or effort. Rotary adenosine triphosphatases (ATPases) are crucial to the maintenance of cellular homeostasis. These enzymes couple the synthesis or hydrolysis of adenosine triphosphate to the use or production of a transmembrane electrochemical ion gradient, respectively. However, the membrane-embedded nature and conformational heterogeneity of intact rotary ATPases have prevented their high-resolution structural analysis to date. Recent application of cryo-EM methods to the different types of rotary ATPase has led to sudden advances in understanding the structure and function of these enzymes, revealing significant conformational heterogeneity and characteristic transmembrane α helices that are highly tilted with respect to the membrane. In this Review, we will discuss what has been learned recently about rotary ATPase structure and function, with a particular focus on the vacuolar-type ATPases. PMID:27532044

  6. Simultaneous Quantitative Imaging of Electrical Properties and Proton Density from B1 Maps Using MRI.

    PubMed

    Liu, Jiaen; Van de Moortele, Pierre-Francois; Zhang, Xiaotong; Wang, Yicun; He, Bin

    2016-03-29

    Electrical conductivity and permittivity of biological tissues are important diagnostic parameters and are useful for calculating subject-specific specific absorption rate distribution. On the other hand, water proton density also has clinical relevance for diagnosis purposes. These two kinds of tissue properties are inevitably associated in the technique of electrical properties tomography (EPT), which can be used to map in vivo electrical properties based on the measured B1 field distribution at Larmor frequency using magnetic resonance imaging (MRI). The signal magnitude in MR images is locally proportional to both the proton density of tissue and the receive B1 field; this is a source of artifact in receive B1-based EPT reconstruction because these two quantities cannot easily be disentangled. In this study, a new method was proposed for simultaneously extracting quantitative conductivity, permittivity and proton density from the measured magnitude of transmit B1 field, proton density-weighted receive B1 field, and transceiver phase, in a multi-channel radiofrequency (RF) coil using MRI, without specific assumptions to derive the proton density distribution. We evaluated the spatial resolution, sensitivity to contrast, and accuracy of the method using numerical simulations of B1 field in a phantom and in a realistic human head model. Using the proposed method, conductivity, permittivity and proton density were then experimentally obtained ex vivo in a pork tissue sample on a 7T MRI scanner equipped with a 16-channel microstrip transceiver RF coil.

  7. Simultaneous Quantitative Imaging of Electrical Properties and Proton Density From B1 Maps Using MRI.

    PubMed

    Jiaen Liu; Van de Moortele, Pierre-Francois; Xiaotong Zhang; Yicun Wang; Bin He

    2016-09-01

    Electrical conductivity and permittivity of biological tissues are important diagnostic parameters and are useful for calculating subject-specific specific absorption rate distribution. On the other hand, water proton density also has clinical relevance for diagnosis purposes. These two kinds of tissue properties are inevitably associated in the technique of electrical properties tomography (EPT), which can be used to map in vivo electrical properties based on the measured B1 field distribution at Larmor frequency using magnetic resonance imaging (MRI). The signal magnitude in MR images is locally proportional to both the proton density of tissue and the receive B1 field; this is a source of artifact in receive B1-based EPT reconstruction because these two quantities cannot easily be disentangled. In this study, a new method was proposed for simultaneously extracting quantitative conductivity, permittivity and proton density from the measured magnitude of transmit B1 field, proton density-weighted receive B1 field, and transceiver phase, in a multi-channel radiofrequency (RF) coil using MRI, without specific assumptions to derive the proton density distribution. We evaluated the spatial resolution, sensitivity to contrast, and accuracy of the method using numerical simulations of B1 field in a phantom and in a realistic human head model. Using the proposed method, conductivity, permittivity and proton density were then experimentally obtained ex vivo in a pork tissue sample on a 7T MRI scanner equipped with a 16-channel microstrip transceiver RF coil.

  8. Tree-centric mapping of forest carbon density from airborne laser scanning and hyperspectral data.

    PubMed

    Dalponte, Michele; Coomes, David A

    2016-10-01

    Forests are a major component of the global carbon cycle, and accurate estimation of forest carbon stocks and fluxes is important in the context of anthropogenic global change. Airborne laser scanning (ALS) data sets are increasingly recognized as outstanding data sources for high-fidelity mapping of carbon stocks at regional scales.We develop a tree-centric approach to carbon mapping, based on identifying individual tree crowns (ITCs) and species from airborne remote sensing data, from which individual tree carbon stocks are calculated. We identify ITCs from the laser scanning point cloud using a region-growing algorithm and identifying species from airborne hyperspectral data by machine learning. For each detected tree, we predict stem diameter from its height and crown-width estimate. From that point on, we use well-established approaches developed for field-based inventories: above-ground biomasses of trees are estimated using published allometries and summed within plots to estimate carbon density.We show this approach is highly reliable: tests in the Italian Alps demonstrated a close relationship between field- and ALS-based estimates of carbon stocks (r(2) = 0·98). Small trees are invisible from the air, and a correction factor is required to accommodate this effect.An advantage of the tree-centric approach over existing area-based methods is that it can produce maps at any scale and is fundamentally based on field-based inventory methods, making it intuitive and transparent. Airborne laser scanning, hyperspectral sensing and computational power are all advancing rapidly, making it increasingly feasible to use ITC approaches for effective mapping of forest carbon density also inside wider carbon mapping programs like REDD++.

  9. Galaxy bias from the Dark Energy Survey Science Verification data: combining galaxy density maps and weak lensing maps

    SciTech Connect

    Chang, C.; Pujol, A.; Gaztañaga, E.; Amara, A.; Réfrégier, A.; Bacon, D.; Becker, M. R.; Bonnett, C.; Carretero, J.; Castander, F. J.; Crocce, M.; Fosalba, P.; Giannantonio, T.; Hartley, W.; Jarvis, M.; Kacprzak, T.; Ross, A. J.; Sheldon, E.; Troxel, M. A.; Vikram, V.; Zuntz, J.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Rosell, A. Carnero; Kind, M. Carrasco; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Eifler, T. F.; Estrada, J.; Evrard, A. E.; Flaugher, B.; Frieman, J.; Goldstein, D. A.; Gruen, D.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; Jain, B.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; Marshall, J. L.; Martini, P.; Melchior, P.; Miller, C. J.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Walker, A. R.

    2016-04-15

    We measure the redshift evolution of galaxy bias from a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a $\\sim$116 deg$^{2}$ area of the Dark Energy Survey (DES) Science Verification data. This method was first developed in Amara et al. (2012) and later re-examined in a companion paper (Pujol et al., in prep) with rigorous simulation tests and analytical treatment of tomographic measurements. In this work we apply this method to the DES SV data and measure the galaxy bias for a magnitude-limited galaxy sample. We find the galaxy bias and 1$\\sigma$ error bars in 4 photometric redshift bins to be 1.33$\\pm$0.18 (z=0.2-0.4), 1.19$\\pm$0.23 (z=0.4-0.6), 0.99$\\pm$0.36 ( z=0.6-0.8), and 1.66$\\pm$0.56 (z=0.8-1.0). These measurements are consistent at the 1-2$\\sigma$ level with mea- surements on the same dataset using galaxy clustering and cross-correlation of galaxies with CMB lensing. In addition, our method provides the only $\\sigma_8$-independent constraint among the three. We forward-model the main observational effects using mock galaxy catalogs by including shape noise, photo-z errors and masking effects. We show that our bias measurement from the data is consistent with that expected from simulations. With the forthcoming full DES data set, we expect this method to provide additional constraints on the galaxy bias measurement from more traditional methods. Furthermore, in the process of our measurement, we build up a 3D mass map that allows further exploration of the dark matter distribution and its relation to galaxy evolution.

  10. Galaxy bias from the Dark Energy Survey Science Verification data: combining galaxy density maps and weak lensing maps

    NASA Astrophysics Data System (ADS)

    Chang, C.; Pujol, A.; Gaztañaga, E.; Amara, A.; Réfrégier, A.; Bacon, D.; Becker, M. R.; Bonnett, C.; Carretero, J.; Castander, F. J.; Crocce, M.; Fosalba, P.; Giannantonio, T.; Hartley, W.; Jarvis, M.; Kacprzak, T.; Ross, A. J.; Sheldon, E.; Troxel, M. A.; Vikram, V.; Zuntz, J.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Rosell, A. Carnero; Kind, M. Carrasco; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Eifler, T. F.; Estrada, J.; Evrard, A. E.; Flaugher, B.; Frieman, J.; Goldstein, D. A.; Gruen, D.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; Jain, B.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; Marshall, J. L.; Martini, P.; Melchior, P.; Miller, C. J.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Walker, A. R.

    2016-07-01

    We measure the redshift evolution of galaxy bias for a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a ˜116 deg2 area of the Dark Energy Survey (DES) Science Verification (SV) data. This method was first developed in Amara et al. and later re-examined in a companion paper with rigorous simulation tests and analytical treatment of tomographic measurements. In this work we apply this method to the DES SV data and measure the galaxy bias for a i < 22.5 galaxy sample. We find the galaxy bias and 1σ error bars in four photometric redshift bins to be 1.12 ± 0.19 (z = 0.2-0.4), 0.97 ± 0.15 (z = 0.4-0.6), 1.38 ± 0.39 (z = 0.6-0.8), and 1.45 ± 0.56 (z = 0.8-1.0). These measurements are consistent at the 2σ level with measurements on the same data set using galaxy clustering and cross-correlation of galaxies with cosmic microwave background lensing, with most of the redshift bins consistent within the 1σ error bars. In addition, our method provides the only σ8 independent constraint among the three. We forward model the main observational effects using mock galaxy catalogues by including shape noise, photo-z errors, and masking effects. We show that our bias measurement from the data is consistent with that expected from simulations. With the forthcoming full DES data set, we expect this method to provide additional constraints on the galaxy bias measurement from more traditional methods. Furthermore, in the process of our measurement, we build up a 3D mass map that allows further exploration of the dark matter distribution and its relation to galaxy evolution.

  11. Galaxy bias from the Dark Energy Survey Science Verification data: Combining galaxy density maps and weak lensing maps

    DOE PAGES

    Chang, C.; Pujol, A.; Gaztañaga, E.; ...

    2016-04-15

    Here, we measure the redshift evolution of galaxy bias for a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a ~116 deg2 area of the Dark Energy Survey (DES) Science Verification data. This method was first developed in Amara et al. (2012) and later re-examined in a companion paper (Pujol et al. 2016) with rigorous simulation tests and analytical treatment of tomographic measurements. In this work we apply this method to the DES SV data and measure the galaxy bias for a i < 22.5 galaxy sample. We find the galaxy bias andmore » 1σ error bars in 4 photometric redshift bins to be 1.12±0.19 (z=0.2-0.4), 0.97±0.15 (z=0.4-0.6), 1.38±0.39 (z=0.6-0.8)), and 1.45±0.56 (z=0.8-1.0). These measurements are consistent at the 2σ level with measurements on the same dataset using galaxy clustering and cross-correlation of galaxies with CMB lensing, with most of the redshift bins consistent within the 1{\\sigma} error bars. In addition, our method provides the only σ8-independent constraint among the three. We forward-model the main observational effects using mock galaxy catalogs by including shape noise, photo-z errors and masking effects. We show that our bias measurement from the data is consistent with that expected from simulations. With the forthcoming full DES data set, we expect this method to provide additional constraints on the galaxy bias measurement from more traditional methods. Furthermore, in the process of our measurement, we build up a 3D mass map that allows further exploration of the dark matter distribution and its relation to galaxy evolution.« less

  12. Galaxy bias from the Dark Energy Survey Science Verification data: Combining galaxy density maps and weak lensing maps

    DOE PAGES

    Chang, C.; Pujol, A.; Gaztañaga, E.; ...

    2016-04-15

    We measure the redshift evolution of galaxy bias for a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a ~116 deg2 area of the Dark Energy Survey (DES) Science Verification (SV) data. This method was first developed in Amara et al. and later re-examined in a companion paper with rigorous simulation tests and analytical treatment of tomographic measurements. In this work we apply this method to the DES SV data and measure the galaxy bias for a i < 22.5 galaxy sample. We find the galaxy bias and 1σ error bars in fourmore » photometric redshift bins to be 1.12 ± 0.19 (z = 0.2–0.4), 0.97 ± 0.15 (z = 0.4–0.6), 1.38 ± 0.39 (z = 0.6–0.8), and 1.45 ± 0.56 (z = 0.8–1.0). These measurements are consistent at the 2σ level with measurements on the same data set using galaxy clustering and cross-correlation of galaxies with cosmic microwave background lensing, with most of the redshift bins consistent within the 1σ error bars. In addition, our method provides the only σ8 independent constraint among the three. We forward model the main observational effects using mock galaxy catalogues by including shape noise, photo-z errors, and masking effects. We show that our bias measurement from the data is consistent with that expected from simulations. With the forthcoming full DES data set, we expect this method to provide additional constraints on the galaxy bias measurement from more traditional methods. Moreover, in the process of our measurement, we build up a 3D mass map that allows further exploration of the dark matter distribution and its relation to galaxy evolution.« less

  13. Galaxy bias from the Dark Energy Survey Science Verification data: Combining galaxy density maps and weak lensing maps

    SciTech Connect

    Chang, C.; Pujol, A.; Gaztañaga, E.; Amara, A.; Réfrégier, A.; Bacon, D.; Becker, M. R.; Bonnett, C.; Carretero, J.; Castander, F. J.; Crocce, M.; Fosalba, P.; Giannantonio, T.; Hartley, W.; Jarvis, M.; Kacprzak, T.; Ross, A. J.; Sheldon, E.; Troxel, M. A.; Vikram, V.; Zuntz, J.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Rosell, A. Carnero; Kind, M. Carrasco; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Eifler, T. F.; Estrada, J.; Evrard, A. E.; Flaugher, B.; Frieman, J.; Goldstein, D. A.; Gruen, D.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; Jain, B.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; Marshall, J. L.; Martini, P.; Melchior, P.; Miller, C. J.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Walker, A. R.

    2016-04-15

    We measure the redshift evolution of galaxy bias for a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a ~116 deg2 area of the Dark Energy Survey (DES) Science Verification (SV) data. This method was first developed in Amara et al. and later re-examined in a companion paper with rigorous simulation tests and analytical treatment of tomographic measurements. In this work we apply this method to the DES SV data and measure the galaxy bias for a i < 22.5 galaxy sample. We find the galaxy bias and 1σ error bars in four photometric redshift bins to be 1.12 ± 0.19 (z = 0.2–0.4), 0.97 ± 0.15 (z = 0.4–0.6), 1.38 ± 0.39 (z = 0.6–0.8), and 1.45 ± 0.56 (z = 0.8–1.0). These measurements are consistent at the 2σ level with measurements on the same data set using galaxy clustering and cross-correlation of galaxies with cosmic microwave background lensing, with most of the redshift bins consistent within the 1σ error bars. In addition, our method provides the only σ8 independent constraint among the three. We forward model the main observational effects using mock galaxy catalogues by including shape noise, photo-z errors, and masking effects. We show that our bias measurement from the data is consistent with that expected from simulations. With the forthcoming full DES data set, we expect this method to provide additional constraints on the galaxy bias measurement from more traditional methods. Moreover, in the process of our measurement, we build up a 3D mass map that allows further exploration of the dark matter distribution and its relation to galaxy evolution.

  14. Spectral density mapping at multiple magnetic fields suitable for 13C NMR relaxation studies

    NASA Astrophysics Data System (ADS)

    Kadeřávek, Pavel; Zapletal, Vojtěch; Fiala, Radovan; Srb, Pavel; Padrta, Petr; Přecechtělová, Jana Pavlíková; Šoltésová, Mária; Kowalewski, Jozef; Widmalm, Göran; Chmelík, Josef; Sklenář, Vladimír; Žídek, Lukáš

    2016-05-01

    Standard spectral density mapping protocols, well suited for the analysis of 15N relaxation rates, introduce significant systematic errors when applied to 13C relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and 13C frequencies can be obtained from data acquired at three magnetic fields for uniformly 13C -labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.

  15. Digital mining claim density map for federal lands in Washington: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Washington as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  16. Digital mining claim density map for federal lands in Colorado: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Colorado as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  17. Digital mining claim density map for federal lands in California: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in California as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  18. Digital mining claim density map for federal lands in New Mexico: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in New Mexico as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  19. Digital mining claim density map for federal lands in Nevada: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Nevada as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate Bureau of Land Management (BLM) State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  20. Digital mining claim density map for federal lands in Arizona: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Arizona as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  1. Digital mining claim density map for federal lands in Utah: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Utah as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  2. Digital mining claim density map for federal lands in Wyoming: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Wyoming as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  3. Digital mining claim density map for federal lands in Idaho: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Idaho as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill and tunnel sites must be recorded at the appropriate Bureau of Land Management (BLM) State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  4. Digital mining claim density map for federal lands in Oregon: 1996

    USGS Publications Warehouse

    Hyndman, Paul C.; Campbell, Harry W.

    1999-01-01

    This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Oregon as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill and tunnel sites must be recorded at the appropriate Bureau of Land Management (BLM) State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

  5. Fabs enable single particle cryoEM studies of small proteins.

    PubMed

    Wu, Shenping; Avila-Sakar, Agustin; Kim, JungMin; Booth, David S; Greenberg, Charles H; Rossi, Andrea; Liao, Maofu; Li, Xueming; Alian, Akram; Griner, Sarah L; Juge, Narinobu; Yu, Yadong; Mergel, Claudia M; Chaparro-Riggers, Javier; Strop, Pavel; Tampé, Robert; Edwards, Robert H; Stroud, Robert M; Craik, Charles S; Cheng, Yifan

    2012-04-04

    In spite of its recent achievements, the technique of single particle electron cryomicroscopy (cryoEM) has not been widely used to study proteins smaller than 100 kDa, although it is a highly desirable application of this technique. One fundamental limitation is that images of small proteins embedded in vitreous ice do not contain adequate features for accurate image alignment. We describe a general strategy to overcome this limitation by selecting a fragment antigen binding (Fab) to form a stable and rigid complex with a target protein, thus providing a defined feature for accurate image alignment. Using this approach, we determined a three-dimensional structure of an ∼65 kDa protein by single particle cryoEM. Because Fabs can be readily generated against a wide range of proteins by phage display, this approach is generally applicable to study many small proteins by single particle cryoEM.

  6. Robust estimation for class averaging in cryo-EM Single Particle Reconstruction.

    PubMed

    Huang, Chenxi; Tagare, Hemant D

    2014-01-01

    Single Particle Reconstruction (SPR) for Cryogenic Electron Microscopy (cryo-EM) aligns and averages the images extracted from micrographs to improve the Signal-to-Noise ratio (SNR). Outliers compromise the fidelity of the averaging. We propose a robust cross-correlation-like w-estimator for combating the effect of outliers on the average images in cryo-EM. The estimator accounts for the natural variation of signal contrast among the images and eliminates the need for a threshold for outlier rejection. We show that the influence function of our estimator is asymptotically bounded. Evaluations of the estimator on simulated and real cryo-EM images show good performance in the presence of outliers.

  7. Does contamination buildup limit throughput for automated cryoEM?

    PubMed

    Cheng, Anchi; Fellmann, Denis; Pulokas, James; Potter, Clinton S; Carragher, Bridget

    2006-06-01

    The development of automated systems for data acquisition in cryo electron microscopy has enabled the possibility of acquiring very large number of images from a single specimen grid. We have demonstrated that over images of 250,000 single particles can be acquired in a 24 h period. This has raised questions as to whether contamination buildup on the specimen limits the quality of the data that can be acquired during these long duration experiments and also whether the data acquisition session could be extended to allow acquisition of more than 1,000,000 particles. We report here a systematic characterization of contamination of specimens maintained for long periods of time at liquid nitrogen temperatures using standard side entry cryo stages. As part of this characterization we developed a more reliable method for accurately estimating specimen ice thickness. Using the method, we were able to calibrate image contrast against ice thickness under a variety of magnifications, objective aperture positions, and defoci, and demonstrated the strong dependence of the calibration curve on these parameters. The results show the anti-contamination aperture is, as expected, critical to the prevention of contamination and that loading film into the microscope dramatically increases the contamination rate, particularly in the first 3 h after the insertion of the film box. In the absence of film, we were able to reproducibly demonstrate that the contamination rate can be limited to a rate of approximately 1 angstrom/h providing reassurance that contamination will not be a major limiting factor for long term cryoEM experiments if a CCD camera is used for the imaging.

  8. B1 mapping with a pure phase encode approach: Quantitative density profiling

    NASA Astrophysics Data System (ADS)

    Vashaee, S.; Newling, B.; MacMillan, B.; Balcom, B. J.

    2013-07-01

    In MRI, it is frequently observed that naturally uniform samples do not have uniform image intensities. In many cases this non-uniform image intensity is due to an inhomogeneous B1 field. The ‘principle of reciprocity' states that the received signal is proportional to the local magnitude of the applied B1 field per unit current. Inhomogeneity in the B1 field results in signal intensity variations that limit the ability of MRI to yield quantitative information. In this paper a novel method is described for mapping B1 inhomogeneities based on measurement of the B1 field employing centric-scan pure phase encode MRI measurements. The resultant B1 map may be employed to correct related non-uniformities in MR images. The new method is based on acquiring successive images with systematically incremented low flip angle excitation pulses. The local image intensity variation is proportional to B12, which ensures high sensitivity to B1 field variations. Pure phase encoding ensures the resultant B1 field maps are free from distortions caused by susceptibility variation, chemical shift and paramagnetic impurities. Hence, the method works well in regions of space that are not accessible to other methods such as in the vicinity of conductive metallic structures, such as the RF probe itself. Quantitative density images result when the centric scan pure phase encode measurement is corrected with a relative or absolute B1 field map. The new technique is simple, reliable and robust.

  9. High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers

    PubMed Central

    Zhang, Qiong; Liu, Chunyan; Liu, Yifei; VanBuren, Robert; Yao, Xiaohong; Zhong, Caihong; Huang, Hongwen

    2015-01-01

    Kiwifruit (Actinidia chinensis Planchon) is an important specialty fruit crop that suffers from narrow genetic diversity stemming from recent global commercialization and limited cultivar improvement. Here, we present high-density RAD-seq-based genetic maps using an interspecific F1 cross between Actinidia rufa ‘MT570001’ and A. chinensis ‘Guihai No4’. The A. rufa (maternal) map consists of 2,426 single-nucleotide polymorphism (SNP) markers with a total length of 2,651 cM in 29 linkage groups (LGs) corresponding to the 29 chromosomes. The A. chinensis (paternal) map consists of 4,214 SNP markers over 3,142 cM in 29 LGs. Using these maps, we were able to anchor an additional 440 scaffolds from the kiwifruit draft genome assembly. Kiwifruit is functionally dioecious, which presents unique challenges for breeding and production. Three sex-specific simple sequence repeats (SSR) markers can be used to accurately sex type male and female kiwifruit in breeding programmes. The sex-determination region (SDR) in kiwifruit was narrowed to a 1-Mb subtelomeric region on chromosome 25. Localizing the SDR will expedite the discovery of genes controlling carpel abortion in males and pollen sterility in females. PMID:26370666

  10. High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers.

    PubMed

    Zhang, Qiong; Liu, Chunyan; Liu, Yifei; VanBuren, Robert; Yao, Xiaohong; Zhong, Caihong; Huang, Hongwen

    2015-10-01

    Kiwifruit (Actinidia chinensis Planchon) is an important specialty fruit crop that suffers from narrow genetic diversity stemming from recent global commercialization and limited cultivar improvement. Here, we present high-density RAD-seq-based genetic maps using an interspecific F1 cross between Actinidia rufa 'MT570001' and A. chinensis 'Guihai No4'. The A. rufa (maternal) map consists of 2,426 single-nucleotide polymorphism (SNP) markers with a total length of 2,651 cM in 29 linkage groups (LGs) corresponding to the 29 chromosomes. The A. chinensis (paternal) map consists of 4,214 SNP markers over 3,142 cM in 29 LGs. Using these maps, we were able to anchor an additional 440 scaffolds from the kiwifruit draft genome assembly. Kiwifruit is functionally dioecious, which presents unique challenges for breeding and production. Three sex-specific simple sequence repeats (SSR) markers can be used to accurately sex type male and female kiwifruit in breeding programmes. The sex-determination region (SDR) in kiwifruit was narrowed to a 1-Mb subtelomeric region on chromosome 25. Localizing the SDR will expedite the discovery of genes controlling carpel abortion in males and pollen sterility in females.

  11. Single-particle cryo-EM data acquisition by using direct electron detection camera

    PubMed Central

    Wu, Shenping; Armache, Jean-Paul; Cheng, Yifan

    2016-01-01

    Recent advances in single-particle electron cryo-microscopy (cryo-EM) were largely facilitated by the application of direct electron detection cameras. These cameras feature not only a significant improvement in detective quantum efficiency but also a high frame rate that enables images to be acquired as ‘movies’ made of stacks of many frames. In this review, we discuss how the applications of direct electron detection cameras in cryo-EM have changed the way the data are acquired. PMID:26546989

  12. A methodology for mapping forest latent heat flux densities using remote sensing

    NASA Technical Reports Server (NTRS)

    Pierce, Lars L.; Congalton, Russell G.

    1988-01-01

    Surface temperatures and reflectances of an upper elevation Sierran mixed conifer forest were monitored using the Thematic Mapper Simulator sensor during the summer of 1985 in order to explore the possibility of using remote sensing to determine the distribution of solar energy on forested watersheds. The results show that the method is capable of quantifying the relative energy allocation relationships between the two cover types defined in the study. It is noted that the method also has the potential to map forest latent heat flux densities.

  13. A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)

    PubMed Central

    Xu, Xuewen; Xu, Ruixue; Zhu, Biyun; Yu, Ting; Qu, Wenqin; Lu, Lu; Xu, Qiang; Qi, Xiaohua; Chen, Xuehao

    2015-01-01

    High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers. PMID:25610449

  14. Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata)

    PubMed Central

    2012-01-01

    Background Brassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing technology. None of the available maps were detailed enough to anchor the sequence scaffolds for the Genome Sequencing Project. This report describes the development of a large number of SSR and SNP markers from the whole genome shotgun sequence data of B. oleracea, and the construction of a high-density genetic linkage map using a double haploid mapping population. Results The B. oleracea high-density genetic linkage map that was constructed includes 1,227 markers in nine linkage groups spanning a total of 1197.9 cM with an average of 0.98 cM between adjacent loci. There were 602 SSR markers and 625 SNP markers on the map. The chromosome with the highest number of markers (186) was C03, and the chromosome with smallest number of markers (99) was C09. Conclusions This first high-density map allowed the assembled scaffolds to be anchored to pseudochromosomes. The map also provides useful information for positional cloning, molecular breeding, and integration of information of genes and traits in B. oleracea. All the markers on the map will be transferable and could be used for the construction of other genetic maps. PMID:23033896

  15. Transport of phase space densities through tetrahedral meshes using discrete flow mapping

    NASA Astrophysics Data System (ADS)

    Bajars, Janis; Chappell, David J.; Søndergaard, Niels; Tanner, Gregor

    2017-01-01

    Discrete flow mapping was recently introduced as an efficient ray based method determining wave energy distributions in complex built up structures. Wave energy densities are transported along ray trajectories through polygonal mesh elements using a finite dimensional approximation of a ray transfer operator. In this way the method can be viewed as a smoothed ray tracing method defined over meshed surfaces. Many applications require the resolution of wave energy distributions in three-dimensional domains, such as in room acoustics, underwater acoustics and for electromagnetic cavity problems. In this work we extend discrete flow mapping to three-dimensional domains by propagating wave energy densities through tetrahedral meshes. The geometric simplicity of the tetrahedral mesh elements is utilised to efficiently compute the ray transfer operator using a mixture of analytic and spectrally accurate numerical integration. The important issue of how to choose a suitable basis approximation in phase space whilst maintaining a reasonable computational cost is addressed via low order local approximations on tetrahedral faces in the position coordinate and high order orthogonal polynomial expansions in momentum space.

  16. Modeling shape and topology of low-resolution density maps of biological macromolecules.

    PubMed Central

    De-Alarcón, Pedro A; Pascual-Montano, Alberto; Gupta, Amarnath; Carazo, Jose M

    2002-01-01

    In the present work we develop an efficient way of representing the geometry and topology of volumetric datasets of biological structures from medium to low resolution, aiming at storing and querying them in a database framework. We make use of a new vector quantization algorithm to select the points within the macromolecule that best approximate the probability density function of the original volume data. Connectivity among points is obtained with the use of the alpha shapes theory. This novel data representation has a number of interesting characteristics, such as 1) it allows us to automatically segment and quantify a number of important structural features from low-resolution maps, such as cavities and channels, opening the possibility of querying large collections of maps on the basis of these quantitative structural features; 2) it provides a compact representation in terms of size; 3) it contains a subset of three-dimensional points that optimally quantify the densities of medium resolution data; and 4) a general model of the geometry and topology of the macromolecule (as opposite to a spatially unrelated bunch of voxels) is easily obtained by the use of the alpha shapes theory. PMID:12124252

  17. Modeling photo-bleaching kinetics to map local variations in rod rhodopsin density

    NASA Astrophysics Data System (ADS)

    Ehler, M.; Dobrosotskaya, J.; King, E. J.; Czaja, W.; Bonner, R. F.

    2011-03-01

    Localized rod photoreceptor and rhodopsin losses have been observed in post mortem histology both in normal aging and in age-related maculopathy. We propose to noninvasively map local rod rhodopsin density through analysis of the brightening of the underlying lipofuscin autofluorescence (LAF) in confocal scanning laser ophthalmoscopy (cSLO) imaging sequences starting in the dark adapted eye. The detected LAF increases as rhodopsin is bleached (time constant ~ 25sec) by the average retinal irradiance of the cSLO 488nm laser beam. We fit parameters of analytical expressions for the kinetics of rhodopsin bleaching that Lamb validated using electroretinogram recordings in human. By performing localized (~ 100μm) kinetic analysis, we create high resolution maps of the rhodopsin density. This new noninvasive imaging and analysis approach appears well-suited for measuring localized changes in the rod photoreceptors and correlating them at high spatial resolution with localized pathological changes of the retinal pigment epithelium (RPE) seen in steady-state LAF images.

  18. Quantitative Autofluorescence and Cell Density Maps of the Human Retinal Pigment Epithelium

    PubMed Central

    Ach, Thomas; Huisingh, Carrie; McGwin, Gerald; Messinger, Jeffrey D.; Zhang, Tianjiao; Bentley, Mark J.; Gutierrez, Danielle B.; Ablonczy, Zsolt; Smith, R. Theodore; Sloan, Kenneth R.; Curcio, Christine A.

    2014-01-01

    Purpose. Lipofuscin (LF) accumulation within RPE cells is considered pathogenic in AMD. To test whether LF contributes to RPE cell loss in aging and to provide a cellular basis for fundus autofluorescence (AF) we created maps of human RPE cell number and histologic AF. Methods. Retinal pigment epithelium–Bruch's membrane flat mounts were prepared from 20 donor eyes (10 ≤ 51 and 10 > 80 years; postmortem: ≤4.2 hours; no retinal pathologies), preserving foveal position. Phalloidin-binding RPE cytoskeleton and LF-AF (488-nm excitation) were imaged at up to 90 predefined positions. Maps were assembled from 83,330 cells in 1470 locations. From Voronoi regions representing each cell, the number of neighbors, cell area, and total AF intensity normalized to an AF standard was determined. Results. Highly variable between individuals, RPE-AF increases significantly with age. A perifoveal ring of high AF mirrors rod photoreceptor topography and fundus-AF. Retinal pigment epithelium cell density peaks at the fovea, independent of age, yet no net RPE cell loss is detectable. The RPE monolayer undergoes considerable lifelong re-modeling. The relationship of cell size and AF, a surrogate for LF concentration, is orderly and linear in both groups. Autofluorescence topography differs distinctly from the topography of age-related rod loss. Conclusions. Digital maps of quantitative AF, cell density, and packing geometry provide metrics for cellular-resolution clinical imaging and model systems. The uncoupling of RPE LF content, cell number, and photoreceptor topography in aging challenges LF's role in AMD. PMID:25034602

  19. A variable-density absorption event in NGC 3227 mapped with Suzaku and Swift

    NASA Astrophysics Data System (ADS)

    Beuchert, T.; Markowitz, A. G.; Krauß, F.; Miniutti, G.; Longinotti, A. L.; Guainazzi, M.; de La Calle Pérez, I.; Malkan, M.; Elvis, M.; Miyaji, T.; Hiriart, D.; López, J. M.; Agudo, I.; Dauser, T.; Garcia, J.; Kreikenbohm, A.; Kadler, M.; Wilms, J.

    2015-12-01

    Context. The morphology of the circumnuclear gas accreting onto supermassive black holes in Seyfert galaxies remains a topic of much debate. As the innermost regions of active galactic nuclei (AGN) are spatially unresolved, X-ray spectroscopy, and in particular line-of-sight absorption variability, is a key diagnostic to map out the distribution of gas. Aims: Observations of variable X-ray absorption in multiple Seyferts and over a wide range of timescales indicate the presence of clumps/clouds of gas within the circumnuclear material. Eclipse events by clumps transiting the line of sight allow us to explore the properties of the clumps over a wide range of radial distances from the optical/UV broad line region (BLR) to beyond the dust sublimation radius. Time-resolved absorption events have been extremely rare so far, but suggest a range of density profiles across Seyferts. We resolve a weeks-long absorption event in the Seyfert NGC 3227. Methods: We examine six Suzaku and 12 Swift observations from a 2008 campaign spanning five weeks. We use a model accounting for the complex spectral interplay of three absorbers with different levels of ionization. We perform time-resolved spectroscopy to discern the absorption variability behavior. We also examine the IR to X-ray spectral energy distribution (SED) to test for reddening by dust. Results: The 2008 absorption event is due to moderately-ionized (log ξ ~ 1.2-1.4) gas covering 90% of the line of sight. We resolve the density profile to be highly irregular, in contrast to a previous symmetric and centrally-peaked event mapped with RXTE in the same object. The UV data do not show significant reddening, suggesting that the cloud is dust-free. Conclusions: The 2008 campaign has revealed a transit by a filamentary, moderately-ionized cloud of variable density that is likely located in the BLR, and possibly part of a disk wind.

  20. Terrestrial gamma radiation baseline mapping using ultra low density sampling methods.

    PubMed

    Kleinschmidt, R; Watson, D

    2016-01-01

    Baseline terrestrial gamma radiation maps are indispensable for providing basic reference information that may be used in assessing the impact of a radiation related incident, performing epidemiological studies, remediating land contaminated with radioactive materials, assessment of land use applications and resource prospectivity. For a large land mass, such as Queensland, Australia (over 1.7 million km(2)), it is prohibitively expensive and practically difficult to undertake detailed in-situ radiometric surveys of this scale. It is proposed that an existing, ultra-low density sampling program already undertaken for the purpose of a nationwide soil survey project be utilised to develop a baseline terrestrial gamma radiation map. Geoelement data derived from the National Geochemistry Survey of Australia (NGSA) was used to construct a baseline terrestrial gamma air kerma rate map, delineated by major drainage catchments, for Queensland. Three drainage catchments (sampled at the catchment outlet) spanning low, medium and high radioelement concentrations were selected for validation of the methodology using radiometric techniques including in-situ measurements and soil sampling for high resolution gamma spectrometry, and comparative non-radiometric analysis. A Queensland mean terrestrial air kerma rate, as calculated from the NGSA outlet sediment uranium, thorium and potassium concentrations, of 49 ± 69 nGy h(-1) (n = 311, 3σ 99% confidence level) is proposed as being suitable for use as a generic terrestrial air kerma rate background range. Validation results indicate that catchment outlet measurements are representative of the range of results obtained across the catchment and that the NGSA geoelement data is suitable for calculation and mapping of terrestrial air kerma rate.

  1. Principal component analysis of the CT density histogram to generate parametric response maps of COPD

    NASA Astrophysics Data System (ADS)

    Zha, N.; Capaldi, D. P. I.; Pike, D.; McCormack, D. G.; Cunningham, I. A.; Parraga, G.

    2015-03-01

    Pulmonary x-ray computed tomography (CT) may be used to characterize emphysema and airways disease in patients with chronic obstructive pulmonary disease (COPD). One analysis approach - parametric response mapping (PMR) utilizes registered inspiratory and expiratory CT image volumes and CT-density-histogram thresholds, but there is no consensus regarding the threshold values used, or their clinical meaning. Principal-component-analysis (PCA) of the CT density histogram can be exploited to quantify emphysema using data-driven CT-density-histogram thresholds. Thus, the objective of this proof-of-concept demonstration was to develop a PRM approach using PCA-derived thresholds in COPD patients and ex-smokers without airflow limitation. Methods: Fifteen COPD ex-smokers and 5 normal ex-smokers were evaluated. Thoracic CT images were also acquired at full inspiration and full expiration and these images were non-rigidly co-registered. PCA was performed for the CT density histograms, from which the components with the highest eigenvalues greater than one were summed. Since the values of the principal component curve correlate directly with the variability in the sample, the maximum and minimum points on the curve were used as threshold values for the PCA-adjusted PRM technique. Results: A significant correlation was determined between conventional and PCA-adjusted PRM with 3He MRI apparent diffusion coefficient (p<0.001), with CT RA950 (p<0.0001), as well as with 3He MRI ventilation defect percent, a measurement of both small airways disease (p=0.049 and p=0.06, respectively) and emphysema (p=0.02). Conclusions: PRM generated using PCA thresholds of the CT density histogram showed significant correlations with CT and 3He MRI measurements of emphysema, but not airways disease.

  2. Visualization of cardiac dipole using a current density map: detection of cardiac current undetectable by electrocardiography using magnetocardiography.

    PubMed

    Ikefuji, Hiroyuki; Nomura, Masahiro; Nakaya, Yutaka; Mori, Toshifumi; Kondo, Noriyasu; Ieishi, Kiyoshi; Fujimoto, Sayuri; Ito, Susumu

    2007-02-01

    A close relationship exists between electric current and the magnetic field. However, electricity and magnetism have different physical characteristics, and magnetocardiography (MCG) may provide information on cardiac current that is difficult to obtain by electrocardiography (ECG). In the present study, we investigated the issue of whether the current density map method, in which cardiac current is estimated from the magnetic gradient, facilitates the visualization of cardiac current undetectable by ECG. The subjects were 50 healthy adults (N group), 40 patients with left ventricular overloading (LVO group), 15 patients with right ventricular overloading (RVO group), 10 patients with an old inferior myocardial infarction (OMI group), and 30 patients with diabetes mellitus (DM group). MCGs were recorded with a second derivative superconducting quantum interference device (SQUID) gradiometer using liquid helium. Isopotential maps and current density maps from unipolar precordial ECG leads and MCGs, respectively, were prepared, and the cardiac electric current was examined. The current density map at the ventricular depolarization phase showed one peak of current density in the N group. However, in the OMI group, the current density map showed multiple peaks of current density areas. In the RVO group, two peaks of current densities were detected at the right superior region and left thoracic region and these two diploles appeared to be from the right and left ventricular derived cardiac currents, respectively. Moreover, there was a significant correlation between the magnitude of the current density from the right ventricle and the systolic pulmonary arterial pressure. The current density map at the ventricular repolarization phase in the N group showed only a single current source. However, abnormal current sources in the current density maps were frequently detected even in patients showing no abnormalities on isopotential maps in the LVO, DM, and OMI groups. The

  3. Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm

    PubMed Central

    Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

    2016-01-01

    In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis. PMID:27959895

  4. Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm.

    PubMed

    Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

    2016-01-01

    In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.

  5. DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.

    PubMed

    Wang, Feng; Gong, Huichao; Liu, Gaochao; Li, Meijing; Yan, Chuangye; Xia, Tian; Li, Xueming; Zeng, Jianyang

    2016-09-01

    Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python.

  6. R-Z Density Mapping and CFD Simulation of Gas Puff Nozzle Flow

    NASA Astrophysics Data System (ADS)

    McKee, Erik; Valenzuela, Julio; Krasheninnikov, Igor; Frazier, Alister; Covington, Aaron; Beg, Farhat; Darling, Tim; Nevada Terawatt Facility Team; University of San Diego Team

    2015-11-01

    Laser induced fluorescence (LIF) is a technique in which a tracer is added to the gas flow for measurement of its spatial and temporal density profile. The Nd:YAG EKSPLA laser 20mJ/150ps at the fourth harmonic 266nm wavelength is focused down to a <1mm pencil beam to excite the acetone tracer. The use of anr ICCD gating camera is necessary because the 4ns short-lived fluorescence state is an order-of-magnitude dimmer than the 200us long-lived phosphorescence state. Mapping the density profile in time and space requires multiple shots. Once the temporal and spatial density profile is obtained, it can be used and benchmarked for two independent CFD software programs using transient solvers: OpenFOAM and FLUENT. The measurements and simulations serve as the initial conditions for (i) Gas Puff experiments that utilize special nozzle contours to inject the gas load between the electrode gap on pulsed-power machines and (ii) use with future MHD modeling efforts. Support for this work is provided by DOE/NNSA grant DE-NA0002075 and funded by the US Department of Energy, ARPA-E, Control Number 1184-1527.

  7. Initial bridges between two ribosomal subunits are formed within 9.4 milliseconds, as studied by time-resolved cryo-EM.

    PubMed

    Shaikh, Tanvir R; Yassin, Aymen S; Lu, Zonghuan; Barnard, David; Meng, Xing; Lu, Toh-Ming; Wagenknecht, Terence; Agrawal, Rajendra K

    2014-07-08

    Association of the two ribosomal subunits during the process of translation initiation is a crucial step of protein synthesis. The two subunits (30S and 50S) of the bacterial 70S ribosome are held together by 12 dynamic bridges involving RNA-RNA, RNA-protein, and protein-protein interactions. The process of bridge formation, such as whether all these bridges are formed simultaneously or in a sequential order, is poorly understood. To understand such processes, we have developed and implemented a class of microfluidic devices that mix two components to completion within 0.4 ms and spray the mixture in the form of microdroplets onto an electron microscopy grid, yielding a minimum reaction time of 9.4 ms before cryofixation. Using these devices, we have obtained cryo-EM data corresponding to reaction times of 9.4 and 43 ms and have determined 3D structures of ribosomal subunit association intermediates. Molecular analyses of the cryo-EM maps reveal that eight intersubunit bridges (bridges B1a, B1b, B2a, B2b, B3, B7a, B7b, and B8) form within 9.4 ms, whereas the remaining four bridges (bridges B2c, B4, B5, and B6) take longer than 43 ms to form, suggesting that bridges are formed in a stepwise fashion. Our approach can be used to characterize sequences of various dynamic functional events on complex macromolecular assemblies such as ribosomes.

  8. Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench).

    PubMed

    Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

    2014-12-01

    For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information.

  9. High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx.

    PubMed

    Ding, Zhanyu; Fu, Zhenglin; Xu, Cong; Wang, Yifan; Wang, Yanxing; Li, Junrui; Kong, Liangliang; Chen, Jinhuan; Li, Na; Zhang, Rongguang; Cong, Yao

    2017-03-01

    The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide. The remaining two subunits, Rpt2 and Rpt6, with empty or only partially occupied nucleotide pocket exhibit pronounced conformational changes in the AAA-ATPase ring, which may represent a collective result of allosteric cooperativity of all the AAA-ATPase subunits responding to ATP hydrolysis. This collective motion of Rpt2 and Rpt6 results in an elevation of their pore loops, which could play an important role in substrate processing of proteasome. Our data also imply that the nucleotide occupancy pattern could be related to the activation status of the complex. Moreover, the HbYX tail insertion may not be sufficient to maintain the gate opening of 20S core particle. Our results provide new insights into the mechanisms of nucleotide-driven allosteric cooperativity of the complex and of the substrate processing by the proteasome.

  10. A High-Density Map for Navigating the Human Polycomb Complexome.

    PubMed

    Hauri, Simon; Comoglio, Federico; Seimiya, Makiko; Gerstung, Moritz; Glatter, Timo; Hansen, Klaus; Aebersold, Ruedi; Paro, Renato; Gstaiger, Matthias; Beisel, Christian

    2016-10-04

    Polycomb group (PcG) proteins are major determinants of gene silencing and epigenetic memory in higher eukaryotes. Here, we systematically mapped the human PcG complexome using a robust affinity purification mass spectrometry approach. Our high-density protein interaction network uncovered a diverse range of PcG complexes. Moreover, our analysis identified PcG interactors linking them to the PcG system, thus providing insight into the molecular function of PcG complexes and mechanisms of recruitment to target genes. We identified two human PRC2 complexes and two PR-DUB deubiquitination complexes, which contain the O-linked N-acetylglucosamine transferase OGT1 and several transcription factors. Finally, genome-wide profiling of PR-DUB components indicated that the human PR-DUB and PRC1 complexes bind distinct sets of target genes, suggesting differential impact on cellular processes in mammals.

  11. [Density equalizing mapping of obesity: analysis of a global epidemic].

    PubMed

    Groneberg, D A; Franke, K; Klingelhöfer, D; Schwarzer, M; Ohlendorf, D

    2015-06-01

    Obesity is a chronic disease whose origin is determined by genetic factors as well as environmental influences. The prevalence has rapidly increased worldwide in the recent decades. This paper evaluated the research on obesity in the period of 1900 - 2009 in the ISI "Web of Science" by Thomson Reuters. For this purpose scientometric methods were used and the results were graphically illustrated by "Density Equalizing Map Projections". From 1900 till 2009 94.987 published items are the basis for the present qualitative and quantitative data analysis. The publication rates show an exponential growth indicating a pronounced research activity. Concerning the country comparison the United States has the highest number of publications and citations, the highest modified h-index and most academic institutions. This manuscript shows the first comprehensive scientometric data on obesity. In this research area, the United States is a leader and is located at the center of global collaborations.

  12. Type 2 Diabetes Research Yield, 1951-2012: Bibliometrics Analysis and Density-Equalizing Mapping.

    PubMed

    Geaney, Fiona; Scutaru, Cristian; Kelly, Clare; Glynn, Ronan W; Perry, Ivan J

    2015-01-01

    The objective of this paper is to provide a detailed evaluation of type 2 diabetes mellitus research output from 1951-2012, using large-scale data analysis, bibliometric indicators and density-equalizing mapping. Data were retrieved from the Science Citation Index Expanded database, one of the seven curated databases within Web of Science. Using Boolean operators "OR", "AND" and "NOT", a search strategy was developed to estimate the total number of published items. Only studies with an English abstract were eligible. Type 1 diabetes and gestational diabetes items were excluded. Specific software developed for the database analysed the data. Information including titles, authors' affiliations and publication years were extracted from all files and exported to excel. Density-equalizing mapping was conducted as described by Groenberg-Kloft et al, 2008. A total of 24,783 items were published and cited 476,002 times. The greatest number of outputs were published in 2010 (n=2,139). The United States contributed 28.8% to the overall output, followed by the United Kingdom (8.2%) and Japan (7.7%). Bilateral cooperation was most common between the United States and United Kingdom (n=237). Harvard University produced 2% of all publications, followed by the University of California (1.1%). The leading journals were Diabetes, Diabetologia and Diabetes Care and they contributed 9.3%, 7.3% and 4.0% of the research yield, respectively. In conclusion, the volume of research is rising in parallel with the increasing global burden of disease due to type 2 diabetes mellitus. Bibliometrics analysis provides useful information to scientists and funding agencies involved in the development and implementation of research strategies to address global health issues.

  13. Type 2 Diabetes Research Yield, 1951-2012: Bibliometrics Analysis and Density-Equalizing Mapping

    PubMed Central

    Geaney, Fiona; Scutaru, Cristian; Kelly, Clare; Glynn, Ronan W.; Perry, Ivan J.

    2015-01-01

    The objective of this paper is to provide a detailed evaluation of type 2 diabetes mellitus research output from 1951-2012, using large-scale data analysis, bibliometric indicators and density-equalizing mapping. Data were retrieved from the Science Citation Index Expanded database, one of the seven curated databases within Web of Science. Using Boolean operators "OR", "AND" and "NOT", a search strategy was developed to estimate the total number of published items. Only studies with an English abstract were eligible. Type 1 diabetes and gestational diabetes items were excluded. Specific software developed for the database analysed the data. Information including titles, authors’ affiliations and publication years were extracted from all files and exported to excel. Density-equalizing mapping was conducted as described by Groenberg-Kloft et al, 2008. A total of 24,783 items were published and cited 476,002 times. The greatest number of outputs were published in 2010 (n=2,139). The United States contributed 28.8% to the overall output, followed by the United Kingdom (8.2%) and Japan (7.7%). Bilateral cooperation was most common between the United States and United Kingdom (n=237). Harvard University produced 2% of all publications, followed by the University of California (1.1%). The leading journals were Diabetes, Diabetologia and Diabetes Care and they contributed 9.3%, 7.3% and 4.0% of the research yield, respectively. In conclusion, the volume of research is rising in parallel with the increasing global burden of disease due to type 2 diabetes mellitus. Bibliometrics analysis provides useful information to scientists and funding agencies involved in the development and implementation of research strategies to address global health issues. PMID:26208117

  14. Development of a high-density genetic linkage map and identification of flowering time QTLs in adzuki bean (Vigna angularis)

    PubMed Central

    Liu, Changyou; Fan, Baojie; Cao, Zhimin; Su, Qiuzhu; Wang, Yan; Zhang, Zhixiao; Tian, Jing

    2016-01-01

    A high-density linkage map is crucial for the identification of quantitative trait loci (QTLs), positional cloning, and physical map assembly. Here, we report the development of a high-density linkage map based on specific length amplified fragment sequencing (SLAF-seq) for adzuki bean and the identification of flowering time-related QTLs. Through SLAF library construction and Illumina sequencing of a recombinant inbred line (RIL) population, a total of 4425 SLAF markers were developed and assigned to 11 linkage groups (LGs). After binning the SLAF markers that represented the same genotype, the final linkage map of 1628.15 cM contained 2032 markers, with an average marker density of 0.80 cM. Comparative analysis showed high collinearity with two adzuki bean physical maps and a high degree of synteny with the reference genome of common bean (Phaseolus vulgaris). Using this map, one major QTL on LG03 and two minor QTLs on LG05 associated with first flowering time (FLD) were consistently identified in tests over a two-year period. These results provide a foundation that will be useful for future genomic research, such as identifying QTLs for other important traits, positional cloning, and comparative mapping in legumes. PMID:28008173

  15. Digital mine claim density map for Federal lands in Montana, 1996

    USGS Publications Warehouse

    Campbell, Harry W.; Hyndman, Paul C.

    1998-01-01

    This report describes a digital map and data files generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim information for Federal lands in Montana as of March, 1997. Statewide, 159,704 claims had been recorded with the Bureau of Land Management since 1975. Of those claims, 21,055 (13%) are still actively held while 138,649 (87%) are closed and are no longer held. Montana contains 147,704 sections (usually 1 section equals 1 square mile) in the Public Land Survey System, with 8,569 sections (6%) containing claim data. Of the sections with claim data, 2,192 (26%) contain actively held claims. Only 1.5% of Montana’s sections contains actively held mining claims. The four types of mining claim are lode, placer, mill, and tunnel. A mill claim may be as much as 5 acres or 1/128th (0.78125%) of a square mile. A lode claim, about 20 acres, would cover 1/32nd (3.125%) of a square mile. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. The digital map and data files that are available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller. Campbell (1996) summarized the methodology and GIS techniques that were used to produce the mining claim density map of the Pacific Northwest. Campbell and Hyndman (1997) displayed mining claim information for the Pacific Northwest that used data acquired in 1994. Appendix A of this report lists the attribute data for the digital data files. Appendix B contains the GIS metadata.

  16. Polycystic ovary syndrome: analysis of the global research architecture using density equalizing mapping.

    PubMed

    Brüggmann, Dörthe; Berges, Lea; Klingelhöfer, Doris; Bauer, Jan; Bendels, Michael; Louwen, Frank; Jaque, Jenny; Groneberg, David A

    2017-03-21

    Polycystic ovary syndrome (PCOS) is the most common cause of female infertility worldwide. Although the related research output is constantly growing, no detailed global map of the scientific architecture has so far been created encompassing quantitative, qualitative, socioeconomic and gender aspects. We used the NewQIS platform to assess all PCOS-related publications indexed between 1900 and 2014 in the Web of Science, and applied density equalizing mapping projections, scientometric techniques and economic benchmarking procedures. A total of 6261 PCOS-specific publications and 703 international research collaborations were found. The USA was identified as the most active country in total and collaborative research activity. In the socioeconomic analysis, the USA was also ranked first (25.49 PCOS-related publications per gross domestic product [GDP]/capita), followed by the UK, Italy and Greece. When research activity was related to population size, Scandinavian countries and Greece were leading the field. For many highly productive countries, gender analysis revealed a high ratio of female scientists working on PCOS with the exception of Japan. In this study, we have created the first picture of global PCOS research, which largely differs from other gynaecologic conditions and indicates that most related research and collaborations originate from high-income countries.

  17. Calibrated and completeness-corrected optical stellar density maps of the northern Galactic plane

    NASA Astrophysics Data System (ADS)

    Farnhill, H. J.; Drew, J. E.; Barentsen, G.; González-Solares, E. A.

    2016-03-01

    Following on from the second release of calibrated photometry from IPHAS, the INT/WFC Photometric Hα Survey of the Northern Galactic Plane, we present incompleteness-corrected stellar density maps in the r and i photometric bands. These have been computed to a range of limiting magnitudes reaching to 20th magnitude in r and 19th in i (Vega system), and with different angular resolutions - the highest resolution available being 1 arcmin2. The maps obtained cover 94 per cent of the 1800 square degree IPHAS footprint, spanning the Galactic latitude range, -5° < b < +5°, north of the celestial equator. The corrections for incompleteness, due to confusion and sensitivity loss at the faint limit, have been deduced by the method of artificial source injection. The presentation of this method is preceded by a discussion of other more approximate methods of determining completeness. Our method takes full account of position-dependent seeing and source ellipticity in the survey data base. The application of the star counts to testing reddened Galactic disc models is previewed by a comparison with predicted counts along three constant-longitude cuts at ℓ ≃ 30°, 90° and 175°: some overprediction of the most heavily reddened ℓ ≃ 30° counts is found, alongside good agreement at ℓ ≃ 90° and 175°.

  18. Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".

    PubMed

    Belnap, D M; Kumar, A; Folk, J T; Smith, T J; Baker, T S

    1999-01-01

    Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15-40 A), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.

  19. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea.

    PubMed

    Khajuria, Yash Paul; Saxena, Maneesha S; Gaur, Rashmi; Chattopadhyay, Debasis; Jain, Mukesh; Parida, Swarup K; Bhatia, Sabhyata

    2015-01-01

    The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM) longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped highest

  20. High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing.

    PubMed

    Zhou, Zunchun; Liu, Shikai; Dong, Ying; Gao, Shan; Chen, Zhong; Jiang, Jingwei; Yang, Aifu; Sun, Hongjuan; Guan, Xiaoyan; Jiang, Bei; Wang, Bai

    2015-01-01

    Sea urchins have long been used as research model organisms for developmental biology and evolutionary studies. Some of them are also important aquaculture species in East Asia. In this work, we report the construction of RAD-tag based high-density genetic maps by genotyping F1 interspecific hybrids derived from a crossing between a female sea urchin Strongylocentrotus nudus and a male Strongylocentrotus intermedius. With polymorphisms present in these two wild individuals, we constructed a female meiotic map containing 3,080 markers for S. nudus, and a male meiotic map for S. intermedius which contains 1,577 markers. Using the linkage maps, we were able to anchor a total of 1,591 scaffolds (495.9 Mb) accounting for 60.8% of the genome assembly of Strongylocentrotus purpuratus. A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM. This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information. The genetic maps are essential for QTL mapping and are useful as framework to order and orientate contiguous scaffolds from sea urchin genome assembly. The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies.

  1. High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing

    PubMed Central

    Dong, Ying; Gao, Shan; Chen, Zhong; Jiang, Jingwei; Yang, Aifu; Sun, Hongjuan; Guan, Xiaoyan; Jiang, Bei; Wang, Bai

    2015-01-01

    Sea urchins have long been used as research model organisms for developmental biology and evolutionary studies. Some of them are also important aquaculture species in East Asia. In this work, we report the construction of RAD-tag based high-density genetic maps by genotyping F1 interspecific hybrids derived from a crossing between a female sea urchin Strongylocentrotus nudus and a male Strongylocentrotus intermedius. With polymorphisms present in these two wild individuals, we constructed a female meiotic map containing 3,080 markers for S. nudus, and a male meiotic map for S. intermedius which contains 1,577 markers. Using the linkage maps, we were able to anchor a total of 1,591 scaffolds (495.9 Mb) accounting for 60.8% of the genome assembly of Strongylocentrotus purpuratus. A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM. This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information. The genetic maps are essential for QTL mapping and are useful as framework to order and orientate contiguous scaffolds from sea urchin genome assembly. The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies. PMID:26398139

  2. Scientometric Analysis and Combined Density-Equalizing Mapping of Environmental Tobacco Smoke (ETS) Research

    PubMed Central

    Vitzthum, Karin; Scutaru, Cristian; Musial-Bright, Lindy; Quarcoo, David; Welte, Tobias; Spallek, Michael; Groneberg-Kloft, Beatrix

    2010-01-01

    Background Passive exposure to environmental tobacco smoke (ETS) is estimated to exert a major burden of disease. Currently, numerous countries have taken legal actions to protect the population against ETS. Numerous studies have been conducted in this field. Therefore, scientometric methods should be used to analyze the accumulated data since there is no such approach available so far. Methods and Results A combination of scientometric methods and novel visualizing procedures were used, including density-equalizing mapping and radar charting techniques. 6,580 ETS-related studies published between 1900 and 2008 were identified in the ISI database. Using different scientometric approaches, a continuous increase of both quantitative and qualitative parameters was found. The combination with density-equalizing calculations demonstrated a leading position of the United States (2,959 items published) in terms of quantitative research activities. Charting techniques demonstrated that there are numerous bi- and multilateral networks between different countries and institutions in this field. Again, a leading position of American institutions was found. Conclusions This is the first comprehensive scientometric analysis of data on global scientific activities in the field of environmental tobacco smoke research. The present findings can be used as a benchmark for funding allocation processes. PMID:20582305

  3. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

    PubMed

    Lindert, Steffen; Alexander, Nathan; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L; Meiler, Jens

    2012-03-07

    Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy or X-ray crystallography. In these density maps, the general arrangement of secondary structure elements (SSEs) is revealed, whereas their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å.

  4. Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain

    PubMed Central

    2011-01-01

    Background Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Methods Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. Results The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. Conclusions In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This

  5. SU-E-J-233: Effect of Brachytherapy Seed Artifacts in T2 and Proton Density Maps in MR Images

    SciTech Connect

    Mashouf, S; Fatemi-Ardekani, A; Song, W

    2015-06-15

    Purpose: This study aims at investigating the influence of brachytherapy seeds on T2 and proton density (PD) maps generated from MR images. Proton density maps can be used to extract water content. Since dose absorbed in tissue surrounding low energy brachytherapy seeds are highly influenced by tissue composition, knowing the water content is a first step towards implementing a heterogeneity correction algorithm using MR images. Methods: An LDR brachytherapy (IsoAid Advantage Pd-103) seed was placed in the middle of an agar-based gel phantom and imaged using a 3T Philips MR scanner with a 168-channel head coil. A multiple echo sequence with TE=20, 40, 60, 80, 100 (ms) with large repetition time (TR=6259ms) was used to extract T2 and PD maps. Results: Seed artifacts were considerably reduced on T2 maps compared to PD maps. The variation of PD around the mean was obtained as −97% to 125% (±1%) while for T2 it was recorded as −71% to 24% (±1%). Conclusion: PD maps which are required for heterogeneity corrections are susceptible to artifacts from seeds. Seed artifacts on T2 maps, however, are significantly reduced due to not being sensitive to B0 field variation.

  6. Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control

    PubMed Central

    2016-01-01

    Three-dimensional Gaussian functions have been shown useful in representing electron microscopy (EM) density maps for studying macromolecular structure and dynamics. Methods that require setting a desired number of Gaussian functions or a maximum number of iterations may result in suboptimal representations of the structure. An alternative is to set a desired error of approximation of the given EM map and then optimize the number of Gaussian functions to achieve this approximation error. In this article, we review different applications of such an approach that uses spherical Gaussian functions of fixed standard deviation, referred to as pseudoatoms. Some of these applications use EM-map normal mode analysis (NMA) with elastic network model (ENM) (applications such as predicting conformational changes of macromolecular complexes or exploring actual conformational changes by normal-mode-based analysis of experimental data) while some other do not use NMA (denoising of EM density maps). In applications based on NMA and ENM, the advantage of using pseudoatoms in EM-map coarse-grain models is that the ENM springs are easily assigned among neighboring grains thanks to their spherical shape and uniformed size. EM-map denoising based on the map coarse-graining was so far only shown using pseudoatoms as grains. PMID:28097146

  7. A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

    PubMed Central

    Di Pierro, Erica A; Gianfranceschi, Luca; Di Guardo, Mario; Koehorst-van Putten, Herma JJ; Kruisselbrink, Johannes W; Longhi, Sara; Troggio, Michela; Bianco, Luca; Muranty, Hélène; Pagliarani, Giulia; Tartarini, Stefano; Letschka, Thomas; Lozano Luis, Lidia; Garkava-Gustavsson, Larisa; Micheletti, Diego; Bink, Marco CAM; Voorrips, Roeland E; Aziz, Ebrahimi; Velasco, Riccardo; Laurens, François; van de Weg, W Eric

    2016-01-01

    Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species. PMID:27917289

  8. Mapping cortical responses to speech using high-density diffuse optical tomography

    PubMed Central

    Hassanpour, Mahlega S.; Eggebrecht, Adam T.; Culver, Joseph P.; Peelle, Jonathan E.

    2015-01-01

    The functional neuroanatomy of speech processing has been investigated using positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) for more than 20 years. However, these approaches have relatively poor temporal resolution and/or challenges of acoustic contamination due to the constraints of echoplanar fMRI. Furthermore, these methods are contraindicated because of safety concerns in longitudinal studies and research with children (PET) or in studies of patients with metal implants (fMRI). High-density diffuse optical tomography (HD-DOT) permits presenting speech in a quiet acoustic environment, has excellent temporal resolution relative to the hemodynamic response, and provides noninvasive and metal-compatible imaging. However, the performance of HD-DOT in imaging the brain regions involved in speech processing is not fully established. In the current study, we use an auditory sentence comprehension task to evaluate the ability of HD-DOT to map the cortical networks supporting speech processes. Using sentences with two levels of linguistic complexity, along with a control condition consisting of unintelligible noise-vocoded speech, we recovered a hierarchical organization of the speech network that matches the results of previous fMRI studies. Specifically, hearing intelligible speech resulted in increased activity in bilateral temporal cortex and left frontal cortex, with syntactically complex speech leading to additional activity in left posterior temporal cortex and left inferior frontal gyrus. These results demonstrate the feasibility of using HD-DOT to map spatially distributed brain networks supporting higher-order cognitive faculties such as spoken language. PMID:26026816

  9. Hot deformation characterization of duplex low-density steel through 3D processing map development

    SciTech Connect

    Mohamadizadeh, A.; Zarei-Hanzaki, A.; Abedi, H.R.; Mehtonen, S.; Porter, D.

    2015-09-15

    The high temperature deformation behavior of duplex low-density Fe–18Mn–8Al–0.8C steel was investigated at temperatures in the range of 600–1000 °C. The primary constitutive analysis indicated that the Zener–Hollomon parameter, which represents the coupled effects of temperature and strain rate, significantly varies with the amount of deformation. Accordingly, the 3D processing maps were developed considering the effect of strain and were used to determine the safe and unsafe deformation conditions in association with the microstructural evolution. The deformation at efficiency domain I (900–1100 °C\\10{sup −} {sup 2}–10{sup −} {sup 3} s{sup −} {sup 1}) was found to be safe at different strains due to the occurrence of dynamic recrystallization in austenite. The safe efficiency domain II (700–900 °C\\1–10{sup −} {sup 1} s{sup −} {sup 1}), which appeared at logarithmic strain of 0.4, was characterized by deformation induced ferrite formation. Scanning electron microscopy revealed that the microband formation and crack initiation at ferrite\\austenite interphases were the main causes of deformation instability at 600–800 °C\\10{sup −} {sup 2}–10{sup −} {sup 3} s{sup −} {sup 1}. The degree of instability was found to decrease by increasing the strain due to the uniformity of microbanded structure obtained at higher strains. The shear band formation at 900–1100 °C\\1–10{sup −} {sup 1} s{sup −} {sup 1} was verified by electron backscattered diffraction. The local dynamic recrystallization of austenite and the deformation induced ferrite formation were observed within shear-banded regions as the results of flow localization. - Graphical abstract: Display Omitted - Highlights: • The 3D processing map is developed for duplex low-density Fe–Mn–Al–C steel. • The efficiency domains shrink, expand or appear with increasing strain. • The occurrence of DRX and DIFF increases the power efficiency. • Crack initiation

  10. Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity

    SciTech Connect

    Long, Feng; Fong, Rachel H.; Austin, Stephen K.; Chen, Zhenguo; Klose, Thomas; Fokine, Andrei; Liu, Yue; Porta, Jason; Sapparapu, Gopal; Akahata, Wataru; Doranz, Benjamin J.; Crowe, James E.; Diamond, Michael S.; Rossmann, Michael G.

    2015-10-26

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. In this paper, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain’s β-ribbon connector of the viral glycoprotein E2. The footprints of these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. Finally, this finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes.

  11. Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity

    DOE PAGES

    Long, Feng; Fong, Rachel H.; Austin, Stephen K.; ...

    2015-10-26

    Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. In this paper, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain’s β-ribbon connector of the viral glycoprotein E2. The footprints ofmore » these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. Finally, this finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes.« less

  12. Focus: The interface between data collection and data processing in cryo-EM.

    PubMed

    Biyani, Nikhil; Righetto, Ricardo D; McLeod, Robert; Caujolle-Bert, Daniel; Castano-Diez, Daniel; Goldie, Kenneth N; Stahlberg, Henning

    2017-03-23

    We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions. The rapid detection of any errors that may occur greatly increases the productivity of recording sessions at the electron microscope.

  13. Denoising and covariance estimation of single particle cryo-EM images.

    PubMed

    Bhamre, Tejal; Zhang, Teng; Singer, Amit

    2016-07-01

    The problem of image restoration in cryo-EM entails correcting for the effects of the Contrast Transfer Function (CTF) and noise. Popular methods for image restoration include 'phase flipping', which corrects only for the Fourier phases but not amplitudes, and Wiener filtering, which requires the spectral signal to noise ratio. We propose a new image restoration method which we call 'Covariance Wiener Filtering' (CWF). In CWF, the covariance matrix of the projection images is used within the classical Wiener filtering framework for solving the image restoration deconvolution problem. Our estimation procedure for the covariance matrix is new and successfully corrects for the CTF. We demonstrate the efficacy of CWF by applying it to restore both simulated and experimental cryo-EM images. Results with experimental datasets demonstrate that CWF provides a good way to evaluate the particle images and to see what the dataset contains even without 2D classification and averaging.

  14. Integration of Self-Organizing Map (SOM) and Kernel Density Estimation (KDE) for network intrusion detection

    NASA Astrophysics Data System (ADS)

    Cao, Yuan; He, Haibo; Man, Hong; Shen, Xiaoping

    2009-09-01

    This paper proposes an approach to integrate the self-organizing map (SOM) and kernel density estimation (KDE) techniques for the anomaly-based network intrusion detection (ABNID) system to monitor the network traffic and capture potential abnormal behaviors. With the continuous development of network technology, information security has become a major concern for the cyber system research. In the modern net-centric and tactical warfare networks, the situation is more critical to provide real-time protection for the availability, confidentiality, and integrity of the networked information. To this end, in this work we propose to explore the learning capabilities of SOM, and integrate it with KDE for the network intrusion detection. KDE is used to estimate the distributions of the observed random variables that describe the network system and determine whether the network traffic is normal or abnormal. Meanwhile, the learning and clustering capabilities of SOM are employed to obtain well-defined data clusters to reduce the computational cost of the KDE. The principle of learning in SOM is to self-organize the network of neurons to seek similar properties for certain input patterns. Therefore, SOM can form an approximation of the distribution of input space in a compact fashion, reduce the number of terms in a kernel density estimator, and thus improve the efficiency for the intrusion detection. We test the proposed algorithm over the real-world data sets obtained from the Integrated Network Based Ohio University's Network Detective Service (INBOUNDS) system to show the effectiveness and efficiency of this method.

  15. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

    PubMed Central

    2012-01-01

    Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

  16. Hirschsprung Disease: Critical Evaluation of the Global Research Architecture Employing Scientometrics and Density-Equalizing Mapping.

    PubMed

    Schöffel, Norman; Gfroerer, Stefan; Rolle, Udo; Bendels, Michael H K; Klingelhöfer, Doris; Groneberg-Kloft, Beatrix

    2016-05-13

    Introduction Hirschsprung disease (HD) is a congenital bowel innervation disorder that involves several clinical specialties. There is an increasing interest on the topic reflected by the number of annually published items. It is therefore difficult for a single scientist to survey all published items and to gauge their scientific importance or value. Thus, tremendous efforts were made to establish sustainable parameters to evaluate scientific work within the past decades. It was the birth of scientometrics. Materials and Methods To quantify the global research activity in this field, a scientometric analysis was conducted. We analyzed the research output of countries, individual institutions, authors, and their collaborative networks by using the Web of Science database. Density-equalizing maps and network diagrams were employed as state of the art visualization techniques. Results The United States is the leading country in terms of published items (n = 685), institutions (n = 347), and cooperation (n = 112). However, although there is dominance in quantity, the most intensive international networks between authors and institutions are not linked to the United States. By contrast, most of the European countries combine the highest impact of publications. Further analysis reveal the influence of international cooperation and associated phenomena on the research field HD. Conclusion We conclude that the field of HD is constantly progressing. The importance of international cooperation in the scientific community is continuously growing.

  17. Caesarean Section--A Density-Equalizing Mapping Study to Depict Its Global Research Architecture.

    PubMed

    Brüggmann, Dörthe; Löhlein, Lena-Katharina; Louwen, Frank; Quarcoo, David; Jaque, Jenny; Klingelhöfer, Doris; Groneberg, David A

    2015-11-17

    Caesarean section (CS) is a common surgical procedure. Although it has been performed in a modern context for about 100 years, there is no concise analysis of the international architecture of caesarean section research output available so far. Therefore, the present study characterizes the global pattern of the related publications by using the NewQIS (New Quality and Quantity Indices in Science) platform, which combines scientometric methods with density equalizing mapping algorithms. The Web of Science was used as a database. 12,608 publications were identified that originated from 131 countries. The leading nations concerning research activity, overall citations and country-specific h-Index were the USA and the United Kingdom. Relation of the research activity to epidemiologic data indicated that Scandinavian countries including Sweden and Finland were leading the field, whereas, in relation to economic data, countries such as Israel and Ireland led. Semi-qualitative indices such as country-specific citation rates ranked Sweden, Norway and Finland in the top positions. International caesarean section research output continues to grow annually in an era where caesarean section rates increased dramatically over the past decades. With regard to increasing employment of scientometric indicators in performance assessment, these findings should provide useful information for those tasked with the improvement of scientific achievements.

  18. Caesarean Section—A Density-Equalizing Mapping Study to Depict Its Global Research Architecture

    PubMed Central

    Brüggmann, Dörthe; Löhlein, Lena-Katharina; Louwen, Frank; Quarcoo, David; Jaque, Jenny; Klingelhöfer, Doris; Groneberg, David A.

    2015-01-01

    Caesarean section (CS) is a common surgical procedure. Although it has been performed in a modern context for about 100 years, there is no concise analysis of the international architecture of caesarean section research output available so far. Therefore, the present study characterizes the global pattern of the related publications by using the NewQIS (New Quality and Quantity Indices in Science) platform, which combines scientometric methods with density equalizing mapping algorithms. The Web of Science was used as a database. 12,608 publications were identified that originated from 131 countries. The leading nations concerning research activity, overall citations and country-specific h-Index were the USA and the United Kingdom. Relation of the research activity to epidemiologic data indicated that Scandinavian countries including Sweden and Finland were leading the field, whereas, in relation to economic data, countries such as Israel and Ireland led. Semi-qualitative indices such as country-specific citation rates ranked Sweden, Norway and Finland in the top positions. International caesarean section research output continues to grow annually in an era where caesarean section rates increased dramatically over the past decades. With regard to increasing employment of scientometric indicators in performance assessment, these findings should provide useful information for those tasked with the improvement of scientific achievements. PMID:26593932

  19. Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome.

    PubMed

    Flores, Samuel Coulbourn

    2014-01-01

    Determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. Case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryo-electron microscopy. Combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. Most existing methods either model all atoms explicitly, resulting in often prohibitive cost, or use approximations that lose interesting structural and dynamical detail. In this work, I introduce Internal Coordinate Flexible Fitting, which uses full atomic forces and flexibility in limited regions of a model, capturing extensive conformational rearrangements at low cost. I use it to turn multiple low-resolution density maps, crystallographic structures and biochemical information into unified all-atoms trajectories of ribosomal translocation. Internal Coordinate Flexible Fitting is three orders of magnitude faster than the most comparable existing method.

  20. Unisensory processing and multisensory integration in schizophrenia: a high-density electrical mapping study.

    PubMed

    Stone, David B; Urrea, Laura J; Aine, Cheryl J; Bustillo, Juan R; Clark, Vincent P; Stephen, Julia M

    2011-10-01

    In real-world settings, information from multiple sensory modalities is combined to form a complete, behaviorally salient percept - a process known as multisensory integration. While deficits in auditory and visual processing are often observed in schizophrenia, little is known about how multisensory integration is affected by the disorder. The present study examined auditory, visual, and combined audio-visual processing in schizophrenia patients using high-density electrical mapping. An ecologically relevant task was used to compare unisensory and multisensory evoked potentials from schizophrenia patients to potentials from healthy normal volunteers. Analysis of unisensory responses revealed a large decrease in the N100 component of the auditory-evoked potential, as well as early differences in the visual-evoked components in the schizophrenia group. Differences in early evoked responses to multisensory stimuli were also detected. Multisensory facilitation was assessed by comparing the sum of auditory and visual evoked responses to the audio-visual evoked response. Schizophrenia patients showed a significantly greater absolute magnitude response to audio-visual stimuli than to summed unisensory stimuli when compared to healthy volunteers, indicating significantly greater multisensory facilitation in the patient group. Behavioral responses also indicated increased facilitation from multisensory stimuli. The results represent the first report of increased multisensory facilitation in schizophrenia and suggest that, although unisensory deficits are present, compensatory mechanisms may exist under certain conditions that permit improved multisensory integration in individuals afflicted with the disorder.

  1. Reduction of ocular artefacts in source current density brain mappings by ARX2 filtering.

    PubMed

    Filligoi, G C; Capitanio, L; Babiloni, F; Fattorini, L; Urbano, A; Cerutti, S

    1995-06-01

    Sweep by sweep analysis of event-related potentials (ERP) of the human scalp represents a reliable tool for both the diagnosis of neurologic diseases and the study of the central nervous system during cognitive tasks. The off-line procedure based on stochastic parametric identification and filtering herewith described, allows an accurate analysis of single-sweep ERP and a drastic reduction of ocular artefacts variously propagating through the skull. Moreover, the spatial distribution of the recorded ERP in bidimensional form was enhanced by using the Laplacian operator in order to get an estimate of the source current density (SCD) flow from the skull into the scalp. Complete single-trial signals were filtered according to an autoregressive model of signal generation with 2 exogenous inputs (ARX2). The ARX2 procedure models the recorded signal as the sum of three signals: (a) the background EEG activity, modelled as an autoregressive process driven by a white noise; (b) a filtered version of a reference signal carrying the average information contained in each sweep; (c) a signal due to the ocular artefact propagation. The evaluation of the effect of artefact suppression on those channels close to the eyes was compared with standard ordinary least squares method (OLS) based on a linear model of the influence of EOG on ERP. Finally, the better results obtainable through ARX filtering on sweep-by-sweep brain mappings are also presented.

  2. Direct electron detection yields cryo-EM reconstructions at resolutions beyond ¾ Nyquist frequency

    PubMed Central

    Bammes, Benjamin E.; Rochat, Ryan H.; Jakana, Joanita; Chen, Dong-Hua; Chiu, Wah

    2012-01-01

    One limitation in electron cryo-microscopy (cryo-EM) is the inability to recover high-resolution signal from the image-recording media at the full-resolution limit of the transmission electron microscope. Direct electron detection using CMOS-based sensors for digitally recording images has the potential to alleviate this shortcoming. Here, we report a practical performance evaluation of a Direct Detection Device (DDD) for biological cryo-EM at two different microscope voltages: 200 and 300 kV. Our DDD images of amorphous and graphitized carbon show strong per-pixel contrast with image resolution near the theoretical sampling limit of the data. Single-particle reconstructions of two frozen-hydrated bacteriophages, P22 and ε15, establish that the DDD is capable of recording usable signal for 3-D reconstructions at about 4/5 of the Nyquist frequency, which is a vast improvement over the performance of conventional imaging media. We anticipate the unparalleled performance of this digital recording device will dramatically benefit cryo-EM for routine tomographic and single-particle structural determination of biological specimens. PMID:22285189

  3. Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity

    PubMed Central

    Nogales, Eva; Scheres, Sjors H.W.

    2015-01-01

    Three-dimensional cryo-electron microscopy (cryo-EM) is an expanding structural biology technique that has recently undergone a quantum leap progression in its achievable resolution and its applicability to the study of challenging biological systems. Because crystallization is not required, only small amounts of sample are needed, and, because images can be classified in a computer, the technique has the potential to deal with compositional and conformational mixtures. Therefore, cryo-EM can be used to investigate complete and fully functional macromolecular complexes in different functional states, providing a richness of biological insight. In this review we underlie some of the principles behind the cryo-EM methodology of single particle analysis and discuss some recent results of its application to challenging systems of paramount biological importance. We place special emphasis on new methodological developments that are leading to an explosion of new studies, many of which are reaching resolutions that could only be dreamed of only a couple of years ago. PMID:26000851

  4. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

    PubMed Central

    Kimanius, Dari; Forsberg, Björn O; Scheres, Sjors HW; Lindahl, Erik

    2016-01-01

    By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation. DOI: http://dx.doi.org/10.7554/eLife.18722.001 PMID:27845625

  5. A SNP Based High-Density Linkage Map of Apis cerana Reveals a High Recombination Rate Similar to Apis mellifera

    PubMed Central

    Huang, Zachary Y.; Wu, Xiao Bo; Zhu, Yong Qiang; Zheng, Hua Jun; Zeng, Zhi Jiang

    2013-01-01

    Background The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. Results F2 workers (N = 103) were genotyped for 126,990 single nucleotide polymorphisms (SNPs). After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM) with the largest linkage group (180 loci) measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. Conclusion We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera. PMID:24130775

  6. Classification and assessment of retrieved electron density maps in coherent X-ray diffraction imaging using multivariate analysis.

    PubMed

    Sekiguchi, Yuki; Oroguchi, Tomotaka; Nakasako, Masayoshi

    2016-01-01

    Coherent X-ray diffraction imaging (CXDI) is one of the techniques used to visualize structures of non-crystalline particles of micrometer to submicrometer size from materials and biological science. In the structural analysis of CXDI, the electron density map of a sample particle can theoretically be reconstructed from a diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction is difficult because diffraction patterns are affected by Poisson noise and miss data in small-angle regions due to the beam stop and the saturation of detector pixels. In contrast to X-ray protein crystallography, in which the phases of diffracted waves are experimentally estimated, phase retrieval in CXDI relies entirely on the computational procedure driven by the PR algorithms. Thus, objective criteria and methods to assess the accuracy of retrieved electron density maps are necessary in addition to conventional parameters monitoring the convergence of PR calculations. Here, a data analysis scheme, named ASURA, is proposed which selects the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a diffraction pattern. Each electron density map composed of J pixels is expressed as a point in a J-dimensional space. Principal component analysis is applied to describe characteristics in the distribution of the maps in the J-dimensional space. When the distribution is characterized by a small number of principal components, the distribution is classified using the k-means clustering method. The classified maps are evaluated by several parameters to assess the quality of the maps. Using the proposed scheme, structure analysis of a diffraction pattern from a non-crystalline particle is conducted in two stages: estimation of the overall shape and determination of the fine structure inside the support shape. In each stage, the most accurate and probable density maps are objectively selected. The validity

  7. A Model of Median Auroral Electron Flux Deduced from Hardy 2008 Model Probability Density Maps

    DTIC Science & Technology

    2013-11-01

    example of the precipitating electron energy flux map in the Northern hemisphere for Kp=3 produced by AF- Geospace software...AF- Geospace Software (Hilmer, 2010) illustrates the precipitating electron energy flux map in the Northern hemisphere for Kp = 3...precipitating electron energy flux map in the Northern hemisphere for Kp=3 produced by AF- Geospace software. The green line specifies the auroral oval

  8. Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass

    PubMed Central

    Liu, Peng; Wang, Le; Wong, Sek-Man; Yue, Gen Hua

    2016-01-01

    Asian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression of Pcdhac2 was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance. PMID:27555039

  9. Cryo-EM structure of the ATP-sensitive potassium channel illuminates mechanisms of assembly and gating

    PubMed Central

    Martin, Gregory M; Yoshioka, Craig; Rex, Emily A; Fay, Jonathan F; Xie, Qing; Whorton, Matthew R; Chen, James Z; Shyng, Show-Ling

    2017-01-01

    KATP channels are metabolic sensors that couple cell energetics to membrane excitability. In pancreatic β-cells, channels formed by SUR1 and Kir6.2 regulate insulin secretion and are the targets of antidiabetic sulfonylureas. Here, we used cryo-EM to elucidate structural basis of channel assembly and gating. The structure, determined in the presence of ATP and the sulfonylurea glibenclamide, at ~6 Å resolution reveals a closed Kir6.2 tetrameric core with four peripheral SUR1s each anchored to a Kir6.2 by its N-terminal transmembrane domain (TMD0). Intricate interactions between TMD0, the loop following TMD0, and Kir6.2 near the proposed PIP2 binding site, and where ATP density is observed, suggest SUR1 may contribute to ATP and PIP2 binding to enhance Kir6.2 sensitivity to both. The SUR1-ABC core is found in an unusual inward-facing conformation whereby the two nucleotide binding domains are misaligned along a two-fold symmetry axis, revealing a possible mechanism by which glibenclamide inhibits channel activity. DOI: http://dx.doi.org/10.7554/eLife.24149.001 PMID:28092267

  10. Architecture of fully occupied GluA2 AMPA receptor-TARP complex elucidated by cryo-EM.

    PubMed

    Zhao, Yan; Chen, Shanshuang; Yoshioka, Craig; Baconguis, Isabelle; Gouaux, Eric

    2016-08-04

    Fast excitatory neurotransmission in the mammalian central nervous system is largely carried out by AMPA-sensitive ionotropic glutamate receptors. Localized within the postsynaptic density of glutamatergic spines, AMPA receptors are composed of heterotetrameric receptor assemblies associated with auxiliary subunits, the most common of which are transmembrane AMPA receptor regulatory proteins (TARPs). The association of TARPs with AMPA receptors modulates receptor trafficking and the kinetics of receptor gating and pharmacology. Here we report the cryo-electron microscopy (cryo-EM) structure of the homomeric rat GluA2 AMPA receptor saturated with TARP γ2 subunits, which shows how the TARPs are arranged with four-fold symmetry around the ion channel domain and make extensive interactions with the M1, M2 and M4 transmembrane helices. Poised like partially opened ‘hands’ underneath the two-fold symmetric ligand-binding domain (LBD) 'clamshells', one pair of TARPs is juxtaposed near the LBD dimer interface, whereas the other pair is near the LBD dimer-dimer interface. The extracellular ‘domains’ of TARP are positioned to not only modulate LBD clamshell closure, but also affect conformational rearrangements of the LBD layer associated with receptor activation and desensitization, while the TARP transmembrane domains buttress the ion channel pore.

  11. A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber

    PubMed Central

    Zhu, Wen-Ying; Huang, Long; Chen, Long; Yang, Jian-Tao; Wu, Jia-Ni; Qu, Mei-Ling; Yao, Dan-Qing; Guo, Chun-Li; Lian, Hong-Li; He, Huan-Le; Pan, Jun-Song; Cai, Run

    2016-01-01

    High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected. PMID:27148281

  12. Construction of high-density genetic linkage maps for orange-spotted grouper Epinephelus coioides using multiplexed shotgun genotyping

    PubMed Central

    2013-01-01

    Background Orange-spotted grouper, Epinephelus coioides, is one of the most valuable fish species in China. Commercial production of orange-spotted grouper could be increased by developing higher growth rates and improving commercially important traits. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. A high-density genetic linkage map is the basis for QTL study, and multiplexed shotgun genotyping (MSG) facilitates the development of single nucleotide polymorphisms (SNPs) and genotyping. In this study, the first high-density genetic linkage maps for groupers were generated on the basis of the MSG method. Results The sex-averaged map contained a total of 4,608 SNPs, which spanned 1581.7 cM, with a mean distance between SNPs of 0.34 cM. The 4,608 SNPs were located in 2,849 unique locations on the linkage map, with an average inter-location space at 0.56 cM. There were 2,516 SNPs on the female map, and the number of unique locus was 1,902. However, the male map contained more numbers of SNP (2,939) and unique locations (2,005). The total length of the female and male maps was 1,370.9 and 1,335.5 cM, respectively. Conclusions The high-resolution genetic linkage maps will be very useful for QTL analyses and marker-assisted selection (MAS) for economically important traits in molecular breeding of the orange-spotted grouper. PMID:24289265

  13. The neurophysiology of human biological motion processing: a high-density electrical mapping study.

    PubMed

    Krakowski, Aaron I; Ross, Lars A; Snyder, Adam C; Sehatpour, Pejman; Kelly, Simon P; Foxe, John J

    2011-05-01

    The neural processing of biological motion (BM) is of profound experimental interest since it is often through the movement of another that we interpret their immediate intentions. Neuroimaging points to a specialized cortical network for processing biological motion. Here, high-density electrical mapping and source-analysis techniques were employed to interrogate the timing of information processing across this network. Participants viewed point-light-displays depicting standard body movements (e.g. jumping), while event-related potentials (ERPs) were recorded and compared to ERPs to scrambled motion control stimuli. In a pair of experiments, three major phases of BM-specific processing were identified: 1) The earliest phase of BM-sensitive modulation was characterized by a positive shift of the ERP between 100 and 200 ms after stimulus onset. This modulation was observed exclusively over the right hemisphere and source-analysis suggested a likely generator in close proximity to regions associated with general motion processing (KO/hMT). 2) The second phase of BM-sensitivity occurred from 200 to 350 ms, characterized by a robust negative-going ERP modulation over posterior middle temporal regions bilaterally. Source-analysis pointed to bilateral generators at or near the posterior superior temporal sulcus (STS). 3) A third phase of processing was evident only in our second experiment, where participants actively attended the BM aspect of the stimuli, and was manifest as a centro-parietal positive ERP deflection, likely related to later cognitive processes. These results point to very early sensory registration of biological motion, and highlight the interactive role of the posterior STS in analyzing the movements of other living organisms.

  14. Functional Connectivity Density Mapping of Depressive Symptoms and Loneliness in Non-Demented Elderly Male

    PubMed Central

    Lan, Chen-Chia; Tsai, Shih-Jen; Huang, Chu-Chung; Wang, Ying-Hsiu; Chen, Tong-Ru; Yeh, Heng-Liang; Liu, Mu-En; Lin, Ching-Po; Yang, Albert C.

    2016-01-01

    Background: Depression and loneliness are prevalent and highly correlated phenomena among the elderly and influence both physical and mental health. Brain functional connectivity changes associated with depressive symptoms and loneliness are not fully understood. Methods: A cross-sectional functional MRI study was conducted among 85 non-demented male elders. Geriatric depression scale-short form (GDS) and loneliness scale were used to evaluate the severity of depressive symptoms and loneliness, respectively. Whole brain voxel-wise resting-state functional connectivity density (FCD) mapping was performed to delineate short-range FCD (SFCD) and long-range FCD (LFCD). Regional correlations between depressive symptoms or loneliness and SFCD or LFCD were examined using general linear model (GLM), with age incorporated as a covariate and depressive symptoms and loneliness as predictors. Results: Positive correlations between depressive symptoms and LFCD were observed in left rectal gyrus, left superior frontal gyrus, right supraorbital gyrus, and left inferior temporal gyrus. Positive correlations between depressive symptoms and SFCD were observed in left middle frontal gyrus, left superior frontal gyrus, bilateral superior medial frontal gyrus, left inferior temporal gyrus, and left middle occipital region. Positive correlations between SFCD and loneliness were centered over bilateral lingual gyrus. Conclusion: Depressive symptoms are associated with FCD changes over frontal and temporal regions, which may involve the cognitive control, affective regulation, and default mode networks. Loneliness is associated with FCD changes in bilateral lingual gyri that are known to be important in social cognition. Depressive symptoms and loneliness may be associated with different brain regions in non-demented elderly male. PMID:26793101

  15. Developing a Penetrometer-Based Mapping System for Visualizing Silage Bulk Density from the Bunker Silo Face

    PubMed Central

    Li, Menghua; Jungbluth, Kerstin H.; Sun, Yurui; Cheng, Qiang; Maack, Christian; Buescher, Wolfgang; Lin, Jianhui; Zhou, Haiyang; Wang, Zhongyi

    2016-01-01

    For silage production, high bulk density (BD) is critical to minimize aerobic deterioration facilitated by oxygen intrusion. To precisely assess packing quality for bunker silos, there is a desire to visualize the BD distribution within the silage. In this study, a penetrometer-based mapping system was developed. The data processing included filtering of the penetration friction component (PFC) out of the penetration resistance (PR), transfer of the corrected penetration resistance (PRc) to BD, incorporation of Kriged interpolation for data expansion and map generation. The experiment was conducted in a maize bunker silo (width: 8 m, middle height: 3 m). The BD distributions near the bunker silo face were represented using two map groups, one related to horizontal- and the other to vertical-density distribution patterns. We also presented a comparison between the map-based BD results and core sampling data. Agreement between the two measurement approaches (RMSE = 19.175 kg·m−3) demonstrates that the developed penetrometer mapping system may be beneficial for rapid assessment of aerobic deterioration potential in bunker silos. PMID:27399703

  16. A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

    PubMed Central

    Shirasawa, Kenta; Tanaka, Masaru; Takahata, Yasuhiro; Ma, Daifu; Cao, Qinghe; Liu, Qingchang; Zhai, Hong; Kwak, Sang-Soo; Cheol Jeong, Jae; Yoon, Ung-Han; Lee, Hyeong-Un; Hirakawa, Hideki; Isobe, Sachiko

    2017-01-01

    Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we used an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops. PMID:28281636

  17. A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping.

    PubMed

    Neves, Leandro Gomide; Davis, John M; Barbazuk, William B; Kirst, Matias

    2014-01-10

    Loblolly pine (Pinus taeda L.) is an economically and ecologically important conifer for which a suite of genomic resources is being generated. Despite recent attempts to sequence the large genome of conifers, their assembly and the positioning of genes remains largely incomplete. The interspecific synteny in pines suggests that a gene-based map would be useful to support genome assemblies and analysis of conifers. To establish a reference gene-based genetic map, we performed exome sequencing of 14729 genes on a mapping population of 72 haploid samples, generating a resource of 7434 sequence variants segregating for 3787 genes. Most markers are single-nucleotide polymorphisms, although short insertions/deletions and multiple nucleotide polymorphisms also were used. Marker segregation in the population was used to generate a high-density, gene-based genetic map. A total of 2841 genes were mapped to pine's 12 linkage groups with an average of one marker every 0.58 cM. Capture data were used to detect gene presence/absence variations and position 65 genes on the map. We compared the marker order of genes previously mapped in loblolly pine and found high agreement. We estimated that 4123 genes had enough sequencing depth for reliable detection of markers, suggesting a high marker conversation rate of 92% (3787/4123). This is possible because a significant portion of the gene is captured and sequenced, increasing the chances of identifying a polymorphic site for characterization and mapping. This sub-centiMorgan genetic map provides a valuable resource for gene positioning on chromosomes and guide for the assembly of a reference pine genome.

  18. The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map.

    PubMed

    Bourke, Peter M; Voorrips, Roeland E; Visser, Richard G F; Maliepaard, Chris

    2015-11-01

    The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. Low levels of multivalents or preferential pairing do not adversely affect map construction when highly informative marker types and phases are used. We reveal the double-reduction landscape in tetraploid potato, clearly showing that this phenomenon increases with distance from the centromeres.

  19. Rapidly calculated density functional theory (DFT) relaxed Iso-potential Phi Si Maps: Beta-cellobiose

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New cellobiose Phi-H/Si-H maps are rapidly generated using a mixed basis set DFT method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are made for different conformational states of cellobiose, showing how glycosidic bond dihe...

  20. Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Tong, Chunfa; Li, Huogen; Wang, Ying; Li, Xuran; Ou, Jiajia; Wang, Deyuan; Xu, Houxi; Ma, Chao; Lang, Xianye; Liu, Guangxin; Zhang, Bo; Shi, Jisen

    2016-01-01

    Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population. PMID:26964097

  1. Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing.

    PubMed

    Tong, Chunfa; Li, Huogen; Wang, Ying; Li, Xuran; Ou, Jiajia; Wang, Deyuan; Xu, Houxi; Ma, Chao; Lang, Xianye; Liu, Guangxin; Zhang, Bo; Shi, Jisen

    2016-01-01

    Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides 'I-69' and male Populus simonii 'L3'. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population.

  2. Development of a high density integrated reference genetic linkage map for the multinational Brassica rapa Genome Sequencing Project.

    PubMed

    Li, Xiaonan; Ramchiary, Nirala; Choi, Su Ryun; Van Nguyen, Dan; Hossain, Md Jamil; Yang, Hyeon Kook; Lim, Yong Pyo

    2010-11-01

    We constructed a high-density Brassica rapa integrated linkage map by combining a reference genetic map of 78 doubled haploid lines derived from Chiifu-401-42 × Kenshin (CKDH) and a new map of 190 F2 lines derived from Chiifu-401-42 × rapid cycling B. rapa (CRF2). The integrated map contains 1017 markers and covers 1262.0 cM of the B. rapa genome, with an average interlocus distance of 1.24 cM. High similarity of marker order and position was observed among the linkage groups of the maps with few short-distance inversions. In total, 155 simple sequence repeat (SSR) markers, anchored to 102 new bacterial artificial chromosomes (BACs) and 146 intron polymorphic (IP) markers were mapped in the integrated map, which would be helpful to align the sequenced BACs in the ongoing multinational Brassica rapa Genome Sequencing Project (BrGSP). Further, comparison of the B. rapa consensus map with the 10 B. juncea A-genome linkage groups by using 98 common IP markers showed high-degree colinearity between the A-genome linkage groups, except for few markers showing inversion or translocation. Suggesting that chromosomes are highly conserved between these Brassica species, although they evolved independently after divergence. The sequence information coming out of BrGSP would be useful for B. juncea breeding. and the identified Arabidopsis chromosomal blocks and known quantitative trait loci (QTL) information of B. juncea could be applied to improve other Brassica crops including B. rapa.

  3. Snakebite Envenoming – A Combined Density Equalizing Mapping and Scientometric Analysis of the Publication History

    PubMed Central

    Groneberg, David A.; Geier, Victoria; Klingelhöfer, Doris; Gerber, Alexander

    2016-01-01

    Estimates suggest that more than 25,000 to 125,000 people die annually from snakebite envenomation worldwide. In contrast to this major disease burden, thorough bibliometric studies do not exist so far that illustrate the overall research activity over a long time span. Therefore, the NewQIS-platform conducted an analysis on snakebite envenoming using the Thomson Reuters database Web of Science. To determine and assess changes regarding the scientific activities and to specifically address the more recent situation we analyzed two time intervals (t). During the first time interval from 1900 to 2007 (t1) 13,015 publications (p) were identified. In the following period (2008–2016 = t2) 4,982 publications were identified by the same search strategy. They originate from 114 (t1) respectively 121 countries (t2), with the USA (p = 3518), Brazil (p = 1100) and Japan (p = 961) being most productive in the first period, and the USA (p = 1087), Brazil (p = 991) and China (p = 378) in the second period, respectively. Setting the publication numbers in relation to GDP/capita, Brazil leads with 92 publications per 10,000 Int$GDP/capita, followed by India with 79 publications per 10000 Int$GDP/capita (t1). Comparing the country’s publication activity with the Human Development Index level indicates that the majority of the publications is published by highly developed countries. When calculating the average citation rates (citations per published item = CR) mainly European countries show the highest ranks: From 1900–2007 Sweden ranks first with a CR = 27, followed by the Netherlands (CR = 24.8), Switzerland (CR = 23), Spain, Austria and the USA (CR = 22). From 2008 to 2016 the highest rate achieves Switzerland with a value of 24.6, followed by Belgium (CR = 18.1), Spain (CR = 16.7), Costa Rica (CR = 14.9) and Netherlands (CR = 14). Compared with this, the USA was placed at rank 13 (CR = 9,5). In summary, the present study represents the first density-equalizing map

  4. Spatial Mapping of Macular Pigment Optical Density and Its Relationship to Contrast Sensitivity and Glare Disability

    NASA Astrophysics Data System (ADS)

    Putnam, Christopher

    This dissertation explored the relationship of the macular pigment optical density (MPOD) spatial profile with measures of contrast sensitivity (CS), glare disability (GD), relative glare disability (RGD) and intraocular light scatter. A novel device capable of measuring MPOD across the central 160 of retina along 8 principle meridians using customized heterochromatic flicker photometry (cHFP) at eccentricities of 00, 20, 40, 60 and 80 was built. MPOD was calculated as both discrete and integrated values at all measured retinal loci. CS was measured using vertical grating stimuli of 3, 6 and 9 cycles per degree (cpd) also presented at 00, 20, 4 0, 60 and 80 eccentricity. GD was calculated as a difference in CS between glare and no glare conditions (CSNo Glare - CSGlare) using the same vertical grating stimuli presented at the same eccentricities. RGD [(CSNo Glare - CSGlare) / CSNo Glare] was calculated to isolate the glare attenuation effects of MPOD by controlling for CS variability among the subject sample. Intraocular scatter was assessed through a direct compensation method using a commercially available device. Statistical analyses of the discrete and integrated MPOD associations with CS, GD, RGD and intraocular scatter were evaluated. The cHFP identified reliable MPOD spatial distribution maps demonstrating a 1 st order exponential decay curve as a function of increasing eccentricity. Foveal MPOD revealed the highest correlation coefficients with RGD using 9cpd stimuli. These results are consistent with the glare attenuation effects of MP at higher spatial frequencies. Further support may be seen from the significant correlations found between corresponding parafoveal MPOD measures and both GD and RGD at 20 and 40 of eccentricity using 9cpd stimuli with greater MPOD being associated with less glare disability. All calculated measures of foveal MPOD shared similar significant correlation coefficients with both GD and RGD using 6cpd and 9cpd stimuli. Discrete

  5. Cryo-EM Imaging of DNA-PK DNA Damage Repair Complexes

    SciTech Connect

    Phoebe L. Stewart

    2005-06-27

    Exposure to low levels of ionizing radiation causes DNA double-strand breaks (DSBs) that must be repaired for cell survival. Higher eukaryotes respond to DSBs by arresting the cell cycle, presumably to repair the DNA lesions before cell division. In mammalian cells, the nonhomologous end-joining DSB repair pathway is mediated by the 470 kDa DNA-dependent protein kinase catalytic subunit (DNA-PKcs) together with the DNA-binding factors Ku70 and Ku80. Mouse knock-out models of these three proteins are all exquisitely sensitive to low doses of ionizing radiation. In the presence of DNA ends, Ku binds to the DNA and then recruits DNA-PKcs. After formation of the complex, the kinase activity associated with DNA-PKcs becomes activated. This kinase activity has been shown to be essential for repairing DNA DSBs in vivo since expression of a kinase-dead form of DNA-PKcs in a mammalian cell line that lacks DNA-PKcs fails to complement the radiosensitive phenotype. The immense size of DNA-PKcs suggests that it may also serve as a docking site for other DNA repair proteins. Since the assembly of the DNA-PK complex onto DNA is a prerequisite for DSB repair, it is critical to obtain structural information on the complex. Cryo-electron microscopy (cryo-EM) and single particle reconstruction methods provide a powerful way to image large macromolecular assemblies at near atomic (10-15 ?) resolution. We have already used cryo-EM methods to examine the structure of the isolated DNA-PKcs protein. This structure reveals numerous cavities throughout the protein that may allow passage of single or double-stranded DNA. Pseudo two-fold symmetry was found for the monomeric protein, suggesting that DNA-PKcs may interact with two DNA ends or two Ku heterodimers simultaneously. Here we propose to study the structure of the cross-linked DNA-PKcs/Ku/DNA complex. Difference imaging with our published DNA-PKcs structure will enable us to elucidate the architecture of the complex. A second

  6. A high-density linkage map of the RN region in pigs.

    PubMed

    Looft, C; Milan, D; Jeon, J T; Paul, S; Reinsch, N; Rogel-Gaillard, C; Rey, V; Amarger, V; Robic, A; Kalm, E; Chardon, P; Andersson, L

    2000-01-01

    The porcine RN locus affects muscle glycogen content and meat quality. We previously mapped the RN locus to chromosome 15. This study describes the identification of polymorphisms for four class I and four class II markers located in the RN region. Resource families were genotyped with F-SSCP markers (fluorescent single strand conformation polymorphism) and microsatellite markers. Subsequent multipoint linkage analysis revealed the order FN1-IGFBP5-S1000-S1001-IL8RB-VIL1-RN-Sw936-Sw906. The gene order is identical to the previously reported porcine RH map of the same region. The described map will facilitate positional cloning of the RN gene.

  7. Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping.

    PubMed

    Schlautman, Brandon; Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Iorizzo, Massimo; Polashock, James; Grygleski, Edward; Vorsa, Nicholi; Zalapa, Juan

    2017-04-03

    The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.

  8. Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping

    PubMed Central

    Schlautman, Brandon; Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Iorizzo, Massimo; Polashock, James; Grygleski, Edward; Vorsa, Nicholi; Zalapa, Juan

    2017-01-01

    The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. PMID:28250016

  9. FAST WAVELET-BASED SINGLE-PARTICLE RECONSTRUCTION IN CRYO-EM.

    PubMed

    Vonesch, Cédric; Wang, Lanhui; Shkolnisky, Yoel; Singer, Amit

    2011-06-09

    This paper presents a novel algorithm for the 3D tomographic inversion problem that arises in single-particle electron cryo-microscopy (Cryo-EM). It is based on two key components: 1) a variational formulation that promotes sparsity in the wavelet domain and 2) the Toeplitz structure of the combined projection/back-projection operator. The first idea has proven to be very effective for the recovery of piecewise-smooth signals, which is confirmed by our numerical experiments. The second idea allows for a computationally efficient implementation of the reconstruction procedure, using only one circulant convolution per iteration.

  10. Using the Volta phase plate with defocus for cryo-EM single particle analysis

    PubMed Central

    Danev, Radostin; Tegunov, Dimitry; Baumeister, Wolfgang

    2017-01-01

    Previously, we reported an in-focus data acquisition method for cryo-EM single-particle analysis with the Volta phase plate (Danev and Baumeister, 2016). Here, we extend the technique to include a small amount of defocus which enables contrast transfer function measurement and correction. This hybrid approach simplifies the experiment and increases the data acquisition speed. It also removes the resolution limit inherent to the in-focus method thus allowing 3D reconstructions with resolutions better than 3 Å. DOI: http://dx.doi.org/10.7554/eLife.23006.001 PMID:28109158

  11. Hotspot detection in pancreatic neuroendocrine tumors: density approximation by α-shape maps

    NASA Astrophysics Data System (ADS)

    Niazi, M. K. K.; Hartman, Douglas J.; Pantanowitz, Liron; Gurcan, Metin N.

    2016-03-01

    The grading of neuroendocrine tumors of the digestive system is dependent on accurate and reproducible assessment of the proliferation with the tumor, either by counting mitotic figures or counting Ki-67 positive nuclei. At the moment, most pathologists manually identify the hotspots, a practice which is tedious and irreproducible. To better help pathologists, we present an automatic method to detect all potential hotspots in neuroendocrine tumors of the digestive system. The method starts by segmenting Ki-67 positive nuclei by entropy based thresholding, followed by detection of centroids for all Ki-67 positive nuclei. Based on geodesic distance, approximated by the nuclei centroids, we compute two maps: an amoeba map and a weighted amoeba map. These maps are later combined to generate the heat map, the segmentation of which results in the hotspots. The method was trained on three and tested on nine whole slide images of neuroendocrine tumors. When evaluated by two expert pathologists, the method reached an accuracy of 92.6%. The current method does not discriminate between tumor, stromal and inflammatory nuclei. The results show that α-shape maps may represent how hotspots are perceived.

  12. Quantification of mammographic masking risk with volumetric breast density maps: how to select women for supplemental screening

    NASA Astrophysics Data System (ADS)

    Holland, Katharina; van Gils, Carla H.; Wanders, Johanna OP; Mann, Ritse M.; Karssemeijer, Nico

    2016-03-01

    The sensitivity of mammograms is low for women with dense breasts, since cancers may be masked by dense tissue. In this study, we investigated methods to identify women with density patterns associated with a high masking risk. Risk measures are derived from volumetric breast density maps. We used the last negative screening mammograms of 93 women who subsequently presented with an interval cancer (IC), and, as controls, 930 randomly selected normal screening exams from women without cancer. Volumetric breast density maps were computed from the mammograms, which provide the dense tissue thickness at each location. These were used to compute absolute and percentage glandular tissue volume. We modeled the masking risk for each pixel location using the absolute and percentage dense tissue thickness and we investigated the effect of taking the cancer location probability distribution (CLPD) into account. For each method, we selected cases with the highest masking measure (by thresholding) and computed the fraction of ICs as a function of the fraction of controls selected. The latter can be interpreted as the negative supplemental screening rate (NSSR). Between the models, when incorporating CLPD, no significant differences were found. In general, the methods performed better when CLPD was included. At higher NSSRs some of the investigated masking measures had a significantly higher performance than volumetric breast density. These measures may therefore serve as an alternative to identify women with a high risk for a masked cancer.

  13. Genome Wide SSR High Density Genetic Map Construction from an Interspecific Cross of Gossypium hirsutum × Gossypium tomentosum

    PubMed Central

    Khan, Muhammad K. R.; Chen, Haodong; Zhou, Zhongli; Ilyas, Muhammad K.; Wang, Xingxing; Cai, Xiaoyan; Wang, Chunying; Liu, Fang; Wang, Kunbo

    2016-01-01

    A high density genetic map was constructed using F2 population derived from an interspecific cross of G. hirsutum × G. tomentosum. The map consisted of 3093 marker loci distributed across all the 26 chromosomes and covered 4365.3 cM of cotton genome with an average inter-marker distance of 1.48 cM. The maximum length of chromosome was 218.38 cM and the minimum was 122.09 cM with an average length of 167.90 cM. A sub-genome covers more genetic distance (2189.01 cM) with an average inter loci distance of 1.53 cM than D sub-genome which covers a length of 2176.29 cM with an average distance of 1.43 cM. There were 716 distorted loci in the map accounting for 23.14% and most distorted loci were distributed on D sub-genome (25.06%), which were more than on A sub-genome (21.23%). In our map 49 segregation hotspots (SDR) were distributed across the genome with more on D sub-genome as compared to A genome. Two post-polyploidization reciprocal translocations of “A2/A3 and A4/A5” were suggested by seven pairs of duplicate loci. The map constructed through these studies is one of the three densest genetic maps in cotton however; this is the first dense genome wide SSR interspecific genetic map between G. hirsutum and G. tomentosum. PMID:27148280

  14. A Fast and Effective Microfluidic Spraying-Plunging Method for High-Resolution Single-Particle Cryo-EM.

    PubMed

    Feng, Xiangsong; Fu, Ziao; Kaledhonkar, Sandip; Jia, Yuan; Shah, Binita; Jin, Amy; Liu, Zheng; Sun, Ming; Chen, Bo; Grassucci, Robert A; Ren, Yukun; Jiang, Hongyuan; Frank, Joachim; Lin, Qiao

    2017-03-06

    We describe a spraying-plunging method for preparing cryoelectron microscopy (cryo-EM) grids with vitreous ice of controllable, highly consistent thickness using a microfluidic device. The new polydimethylsiloxane (PDMS)-based sprayer was tested with apoferritin. We demonstrate that the structure can be solved to high resolution with this method of sample preparation. Besides replacing the conventional pipetting-blotting-plunging method, one of many potential applications of the new sprayer is in time-resolved cryo-EM, as part of a PDMS-based microfluidic reaction channel to study short-lived intermediates on the timescale of 10-1,000 ms.

  15. Plasticity in PYD assembly revealed by cryo-EM structure of the PYD filament of AIM2.

    PubMed

    Lu, Alvin; Li, Yang; Yin, Qian; Ruan, Jianbin; Yu, Xiong; Egelman, Edward; Wu, Hao

    Absent in melanoma 2 (AIM2) is an essential cytosolic double-stranded DNA receptor that assembles with the adaptor, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and caspase-1 to form the AIM2 inflammasome, which leads to proteolytic maturation of cytokines and pyroptotic cell death. AIM2 contains an N-terminal Pyrin domain (PYD) that interacts with ASC through PYD/PYD interactions and nucleates ASC(PYD) filament formation. To elucidate the molecular basis of AIM2-induced ASC(PYD) polymerization, we generated AIM2(PYD) filaments fused to green fluorescent protein (GFP) and determined its cryo-electron microscopic (cryo-EM) structure. The map showed distinct definition of helices, allowing fitting of the crystal structure. Surprisingly, the GFP-AIM2(PYD) filament is a 1-start helix with helical parameters distinct from those of the 3-start ASC(PYD) filament. However, despite the apparent symmetry difference, helical net and detailed interface analyses reveal minimal changes in subunit packing. GFP-AIM2(PYD) nucleated ASC(PYD) filament formation in comparable efficiency as untagged AIM2(PYD), suggesting assembly plasticity in both AIM2(PYD) and ASC(PYD). The DNA-binding domain of AIM2 is able to form AIM2/DNA filaments, within which the AIM2(PYD) is brought into proximity to template ASC(PYD) filament assembly. Because ASC is able to interact with many PYD-containing receptors for the formation of inflammasomes, the observed structural plasticity may be critically important for this versatility in the PYD/PYD interactions.

  16. Plasticity in PYD assembly revealed by cryo-EM structure of the PYD filament of AIM2

    PubMed Central

    Lu, Alvin; Li, Yang; Yin, Qian; Ruan, Jianbin; Yu, Xiong; Egelman, Edward; Wu, Hao

    2015-01-01

    Absent in melanoma 2 (AIM2) is an essential cytosolic double-stranded DNA receptor that assembles with the adaptor, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and caspase-1 to form the AIM2 inflammasome, which leads to proteolytic maturation of cytokines and pyroptotic cell death. AIM2 contains an N-terminal Pyrin domain (PYD) that interacts with ASC through PYD/PYD interactions and nucleates ASCPYD filament formation. To elucidate the molecular basis of AIM2-induced ASCPYD polymerization, we generated AIM2PYD filaments fused to green fluorescent protein (GFP) and determined its cryo-electron microscopic (cryo-EM) structure. The map showed distinct definition of helices, allowing fitting of the crystal structure. Surprisingly, the GFP-AIM2PYD filament is a 1-start helix with helical parameters distinct from those of the 3-start ASCPYD filament. However, despite the apparent symmetry difference, helical net and detailed interface analyses reveal minimal changes in subunit packing. GFP-AIM2PYD nucleated ASCPYD filament formation in comparable efficiency as untagged AIM2PYD, suggesting assembly plasticity in both AIM2PYD and ASCPYD. The DNA-binding domain of AIM2 is able to form AIM2/DNA filaments, within which the AIM2PYD is brought into proximity to template ASCPYD filament assembly. Because ASC is able to interact with many PYD-containing receptors for the formation of inflammasomes, the observed structural plasticity may be critically important for this versatility in the PYD/PYD interactions. PMID:26583071

  17. MODELING THE ANOMALY OF SURFACE NUMBER DENSITIES OF GALAXIES ON THE GALACTIC EXTINCTION MAP DUE TO THEIR FIR EMISSION CONTAMINATION

    SciTech Connect

    Kashiwagi, Toshiya; Suto, Yasushi; Taruya, Atsushi; Yahata, Kazuhiro; Kayo, Issha; Nishimichi, Takahiro

    2015-02-01

    The most widely used Galactic extinction map is constructed assuming that the observed far-infrared (FIR) fluxes come entirely from Galactic dust. According to the earlier suggestion by Yahata et al., we consider how FIR emission of galaxies affects the SFD map. We first compute the surface number density of Sloan Digital Sky Survey (SDSS) DR7 galaxies as a function of the r-band extinction, A {sub r,} {sub SFD}. We confirm that the surface densities of those galaxies positively correlate with A {sub r,} {sub SFD} for A {sub r,} {sub SFD} < 0.1, as first discovered by Yahata et al. for SDSS DR4 galaxies. Next we construct an analytical model to compute the surface density of galaxies, taking into account the contamination of their FIR emission. We adopt a log-normal probability distribution for the ratio of 100 μm and r-band luminosities of each galaxy, y ≡ (νL){sub 100} {sub μm}/(νL) {sub r}. Then we search for the mean and rms values of y that fit the observed anomaly, using the analytical model. The required values to reproduce the anomaly are roughly consistent with those measured from the stacking analysis of SDSS galaxies. Due to the limitation of our statistical modeling, we are not yet able to remove the FIR contamination of galaxies from the extinction map. Nevertheless, the agreement with the model prediction suggests that the FIR emission of galaxies is mainly responsible for the observed anomaly. Whereas the corresponding systematic error in the Galactic extinction map is 0.1-1 mmag, it is directly correlated with galaxy clustering and thus needs to be carefully examined in precision cosmology.

  18. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

    DOE PAGES

    Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei; ...

    2015-08-17

    Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report that EMRinger is a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

  19. High-density linkage mapping and distribution of segregation distortion regions in the oak genome

    PubMed Central

    Bodénès, Catherine; Chancerel, Emilie; Ehrenmann, François; Kremer, Antoine; Plomion, Christophe

    2016-01-01

    We developed the densest single-nucleotide polymorphism (SNP)-based linkage genetic map to date for the genus Quercus. An 8k gene-based SNP array was used to genotype more than 1,000 full-sibs from two intraspecific and two interspecific full-sib families of Quercus petraea and Quercus robur. A high degree of collinearity was observed between the eight parental maps of the two species. A composite map was then established with 4,261 SNP markers spanning 742 cM over the 12 linkage groups (LGs) of the oak genome. Nine genomic regions from six LGs displayed highly significant distortions of segregation. Two main hypotheses concerning the mechanisms underlying segregation distortion are discussed: genetic load vs. reproductive barriers. Our findings suggest a predominance of pre-zygotic to post-zygotic barriers. PMID:27013549

  20. Use of density equalizing map projections (DEMP) in the analysis of childhood cancer in four California counties

    SciTech Connect

    Merrill, D.W.; Selvin, S.; Close, E.R.; Holmes, H.H.

    1995-01-01

    In studying geographic disease distributions, one normally compares rates of arbitrarily defined geographic subareas (e.g. census tracts), thereby sacrificing the geographic detail of the original data. The sparser the data, the larger the subareas must be in order to calculate stable rates. This dilemma is avoided with the technique of Density Equalizing Map Projections (DEMP). Boundaries of geographic subregions are adjusted to equalize population density over the entire study area. Case locations plotted on the transformed map should have a uniform distribution if the underlying disease-rates are constant. On the transformed map, the statistical analysis of the observed distribution is greatly simplified. Even for sparse distributions, the statistical significance of a supposed disease cluster can be reliably calculated. The present report describes the first successful application of the DEMP technique to a sizeable ``real-world`` data set of epidemiologic interest. An improved DEMP algorithm [GUSE93, CLOS94] was applied to a data set previously analyzed with conventional techniques [SATA90, REYN91]. The results from the DEMP analysis and a conventional analysis are compared.

  1. Quantifying volcanic hazard at Campi Flegrei caldera (Italy) with uncertainty assessment: 2. Pyroclastic density current invasion maps

    NASA Astrophysics Data System (ADS)

    Neri, Augusto; Bevilacqua, Andrea; Esposti Ongaro, Tomaso; Isaia, Roberto; Aspinall, Willy P.; Bisson, Marina; Flandoli, Franco; Baxter, Peter J.; Bertagnini, Antonella; Iannuzzi, Enrico; Orsucci, Simone; Pistolesi, Marco; Rosi, Mauro; Vitale, Stefano

    2015-04-01

    Campi Flegrei (CF) is an example of an active caldera containing densely populated settlements at very high risk of pyroclastic density currents (PDCs). We present here an innovative method for assessing background spatial PDC hazard in a caldera setting with probabilistic invasion maps conditional on the occurrence of an explosive event. The method encompasses the probabilistic assessment of potential vent opening positions, derived in the companion paper, combined with inferences about the spatial density distribution of PDC invasion areas from a simplified flow model, informed by reconstruction of deposits from eruptions in the last 15 ka. The flow model describes the PDC kinematics and accounts for main effects of topography on flow propagation. Structured expert elicitation is used to incorporate certain sources of epistemic uncertainty, and a Monte Carlo approach is adopted to produce a set of probabilistic hazard maps for the whole CF area. Our findings show that, in case of eruption, almost the entire caldera is exposed to invasion with a mean probability of at least 5%, with peaks greater than 50% in some central areas. Some areas outside the caldera are also exposed to this danger, with mean probabilities of invasion of the order of 5-10%. Our analysis suggests that these probability estimates have location-specific uncertainties which can be substantial. The results prove to be robust with respect to alternative elicitation models and allow the influence on hazard mapping of different sources of uncertainty, and of theoretical and numerical assumptions, to be quantified.

  2. Use of Density Equalizing Map Projections (DEMP) in the analysis of childhood cancer in four California counties. Revision 2

    SciTech Connect

    Merrill, D.W.; Close, E.R.; Holmes, H.H.; Selvin, S. |

    1995-10-01

    In studying geographic disease distributions, one normally compares rates among arbitrarily defined geographic subareas (e.g. census tracts), thereby sacrificing the geographic detail of the original data. The sparser the data, the larger the subareas must be in order to calculate stable rates. This dilemma is avoided with the technique of Density Equalizing Map Projections (DEMP). Boundaries of geographic subregions are adjusted to equalize population density over the entire study area. Case locations plotted on the transformed map should have a uniform distribution if the underlying disease rates are constant. The present report describes the application of the DEMP technique to 401 childhood cancer cases occurring between 1980 and 1988 in four California counties, with the use of map files and population data for the 262 tracts of the 1980 Census. A k`th nearest neighbor analysis provides strong evidence for geographic non-uniformity in tract rates (p < 10{sup {minus}4}). No such effect is observed for artificial cases generated under the assumption of constant rates. Work is in progress to repeat the analysis with improved population estimates derived from both 1980 and 1990 Census data. Final epidemiologic conclusions will be reported when that analysis is complete.

  3. An approach to automated acquisition of cryoEM images from lacey carbon grids.

    PubMed

    Nicholson, William V; White, Howard; Trinick, John

    2010-12-01

    An approach to automated acquisition of cryoEM image data from lacey carbon grids using the Leginon program is described. Automated liquid nitrogen top up of the specimen holder dewar was used as a step towards full automation, without operator intervention during the course of data collection. During cryoEM studies of actin labelled with myosin V, we have found it necessary to work with lacey grids rather than Quantifoil or C-flat grids due to interaction of myosin V with the support film. Lacey grids have irregular holes of variable shape and size, in contrast to Quantifoil or C-flat grids which have a regular array of similar circular holes on each grid square. Other laboratories also prefer to work with grids with irregular holes for a variety of reasons. Therefore, it was necessary to develop a different strategy from normal Leginon usage for working with lacey grids for targeting holes for image acquisition and suitable areas for focussing prior to image acquisition. This approach was implemented by using the extensible framework provided by Leginon and by developing a new MSI application within that framework which includes a new Leginon node (for a novel method for finding focus targets).

  4. Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM

    PubMed Central

    Zhou, Anna; Rohou, Alexis; Schep, Daniel G; Bason, John V; Montgomery, Martin G; Walker, John E; Grigorieff, Nikolaus; Rubinstein, John L

    2015-01-01

    Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases. DOI: http://dx.doi.org/10.7554/eLife.10180.001 PMID:26439008

  5. Design of a molecular support for cryo-EM structure determination

    PubMed Central

    Martin, Thomas G.; Bharat, Tanmay A. M.; Joerger, Andreas C.; Bai, Xiao-chen; Praetorius, Florian; Fersht, Alan R.; Dietz, Hendrik

    2016-01-01

    Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air–water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA. The support structures spontaneously form monolayers of preoriented particles in a thin film of water, and offer advantages in particle picking and sorting. By controlling the position of the binding sequence on a single helix that spans the hollow support structure, we also sought to control the orientation of individual p53 complexes. Although the latter did not yet yield the desired results, the support structures did provide partial information about the relative orientations of individual p53 complexes. We used this information to calculate a tomographic 3D reconstruction, and refined this structure to a final resolution of ∼15 Å. This structure settles an ongoing debate about the symmetry of the p53 tetramer bound to DNA. PMID:27821763

  6. Symmetry-restrained flexible fitting for symmetric EM maps

    PubMed Central

    Chan, Kwok-Yan; Gumbart, James; McGreevy, Ryan; Watermeyer, Jean M.; Sewell, B. Trevor; Schulten, Klaus

    2011-01-01

    Summary Many large biological macromolecules have inherent structural symmetry, being composed of a few distinct subunits, repeated in a symmetric array. These complexes are often not amenable to traditional high-resolution structural determination methods, but can be imaged in functionally relevant states using cryo-electron microscopy (cryo-EM). A number of methods for fitting atomic-scale structures into cryo-EM maps have been developed, including the molecular dynamics flexible fitting (MDFF) method. However, quality and resolution of the cryo-EM map are the major determinants of a method’s success. In order to incorporate knowledge of structural symmetry into the fitting procedure, we developed the symmetry-restrained MDFF method. The new method adds to the cryo-EM map-derived potential further restraints on the allowed conformations of a complex during fitting, thereby improving the quality of the resultant structure. The benefit of using symmetry-based restraints during fitting, particularly for medium to low-resolution data, is demonstrated for three different systems. PMID:21893283

  7. Pyroclastic density current hazard maps at Campi Flegrei caldera (Italy): the effects of event scale, vent location and time forecasts.

    NASA Astrophysics Data System (ADS)

    Bevilacqua, Andrea; Neri, Augusto; Esposti Ongaro, Tomaso; Isaia, Roberto; Flandoli, Franco; Bisson, Marina

    2016-04-01

    Today hundreds of thousands people live inside the Campi Flegrei caldera (Italy) and in the adjacent part of the city of Naples making a future eruption of such volcano an event with huge consequences. Very high risks are associated with the occurrence of pyroclastic density currents (PDCs). Mapping of background or long-term PDC hazard in the area is a great challenge due to the unknown eruption time, scale and vent location of the next event as well as the complex dynamics of the flow over the caldera topography. This is additionally complicated by the remarkable epistemic uncertainty on the eruptive record, affecting the time of past events, the location of vents as well as the PDCs areal extent estimates. First probability maps of PDC invasion were produced combining a vent-opening probability map, statistical estimates concerning the eruptive scales and a Cox-type temporal model including self-excitement effects, based on the eruptive record of the last 15 kyr. Maps were produced by using a Monte Carlo approach and adopting a simplified inundation model based on the "box model" integral approximation tested with 2D transient numerical simulations of flow dynamics. In this presentation we illustrate the independent effects of eruption scale, vent location and time of forecast of the next event. Specific focus was given to the remarkable differences between the eastern and western sectors of the caldera and their effects on the hazard maps. The analysis allowed to identify areas with elevated probabilities of flow invasion as a function of the diverse assumptions made. With the quantification of some sources of uncertainty in relation to the system, we were also able to provide mean and percentile maps of PDC hazard levels.

  8. a New Method to Calculate the Density Map of Magnetic Equatorial Plane of the Plasmasphere from the EUV Data

    NASA Astrophysics Data System (ADS)

    Zheng, Jie

    The Extreme Ultraviolet (EUV) data was collected by the EUV sensor on the American IMAGE satellite which represented the line integrals of the density of He+ along the EUV radiation. In this paper, we introduce a new method which can be used to calculate the density map of magnetic equatorial plane of the plasmasphere from the EUV data. The new method is derived from the ART algorithm in computed tomography (CT) which is different from the several existing methods. The value of each element of the EUV data is back-projected to the corresponded L-curves. It is assumed that the He+ density is constant along L-curve. Different from the existing methods, each element of EUV data is considered as a sum of all the He+ densities on the L-curves which are passed though by the corresponding EUV radiation ray. Finally, the numerical experimental results are presented to verify our new method for the plasmasphere density in the magnetic equatorial plane.

  9. Construction of High Density Sweet Cherry (Prunus avium L.) Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS).

    PubMed

    Guajardo, Verónica; Solís, Simón; Sagredo, Boris; Gainza, Felipe; Muñoz, Carlos; Gasic, Ksenija; Hinrichsen, Patricio

    2015-01-01

    Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs) and, recently, using single nucleotide polymorphism markers (SNPs) from a cherry 6K SNP array. Genotyping-by-sequencing (GBS), a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a 'Rainier' x 'Rivedel' (Ra x Ri) cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in 'Rainier', 'Rivedel' and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for 'Rainier', 'Rivedel' and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both 'Rainier' and 'Rivedel' maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.

  10. Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat

    PubMed Central

    Holtz, Yan; Ardisson, Morgane; Ranwez, Vincent; Besnard, Alban; Leroy, Philippe; Poux, Gérard; Roumet, Pierre; Viader, Véronique; Santoni, Sylvain; David, Jacques

    2016-01-01

    Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays. PMID:27171472

  11. Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat.

    PubMed

    Holtz, Yan; Ardisson, Morgane; Ranwez, Vincent; Besnard, Alban; Leroy, Philippe; Poux, Gérard; Roumet, Pierre; Viader, Véronique; Santoni, Sylvain; David, Jacques

    2016-01-01

    Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays.

  12. Image of Fomalhaut Dust Ring at 350 Microns: The Relative Column Density Map Shows Pericenter-Apocenter Asymmetry

    NASA Technical Reports Server (NTRS)

    Marsh, K. A.; Velusamy, T.; Dowell, C. D.; Grogan, K.; Beichman, C. A.

    2005-01-01

    We have imaged the circumstellar disk of Fomalhaut at 350 mm wavelength, using SHARC II (Submillimeter High Angular Resolution Camera II) at the Caltech Submillimeter Observatory. The spatial resolution of the raw images (9") has been enhanced by a factor of 3 using the HiRes deconvolution procedure. We find that at this wavelength and signal-to-noise ratio (approx.12), the observed morphology is that of a simple inclined ring (i approx. 70 deg), with little or no other apparent structure--this is the first observation that shows clearly the ring morphology of the disk. We have combined our 350 mm data with Spitzer Space Telescope images at 24, 70, and 160 mm in order to estimate the two-dimensional spatial variation of relative column density ("tau map") using our DISKFIT procedure. The tau map is based on the following physical assumptions: (1) the wavelength variation of opacity is the same throughout the disk, (2) the radial variation of dust temperature is dictated by the energy balance of individual grains in the stellar radiation field, and (3) the vertical scale height of the disk follows a power-law radial variation. The results confirm the ringlike morphology but also show that the geometric center is displaced from the star by about 8 AU and that the ring has an apocentric enhancement of approximately 14% in integrated column density. If we interpret the displacement in terms of elliptical orbital motion due to gravitational perturbation by an unseen planet, then the implied forced eccentricity is 0.06; dynamical modeling then predicts an apocentric density enhancement consistent with that inferred from the tau map.

  13. Mapping axonal density and average diameter using non-monotonic time-dependent gradient-echo MRI

    NASA Astrophysics Data System (ADS)

    Nunes, Daniel; Cruz, Tomás L.; Jespersen, Sune N.; Shemesh, Noam

    2017-04-01

    White Matter (WM) microstructures, such as axonal density and average diameter, are crucial to the normal function of the Central Nervous System (CNS) as they are closely related with axonal conduction velocities. Conversely, disruptions of these microstructural features may result in severe neurological deficits, suggesting that their noninvasive mapping could be an important step towards diagnosing and following pathophysiology. Whereas diffusion based MRI methods have been proposed to map these features, they typically entail the application of powerful gradients, which are rarely available in the clinic, or extremely long acquisition schemes to extract information from parameter-intensive models. In this study, we suggest that simple and time-efficient multi-gradient-echo (MGE) MRI can be used to extract the axon density from susceptibility-driven non-monotonic decay in the time-dependent signal. We show, both theoretically and with simulations, that a non-monotonic signal decay will occur for multi-compartmental microstructures - such as axons and extra-axonal spaces, which were here used as a simple model for the microstructure - and that, for axons parallel to the main magnetic field, the axonal density can be extracted. We then experimentally demonstrate in ex-vivo rat spinal cords that its different tracts - characterized by different microstructures - can be clearly contrasted using the MGE-derived maps. When the quantitative results are compared against ground-truth histology, they reflect the axonal fraction (though with a bias, as evident from Bland-Altman analysis). As well, the extra-axonal fraction can be estimated. The results suggest that our model is oversimplified, yet at the same time evidencing a potential and usefulness of the approach to map underlying microstructures using a simple and time-efficient MRI sequence. We further show that a simple general-linear-model can predict the average axonal diameters from the four model parameters, and

  14. Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage.

    PubMed

    Li, Xueming; Zheng, Shawn; Agard, David A; Cheng, Yifan

    2015-11-01

    Newly developed direct electron detection cameras have a high image output frame rate that enables recording dose fractionated image stacks of frozen hydrated biological samples by electron cryomicroscopy (cryoEM). Such novel image acquisition schemes provide opportunities to analyze cryoEM data in ways that were previously impossible. The file size of a dose fractionated image stack is 20-60 times larger than that of a single image. Thus, efficient data acquisition and on-the-fly analysis of a large number of dose-fractionated image stacks become a serious challenge to any cryoEM data acquisition system. We have developed a computer-assisted system, named UCSFImage4, for semi-automated cryo-EM image acquisition that implements an asynchronous data acquisition scheme. This facilitates efficient acquisition, on-the-fly motion correction, and CTF analysis of dose fractionated image stacks with a total time of ∼60s/exposure. Here we report the technical details and configuration of this system.

  15. Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components.

    PubMed

    Yu, Guimei; Yan, Rui; Zhang, Chuan; Mao, Chengde; Jiang, Wen

    2015-10-01

    Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components.

  16. Assessing Accuracy in Varying LIDAR Data Point Densities in Digital Elevation Maps

    DTIC Science & Technology

    2008-09-01

    burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instruction, searching ...collected by the National Geospatial Intelligence Agency in February 2008 in areas of differing ground cover amounts. 2 The following chapters will...a greater area collected (and mapped) for each pass. This becomes important when collecting against hostile targets in a military or intelligence

  17. High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L.

    PubMed Central

    Wang, Xiaodong; Yu, Kunjiang; Li, Hongge; Peng, Qi; Chen, Feng; Zhang, Wei; Chen, Song; Hu, Maolong; Zhang, Jiefu

    2015-01-01

    The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line ‘APL01’ and a normally petalled variety ‘Holly’. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus. PMID:26779193

  18. A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus

    PubMed Central

    2011-01-01

    Background Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. Results SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. Conclusions The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping

  19. Mapping brucellosis increases relative to elk density using hierarchical Bayesian models

    USGS Publications Warehouse

    Cross, Paul C.; Heisey, Dennis M.; Scurlock, Brandon M.; Edwards, William H.; Brennan, Angela; Ebinger, Michael R.

    2010-01-01

    The relationship between host density and parasite transmission is central to the effectiveness of many disease management strategies. Few studies, however, have empirically estimated this relationship particularly in large mammals. We applied hierarchical Bayesian methods to a 19-year dataset of over 6400 brucellosis tests of adult female elk (Cervus elaphus) in northwestern Wyoming. Management captures that occurred from January to March were over two times more likely to be seropositive than hunted elk that were killed in September to December, while accounting for site and year effects. Areas with supplemental feeding grounds for elk had higher seroprevalence in 1991 than other regions, but by 2009 many areas distant from the feeding grounds were of comparable seroprevalence. The increases in brucellosis seroprevalence were correlated with elk densities at the elk management unit, or hunt area, scale (mean 2070 km2; range = [95–10237]). The data, however, could not differentiate among linear and non-linear effects of host density. Therefore, control efforts that focus on reducing elk densities at a broad spatial scale were only weakly supported. Additional research on how a few, large groups within a region may be driving disease dynamics is needed for more targeted and effective management interventions. Brucellosis appears to be expanding its range into new regions and elk populations, which is likely to further complicate the United States brucellosis eradication program. This study is an example of how the dynamics of host populations can affect their ability to serve as disease reservoirs.

  20. Mapping Human Population Density in and Around New Hapmshire's Loon Lakes: A Comparison of Dasymetric Methods

    EPA Science Inventory

    The impact of anthropogenic stressors on ecosystems is directly related to the pattern of human population density across the landscape; thus, accurate information on the distribution of human populations is critical for associating the impact of human population and ecological r...

  1. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Btau_4.0 and UMD3.1 are two distinct cattle reference genome assemblies. In our previous study using the low density BovineSNP50 array, we reported a copy number variation (CNV) analysis on Btau_4.0 with 521 animals of 21 cattle breeds, yielding 682 CNV regions with a total length of 139.8 megabases...

  2. Development of high-density linkage map and tagging leaf spot resistance in pearl millet using genotyping-by-sequencing markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pearl millet is an important forage and grain crop in many parts of the world. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-by-Sequencing (GBS) markers can be used to build high density linkage maps even in species lacking a reference genome. A re...

  3. Addition of four-hundred fifty-five microsatellite marker loci to the high density Gossypium hirsutum TM-1 x G. barbadense 3-79 genetic map

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A high density genetic linkage map plays important roles in understanding genome structure of tetraploid cotton, dissecting economically important traits, identifying molecular markers associated with a trait, and cloning a gene of interest through map-based cloning strategy. Four hundred fifty f...

  4. A high density linkage map of the ancestral diploid strawberry F. iinumae using SNP markers from the ISTRAW90 array and GBS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fragaria iinumae is recognized as an ancestor of the octoploid strawberry species, including the cultivated strawberry, Fragaria ×ananassa. Here we report the construction of the first high density linkage map for F. iinumae. The map is based on two high-throughput techniques of single nucleotide p...

  5. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 datasets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum...

  6. Drowning - a scientometric analysis and data acquisition of a constant global problem employing density equalizing mapping and scientometric benchmarking procedures

    PubMed Central

    2011-01-01

    Background Drowning is a constant global problem which claims approximately half a million victims worldwide each year, whereas the number of near-drowning victims is considerably higher. Public health strategies to reduce the burden of death are still limited. While research activities in the subject drowning grow constantly, yet there is no scientometric evaluation of the existing literature at the present time. Methods The current study uses classical bibliometric tools and visualizing techniques such as density equalizing mapping to analyse and evaluate the scientific research in the field of drowning. The interpretation of the achieved results is also implemented in the context of the data collection of the WHO. Results All studies related to drowning and listed in the ISI-Web of Science database since 1900 were identified using the search term "drowning". Implementing bibliometric methods, a constant increase in quantitative markers such as number of publications per state, publication language or collaborations as well as qualitative markers such as citations were observed for research in the field of drowning. The combination with density equalizing mapping exposed different global patterns for research productivity and the total number of drowning deaths and drowning rates respectively. Chart techniques were used to illustrate bi- and multilateral research cooperation. Conclusions The present study provides the first scientometric approach that visualizes research activity on the subject of drowning. It can be assumed that the scientific approach to this topic will achieve even greater dimensions because of its continuing actuality. PMID:21999813

  7. Construction of the first high-density genetic linkage map of Salvia miltiorrhiza using specific length amplified fragment (SLAF) sequencing

    PubMed Central

    Liu, Tian; Guo, Linlin; Pan, Yuling; Zhao, Qi; Wang , Jianhua; Song, Zhenqiao

    2016-01-01

    Salvia miltiorrhiza is an important medicinal crop in traditional Chinese medicine (TCM). Knowledge of its genetic foundation is limited because sufficient molecular markers have not been developed, and therefore a high-density genetic linkage map is incomplete. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-throughput strategy for large-scale SNP (Single Nucleotide Polymorphisms) discovery and genotyping based on next generation sequencing (NGS). In this study, genomic DNA extracted from two parents and their 96 F1 individuals was subjected to high-throughput sequencing and SLAF library construction. A total of 155.96 Mb of data containing 155,958,181 pair-end reads were obtained after preprocessing. The average coverage of each SLAF marker was 83.43-fold for the parents compared with 10.36-fold for the F1 offspring. The final linkage map consists of 5,164 SLAFs in 8 linkage groups (LGs) and spans 1,516.43 cM, with an average distance of 0.29 cM between adjacent markers. The results will not only provide a platform for mapping quantitative trait loci but also offer a critical new tool for S. miltiorrhiza biotechnology and comparative genomics as well as a valuable reference for TCM studies. PMID:27040179

  8. Automated, foot-bone registration using subdivision-embedded atlases for spatial mapping of bone mineral density.

    PubMed

    Liu, Lu; Commean, Paul K; Hildebolt, Charles; Sinacore, Dave; Prior, Fred; Carson, James P; Kakadiaris, Ioannis; Ju, Tao

    2013-06-01

    We present an atlas-based registration method for bones segmented from quantitative computed tomography (QCT) scans, with the goal of mapping their interior bone mineral densities (BMDs) volumetrically. We introduce a new type of deformable atlas, called subdivision-embedded atlas, which consists of a control grid represented as a tetrahedral subdivision mesh and a template bone surface embedded within the grid. Compared to a typical lattice-based deformation grid, the subdivision control grid possesses a relatively small degree of freedom tailored to the shape of the bone, which allows efficient fitting onto subjects. Compared with previous subdivision atlases, the novelty of our atlas lies in the addition of the embedded template surface, which further increases the accuracy of the fitting. Using this new atlas representation, we developed an efficient and fully automated pipeline for registering atlases of 12 tarsal and metatarsal bones to a segmented QCT scan of a human foot. Our evaluation shows that the mapping of BMD enabled by the registration is consistent for bones in repeated scans, and the regional BMD automatically computed from the mapping is not significantly different from expert annotations. The results suggest that our improved subdivision-based registration method is a reliable, efficient way to replace manual labor for measuring regional BMD in foot bones in QCT scans.

  9. Construction of the first high-density genetic linkage map of Salvia miltiorrhiza using specific length amplified fragment (SLAF) sequencing.

    PubMed

    Liu, Tian; Guo, Linlin; Pan, Yuling; Zhao, Qi; Wang, Jianhua; Song, Zhenqiao

    2016-04-04

    Salvia miltiorrhiza is an important medicinal crop in traditional Chinese medicine (TCM). Knowledge of its genetic foundation is limited because sufficient molecular markers have not been developed, and therefore a high-density genetic linkage map is incomplete. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-throughput strategy for large-scale SNP (Single Nucleotide Polymorphisms) discovery and genotyping based on next generation sequencing (NGS). In this study, genomic DNA extracted from two parents and their 96 F1 individuals was subjected to high-throughput sequencing and SLAF library construction. A total of 155.96 Mb of data containing 155,958,181 pair-end reads were obtained after preprocessing. The average coverage of each SLAF marker was 83.43-fold for the parents compared with 10.36-fold for the F1 offspring. The final linkage map consists of 5,164 SLAFs in 8 linkage groups (LGs) and spans 1,516.43 cM, with an average distance of 0.29 cM between adjacent markers. The results will not only provide a platform for mapping quantitative trait loci but also offer a critical new tool for S. miltiorrhiza biotechnology and comparative genomics as well as a valuable reference for TCM studies.

  10. Surface Current Density Mapping for Identification of Gastric Slow Wave Propagation

    PubMed Central

    Bradshaw, L. A.; Cheng, L. K.; Richards, W. O.; Pullan, A. J.

    2009-01-01

    The magnetogastrogram records clinically relevant parameters of the electrical slow wave of the stomach noninvasively. Besides slow wave frequency, gastric slow wave propagation velocity is a potentially useful clinical indicator of the state of health of gastric tissue, but it is a difficult parameter to determine from noninvasive bioelectric or biomagnetic measurements. We present a method for computing the surface current density (SCD) from multichannel magnetogastrogram recordings that allows computation of the propagation velocity of the gastric slow wave. A moving dipole source model with hypothetical as well as realistic biomagnetometer parameters demonstrates that while a relatively sparse array of magnetometer sensors is sufficient to compute a single average propagation velocity, more detailed information about spatial variations in propagation velocity requires higher density magnetometer arrays. Finally, the method is validated with simultaneous MGG and serosal EMG measurements in a porcine subject. PMID:19403355

  11. Collinearity Analysis and High-Density Genetic Mapping of the Wheat Powdery Mildew Resistance Gene Pm40 in PI 672538

    PubMed Central

    Fatima, Syeda Akash; Yang, Jiezhi; Chen, Wanquan; Liu, Taiguo; Hu, Yuting; Li, Qing; Guo, Jingwei; Zhang, Min; Lei, Li; Li, Xin; Tang, Shengwen; Luo, Peigao

    2016-01-01

    The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6.18 cM and average spacing between markers of 0.48 cM.Pm40 is flanked by Xwmc335 and BF291338 at genetic distances of 0.58 cM and 0.26 cM, respectively, in deletion bin C-7BS-1-0.27. Comparative genomic analysis based on EST-STS markers established a high level of collinearity of the Pm40 genomic region with a 1.09-Mbp genomic region on Brachypodium chromosome 3, a 1.16-Mbp genomic region on rice chromosome 8, and a 1.62-Mbp genomic region on sorghum chromosome 7. We further anchored the Pm40 target intervals to the wheat genome sequence. A putative linear index of 85 wheat contigs containing 97 genes on 7BS was constructed. In total, 9 genes could be considered as candidates for the resistances to powdery mildew in the target genomic regions, which encoded proteins that were involved in the plant defense and response to pathogen attack. These results will facilitate the development of new markers for map-based cloning and marker-assisted selection of Pm40 in wheat breeding programs. PMID:27755575

  12. Collinearity Analysis and High-Density Genetic Mapping of the Wheat Powdery Mildew Resistance Gene Pm40 in PI 672538.

    PubMed

    Zhong, Shengfu; Ma, Lixia; Fatima, Syeda Akash; Yang, Jiezhi; Chen, Wanquan; Liu, Taiguo; Hu, Yuting; Li, Qing; Guo, Jingwei; Zhang, Min; Lei, Li; Li, Xin; Tang, Shengwen; Luo, Peigao

    2016-01-01

    The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6.18 cM and average spacing between markers of 0.48 cM.Pm40 is flanked by Xwmc335 and BF291338 at genetic distances of 0.58 cM and 0.26 cM, respectively, in deletion bin C-7BS-1-0.27. Comparative genomic analysis based on EST-STS markers established a high level of collinearity of the Pm40 genomic region with a 1.09-Mbp genomic region on Brachypodium chromosome 3, a 1.16-Mbp genomic region on rice chromosome 8, and a 1.62-Mbp genomic region on sorghum chromosome 7. We further anchored the Pm40 target intervals to the wheat genome sequence. A putative linear index of 85 wheat contigs containing 97 genes on 7BS was constructed. In total, 9 genes could be considered as candidates for the resistances to powdery mildew in the target genomic regions, which encoded proteins that were involved in the plant defense and response to pathogen attack. These results will facilitate the development of new markers for map-based cloning and marker-assisted selection of Pm40 in wheat breeding programs.

  13. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS).

    PubMed

    Pootakham, Wirulda; Ruang-Areerate, Panthita; Jomchai, Nukoon; Sonthirod, Chutima; Sangsrakru, Duangjai; Yoocha, Thippawan; Theerawattanasuk, Kanikar; Nirapathpongporn, Kanlaya; Romruensukharom, Phayao; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2015-01-01

    Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.

  14. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)

    PubMed Central

    Pootakham, Wirulda; Ruang-Areerate, Panthita; Jomchai, Nukoon; Sonthirod, Chutima; Sangsrakru, Duangjai; Yoocha, Thippawan; Theerawattanasuk, Kanikar; Nirapathpongporn, Kanlaya; Romruensukharom, Phayao; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2015-01-01

    Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23–1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species. PMID:26074933

  15. Cryo-EM structure of a 3D DNA-origami object

    PubMed Central

    Bai, Xiao-chen; Martin, Thomas G.; Scheres, Sjors H. W.; Dietz, Hendrik

    2012-01-01

    A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback. PMID:23169645

  16. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome.

    PubMed

    Passos, Dario Oliveira; Li, Min; Yang, Renbin; Rebensburg, Stephanie V; Ghirlando, Rodolfo; Jeon, Youngmin; Shkriabai, Nikoloz; Kvaratskhelia, Mamuka; Craigie, Robert; Lyumkis, Dmitry

    2017-01-06

    Like all retroviruses, HIV-1 irreversibly inserts a viral DNA (vDNA) copy of its RNA genome into host target DNA (tDNA). The intasome, a higher-order nucleoprotein complex composed of viral integrase (IN) and the ends of linear vDNA, mediates integration. Productive integration into host chromatin results in the formation of the strand transfer complex (STC) containing catalytically joined vDNA and tDNA. HIV-1 intasomes have been refractory to high-resolution structural studies. We used a soluble IN fusion protein to facilitate structural studies, through which we present a high-resolution cryo-electron microscopy (cryo-EM) structure of the core tetrameric HIV-1 STC and a higher-order form that adopts carboxyl-terminal domain rearrangements. The distinct STC structures highlight how HIV-1 can use the common retroviral intasome core architecture to accommodate different IN domain modules for assembly.

  17. Analysis of low-density lipoprotein-associated proteins using the method of digitized native protein mapping.

    PubMed

    Jin, Ya; Chen, Jin; Wang, Ahui; Zhang, Jun; Chen, Shumin; Manabe, Takashi; Tan, Wen

    2016-07-01

    The method of digitized native protein mapping, combining nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS (in data-independent acquisition mode, or MS(E) ), was improved by using a new MS/MS mode, ion mobility separation enhanced-MS(E) (HDMS(E) ), and applied to analyze the area of human plasma low-density lipoprotein (LDL). An 18 mm × 4.8 mm rectangular area which included LDL on a nondenaturing micro 2D gel of human plasma was grid-cut into 72 square gel pieces and subjected to quantitative LC-MS/MS. Compared with MS(E) , HDMS(E) showed significantly higher performance, by assigning 50% more proteins and detecting each protein in more squares. A total of 253 proteins were assigned with LC-HDMS(E) and the quantity distribution of each was reconstructed as a native protein map. The maps showed that Apo B-100 was the most abundant protein in the grid-cut area, concentrated at pI ca. 5.4-6.1 and apparent mass ca. 1000 kDa, which corresponded to four gel pieces, squares 39-42. An Excel macro was prepared to search protein maps which showed protein quantity peaks localized within this concentrated region of Apo B-100. Twenty-two proteins out of the 252 matched this criterion, in which 19 proteins have been reported to be associated with LDL. This method only requires several microliters of a plasma sample and the principle of the protein separation is totally different from the commonly used ultracentrifugation. The results obtained by this method would provide new insights on the structure and function of LDL.

  18. High-Density Genetic Mapping Identifies New Major Loci for Tolerance to Low-Phosphorus Stress in Soybean

    PubMed Central

    Zhang, Dan; Li, Hongyan; Wang, Jinshe; Zhang, Hengyou; Hu, Zhenbin; Chu, Shanshan; Lv, Haiyan; Yu, Deyue

    2016-01-01

    Phosphorus (P) is essential for all living cells and organisms, and low-P stress represents a major constraint on plant growth and yield worldwide. Soybean is an important economical resource of protein and oil for human and animals, and soybean is also a high-P demand species that is sensitive to low-P stress, which is considered a major constraint on soybean production. However, P efficiency is an important complex quantitative trait involving multiple genes, and the mechanisms underlying soybean P efficiency are largely unknown. Here, we reported the construction of a high-density genetic map using a specific-locus amplified fragment sequencing (SLAF-seq) strategy in soybean. This map, spanning 3020.59 cM in length, contained 6159 markers on 20 chromosomes, with an average distance of 0.49 cM between adjacent markers. Based on this map, 20 loci, including eight novel loci, associated with P efficiency-related traits were identified across multiple years and treatments. The confidence intervals of almost all QTLs were refined significantly, and the accuracy of this map was evidenced by coincident detections of the previously identified P efficiency-related genes GmACP1 and GmPT1. Notably, a highly significant novel QTL located on chromosome 4, q4-2, was identified across traits, years and treatments. Several candidate genes, such as a pectin methylesterase-encoding gene (Glyma.04G214000) and a protein kinase gene (Glyma.13G161900), with significantly differential expression upon low-P stress were considered as promising candidates involved in regulating soybean P efficiency. Markers that tightly associated with P efficiency could be used for marker-assisted selection in a soybean P efficient breeding program. Further, dissection of these QTLs will facilitate gene cloning underlying P efficiency in soybean, and increase our understanding of efficient use of P in enhancing crop yield. PMID:27065041

  19. Conceptual design of a neutron diagnostic for 2-D deuterium power density map reconstruction in MITICA

    NASA Astrophysics Data System (ADS)

    Rebai, M.; Croci, G.; Grosso, G.; Muraro, A.; Perelli Cippo, E.; Tardocchi, M.; Dalla Palma, M.; Pasqualotto, R.; Tollin, M.; Murtas, F.; Cavenago, M.; Gorini, G.

    2017-01-01

    A neutron diagnostic based on Gas Electron Multiplier is proposed for the MITICA beam injector test facility. The detection system is called Close-contact Neutron Emission Surface Mapping (CNESM) and aims at providing the beam intensity profile on the horizontal direction by measuring the neutron emission from the beam dump surface by placing a detector right behind the dump. CNESM uses Gas Electron Multiplier detectors equipped with a cathode that also serves as neutron-proton converter foil, named nGEM. The cathode, made of a thin polythene film and an aluminium film, is designed for detection of neutrons emitted with and angle between 30 and 70 degrees with respect to the deuterium beam axis. Neutron scattering in the dump and neutron detection with the nGEM were simulated with the MCNP6.1.1 code.

  20. Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei

    PubMed Central

    Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai

    2015-01-01

    The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species. PMID:26503227

  1. Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei.

    PubMed

    Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai

    2015-10-27

    The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species.

  2. Bacterial Meningitis: A Density-Equalizing Mapping Analysis of the Global Research Architecture

    PubMed Central

    Pleger, Niklas; Kloft, Beatrix; Quarcoo, David; Zitnik, Simona; Mache, Stefanie; Klingelhoefer, Doris; Groneberg, David A

    2014-01-01

    Bacterial meningitis is caused by a variety of pathogens and displays an important public health threat all over the world. Despite the necessity to develop customized public health-related research projects, a thorough study of global meningitis research is not present, so far. Therefore, the aim of this study was a combined density-equalizing and scientometric study. To evaluate the scientific efforts of bibliometric methods, density-equalizing algorithms and large-scale data analysis of the Web of Science were applied in the period between 1900 and 2007. From this, 7998 publications on bacterial meningitis have been found. With a number of 2698, most publications have been written by U.S. authors, followed by the UK (912), Germany (749) and France (620). This dominance can also be shown in the international cooperation. The specific citation analyses reveal that the nation with the highest average citation rate (citations per publications) was Norway (26.36), followed by Finland (24.16) and the U.S. (24.06). This study illustrates the architecture of global research on bacterial meningitis and points to the need for customized research programs with a focus on local public health issues in countries with a low development index, but high incidences, to target this global public health problem. PMID:25272079

  3. High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers

    PubMed Central

    Wu, Jun; Li, Lei-Ting; Li, Meng; Khan, M. Awais; Li, Xiu-Gen; Chen, Hui; Yin, Hao; Zhang, Shao-Ling

    2014-01-01

    Pear (Pyrus spp) is an important fruit crop, grown in all temperate regions of the world, with global production ranked after grape and apples among deciduous tree crops. A high-density linkage map is a valuable tool for fine mapping quantitative trait loci (QTL) and map-based gene cloning. In this study, we firstly constructed a high-density linkage map of pear using SNPs integrated with SSRs, developed by the rapid and robust technology of restriction-associated DNA sequencing (RADseq). The linkage map consists of 3143 SNP markers and 98 SSRs, 3241 markers in total, spanning 2243.4 cM, with an average marker distance of 0.70 cM. Anchoring SSRs were able to anchor seventeen linkage groups to their corresponding chromosomes. Based on this high-density integrated pear linkage map and two years of fruit phenotyping, a total of 32 potential QTLs for 11 traits, including length of pedicel (LFP), single fruit weight (SFW), soluble solid content (SSC), transverse diameter (TD), vertical diameter (VD), calyx status (CS), flesh colour (FC), juice content (JC), number of seeds (NS), skin colour (SC), and skin smooth (SS), were identified and positioned on the genetic map. Among them, some important fruit-related traits have for the first time been identified, such as calyx status, length of pedicel, and flesh colour, and reliable localization of QTLs were verified repeatable. This high-density linkage map of pear is a worthy reference for mapping important fruit traits, QTL identification, and comparison and combination of different genetic maps. PMID:25129128

  4. Doppler Spectrometry for Ultrafast Temporal Mapping of Density Dynamics in Laser-Induced Plasmas

    SciTech Connect

    Mondal, S.; Lad, Amit D.; Ahmed, Saima; Narayanan, V.; Pasley, J.; Rajeev, P. P.; Robinson, A. P. L.; Kumar, G. Ravindra

    2010-09-03

    We present high resolution measurements of the ultrafast temporal dynamics of the critical surface in moderately overdense, hot plasma by using two-color, pump-probe Doppler spectrometry. Our measurements clearly capture the initial inward motion of the plasma inside the critical surface of the pump laser which is followed by outward expansion. The measured instantaneous velocity and acceleration profiles are very well reproduced by a hybrid simulation that uses a 1D electromagnetic particle-in-cell simulation for the initial evolution and a hydrodynamics simulation for the later times. The combination of high temporal resolution and dynamic range in our measurements clearly provides quantitative unraveling of the dynamics in this important region, enabling this as a powerful technique to obtain ultrafast snapshots of plasma density and temperature profiles for providing benchmarks for simulations.

  5. Refining a model electron-density map via the Phantom Derivative method.

    PubMed

    Burla, Maria Cristina; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Polidori, Giampiero

    2015-09-01

    The Phantom Derivative (PhD) method [Giacovazzo (2015), Acta Cryst. A71, 483-512] has recently been described for ab initio and non-ab initio phasing. It is based on the random generation of structures with the same unit cell and the same space group as the target structure (called ancil structures), which are used to create derivatives devoid of experimental diffraction amplitudes. In this paper, the non-ab initio variant of the method was checked using phase sets obtained by molecular-replacement techniques as a starting point for phase extension and refinement. It has been shown that application of PhD is able to extend and refine phases in a way that is competitive with other electron-density modification techniques.

  6. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis.

    PubMed

    Eyre, Steve; Bowes, John; Diogo, Dorothée; Lee, Annette; Barton, Anne; Martin, Paul; Zhernakova, Alexandra; Stahl, Eli; Viatte, Sebastien; McAllister, Kate; Amos, Christopher I; Padyukov, Leonid; Toes, Rene E M; Huizinga, Tom W J; Wijmenga, Cisca; Trynka, Gosia; Franke, Lude; Westra, Harm-Jan; Alfredsson, Lars; Hu, Xinli; Sandor, Cynthia; de Bakker, Paul I W; Davila, Sonia; Khor, Chiea Chuen; Heng, Khai Koon; Andrews, Robert; Edkins, Sarah; Hunt, Sarah E; Langford, Cordelia; Symmons, Deborah; Concannon, Pat; Onengut-Gumuscu, Suna; Rich, Stephen S; Deloukas, Panos; Gonzalez-Gay, Miguel A; Rodriguez-Rodriguez, Luis; Ärlsetig, Lisbeth; Martin, Javier; Rantapää-Dahlqvist, Solbritt; Plenge, Robert M; Raychaudhuri, Soumya; Klareskog, Lars; Gregersen, Peter K; Worthington, Jane

    2012-12-01

    Using the Immunochip custom SNP array, which was designed for dense genotyping of 186 loci identified through genome-wide association studies (GWAS), we analyzed 11,475 individuals with rheumatoid arthritis (cases) of European ancestry and 15,870 controls for 129,464 markers. We combined these data in a meta-analysis with GWAS data from additional independent cases (n = 2,363) and controls (n = 17,872). We identified 14 new susceptibility loci, 9 of which were associated with rheumatoid arthritis overall and five of which were specifically associated with disease that was positive for anticitrullinated peptide antibodies, bringing the number of confirmed rheumatoid arthritis risk loci in individuals of European ancestry to 46. We refined the peak of association to a single gene for 19 loci, identified secondary independent effects at 6 loci and identified association to low-frequency variants at 4 loci. Bioinformatic analyses generated strong hypotheses for the causal SNP at seven loci. This study illustrates the advantages of dense SNP mapping analysis to inform subsequent functional investigations.

  7. A Spatially Focused Method for High Density Electrode-Based Functional Brain Mapping Applications.

    PubMed

    Chang, Chih-Wei; Hsin, Yue-Loong; Liu, Wentai

    2016-10-01

    Mapping the electric field of the brain with electrodes benefits from its superior temporal resolution but is prone to low spatial resolution property comparing with other modalities such as fMRI, which can directly impact the precision of clinical diagnosis. Simulations show that dense arrays with straightforwardly miniaturized electrodes in terms of size and pitch may not improve the spatial resolution but only strengthen the cross coupling between adjacent channels due to volume conduction. We present a new spatially focused method to improve the electrode spatial selectivity and consequently suppress the neural signal coupling from the sources in the vicinity. Compared with existing spatial filtering methods with fixed coefficients, the proposed method is adaptively optimized for the geometric parameters of the recording electrode arrays, including electrode size, pitch and source depth. The effective spatial bandwidth, characterized as Radius of Half Power, can be reduced by about 70% for ECoG and the case of distant sources scenarios. The proposed method has been applied to the analysis of high-frequency oscillations (HFOs) in seizures to study the ictal pathway in the epileptogenic region. The results reveal lucid HFO wavefront propagation in both preictal and ictal stages due to a 75% reduction in the coupling effect. The results also show that a specific power threshold of preictal HFOs is needed in order to initiate an epileptic seizure. This demonstrates that our method indeed facilitates the investigation of complex neurobiological signals preprocessing applications.

  8. A Spatially Focused Method for High Density Electrode-Based Functional Brain Mapping Applications.

    PubMed

    Chang, Chih-Wei; Hsin, Yue-Loong; Liu, Wentai

    2016-03-07

    Mapping the electric field of the brain with electrodes benefits from its superior temporal resolution but is prone to low spatial resolution property comparing with other modalities such as fMRI, which can directly impact the precision of clinical diagnosis. Simulations show that dense arrays with straightforwardly miniaturized electrodes in terms of size and pitch may not improve the spatial resolution but only strengthen the cross coupling between adjacent channels due to volume conduction. We present a new spatially focused method to improve the electrode spatial selectivity and consequently suppress the neural signal coupling from the sources in the vicinity. Compared with existing spatial filtering methods with fixed coefficients, the proposed method is adaptively optimized for the geometric parameters of the recording electrode arrays, including electrode size, pitch and source depth. The effective spatial bandwidth, characterized as Radius of Half Power, can be reduced by about 70% for ECoG and the case of distant sources scenarios. The proposed method has been applied to the analysis of high-frequency oscillations (HFOs) in seizures to study the ictal pathway in the epileptogenic region. The results reveal lucid HFO wavefront propagation in both preictal and ictal stages due to a 75% reduction in the coupling effect. The results also show that a specific power threshold of preictal HFOs is needed in order to initiate an epileptic seizure. This demonstrates that our method indeed facilitates the investigation of complex neurobiological signals preprocessing applications.

  9. Mapping the polarity and stimulus density requirements for T-cell activation

    NASA Astrophysics Data System (ADS)

    Wei, Xunbin; Krasieva, Tatiana B.; Zhang, Zhanxiang; Negulescu, Paul A.; Sun, Chung-Ho; Berns, Michael W.; Cahalan, Michael D.; Tromberg, Bruce J.

    1998-08-01

    T-cell contact with antigen-presenting cells (APC) initiates an activation cascade which includes an increase in T-cell intracellular calcium [(Ca2+)i] and leads to T-cell proliferation and differentiation. Although T-cell/APC physical contact is required for an immune response, little is known about the patterns of cellular interaction and their relation to activation. We have combined fluorescence spectroscopy and imaging with optical manipulation to investigate the contact requirements for T-cell activation, using optical tweezers to control the orientation of T- cell/APC pairs and fluorescence microscopy to measure the subsequent (Ca2+)i response, detected as an emission shift from the combination of fura-red and oregon- green, two cytoplasmic (Ca2+) indicators. APCs or beads coated with antibodies to the T-cell receptor (TCR) are trapped with a near-infrared titanium-sapphire laser and placed at different locations along the T-cell, which has a polarized appearance defined by the shape and direction of crawling (2-5 micrometers /min). T cells contacted with antigen- presenting cells or antibody-coated beads entered a dynamic and reproducible program in the first 10 - 20 mins, including (Ca2+)i increase, changes in shape and motility, engulfment, and stable contact. T cells presented with antigen at the leading edge had a higher probability of responding (85%) and a shorter latency of response (50 secs) than those contacting APCs or beads with their trailing end (APCs: 30%, 150 secs; beads: 6%, 300 secs). Alterations in antibody density, quantified by FACS analysis, and bead size were used to determine the spatial requirements for T cell activation and the minimum number of receptors which must be engaged in order to transmit a positive signal. Preliminary data show that T cell responses [response percentage, latency and (Ca2+)i pattern] depend on both antibody density and bead size.

  10. Magnetic Resonance Q Mapping Reveals a Decrease in Microvessel Density in the arcAβ Mouse Model of Cerebral Amyloidosis

    PubMed Central

    Ielacqua, Giovanna D.; Schlegel, Felix; Füchtemeier, Martina; Xandry, Jael; Rudin, Markus; Klohs, Jan

    2016-01-01

    Alterations in density and morphology of the cerebral microvasculature have been reported to occur in Alzheimer's disease patients and animal models of the disease. In this study we compared magnetic resonance imaging (MRI) techniques for their utility to detect age-dependent changes of the cerebral vasculature in the arcAβ mouse model of cerebral amyloidosis. Dynamic susceptibility contrast (DSC)-MRI was performed by tracking the passage of a superparamagnetic iron oxide nanoparticle in the brain with dynamic gradient echo planar imaging (EPI). From this measurements relative cerebral blood volume [rCBV(DSC)] and relative cerebral blood flow (rCBF) were estimated. For the same animal maps of the relaxation shift index Q were computed from high resolution gradient echo and spin echo data that were acquired before and after superparamagnetic iron oxide (SPIO) nanoparticle injection. Q-values were used to derive estimates of microvessel density. The change in the relaxation rates ΔR2* obtained from pre- and post-contrast gradient echo data was used for the alternative determination of rCBV [rCBV(ΔR2*)]. Linear mixed effects modeling found no significant association between rCBV(DSC), rCBV(ΔR2*), rCBF, and Q with genotype in 13-month old mice [compared to age-matched non-transgenic littermates (NTLs)] for any of the evaluated brain regions. In 24-month old mice there was a significant association for rCBV(DSC) with genotype in the cerebral cortex, and for rCBV(ΔR2*) in the cerebral cortex and cerebellum. For rCBF there was a significant association in the cerebellum but not in other brain regions. Q-values in the olfactory bulb, cerebral cortex, striatum, hippocampus, and cerebellum in 24-month old mice were significantly associated with genotype. In those regions Q-values were reduced between 11 and 26% in arcAβ mice compared to age-matched NTLs. Vessel staining with CD31 immunohistochemistry confirmed a reduction of microvessel density in the old arcAβ mice

  11. Magnetic Resonance Q Mapping Reveals a Decrease in Microvessel Density in the arcAβ Mouse Model of Cerebral Amyloidosis.

    PubMed

    Ielacqua, Giovanna D; Schlegel, Felix; Füchtemeier, Martina; Xandry, Jael; Rudin, Markus; Klohs, Jan

    2015-01-01

    Alterations in density and morphology of the cerebral microvasculature have been reported to occur in Alzheimer's disease patients and animal models of the disease. In this study we compared magnetic resonance imaging (MRI) techniques for their utility to detect age-dependent changes of the cerebral vasculature in the arcAβ mouse model of cerebral amyloidosis. Dynamic susceptibility contrast (DSC)-MRI was performed by tracking the passage of a superparamagnetic iron oxide nanoparticle in the brain with dynamic gradient echo planar imaging (EPI). From this measurements relative cerebral blood volume [rCBV(DSC)] and relative cerebral blood flow (rCBF) were estimated. For the same animal maps of the relaxation shift index Q were computed from high resolution gradient echo and spin echo data that were acquired before and after superparamagnetic iron oxide (SPIO) nanoparticle injection. Q-values were used to derive estimates of microvessel density. The change in the relaxation rates [Formula: see text] obtained from pre- and post-contrast gradient echo data was used for the alternative determination of rCBV [rCBV([Formula: see text])]. Linear mixed effects modeling found no significant association between rCBV(DSC), rCBV([Formula: see text]), rCBF, and Q with genotype in 13-month old mice [compared to age-matched non-transgenic littermates (NTLs)] for any of the evaluated brain regions. In 24-month old mice there was a significant association for rCBV(DSC) with genotype in the cerebral cortex, and for rCBV([Formula: see text]) in the cerebral cortex and cerebellum. For rCBF there was a significant association in the cerebellum but not in other brain regions. Q-values in the olfactory bulb, cerebral cortex, striatum, hippocampus, and cerebellum in 24-month old mice were significantly associated with genotype. In those regions Q-values were reduced between 11 and 26% in arcAβ mice compared to age-matched NTLs. Vessel staining with CD31 immunohistochemistry confirmed a

  12. The chronoarchitecture of human sexual desire: a high-density electrical mapping study.

    PubMed

    Ortigue, Stephanie; Bianchi-Demicheli, Francesco

    2008-11-01

    Recent neuroimaging research suggests that human sexual desire (SD) recruits both the limbic system and higher-order cognitive brain areas. Because of the temporal limitation of this technique, the chronoarchitecture of SD remains however unresolved. Here, we investigated the spatio-temporal dynamics of SD by combining a behavioral desire decision task with high-density visual event-related potential (VEP) recordings and brain source estimations. VEPs were recorded from thirteen healthy participants when presented with pictures from two different stimulus categories (i.e., high and low desirability). In agreement with the literature, behavioral results showed that participants were faster to rate non-desired stimuli than desired stimuli (p=0.028). Electrophysiological results extended these behavioral data. Group-averaged VEPs peaked at 90 to 140 ms (P100), at 142 to 220 ms (N200), and at 222 to 360 ms (P300). Desired stimuli (DS) were distinguished from non-desired stimuli (NDS) over the N200 period, notably from 142 to 187 ms. Over this time period, DS processing was characterized by a significant scalp potential field. Although both conditions (DS and NDS) showed the recruitment of the occipito-temporal region (including the extrastriate body area, EBA), LAURA source estimation of the DS scalp potential field revealed a more right-lateralized current source density maximum in the posterior superior temporal sulcus (STS) extending to the temporo-parietal junction (TPJ). The recruitment of STS and TPJ for desired stimuli indicates that these brain areas, known to be respectively involved in social cognition, attention, integration of body-related information and self-processing, play a crucial role for the coding of desirability of visual sexual human stimuli within the first 200 ms after stimulus onset. These findings support the hypothesis that complex cognitive processing for desire occurs much faster than previously thought and open new perspectives with

  13. The link between diffusion MRI and tumor heterogeneity: Mapping cell eccentricity and density by diffusional variance decomposition (DIVIDE).

    PubMed

    Szczepankiewicz, Filip; van Westen, Danielle; Englund, Elisabet; Westin, Carl-Fredrik; Ståhlberg, Freddy; Lätt, Jimmy; Sundgren, Pia C; Nilsson, Markus

    2016-11-15

    only to cell density variance. The variance in meningiomas was caused primarily by microscopic anisotropy (mean±s.d.) MKA=1.11±0.33 vs MKI=0.44±0.20 (p<10(-3)), whereas in the gliomas, it was mostly caused by isotropic heterogeneity MKI=0.57±0.30 vs MKA=0.26±0.11 (p<0.05). In conclusion, DIVIDE allows non-invasive mapping of parameters that reflect variable cell eccentricity and density. These results constitute convincing evidence that a link exists between specific aspects of tissue heterogeneity and parameters from dMRI. Decomposing effects of microscopic anisotropy and isotropic heterogeneity facilitates an improved interpretation of tumor heterogeneity as well as diffusion anisotropy on both the microscopic and macroscopic scale.

  14. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.

    PubMed

    Talukder, Zahirul I; Gong, Li; Hulke, Brent S; Pegadaraju, Venkatramana; Song, Qijian; Schultz, Quentin; Qi, Lili

    2014-01-01

    A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.

  15. Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species.

    PubMed

    Hill, Theresa; Ashrafi, Hamid; Chin-Wo, Sebastian Reyes; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard; Van Deynze, Allen

    2015-09-08

    Our ability to assemble complex genomes and construct ultradense genetic maps now allows the determination of recombination rates, translocations, and the extent of genomic collinearity between populations, species, and genera. We developed two ultradense genetic linkage maps for pepper from single-position polymorphisms (SPPs) identified de novo with a 30,173 unigene pepper genotyping array. The Capsicum frutescens × C. annuum interspecific and the C. annuum intraspecific genetic maps were constructed comprising 16,167 and 3,878 unigene markers in 2108 and 783 genetic bins, respectively. Accuracies of marker groupings and orders are validated by the high degree of collinearity between the two maps. Marker density was sufficient to locate the chromosomal breakpoint resulting in the P1/P8 translocation between C. frutescens and C. annuum to a single bin. The two maps aligned to the pepper genome showed varying marker density along the chromosomes. There were extensive chromosomal regions with suppressed recombination and reduced intraspecific marker density. These regions corresponded to the pronounced nonrecombining pericentromeric regions in tomato, a related Solanaceous species. Similar to tomato, the extent of reduced recombination appears to be more pronounced in pepper than in other plant species. Alignment of maps with the tomato and potato genomes shows the presence of previously known translocations and a translocation event that was not observed in previous genetic maps of pepper.

  16. A high-density genetic map identifies a novel major QTL for boron efficiency in oilseed rape (Brassica napus L.).

    PubMed

    Zhang, Didi; Hua, Yingpeng; Wang, Xiaohua; Zhao, Hua; Shi, Lei; Xu, Fangsen

    2014-01-01

    Low boron (B) seriously limits the growth of oilseed rape (Brassica napus L.), a high B demand species that is sensitive to low B conditions. Significant genotypic variations in response to B deficiency have been observed among B. napus cultivars. To reveal the genetic basis for B efficiency in B. napus, quantitative trait loci (QTLs) for the plant growth traits, B uptake traits and the B efficiency coefficient (BEC) were analyzed using a doubled haploid (DH) population derived from a cross between a B-efficient parent, Qingyou 10, and a B-inefficient parent, Westar 10. A high-density genetic map was constructed based on single nucleotide polymorphisms (SNPs) assayed using Brassica 60 K Infinium BeadChip Array, simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). The linkage map covered a total length of 2139.5 cM, with 19 linkage groups (LGs) and an average distance of 1.6 cM between adjacent markers. Based on hydroponic evaluation of six B efficiency traits measured in three separate repeated trials, a total of 52 QTLs were identified, accounting for 6.14-46.27% of the phenotypic variation. A major QTL for BEC, qBEC-A3a, was co-located on A3 with other QTLs for plant growth and B uptake traits under low B stress. Using a subset of substitution lines, qBEC-A3a was validated and narrowed down to the interval between CNU384 and BnGMS436. The results of this study provide a novel major locus located on A3 for B efficiency in B. napus that will be suitable for fine mapping and marker-assisted selection breeding for B efficiency in B. napus.

  17. A High-Density Genetic Map Identifies a Novel Major QTL for Boron Efficiency in Oilseed Rape (Brassica napus L.)

    PubMed Central

    Wang, Xiaohua; Zhao, Hua; Shi, Lei; Xu, Fangsen

    2014-01-01

    Low boron (B) seriously limits the growth of oilseed rape (Brassica napus L.), a high B demand species that is sensitive to low B conditions. Significant genotypic variations in response to B deficiency have been observed among B. napus cultivars. To reveal the genetic basis for B efficiency in B. napus, quantitative trait loci (QTLs) for the plant growth traits, B uptake traits and the B efficiency coefficient (BEC) were analyzed using a doubled haploid (DH) population derived from a cross between a B-efficient parent, Qingyou 10, and a B-inefficient parent, Westar 10. A high-density genetic map was constructed based on single nucleotide polymorphisms (SNPs) assayed using Brassica 60 K Infinium BeadChip Array, simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). The linkage map covered a total length of 2139.5 cM, with 19 linkage groups (LGs) and an average distance of 1.6 cM between adjacent markers. Based on hydroponic evaluation of six B efficiency traits measured in three separate repeated trials, a total of 52 QTLs were identified, accounting for 6.14–46.27% of the phenotypic variation. A major QTL for BEC, qBEC-A3a, was co-located on A3 with other QTLs for plant growth and B uptake traits under low B stress. Using a subset of substitution lines, qBEC-A3a was validated and narrowed down to the interval between CNU384 and BnGMS436. The results of this study provide a novel major locus located on A3 for B efficiency in B. napus that will be suitable for fine mapping and marker-assisted selection breeding for B efficiency in B. napus. PMID:25375356

  18. Three-dimensional T(1), T(2) and proton density mapping with inversion recovery balanced SSFP.

    PubMed

    Newbould, Rexford D; Skare, Stefan T; Alley, Marcus T; Gold, Garry E; Bammer, Roland

    2010-11-01

    By combining a balanced steady-state free precession (bSSFP) readout with an initial inversion pulse, all three contrast parameters, T(1), T(2) and proton density (M(0)), may be rapidly calculated from the signal progression in time. However, here it is shown that this technique is quite sensitive to variation in the applied transmit RF (B(1)) field, leading to pronounced errors in calculated values. Two-dimensional (2D) acquisitions are taxed to accurately quantify the relaxation, as the short RF pulses required by SSFP's rapid TR contain a broad spectrum of excitation angles. A 3D excitation using a large diameter excitation coil was able to correctly quantify the parameters. While the extreme B(1) sensitivity was previously problematic and has precluded use of IR-bSSFP for relaxometry, in this work these obstacles were significantly reduced, allowing the rapid quantification of T(1), T(2) and M(0). The results may further be used to simulate image contrast from common sequences, such as a T(1)-weighted or fluid-attenuated inversion recovery (FLAIR) examination.

  19. Executive Dysfunction and Reward Dysregulation: A High-Density Electrical Mapping Study in Cocaine Abusers

    PubMed Central

    Morie, Kristen P.; De Sanctis, Pierfilippo; Garavan, Hugh; Foxe, John J.

    2015-01-01

    Executive function deficits and reward dysregulation, which mainly manifests as anhedonia, are well documented in drug abusers. We investigated specific aspects of executive function (inhibitory control and cognitive control), as well as anhedonia, in a cohort of current cocaine abusers in order to ascertain to what extent these factors are associated with more severe drug dependence. Participants filled out questionnaires relating to anhedonia and their addiction history. Participants also performed a response inhibition task while high-density event-related potentials (ERPs) were recorded. Electrophysiological responses to successful inhibitions (N2/P3 components) and to commission errors (ERN/Pe components) were compared between 23 current users of cocaine and 27 non-using controls. A regression model was performed to determine the association of our measures of reward dysregulation and executive function with addiction severity. As expected, cocaine users performed more poorly than controls on the inhibitory control task and showed significant electrophysiological differences. They were also generally more anhedonic than controls. Higher levels of anhedonia were associated with more severe substance use, whereas the level of executive dysfunction was not associated with more severe substance use. However, N2 amplitude was associated with duration of drug use. Further, inhibitory control and anhedonia were correlated, but only in controls. These data suggest that while executive dysfunction characterizes drug abuse, it is anhedonia, independent of executive dysfunction, that is most strongly associated with more severe use. PMID:24911989

  20. Three Dimensional T1, T2, and Proton Density Mapping with Inversion Recovery Balanced SSFP

    PubMed Central

    Newbould, Rexford D.; Skare, Stefan T.; Alley, Marcus T.; Gold, Garry E.; Bammer, Roland

    2010-01-01

    By combining a bSSFP readout with an initial inversion pulse, all three contrast parameters, T1, T2, and proton density (M0), may be rapidly calculated from the signal progression in time. However, here it is shown that this technique is quite sensitive to variation in the applied transmit RF (B1) field, leading to pronounced errors in calculated values. 2D acquisitions are taxed to accurately quantify the relaxation, as the short RF pulses required by SSFP's rapid TR contain a broad spectrum of excitation angles. A 3D excitation using a large diameter excitation coil was able to correctly quantify the parameters. While the extreme B1 sensitivity was previously problematic, and has precluded use of IR-bSSFP for relaxometry, in this work these obstacles were significantly reduced, allowing the rapid quantification of T1, T2, and M0. The results may further be used to simulate image contrast from common sequences, such as a T1-weighted or FLAIR examination. PMID:20692784

  1. Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.).

    PubMed

    Liu, Dexin; Liu, Fang; Shan, Xiaoru; Zhang, Jian; Tang, Shiyi; Fang, Xiaomei; Liu, Xueying; Wang, Wenwen; Tan, Zhaoyun; Teng, Zhonghua; Zhang, Zhengsheng; Liu, Dajun

    2015-10-01

    Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5-62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.

  2. Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance

    PubMed Central

    Schep, Daniel G.; Rubinstein, John L.

    2016-01-01

    Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases. PMID:26951669

  3. Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance.

    PubMed

    Schep, Daniel G; Zhao, Jianhua; Rubinstein, John L

    2016-03-22

    Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases.

  4. A High-Density Genetic Map with Array-Based Markers Facilitates Structural and Quantitative Trait Locus Analyses of the Common Wheat Genome

    PubMed Central

    Iehisa, Julio Cesar Masaru; Ohno, Ryoko; Kimura, Tatsuro; Enoki, Hiroyuki; Nishimura, Satoru; Okamoto, Yuki; Nasuda, Shuhei; Takumi, Shigeo

    2014-01-01

    The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map. PMID:24972598

  5. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    SciTech Connect

    Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

    2015-03-01

    A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

  6. Monolayer-crystal streptavidin support films provide an internal standard of cryo-EM image quality.

    PubMed

    Han, Bong-Gyoon; Watson, Zoe; Cate, Jamie H D; Glaeser, Robert M

    2017-03-01

    Analysis of images of biotinylated Escherichia coli 70S ribosome particles, bound to streptavidin affinity grids, demonstrates that the image-quality of particles can be predicted by the image-quality of the monolayer crystalline support film. The quality of the Thon rings is also a good predictor of the image-quality of particles, but only when images of the streptavidin crystals extend to relatively high resolution. When the estimated resolution of streptavidin was 5Å or worse, for example, the ribosomal density map obtained from 22,697 particles went to only 9.5Å, while the resolution of the map reached 4.0Å for the same number of particles, when the estimated resolution of streptavidin crystal was 4Å or better. It thus is easy to tell which images in a data set ought to be retained for further work, based on the highest resolution seen for Bragg peaks in the computed Fourier transforms of the streptavidin component. The refined density map obtained from 57,826 particles obtained in this way extended to 3.6Å, a marked improvement over the value of 3.9Å obtained previously from a subset of 52,433 particles obtained from the same initial data set of 101,213 particles after 3-D classification. These results are consistent with the hypothesis that interaction with the air-water interface can damage particles when the sample becomes too thin. Streptavidin monolayer crystals appear to provide a good indication of when that is the case.

  7. A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12

    PubMed Central

    Talukder, Zahirul I.; Gong, Li; Hulke, Brent S.; Pegadaraju, Venkatramana; Song, Qijian; Schultz, Quentin; Qi, Lili

    2014-01-01

    A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping. PMID:25014030

  8. Chromosomal mapping of human genes by radioactive hybridization of cDNAs to Centre d'Etude du Polymorphisme humain high density gridded filter sets.

    PubMed

    Claas, A; Savelyeva, L; Pillmann, A; Schwab, M

    2000-08-01

    Chromosomal assignment of human transcribed sequences has been done mainly by high throughput genome analysis in specialized genome centres and, in a more classical fashion, by fluorescence in-site hybridization (FISH) analysis. Not every laboratory has the ability to map cDNAs by FISH analysis. We here report a rapid mapping approach that is based on the hybridization of cDNA probes to high density gridded Centre d'Etude du Polymorphisme Humain filters followed by subsequent computational analysis by database searches in the internet. Not only transcribed sequences but also genomic DNA could be subjected to this mapping approach. The presented approach allows to map human transcribed and genomic DNAs within 1-3 days and with a high level of resolution that will constantly increase in line with the incorporation of data deriving from high throughput genome mapping.

  9. Constructing a high-density linkage map for Gossypium hirsutum × Gossypium barbadense and identifying QTLs for lint percentage.

    PubMed

    Shi, Yuzhen; Li, Wentan; Li, Aiguo; Ge, Ruihua; Zhang, Baocai; Li, Junzhi; Liu, Guangping; Li, Junwen; Liu, Aiying; Shang, Haihong; Gong, Juwu; Gong, Wankui; Yang, Zemao; Tang, Feiyü; Liu, Zhi; Zhu, Weiping; Jiang, Jianxiong; Yu, Xiaonan; Wang, Tao; Wang, Wei; Chen, Tingting; Wang, Kunbo; Zhang, Zhengsheng; Yuan, Youlu

    2015-05-01

    To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high-density simple sequence repeat (SSR) genetic linkage map was developed from a BC1 F1 population of Gossypium hirsutum × Gossypium barbadense. The map comprised 2,292 loci and covered 5115.16 centiMorgan (cM) of the cotton AD genome, with an average marker interval of 2.23 cM. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five published high-density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty-six quantitative trait loci (QTLs) for lint percentage (LP) were identified on nine chromosomes. Nine stable or common QTLs could be used for marker-assisted selection. Fifty percent of the QTLs were from G. barbadense and increased LP by 1.07%-2.41%. These results indicated that the map could be used for screening chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality.

  10. High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

    PubMed Central

    Cui, Z; Hui, M; Liu, Y; Song, C; Li, X; Li, Y; Liu, L; Shi, G; Wang, S; Li, F; Zhang, X; Liu, C; Xiang, J; Chu, K H

    2015-01-01

    The sex determination system in crabs is believed to be XY-XX from karyotypy, but centromeres could not be identified in some chromosomes and their morphology is not completely clear. Using quantitative trait locus mapping of the gender phenotype, we revealed a ZW-ZZ sex determination system in Eriocheir sinensis and presented a high-density linkage map covering ~98.5% of the genome, with 73 linkage groups corresponding to the haploid chromosome number. All sex-linked markers in the family we used were located on a single linkage group, LG60, and sex linkage was confirmed by genome-wide association studies (GWAS). Forty-six markers detected by GWAS were heterozygous and segregated only in the female parent. The female LG60 was thus the putative W chromosome, with the homologous male LG60 as the Z chromosome. The putative Z and W sex chromosomes were identical in size and carried many homologous loci. Sex ratio (5:1) skewing towards females in induced triploids using unrelated animals also supported a ZW-ZZ system. Transcriptome data were used to search for candidate sex-determining loci, but only one LG60 gene was identified as an ankyrin-2 gene. Double sex- and mab3-related transcription factor 1 (Dmrt1), a Z-linked gene in birds, was located on a putative autosome. With complete genome sequencing and transcriptomic data, more genes on putative sex chromosomes will be characterised, thus leading towards a comprehensive understanding of the sex determination and differentiation mechanisms of E. sinensis, and decapod crustaceans in general. PMID:25873149

  11. A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map.

    PubMed

    Cai, Guangqin; Yang, Qingyong; Yi, Bin; Fan, Chuchuan; Edwards, David; Batley, Jacqueline; Zhou, Yongming

    2014-01-01

    Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.

  12. VizieR Online Data Catalog: HI4PI spectra and column density maps (HI4PI team+, 2016)

    NASA Astrophysics Data System (ADS)

    Hi4PI Collaboration; Ben Bekhti, N.; Floeer, L.; Keller, R.; Kerp, J.; Lenz, D.; Winkel, B.; Bailin, J.; Calabretta, M. R.; Dedes, L.; Ford, H. A.; Gibson, B. K.; Haud, U.; Janowiecki, S.; Kalberla, P. M. W.; Lockman, F. J.; McClure-Griffiths, N. M.; Murphy, T.; Nakanishi, H.; Pisano, D. J.; Staveley-Smith, L.

    2016-09-01

    The HI4PI data release comprises 21-cm neutral atomic hydrogen data of the Milky Way (-600km/s0°; -470km/smap projections, AIT, CAR, MOL, and SFL; see world-coordinate-system, WCS, references: Greisen & Calabretta, 2002A&A...395.1061G, Calabretta & Greisen, 2002A&A...395.1077C, Greisen et al., 2006A&A...446..747G (2) Smaller FITS data cubes, each having a size of about 20x20 sq.deg. For convenience, we provide four different map projections, CAR, SFL, SIN, and TAN (again see WCS references). Note, size in longitude is 20° in absolute coordinates for CAR projection, and 20° true-angular size for SFL, SIN, and TAN projections. Again, Equatorial and Galactic coordinate systems are provided. (3) FITS binary tables containing lists of spectra sampled on a HealPIX grid (nside=1024, Galactic coordinates, Ring indexing scheme, Gorski et al., 2005ApJ...622..759G). To make handling of the data easier, the table is split into smaller files. Each of these contains spectra belonging to one of the 192 base/parent pixels of the nside=4 pixelization. For convenience, the binary tables also contain EQ2000 and Galactic coordinate positions for each individual spectrum, as well as the associated HealPIX index. Furthermore, we provide the full-sky HI column density distribution, both, in a (1) HealPIX-grid binary table (nside=1024, Galactic coordinates, Ring indexing scheme), and (2) Standard FITS 2D images in four map projections, AIT, CAR, MOL, and SFL. Various velocity intervals were applied to calculate NHI. Equatorial and Galactic coordinate systems are provided. (16 data files).

  13. Uncoating Mechanism of Carnation Mottle Virus Revealed by Cryo-EM Single Particle Analysis

    PubMed Central

    Wang, Chun-Yan; Zhang, Qin-Fen; Gao, Yuan-Zhu; Xie, Li; Li, Hong-Mei; Hong, Jian; Zhang, Chuan-Xi

    2015-01-01

    Genome uncoating is a prerequisite for the successful infection of plant viruses in host plants. Thus far, little is known about the genome uncoating of the Carnation mottle virus (CarMV). Here, we obtained two reconstructions of CarMV at pH7 in the presence (Ca-pH7) and absence (EDTA-pH7) of calcium ions by Cryo-EM single particle analysis, which achieved 6.4 Å and 8 Å resolutions respectively. Our results showed that chelation of the calcium ions under EDTA-pH7 resulted in reduced interaction between the subunits near the center of the asymmetric unit but not overall size change of the viral particles, which indicated that the role of the calcium ions in CarMV was not predominantly for the structural preservation. Part of the genomic RNA closest to the capsid was found to be located near the center of the asymmetric unit, which might result from the interaction between genomic RNA and Lys194 residues. Together with the electrostatic potential analysis on the inner surface of the asymmetric unit, the reduced interaction near the center of the asymmetric unit under EDTA-pH7 suggested that the genome release of CarMV might be realized through the center of the asymmetric unit. PMID:26442593

  14. Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM

    PubMed Central

    Iadanza, Matthew G.; Higgins, Anna J.; Schiffrin, Bob; Calabrese, Antonio N.; Brockwell, David J.; Ashcroft, Alison E.; Radford, Sheena E.; Ranson, Neil A.

    2016-01-01

    The β-barrel assembly machinery (BAM) is a ∼203 kDa complex of five proteins (BamA–E), which is essential for viability in E. coli. BAM promotes the folding and insertion of β-barrel proteins into the outer membrane via a poorly understood mechanism. Several current models suggest that BAM functions through a ‘lateral gating' motion of the β-barrel of BamA. Here we present a cryo-EM structure of the BamABCDE complex, at 4.9 Å resolution. The structure is in a laterally open conformation showing that gating is independent of BamB binding. We describe conformational changes throughout the complex and interactions between BamA, B, D and E, and the detergent micelle that suggest communication between BAM and the lipid bilayer. Finally, using an enhanced reconstitution protocol and functional assays, we show that for the outer membrane protein OmpT, efficient folding in vitro requires lateral gating in BAM. PMID:27686148

  15. Characterization and Reconstruction of Nanolipoprotein Particles (Nlps) by Cryo-EM and Image Reconstruction

    SciTech Connect

    Pesavento, J B; Morgan, D; Bermingham, R; Zamora, D; Chromy, B; Segelke, B; Coleman, M; Xing, L; Cheng, H; Bench, G; Hoeprich, P

    2007-06-07

    Nanolipoprotein particles (NLPs) are small 10-20 nm diameter assemblies of apolipoproteins and lipids. At Lawrence Livermore National Laboratory (LLNL), they have constructed multiple variants of these assemblies. NLPs have been generated from a variety of lipoproteins, including apolipoprotein Al, apolipophorin III, apolipoprotein E4 22K, and MSP1T2 (nanodisc, Inc.). Lipids used included DMPC (bulk of the bilayer material), DMPE (in various amounts), and DPPC. NLPs were made in either the absence or presence of the detergent cholate. They have collected electron microscopy data as a part of the characterization component of this research. Although purified by size exclusion chromatography (SEC), samples are somewhat heterogeneous when analyzed at the nanoscale by negative stained cryo-EM. Images reveal a broad range of shape heterogeneity, suggesting variability in conformational flexibility, in fact, modeling studies point to dynamics of inter-helical loop regions within apolipoproteins as being a possible source for observed variation in NLP size. Initial attempts at three-dimensional reconstructions have proven to be challenging due to this size and shape disparity. They are pursuing a strategy of computational size exclusion to group particles into subpopulations based on average particle diameter. They show here results from their ongoing efforts at statistically and computationally subdividing NLP populations to realize greater homogeneity and then generate 3D reconstructions.

  16. Cryo-EM reveals a novel octameric integrase structure for β-retroviral intasome function

    PubMed Central

    Ballandras-Colas, Allison; Brown, Monica; Cook, Nicola J.; Dewdney, Tamaria G.; Demeler, Borries; Cherepanov, Peter; Lyumkis, Dmitry; Engelman, Alan N.

    2016-01-01

    Retroviral integrase (IN) catalyzes the integration of viral DNA (vDNA) into host target (tDNA), which is an essential step in the lifecycle of all retroviruses1. Prior structural characterization of IN-vDNA complexes, or intasomes, from the spumavirus prototype foamy virus (PFV) revealed a functional IN tetramer2–5, and it is generally believed that intasomes derived from other retroviral genera will employ tetrameric IN6–9. However, the intasomes of orthoretroviruses, which include all known pathogenic species, have not been characterized structurally. Using single-particle cryo-electron microscopy (cryo-EM) and X-ray crystallography, we determine here an unexpected octameric IN architecture for the β-retrovirus mouse mammary tumor virus (MMTV) intasome. The structure is composed of two core IN dimers, which interact with the vDNA ends and structurally mimic the PFV IN tetramer, and two flanking IN dimers that engage the core structure via their IN C-terminal domains (CTDs). Contrary to the belief that tetrameric IN components are sufficient to catalyze integration, the flanking IN dimers were necessary for MMTV IN activity. The IN octamer solves a conundrum for the β- as well as α-retroviruses by providing critical CTDs to the intasome core that cannot be provided in cis due to evolutionarily restrictive catalytic core domain (CCD)-CTD linker regions. The octameric architecture of the MMTV intasome provides a new paradigm for the structural basis of retroviral DNA integration. PMID:26887496

  17. Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein

    PubMed Central

    Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.

    2016-01-01

    Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel. PMID:27048994

  18. Near-atomic cryo-EM structure of PRC1 bound to the microtubule

    PubMed Central

    Kellogg, Elizabeth H.; Howes, Stuart; Ti, Shih-Chieh; Ramírez-Aportela, Erney; Kapoor, Tarun M.; Chacón, Pablo; Nogales, Eva

    2016-01-01

    Proteins that associate with microtubules (MTs) are crucial to generate MT arrays and establish different cellular architectures. One example is PRC1 (protein regulator of cytokinesis 1), which cross-links antiparallel MTs and is essential for the completion of mitosis and cytokinesis. Here we describe a 4-Å–resolution cryo-EM structure of monomeric PRC1 bound to MTs. Residues in the spectrin domain of PRC1 contacting the MT are highly conserved and interact with the same pocket recognized by kinesin. We additionally found that PRC1 promotes MT assembly even in the presence of the MT stabilizer taxol. Interestingly, the angle of the spectrin domain on the MT surface corresponds to the previously observed cross-bridge angle between MTs cross-linked by full-length, dimeric PRC1. This finding, together with molecular dynamic simulations describing the intrinsic flexibility of PRC1, suggests that the MT–spectrin domain interface determines the geometry of the MT arrays cross-linked by PRC1. PMID:27493215

  19. Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein

    NASA Astrophysics Data System (ADS)

    Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.

    2016-04-01

    Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel.

  20. Cryo-EM study of start codon selection during archaeal translation initiation

    PubMed Central

    Coureux, Pierre-Damien; Lazennec-Schurdevin, Christine; Monestier, Auriane; Larquet, Eric; Cladière, Lionel; Klaholz, Bruno P.; Schmitt, Emmanuelle; Mechulam, Yves

    2016-01-01

    Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNAiMet) and mRNA bound to the small ribosomal subunit. e/aIF2 plays a crucial role in this process but how this factor controls start codon selection remains unclear. Here, we present cryo-EM structures of the full archaeal 30S initiation complex showing two conformational states of the TC. In the first state, the TC is bound to the ribosome in a relaxed conformation with the tRNA oriented out of the P site. In the second state, the tRNA is accommodated within the peptidyl (P) site and the TC becomes constrained. This constraint is compensated by codon/anticodon base pairing, whereas in the absence of a start codon, aIF2 contributes to swing out the tRNA. This spring force concept highlights a mechanism of codon/anticodon probing by the initiator tRNA directly assisted by aIF2. PMID:27819266

  1. A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments.

    PubMed

    Gardner, Keith A; Wittern, Lukas M; Mackay, Ian J

    2016-06-01

    Multiparent Advanced Generation Intercross (MAGIC) mapping populations offer unique opportunities and challenges for marker and QTL mapping in crop species. We have constructed the first eight-parent MAGIC genetic map for wheat, comprising 18 601 SNP markers. We validated the accuracy of our map against the wheat genome sequence and found an improvement in accuracy compared to published genetic maps. Our map shows a notable increase in precision resulting from the three generations of intercrossing required to create the population. This is most pronounced in the pericentromeric regions of the chromosomes. Sixteen percent of mapped markers exhibited segregation distortion (SD) with many occurring in long (>20 cM) blocks. Some of the longest and most distorted blocks were collinear with noncentromeric high-marker-density regions of the genome, suggesting they were candidates for introgression fragments introduced into the bread wheat gene pool from other grass species. We investigated two of these linkage blocks in detail and found strong evidence that one on chromosome 4AL, showing SD against the founder Robigus, is an interspecific introgression fragment. The completed map is available from http://www.niab.com/pages/id/326/Resources.

  2. High-resolution EEG analysis of power spectral density maps and coherence networks in a proportional reasoning task.

    PubMed

    Vecchiato, Giovanni; Susac, Ana; Margeti, Stavroula; De Vico Fallani, Fabrizio; Maglione, Anton Giulio; Supek, Selma; Planinic, Maja; Babiloni, Fabio

    2013-04-01

    Proportional reasoning is very important logical skill required in mathematics and science problem solving as well as in everyday life decisions. However, there is a lack of studies on neurophysiological correlates of proportional reasoning. To explore the brain activity of healthy adults while performing a balance scale task, we used high-resolution EEG techniques and graph-theory based connectivity analysis. After unskilled subjects learned how to properly solve the task, their cortical power spectral density (PSD) maps revealed an increased parietal activity in the beta band. This indicated that subjects started to perform calculations. In addition, the number of inter-hemispheric connections decreased after learning, implying a rearrangement of the brain activity. Repeated performance of the task led to the PSD decrease in the beta and gamma bands among parietal and frontal regions along with a synchronization of lower frequencies. These findings suggest that repetition led to a more automatic task performance. Subjects were also divided in two groups according to their scores on the test of logical thinking (TOLT). Although no group differences in the accuracy and reaction times were found, EEG data showed higher activity in the beta and gamma bands for the group that scored better on TOLT. Learning and repetition induced changes in the pattern of functional connectivity were evident for all frequency bands. Overall, the results indicated that higher frequency oscillations in frontal and parietal regions are particularly important for proportional reasoning.

  3. Structure, evolution, and comparative genomics of tetraploid cotton based on a high-density genetic linkage map.

    PubMed

    Li, Ximei; Jin, Xin; Wang, Hantao; Zhang, Xianlong; Lin, Zhongxu

    2016-06-01

    A high-density linkage map was constructed using 1,885 newly obtained loci and 3,747 previously published loci, which included 5,152 loci with 4696.03 cM in total length and 0.91 cM in mean distance. Homology analysis in the cotton genome further confirmed the 13 expected homologous chromosome pairs and revealed an obvious inversion on Chr10 or Chr20 and repeated inversions on Chr07 or Chr16. In addition, two reciprocal translocations between Chr02 and Chr03 and between Chr04 and Chr05 were confirmed. Comparative genomics between the tetraploid cotton and the diploid cottons showed that no major structural changes exist between DT and D chromosomes but rather between AT and A chromosomes. Blast analysis between the tetraploid cotton genome and the mixed genome of two diploid cottons showed that most AD chromosomes, regardless of whether it is from the AT or DT genome, preferentially matched with the corresponding homologous chromosome in the diploid A genome, and then the corresponding homologous chromosome in the diploid D genome, indicating that the diploid D genome underwent converted evolution by the diploid A genome to form the DT genome during polyploidization. In addition, the results reflected that a series of chromosomal translocations occurred among Chr01/Chr15, Chr02/Chr14, Chr03/Chr17, Chr04/Chr22, and Chr05/Chr19.

  4. First Case of Automatic His Potential Detection With a Novel Ultra High-density Electroanatomical Mapping System for AV Nodal Ablation

    PubMed Central

    Hilbert, Sebastian; Kosiuk, Jedrzej; John, Silke; Hindricks, Gerhard; Bollmann, Andreas

    2016-01-01

    A 74-year old was considered for atrioventricular (AV) nodal ablation in view of atrial fibrillation (AF) with poorly controlled ventricular rate despite being on amiodarone. Targeted AV nodal ablation was successfully performed after identifying the target site for ablation by reviewing an ultra high-density map of the His region produced by automatic electrogram annotation. PMID:25852249

  5. Genetic dissection of yield and its component traits using high-density composite map of wheat chromosome 3A: bridging gaps between QTLs and underlying genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Earlier we identified wheat (Triticum aestivum L.) chromosome 3A as a major determinant of grain yield and its component traits. In the present study, a high-density genetic linkage map of 81 chromosome 3A-specific markers was developed to increase the precision of previously identified yield compon...

  6. Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High-throughput genotyping arrays provide a standardized resource for crop research communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), candidate marker and quantitative trait loci (QTL) ide...

  7. A High-Density SNP-Based Linkage Map of the Chicken Genome Reveals Sequence Features Correlated With Recombination Rate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The resolution of the widely used chicken consensus linkage map was highly enlarged by genotyping a total of 12,945 SNPs on the three existing mapping populations in chicken; the Wageningen (WU), East Lansing (EL) and Uppsala (UPP) mapping populations. A total of 8608 SNPs could be included on the m...

  8. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq)

    PubMed Central

    Luo, Chun; Shu, Bo; Yao, Quangsheng; Wu, Hongxia; Xu, Wentian; Wang, Songbiao

    2016-01-01

    Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. “Jin-Hwang” and M. indica L. “Irwin” and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango. PMID:27625670

  9. A mechanism of viral immune evasion revealed by cryo-EM analysis of the TAP transporter

    PubMed Central

    Oldham, Michael L.; Hite, Richard K.; Steffen, Alanna M.; Damko, Ermelinda; Li, Zongli; Walz, Thomas; Chen, Jue

    2015-01-01

    Cellular immunity against viral infection and tumor cells depends on antigen presentation by the major histocompatibility complex class 1 molecules (MHC I). Intracellular antigenic peptides are transported into the endoplasmic reticulum (ER) by the transporter associated with antigen processing (TAP) and then loaded onto the nascent MHC I, which are exported to the cell surface and present peptides to the immune system1. Cytotoxic T lymphocytes recognize non-self peptides and program the infected or malignant cells for apoptosis. Defects in TAP account for immunodeficiency and tumor development. To escape immune surveillance, some viruses have evolved strategies to either down-regulate TAP expression or directly inhibit TAP activity. To date neither the architecture of TAP nor the mechanism of viral inhibition has been elucidated at the structural level. In this study we describe the cryo-electron microscopy (cryo-EM) structure of human TAP in complex with its inhibitor ICP47, a small protein produced by the herpes simplex virus I. We show that the twelve transmembrane helices and two cytosolic nucleotide-binding domains (NBDs) of the transporter adopt an inward-facing conformation with the two NBDs separated. The viral inhibitor ICP47 forms a long helical hairpin, which plugs the translocation pathway of TAP from the cytoplasmic side. Association of ICP47 precludes substrate binding and also prevents NBD closure necessary for ATP hydrolysis. This work illustrates a striking example of immune evasion by persistent viruses. By blocking viral antigens from entering the ER, herpes simplex virus is hidden from cytotoxic T lymphocytes, which may contribute to establishing a lifelong infection in the host. PMID:26789246

  10. Dynamical Mapping of Anopheles darlingi Densities in a Residual Malaria Transmission Area of French Guiana by Using Remote Sensing and Meteorological Data

    PubMed Central

    Adde, Antoine; Roux, Emmanuel; Mangeas, Morgan; Dessay, Nadine; Nacher, Mathieu; Dusfour, Isabelle; Girod, Romain; Briolant, Sébastien

    2016-01-01

    Local variation in the density of Anopheles mosquitoes and the risk of exposure to bites are essential to explain the spatial and temporal heterogeneities in the transmission of malaria. Vector distribution is driven by environmental factors. Based on variables derived from satellite imagery and meteorological observations, this study aimed to dynamically model and map the densities of Anopheles darlingi in the municipality of Saint-Georges de l’Oyapock (French Guiana). Longitudinal sampling sessions of An. darlingi densities were conducted between September 2012 and October 2014. Landscape and meteorological data were collected and processed to extract a panel of variables that were potentially related to An. darlingi ecology. Based on these data, a robust methodology was formed to estimate a statistical predictive model of the spatial-temporal variations in the densities of An. darlingi in Saint-Georges de l’Oyapock. The final cross-validated model integrated two landscape variables—dense forest surface and built surface—together with four meteorological variables related to rainfall, evapotranspiration, and the minimal and maximal temperatures. Extrapolation of the model allowed the generation of predictive weekly maps of An. darlingi densities at a resolution of 10-m. Our results supported the use of satellite imagery and meteorological data to predict malaria vector densities. Such fine-scale modeling approach might be a useful tool for health authorities to plan control strategies and social communication in a cost-effective, targeted, and timely manner. PMID:27749938

  11. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

    PubMed

    Hulse-Kemp, Amanda M; Lemm, Jana; Plieske, Joerg; Ashrafi, Hamid; Buyyarapu, Ramesh; Fang, David D; Frelichowski, James; Giband, Marc; Hague, Steve; Hinze, Lori L; Kochan, Kelli J; Riggs, Penny K; Scheffler, Jodi A; Udall, Joshua A; Ulloa, Mauricio; Wang, Shirley S; Zhu, Qian-Hao; Bag, Sumit K; Bhardwaj, Archana; Burke, John J; Byers, Robert L; Claverie, Michel; Gore, Michael A; Harker, David B; Islam, Md S; Jenkins, Johnie N; Jones, Don C; Lacape, Jean-Marc; Llewellyn, Danny J; Percy, Richard G; Pepper, Alan E; Poland, Jesse A; Mohan Rai, Krishan; Sawant, Samir V; Singh, Sunil Kumar; Spriggs, Andrew; Taylor, Jen M; Wang, Fei; Yourstone, Scott M; Zheng, Xiuting; Lawley, Cindy T; Ganal, Martin W; Van Deynze, Allen; Wilson, Iain W; Stelly, David M

    2015-04-22

    High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.

  12. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

    PubMed Central

    Hulse-Kemp, Amanda M.; Lemm, Jana; Plieske, Joerg; Ashrafi, Hamid; Buyyarapu, Ramesh; Fang, David D.; Frelichowski, James; Giband, Marc; Hague, Steve; Hinze, Lori L.; Kochan, Kelli J.; Riggs, Penny K.; Scheffler, Jodi A.; Udall, Joshua A.; Ulloa, Mauricio; Wang, Shirley S.; Zhu, Qian-Hao; Bag, Sumit K.; Bhardwaj, Archana; Burke, John J.; Byers, Robert L.; Claverie, Michel; Gore, Michael A.; Harker, David B.; Islam, Md S.; Jenkins, Johnie N.; Jones, Don C.; Lacape, Jean-Marc; Llewellyn, Danny J.; Percy, Richard G.; Pepper, Alan E.; Poland, Jesse A.; Mohan Rai, Krishan; Sawant, Samir V.; Singh, Sunil Kumar; Spriggs, Andrew; Taylor, Jen M.; Wang, Fei; Yourstone, Scott M.; Zheng, Xiuting; Lawley, Cindy T.; Ganal, Martin W.; Van Deynze, Allen; Wilson, Iain W.; Stelly, David M.

    2015-01-01

    High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community. PMID:25908569

  13. High-density genetic maps for loci involved in nuclear male sterility (NMS1) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L., Asteraceae).

    PubMed

    Gonthier, Lucy; Blassiau, Christelle; Mörchen, Monika; Cadalen, Thierry; Poiret, Matthieu; Hendriks, Theo; Quillet, Marie-Christine

    2013-08-01

    High-density genetic maps were constructed for loci involved in nuclear male sterility (NMS1-locus) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L.). The mapping population consisted of 389 F1' individuals derived from a cross between two plants, K28 (male-sterile) and K59 (pollen-fertile), both heterozygous at the S-locus. This F1' mapping population segregated for both male sterility (MS) and strong self-incompatibility (SI) phenotypes. Phenotyping F1' individuals for MS allowed us to map the NMS1-locus to linkage group (LG) 5, while controlled diallel and factorial crosses to identify compatible/incompatible phenotypes mapped the S-locus to LG2. To increase the density of markers around these loci, bulked segregant analysis was used. Bulks and parental plants K28 and K59 were screened using amplified fragment length polymorphism (AFLP) analysis, with a complete set of 256 primer combinations of EcoRI-ANN and MseI-CNN. A total of 31,000 fragments were generated, of which 2,350 showed polymorphism between K59 and K28. Thirteen AFLP markers were identified close to the NMS1-locus and six in the vicinity of the S-locus. From these AFLP markers, eight were transformed into sequence-characterized amplified region (SCAR) markers and of these five showed co-dominant polymorphism. The chromosomal regions containing the NMS1-locus and the S-locus were each confined to a region of 0.8 cM. In addition, we mapped genes encoding proteins similar to S-receptor kinase, the female determinant of sporophytic SI in the Brasicaceae, and also markers in the vicinity of the putative S-locus of sunflower, but none of these genes or markers mapped close to the chicory S-locus.

  14. High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS)

    PubMed Central

    Verma, Subodh; Gupta, Shefali; Bandhiwal, Nitesh; Kumar, Tapan; Bharadwaj, Chellapilla; Bhatia, Sabhyata

    2015-01-01

    This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea. PMID:26631981

  15. High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS).

    PubMed

    Verma, Subodh; Gupta, Shefali; Bandhiwal, Nitesh; Kumar, Tapan; Bharadwaj, Chellapilla; Bhatia, Sabhyata

    2015-12-03

    This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea.

  16. A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid.

    PubMed

    Kang, Bum-Yong; Major, John E; Rajora, Om P

    2011-02-01

    Genetic maps provide an important genomic resource of basic and applied significance. Spruce (Picea) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5-24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL-MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.

  17. Scanning micro-Hall probe mapping of magnetic flux distributions and current densities in YBa2Cu3O7 thin films

    NASA Technical Reports Server (NTRS)

    Xing, W.; Heinrich, B.; Zhou, HU; Fife, A. A.; Cragg, A. R.; Grant, P. D.

    1995-01-01

    Mapping of the magnetic flux density B(sub z) (perpendicular to the film plane) for a YBa2Cu3O7 thin-film sample was carried out using a scanning micro-Hall probe. The sheet magnetization and sheet current densities were calculated from the B(sub z) distributions. From the known sheet magnetization, the tangential (B(sub x,y)) and normal components of the flux density B were calculated in the vicinity of the film. It was found that the sheet current density was mostly determined by 2B(sub x,y)/d, where d is the film thickness. The evolution of flux penetration as a function of applied field will be shown.

  18. Scanning micro-Hall probe mapping of magnetic flux distributions and current densities in YBa{sub 2}Cu{sub 3}O{sub 7}

    SciTech Connect

    Xing, W.; Heinrich, B.; Zhou, H.

    1994-12-31

    Mapping of the magnetic flux density B{sub z} (perpendicular to the film plane) for a YBa{sub 2}Cu{sub 3}O{sub 7} thin-film sample was carried out using a scanning micro-Hall probe. The sheet magnetization and sheet current densities were calculated from the B{sub z} distributions. From the known sheet magnetization, the tangential (B{sub x,y}) and normal components of the flux density B were calculated in the vicinity of the film. It was found that the sheet current density was mostly determined by 2B{sub x,y}/d, where d is the film thickness. The evolution of flux penetration as a function of applied field will be shown.

  19. Mixed Modeling of Meta-Analysis P-Values (MixMAP) Suggests Multiple Novel Gene Loci for Low Density Lipoprotein Cholesterol

    PubMed Central

    Foulkes, Andrea S.; Matthews, Gregory J.; Das, Ujjwal; Ferguson, Jane F.; Lin, Rongheng; Reilly, Muredach P.

    2013-01-01

    Informing missing heritability for complex disease will likely require leveraging information across multiple SNPs within a gene region simultaneously to characterize gene and locus-level contributions to disease phenotypes. To this aim, we introduce a novel strategy, termed Mixed modeling of Meta-Analysis P-values (MixMAP), that draws on a principled statistical modeling framework and the vast array of summary data now available from genetic association studies, to test formally for locus level association. The primary inputs to this approach are: (a) single SNP level p-values for tests of association; and (b) the mapping of SNPs to genomic regions. The output of MixMAP is comprised of locus level estimates and tests of association. In application of MixMAP to summary data from the Global Lipids Gene Consortium, we suggest twelve new loci (PKN, FN1, UGT1A1, PPARG, DMDGH, PPARD, CDK6, VPS13B, GAD2, GAB2, APOH and NPC1) for low-density lipoprotein cholesterol (LDL-C), a causal risk factor for cardiovascular disease and we also demonstrate the potential utility of MixMAP in small data settings. Overall, MixMAP offers novel and complementary information as compared to SNP-based analysis approaches and is straightforward to implement with existing open-source statistical software tools. PMID:23405096

  20. Genome-Wide Single-Nucleotide Polymorphisms Discovery and High-Density Genetic Map Construction in Cauliflower Using Specific-Locus Amplified Fragment Sequencing.

    PubMed

    Zhao, Zhenqing; Gu, Honghui; Sheng, Xiaoguang; Yu, Huifang; Wang, Jiansheng; Huang, Long; Wang, Dan

    2016-01-01

    Molecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequencing strategy was employed for large-scale single nucleotide polymorphism (SNP) discovery and high-density genetic map construction in a double-haploid, segregating population of cauliflower. A total of 12.47 Gb raw data containing 77.92 M pair-end reads were obtained after processing and 6815 polymorphic SLAFs between the two parents were detected. The average sequencing depths reached 52.66-fold for the female parent and 49.35-fold for the male parent. Subsequently, these polymorphic SLAFs were used to genotype the population and further filtered based on several criteria to construct a genetic linkage map of cauliflower. Finally, 1776 high-quality SLAF markers, including 2741 SNPs, constituted the linkage map with average data integrity of 95.68%. The final map spanned a total genetic length of 890.01 cM with an average marker interval of 0.50 cM, and covered 364.9 Mb of the reference genome. The markers and genetic map developed in this study could provide an important foundation not only for comparative genomics studies within Brassica oleracea species but also for quantitative trait loci identification and molecular breeding of cauliflower.

  1. Percutaneous transapical access for pulmonary vein mapping and ablation in a porcine model with a new high-density electroanatomical mapping system

    PubMed Central

    Bollmann, Andreas; Kosiuk, Jedrzej; Hilbert, Sebastian; John, Silke; Hindricks, Gerhard

    2015-01-01

    Introduction: The porcine model is generally accepted for the development and testing of new forms oftherapy including ablation of atrial fibrillation (AF). However, the challenging left atrial (LA) and pulmonary vein (PV) anatomy enables only limited percutaneous catheter-based PV access. Results: Here we present I) an alternative percutaneous transapical access, which enables easy and safe retrograde transmitral LA and PV mapping and ablation; II) early experience of LA mapping and successful circumferential PV isolation with novel mapping system (RhythmiaTM) and new generation of ablation catheter equipped with micro electrodes (IntellaTip MiFi). Conclusion: Although the experience with the transapical approach is limited, the initial results are promising as this may offer an alternative approach for tasting new technologies and translational research. PMID:26550175

  2. An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73'×'Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http:...

  3. Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryo-EM

    PubMed Central

    Chen, Bo; Kaledhonkar, Sandip; Sun, Ming; Shen, Bingxin; Lu, Zonghuan; Barnard, David; Lu, Toh-Ming; Gonzalez, Ruben L.; Frank, Joachim

    2015-01-01

    Ribosomal subunit association is a key checkpoint in translation initiation, but its structural dynamics are poorly understood. Here, we used a recently developed mixing-spraying, time-resolved, cryogenic electron microscopy (cryo-EM) method to study ribosomal subunit association in the sub-second time range. We have improved this method and increased the cryo-EM data yield by tenfold. Pre-equilibrium states of the association reaction were captured by reacting the mixture of ribosomal subunits for 60 ms and 140 ms. We also identified three distinct ribosome conformations in the associated ribosomes. The observed proportions of these conformations are the same in these two time points, suggesting that ribosomes equilibrate among the three conformations within less than 60 ms upon formation. Our results demonstrate that the mixing-spraying method can capture multiple states of macromolecules during a sub-second reaction. Other fast processes, such as translation initiation, decoding and ribosome recycling, are amenable to study with this method. PMID:26004440

  4. Insights into remodeling events during eukaryotic large ribosomal subunit assembly provided by high resolution cryo-EM structures.

    PubMed

    Biedka, Stephanie; Wu, Shan; LaPeruta, Amber J; Gao, Ning; Woolford, John L

    2017-03-07

    Ribosomes are responsible for translating the genome, in the form of mRNA, into the proteome in all organisms. Biogenesis of ribosomes in eukaryotes is a complex process involving numerous remodeling events driven in part by the concerted actions of hundreds of protein assembly factors. A major challenge in studying eukaryotic ribosome assembly has, until recently, been a lack of structural data to facilitate understanding of the conformational and compositional changes the pre-ribosome undergoes during its construction. Cryo-electron microscopy (cryo-EM) has begun filling these gaps; recent advances in cryo-EM have enabled the determination of several high resolution pre-ribosome structures. This review focuses mainly on lessons learned from the study of pre-60S particles purified from yeast using the assembly factor Nog2 as bait. These Nog2 particles provide insight into many aspects of nuclear stages of 60S subunit assembly, including construction of major 60S subunit functional centers and processing of the ITS2 spacer RNA.

  5. Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.

    PubMed

    Graf, Michael; Arenz, Stefan; Huter, Paul; Dönhöfer, Alexandra; Nováček, Jiří; Wilson, Daniel N

    2016-12-15

    Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking. Here we present a cryo-EM structure of the spinach chloroplast 70S ribosome, with an average resolution of 5.4 Å for the small 30S subunit and 3.6 Å for the large 50S ribosomal subunit. The structure reveals the location of the plastid-specific ribosomal proteins (RPs) PSRP1, PSRP4, PSRP5 and PSRP6 as well as the numerous plastid-specific extensions of the RPs. We discover many features by which the plastid-specific extensions stabilize the ribosome via establishing additional interactions with surrounding ribosomal RNA and RPs. Moreover, we identify a large conglomerate of plastid-specific protein mass adjacent to the tunnel exit site that could facilitate interaction of the chloroplast ribosome with the thylakoid membrane and the protein-targeting machinery. Comparing the Escherichia coli 70S ribosome with that of the spinach chloroplast ribosome provides detailed insight into the co-evolution of RP and rRNA.

  6. Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.)

    PubMed Central

    Huang, Li; Ren, Xiaoping; Wu, Bei; Li, Xinping; Chen, Weigang; Zhou, Xiaojing; Chen, Yuning; Pandey, Manish K.; Jiao, Yongqing; Luo, Huaiyong; Lei, Yong; Varshney, Rajeev K.; Liao, Boshou; Jiang, Huifang

    2016-01-01

    Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 individuals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut. PMID:27995991

  7. High-dynamic-range extinction mapping of infrared dark clouds. Dependence of density variance with sonic Mach number in molecular clouds

    NASA Astrophysics Data System (ADS)

    Kainulainen, J.; Tan, J. C.

    2013-01-01

    Context. Measuring the mass distribution of infrared dark clouds (IRDCs) over the wide dynamic range of their column densities is a fundamental obstacle in determining the initial conditions of high-mass star formation and star cluster formation. Aims: We present a new technique to derive high-dynamic-range, arcsecond-scale resolution column density data for IRDCs and demonstrate the potential of such data in measuring the density variance - sonic Mach number relation in molecular clouds. Methods: We combine near-infrared data from the UKIDSS/Galactic Plane Survey with mid-infrared data from the Spitzer/GLIMPSE survey to derive dust extinction maps for a sample of ten IRDCs. We then examine the linewidths of the IRDCs using 13CO line emission data from the FCRAO/Galactic Ring Survey and derive a column density - sonic Mach number relation for them. For comparison, we also examine the relation in a sample of nearby molecular clouds. Results: The presented column density mapping technique provides a very capable, temperature independent tool for mapping IRDCs over the column density range equivalent to AV ≃ 1-100 mag at a resolution of 2″. Using the data provided by the technique, we present the first direct measurement of the relationship between the column density dispersion, σN/⟨N⟩, and sonic Mach number, ℳs, in molecular clouds. We detect correlation between the variables with about 3-σ confidence. We derive the relation σN/⟨N⟩ ≈ (0.047 ± 0.016)ℳs, which is suggestive of the correlation coefficient between the volume density and sonic Mach number, σρ/⟨ρ⟩ ≈ (0.20-0.22+0.37)ℳs, in which the quoted uncertainties indicate the 3-σ range. When coupled with the results of recent numerical works, the existence of the correlation supports the picture of weak correlation between the magnetic field strength and density in molecular clouds (i.e., B ∝ ρ0.5). While our results remain suggestive because of the small number of clouds in our

  8. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability.

    PubMed

    Isobe, Sachiko N; Hirakawa, Hideki; Sato, Shusei; Maeda, Fumi; Ishikawa, Masami; Mori, Toshiki; Yamamoto, Yuko; Shirasawa, Kenta; Kimura, Mitsuhiro; Fukami, Masanobu; Hashizume, Fujio; Tsuji, Tomoko; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Tsuruoka, Hisano; Minami, Chiharu; Takahashi, Chika; Wada, Tsuyuko; Ono, Akiko; Kawashima, Kumiko; Nakazaki, Naomi; Kishida, Yoshie; Kohara, Mitsuyo; Nakayama, Shinobu; Yamada, Manabu; Fujishiro, Tsunakazu; Watanabe, Akiko; Tabata, Satoshi

    2013-02-01

    The cultivated strawberry (Fragaria × ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA'A'BBB'B' model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers.

  9. High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex

    PubMed Central

    Brelsford, A; Dufresnes, C; Perrin, N

    2016-01-01

    Identifying homology between sex chromosomes of different species is essential to understanding the evolution of sex determination. Here, we show that the identity of a homomorphic sex chromosome pair can be established using a linkage map, without information on offspring sex. By comparing sex-specific maps of the European tree frog Hyla arborea, we find that the sex chromosome (linkage group 1) shows a threefold difference in marker number between the male and female maps. In contrast, the number of markers on each autosome is similar between the two maps. We also find strongly conserved synteny between H. arborea and Xenopus tropicalis across 200 million years of evolution, suggesting that the rate of chromosomal rearrangement in anurans is low. Finally, we show that recombination in males is greatly reduced at the centers of large chromosomes, consistent with previous cytogenetic findings. Our research shows the importance of high-density linkage maps for studies of recombination, chromosomal rearrangement and the genetic architecture of ecologically or economically important traits. PMID:26374238

  10. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    SciTech Connect

    Carr, J. K.; Roy, S.; Skinner, J. L.; Zabuga, A. V.; Rizzo, T. R.

    2014-06-14

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala){sub 5}-Lys-H{sup +} in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly {sup 13}C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and {sup 13}C{sup 18}O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm{sup −1} for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

  11. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations.

    PubMed

    Carr, J K; Zabuga, A V; Roy, S; Rizzo, T R; Skinner, J L

    2014-06-14

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H(+) in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly (13)C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and (13)C(18)O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm(-1) for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

  12. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Carr, J. K.; Zabuga, A. V.; Roy, S.; Rizzo, T. R.; Skinner, J. L.

    2014-06-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H+ in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13C18O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm-1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

  13. Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

    PubMed Central

    Nunes, José de Ribamar da Silva; Liu, Shikai; Pértille, Fábio; Perazza, Caio Augusto; Villela, Priscilla Marqui Schmidt; de Almeida-Val, Vera Maria Fonseca; Hilsdorf, Alexandre Wagner Silva; Liu, Zhanjiang; Coutinho, Luiz Lehmann

    2017-01-01

    Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs. PMID:28387238

  14. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    PubMed Central

    Carr, J. K.; Zabuga, A. V.; Roy, S.; Rizzo, T. R.; Skinner, J. L.

    2014-01-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H+ in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13C18O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm−1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides. PMID:24929378

  15. A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data.

    PubMed

    Biswas, Abhishek; Ranjan, Desh; Zubair, Mohammad; He, Jing

    2015-09-01

    The determination of secondary structure topology is a critical step in deriving the atomic structures from the protein density maps obtained from electron cryomicroscopy technique. This step often relies on matching the secondary structure traces detected from the protein density map to the secondary structure sequence segments predicted from the amino acid sequence. Due to inaccuracies in both sources of information, a pool of possible secondary structure positions needs to be sampled. One way to approach the problem is to first derive a small number of possible topologies using existing matching algorithms, and then find the optimal placement for each possible topology. We present a dynamic programming method of Θ(Nq(2)h) to find the optimal placement for a secondary structure topology. We show that our algorithm requires significantly less computational time than the brute force method that is in the order of Θ(q(N) h).

  16. Mapping the energy density of shaped waves in scattering media onto a complete set of diffusion modes.

    PubMed

    Ojambati, Oluwafemi S; Mosk, Allard P; Vellekoop, Ivo M; Lagendijk, Ad; Vos, Willem L

    2016-08-08

    We study the energy density of shaped waves inside a quasi-1D disordered waveguide. We find that the spatial energy density of optimally shaped waves, when expanded in the complete set of eigenfunctions of the diffusion equation, is well described by considering only a few of the lowest eigenfunctions. Taking into account only the fundamental eigenfunction, the total internal energy inside the sample is underestimated by only 2%. The spatial distribution of the shaped energy density is very similar to the fundamental eigenfunction, up to a cosine distance of about 0.01. We obtain the energy density of transmission eigenchannels inside the sample by numerical simulation of the scattering matrix. Computing the transmission-averaged energy density over all transmission channels yields the ensemble averaged energy density of shaped waves. From the averaged energy density, we reconstruct its spatial distribution using the eigenfunctions of the diffusion equation. The results of our study have exciting applications in controlled biomedical imaging, efficient light harvesting in solar cells, enhanced energy conversion in solid-state lighting, and low threshold random lasers.

  17. Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq

    PubMed Central

    Zhao, Xinxin; Huang, Linkai; Zhang, Xinquan; Wang, Jianping; Yan, Defei; Li, Ji; Tang, Lu; Li, Xiaolong; Shi, Tongwei

    2016-01-01

    Orchardgrass (Dactylis glomerata L.) is one of the most economically important perennial, cool-season forage species grown and pastured worldwide. High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this study, we developed 447,177 markers based on SLAF-seq and used them to perform a comparative genomics analysis. Perennial ryegrass sequences were the most similar (5.02%) to orchardgrass sequences. A high-density linkage map of orchardgrass was constructed using 2,467 SLAF markers and 43 SSRs, which were distributed on seven linkage groups spanning 715.77 cM. The average distance between adjacent markers was 0.37 cM. Based on phenotyping in four environments, 11 potentially significant quantitative trait loci (QTLs) for two target traits–heading date (HD) and flowering time (FT)–were identified and positioned on linkage groups LG1, LG3, and LG5. Significant QTLs explained 8.20–27.00% of the total phenotypic variation, with the LOD ranging from 3.85–12.21. Marker167780 and Marker139469 were associated with FT and HD at the same location (Ya’an) over two different years. The utility of SLAF markers for rapid generation of genetic maps and QTL analysis has been demonstrated for heading date and flowering time in a global forage grass. PMID:27389619

  18. Investigating the Capability of IRS-P6-LISS IV Satellite Image for Pistachio Forests Density Mapping (case Study: Northeast of Iran)

    NASA Astrophysics Data System (ADS)

    Hoseini, F.; Darvishsefat, A. A.; Zargham, N.

    2012-07-01

    In order to investigate the capability of satellite images for Pistachio forests density mapping, IRS-P6-LISS IV data were analyzed in an area of 500 ha in Iran. After geometric correction, suitable training areas were determined based on fieldwork. Suitable spectral transformations like NDVI, PVI and PCA were performed. A ground truth map included of 34 plots (each plot 1 ha) were prepared. Hard and soft supervised classifications were performed with 5 density classes (0-5%, 5-10%, 10-15%, 15-20% and > 20%). Because of low separability of classes, some classes were merged and classifications were repeated with 3 classes. Finally, the highest overall accuracy and kappa coefficient of 70% and 0.44, respectively, were obtained with three classes (0-5%, 5-20%, and > 20%) by fuzzy classifier. Considering the low kappa value obtained, it could be concluded that the result of the classification was not desirable. Therefore, this approach is not appropriate for operational mapping of these valuable Pistachio forests.

  19. The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing.

    PubMed

    Cai, Changfu; Cheng, Fang-Yun; Wu, Jing; Zhong, Yuan; Liu, Gaixiu

    2015-01-01

    Genetic linkage maps, permitting the elucidation of genome structure, are one of most powerful genomic tools to accelerate marker-assisted breeding. However, due to a lack of sufficient user-friendly molecular markers, no genetic linkage map has been developed for tree peonies (Paeonia Sect. Moutan), a group of important horticultural plants worldwide. Specific-locus amplified fragment sequencing (SLAF-seq) is a recent molecular marker development technology that enable the large-scale discovery and genotyping of sequence-based marker in genome-wide. In this study, we performed SLAF sequencing of an F1 population, derived from the cross P. ostti 'FenDanBai' × P. × suffruticosa 'HongQiao', to identify sufficient high-quality markers for the construction of high-density genetic linkage map in tree peonies. After SLAF sequencing, a total of 78 Gb sequencing data and 285,403,225 pair-end reads were generated. We detected 309,198 high-quality SLAFs from these data, of which 85,124 (27.5%) were polymorphic. Subsequently, 3518 of the polymorphic markers, which were successfully encoded in to Mendelian segregation types, and were in conformity with the criteria of high-quality markers, were defined as effective markers and used for genetic linkage mapping. Finally, we constructed an integrated genetic map, which comprised 1189 markers on the five linkage groups, and spanned 920.699 centiMorgans (cM) with an average inter-marker distance of 0.774 cM. There were 1115 'SNP-only' markers, 18 'InDel-only' markers, and 56 'SNP&InDel' markers on the map. Among these markers, 450 (37.85%) showed significant segregation distortion (P < 0.05). In conclusion, this investigation reported the first large-scale marker development and high-density linkage map construction for tree peony. The results of this study will serve as a solid foundation not only for marker-assisted breeding, but also for genome sequence assembly for tree peony.

  20. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton genome complexity was investigated with a saturated molecular genetic map that combined several sets of microsatellites or simple sequence repeats (SSR) and the first major public set of single nucleotide polymorphism (SNP) markers in cotton genomes (Gossypium spp.), and that was constructed ...

  1. Shell stability and conditions analyzed using a new method of extracting shell areal density maps from spectrally resolved images of direct-drive inertial confinement fusion implosions

    DOE PAGES

    Johns, H. M.; Mancini, R. C.; Nagayama, T.; ...

    2016-01-25

    In warm target direct-drive ICF implosion experiments performed at the OMEGA laser facility, plastic microballoons doped with a titanium tracer layer in the shell and filled with deuterium gas were imploded using a low-adiabat shaped laser pulse. Continuum radiation emitted in the core is transmitted through the tracer layer and the resulting spectrum recorded with a gated multi-monochromatic x-ray imager (MMI). Titanium K-shell line absorption spectra observed in the data are due to transitions in L-shell titanium ions driven by the backlighting continuum. The MMI data consist of an array of spectrally resolved images of the implosion. These 2-D space-resolvedmore » titanium spectral features constrain the plasma conditions and areal density of the titanium doped region of the shell. The MMI data were processed to obtain narrow-band images and space resolved spectra of titanium spectral features. Shell areal density maps, ρL(x,y), extracted using a new method using both narrow-band images and space resolved spectra are confirmed to be consistent within uncertainties. We report plasma conditions in the titanium-doped region of electron temperature (Te) = 400±28eV, electron number density (Ne) = 8.5x1024±2.5x1024 cm-3, and average areal density <ρR> = 86±7mg/cm2. Fourier analysis of areal density maps reveals shell modulations caused by hydrodynamic instability growth near the fuel-shell interface in the deceleration phase. We observe significant structure in modes l = 2-9, dominated by l = 2. We extract a target breakup fraction of 7.1±1.5% from our Fourier analysis. A new method for estimating mix width is evaluated against existing literature and our target breakup fraction. We estimate a mix width of 10.5±1μm.« less

  2. Gate-control efficiency and interface state density evaluated from capacitance-frequency-temperature mapping for GaN-based metal-insulator-semiconductor devices

    SciTech Connect

    Shih, Hong-An; Kudo, Masahiro; Suzuki, Toshi-kazu

    2014-11-14

    We present an analysis method for GaN-based metal-insulator-semiconductor (MIS) devices by using capacitance-frequency-temperature (C-f-T) mapping to evaluate the gate-control efficiency and the interface state density, both exhibiting correlations with the linear-region intrinsic transconductance. The effectiveness of the method was exemplified by application to AlN/AlGaN/GaN MIS devices to elucidate the properties of AlN-AlGaN interfaces depending on their formation processes. Using the C-f-T mapping, we extract the gate-bias-dependent activation energy with its derivative giving the gate-control efficiency, from which we evaluate the AlN-AlGaN interface state density through the Lehovec equivalent circuit in the DC limit. It is shown that the gate-control efficiency and the interface state density have correlations with the linear-region intrinsic transconductance, all depending on the interface formation processes. In addition, we give characterization of the AlN-AlGaN interfaces by using X-ray photoelectron spectroscopy, in relation with the results of the analysis.

  3. NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps.

    PubMed

    Suhre, Karsten; Navaza, Jorge; Sanejouand, Yves Henri

    2006-09-01

    This paper describes a freely available software suite that allows the modelling of large conformational changes of high-resolution three-dimensional protein structures under the constraint of a low-resolution electron-density map. Typical applications are the interpretation of electron-microscopy data using atomic scale X-ray structural models. The software package provided should enable the interested user to perform flexible fitting on new cases without encountering major technical difficulties. The NORMA software suite including three fully executable reference cases and extensive user instructions are available at http://www.elnemo.org/NORMA/.

  4. Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation

    PubMed Central

    van de Bunt, Martijn; Surakka, Ida; Sarin, Antti-Pekka; Mahajan, Anubha; Marullo, Letizia; Thorleifsson, Gudmar; Hӓgg, Sara; Hottenga, Jouke-Jan; Ladenvall, Claes; Ried, Janina S.; Winkler, Thomas W.; Willems, Sara M.; Pervjakova, Natalia; Esko, Tõnu; Beekman, Marian; Nelson, Christopher P.; Willenborg, Christina; Ferreira, Teresa; Fernandez, Juan; Gaulton, Kyle J.; Steinthorsdottir, Valgerdur; Hamsten, Anders; Magnusson, Patrik K. E.; Willemsen, Gonneke; Milaneschi, Yuri; Robertson, Neil R.; Groves, Christopher J.; Bennett, Amanda J.; Lehtimӓki, Terho; Viikari, Jorma S.; Rung, Johan; Lyssenko, Valeriya; Perola, Markus; Heid, Iris M.; Herder, Christian; Grallert, Harald; Müller-Nurasyid, Martina; Roden, Michael; Hypponen, Elina; Isaacs, Aaron; van Leeuwen, Elisabeth M.; Karssen, Lennart C.; Mihailov, Evelin; Houwing-Duistermaat, Jeanine J.; de Craen, Anton J. M.; Deelen, Joris; Havulinna, Aki S.; Blades, Matthew; Hengstenberg, Christian; Erdmann, Jeanette; Schunkert, Heribert; Kaprio, Jaakko; Tobin, Martin D.; Samani, Nilesh J.; Lind, Lars; Salomaa, Veikko; Lindgren, Cecilia M.; Slagboom, P. Eline; Metspalu, Andres; van Duijn, Cornelia M.; Eriksson, Johan G.; Peters, Annette; Gieger, Christian; Jula, Antti; Groop, Leif; Raitakari, Olli T.; Power, Chris; Penninx, Brenda W. J. H.; de Geus, Eco; Smit, Johannes H.; Boomsma, Dorret I.; Pedersen, Nancy L.; Ingelsson, Erik; Thorsteinsdottir, Unnur; Stefansson, Kari; Ripatti, Samuli; Prokopenko, Inga; McCarthy, Mark I.; Morris, Andrew P.

    2015-01-01

    Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated. PMID:26132169

  5. MO-F-CAMPUS-J-04: Tissue Segmentation-Based MR Electron Density Mapping Method for MR-Only Radiation Treatment Planning of Brain

    SciTech Connect

    Yu, H; Lee, Y; Ruschin, M; Karam, I; Sahgal, A

    2015-06-15

    Purpose: Automatically derive electron density of tissues using MR images and generate a pseudo-CT for MR-only treatment planning of brain tumours. Methods: 20 stereotactic radiosurgery (SRS) patients’ T1-weighted MR images and CT images were retrospectively acquired. First, a semi-automated tissue segmentation algorithm was developed to differentiate tissues with similar MR intensities and large differences in electron densities. The method started with approximately 12 slices of manually contoured spatial regions containing sinuses and airways, then air, bone, brain, cerebrospinal fluid (CSF) and eyes were automatically segmented using edge detection and anatomical information including location, shape, tissue uniformity and relative intensity distribution. Next, soft tissues - muscle and fat were segmented based on their relative intensity histogram. Finally, intensities of voxels in each segmented tissue were mapped into their electron density range to generate pseudo-CT by linearly fitting their relative intensity histograms. Co-registered CT was used as a ground truth. The bone segmentations of pseudo-CT were compared with those of co-registered CT obtained by using a 300HU threshold. The average distances between voxels on external edges of the skull of pseudo-CT and CT in three axial, coronal and sagittal slices with the largest width of skull were calculated. The mean absolute electron density (in Hounsfield unit) difference of voxels in each segmented tissues was calculated. Results: The average of distances between voxels on external skull from pseudo-CT and CT were 0.6±1.1mm (mean±1SD). The mean absolute electron density differences for bone, brain, CSF, muscle and fat are 78±114 HU, and 21±8 HU, 14±29 HU, 57±37 HU, and 31±63 HU, respectively. Conclusion: The semi-automated MR electron density mapping technique was developed using T1-weighted MR images. The generated pseudo-CT is comparable to that of CT in terms of anatomical position of

  6. Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

    SciTech Connect

    Mardirossian, Narbe; Head-Gordon, Martin

    2015-02-21

    A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 10{sup 10} choices carved out of a functional space of almost 10{sup 40} possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.

  7. High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster.

    PubMed

    Freaney, Jonathan E; Zhang, Quanwei; Yigit, Erbay; Kim, Rebecca; Widom, Jonathan; Wang, Ji-Ping; Horvath, Curt M

    2014-09-01

    Genome-wide investigations have dramatically increased our understanding of nucleosome positioning and the role of chromatin in gene regulation, yet some genomic regions have been poorly represented in human nucleosome maps. One such region is represented by human chromosome 9p21-22, which contains the type I interferon gene cluster that includes 16 interferon alpha genes and the single interferon beta, interferon epsilon, and interferon omega genes. A high-density nucleosome mapping strategy was used to generate locus-wide maps of the nucleosome organization of this biomedically important locus at a steady state and during a time course of infection with Sendai virus, an inducer of interferon gene expression. Detailed statistical and computational analysis illustrates that nucleosomes in this locus exhibit preferences for particular dinucleotide and oligomer DNA sequence motifs in vivo, which are similar to those reported for lower eukaryotic nucleosome-DNA interactions. These data were used to visualize the region's chromatin architecture and reveal features that are common to the organization of all the type I interferon genes, indicating a common nucleosome-mediated gene regulatory paradigm. Additionally, this study clarifies aspects of the dynamic changes that occur with the nucleosome occupying the transcriptional start site of the interferon beta gene after virus infection.

  8. Geostatistical analysis of disease data: accounting for spatial support and population density in the isopleth mapping of cancer mortality risk using area-to-point Poisson kriging

    PubMed Central

    Goovaerts, Pierre

    2006-01-01

    Background Geostatistical techniques that account for spatially varying population sizes and spatial patterns in the filtering of choropleth maps of cancer mortality were recently developed. Their implementation was facilitated by the initial assumption that all geographical units are the same size and shape, which allowed the use of geographic centroids in semivariogram estimation and kriging. Another implicit assumption was that the population at risk is uniformly distributed within each unit. This paper presents a generalization of Poisson kriging whereby the size and shape of administrative units, as well as the population density, is incorporated into the filtering of noisy mortality rates and the creation of isopleth risk maps. An innovative procedure to infer the point-support semivariogram of the risk from aggregated rates (i.e. areal data) is also proposed. Results The novel methodology is applied to age-adjusted lung and cervix cancer mortality rates recorded for white females in two contrasted county geographies: 1) state of Indiana that consists of 92 counties of fairly similar size and shape, and 2) four states in the Western US (Arizona, California, Nevada and Utah) forming a set of 118 counties that are vastly different geographical units. Area-to-point (ATP) Poisson kriging produces risk surfaces that are less smooth than the maps created by a naïve point kriging of empirical Bayesian smoothed rates. The coherence constraint of ATP kriging also ensures that the population-weighted average of risk estimates within each geographical unit equals the areal data for this unit. Simulation studies showed that the new approach yields more accurate predictions and confidence intervals than point kriging of areal data where all counties are simply collapsed into their respective polygon centroids. Its benefit over point kriging increases as the county geography becomes more heterogeneous. Conclusion A major limitation of choropleth maps is the common biased

  9. SNP discovery and high-density genetic mapping in faba bean (Vicia faba L.) permits identification of QTLs for ascochyta blight resistance.

    PubMed

    Kaur, Sukhjiwan; Kimber, Rohan B E; Cogan, Noel O I; Materne, Michael; Forster, John W; Paull, Jeffrey G

    2014-03-01

    Ascochyta blight, caused by the fungus Ascochyta fabae Speg., is a common and destructive disease of faba bean (Vicia faba L.) on a global basis. Yield losses vary from typical values of 35-40% to 90% under specific environmental conditions. Several sources of resistance have been identified and used in breeding programs. However, introgression of the resistance gene determinants into commercial cultivars as a gene pyramiding approach is reliant on selection of closely linked genetic markers. A total of 14,552 base variants were identified from a faba bean expressed sequence tag (EST) database, and were further quality assessed to obtain a set of 822 high-quality single nucleotide polymorphisms (SNPs). Sub-sets of 336 EST-derived simple sequence repeats (SSRs) and 768 SNPs were further used for high-density genetic mapping of a biparental faba bean mapping population (Icarus×Ascot) that segregates for resistance to ascochyta blight. The linkage map spanned a total length of 1216.8 cM with 12 linkage groups (LGs) and an average marker interval distance of 2.3 cM. Comparison of map structure to the genomes of closely related legume species revealed a high degree of conserved macrosynteny, as well as some rearrangements. Based on glasshouse evaluation of ascochyta blight resistance performed over two years, four genomic regions controlling resistance were identified on Chr-II, Chr-VI and two regions on Chr-I.A. Of these, one (QTL-3) may be identical with quantitative trait loci (QTLs) identified in prior studies, while the others (QTL-1, QTL-2 and QTL-4) may be novel. Markers in close linkage to ascochyta blight resistance genes identified in this study can be further validated and effectively implemented in faba bean breeding programs.

  10. High-Density Genetic Linkage Mapping in Turbot (Scophthalmus maximus L.) Based on SNP Markers and Major Sex- and Growth-Related Regions Detection

    PubMed Central

    Wang, Weiji; Hu, Yulong; Ma, Yu; Xu, Liyong; Guan, Jiantao; Kong, Jie

    2015-01-01

    This paper describes the development of a high density consensus genetic linkage map of a turbot (Scophthalmus maximus L.) family composed of 149 mapping individuals using Single Nucleotide Polymorphisms (SNP) developed using the restriction-site associated DNA (RAD) sequencing technique with the restriction enzyme, PstI. A total of 6,647 SNPs were assigned to 22 linkage groups, which is equal to the number of chromosome pairs in turbot. For the first time, the average marker interval reached 0.3958 cM, which is equal to approximately 0.1203 Mb of the turbot genome. The observed 99.34% genome coverage indicates that the linkage map was genome-wide. A total of 220 Quantitative Traits Locus (QTLs) associated with two body length traits, two body weight traits in different growth periods and sex determination were detected with an LOD > 5.0 in 12 linkage groups (LGs), which explained the corresponding phenotypic variance (R2), ranging from 14.4–100%. Among them, 175 overlapped with linked SNPs, and the remaining 45 were located in regions between contiguous SNPs. According to the QTLs related to growth trait distribution and the changing of LGs during different growth periods, the growth traits are likely controlled by multi-SNPs distributed on several LGs; the effect of these SNPs changed during different growth periods. Most sex-related QTLs were detected at LG 21 with a linkage span of 70.882 cM. Additionally, a small number of QTLs with high feasibility and a narrow R2 distribution were also observed on LG7 and LG14, suggesting that multi LGs or chromosomes might be involved in sex determination. High homology was recorded between LG21 in Cynoglossus semilaevis and turbot. This high-saturated turbot RAD-Seq linkage map is undoubtedly a promising platform for marker assisted selection (MAS) and flatfish genomics research. PMID:25775256

  11. Diffusion-Based Density-Equalizing Maps: an Interdisciplinary Approach to Visualizing Homicide Rates and Other Georeferenced Statistical Data

    NASA Astrophysics Data System (ADS)

    Mazzitello, Karina I.; Candia, Julián

    2012-12-01

    In every country, public and private agencies allocate extensive funding to collect large-scale statistical data, which in turn are studied and analyzed in order to determine local, regional, national, and international policies regarding all aspects relevant to the welfare of society. One important aspect of that process is the visualization of statistical data with embedded geographical information, which most often relies on archaic methods such as maps colored according to graded scales. In this work, we apply nonstandard visualization techniques based on physical principles. We illustrate the method with recent statistics on homicide rates in Brazil and their correlation to other publicly available data. This physics-based approach provides a novel tool that can be used by interdisciplinary teams investigating statistics and model projections in a variety of fields such as economics and gross domestic product research, public health and epidemiology, sociodemographics, political science, business and marketing, and many others.

  12. Precision Mapping of Laser-Driven Magnetic Fields and Their Evolution in High-Energy-Density Plasmas

    NASA Astrophysics Data System (ADS)

    Gao, Lan; Nilson, P.; Igumenshchev, I.; Haines, M. G.; Froula, D. H.; Betti, R.; Meyerhofer, D. D.

    2016-10-01

    The magnetic fields generated at the surface of a laser-irradiated planar solid target are mapped using ultrafast proton radiography. Thick (50 μm) plastic foils are irradiated with 4-kJ, 2.5-ns laser pulses focused to an intensity of 4 x 1014 W/cm2. The data show magnetic fields concentrated at the edge of the laser-focal region, well within the expanding coronal plasma. The magnetic-field spatial distribution is tracked and shows good agreement with 2D resistive magnetohydrodynamic simulations using the code DRACO when the Biermann battery source, fluid and Nernst advection, resistive magnetic diffusion, and Righi-Leduc heat flow are included. The work provides significant insight into the generation and transport of Biermann fields in laser-produced plasmas, particularly those used in laser-driven magnetic reconnection and laboratory astrophysics experiments. deceased.

  13. Mapping the conjugate and corotating storm-enhanced density during 17 March 2013 storm through data assimilation

    NASA Astrophysics Data System (ADS)

    Yue, Xinan; Wan, Weixing; Liu, Libo; Liu, Jing; Zhang, Shunrong; Schreiner, William S.; Zhao, Biqiang; Hu, Lianhuan

    2016-12-01

    The storm-enhanced density (SED) is an electron density enhancement phenomenon extending from the later afternoon at middle latitude to the noontime in high latitude within a narrow band during early stage of geomagnetic storm. Previous investigations were mostly focused on the northern America region due to sparse data coverage in other regions. Recent observational analysis and simulation studies have shown that the SED might be quite complicated both physically and spatial/temporal evolution. In this paper, we obtained the global ionospheric electron density with the spatial/temporal resolution of 5° in latitude, 10° in longitude, 30 km around F2 peak, and 0.5 h in time, during 17 March 2013 geomagnetic storm through assimilating ground and LEO-based total electron content (TEC) data into the model. A total of 450 ground-based Global Navigation Satellite Systems stations' and 10 LEO satellites' observations were applied in the assimilation. Of all the data, six satellites with ionospheric radio occultation profiling capability provided the key altitudinal variation information. The SED associated with the tongue of ionization (TOI) and boundary blob can be well identified from the data assimilation results, although their amplitude of enhancement was only up to 6 TECU (TEC unit, 1 TECU = 1016 el m-2). All structures show very dynamic and complicated time evolution features. During this storm time, we identified two separate SED/TOI/blob structures corotating from Europe to American with conjugate occurrence. This partly supports the mechanism of convection expansion. Given a significant amount of radio occultation will be available in the near future, this method will help up us to resolve global large-scale ionospheric disturbance down to very small spatial and temporal scale in storm time.

  14. An Atlas-Based Electron Density Mapping Method for Magnetic Resonance Imaging (MRI)-Alone Treatment Planning and Adaptive MRI-Based Prostate Radiation Therapy

    SciTech Connect

    Dowling, Jason A.; Lambert, Jonathan; Parker, Joel; Salvado, Olivier; Fripp, Jurgen; Capp, Anne; Wratten, Chris; Denham, James W.; Greer, Peter B.

    2012-05-01

    Purpose: Prostate radiation therapy dose planning directly on magnetic resonance imaging (MRI) scans would reduce costs and uncertainties due to multimodality image registration. Adaptive planning using a combined MRI-linear accelerator approach will also require dose calculations to be performed using MRI data. The aim of this work was to develop an atlas-based method to map realistic electron densities to MRI scans for dose calculations and digitally reconstructed radiograph (DRR) generation. Methods and Materials: Whole-pelvis MRI and CT scan data were collected from 39 prostate patients. Scans from 2 patients showed significantly different anatomy from that of the remaining patient population, and these patients were excluded. A whole-pelvis MRI atlas was generated based on the manually delineated MRI scans. In addition, a conjugate electron-density atlas was generated from the coregistered computed tomography (CT)-MRI scans. Pseudo-CT scans for each patient were automatically generated by global and nonrigid registration of the MRI atlas to the patient MRI scan, followed by application of the same transformations to the electron-density atlas. Comparisons were made between organ segmentations by using the Dice similarity coefficient (DSC) and point dose calculations for 26 patients on planning CT and pseudo-CT scans. Results: The agreement between pseudo-CT and planning CT was quantified by differences in the point dose at isocenter and distance to agreement in corresponding voxels. Dose differences were found to be less than 2%. Chi-squared values indicated that the planning CT and pseudo-CT dose distributions were equivalent. No significant differences (p > 0.9) were found between CT and pseudo-CT Hounsfield units for organs of interest. Mean {+-} standard deviation DSC scores for the atlas-based segmentation of the pelvic bones were 0.79 {+-} 0.12, 0.70 {+-} 0.14 for the prostate, 0.64 {+-} 0.16 for the bladder, and 0.63 {+-} 0.16 for the rectum

  15. Shell stability and conditions analyzed using a new method of extracting shell areal density maps from spectrally resolved images of direct-drive inertial confinement fusion implosions

    SciTech Connect

    Johns, H. M.; Mancini, R. C.; Nagayama, T.; Mayes, D. C.; Tommasini, R.; Smalyuk, V. A.; Regan, S. P.; Delettrez, J. A.

    2016-01-25

    In warm target direct-drive ICF implosion experiments performed at the OMEGA laser facility, plastic microballoons doped with a titanium tracer layer in the shell and filled with deuterium gas were imploded using a low-adiabat shaped laser pulse. Continuum radiation emitted in the core is transmitted through the tracer layer and the resulting spectrum recorded with a gated multi-monochromatic x-ray imager (MMI). Titanium K-shell line absorption spectra observed in the data are due to transitions in L-shell titanium ions driven by the backlighting continuum. The MMI data consist of an array of spectrally resolved images of the implosion. These 2-D space-resolved titanium spectral features constrain the plasma conditions and areal density of the titanium doped region of the shell. The MMI data were processed to obtain narrow-band images and space resolved spectra of titanium spectral features. Shell areal density maps, ρL(x,y), extracted using a new method using both narrow-band images and space resolved spectra are confirmed to be consistent within uncertainties. We report plasma conditions in the titanium-doped region of electron temperature (Te) = 400±28eV, electron number density (Ne) = 8.5x1024±2.5x1024 cm-3, and average areal density <ρR> = 86±7mg/cm2. Fourier analysis of areal density maps reveals shell modulations caused by hydrodynamic instability growth near the fuel-shell interface in the deceleration phase. We observe significant structure in modes l = 2-9, dominated by l = 2. We extract a target breakup fraction of 7.1±1.5% from our Fourier analysis. A new method for estimating mix width is evaluated against existing literature and our target breakup fraction. We estimate a mix width of 10.5±1μm.

  16. Dynamic drag force based on iterative density mapping: A new numerical tool for three-dimensional analysis of particle trajectories in a dielectrophoretic system.

    PubMed

    Knoerzer, Markus; Szydzik, Crispin; Tovar-Lopez, Francisco Javier; Tang, Xinke; Mitchell, Arnan; Khoshmanesh, Khashayar

    2016-02-01

    Dielectrophoresis is a widely used means of manipulating suspended particles within microfluidic systems. In order to efficiently design such systems for a desired application, various numerical methods exist that enable particle trajectory plotting in two or three dimensions based on the interplay of hydrodynamic and dielectrophoretic forces. While various models are described in the literature, few are capable of modeling interactions between particles as well as their surrounding environment as these interactions are complex, multifaceted, and computationally expensive to the point of being prohibitive when considering a large number of particles. In this paper, we present a numerical model designed to enable spatial analysis of the physical effects exerted upon particles within microfluidic systems employing dielectrophoresis. The model presents a means of approximating the effects of the presence of large numbers of particles through dynamically adjusting hydrodynamic drag force based on particle density, thereby introducing a measure of emulated particle-particle and particle-liquid interactions. This model is referred to as "dynamic drag force based on iterative density mapping." The resultant numerical model is used to simulate and predict particle trajectory and velocity profiles within a microfluidic system incorporating curved dielectrophoretic microelectrodes. The simulated data are compared favorably with experimental data gathered using microparticle image velocimetry, and is contrasted against simulated data generated using traditional "effective moment Stokes-drag method," showing more accurate particle velocity profiles for areas of high particle density.

  17. Near-Atomic Resolution Structure Determination of a Cypovirus Capsid and Polymerase Complex Using Cryo-EM at 200kV.

    PubMed

    Li, Xiaowu; Zhou, Niyun; Chen, Wenyuan; Zhu, Bin; Wang, Xurong; Xu, Bin; Wang, Jiawei; Liu, Hongrong; Cheng, Lingpeng

    2017-01-06

    Single-particle cryo-electron microscopy (cryo-EM) allows the high-resolution structural determination of biological assemblies in a near-native environment. However, all high-resolution (better than 3.5Å) cryo-EM structures reported to date were obtained by using 300kV transmission electron microscopes (TEMs). We report here the structures of a cypovirus capsid of 750-Å diameter at 3.3-Å resolution and of RNA-dependent RNA polymerase (RdRp) complexes within the capsid at 3.9-Å resolution using a 200-kV TEM. The newly resolved structure revealed conformational changes of two subdomains in the RdRp. These conformational changes, which were involved in RdRp's switch from non-transcribing to transcribing mode, suggest that the RdRp may facilitate the unwinding of genomic double-stranded RNA. The possibility of 3-Å resolution structural determinations for biological assemblies of relatively small sizes using cryo-EM at 200kV was discussed.

  18. High-density linkage maps fail to detect any genetic component to sex determination in a Rana temporaria family.

    PubMed

    Brelsford, A; Rodrigues, N; Perrin, N

    2016-01-01

    Sex chromosome differentiation in Rana temporaria varies strikingly among populations or families: whereas some males display well-differentiated Y haplotypes at microsatellite markers on linkage group 2 (LG2), others are genetically undistinguishable from females. We analysed with RADseq markers one family from a Swiss lowland population with no differentiated sex chromosomes, and where sibship analyses had failed to detect any association between the phenotypic sex of progeny and parental haplotypes. Offspring were reared in a common tank in outdoor conditions and sexed at the froglet stage. We could map a total of 2177 SNPs (1123 in the mother, 1054 in the father), recovering in both adults 13 linkage groups (= chromosome pairs) that were strongly syntenic to Xenopus tropicalis despite > 200 My divergence. Sexes differed strikingly in the localization of crossovers, which were uniformly distributed in the female but limited to chromosome ends in the male. None of the 2177 markers showed significant association with offspring sex. Considering the very high power of our analysis, we conclude that sex determination was not genetic in this family; which factors determined sex remain to be investigated.

  19. Computational neuroanatomy: mapping cell-type densities in the mouse brain, simulations from the Allen Brain Atlas

    NASA Astrophysics Data System (ADS)

    Grange, Pascal

    2015-09-01

    The Allen Brain Atlas of the adult mouse (ABA) consists of digitized expression profiles of thousands of genes in the mouse brain, co-registered to a common three-dimensional template (the Allen Reference Atlas).This brain-wide, genome-wide data set has triggered a renaissance in neuroanatomy. Its voxelized version (with cubic voxels of side 200 microns) is available for desktop computation in MATLAB. On the other hand, brain cells exhibit a great phenotypic diversity (in terms of size, shape and electrophysiological activity), which has inspired the names of some well-studied cell types, such as granule cells and medium spiny neurons. However, no exhaustive taxonomy of brain cell is available. A genetic classification of brain cells is being undertaken, and some cell types have been chraracterized by their transcriptome profiles. However, given a cell type characterized by its transcriptome, it is not clear where else in the brain similar cells can be found. The ABA can been used to solve this region-specificity problem in a data-driven way: rewriting the brain-wide expression profiles of all genes in the atlas as a sum of cell-type-specific transcriptome profiles is equivalent to solving a quadratic optimization problem at each voxel in the brain. However, the estimated brain-wide densities of 64 cell types published recently were based on one series of co-registered coronal in situ hybridization (ISH) images per gene, whereas the online ABA contains several image series per gene, including sagittal ones. In the presented work, we simulate the variability of cell-type densities in a Monte Carlo way by repeatedly drawing a random image series for each gene and solving the optimization problem. This yields error bars on the region-specificity of cell types.

  20. Synthetic observations of molecular clouds in a galactic centre environment - I. Studying maps of column density and integrated intensity

    NASA Astrophysics Data System (ADS)

    Bertram, Erik; Glover, Simon C. O.; Clark, Paul C.; Ragan, Sarah E.; Klessen, Ralf S.

    2016-02-01

    We run numerical simulations of molecular clouds, adopting properties similar to those found in the central molecular zone (CMZ) of the Milky Way. For this, we employ the moving mesh code AREPO and perform simulations which account for a simplified treatment of time-dependent chemistry and the non-isothermal nature of gas and dust. We perform simulations using an initial density of n0 = 103 cm-3 and a mass of 1.3 × 105 M⊙. Furthermore, we vary the virial parameter, defined as the ratio of kinetic and potential energy, α = Ekin/|Epot|, by adjusting the velocity dispersion. We set it to α = 0.5, 2.0 and 8.0, in order to analyse the impact of the kinetic energy on our results. We account for the extreme conditions in the CMZ and increase both the interstellar radiation field (ISRF) and the cosmic ray flux (CRF) by a factor of 1000 compared to the values found in the solar neighbourhood. We use the radiative transfer code RADMC-3D to compute synthetic images in various diagnostic lines. These are [C II] at 158 μm, [O I] (145 μm), [O I] (63 μm), 12CO (J = 1 → 0) and 13CO (J = 1 → 0) at 2600 and 2720 μm, respectively. When α is large, the turbulence disperses much of the gas in the cloud, reducing its mean density and allowing the ISRF to penetrate more deeply into the cloud's interior. This significantly alters the chemical composition of the cloud, leading to the dissociation of a significant amount of the molecular gas. On the other hand, when α is small, the cloud remains compact, allowing more of the molecular gas to survive. We show that in each case the atomic tracers accurately reflect most of the physical properties of both the H2 and the total gas of the cloud and that they provide a useful alternative to molecular lines when studying the interstellar medium in the CMZ.

  1. Computer controlled performance mapping of thermionic converters: effect of collector, guard-ring potential imbalances on the observed collector current-density, voltage characteristics and limited range performance map of an etched-rhenium, niobium planar converter

    NASA Technical Reports Server (NTRS)

    Manista, E. J.

    1972-01-01

    The effect of collector, guard-ring potential imbalance on the observed collector-current-density J, collector-to-emitter voltage V characteristic was evaluated in a planar, fixed-space, guard-ringed thermionic converter. The J,V characteristic was swept in a period of 15 msec by a variable load. A computerized data acquisition system recorded test parameters. The results indicate minimal distortion of the J,V curve in the power output quadrant for the nominal guard-ring circuit configuration. Considerable distortion, along with a lowering of the ignited-mode striking voltage, was observed for the configuration with the emitter shorted to the guard ring. A limited-range performance map of an etched-rhenium, niobium, planar converter was obtained by using an improved computer program for the data acquisition system.

  2. A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

    PubMed Central

    Kawakami, Takeshi; Smeds, Linnéa; Backström, Niclas; Husby, Arild; Qvarnström, Anna; Mugal, Carina F; Olason, Pall; Ellegren, Hans

    2014-01-01

    Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high-density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132 cm and a mean genetic distance between markers of 0.12 cm. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cm/Mb and correlated closely with chromosome size, from 2 cm/Mb for chromosomes >100 Mb to >10 cm/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cm was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes. PMID:24863701

  3. Mobile brain/body imaging (MoBI): High-density electrical mapping of inhibitory processes during walking.

    PubMed

    De Sanctis, Pierfilippo; Butler, John S; Green, Jason M; Snyder, Adam C; Foxe, John J

    2012-01-01

    The present study investigated the feasibility of acquiring high-density event-related brain potential (ERP) recordings during treadmill walking in human subjects. The work builds upon recent studies testing the applicability of real-world tasks while obtaining electroencephalographic (EEG) recordings. Participants performed a response inhibition GO/NOGO task - designed to evoke a P3 component for correct response inhibitions and an error-related negativity (ERN) for incorrect commission errors - while speed of walking was experimentally manipulated. Robust P3 and ERN components were obtained under all experimental conditions - while participants were sitting, walking at moderate speed (2.4 km/hour), or walking rapidly (5 km/hour). Signal-to-noise ratios were remarkably similar across conditions, pointing to the feasibility of high-fidelity ERP recordings under relatively vigorous activity regimens. There is considerable research and clinical motivation to obtain high quality neurophysiological measures under more naturalistic environmental settings such as these. Strong links between cognitive load and gait abnormalities are seen in a number of clinical populations and these MoBI technologies provide highly promising methods for gaining insights into the underlying pathophysiology.

  4. Mapping of cortical activity in the first two decades of life: a high-density sleep electroencephalogram study.

    PubMed

    Kurth, Salomé; Ringli, Maya; Geiger, Anja; LeBourgeois, Monique; Jenni, Oskar G; Huber, Reto

    2010-10-06

    Evidence that electroencephalography (EEG) slow-wave activity (SWA) (EEG spectral power in the 1-4.5 Hz band) during non-rapid eye movement sleep (NREM) reflects plastic changes is increasing (Tononi and Cirelli, 2006). Regional assessment of gray matter development from neuroimaging studies reveals a posteroanterior trajectory of cortical maturation in the first three decades of life (Shaw et al., 2008). Our aim was to test whether this regional cortical maturation is reflected in regional changes of sleep SWA. We evaluated all-night high-density EEG (128 channels) in 55 healthy human subjects (2.4-19.4 years) and assessed age-related changes in NREM sleep topography. As in adults, we observed frequency-specific topographical distributions of sleep EEG power in all subjects. However, from early childhood to late adolescence, the location on the scalp showing maximal SWA underwent a shift from posterior to anterior regions. This shift along the posteroanterior axis was only present in the SWA frequency range and remained stable across the night. Changes in the topography of SWA during sleep parallel neuroimaging study findings indicating cortical maturation starts early in posterior areas and spreads rostrally over the frontal cortex. Thus, SWA might reflect the underlying processes of cortical maturation. In the future, sleep SWA assessments may be used as a clinical tool to detect aberrations in cortical maturation.

  5. Detailed deposition density maps constructed by large-scale soil sampling for gamma-ray emitting radioactive nuclides from the Fukushima Dai-ichi Nuclear Power Plant accident.

    PubMed

    Saito, Kimiaki; Tanihata, Isao; Fujiwara, Mamoru; Saito, Takashi; Shimoura, Susumu; Otsuka, Takaharu; Onda, Yuichi; Hoshi, Masaharu; Ikeuchi, Yoshihiro; Takahashi, Fumiaki; Kinouchi, Nobuyuki; Saegusa, Jun; Seki, Akiyuki; Takemiya, Hiroshi; Shibata, Tokushi

    2015-01-01

    Soil deposition density maps of gamma-ray emitting radioactive nuclides from the Fukushima Dai-ichi Nuclear Power Plant (NPP) accident were constructed on the basis of results from large-scale soil sampling. In total 10,915 soil samples were collected at 2168 locations. Gamma rays emitted from the samples were measured by Ge detectors and analyzed using a reliable unified method. The determined radioactivity was corrected to that of June 14, 2011 by considering the intrinsic decay constant of each nuclide. Finally the deposition maps were created for (134)Cs, (137)Cs, (131)I, (129m)Te and (110m)Ag. The radioactivity ratio of (134)Cs-(137)Cs was almost constant at 0.91 regardless of the locations of soil sampling. The radioactivity ratios of (131)I and (129m)Te-(137)Cs were relatively high in the regions south of the Fukushima NPP site. Effective doses for 50 y after the accident were evaluated for external and inhalation exposures due to the observed radioactive nuclides. The radiation doses from radioactive cesium were found to be much higher than those from the other radioactive nuclides.

  6. A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses.

    PubMed Central

    Bowers, John E; Abbey, Colette; Anderson, Sharon; Chang, Charlene; Draye, Xavier; Hoppe, Alison H; Jessup, Russell; Lemke, Cornelia; Lennington, Jennifer; Li, Zhikang; Lin, Yann-Rong; Liu, Sin-Chieh; Luo, Lijun; Marler, Barry S; Ming, Reiguang; Mitchell, Sharon E; Qiang, Dou; Reischmann, Kim; Schulze, Stefan R; Skinner, D Neil; Wang, Yue-Wen; Kresovich, Stephen; Schertz, Keith F; Paterson, Andrew H

    2003-01-01

    We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM ( approximately 300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of density are related to possible centromeric regions and to probable chromosome structural rearrangements between Sorghum bicolor and S. propinquum, but not to variation in levels of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny-in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops. PMID:14504243

  7. The neural dynamics of somatosensory processing and adaptation across childhood: a high-density electrical mapping study

    PubMed Central

    Uppal, Neha; Foxe, John J.; Butler, John S.; Acluche, Frantzy

    2016-01-01

    Young children are often hyperreactive to somatosensory inputs hardly noticed by adults, as exemplified by irritation to seams or labels in clothing. The neurodevelopmental mechanisms underlying changes in sensory reactivity are not well understood. Based on the idea that neurodevelopmental changes in somatosensory processing and/or changes in sensory adaptation might underlie developmental differences in somatosensory reactivity, high-density electroencephalography was used to examine how the nervous system responds and adapts to repeated vibrotactile stimulation over childhood. Participants aged 6–18 yr old were presented with 50-ms vibrotactile stimuli to the right wrist over the median nerve at 5 blocked interstimulus intervals (ranging from ∼7 to ∼1 stimulus per second). Somatosensory evoked potentials (SEPs) revealed three major phases of activation within the first 200 ms, with scalp topographies suggestive of neural generators in contralateral somatosensory cortex. Although overall SEPs were highly similar for younger, middle, and older age groups (6.1–9.8, 10.0–12.9, and 13.0–17.8 yr old), there were significant age-related amplitude differences in initial and later phases of the SEP. In contrast, robust adaptation effects for fast vs. slow presentation rates were observed that did not differ as a function of age. A greater amplitude response in the later portion of the SEP was observed for the youngest group and may be related to developmental changes in responsivity to somatosensory stimuli. These data suggest the protracted development of the somatosensory system over childhood, whereas adaptation, as assayed in this study, is largely in place by ∼7 yr of age. PMID:26763781

  8. Fine Mapping of Five Loci Associated with Low-Density Lipoprotein Cholesterol Detects Variants That Double the Explained Heritability

    PubMed Central

    Sidore, Carlo; Kang, Hyun M.; Jackson, Anne U.; Piras, Maria Grazia; Usala, Gianluca; Maninchedda, Giuseppe; Sassu, Alessandro; Serra, Fabrizio; Palmas, Maria Antonietta; Wood, William H.; Njølstad, Inger; Laakso, Markku; Hveem, Kristian; Tuomilehto, Jaakko; Lakka, Timo A.; Rauramaa, Rainer; Boehnke, Michael; Cucca, Francesco; Uda, Manuela; Schlessinger, David; Nagaraja, Ramaiah; Abecasis, Gonçalo R.

    2011-01-01

    Complex trait genome-wide association studies (GWAS) provide an efficient strategy for evaluating large numbers of common variants in large numbers of individuals and for identifying trait-associated variants. Nevertheless, GWAS often leave much of the trait heritability unexplained. We hypothesized that some of this unexplained heritability might be due to common and rare variants that reside in GWAS identified loci but lack appropriate proxies in modern genotyping arrays. To assess this hypothesis, we re-examined 7 genes (APOE, APOC1, APOC2, SORT1, LDLR, APOB, and PCSK9) in 5 loci associated with low-density lipoprotein cholesterol (LDL-C) in multiple GWAS. For each gene, we first catalogued genetic variation by re-sequencing 256 Sardinian individuals with extreme LDL-C values. Next, we genotyped variants identified by us and by the 1000 Genomes Project (totaling 3,277 SNPs) in 5,524 volunteers. We found that in one locus (PCSK9) the GWAS signal could be explained by a previously described low-frequency variant and that in three loci (PCSK9, APOE, and LDLR) there were additional variants independently associated with LDL-C, including a novel and rare LDLR variant that seems specific to Sardinians. Overall, this more detailed assessment of SNP variation in these loci increased estimates of the heritability of LDL-C accounted for by these genes from 3.1% to 6.5%. All association signals and the heritability estimates were successfully confirmed in a sample of ∼10,000 Finnish and Norwegian individuals. Our results thus suggest that focusing on variants accessible via GWAS can lead to clear underestimates of the trait heritability explained by a set of loci. Further, our results suggest that, as prelude to large-scale sequencing efforts, targeted re-sequencing efforts paired with large-scale genotyping will increase estimates of complex trait heritability explained by known loci. PMID:21829380

  9. Spatio-temporal dynamics of adaptation in the human visual system: A high-density electrical mapping study

    PubMed Central

    Andrade, Gizely N.; Butler, John S.; Mercier, Manuel R.; Molholm, Sophie; Foxe, John J.

    2015-01-01

    When sensory inputs are presented serially, response amplitudes to stimulus repetitions generally decrease as a function of presentation rate, diminishing rapidly as inter-stimulus-intervals (ISIs) fall below a second. This “adaptation” is believed to represent mechanisms by which sensory systems reduce responsivity to consistent environmental inputs, freeing resources to respond to potentially more relevant inputs. While auditory adaptation functions have been relatively well-characterized, considerably less is known about visual adaptation in humans. Here, high-density visual evoked potentials (VEPs) were recorded while two paradigms were used to interrogate visual adaptation. The first presented stimulus pairs with varying ISIs, comparing VEP amplitude to the second stimulus to that of the first (paired-presentation). The second involved blocks of stimulation (N=100) at various ISIs and comparison of VEP amplitude between blocks of differing ISIs (block-presentation). Robust VEP modulations were evident as a function of presentation rate in the block-paradigm with strongest modulations in the 130–150ms and 160–180ms visual processing phases. In paired-presentations, with ISIs of just 200–300 ms, an enhancement of VEP was evident when comparing S2 to S1, with no significant effect of presentation rate. Importantly, in block-presentations, adaptation effects were statistically robust at the individual participant level. These data suggest that a more taxing block-presentation paradigm is better suited to engage visual adaptation mechanisms than a paired-presentation design. The increased sensitivity of the visual processing metric obtained in the block-paradigm has implications for the examination of visual processing deficits in clinical populations. PMID:25688539

  10. Multisensory representation of frequency across audition and touch: High density electrical mapping reveals early sensory-perceptual coupling

    PubMed Central

    Butler, John S.; Foxe, John J.; Fiebelkorn, Ian C.; Mercier, Manuel; Molholm, Sophie

    2013-01-01

    The frequency of environmental vibrations is sampled by two of the major sensory systems, audition and touch, notwithstanding that these signals are transduced through very different physical media and entirely separate sensory epithelia. Psychophysical studies have shown that manipulating frequency in audition or touch can have a significant cross-sensory impact on perceived frequency in the other sensory system, pointing to intimate links between these senses during computation of frequency. In this regard, the frequency of a vibratory event can be thought of as a multisensory perceptual construct. In turn, electrophysiological studies point to temporally early multisensory interactions that occur in hierarchically early sensory regions where convergent inputs from the auditory and somatosensory systems are to be found. A key question pertains to the level of processing at which the multisensory integration of featural information such as frequency occurs. Do the sensory systems calculate frequency independently before this information is combined, or is this feature calculated in an integrated fashion during pre-attentive sensory processing? The well-characterized mismatch negativity, an electrophysiological response that indexes pre-attentive detection of a change within the context of a regular pattern of stimulation, served as our dependent measure. High-density electrophysiological recordings were made in humans while they were presented with separate blocks of somatosensory, auditory, and audio-somatosensory “standards” and “deviants”, where the deviant differed in frequency. Multisensory effects were identified beginning at ~200ms, with the multisensory MMN significantly different from the sum of the unisensory MMNs. This provides compelling evidence for preattentive coupling between the somatosensory and auditory channels in the cortical representation of frequency. PMID:23115172

  11. Spatio-temporal dynamics of adaptation in the human visual system: a high-density electrical mapping study.

    PubMed

    Andrade, Gizely N; Butler, John S; Mercier, Manuel R; Molholm, Sophie; Foxe, John J

    2015-04-01

    When sensory inputs are presented serially, response amplitudes to stimulus repetitions generally decrease as a function of presentation rate, diminishing rapidly as inter-stimulus intervals (ISIs) fall below 1 s. This 'adaptation' is believed to represent mechanisms by which sensory systems reduce responsivity to consistent environmental inputs, freeing resources to respond to potentially more relevant inputs. While auditory adaptation functions have been relatively well characterized, considerably less is known about visual adaptation in humans. Here, high-density visual-evoked potentials (VEPs) were recorded while two paradigms were used to interrogate visual adaptation. The first presented stimulus pairs with varying ISIs, comparing VEP amplitude to the second stimulus with that of the first (paired-presentation). The second involved blocks of stimulation (N = 100) at various ISIs and comparison of VEP amplitude between blocks of differing ISIs (block-presentation). Robust VEP modulations were evident as a function of presentation rate in the block-paradigm, with strongest modulations in the 130-150 ms and 160-180 ms visual processing phases. In paired-presentations, with ISIs of just 200-300 ms, an enhancement of VEP was evident when comparing S2 with S1, with no significant effect of presentation rate. Importantly, in block-presentations, adaptation effects were statistically robust at the individual participant level. These data suggest that a more taxing block-presentation paradigm is better suited to engage visual adaptation mechanisms than a paired-presentation design. The increased sensitivity of the visual processing metric obtained in the block-paradigm has implications for the examination of visual processing deficits in clinical populations.

  12. A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest

    PubMed Central

    Arenz, Stefan; Bock, Lars V.; Graf, Michael; Innis, C. Axel; Beckmann, Roland; Grubmüller, Helmut; Vaiana, Andrea C.; Wilson, Daniel N.

    2016-01-01

    Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-Å-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation. PMID:27380950

  13. Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage [psi]29 tail

    SciTech Connect

    Xiang, Ye; Morais, Marc C.; Cohen, Daniel N.; Bowman, Valorie D.; Anderson, Dwight L.; Rossmann, Michael G.

    2009-08-28

    The small bacteriophage {phi}29 must penetrate the {approx}250-{angstrom} thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome through its tail into the bacterial cytoplasm. The tail of bacteriophage {phi}29 is noncontractile and {approx}380 {angstrom} long. A 1.8-{angstrom} resolution crystal structure of gene product 13 (gp13) shows that this tail protein has spatially well separated N- and C-terminal domains, whose structures resemble lysozyme-like enzymes and metallo-endopeptidases, respectively. CryoEM reconstructions of the WT bacteriophage and mutant bacteriophages missing some or most of gp13 shows that this enzyme is located at the distal end of the {phi}29 tail knob. This finding suggests that gp13 functions as a tail-associated, peptidoglycan-degrading enzyme able to cleave both the polysaccharide backbone and peptide cross-links of the peptidoglycan cell wall. Comparisons of the gp13{sup -} mutants with the {phi}29 mature and emptied phage structures suggest the sequence of events that occur during the penetration of the tail through the peptidoglycan layer.

  14. Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution

    NASA Astrophysics Data System (ADS)

    Quade, Nick; Boehringer, Daniel; Leibundgut, Marc; van den Heuvel, Joop; Ban, Nenad

    2015-07-01

    Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome-HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs.

  15. Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution

    PubMed Central

    Quade, Nick; Boehringer, Daniel; Leibundgut, Marc; van den Heuvel, Joop; Ban, Nenad

    2015-01-01

    Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5′-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome–HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs. PMID:26155016

  16. A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest

    NASA Astrophysics Data System (ADS)

    Arenz, Stefan; Bock, Lars V.; Graf, Michael; Innis, C. Axel; Beckmann, Roland; Grubmüller, Helmut; Vaiana, Andrea C.; Wilson, Daniel N.

    2016-07-01

    Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-Å-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation.

  17. Cryo-EM study of slow bee paralysis virus at low pH reveals iflavirus genome release mechanism

    PubMed Central

    Kalynych, Sergei; Füzik, Tibor; Přidal, Antonín; de Miranda, Joachim; Plevka, Pavel

    2017-01-01

    Viruses from the family Iflaviridae are insect pathogens. Many of them, including slow bee paralysis virus (SBPV), cause lethal diseases in honeybees and bumblebees, resulting in agricultural losses. Iflaviruses have nonenveloped icosahedral virions containing single-stranded RNA genomes. However, their genome release mechanism is unknown. Here, we show that low pH promotes SBPV genome release, indicating that the virus may use endosomes to enter host cells. We used cryo-EM to study a heterogeneous population of SBPV virions at pH 5.5. We determined the structures of SBPV particles before and after genome release to resolutions of 3.3 and 3.4 Å, respectively. The capsids of SBPV virions in low pH are not expanded. Thus, SBPV does not appear to form “altered” particles with pores in their capsids before genome release, as is the case in many related picornaviruses. The egress of the genome from SBPV virions is associated with a loss of interpentamer contacts mediated by N-terminal arms of VP2 capsid proteins, which result in the expansion of the capsid. Pores that are 7 Å in diameter form around icosahedral threefold symmetry axes. We speculate that they serve as channels for the genome release. Our findings provide an atomic-level characterization of the genome release mechanism of iflaviruses. PMID:28053231

  18. Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.

    PubMed

    Zhang, Junjie; Ma, Boxue; DiMaio, Frank; Douglas, Nicholai R; Joachimiak, Lukasz A; Baker, David; Frydman, Judith; Levitt, Michael; Chiu, Wah

    2011-05-11

    Chaperonins are large ATP-driven molecular machines that mediate cellular protein folding. Group II chaperonins use their "built-in lid" to close their central folding chamber. Here we report the structure of an archaeal group II chaperonin in its prehydrolysis ATP-bound state at subnanometer resolution using single particle cryo-electron microscopy (cryo-EM). Structural comparison of Mm-cpn in ATP-free, ATP-bound, and ATP-hydrolysis states reveals that ATP binding alone causes the chaperonin to close slightly with a ∼45° counterclockwise rotation of the apical domain. The subsequent ATP hydrolysis drives each subunit to rock toward the folding chamber and to close the lid completely. These motions are attributable to the local interactions of specific active site residues with the nucleotide, the tight couplings between the apical and intermediate domains within the subunit, and the aligned interactions between two subunits across the rings. This mechanism of structural changes in response to ATP is entirely different from those found in group I chaperonins.

  19. Cryo-EM visualization of the ribosome in termination complex with apo-RF3 and RF1.

    PubMed

    Pallesen, Jesper; Hashem, Yaser; Korkmaz, Gürkan; Koripella, Ravi Kiran; Huang, Chenhui; Ehrenberg, Måns; Sanyal, Suparna; Frank, Joachim

    2013-06-04

    Termination of messenger RNA translation in Bacteria and Archaea is initiated by release factors (RFs) 1 or 2 recognizing a stop codon in the ribosomal A site and releasing the peptide from the P-site transfer RNA. After release, RF-dissociation is facilitated by the G-protein RF3. Structures of ribosomal complexes with RF1 or RF2 alone or with RF3 alone-RF3 bound to a non-hydrolyzable GTP-analog-have been reported. Here, we present the cryo-EM structure of a post-termination ribosome containing both apo-RF3 and RF1. The conformation of RF3 is distinct from those of free RF3•GDP and ribosome-bound RF3•GDP(C/N)P. Furthermore, the conformation of RF1 differs from those observed in RF3-lacking ribosomal complexes. Our study provides structural keys to the mechanism of guanine nucleotide exchange on RF3 and to an L12-mediated ribosomal recruitment of RF3. In conjunction with previous observations, our data provide the foundation to structurally characterize the complete action cycle of the G-protein RF3. DOI:http://dx.doi.org/10.7554/eLife.00411.001.

  20. Cryo-EM visualization of the ribosome in termination complex with apo-RF3 and RF1

    PubMed Central

    Pallesen, Jesper; Hashem, Yaser; Korkmaz, Gürkan; Koripella, Ravi Kiran; Huang, Chenhui; Ehrenberg, Måns; Sanyal, Suparna; Frank, Joachim

    2013-01-01

    Termination of messenger RNA translation in Bacteria and Archaea is initiated by release factors (RFs) 1 or 2 recognizing a stop codon in the ribosomal A site and releasing the peptide from the P-site transfer RNA. After release, RF-dissociation is facilitated by the G-protein RF3. Structures of ribosomal complexes with RF1 or RF2 alone or with RF3 alone—RF3 bound to a non-hydrolyzable GTP-analog—have been reported. Here, we present the cryo-EM structure of a post-termination ribosome containing both apo-RF3 and RF1. The conformation of RF3 is distinct from those of free RF3•GDP and ribosome-bound RF3•GDP(C/N)P. Furthermore, the conformation of RF1 differs from those observed in RF3-lacking ribosomal complexes. Our study provides structural keys to the mechanism of guanine nucleotide exchange on RF3 and to an L12-mediated ribosomal recruitment of RF3. In conjunction with previous observations, our data provide the foundation to structurally characterize the complete action cycle of the G-protein RF3. DOI: http://dx.doi.org/10.7554/eLife.00411.001 PMID:23755360

  1. Aging alterations in whole-brain networks during adulthood mapped with the minimum spanning tree indices: the interplay of density, connectivity cost and life-time trajectory.

    PubMed

    Otte, Willem M; van Diessen, Eric; Paul, Subhadip; Ramaswamy, Rajiv; Subramanyam Rallabandi, V P; Stam, Cornelis J; Roy, Prasun K

    2015-04-01

    The organizational network changes in the human brain across the lifespan have been mapped using functional and structural connectivity data. Brain network changes provide valuable insights into the processes underlying senescence. Nonetheless, the altered network density in the elderly severely compromises the usefulness of network analysis to study the aging brain. We successfully circumvented this problem by focusing on the critical structural network backbone, using a robust tree representation. Whole-brain networks' minimum spanning trees were determined in a dataset of diffusion-weighted images from 382 healthy subjects, ranging in age from 20.2 to 86.2 years. Tree-based metrics were compared with classical network metrics. In contrast to the tree-based metrics, classical metrics were highly influenced by age-related changes in network density. Tree-based metrics showed linear and non-linear correlation across adulthood and are in close accordance with results from previous histopathological characterizations of the changes in white matter integrity in the aging brain.

  2. CXCL13/CXCR5 enhances sodium channel Nav1.8 current density via p38 MAP kinase in primary sensory neurons following inflammatory pain.

    PubMed

    Wu, Xiao-Bo; Cao, De-Li; Zhang, Xin; Jiang, Bao-Chun; Zhao, Lin-Xia; Qian, Bin; Gao, Yong-Jing

    2016-10-06

    CXCL13 is a B lymphocyte chemoattractant and activates CXCR5 receptor in the immune system. Here we investigated whether CXCL13/CXCR5 mediates inflammatory pain in dorsal root ganglia (DRG) and the underlying mechanisms. Peripheral injection of complete Freund's Adjuvant (CFA) increased the expression of CXCL13 and CXCR5 in DRG neurons. In Cxcr5(-/-) mice, CFA-induced pain hypersensitivity were attenuated. Whole-cell patch-clamp recording showed that the excitability of dissociated DRG neurons was increased after CFA injection or CXCL13 incubation from wild-type (WT) mice, but not from Cxcr5(-/-) mice. Additionally, sodium channel Nav1.8 was co-expressed with CXCR5 in dissociated DRG neurons, and the increased neuronal excitability induced by CFA or CXCL13 was reduced by Nav1.8 blocker. Intrathecal injection of Nav1.8 blocker also attenuated intrathecal injection of CXCL13-induced pain hypersensitivity. Furthermore, CXCL13 increased Nav1.8 current density in DRG neurons, which was inhibited by p38 MAP kinase inhibitor. CFA and CXCL13 increased p38 phosphorylation in the DRG of WT mice but not Cxcr5(-/-) mice. Finally, intrathecal p38 inhibitor alleviated CXCL13-induced pain hypersensitivity. Taken together, these results demonstrated that CXCL13, upregulated by peripheral inflammation, acts on CXCR5 on DRG neurons and activates p38, which increases Nav1.8 current density and further contributes to the maintenance of inflammatory pain.

  3. Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

    PubMed Central

    Baker, Matthew L.; Hryc, Corey F.; Zhang, Qinfen; Wu, Weimin; Jakana, Joanita; Haase-Pettingell, Cameron; Afonine, Pavel V.; Adams, Paul D.; King, Jonathan A.; Jiang, Wen; Chiu, Wah

    2013-01-01

    High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidrug-resistant bacteria. Here, we improved upon our previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution sufficient to determine the tertiary structures of both gp7 and gp10 protein subunits that form the T = 7 icosahedral lattice. This study utilizes recently established best practice for near-atomic to high-resolution (3–5 Å) electron cryomicroscopy data evaluation. The resolution and reliability of the density map were cross-validated by multiple reconstructions from truly independent data sets, whereas the models of the individual protein subunits were validated adopting the best practices from X-ray crystallography. Some sidechain densities are clearly resolved and show the subunit–subunit interactions within and across the capsomeres that are required to stabilize the virus. The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages. PMID:23840063

  4. Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map

    PubMed Central

    Haile, Jemanesh K.; Cory, Aron T.; Clarke, Fran R.; Clarke, John M.; Knox, Ron E.; Pozniak, Curtis J.

    2017-01-01

    Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype

  5. Dissection of Genetic Factors underlying Wheat Kernel Shape and Size in an Elite × Nonadapted Cross using a High Density SNP Linkage Map.

    PubMed

    Kumar, Ajay; Mantovani, E E; Seetan, R; Soltani, A; Echeverry-Solarte, M; Jain, S; Simsek, S; Doehlert, D; Alamri, M S; Elias, E M; Kianian, S F; Mergoum, M

    2016-03-01

    Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL), developed using an elite (ND 705) and a nonadapted genotype (PI 414566), was extensively phenotyped in replicated field trials and genotyped using Infinium iSelect 90K assay to gain insight into the genetic architecture of kernel shape and size. A high density genetic map consisting of 10,172 single nucleotide polymorphism (SNP) markers, with an average marker density of 0.39 cM/marker, identified a total of 29 genomic regions associated with six grain shape and size traits; ∼80% of these regions were associated with multiple traits. The analyses showed that kernel length (KL) and width (KW) are genetically independent, while a large number (∼59%) of the quantitative trait loci (QTL) for kernel shape traits were in common with genomic regions associated with kernel size traits. The most significant QTL was identified on chromosome 4B, and could be an ortholog of major rice grain size and shape gene or . Major and stable loci also were identified on the homeologous regions of Group 5 chromosomes, and in the regions of (6A) and (7A) genes. Both parental genotypes contributed equivalent positive QTL alleles, suggesting that the nonadapted germplasm has a great potential for enhancing the gene pool for grain shape and size. This study provides new knowledge on the genetic dissection of kernel morphology, with a much higher resolution, which may aid further improvement in wheat yield and quality using genomic tools.

  6. CXCL13/CXCR5 enhances sodium channel Nav1.8 current density via p38 MAP kinase in primary sensory neurons following inflammatory pain

    PubMed Central

    Wu, Xiao-Bo; Cao, De-Li; Zhang, Xin; Jiang, Bao-Chun; Zhao, Lin-Xia; Qian, Bin; Gao, Yong-Jing

    2016-01-01

    CXCL13 is a B lymphocyte chemoattractant and activates CXCR5 receptor in the immune system. Here we investigated whether CXCL13/CXCR5 mediates inflammatory pain in dorsal root ganglia (DRG) and the underlying mechanisms. Peripheral injection of complete Freund’s Adjuvant (CFA) increased the expression of CXCL13 and CXCR5 in DRG neurons. In Cxcr5−/− mice, CFA-induced pain hypersensitivity were attenuated. Whole-cell patch-clamp recording showed that the excitability of dissociated DRG neurons was increased after CFA injection or CXCL13 incubation from wild-type (WT) mice, but not from Cxcr5−/− mice. Additionally, sodium channel Nav1.8 was co-expressed with CXCR5 in dissociated DRG neurons, and the increased neuronal excitability induced by CFA or CXCL13 was reduced by Nav1.8 blocker. Intrathecal injection of Nav1.8 blocker also attenuated intrathecal injection of CXCL13-induced pain hypersensitivity. Furthermore, CXCL13 increased Nav1.8 current density in DRG neurons, which was inhibited by p38 MAP kinase inhibitor. CFA and CXCL13 increased p38 phosphorylation in the DRG of WT mice but not Cxcr5−/− mice. Finally, intrathecal p38 inhibitor alleviated CXCL13-induced pain hypersensitivity. Taken together, these results demonstrated that CXCL13, upregulated by peripheral inflammation, acts on CXCR5 on DRG neurons and activates p38, which increases Nav1.8 current density and further contributes to the maintenance of inflammatory pain. PMID:27708397

  7. Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions

    PubMed Central

    Guo, Fei; Liu, Zheng; Fang, Ping-An; Zhang, Qinfen; Wright, Elena T.; Wu, Weimin; Zhang, Ci; Vago, Frank; Ren, Yue; Jakana, Joanita; Chiu, Wah; Serwer, Philip; Jiang, Wen

    2014-01-01

    Many dsDNA viruses first assemble a DNA-free procapsid, using a scaffolding protein-dependent process. The procapsid, then, undergoes dramatic conformational maturation while packaging DNA. For bacteriophage T7 we report the following four single-particle cryo-EM 3D reconstructions and the derived atomic models: procapsid (4.6-Å resolution), an early-stage DNA packaging intermediate (3.5 Å), a later-stage packaging intermediate (6.6 Å), and the final infectious phage (3.6 Å). In the procapsid, the N terminus of the major capsid protein, gp10, has a six-turn helix at the inner surface of the shell, where each skewed hexamer of gp10 interacts with two scaffolding proteins. With the exit of scaffolding proteins during maturation the gp10 N-terminal helix unfolds and swings through the capsid shell to the outer surface. The refolded N-terminal region has a hairpin that forms a novel noncovalent, joint-like, intercapsomeric interaction with a pocket formed during shell expansion. These large conformational changes also result in a new noncovalent, intracapsomeric topological linking. Both interactions further stabilize the capsids by interlocking all pentameric and hexameric capsomeres in both DNA packaging intermediate and phage. Although the final phage shell has nearly identical structure to the shell of the DNA-free intermediate, surprisingly we found that the icosahedral faces of the phage are slightly (∼4 Å) contracted relative to the faces of the intermediate, despite the internal pressure from the densely packaged DNA genome. These structures provide a basis for understanding the capsid maturation process during DNA packaging that is essential for large numbers of dsDNA viruses. PMID:25313071

  8. Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions.

    PubMed

    Guo, Fei; Liu, Zheng; Fang, Ping-An; Zhang, Qinfen; Wright, Elena T; Wu, Weimin; Zhang, Ci; Vago, Frank; Ren, Yue; Jakana, Joanita; Chiu, Wah; Serwer, Philip; Jiang, Wen

    2014-10-28

    Many dsDNA viruses first assemble a DNA-free procapsid, using a scaffolding protein-dependent process. The procapsid, then, undergoes dramatic conformational maturation while packaging DNA. For bacteriophage T7 we report the following four single-particle cryo-EM 3D reconstructions and the derived atomic models: procapsid (4.6-Å resolution), an early-stage DNA packaging intermediate (3.5 Å), a later-stage packaging intermediate (6.6 Å), and the final infectious phage (3.6 Å). In the procapsid, the N terminus of the major capsid protein, gp10, has a six-turn helix at the inner surface of the shell, where each skewed hexamer of gp10 interacts with two scaffolding proteins. With the exit of scaffolding proteins during maturation the gp10 N-terminal helix unfolds and swings through the capsid shell to the outer surface. The refolded N-terminal region has a hairpin that forms a novel noncovalent, joint-like, intercapsomeric interaction with a pocket formed during shell expansion. These large conformational changes also result in a new noncovalent, intracapsomeric topological linking. Both interactions further stabilize the capsids by interlocking all pentameric and hexameric capsomeres in both DNA packaging intermediate and phage. Although the final phage shell has nearly identical structure to the shell of the DNA-free intermediate, surprisingly we found that the icosahedral faces of the phage are slightly (∼4 Å) contracted relative to the faces of the intermediate, despite the internal pressure from the densely packaged DNA genome. These structures provide a basis for understanding the capsid maturation process during DNA packaging that is essential for large numbers of dsDNA viruses.

  9. Cryo-EM analysis of a domain antibody bound rotary ATPase complex.

    PubMed

    Davies, Roberta B; Smits, Callum; Wong, Andrew S W; Stock, Daniela; Christie, Mary; Sandin, Sara; Stewart, Alastair G

    2017-03-01

    The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins. Although previous studies suggested that the presence of fluoroaluminate in this complex could change the rotary state of this enzyme, we observed no gross structural rearrangements under these conditions.

  10. Analyzing the spatio-temporal relationship between dengue vector larval density and land-use using factor analysis and spatial ring mapping

    PubMed Central

    2012-01-01

    Background Dengue, a mosquito-borne febrile viral disease, is found in tropical and sub-tropical regions and is now extending its range to temperate regions. The spread of the dengue viruses mainly depends on vector population (Aedes aegypti and Aedes albopictus), which is influenced by changing climatic conditions and various land-use/land-cover types. Spatial display of the relationship between dengue vector density and land-cover types is required to describe a near-future viral outbreak scenario. This study is aimed at exploring how land-cover types are linked to the behavior of dengue-transmitting mosquitoes. Methods Surveys were conducted in 92 villages of Phitsanulok Province Thailand. The sampling was conducted on three separate occasions in the months of March, May and July. Dengue indices, i.e. container index (C.I.), house index (H.I.) and Breteau index (B.I.) were used to map habitats conducible to dengue vector growth. Spatial epidemiological analysis using Bivariate Pearson’s correlation was conducted to evaluate the level of interdependence between larval density and land-use types. Factor analysis using principal component analysis (PCA) with varimax rotation was performed to ascertain the variance among land-use types. Furthermore, spatial ring method was used as to visualize spatially referenced, multivariate and temporal data in single information graphic. Results Results of dengue indices showed that the settlements around gasoline stations/workshops, in the vicinity of marsh/swamp and rice paddy appeared to be favorable habitat for dengue vector propagation at highly significant and positive correlation (p = 0.001) in the month of May. Settlements around the institutional areas were highly significant and positively correlated (p = 0.01) with H.I. in the month of March. Moreover, dengue indices in the month of March showed a significant and positive correlation (p <= 0.05) with deciduous forest. The H.I. of people living around horticulture

  11. CryoEM and Molecular Dynamics of the Circadian KaiB-KaiC Complex Indicates That KaiB Monomers Interact with KaiC and Block ATP Binding Clefts

    SciTech Connect

    Villarreal, Seth A.; Pattanayek, Rekha; Williams, Dewight R.; Mori, Tetsuya; Qin, Ximing; Johnson, Carl H.; Egli, Martin; Stewart, Phoebe L.

    2014-10-02

    The circadian control of cellular processes in cyanobacteria is regulated by a posttranslational oscillator formed by three Kai proteins. During the oscillator cycle, KaiA serves to promote autophosphorylation of KaiC while KaiB counteracts this effect. Here, we present a crystallographic structure of the wild-type Synechococcus elongatus KaiB and a cryo-electron microscopy (cryoEM) structure of a KaiBC complex. The crystal structure shows the expected dimer core structure and significant conformational variations of the KaiB C-terminal region, which is functionally important in maintaining rhythmicity. The KaiBC sample was formed with a C-terminally truncated form of KaiC, KaiC-Δ489, which is persistently phosphorylated. The KaiB–KaiC-Δ489 structure reveals that the KaiC hexamer can bind six monomers of KaiB, which form a continuous ring of density in the KaiBC complex. We performed cryoEM-guided molecular dynamics flexible fitting simulations with crystal structures of KaiB and KaiC to probe the KaiBC protein–protein interface. This analysis indicated a favorable binding mode for the KaiB monomer on the CII end of KaiC, involving two adjacent KaiC subunits and spanning an ATP binding cleft. A KaiC mutation, R468C, which has been shown to affect the affinity of KaiB for KaiC and lengthen the period in a bioluminescence rhythm assay, is found within the middle of the predicted KaiBC interface. The proposed KaiB binding mode blocks access to the ATP binding cleft in the CII ring of KaiC, which provides insight into how KaiB might influence the phosphorylation status of KaiC.

  12. Statistical density modification using local pattern matching

    DOEpatents

    Terwilliger, Thomas C.

    2007-01-23

    A computer implemented method modifies an experimental electron density map. A set of selected known experimental and model electron density maps is provided and standard templates of electron density are created from the selected experimental and model electron density maps by clustering and averaging values of electron density in a spherical region about each point in a grid that defines each selected known experimental and model electron density maps. Histograms are also created from the selected experimental and model electron density maps that relate the value of electron density at the center of each of the spherical regions to a correlation coefficient of a density surrounding each corresponding grid point in each one of the standard templates. The standard templates and the histograms are applied to grid points on the experimental electron density map to form new estimates of electron density at each grid point in the experimental electron density map.

  13. Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map.

    PubMed

    Tayeh, Nadim; Aluome, Christelle; Falque, Matthieu; Jacquin, Françoise; Klein, Anthony; Chauveau, Aurélie; Bérard, Aurélie; Houtin, Hervé; Rond, Céline; Kreplak, Jonathan; Boucherot, Karen; Martin, Chantal; Baranger, Alain; Pilet-Nayel, Marie-Laure; Warkentin, Thomas D; Brunel, Dominique; Marget, Pascal; Le Paslier, Marie-Christine; Aubert, Grégoire; Burstin, Judith

    2015-12-01

    Single nucleotide polymorphism (SNP) arrays represent important genotyping tools for innovative strategies in both basic research and applied breeding. Pea is an important food, feed and sustainable crop with a large (about 4.45 Gbp) but not yet available genome sequence. In the present study, 12 pea recombinant inbred line populations were genotyped using the newly developed GenoPea 13.2K SNP Array. Individual and consensus genetic maps were built providing insights into the structure and organization of the pea genome. Largely collinear genetic maps of 3918-8503 SNPs were obtained from all mapping populations, and only two of these exhibited putative chromosomal rearrangement signatures. Similar distortion patterns in different populations were noted. A total of 12 802 transcript-derived SNP markers placed on a 15 079-marker high-density, high-resolution consensus map allowed the identification of ohnologue-rich regions within the pea genome and the localization of local duplicates. Dense syntenic networks with sequenced legume genomes were further established, paving the way for the identification of the molecular bases of important agronomic traits segregating in the mapping populations. The information gained on the structure and organization of the genome from this research will undoubtedly contribute to the understanding of the evolution of the pea genome and to its assembly. The GenoPea 13.2K SNP Array and individual and consensus genetic maps are valuable genomic tools for plant scientists to strengthen pea as a model for genetics and physiology and enhance breeding.

  14. Auditory processing in schizophrenia during the middle latency period (10–50 ms): high-density electrical mapping and source analysis reveal subcortical antecedents to early cortical deficits

    PubMed Central

    Leavitt, Victoria M.; Molholm, Sophie; Ritter, Walter; Shpaner, Marina; Foxe, John J.

    2007-01-01

    Introduction Auditory sensory processing dysfunction is a core component of schizophrenia, with deficits occurring at 50 ms post-stimulus firmly established in the literature. Given that the initial afference of primary auditory cortex occurs at least 35 ms earlier, however, an essential question remains: how early in sensory processing do such deficits arise, and do they occur during initial cortical afference or earlier, which would implicate subcortical auditory dysfunction. Objective To establish the onset of the earliest deficits in auditory processing, we examined the time window demarcating the transition from subcortical to cortical processing: 10 ms to 50 ms during the so-called middle latency responses (MLRs). These remain to be adequately characterized in patients with schizophrenia. Methods We recorded auditory evoked potentials (AEPs) to simple tone-pips from 15 control subjects and 21 medicated patients with longer-term schizophrenia or schizoaffective disorder (illness duration 16 yr, standard deviation [SD] 9.4 yr), using high-density electrical scalp recordings. Between-group analyses assessed the integrity of the MLRs across groups. In addition, 2 source-localization models were conducted to address whether a distinction between subcortical and cortical generators of the MLRs can be made and whether evidence for differential dorsal and ventral pathway contributions to auditory processing deficits can be established. Results Robust auditory processing deficits were found for patients as early as 15 ms. Evidence for subcortical generators of the earliest MLR component (P20) was provided by source analysis. Topographical mapping and source localization also pointed to greater decrements in processing in the dorsal auditory pathway of patients, providing support for a theory of pervasive deficits that are organized along the lines of a dorsal–ventral distinction. Conclusions Auditory sensory dysfunction in schizophrenia begins extremely early in

  15. A 1. 8-Mb YAC contig in Xp11. 23: Identification of Cpg islands and physical mapping of CA repeats in a region of high gene density

    SciTech Connect

    Coleman, M.P.; Nemeth, A.H.; Campbell, L.; Raut, C.P.; Davies, K.E. ); Weissenbach, J. )

    1994-05-15

    The genes ARAF1, SYN1, TIMP, and PFC are clustered within 70 kb of one another, and, as reported in the accompanying paper, at least four more genes map within 400 kb: a cluster of Krueppel-type zinc finger genes (including ZNF21, ZNF41, and ZNF81) and ELK-1, a member of the ets oncogene superfamily. This gene-rich region is of particular interest because of the large number of disease genes mapping to Xp11.23: At least three eye diseases (retinitis pigmentosa type 2, congenital stationary night blindness CSNB1, and Aland Island eye disease), Wiskott-Aldrich syndrome, X-linked nephrolithiasis, and a translocation breakpoint associated with synovial sarcoma. The authors have constructed a 1.8-Mb YAC contig in this region, confirming the link between TIMP and OATL1 reported by Knight et al. (1994) and extending the map in the distal direction. To investigate the likelihood that more genes are located within this region, they have carried out detailed mapping of rare-cutter restriction sites in these YACs and identified seven CpG islands. At least six of these islands are located over 50 kb from any known gene locations, suggesting that the region contains at least this many as yet unidentified genes. They have also mapped the physical locations of six highly polymorphic CA repeats within the contig, thus integrating the physical, genetic, and transcriptional maps of the region and facilitating the mapping and identification of disease genes. Together with the report by Knight et al., these data indicate the following order of loci: Xpter-DXS1264-DXS1055-DXS1003-DXS1146-DXS1266-(ZNF41, ARAF1)-SYN1 CA repeat-SYN1 (3[prime] end)-TIMP-SYN1 (5[prime] end)-PFC CA repeat-PFC-(DXS426, ELK1)-(DXS1265, ZNF81)-ZNF21-DXS1267-OATL1-Xcen. 40 refs., 4 figs., 3 tabs.

  16. Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

    PubMed

    Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

    2003-12-01

    Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

  17. Mapping the Baby Universe

    NASA Technical Reports Server (NTRS)

    Wanjek, Christopher

    2003-01-01

    In June, NASA plans to launch the Microwave Anisotropy Probe (MAP) to survey the ancient radiation in unprecedented detail. MAP will map slight temperature fluctuations within the microwave background that vary by only 0.00001 C across a chilly radiation that now averages 2.73 C above absolute zero. The temperature differences today point back to density differences in the fiery baby universe, in which there was a little more matter here and a little less matter there. Areas of slightly enhanced density had stronger gravity than low-density areas. The high-density areas pulled back on the background radiation, making it appear slightly cooler in those directions.

  18. Comparative High-Density Linkage Mapping Reveals Conserved Genome Structure but Variation in Levels of Heterochiasmy and Location of Recombination Cold Spots in the Common Frog

    PubMed Central

    Palomar, Gemma; Ahmad, Freed; Vasemägi, Anti; Matsuba, Chikako; Nicieza, Alfredo G.; Cano, José Manuel

    2016-01-01

    By combining 7077 SNPs and 61 microsatellites, we present the first linkage map for some of the early diverged lineages of the common frog, Rana temporaria, and the densest linkage map to date for this species. We found high homology with the published linkage maps of the Eastern and Western lineages but with differences in the order of some markers. Homology was also strong with the genome of the Tibetan frog Nanorana parkeri and we found high synteny with the clawed frog Xenopus tropicalis. We confirmed marked heterochiasmy between sexes and detected nonrecombining regions in several groups of the male linkage map. Contrary to the expectations set by the male heterogamety of the common frog, we did not find male heterozygosity excess in the chromosome previously shown to be linked to sex determination. Finally, we found blocks of loci showing strong transmission ratio distortion. These distorted genomic regions might be related to genetic incompatibilities between the parental populations, and are promising candidates for further investigation into the genetic basis of speciation and adaptation in the common frog. PMID:28040782

  19. SU-E-J-122: The CBCT Dose Calculation Using a Patient Specific CBCT Number to Mass Density Conversion Curve Based On a Novel Image Registration and Organ Mapping Method in Head-And-Neck Radiation Therapy

    SciTech Connect

    Zhou, J; Lasio, G; Chen, S; Zhang, B; Langen, K; Prado, K; D’Souza, W; Yi, B; Huang, J

    2015-06-15

    Purpose: To develop a CBCT HU correction method using a patient specific HU to mass density conversion curve based on a novel image registration and organ mapping method for head-and-neck radiation therapy. Methods: There are three steps to generate a patient specific CBCT HU to mass density conversion curve. First, we developed a novel robust image registration method based on sparseness analysis to register the planning CT (PCT) and the CBCT. Second, a novel organ mapping method was developed to transfer the organs at risk (OAR) contours from the PCT to the CBCT and corresponding mean HU values of each OAR were measured in both the PCT and CBCT volumes. Third, a set of PCT and CBCT HU to mass density conversion curves were created based on the mean HU values of OARs and the corresponding mass density of the OAR in the PCT. Then, we compared our proposed conversion curve with the traditional Catphan phantom based CBCT HU to mass density calibration curve. Both curves were input into the treatment planning system (TPS) for dose calculation. Last, the PTV and OAR doses, DVH and dose distributions of CBCT plans are compared to the original treatment plan. Results: One head-and-neck cases which contained a pair of PCT and CBCT was used. The dose differences between the PCT and CBCT plans using the proposed method are −1.33% for the mean PTV, 0.06% for PTV D95%, and −0.56% for the left neck. The dose differences between plans of PCT and CBCT corrected using the CATPhan based method are −4.39% for mean PTV, 4.07% for PTV D95%, and −2.01% for the left neck. Conclusion: The proposed CBCT HU correction method achieves better agreement with the original treatment plan compared to the traditional CATPhan based calibration method.

  20. High-density physical mapping of a 3-Mb region in Xp22.3 and refined localization of the gene for X-linked recessive chondrodysplasia punctata (CDPX1)

    SciTech Connect

    Wang, I.; Levilliers, J.; Petit, C.

    1995-03-20

    The study of patients with chromosomal rearrangements has led to the mapping of the gene responsible for X-linked recessive chondrodysplasia punctata (CDPX1; MIM 302950) to the distal part of the Xp22.3 region, between the loci PABX and DXS31. To refine this mapping, a yeast artificial chromosome (YAC) contig map spanning this region has been constructed. Together with the YAC contig of the pseudo-autosomal region that we previously established, this map covers the terminal 6 Mb of Xp, with an average density of 1 probe every 100 kb. Newly isolated probes that detect segmental X-Y homologies on Yp and Yq suggest multiple complex rearrangements of the ancestral pseudoautosomal region during evolution. Compilation of the data obtained from the study of individuals carrying various Xp22.3 deletions led us to conclude that the CDPX disease displays incomplete penetrance and, consequently, to refine the localization of CDPX1 to a 600-kb interval immediately adjacent to the pseudoautosomal boundary. This interval, in which 12 probes are ordered, provides the starting point for the isolation of CDPX1. 67 refs., 3 figs., 2 tabs.

  1. Risk Mapping of Anopheles gambiae s.l. Densities Using Remotely-Sensed Environmental and Meteorological Data in an Urban Area: Dakar, Senegal

    PubMed Central

    Machault, Vanessa; Vignolles, Cécile; Pagès, Frédéric; Gadiaga, Libasse; Tourre, Yves M.; Gaye, Abdoulaye; Sokhna, Cheikh; Trape, Jean-François; Lacaux, Jean-Pierre; Rogier, Christophe

    2012-01-01

    Introduction High malaria transmission heterogeneity in an urban environment is basically due to the complex distribution of Anopheles larval habitats, sources of vectors. Understanding 1) the meteorological and ecological factors associated with differential larvae spatio-temporal distribution and 2) the vectors dynamic, both may lead to improving malaria control measures with remote sensing and high resolution data as key components. In this study a robust operational methodology for entomological malaria predictive risk maps in urban settings is developed. Methods The Tele-epidemiology approach, i.e., 1) intensive ground measurements (Anopheles larval habitats and Human Biting Rate, or HBR), 2) selection of the most appropriate satellite data (for mapping and extracting environmental and meteorological information), and 3) use of statistical models taking into account the spatio-temporal data variability has been applied in Dakar, Senegal. Results First step was to detect all water bodies in Dakar. Secondly, environmental and meteorological conditions in the vicinity of water bodies favoring the presence of Anopheles gambiae s.l. larvae were added. Then relationship between the predicted larval production and the field measured HBR was identified, in order to generate An. gambiae s.l. HBR high resolution maps (daily, 10-m pixel in space). Discussion and Conclusion A robust operational methodology for dynamic entomological malaria predictive risk maps in an urban setting includes spatio-temporal variability of An. gambiae s.l. larval habitats and An. gambiae s.l. HBR. The resulting risk maps are first examples of high resolution products which can be included in an operational warning and targeting system for the implementation of vector control measures. PMID:23226351

  2. Detection of Traumatic Bone Marrow Lesions after Knee Trauma: Comparison of ADC Maps Derived from Diffusion-weighted Imaging with Standard Fat-saturated Proton Density-weighted Turbo Spin-Echo Sequences.

    PubMed

    Klengel, Alexis; Stumpp, Patrick; Klengel, Steffen; Böttger, Ina; Rönisch, Nadja; Kahn, Thomas

    2016-10-24

    Purpose To compare single-shot echo-planar diffusion-weighted imaging-derived apparent diffusion coefficient (ADC) maps with fat-saturated (FS) proton density (PD)-weighted turbo spin-echo (TSE) imaging in the detection of bone marrow lesions (BMLs) after knee trauma. Materials and Methods Institutional review board approval was obtained from Leipzig University. Written informed consent was waived. Three radiologists retrospectively re-examined 97 consecutive patients with reported knee trauma who underwent 1.5-T magnetic resonance (MR) imaging within 90 days of knee trauma. The following sequences were used: (a) sagittal T1-weighted TSE and FS PD-weighted TSE and (b) sagittal T1-weighted TSE and single-shot echo-planar diffusion-weighted imaging-derived ADC mapping. BMLs on the lateral and medial femoral condyle, lateral and medial aspect of the tibial plateau, and patella were documented. Volumetry was performed on BMLs with a thickness of at least 15 mm (major BMLs). ADC values were measured in intact bone marrow and major BMLs. A McNemar test and t tests were used as appropriate to test for significant differences between BML number and volume at an α level of .05. Results Significantly more patients showed at least one BML on ADC maps (98%, 95 of 97 patients) than on FS PD-weighted TSE images (86%, 84 of 97 patients) (P < .001). Of the affected regions detected on FS PD-weighted TSE images, 97% (170 of 175 regions) were identified consistently on ADC maps. Only 58% of the affected regions detected on ADC maps (170 of 293 regions) were identified on FS PD-weighted TSE images (P < .001). Median volume of concordant major BML was approximately two times larger on ADC maps (81 cm(3)) than on FS PD-weighted TSE images (39 cm(3)) (P < .001). The ADC values of intact bone marrow and BMLs did not overlap. Conclusion ADC maps are more sensitive than corresponding FS PD-weighted TSE images for detection of BML after knee trauma and allow detection of significantly more

  3. Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus.

    PubMed

    Wang, Xiaodong; Wang, Hao; Long, Yan; Li, Dianrong; Yin, Yongtai; Tian, Jianhua; Chen, Li; Liu, Liezhao; Zhao, Weiguo; Zhao, Yajun; Yu, Longjiang; Li, Maoteng

    2013-01-01

    Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between 'KenC-8' and 'N53-2', two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64-17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.

  4. Genome-Wide Single Nucleotide Polymorphism Discovery and the Construction of a High-Density Genetic Map for Melon (Cucumis melo L.) Using Genotyping-by-Sequencing.

    PubMed

    Chang, Che-Wei; Wang, Yu-Hua; Tung, Chih-Wei

    2017-01-01

    Although genotyping-by-sequencing (GBS) enables the efficient and low-cost generation of large numbers of markers, the utility of resultant genotypes are limited, because they are enormously error-prone and contain high proportions of missing data. In this study, we generated single nucleotide polymorphism (SNP) markers for 109 recombinant inbred lines of melon (Cucumis melo L.) using the GBS approach and ordered them according to their physical position on the draft double haploid line DHL92 genome. Next, by investigating associations between these SNPs, we discovered that some segments on the physical map conflict with linkage relationships. Therefore, to filter out error-prone loci, 4,110 SNPs in which we have a high degree of confidence were selected as anchors to test independence with respect to unselected markers, and the resultant dataset was then analyzed using the Full-Sib Family Haplotype (FSFHap) algorithm in the software TASSEL 5.2. On the basis of this analysis, 22,933 loci that have an average rate of missing data of 0.281% were used to construct a genetic map, which spans 1,088.3 cM across 12 chromosomes and has a maximum spacing of 6.0 cM. Use of this high-quality linkage map enabled the identification of several quantitative trait loci (QTL) known to control traits in fruit and validated our approach. This study highlights the utility of GBS markers for the identification of trait-associated QTLs in melon and facilitates further investigation of genome structure.

  5. Genome-Wide Single Nucleotide Polymorphism Discovery and the Construction of a High-Density Genetic Map for Melon (Cucumis melo L.) Using Genotyping-by-Sequencing

    PubMed Central

    Chang, Che-Wei; Wang, Yu-Hua; Tung, Chih-Wei

    2017-01-01

    Although genotyping-by-sequencing (GBS) enables the efficient and low-cost generation of large numbers of markers, the utility of resultant genotypes are limited, because they are enormously error-prone and contain high proportions of missing data. In this study, we generated single nucleotide polymorphism (SNP) markers for 109 recombinant inbred lines of melon (Cucumis melo L.) using the GBS approach and ordered them according to their physical position on the draft double haploid line DHL92 genome. Next, by investigating associations between these SNPs, we discovered that some segments on the physical map conflict with linkage relationships. Therefore, to filter out error-prone loci, 4,110 SNPs in which we have a high degree of confidence were selected as anchors to test independence with respect to unselected markers, and the resultant dataset was then analyzed using the Full-Sib Family Haplotype (FSFHap) algorithm in the software TASSEL 5.2. On the basis of this analysis, 22,933 loci that have an average rate of missing data of 0.281% were used to construct a genetic map, which spans 1,088.3 cM across 12 chromosomes and has a maximum spacing of 6.0 cM. Use of this high-quality linkage map enabled the identification of several quantitative trait loci (QTL) known to control traits in fruit and validated our approach. This study highlights the utility of GBS markers for the identification of trait-associated QTLs in melon and facilitates further investigation of genome structure. PMID:28220139

  6. High-density single-nucleotide polymorphism (SNP) map in the 96-kb region containing the entire human DiGeorge syndrome critical region 2 (DGCR2) gene at 22q11.2.

    PubMed

    Iida, A; Ohnishi, Y; Ozaki, K; Ariji, Y; Nakamura, Y; Tanaka, T

    2001-01-01

    We constructed a high-density single-nucleotide polymorphism (SNP) map in the 96-kb region containing the DiGeorge syndrome critical region 2 (DGCR2) gene at chromosome 22q11.2, a human counterpart of mouse seizure-related gene SEZ-12. A total of 102 SNPs were isolated from the region by systematic screening among 48 Japanese individuals: 9 SNPs in the 5' flanking region, 3 in the 5' untranslated region, 2 in the coding regions, 77 in introns, 7 in the 3' untranslated region, and 4 in the 3' flanking region. By a comparison of our data with SNPs deposited in the dbSNP database in the National Center for Biotechnology Information, 80 SNPs (78.4%) were considered to be novel. The ratio of transition to transversion was 3.08:1. In addition, eight other types of genetic variations (one GA dinucleotide polymorphism and seven insertion/deletion polymorphisms) were discovered. The high-resolution map that we constructed will be a useful resource for analyzing gene scans of complex diseases mapped to this local segment on chromosome 22.

  7. Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci.

    PubMed

    Kachuri, Linda; Amos, Christopher I; McKay, James D; Johansson, Mattias; Vineis, Paolo; Bueno-de-Mesquita, H Bas; Boutron-Ruault, Marie-Christine; Johansson, Mikael; Quirós, J Ramón; Sieri, Sabina; Travis, Ruth C; Weiderpass, Elisabete; Le Marchand, Loic; Henderson, Brian E; Wilkens, Lynne; Goodman, Gary E; Chen, Chu; Doherty, Jennifer A; Christiani, David C; Wei, Yongyue; Su, Li; Tworoger, Shelley; Zhang, Xuehong; Kraft, Peter; Zaridze, David; Field, John K; Marcus, Michael W; Davies, Michael P A; Hyde, Russell; Caporaso, Neil E; Landi, Maria Teresa; Severi, Gianluca; Giles, Graham G; Liu, Geoffrey; McLaughlin, John R; Li, Yafang; Xiao, Xiangjun; Fehringer, Gord; Zong, Xuchen; Denroche, Robert E; Zuzarte, Philip C; McPherson, John D; Brennan, Paul; Hung, Rayjean J

    2016-01-01

    Chromosome 5p15.33 has been identified as a lung cancer susceptibility locus, however the underlying causal mechanisms were not fully elucidated. Previous fine-mapping studies of this locus have relied on imputation or investigated a small number of known, common variants. This study represents a significant advance over previous research by investigating a large number of novel, rare variants, as well as their underlying mechanisms through telomere length. Variants for this fine-mapping study were identified through a targeted deep sequencing (average depth of coverage greater than 4000×) of 576 individuals. Subsequently, 4652 SNPs, including 1108 novel SNPs, were genotyped in 5164 cases and 5716 controls of European ancestry. After adjusting for known risk loci, rs2736100 and rs401681, we identified a new, independent lung cancer susceptibility variant in LPCAT1: rs139852726 (OR = 0.46, P = 4.73×10(-9)), and three new adenocarcinoma risk variants in TERT: rs61748181 (OR = 0.53, P = 2.64×10(-6)), rs112290073 (OR = 1.85, P = 1.27×10(-5)), rs138895564 (OR = 2.16, P = 2.06×10(-5); among young cases, OR = 3.77, P = 8.41×10(-4)). In addition, we found that rs139852726 (P = 1.44×10(-3)) was associated with telomere length in a sample of 922 healthy individuals. The gene-based SKAT-O analysis implicated TERT as the most relevant gene in the 5p15.33 region for adenocarcinoma (P = 7.84×10(-7)) and lung cancer (P = 2.37×10(-5)) risk. In this largest fine-mapping study to investigate a large number of rare and novel variants within 5p15.33, we identified novel lung and adenocarcinoma susceptibility loci with large effects and provided support for the role of telomere length as the potential underlying mechanism.

  8. A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata) Using Genotyping-by-Sequencing

    PubMed Central

    Wang, Jinpeng; Li, Li; Zhang, Guofan

    2016-01-01

    Oysters are among the most important species in global aquaculture. Crassostrea gigas, and its subspecies C. angulata, are the major cultured species. To determine the genetic basis of growth-related traits in oysters, we constructed a second-generation linkage map from 3367 single-nucleotide polymorphisms (SNPs) based on genotyping-by-sequencing, genotyped from a C. gigas × C. angulata hybrid family. These 3367 SNPs were distributed on 1695 markers, which were assigned to 10 linkage groups. The genetic linkage map had a total length of 1084.3 cM, with an average of 0.8 cM between markers; it thus represents the densest genetic map constructed for oysters to date. Twenty-seven quantitative trait loci (QTL) for five growth-related traits were detected. These QTL could explain 4.2–7.7% (mean = 5.4%) of the phenotypic variation. In total, 50.8% of phenotypic variance for shell width, 7.7% for mass weight, and 34.1% for soft tissue weight were explained. The detected QTL were distributed among eight linkage groups, and more than half (16) were concentrated within narrow regions in their respective linkage groups. Thirty-eight annotated genes were identified within the QTL regions, two of which are key genes for carbohydrate metabolism. Other genes were found to participate in assembly and regulation of the actin cytoskeleton, signal transduction, and regulation of cell differentiation and development. The newly developed high-density genetic map, and the QTL and candidate genes identified provide a valuable genetic resource and a basis for marker-assisted selection for C. gigas and C. angulata. PMID:26994291

  9. Solving the Secondary Structure Matching Problem in Cryo-EM De Novo Modeling Using a Constrained K-Shortest Path Graph Algorithm.

    PubMed

    Al Nasr, Kamal; Ranjan, Desh; Zubair, Mohammad; Chen, Lin; He, Jing

    2014-01-01

    Electron cryomicroscopy is becoming a major experimental technique in solving the structures of large molecular assemblies. More and more three-dimensional images have been obtained at the medium resolutions between 5 and 10 Å. At this resolution range, major α-helices can be detected as cylindrical sticks and β-sheets can be detected as plain-like regions. A critical question in de novo modeling from cryo-EM images is to determine the match between the detected secondary structures from the image and those on the protein sequence. We formulate this matching problem into a constrained graph problem and present an O(Δ(2)N(2)2(N)) algorithm to this NP-Hard problem. The algorithm incorporates the dynamic programming approach into a constrained K-shortest path algorithm. Our method, DP-TOSS, has been tested using α-proteins with maximum 33 helices and α-β proteins up to five helices and 12 β-strands. The correct match was ranked within the top 35 for 19 of the 20 α-proteins and all nine α-β proteins tested. The results demonstrate that DP-TOSS improves accuracy, time and memory space in deriving the topologies of the secondary structure elements for proteins with a large number of secondary structures and a complex skeleton.

  10. CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pili.

    PubMed

    Poweleit, Nicole; Ge, Peng; Nguyen, Hong H; Loo, Rachel R Ogorzalek; Gunsalus, Robert P; Zhou, Z Hong

    2016-12-05

    Archaea use flagella known as archaella-distinct both in protein composition and structure from bacterial flagella-to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4 Å resolution. Each archaellum contains ∼61,500 archaellin subunits organized into a curved helix with a diameter of 10 nm and average length of 10,000 nm. The tadpole-shaped archaellin monomer has two domains, a β-barrel domain and a long, mildly kinked α-helix tail. Our structure reveals multiple post-translational modifications to the archaella, including six O-linked glycans and an unusual N-linked modification. The extensive interactions among neighbouring archaellins explain how the long but thin archaellum maintains the structural integrity required for motility-driving rotation. These extensive inter-subunit interactions and the absence of a central pore in the archaellum distinguish it from both the bacterial flagellum and type IV pili.

  11. CryoEM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution

    PubMed Central

    Bai, Xiao-chen; Oubridge, Chris; Newman, Andrew J.; Scheres, Sjors H. W.; Nagai, Kiyoshi

    2016-01-01

    U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryoEM structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 snRNAs. The structure reveals striking interweaving interactions of the protein and RNA components including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5′-splice site during catalytic activation, forms a hairpin stabilised by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in Prp8’s N-terminal domain. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre. PMID:26829225

  12. Cryo-EM structure of a helicase loading intermediate containing ORC–Cdc6–Cdt1–MCM2-7 bound to DNA

    SciTech Connect

    Sun, Jingchuan; Evrin, Cecile; Samel, Stefan A.; Fernández-Cid, Alejandra; Riera, Alberto; Kawakami, Hironori; Stillman, Bruce; Speck, Christian; Li, Huilin

    2013-07-14

    In eukaryotes, the Cdt1-bound replicative helicase core MCM2-7 is loaded onto DNA by the ORC–Cdc6 ATPase to form a prereplicative complex (pre-RC) with an MCM2-7 double hexamer encircling DNA. Using purified components in the presence of ATP-γS, we have captured in vitro an intermediate in pre-RC assembly that contains a complex between the ORC–Cdc6 and Cdt1–MCM2-7 heteroheptamers called the OCCM. Cryo-EM studies of this 14-subunit complex reveal that the two separate heptameric complexes are engaged extensively, with the ORC–Cdc6 N-terminal AAA+ domains latching onto the C-terminal AAA+ motor domains of the MCM2-7 hexamer. The conformation of ORC–Cdc6 undergoes a concerted change into a right-handed spiral with helical symmetry that is identical to that of the DNA double helix. The resulting ORC–Cdc6 helicase loader shows a notable structural similarity to the replication factor C clamp loader, suggesting a conserved mechanism of action.

  13. Methodology and applications of automatic electron-density map interpretation by six-dimensional rotational and translational search for molecular fragments.

    PubMed

    Pavelcik, Frantisek; Zelinka, Jan; Otwinowski, Zbyszek

    2002-02-01

    The electron density for a search fragment and for the crystal is expanded in the space of spherical harmonics Bessel functions. The fast rotation function is evaluated for each grid point to test if the fragment can be orientated there. For the best scoring points, the six-dimensional coordinates of the fragment are refined by the second-derivative block-diagonal procedure. The method is able to locate fragments precisely over a wide range of resolutions for structure types from small organic molecules to proteins.

  14. QTL Analysis of Spike Morphological Traits and Plant Height in Winter Wheat (Triticum aestivum L.) Using a High-Density SNP and SSR-Based Linkage Map

    PubMed Central

    Zhai, Huijie; Feng, Zhiyu; Li, Jiang; Liu, Xinye; Xiao, Shihe; Ni, Zhongfu; Sun, Qixin

    2016-01-01

    Wheat yield can be enhanced by modifying the spike morphology and the plant height. In this study, a population of 191 F9 recombinant inbred lines (RILs) was developed from a cross between two winter cultivars Yumai 8679 and Jing 411. A dense genetic linkage map with 10,816 markers was constructed by incorporating single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker information. Five spike morphological traits and plant height were evaluated under nine environments for the RILs and parental lines, and the number of detected environmentally stable QTLs were 18 and three, respectively. The 1RS/1BL (rye) translocation increased both spike length and spikelet number with constant spikelet compactness. The QPht.cau-2D.1 was identical to gene Rht8, which decreased spike length without modifying spikelet number. Notably, four novel QTLs locating on chromosomes 1AS (QSc.cau-1A.1), 2DS (QSc.cau-2D.1), and 7BS (QSl.cau-7B.1 and QSl.cau-7B.2) were firstly identified in this study, which provide further insights into the genetic factors that shaped the spike morphology in wheat. Moreover, SNP markers tightly linked to previously reported QTLs will eventually facilitate future studies including their positional cloning or marker-assisted selection. PMID:27872629

  15. Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.).

    PubMed

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-10-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction-mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another.

  16. High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus

    PubMed Central

    Avia, Komlan; Coelho, Susana M.; Montecinos, Gabriel J.; Cormier, Alexandre; Lerck, Fiona; Mauger, Stéphane; Faugeron, Sylvain; Valero, Myriam; Cock, J. Mark; Boudry, Pierre

    2017-01-01

    Deciphering the genetic architecture of adaptation of brown algae to environmental stresses such as temperature and salinity is of evolutionary as well as of practical interest. The filamentous brown alga Ectocarpus sp. is a model for the brown algae and its genome has been sequenced. As sessile organisms, brown algae need to be capable of resisting the various abiotic stressors that act in the intertidal zone (e.g. osmotic pressure, temperature, salinity, UV radiation) and previous studies have shown that an important proportion of the expressed genes is regulated in response to hyposaline, hypersaline or oxidative stress conditions. Using the double digest RAD sequencing method, we constructed a dense genetic map with 3,588 SNP markers and identified 39 QTLs for growth-related traits and their plasticity under different temperature and salinity conditions (tolerance to high temperature and low salinity). GO enrichment tests within QTL intervals highlighted membrane transport processes such as ion transporters. Our study represents a significant step towards deciphering the genetic basis of adaptation of Ectocarpus sp. to stress conditions and provides a substantial resource to the increasing list of tools generated for the species. PMID:28256542

  17. Extensive Chromosome Homoeology among Brassiceae Species Were Revealed by Comparative Genetic Mapping with High-Density EST-Based SNP Markers in Radish (Raphanus sativus L.)‡

    PubMed Central

    Li, Feng; Hasegawa, Yoichi; Saito, Masako; Shirasawa, Sachiko; Fukushima, Aki; Ito, Toyoaki; Fujii, Hiroshi; Kishitani, Sachie; Kitashiba, Hiroyasu; Nishio, Takeshi

    2011-01-01

    A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction–mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another. PMID:21816873

  18. High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus.

    PubMed

    Avia, Komlan; Coelho, Susana M; Montecinos, Gabriel J; Cormier, Alexandre; Lerck, Fiona; Mauger, Stéphane; Faugeron, Sylvain; Valero, Myriam; Cock, J Mark; Boudry, Pierre

    2017-03-03

    Deciphering the genetic architecture of adaptation of brown algae to environmental stresses such as temperature and salinity is of evolutionary as well as of practical interest. The filamentous brown alga Ectocarpus sp. is a model for the brown algae and its genome has been sequenced. As sessile organisms, brown algae need to be capable of resisting the various abiotic stressors that act in the intertidal zone (e.g. osmotic pressure, temperature, salinity, UV radiation) and previous studies have shown that an important proportion of the expressed genes is regulated in response to hyposaline, hypersaline or oxidative stress conditions. Using the double digest RAD sequencing method, we constructed a dense genetic map with 3,588 SNP markers and identified 39 QTLs for growth-related traits and their plasticity under different temperature and salinity conditions (tolerance to high temperature and low salinity). GO enrichment tests within QTL intervals highlighted membrane transport processes such as ion transporters. Our study represents a significant step towards deciphering the genetic basis of adaptation of Ectocarpus sp. to stress conditions and provides a substantial resource to the increasing list of tools generated for the species.

  19. Intensity-Based Skeletonization of CryoEM Gray-Scale Images Using a True Segmentation-Free Algorithm

    PubMed Central

    Nasr, Kamal Al; Liu, Chunmei; Rwebangira, Mugizi; Burge, Legand; He, Jing

    2014-01-01

    Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the image can be captured using a single segmentation. In this paper, we present a segmentation-free approach to extract the gray-scale curve-like skeletons. The approach relies on a novel representation of the 3D image, where the image is modeled as a graph and a set of volume trees. A test containing 36 synthesized maps and one authentic map shows that our approach can improve the performance of the two tested tools used in de novo modeling. The improvements were 62 and 13 percent for Gorgon and DP-TOSS, respectively. PMID:24384713

  20. Achievement of a short term three dimensional electron density mapping of the ionosphere in the European sector: Comparisons with the IRI model for quiet-moderate geomagnetic-ionospheric conditions

    NASA Astrophysics Data System (ADS)

    Pietrella, M.

    2016-10-01

    In this paper will be described the procedure followed for the achievement of a short term three dimensional (3-D) electron density mapping of the ionosphere in the European area. It consists of three main steps: (1) foF2 and M(3000)F2 short-term forecasts, (foF2STF) and (M3000F2STF), are calculated at 12 ionospheric observatories scattered in the European area; (2) the values of foF2STF and M3000F2STF on a grid of equi-spaced points, (foF2STF,GP) and (M3000F2STF,GP), are calculated by means of an appropriate interpolation algorithm by using the foF2STF and M3000F2STF data; (3) foF2STF,GP and M3000F2STF,GP data ingestion into the IRI model is employed to produce a short term 3-D electron density mapping (ST-3D-M) of the ionosphere. The electron density profiles provided by the ST-3D-M and IRI models, were compared with the electron density profiles autoscaled by the Automatic Real-Time Ionogram Scaler with True-height (ARTIST) system, which are here considered as the truth profiles. The results of these comparisons, shown for a certain number of epochs during quiet-moderate geomagnetic-ionospheric conditions, in the truth-sites of Athens (38○.0‧N, 23○.5‧E), Chilton (51○.5‧N, -0○.6‧W), Dourbes (50○.1‧ N, 4○.6‧E), Pruhonice (50○.0‧N, 14○.6‧E), Rome (41○.9‧N, 12○.5‧E), and Tortosa (40○.8‧N, 0○.5‧E), indicate that the ST-3D-M as forecasting tool can be considered generally reliable.

  1. A Genetic Relationship between Phosphorus Efficiency and Photosynthetic Traits in Soybean As Revealed by QTL Analysis Using a High-Density Genetic Map

    PubMed Central

    Li, Hongyan; Yang, Yuming; Zhang, Hengyou; Chu, Shanshan; Zhang, Xingguo; Yin, Dongmei; Yu, Deyue; Zhang, Dan

    2016-01-01

    Plant productivity relies on photosynthesis, and the photosynthetic process relies on phosphorus (P). The genetic basis of photosynthesis and P efficiency (PE) affecting yield has been separately characterized in various crop plants. However, the genetic relationship between PE and photosynthesis remains to be elucidated. In this study, we used a combined analysis of phenotypic correlation, linkage mapping, and expression analysis to dissect the relationship between PE and photosynthesis. We found significant phenotypic correlations between PE and photosynthetic related traits, particularly under low P stress. A total of 172 QTLs for both traits were detected and classified into 29 genomic regions. 12 (41.4%) of 29 regions were detected to be associated with both PE and photosynthetic related traits. Three major QTLs, q14-2, q15-2, and q19-2, were found to be associated with both traits and explained 6.6–58.9% of phenotypic variation. A photosynthetic-specific QTL cluster, q12-1, was detected under both normal and low P conditions, suggesting that genes responsible for this region were less effected by low P stress, and could be used in high photosynthetic efficiency breeding programs. In addition, several candidate genes with significantly differential expression upon low P stress, such as a purple acid phosphatase gene (Glyma.19G193900) within q19-2 region, were considered as promising candidates involved in regulating both soybean PE and photosynthetic capacity. Our results reveal a significant genetic relationship between PE and photosynthetic traits, and uncover several major genomic regions specific or common to these traits. The markers linked closely to these major QTLs may be used for selection of soybean varieties with improved P efficiency and photosynthetic capacity. PMID:27446154

  2. A Genetic Relationship between Phosphorus Efficiency and Photosynthetic Traits in Soybean As Revealed by QTL Analysis Using a High-Density Genetic Map.

    PubMed

    Li, Hongyan; Yang, Yuming; Zhang, Hengyou; Chu, Shanshan; Zhang, Xingguo; Yin, Dongmei; Yu, Deyue; Zhang, Dan

    2016-01-01

    Plant productivity relies on photosynthesis, and the photosynthetic process relies on phosphorus (P). The genetic basis of photosynthesis and P efficiency (PE) affecting yield has been separately characterized in various crop plants. However, the genetic relationship between PE and photosynthesis remains to be elucidated. In this study, we used a combined analysis of phenotypic correlation, linkage mapping, and expression analysis to dissect the relationship between PE and photosynthesis. We found significant phenotypic correlations between PE and photosynthetic related traits, particularly under low P stress. A total of 172 QTLs for both traits were detected and classified into 29 genomic regions. 12 (41.4%) of 29 regions were detected to be associated with both PE and photosynthetic related traits. Three major QTLs, q14-2, q15-2, and q19-2, were found to be associated with both traits and explained 6.6-58.9% of phenotypic variation. A photosynthetic-specific QTL cluster, q12-1, was detected under both normal and low P conditions, suggesting that genes responsible for this region were less effected by low P stress, and could be used in high photosynthetic efficiency breeding programs. In addition, several candidate genes with significantly differential expression upon low P stress, such as a purple acid phosphatase gene (Glyma.19G193900) within q19-2 region, were considered as promising candidates involved in regulating both soybean PE and photosynthetic capacity. Our results reveal a significant genetic relationship between PE and photosynthetic traits, and uncover several major genomic regions specific or common to these traits. The markers linked closely to these major QTLs may be used for selection of soybean varieties with improved P efficiency and photosynthetic capacity.

  3. A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies

    PubMed Central

    McCue, Molly E.; Bannasch, Danika L.; Petersen, Jessica L.; Gurr, Jessica; Bailey, Ernie; Binns, Matthew M.; Distl, Ottmar; Guérin, Gérard; Hasegawa, Telhisa; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Penedo, M. Cecilia T.; Røed, Knut H.; Ryder, Oliver A.; Swinburne, June E.; Tozaki, Teruaki; Valberg, Stephanie J.; Vaudin, Mark; Lindblad-Toh, Kerstin

    2012-01-01

    An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species. PMID:22253606

  4. High density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis

    PubMed Central

    Goyette, Philippe; Boucher, Gabrielle; Mallon, Dermot; Ellinghaus, Eva; Jostins, Luke; Huang, Hailiang; Ripke, Stephan; Gusareva, Elena S; Annese, Vito; Hauser, Stephen L; Oksenberg, Jorge R; Thomsen, Ingo; Leslie, Stephen; Daly, Mark J; Van Steen, Kristel; Duerr, Richard H; Barrett, Jeffrey C; McGovern, Dermot PB; Schumm, L Philip; Traherne, James A; Carrington, Mary N; Kosmoliaptsis, Vasilis; Karlsen, Tom H; Franke, Andre; Rioux, John D

    2014-01-01

    Genome-wide association studies of the related chronic inflammatory bowel diseases (IBD) known as Crohn’s disease and ulcerative colitis have shown strong evidence of association to the major histocompatibility complex (MHC). This region encodes a large number of immunological candidates, including the antigen-presenting classical HLA molecules1. Studies in IBD have indicated that multiple independent associations exist at HLA and non-HLA genes, but lacked the statistical power to define the architecture of association and causal alleles2,3. To address this, we performed high-density SNP typing of the MHC in >32,000 patients with IBD, implicating multiple HLA alleles, with a primary role for HLA-DRB1*01:03 in both Crohn’s disease and ulcerative colitis. Significant differences were observed between these diseases, including a predominant role of class II HLA variants and heterozygous advantage observed in ulcerative colitis, suggesting an important role of the adaptive immune response to the colonic environment in the pathogenesis of IBD. PMID:25559196

  5. The Development of Multisensory Integration in High-Functioning Autism: High-Density Electrical Mapping and Psychophysical Measures Reveal Impairments in the Processing of Audiovisual Inputs

    PubMed Central

    Brandwein, Alice B.; Foxe, John J.; Butler, John S.; Russo, Natalie N.; Altschuler, Ted S.; Gomes, Hilary; Molholm, Sophie

    2013-01-01

    Successful integration of auditory and visual inputs is crucial for both basic perceptual functions and for higher-order processes related to social cognition. Autism spectrum disorders (ASD) are characterized by impairments in social cognition and are associated with abnormalities in sensory and perceptual processes. Several groups have reported that individuals with ASD are impaired in their ability to integrate socially relevant audiovisual (AV) information, and it has been suggested that this contributes to the higher-order social and cognitive deficits observed in ASD. However, successful integration of auditory and visual inputs also influences detection and perception of nonsocial stimuli, and integration deficits may impair earlier stages of information processing, with cascading downstream effects. To assess the integrity of basic AV integration, we recorded high-density electrophysiology from a cohort of high-functioning children with ASD (7–16 years) while they performed a simple AV reaction time task. Children with ASD showed considerably less behavioral facilitation to multisensory inputs, deficits that were paralleled by less effective neural integration. Evidence for processing differences relative to typically developing children was seen as early as 100 ms poststimulation, and topographic analysis suggested that children with ASD relied on different cortical networks during this early multisensory processing stage. PMID:22628458

  6. Anticipatory attentional suppression of visual features indexed by oscillatory alpha-band power increases: a high-density electrical mapping study.

    PubMed

    Snyder, Adam C; Foxe, John J

    2010-03-17

    Retinotopically specific increases in alpha-band ( approximately 10 Hz) oscillatory power have been strongly implicated in the suppression of processing for irrelevant parts of the visual field during the deployment of visuospatial attention. Here, we asked whether this alpha suppression mechanism also plays a role in the nonspatial anticipatory biasing of feature-based attention. Visual word cues informed subjects what the task-relevant feature of an upcoming visual stimulus (S2) was, while high-density electroencephalographic recordings were acquired. We examined anticipatory oscillatory activity in the Cue-to-S2 interval ( approximately 2 s). Subjects were cued on a trial-by-trial basis to attend to either the color or direction of motion of an upcoming dot field array, and to respond when they detected that a subset of the dots differed from the majority along the target feature dimension. We used the features of color and motion, expressly because they have well known, spatially separated cortical processing areas, to distinguish shifts in alpha power over areas processing each feature. Alpha power from dorsal regions increased when motion was the irrelevant feature (i.e., color was cued), and alpha power from ventral regions increased when color was irrelevant. Thus, alpha-suppression mechanisms appear to operate during feature-based selection in much the same manner as has been shown for space-based attention.

  7. High-density Association Mapping and Interaction Analysis of PLA2R1 and HLA Regions with Idiopathic Membranous Nephropathy in Japanese

    PubMed Central

    Thiri, Myo; Honda, Kenjiro; Kashiwase, Koichi; Mabuchi, Akihiko; Suzuki, Hodaka; Watanabe, Kimio; Nakayama, Masaaki; Watanabe, Tsuyoshi; Doi, Kent; Tokunaga, Katsushi; Noiri, Eisei

    2016-01-01

    Although recent studies showed anti-PLA2R antibody plays a crucial role in idiopathic membranous nephropathy (IMN), detailed HLA mapping and interaction between the HLA genes and PLA2R1 have not been investigated in IMN. We genotyped across the PLA2R1 gene and the HLA region, using 183 IMN patients and 811 healthy controls. Five SNPs around the PLA2R1 gene were significantly associated with IMN. In addition to the two SNPs previously reported to be strongly associated with IMN, rs3749119 and rs35771982 (OR 3.02 and 2.93, P = 3.24E-14 and 4.64E-14, respectively), two novel intronic SNPs (rs2715928 and rs16844715) were also identified as IMN-associated SNPs (OR = 2.30 and 2.51, P = 3.15E-10 and 5.66E-13, respectively). In the HLA gene analysis, DRB1*1501 and DQB1*0602 were strongly associated with IMN (P = 1.14E-11 and 1.25E-11, respectively). The interaction was strongest between HLA-DRB1*15:01 - HLA-DQB1*06:02 and the intronic SNP rs2715928 (OR = 17.53, P = 4.26E-26). Furthermore, positive interaction was also observed between HLA-DRB1*15:01 - HLA-DQB1*06:02 and the missense SNP rs35771982 (OR = 15.91, P = 2.76E-29), which is in strong linkage disequilibrium with 5′UTR SNP rs3749119, and intronic SNP rs16844715 (OR = 15.91, P = 2.30E-26) for IMN. Neither HLA-DRB1*15:01 nor HLA-DQB1*06:02 was associated with steroid responsiveness, overall survival and renal survival during the observation period of mean 11 years though limited number of analysis. PMID:27934873

  8. From hot rocks to glowing avalanches: Numerical modelling of gravity-induced pyroclastic density currents and hazard maps at the Stromboli volcano (Italy)

    NASA Astrophysics Data System (ADS)

    Salvatici, Teresa; Di Roberto, Alessio; Di Traglia, Federico; Bisson, Marina; Morelli, Stefano; Fidolini, Francesco; Bertagnini, Antonella; Pompilio, Massimo; Hungr, Oldrich; Casagli, Nicola

    2016-11-01

    Gravity-induced pyroclastic density currents (PDCs) can be produced by the collapse of volcanic crater rims or due to the gravitational instability of materials deposited in proximal areas during explosive activity. These types of PDCs, which are also known as "glowing avalanches", have been directly observed, and their deposits have been widely identified on the flanks of several volcanoes that are fed by mafic to intermediate magmas. In this research, the suitability of landslide numerical models for simulating gravity-induced PDCs to provide hazard assessments was tested. This work also presents the results of a back-analysis of three events that occurred in 1906, 1930 and 1944 at the Stromboli volcano by applying a depth-averaged 3D numerical code named DAN-3D. The model assumes a frictional internal rheology and a variable basal rheology (i.e., frictional, Voellmy and plastic). The numerical modelling was able to reproduce the gravity-induced PDCs' extension and deposit thicknesses to an order of magnitude of that reported in the literature. The best results when compared with field data were obtained using a Voellmy model with a frictional coefficient of f = 0.19 and a turbulence parameter ξ = 1000 m s- 1. The results highlight the suitability of this numerical code, which is generally used for landslides, to reproduce the destructive potential of these events in volcanic environments and to obtain information on hazards connected with explosive-related, mass-wasting phenomena in Stromboli Island and at volcanic systems characterized by similar phenomena.

  9. The response of the inductively coupled argon plasma to solvent plasma load: spatially resolved maps of electron density obtained from the intensity of one argon line

    NASA Astrophysics Data System (ADS)

    Weir, D. G. J.; Blades, M. W.

    1994-12-01

    A survey of spatially resolved electron number density ( ne) in the tail cone of the inductively coupled argon plasma (ICAP) is presented: all of the results of the survey have been radially inverted by numerical, asymmetric Abel inversion. The survey extends over the entire volume of the plasma beyond the exit of the ICAP torch; It extends over distances of z = 5-25 mm downstream from the induction coil, and over radial distances of ± 8 mm from the discharge axis. The survey also explores a range of inner argon flow rates ( QIN), solvent plasma load ( Qspl) and r.f. power: moreover, it explores loading by water, methanol and chloroform. Throughout the survey, ne was determined from the intensity of one, optically thin argon line, by a method which assumes that the atomic state distribution function (ASDF) for argon lies close to local thermal equilibrium (LTE). The validity of this assumption is reviewed. Also examined are the discrepancies between ne from this method and ne from Stark broadening measurements. With the error taken into account, the results of the survey reveal how time averaged values of ne in the ICAP respond over an extensive, previously unexplored range of experimental parameters. Moreover, the spatial information lends insight into how the thermal conditions and the transport of energy respond. Overall, the response may be described in terms of energy consumption along the axial channel and thermal pinch within the induction region. The predominating effect depends on the solvent plasma load, the solvent composition, the robustness of the discharge, and the distribution of solvent material over the argon stream.

  10. Two novel susceptibility loci for non-small cell lung cancer map to low-density lipoprotein receptor-related protein 5

    PubMed Central

    Wang, Ying; Zhang, Yongjun; Fang, Meiyu; Bao, Wenglong; Deng, Dehou

    2016-01-01

    This study investigated the effect of single-nucleotide polymorphisms (SNPs) of low-density lipoprotein receptor-related protein 5 (LRP5) on the risk of developing non-small cell lung cancer (NSCLC). A total of 500 NSCLC patients and 500 healthy controls were recruited for genotyping of 11 SNPs of LRP5. The association between genotype and NSCLC risk was evaluated by computing the odds ratio (OR) and 95% confidence interval (CI) from multivariate unconditional logistic regression analyses. Eleven Tag SNPs were detected. The frequency of the LRP5 rs3736228 T allele (18.9% in male NSCLC cases and 23.9% in male controls) was statistically different between male NSCLCs and male controls (P=0.03), and the T allele was associated with a lower risk of NSCLC (OR=0.74; 95% CI, 0.56–0.67), whereas the C/C homozygous genotype and the LRP5 rs64843 T/T genotype were associated with an increased risk of NSCLC and squamous cell carcinoma (SCC), respectively (OR=1.43 and 1.77, respectively). Using Haploview software, the frequency of the haplotypes of rs312009/rs3120015/rs3120014 CCC was was significantly higher in female SCC cases compared with female controls (0.064 vs. 0.009, P=0.04). LRP5 rs3736228 and rs64843 SNPs were significantly associated with an increased risk of NSCLC and SCC, respectively. Further studies are required to investigate the functional changes in LRP5 expression and activity in NSCLC in vitro. PMID:27698794

  11. Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.

    PubMed

    Dastani, Zari; Pajukanta, Päivi; Marcil, Michel; Rudzicz, Nicholas; Ruel, Isabelle; Bailey, Swneke D; Lee, Jenny C; Lemire, Mathieu; Faith, Janet; Platko, Jill; Rioux, John; Hudson, Thomas J; Gaudet, Daniel; Engert, James C; Genest, Jacques

    2010-03-01

    Low levels of high-density lipoprotein cholesterol (HDL-C) are an independent risk factor for cardiovascular disease. To identify novel genetic variants that contribute to HDL-C, we performed genome-wide scans and quantitative association studies in two study samples: a Quebec-wide study consisting of 11 multigenerational families and a study of 61 families from the Saguenay-Lac St-Jean (SLSJ) region of Quebec. The heritability of HDL-C in these study samples was 0.73 and 0.49, respectively. Variance components linkage methods identified a LOD score of 2.61 at 98 cM near the marker D16S515 in Quebec-wide families and an LOD score of 2.96 at 86 cM near the marker D16S2624 in SLSJ families. In the Quebec-wide sample, four families showed segregation over a 25.5-cM (18 Mb) region, which was further reduced to 6.6 Mb with additional markers. The coding regions of all genes within this region were sequenced. A missense variant in CHST6 segregated in four families and, with additional families, we observed a P value of 0.015 for this variant. However, an association study of this single-nucleotide polymorphism (SNP) in unrelated Quebec-wide samples was not significant. We also identified an SNP (rs11646677) in the same region, which was significantly associated with a low HDL-C (P=0.016) in the SLSJ study sample. In addition, RT-PCR results from cultured cells showed a significant difference in the expression of CHST6 and KIAA1576, another gene in the region. Our data constitute additional evidence for a locus on chromosome 16q23-24 that affects HDL-C levels in two independent French-Canadian studies.

  12. Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ

    PubMed Central

    Gorzelnik, Karl V.; Cui, Zhicheng; Reed, Catrina A.; Jakana, Joanita; Young, Ry; Zhang, Junjie

    2016-01-01

    Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A2, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A2 and the gRNA. A2 contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA–coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly. PMID:27671640

  13. Genetic Mapping

    MedlinePlus

    ... Fact Sheets Fact Sheets En Español: Mapeo Genético Genetic Mapping What is genetic mapping? How do researchers ... genetic map? What are genetic markers? What is genetic mapping? Among the main goals of the Human ...

  14. Martian drainage densities

    USGS Publications Warehouse

    Carr, M.H.; Chuang, F.C.

    1997-01-01

    Drainage densities on Mars range from zero over large areas of volcanic plains to 0.3-0.5 km-1 locally on some volcanoes. These values refer to geologic units, not to drainage basins, as is normal for terrestrial drainage densities. The highest values are close to the lowest terrestrial values derived by similar techniques. Drainage densities were determined for every geologic unit portrayed on the 1:15,000,000 geologic map of Mars. Except for volcanoes the geologic unit with the highest drainage density is the dissected Noachian plains with a drainage density of 0.0074 km-1. The average drainage density for Noachian units is 0.0032 km-1, for Hesperian units is 0.00047 km-1, and for Amazonian units is 0.00007 km-1, excluding the volcanoes. These values are 2-3 orders of magnitude lower than typical terrestrial densities as determined by similar techniques from Landsat images. The low drainage densities, despite a cumulative record that spans billions of years, indicate that compared with the Earth, the channel-forming processes have been very inefficient or have operated only rarely or that the surface is extremely permeable. The high drainage density on volcanoes is attributed to a local cause, such as hydrothermal activity, rather than to a global cause such as climate change. Copyright. Published in 1997 by the American Geophysical Union.

  15. Planetary maps

    USGS Publications Warehouse

    ,

    1992-01-01

    An important goal of the USGS planetary mapping program is to systematically map the geology of the Moon, Mars, Venus, and Mercury, and the satellites of the outer planets. These geologic maps are published in the USGS Miscellaneous Investigations (I) Series. Planetary maps on sale at the USGS include shaded-relief maps, topographic maps, geologic maps, and controlled photomosaics. Controlled photomosaics are assembled from two or more photographs or images using a network of points of known latitude and longitude. The images used for most of these planetary maps are electronic images, obtained from orbiting television cameras, various optical-mechanical systems. Photographic film was only used to map Earth's Moon.

  16. Joint Impact Proposal: A complete velocity resolved 3-D [CII] map of the M51 grand-design spiral galaxy: Unraveling the impact of spiral density waves on the evolution of the ISM and star formation.

    NASA Astrophysics Data System (ADS)

    Stutzki, Juergen

    2015-10-01

    We propose to obtain the first complete, velocity resolved [CII] 158um image of the M51 grand-design spiral galaxy with the upGREAT and FIFI-LS instruments on SOFIA. Spiral density waves play a fundamental role on the conversion of atomic to molecular gas, leading to gravitational contraction and thus to star formation. Understanding the impact of spiral density waves on the lifecycle of the interstellar medium and on star formation in galaxies is thus critical for our understanding of galaxy evolution. The [CII] line (in combination with the low-J CO lines and HI 21 cm) is an important tool to diagnose the physical state of the ISM. It can reveal the distribution of the gas that is making a transition between atomic and molecular phases, including the CO-dark H2 gas (hydrogen molecular but carbon ionized, and thus not traced by either HI or CO) in the spiral arms and interarm regions of M51. We will use the high spectral resolution of the upGREAT instrument to resolve spiral arms in velocity, allowing us to study the flow of gas through spiral arms and measure line widths and determine the dynamical state of prominent interarm clouds. The significantly more sensitive FIFI-LS will be used to detect extended faint [CII] emission in the interarm regions and outskirts of the galaxy, including the gas connection to the companion galaxy. The 3-D data cube of velocity-resolved [CII] in this nearby galaxy, combined with the wealth of ancillary data, can be used for a large set of investigations by the broader astronomical community. It will provide for the first time the link between the detailed physical processes in the star-forming ISM in the Milky Way and the average properties of distant external galaxies. This complete map will be also an excellent showcase of SOFIA's capabilities for years to come.

  17. Joint Impact Proposal: A complete velocity resolved 3-D [CII] map of the M51 grand-design spiral galaxy: Unraveling the impact of spiral density waves on the evolution of the ISM and star formation.

    NASA Astrophysics Data System (ADS)

    Pineda, Jorge

    2015-10-01

    We propose to obtain the first complete, velocity resolved [CII] 158um image of the M51 grand-design spiral galaxy with the upGREAT and FIFI-LS instruments on SOFIA. Spiral density waves play a fundamental role on the conversion of atomic to molecular gas, leading to gravitational contraction and thus to star formation. Understanding the impact of spiral density waves on the lifecycle of the interstellar medium and on star formation in galaxies is thus critical for our understanding of galaxy evolution. The [CII] line (in combination with the low-J CO lines and HI 21 cm) is an important tool to diagnose the physical state of the ISM. It can reveal the distribution of the gas that is making a transition between atomic and molecular phases, including the CO-dark H2 gas (hydrogen molecular but carbon ionized, and thus not traced by either HI or CO) in the spiral arms and interarm regions of M51. We will use the high spectral resolution of the upGREAT instrument to resolve spiral arms in velocity, allowing us to study the flow of gas through spiral arms and measure line widths and determine the dynamical state of prominent interarm clouds. The significantly more sensitive FIFI-LS will be used to detect extended faint [CII] emission in the interarm regions and outskirts of the galaxy, including the gas connection to the companion galaxy. The 3-D data cube of velocity--resolved [CII] in this nearby galaxy, combined with the wealth of ancillary data, can be used for a large set of investigations by the broader astronomical community. It will provide for the first time the link between the detailed physical processes in the star-forming ISM in the Milky Way and the average properties of distant external galaxies. This complete map will be also an excellent showcase of SOFIA's capabilities for years to come.

  18. Antagonistic properties of a natural product - Bicuculline with the gamma-aminobutyric acid recep