WorldWideScience

Sample records for single organelle analyses

  1. Robust organelle size extractions from elastic scattering measurements of single cells (Conference Presentation)

    Science.gov (United States)

    Cannaday, Ashley E.; Draham, Robert; Berger, Andrew J.

    2016-04-01

    The goal of this project is to estimate non-nuclear organelle size distributions in single cells by measuring angular scattering patterns and fitting them with Mie theory. Simulations have indicated that the large relative size distribution of organelles (mean:width≈2) leads to unstable Mie fits unless scattering is collected at polar angles less than 20 degrees. Our optical system has therefore been modified to collect angles down to 10 degrees. Initial validations will be performed on polystyrene bead populations whose size distributions resemble those of cell organelles. Unlike with the narrow bead distributions that are often used for calibration, we expect to see an order-of-magnitude improvement in the stability of the size estimates as the minimum angle decreases from 20 to 10 degrees. Scattering patterns will then be acquired and analyzed from single cells (EMT6 mouse cancer cells), both fixed and live, at multiple time points. Fixed cells, with no changes in organelle sizes over time, will be measured to determine the fluctuation level in estimated size distribution due to measurement imperfections alone. Subsequent measurements on live cells will determine whether there is a higher level of fluctuation that could be attributed to dynamic changes in organelle size. Studies on unperturbed cells are precursors to ones in which the effects of exogenous agents are monitored over time.

  2. A single origin of the photosynthetic organelle in different Paulinella lineages

    Directory of Open Access Journals (Sweden)

    Ishida Ken-ichiro

    2009-05-01

    Full Text Available Abstract Background Gaining the ability to photosynthesize was a key event in eukaryotic evolution because algae and plants form the base of the food chain on our planet. The eukaryotic machines of photosynthesis are plastids (e.g., chloroplast in plants that evolved from cyanobacteria through primary endosymbiosis. Our knowledge of plastid evolution, however, remains limited because the primary endosymbiosis occurred more than a billion years ago. In this context, the thecate "green amoeba" Paulinella chromatophora is remarkable because it very recently (i.e., minimum age of ≈ 60 million years ago acquired a photosynthetic organelle (termed a "chromatophore"; i.e., plastid via an independent primary endosymbiosis involving a Prochlorococcus or Synechococcus-like cyanobacterium. All data regarding P. chromatophora stem from a single isolate from Germany (strain M0880/a. Here we brought into culture a novel photosynthetic Paulinella strain (FK01 and generated molecular sequence data from these cells and from four different cell samples, all isolated from freshwater habitats in Japan. Our study had two aims. The first was to compare and contrast cell ultrastructure of the M0880/a and FK01 strains using scanning electron microscopy. The second was to assess the phylogenetic diversity of photosynthetic Paulinella to test the hypothesis they share a vertically inherited plastid that originated in their common ancestor. Results Comparative morphological analyses show that Paulinella FK01 cells are smaller than M0880/a and differ with respect to the number of scales per column. There are more distinctive, multiple fine pores on the external surface of FK01 than in M0880/a. Molecular phylogenetic analyses using multiple gene markers demonstrate these strains are genetically distinct and likely comprise separate species. The well-supported monophyly of the Paulinella chromatophora strains analyzed here using plastid-encoded 16S rRNA suggests strongly

  3. Biochemical characterization of the bi-lobe reveals a continuous structural network linking the bi-lobe to other single-copied organelles in Trypanosoma brucei.

    Science.gov (United States)

    Gheiratmand, Ladan; Brasseur, Anais; Zhou, Qing; He, Cynthia Y

    2013-02-01

    Trypanosoma brucei, a unicellular parasite, contains several single-copied organelles that duplicate and segregate in a highly coordinated fashion during the cell cycle. In the procyclic stage, a bi-lobed structure is found adjacent to the single ER exit site and Golgi apparatus, forming both stable and dynamic association with other cytoskeletal components including the basal bodies that seed the flagellum and the flagellar pocket collar that is critical for flagellar pocket biogenesis. To further understand the bi-lobe and its association with adjacent organelles, we performed proteomic analyses on the immunoisolated bi-lobe complex. Candidate proteins were localized to the flagellar pocket, the basal bodies, a tripartite attachment complex linking the basal bodies to the kinetoplast, and a segment of microtubule quartet linking the flagellar pocket collar and bi-lobe to the basal bodies. These results supported an extensive connection among the single-copied organelles in T. brucei, a strategy employed by the parasite for orderly organelle assembly and inheritance during the cell cycle.

  4. Manipulation and Motion of Organelles and Single Molecules in Living Cells

    DEFF Research Database (Denmark)

    Norregaard, Kamilla; Metzler, Ralf; Ritter, Christine M.

    2017-01-01

    driving many cellular processes. The forces on a molecular scale are exactly in the range that can be manipulated and probed with single molecule force spectroscopy. The natural environment of a biomolecule is inside a living cell, hence, this is the most relevant environment for probing their function....... In vivo studies are, however, challenged by the complexity of the cell. In this review, we start with presenting relevant theoretical tools for analyzing single molecule data obtained in intracellular environments followed by a description of state-of-the art visualization techniques. The most commonly...

  5. Single crystal analyser accepting the narrowest neutron angular profile

    International Nuclear Information System (INIS)

    Abbas, Sohrab; Wagh, Apoorva G.; Strobl, Markus; Treimer, Wolfgang

    2007-01-01

    We have designed, fabricated and tested a novel silicon single crystal analyser. It accepts a 0.21 arcsec (FWHM) wide angular profile of a monochromatic 5.24 A neutron beam, in agreement with its design. This is the narrowest and sharpest acceptance angular profile attained to date in the world with a neutron analyser. This analyser will facilitate SUSANS experiments probing wave vector transfers Q ∼ 10 -6 A -1 . (author)

  6. Pareto optimality in organelle energy metabolism analysis.

    Science.gov (United States)

    Angione, Claudio; Carapezza, Giovanni; Costanza, Jole; Lió, Pietro; Nicosia, Giuseppe

    2013-01-01

    In low and high eukaryotes, energy is collected or transformed in compartments, the organelles. The rich variety of size, characteristics, and density of the organelles makes it difficult to build a general picture. In this paper, we make use of the Pareto-front analysis to investigate the optimization of energy metabolism in mitochondria and chloroplasts. Using the Pareto optimality principle, we compare models of organelle metabolism on the basis of single- and multiobjective optimization, approximation techniques (the Bayesian Automatic Relevance Determination), robustness, and pathway sensitivity analysis. Finally, we report the first analysis of the metabolic model for the hydrogenosome of Trichomonas vaginalis, which is found in several protozoan parasites. Our analysis has shown the importance of the Pareto optimality for such comparison and for insights into the evolution of the metabolism from cytoplasmic to organelle bound, involving a model order reduction. We report that Pareto fronts represent an asymptotic analysis useful to describe the metabolism of an organism aimed at maximizing concurrently two or more metabolite concentrations.

  7. Optogenetic control of organelle transport and positioning

    NARCIS (Netherlands)

    van Bergeijk, Petra|info:eu-repo/dai/nl/338805508; Adrian, Max|info:eu-repo/dai/nl/369490959; Hoogenraad, Casper C|info:eu-repo/dai/nl/227263502; Kapitein, Lukas C|info:eu-repo/dai/nl/298806630

    2015-01-01

    Proper positioning of organelles by cytoskeleton-based motor proteins underlies cellular events such as signalling, polarization and growth. For many organelles, however, the precise connection between position and function has remained unclear, because strategies to control intracellular organelle

  8. Proteomics of a fuzzy organelle: interphase chromatin

    Science.gov (United States)

    Kustatscher, Georg; Hégarat, Nadia; Wills, Karen L H; Furlan, Cristina; Bukowski-Wills, Jimi-Carlo; Hochegger, Helfrid; Rappsilber, Juri

    2014-01-01

    Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead, we propose a new approach that provides a quantitative assessment of a protein's probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. We demonstrate the power of our large-scale data-driven annotation during the analysis of cyclin-dependent kinase (CDK) regulation in chromatin. Quantitative protein ontologies may provide a general alternative to list-based investigations of organelles and complement Gene Ontology. PMID:24534090

  9. Symbiosomes: temporary moonlighting organelles.

    Science.gov (United States)

    Emerich, David W; Krishnan, Hari B

    2014-05-15

    Symbiosomes are a unique structural entity that performs the role of biological nitrogen fixation, an energy-demanding process that is the primary entryway of fixed nitrogen into the biosphere. Symbiosomes result from the infection of specific rhizobial strains into the roots of an appropriate leguminous host plant forming an organ referred to as a nodule. Within the infected plant cells of the nodule, the rhizobia are encased within membrane-bounded structures that develop into symbiosomes. Mature symbiosomes create an environment that allows the rhizobia to differentiate into a nitrogen-fixing form called bacteroids. The bacteroids are surrounded by the symbiosome space, which is populated by proteins from both eukaryotic and prokaryotic symbionts, suggesting this space is the quintessential component of symbiosis: an inter-kingdom environment with the single purpose of symbiotic nitrogen fixation. Proteins associated with the symbiosome membrane are largely plant-derived proteins and are non-metabolic in nature. The proteins of the symbiosome space are mostly derived from the bacteroid with annotated functions of carbon metabolism, whereas relatively few are involved in nitrogen metabolism. An appreciable portion of both the eukaryotic and prokaryotic proteins in the symbiosome are also 'moonlighting' proteins, which are defined as proteins that perform roles unrelated to their annotated activities when found in an unexpected physiological environment. The essential functions of symbiotic nitrogen fixation of the symbiosome are performed by co-operative interactions of proteins from both symbionts some of which may be performing unexpected roles.

  10. Organelle DNA haplotypes reflect crop-use characteristics and geographic origins of Cannabis sativa.

    Science.gov (United States)

    Gilmore, Simon; Peakall, Rod; Robertson, James

    2007-10-25

    Comparative sequencing of cannabis individuals across 12 chloroplast and mitochondrial DNA loci revealed 7 polymorphic sites, including 5 length variable regions and 2 single nucleotide polymorphisms. Simple PCR assays were developed to assay these polymorphisms, and organelle DNA haplotypes were obtained for 188 cannabis individuals from 76 separate populations, including drug-type, fibre-type and wild populations. The haplotype data were analysed using parsimony, UPGMA and neighbour joining methods. Three haplotype groups were recovered by each analysis method, and these groups are suggestive of the crop-use characteristics and geographical origin of the populations, although not strictly diagnostic. We discuss the relationship between our haplotype data and taxonomic opinions of cannabis, and the implications of organelle DNA haplotyping to forensic investigations of cannabis.

  11. GOBASE: an organelle genome database

    OpenAIRE

    O?Brien, Emmet A.; Zhang, Yue; Wang, Eric; Marie, Veronique; Badejoko, Wole; Lang, B. Franz; Burger, Gertraud

    2008-01-01

    The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (?913 000) and chloroplast-encoded sequences (?250 000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene products and taxonomy is available, as well as selected genome maps and RNA secondary structures. Recent major enhancements to database functionality include: (i) addition of an interface for RNA editing...

  12. Component Analyses Using Single-Subject Experimental Designs: A Review

    Science.gov (United States)

    Ward-Horner, John; Sturmey, Peter

    2010-01-01

    A component analysis is a systematic assessment of 2 or more independent variables or components that comprise a treatment package. Component analyses are important for the analysis of behavior; however, previous research provides only cursory descriptions of the topic. Therefore, in this review the definition of "component analysis" is discussed,…

  13. Protein Expression Analyses at the Single Cell Level

    Directory of Open Access Journals (Sweden)

    Masae Ohno

    2014-09-01

    Full Text Available The central dogma of molecular biology explains how genetic information is converted into its end product, proteins, which are responsible for the phenotypic state of the cell. Along with the protein type, the phenotypic state depends on the protein copy number. Therefore, quantification of the protein expression in a single cell is critical for quantitative characterization of the phenotypic states. Protein expression is typically a dynamic and stochastic phenomenon that cannot be well described by standard experimental methods. As an alternative, fluorescence imaging is being explored for the study of protein expression, because of its high sensitivity and high throughput. Here we review key recent progresses in fluorescence imaging-based methods and discuss their application to proteome analysis at the single cell level.

  14. The effect of organelle discovery upon sub-cellular protein localisation.

    Science.gov (United States)

    Breckels, L M; Gatto, L; Christoforou, A; Groen, A J; Lilley, K S; Trotter, M W B

    2013-08-02

    Prediction of protein sub-cellular localisation by employing quantitative mass spectrometry experiments is an expanding field. Several methods have led to the assignment of proteins to specific subcellular localisations by partial separation of organelles across a fractionation scheme coupled with computational analysis. Methods developed to analyse organelle data have largely employed supervised machine learning algorithms to map unannotated abundance profiles to known protein-organelle associations. Such approaches are likely to make association errors if organelle-related groupings present in experimental output are not included in data used to create a protein-organelle classifier. Currently, there is no automated way to detect organelle-specific clusters within such datasets. In order to address the above issues we adapted a phenotype discovery algorithm, originally created to filter image-based output for RNAi screens, to identify putative subcellular groupings in organelle proteomics experiments. We were able to mine datasets to a deeper level and extract interesting phenotype clusters for more comprehensive evaluation in an unbiased fashion upon application of this approach. Organelle-related protein clusters were identified beyond those sufficiently annotated for use as training data. Furthermore, we propose avenues for the incorporation of observations made into general practice for the classification of protein-organelle membership from quantitative MS experiments. Protein sub-cellular localisation plays an important role in molecular interactions, signalling and transport mechanisms. The prediction of protein localisation by quantitative mass-spectrometry (MS) proteomics is a growing field and an important endeavour in improving protein annotation. Several such approaches use gradient-based separation of cellular organelle content to measure relative protein abundance across distinct gradient fractions. The distribution profiles are commonly mapped in

  15. Membranes on nanopores for multiplexed single-transporter analyses

    International Nuclear Information System (INIS)

    Urban, Michael; Tampé, Robert

    2016-01-01

    The study of membrane proteins as prime drug targets has led to intensified efforts to characterize their structure and function. With regards to the structural analysis of membrane proteins, there have been considerable technological innovations in cryo-EM and X-ray crystallography, but advancements in the elucidation of membrane protein function, especially on a single-molecule level, have been struggling to bridge from basic science to high-throughput applications. There is a need for advanced biosensor platforms allowing membrane protein-mediated transport and potential suppressor libraries to be characterized. Membrane proteins facilitating the translocation of non-electrogenic substrates particularly suffer from a lack of such techniques to date. Here, we summarize recent developments in the field of membrane protein analysis, with a special focus on micro- and nanostructured platforms for purpose of high-throughput screening using fluorescent read-out systems. Additionally, their use as novel biosensor platforms to elucidate non-electrogenic substrate translocation is described. This overview contains 82 references. (author)

  16. Single-stage mass spectrometric analyses of resin bead samples

    Energy Technology Data Exchange (ETDEWEB)

    Smith, D. H.; Walker, R. L.; Bertram, L. K.; Carter, J. A.

    1978-10-01

    Plutonium and uranium from dissolver solutions loaded on resin beads can be analyzed on single-stage mass spectrometers with little or no degradation of results provided proper care is exercised with regard to sample handling techniques. Additionally, storage of samples on resin beads is feasible for periods at least as long as six months provided the beads are not exposed to residual HNO/sub 3/ and air; it is probable that beads will retain their integrity much longer than six months when stored under collodion, but as yet no data to support this contention have been collected. Conventional or commercial mass spectrometers can readily be adapted to the resin bead technique by installing a pulse-counting detection system. The cost of such conversion will vary depending on whether or not a data acquisition system will be needed. A reasonable estimate is that the cost will be in the neighborhood of $15,000; this figure includes the price of a multi-channel analyzer to serve as a temporary data storage device, but does not include the cost of a computer. It does not appear that it will be practicable to switch easily back and forth between pulse-counting and current integration modes unless the instrument is provided with a movable Faraday cup. Using the same multiplier in both modes would undoubtedly degrade its performance in each. The requirements of low background counting rates and high gain for pulse counting, and of relatively high signal handling capacity in current integration are mutually incompatible if demanded of the same multiplier.

  17. Accelerated safety analyses - structural analyses Phase I - structural sensitivity evaluation of single- and double-shell waste storage tanks

    International Nuclear Information System (INIS)

    Becker, D.L.

    1994-11-01

    Accelerated Safety Analyses - Phase I (ASA-Phase I) have been conducted to assess the appropriateness of existing tank farm operational controls and/or limits as now stipulated in the Operational Safety Requirements (OSRs) and Operating Specification Documents, and to establish a technical basis for the waste tank operating safety envelope. Structural sensitivity analyses were performed to assess the response of the different waste tank configurations to variations in loading conditions, uncertainties in loading parameters, and uncertainties in material characteristics. Extensive documentation of the sensitivity analyses conducted and results obtained are provided in the detailed ASA-Phase I report, Structural Sensitivity Evaluation of Single- and Double-Shell Waste Tanks for Accelerated Safety Analysis - Phase I. This document provides a summary of the accelerated safety analyses sensitivity evaluations and the resulting findings

  18. Immobilised multienzyme systems and organelles

    Energy Technology Data Exchange (ETDEWEB)

    Legoy, M.D.; Gellf, G.; Ergan, F.; Cocquempot, M.F.; Larreta Garde, V.; Thomas, D.

    1982-01-01

    Enzyme technology has demonstrated its economic and industrial potentials by the successful development of the 'first generation' of immobilised enzymes which concern simple degradative enzymes which by hydrolysis, oxidation and isomerisation yield products with rather limited added values. A new objective is to prepare industries to develop a 'second generation' of enzyme reactors in which sophisticated multienzyme systems will catalyse the synthesis of fine chemicals of high added value. There are two kinds of solutions to develop such new systems: immobilisation of subcellular organelles such as mitochondria, whole bacteria or fragments (chromatophores), chloroplasts (thylakoids), etc.; immobilisation of multienzymes systems including cofactor regeneration and realisation of multienzyme reactors like continuous stirred-tank reactor. Experimental examples dealing with both topics are described. (Refs. 50).

  19. HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching.

    Science.gov (United States)

    Bi, Guiqi; Mao, Yunxiang; Xing, Qikun; Cao, Min

    2018-01-01

    Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multiple sequence alignment. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multiple sequence alignment in a few hours. In addition, HomBlocks supports organelle genomes without annotation and makes adjustment to different taxon datasets, thereby enabling the inclusion of as many common genes as possible. Topology comparison of trees built by conventional multi-gene and HomBlocks alignments implemented in different taxon categories shows that the same efficiency can be achieved by HomBlocks as when using the traditional method. The availability of Homblocks makes organelle phylogenetic analyses more accessible to non-bioinformaticians, thereby promising to lead to a better understanding of phylogenic relationships at an organelle genome level. HomBlocks is implemented in Perl and is supported by Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download from https://github.com/fenghen360/HomBlocks.git, and documentation and tutorials are available at https://github.com/fenghen360/HomBlocks. yxmao@ouc.edu.cn or fenghen360@126.com. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. GOBASE--a database of organelle and bacterial genome information.

    Science.gov (United States)

    O'Brien, Emmet A; Zhang, Yue; Yang, LiuSong; Wang, Eric; Marie, Veronique; Lang, B Franz; Burger, Gertraud

    2006-01-01

    The organelle genome database GOBASE is now in its twelfth release, and includes 350,000 mitochondrial sequences and 118,000 chloroplast sequences, roughly a 3-fold expansion since previously documented. GOBASE also includes a fully reannotated genome sequence of Rickettsia prowazekii, one of the closest bacterial relatives of mitochondria, and will shortly expand to contain more data from bacteria from which organelles originated. All these sequences are now accessible through a single unified interface. Enhancements to the functionality of GOBASE include addition of pages for RNA structures and a page compiling data about the taxonomic distribution of organelle-encoded genes; incorporation of Gene Ontology terms; addition of features deduced from incomplete annotations to sequences in GenBank; marking of type examples in cases where single genes in single species are oversampled within GenBank; and addition of graphics illustrating gene structure and the position of neighbouring genes on a sequence. The database has been reimplemented in PostgreSQL to facilitate development and maintenance, and structural modifications have been made to speed up queries, particularly those related to taxonomy. The GOBASE database can be queried at http://gobase.bcm.umontreal.ca/ and inquiries should be directed to gobase@bch.umontreal.ca.

  1. GOBASE—a database of organelle and bacterial genome information

    Science.gov (United States)

    O'Brien, Emmet A.; Zhang, Yue; Yang, LiuSong; Wang, Eric; Marie, Veronique; Lang, B. Franz; Burger, Gertraud

    2006-01-01

    The organelle genome database GOBASE is now in its twelfth release, and includes 350 000 mitochondrial sequences and 118 000 chloroplast sequences, roughly a 3-fold expansion since previously documented. GOBASE also includes a fully reannotated genome sequence of Rickettsia prowazekii, one of the closest bacterial relatives of mitochondria, and will shortly expand to contain more data from bacteria from which organelles originated. All these sequences are now accessible through a single unified interface. Enhancements to the functionality of GOBASE include addition of pages for RNA structures and a page compiling data about the taxonomic distribution of organelle-encoded genes; incorporation of Gene Ontology terms; addition of features deduced from incomplete annotations to sequences in GenBank; marking of type examples in cases where single genes in single species are oversampled within GenBank; and addition of graphics illustrating gene structure and the position of neighbouring genes on a sequence. The database has been reimplemented in PostgreSQL to facilitate development and maintenance, and structural modifications have been made to speed up queries, particularly those related to taxonomy. The GOBASE database can be queried at and inquiries should be directed to gobase@bch.umontreal.ca. PMID:16381962

  2. RNA editing machinery in plant organelles.

    Science.gov (United States)

    Yan, Junjie; Zhang, Qunxia; Yin, Ping

    2018-02-01

    RNA editing is a type of post-transcriptional modification that includes nucleotide insertion/deletion or conversion. Different categories of RNA editing have been widely observed in distinct RNAs from divergent organisms. In flowering plants, RNA editing usually alters cytidine to uridine in plastids and mitochondria, playing important roles in various plant developmental processes, including organelle biogenesis, adaptation to environmental changes, and signal transduction. Numerous studies have demonstrated that a number of factors are involved in plant RNA editing, such as pentatricopeptide repeat (PPR) proteins, multiple organelle RNA editing factors (MORF, also known as RIP), organelle RNA recognition motif (ORRM) containing proteins, protoporphyrinogen IX oxidase 1 (PPO1) and organelle zinc finger 1 (OZ1). These factors play diverse roles in plant RNA editing due to their distinct characteristics. In this review, we discuss the functional roles of the individual editing factors and their associations in plant RNA editing.

  3. Proposal for a rotating analyser single crystal spectrometer at a pulsed neutron source

    International Nuclear Information System (INIS)

    Geick, R.; Tietze, H.

    1986-01-01

    We propose a new type of crystal analyser time-of-flight spectrometer for elastic and inelastic single crystal measurements at a pulsed neutron source. Using a nonuniformly rotating analyser, a flexibility of the spectrometer is achieved intermediate between that of the crystal analyser time-of-flight spectrometers like MAX and Constant-Q and the triple axis spectrometer. In detail, we discuss constant-(h/2π)ω and constant-(Q/vertical strokeQvertical stroke) scans for our spectrometer and the nonuniform rotation of the analyser necessary for these special scans. (orig.)

  4. Stochastic Model of Vesicular Sorting in Cellular Organelles

    Science.gov (United States)

    Vagne, Quentin; Sens, Pierre

    2018-02-01

    The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intracellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations, considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values lead to fast sorting but result in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well-defined sorted compartments but sorting is exponentially slow. Our results suggest an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components and highlight the importance of stochastic effects for the steady-state organization of intracellular compartments.

  5. Single Microfluidic Electrochemical Sensor System for Simultaneous Multi-Pulmonary Hypertension Biomarker Analyses

    OpenAIRE

    Lee, GeonHui; Lee, JuKyung; Kim, JeongHoon; Choi, Hak Soo; Kim, Jonghan; Lee, SangHoon; Lee, HeaYeon

    2017-01-01

    Miniaturized microfluidic biosensors have recently been advanced for portable point-of-care diagnostics by integrating lab-on-a-chip technology and electrochemical analysis. However, the design of a small, integrated, and reliable biosensor for multiple and simultaneous electrochemical analyses in a single device remains a challenge. Here, we present a simultaneous microfluidic electrochemical biosensing system to detect multiple biomarkers of pulmonary hypertension diseases in a single devic...

  6. Understanding gene expression variability in its biological context using theoretical and experimental analyses of single cells

    NARCIS (Netherlands)

    Kempe, H.

    2017-01-01

    Traditional gene expression studies have largely ignored cell-to-cell variability in transcription. Current methods allow for single cell analyses and have shown considerable variability in gene expression, even in populations of isogenic cells exposed to the same growth environment. In this thesis,

  7. Nanotubular Highways for Intercellular Organelle Transport

    Science.gov (United States)

    Rustom, Amin; Saffrich, Rainer; Markovic, Ivanka; Walther, Paul; Gerdes, Hans-Hermann

    2004-02-01

    Cell-to-cell communication is a crucial prerequisite for the development and maintenance of multicellular organisms. To date, diverse mechanisms of intercellular exchange of information have been documented, including chemical synapses, gap junctions, and plasmodesmata. Here, we describe highly sensitive nanotubular structures formed de novo between cells that create complex networks. These structures facilitate the selective transfer of membrane vesicles and organelles but seem to impede the flow of small molecules. Accordingly, we propose a novel biological principle of cell-to-cell interaction based on membrane continuity and intercellular transfer of organelles.

  8. Organelle proteomics experimental designs and analysis.

    Science.gov (United States)

    Gatto, Laurent; Vizcaíno, Juan Antonio; Hermjakob, Henning; Huber, Wolfgang; Lilley, Kathryn S

    2010-11-01

    In biology, localisation is function: knowledge of the localisation of proteins is of paramount importance to assess and study their function. This supports the need for reliable protein sub-cellular localisation assignment. Concomitant with recent technological advances in organelle proteomics, there is a requirement for more rigorous experimental and analysis design planning and description. In this review, we present an overview of current experimental designs in qualitative and quantitative organelle proteomics as well as associated data analysis. We also consider the major benefits associated with careful description and dissemination of the experiment and analysis designs, namely (i) comparison and optimisation of experimental designs and analysis pipelines, (ii) data validation, (iii) reproducible research, (iv) efficient repository submission and retrieval and (v) meta analysis. Formalization of experimental design and analysis work flows is of direct benefit for the organelle proteomics researchers and will result in providing organelle localisation data of highest quality for the wider research community. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Thermographic analyses of the growth of Cd1-xZnxTe single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kopach, O.V.; Bolotnikov, A.; Shcherbak, Larysa P.; Fochuk, Petro M.; and James, Ralph B.

    2010-08-01

    Bulk Cd1-xZnxTe (0single crystals for gamma-ray detectors are grown mainly from near-stoichiometric melts. We discuss the influence of the thermal pre-history of the melts (superheating, thermo-cycling, and cooling rate) on various physical properties based on our thermographic analyses, electrical conductivity and viscosity measurements. Increasing the Zn content causes non-monotonic dependencies in the quality of the crystals structure.

  10. Polysilicon nanogap lab-on-chip facilitates multiplex analyses with single analyte.

    Science.gov (United States)

    Balakrishnan, Sharma Rao; Hashim, U; Gopinath, Subash C B; Poopalan, P; Ramayya, H R; Veeradasan, P; Haarindraprasad, R; Ruslinda, A R

    2016-10-15

    Rationally designed biosensing system supports multiplex analyses is warranted for medical diagnosis to determine the level of analyte interaction. The chemically functionalized novel multi-electrode polysilicon nanogap (PSNG) lab-on-chip is designed in this study, facilitates multiplex analyses for a single analyte. On the fabricated 69nm PSNG, biocompatibility and structural characteristics were verified for the efficient binding of Human Chorionic Gonadotropin (hCG). With the assistance of microfluidics, hCG sample was delivered via single-injection to 3-Aminopropyl(triethoxy)silane (APTES) and Glycidoxypropyl(trimethoxy)silane (GPMS) modified PSNG electrodes and the transduced signal was used to investigate the dielectric mechanisms for multiplex analyses. The results from amperometric response and impedance measurement delivered the scale of interaction between anti-hCG antibody and hCG that exhibited 6.5 times higher sensitivity for the chemical linker, APTES than GPMS. Under optimized experimental conditions, APTES and GPMS modified immunosensor has a limit of detection as 0.56mIU/ml and 2.93mIU/ml (at S/N=3), with dissociation constants (Kd) of 5.65±2.5mIU/ml and 7.28±2.6mIU/ml, respectively. These results suggest that multiplex analysis of single target could enhance the accuracy of detection and reliable for real-time comparative analyses. The designed PSNG is simple, feasible, requires low sample consumption and could be applied for any given multiplex analyses. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Mechanical properties of organelles driven by microtubule-dependent molecular motors in living cells.

    Directory of Open Access Journals (Sweden)

    Luciana Bruno

    2011-04-01

    Full Text Available The organization of the cytoplasm is regulated by molecular motors which transport organelles and other cargoes along cytoskeleton tracks. Melanophores have pigment organelles or melanosomes that move along microtubules toward their minus and plus end by the action of cytoplasmic dynein and kinesin-2, respectively. In this work, we used single particle tracking to characterize the mechanical properties of motor-driven organelles during transport along microtubules. We tracked organelles with high temporal and spatial resolutions and characterized their dynamics perpendicular to the cytoskeleton track. The quantitative analysis of these data showed that the dynamics is due to a spring-like interaction between melanosomes and microtubules in a viscoelastic microenvironment. A model based on a generalized Langevin equation explained these observations and predicted that the stiffness measured for the motor complex acting as a linker between organelles and microtubules is ∼ one order smaller than that determined for motor proteins in vitro. This result suggests that other biomolecules involved in the interaction between motors and organelles contribute to the mechanical properties of the motor complex. We hypothesise that the high flexibility observed for the motor linker may be required to improve the efficiency of the transport driven by multiple copies of motor molecules.

  12. Single Microfluidic Electrochemical Sensor System for Simultaneous Multi-Pulmonary Hypertension Biomarker Analyses.

    Science.gov (United States)

    Lee, GeonHui; Lee, JuKyung; Kim, JeongHoon; Choi, Hak Soo; Kim, Jonghan; Lee, SangHoon; Lee, HeaYeon

    2017-08-08

    Miniaturized microfluidic biosensors have recently been advanced for portable point-of-care diagnostics by integrating lab-on-a-chip technology and electrochemical analysis. However, the design of a small, integrated, and reliable biosensor for multiple and simultaneous electrochemical analyses in a single device remains a challenge. Here, we present a simultaneous microfluidic electrochemical biosensing system to detect multiple biomarkers of pulmonary hypertension diseases in a single device. The miniaturized biosensor, which is composed of five chambers, is precisely and individually controlled using in-house-built pneumatic microvalves to manipulate the flow pathway. Each chamber is connected to an electrochemical sensor designed to detect four different biomarkers plus a reference control. Our design allows for loading of multiple reagents for simultaneous analyses. On the basis of the developed microfluidic electrochemical sensor system, we successfully detected four well-defined pulmonary hypertension-associated biomarkers, namely, fibrinogen, adiponectin, low-density lipoprotein, and 8-isoprostane. This novel approach offers a new platform for a rapid, miniaturized, and sensitive diagnostic sensor in a single device for various human diseases.

  13. Right Time, Right Place : Probing the Functions of Organelle Positioning

    NARCIS (Netherlands)

    van Bergeijk, Petra; Hoogenraad, Casper C; Kapitein, Lukas C

    2016-01-01

    The proper spatial arrangement of organelles underlies many cellular processes including signaling, polarization, and growth. Despite the importance of local positioning, the precise connection between subcellular localization and organelle function is often not fully understood. To address this,

  14. Development of NUPREP PC Version and Input Structures for NUCIRC Single Channel Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Churl; Jun, Ji Su; Park, Joo Hwan

    2007-12-15

    The input file for a steady-state thermal-hydraulic code NUCIRC consists of common channel input data and specific channel input data in a case of single channel analysis. Even when all the data is ready for the 380 channels' single channel analyses, it takes long time and requires enormous effort to compose an input file by hand-editing. The automatic pre-processor for this tedious job is a NUPREP code. In this study, a NUPREP PC version has been developed from the source list in the program manual of NUCIRC-MOD2.000 that is imported in a form of an execution file. In this procedure, some errors found in PC executions and lost statements are fixed accordingly. It is confirmed that the developed NUPREP code produces input file correctly for the CANDU-6 single channel analysis. Additionally, the NUCIRC input structure and data format are summarized for a single channel analysis and the input CARDs required for the creep information of aged channels are listed.

  15. Development of NUPREP PC Version and Input Structures for NUCIRC Single Channel Analyses

    International Nuclear Information System (INIS)

    Yoon, Churl; Jun, Ji Su; Park, Joo Hwan

    2007-12-01

    The input file for a steady-state thermal-hydraulic code NUCIRC consists of common channel input data and specific channel input data in a case of single channel analysis. Even when all the data is ready for the 380 channels' single channel analyses, it takes long time and requires enormous effort to compose an input file by hand-editing. The automatic pre-processor for this tedious job is a NUPREP code. In this study, a NUPREP PC version has been developed from the source list in the program manual of NUCIRC-MOD2.000 that is imported in a form of an execution file. In this procedure, some errors found in PC executions and lost statements are fixed accordingly. It is confirmed that the developed NUPREP code produces input file correctly for the CANDU-6 single channel analysis. Additionally, the NUCIRC input structure and data format are summarized for a single channel analysis and the input CARDs required for the creep information of aged channels are listed

  16. Deleterious mutation accumulation in organelle genomes.

    Science.gov (United States)

    Lynch, M; Blanchard, J L

    1998-01-01

    It is well established on theoretical grounds that the accumulation of mildly deleterious mutations in nonrecombining genomes is a major extinction risk in obligately asexual populations. Sexual populations can also incur mutational deterioration in genomic regions that experience little or no recombination, i.e., autosomal regions near centromeres, Y chromosomes, and organelle genomes. Our results suggest, for a wide array of genes (transfer RNAs, ribosomal RNAs, and proteins) in a diverse collection of species (animals, plants, and fungi), an almost universal increase in the fixation probabilities of mildly deleterious mutations arising in mitochondrial and chloroplast genomes relative to those arising in the recombining nuclear genome. This enhanced width of the selective sieve in organelle genomes does not appear to be a consequence of relaxed selection, but can be explained by the decline in the efficiency of selection that results from the reduction of effective population size induced by uniparental inheritance. Because of the very low mutation rates of organelle genomes (on the order of 10(-4) per genome per year), the reduction in fitness resulting from mutation accumulation in such genomes is a very long-term process, not likely to imperil many species on time scales of less than a million years, but perhaps playing some role in phylogenetic lineage sorting on time scales of 10 to 100 million years.

  17. A Breast Cell Atlas: Organelle analysis of the MDA-MB-231 cell line by density-gradient fractionation using isotopic marking and label-free analysis

    Directory of Open Access Journals (Sweden)

    Marianne Sandin

    2015-09-01

    Full Text Available Protein translocation between organelles in the cell is an important process that regulates many cellular functions. However, organelles can rarely be isolated to purity so several methods have been developed to analyse the fractions obtained by density gradient centrifugation. We present an analysis of the distribution of proteins amongst organelles in the human breast cell line, MDA-MB-231 using two approaches: an isotopic labelling and a label-free approach.

  18. Optimizing the photon selection of the CMS Single-Photon search for Supersymmetry using multivariate analyses

    CERN Document Server

    Lange, Johannes

    2014-01-01

    The purpose of this thesis is to improve the photon selection of the CMS SinglePhoton search for Supersymmetry by using multivariate analyses.The Single-Photon search aims to find Supersymmetry (SUSY) in data taken by theCompact Muon Solenoid (CMS) detector at the Large Hadron Collider located atthe research center CERN. SUSY is an extension of the standard model of particlephysics. The search is designed for a general gauge mediation scenario, which describes the gauge mediated SUSY breaking. The analysis uses final states with jets,at least one photon and missing transverse energy. A data-driven prediction of themultijet background is performed for the analysis. For this purpose, photon candidates have to be classified into two selections.In this thesis the usage of multivariate analyses for the photon candidate classification is studied. The methods used are Fisher Discriminant, Boosted Decision Treesand Artificial Neural Networks. Their performance is evaluated with respect to different aspects impor...

  19. Multi-level Bayesian analyses for single- and multi-vehicle freeway crashes.

    Science.gov (United States)

    Yu, Rongjie; Abdel-Aty, Mohamed

    2013-09-01

    This study presents multi-level analyses for single- and multi-vehicle crashes on a mountainous freeway. Data from a 15-mile mountainous freeway section on I-70 were investigated. Both aggregate and disaggregate models for the two crash conditions were developed. Five years of crash data were used in the aggregate investigation, while the disaggregate models utilized one year of crash data along with real-time traffic and weather data. For the aggregate analyses, safety performance functions were developed for the purpose of revealing the contributing factors for each crash type. Two methodologies, a Bayesian bivariate Poisson-lognormal model and a Bayesian hierarchical Poisson model with correlated random effects, were estimated to simultaneously analyze the two crash conditions with consideration of possible correlations. Except for the factors related to geometric characteristics, two exposure parameters (annual average daily traffic and segment length) were included. Two different sets of significant explanatory and exposure variables were identified for the single-vehicle (SV) and multi-vehicle (MV) crashes. It was found that the Bayesian bivariate Poisson-lognormal model is superior to the Bayesian hierarchical Poisson model, the former with a substantially lower DIC and more significant variables. In addition to the aggregate analyses, microscopic real-time crash risk evaluation models were developed for the two crash conditions. Multi-level Bayesian logistic regression models were estimated with the random parameters accounting for seasonal variations, crash-unit-level diversity and segment-level random effects capturing unobserved heterogeneity caused by the geometric characteristics. The model results indicate that the effects of the selected variables on crash occurrence vary across seasons and crash units; and that geometric characteristic variables contribute to the segment variations: the more unobserved heterogeneity have been accounted, the better

  20. Analyzing Lysosome-Related Organelles by Electron Microscopy

    KAUST Repository

    Hurbain, Ilse

    2017-04-29

    Intracellular organelles have a particular morphological signature that can only be appreciated by ultrastructural analysis at the electron microscopy level. Optical imaging and associated methodologies allow to explore organelle localization and their dynamics at the cellular level. Deciphering the biogenesis and functions of lysosomes and lysosome-related organelles (LROs) and their dysfunctions requires their visualization and detailed characterization at high resolution by electron microscopy. Here, we provide detailed protocols for studying LROs by transmission electron microscopy. While conventional electron microscopy and its recent improvements is the method of choice to investigate organelle morphology, immunoelectron microscopy allows to localize organelle components and description of their molecular make up qualitatively and quantitatively.

  1. Multicompartment Artificial Organelles Conducting Enzymatic Cascade Reactions inside Cells

    DEFF Research Database (Denmark)

    Gallardo, Maria Godoy; Labay, Cédric Pierre; Trikalitis, Vasileios

    2017-01-01

    Cell organelles are subcellular structures entrapping a set of enzymes to achieve a specific functionality. The incorporation of artificial organelles into cells is a novel medical paradigm which might contribute to the treatment of various cell disorders by replacing malfunctioning organelles....... In particular, artificial organelles are expected to be a powerful solution in the context of enzyme replacement therapy since enzymatic malfunction is the primary cause of organelle dysfunction. Although several attempts have been made to encapsulate enzymes within a carrier vehicle, only few intracellularly...

  2. Multivariate statistical analyses demonstrate unique host immune responses to single and dual lentiviral infection.

    Directory of Open Access Journals (Sweden)

    Sunando Roy

    2009-10-01

    Full Text Available Feline immunodeficiency virus (FIV and human immunodeficiency virus (HIV are recently identified lentiviruses that cause progressive immune decline and ultimately death in infected cats and humans. It is of great interest to understand how to prevent immune system collapse caused by these lentiviruses. We recently described that disease caused by a virulent FIV strain in cats can be attenuated if animals are first infected with a feline immunodeficiency virus derived from a wild cougar. The detailed temporal tracking of cat immunological parameters in response to two viral infections resulted in high-dimensional datasets containing variables that exhibit strong co-variation. Initial analyses of these complex data using univariate statistical techniques did not account for interactions among immunological response variables and therefore potentially obscured significant effects between infection state and immunological parameters.Here, we apply a suite of multivariate statistical tools, including Principal Component Analysis, MANOVA and Linear Discriminant Analysis, to temporal immunological data resulting from FIV superinfection in domestic cats. We investigated the co-variation among immunological responses, the differences in immune parameters among four groups of five cats each (uninfected, single and dual infected animals, and the "immune profiles" that discriminate among them over the first four weeks following superinfection. Dual infected cats mount an immune response by 24 days post superinfection that is characterized by elevated levels of CD8 and CD25 cells and increased expression of IL4 and IFNgamma, and FAS. This profile discriminates dual infected cats from cats infected with FIV alone, which show high IL-10 and lower numbers of CD8 and CD25 cells.Multivariate statistical analyses demonstrate both the dynamic nature of the immune response to FIV single and dual infection and the development of a unique immunological profile in dual

  3. The exception proves the rule? Dual targeting of nuclear-encoded proteins into endosymbiotic organelles.

    Science.gov (United States)

    Baudisch, Bianca; Langner, Uwe; Garz, Ingo; Klösgen, Ralf Bernd

    2014-01-01

    Plant cells harbor two types of endosymbiotic organelle: mitochondria and chloroplasts. As a consequence of endosymbiotic gene transfer, the majority of their proteins are encoded in the nucleus and post-translationally 're'-imported into the respective target organelle. The corresponding transport signals are usually selective for a single organelle, but several proteins are transported into both the mitochondria and chloroplasts. To estimate the number of proteins with such dual targeting properties in Arabidopsis, we classified the proteins encoded by nuclear genes of endosymbiotic origin according to the respective targeting specificity of their N-terminal transport signals as predicted by the TargetP software package. Selected examples of the resulting protein classes were subsequently analyzed by transient transformation assays as well as by in organello protein transport experiments. It was found that most proteins with high prediction values for both organelles show dual targeting with both experimental approaches. Unexpectedly, however, dual targeting was even found among those proteins that are predicted to be localized solely in one of the two endosymbiotic organelles. In total, among the 16 candidate proteins analyzed, we identified 10 proteins with dual targeting properties. This unexpectedly high proportion suggests that such transport properties are much more abundant than anticipated. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  4. MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.; Burnum-Johnson, Kristin E.; Kim, Young-Mo; Kyle, Jennifer E.; Matzke, Melissa M.; Shukla, Anil K.; Chu, Rosalie K.; Schepmoes, Athena A.; Jacobs, Jon M.; Baric, Ralph S.; Webb-Robertson, Bobbie-Jo; Smith, Richard D.; Metz, Thomas O.; Chia, Nicholas

    2016-05-03

    ABSTRACT

    Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. Themetabolite,protein, andlipidextraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental,in vitro, and clinical).

    IMPORTANCEIn systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated

  5. Composition of the von Willebrand factor storage organelle (Weibel-Palade body) isolated from cultured human umbilical vein endothelial cells.

    Science.gov (United States)

    Ewenstein, B M; Warhol, M J; Handin, R I; Pober, J S

    1987-05-01

    von Willebrand factor (VWF) is a large, adhesive glycoprotein that is biosynthesized and secreted by cultured endothelial cells (EC). Although these cells constitutively release VWF, they also contain a storage pool of this protein that can be rapidly mobilized. In this study, a dense organelle fraction was isolated from cultured umbilical vein endothelial cells by centrifugation on a self-generated Percoll gradient. Stimulation of EC by 4-phorbol 12-myristate 13-acetate (PMA) resulted in the disappearance of this organelle fraction and the synchronous loss of Weibel-Palade bodies as judged by immunoelectron microscopy. Electrophoretic and serologic analyses of biosynthetically labeled dense organelle fraction revealed that it is comprised almost exclusively of VWF and its cleaved pro sequence. These two polypeptides were similarly localized exclusively to Weibel-Palade bodies by ultrastructural immunocytochemistry. The identity of the dense organelle as the Weibel-Palade body was further established by direct morphological examination of the dense organelle fraction. The VWF derived from this organelle is distributed among unusually high molecular weight multimers composed of fully processed monomeric subunits and is rapidly and quantitatively secreted in unmodified form after PMA stimulation. These studies: establish that the Weibel-Palade body is the endothelial-specific storage organelle for regulated VWF secretion; demonstrate that in cultured EC, the VWF concentrated in secretory organelles is of unusually high molecular weight and that this material may be rapidly mobilized in unmodified form; imply that proteolytic processing of VWF involved in regulated secretion takes place after translocation to the secretory organelle; provide a basis for further studies of intracellular protein trafficking in EC.

  6. Requirements and standards for organelle genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.

    2006-01-09

    Mitochondria and plastids (collectively called organelles)descended from prokaryotes that adopted an intracellular, endosymbioticlifestyle within early eukaryotes. Comparisons of their remnant genomesaddress a wide variety of biological questions, especially when includingthe genomes of their prokaryotic relatives and the many genes transferredto the eukaryotic nucleus during the transitions from endosymbiont toorganelle. The pace of producing complete organellar genome sequences nowmakes it unfeasible to do broad comparisons using the primary literatureand, even if it were feasible, it is now becoming uncommon for journalsto accept detailed descriptions of genome-level features. Unfortunatelyno database is currently useful for this task, since they have littlestandardization and are riddled with error. Here I outline what iscurrently wrong and what must be done to make this data useful to thescientific community.

  7. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

    Science.gov (United States)

    Boldt, Karsten; van Reeuwijk, Jeroen; Lu, Qianhao; Koutroumpas, Konstantinos; Nguyen, Thanh-Minh T; Texier, Yves; van Beersum, Sylvia E C; Horn, Nicola; Willer, Jason R; Mans, Dorus A; Dougherty, Gerard; Lamers, Ideke J C; Coene, Karlien L M; Arts, Heleen H; Betts, Matthew J; Beyer, Tina; Bolat, Emine; Gloeckner, Christian Johannes; Haidari, Khatera; Hetterschijt, Lisette; Iaconis, Daniela; Jenkins, Dagan; Klose, Franziska; Knapp, Barbara; Latour, Brooke; Letteboer, Stef J F; Marcelis, Carlo L; Mitic, Dragana; Morleo, Manuela; Oud, Machteld M; Riemersma, Moniek; Rix, Susan; Terhal, Paulien A; Toedt, Grischa; van Dam, Teunis J P; de Vrieze, Erik; Wissinger, Yasmin; Wu, Ka Man; Apic, Gordana; Beales, Philip L; Blacque, Oliver E; Gibson, Toby J; Huynen, Martijn A; Katsanis, Nicholas; Kremer, Hannie; Omran, Heymut; van Wijk, Erwin; Wolfrum, Uwe; Kepes, François; Davis, Erica E; Franco, Brunella; Giles, Rachel H; Ueffing, Marius; Russell, Robert B; Roepman, Ronald

    2016-05-13

    Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine.

  8. Engineering carbon fixation with artificial protein organelles.

    Science.gov (United States)

    Giessen, Tobias W; Silver, Pamela A

    2017-08-01

    Based on projections for global population growth, current techniques for improving agricultural yields will not be able to address future demands for major food crops. Improving photosynthetic efficiency by engineering carbon fixation has been identified as one of the most important approaches for increasing agricultural output. Recent studies indicate that introducing cyanobacterial-like carbon concentrating mechanisms (CCMs) into plant chloroplasts represents a promising strategy for enhancing plant photosynthesis. Here, we give a general outline for transferring CCMs to plants. The proposed trajectory includes introducing bicarbonate transporters and CO 2 -fixing organelles into plant chloroplasts as well as minimizing stromal carbonic anhydrase (CA) activity. We focus on different approaches for constructing compartments that co-localize the CO 2 -fixing enzyme d-ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and CA, aimed at increasing RuBisCO turnover and decreasing wasteful photorespiration. We consider strategies based on cyanobacterial carboxysomes and on other protein-based compartments, specifically encapsulin nanocompartments. Finally, recent advances in expressing catalytic and structural carboxysomal components in plants will be highlighted. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Extracting physics of life at the molecular level: A review of single-molecule data analyses.

    Science.gov (United States)

    Colomb, Warren; Sarkar, Susanta K

    2015-06-01

    Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Analysing Discursive Practices in Legal Research : How a Single Remark Implies a Paradigm

    NARCIS (Netherlands)

    van den Hoven, P.J.

    2017-01-01

    Different linguistic theories of meaning (semantic theories) imply different methods to discuss meaning. Discussing meaning is what legal practitioners frequently do to decide legal issues and, subsequently, legal scholars analyse in their studies these discursive practices of parties, judges and

  11. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase

    NARCIS (Netherlands)

    Buganim, Y.; Faddah, D.A.; Cheng, A.W.; Itskovich, E.; Markoulaki, S.; Ganz, K.; Klemm, S.L.; van Oudenaarden, A.; Jaenisch, R.

    2012-01-01

    During cellular reprogramming, only a small fraction of cells become induced pluripotent stem cells (iPSCs). Previous analyses of gene expression during reprogramming were based on populations of cells, impeding single-cell level identification of reprogramming events. We utilized two gene

  12. Generalized Single-Case Randomization Tests: Flexible Analyses for a Variety of Situations.

    Science.gov (United States)

    Levin, Joel R.; Wampold, Bruce E.

    1999-01-01

    Presents a general class of single-case statistical procedures derived from previously developed nonparametric randomization tests. Designs are illustrated that focus on the general and comparative effectiveness of alternative interventions, multiple units with differentiable characteristics, and multiple outcome measures. Provides operational…

  13. Ultrastructural relationship of the phagophore with surrounding organelles.

    Science.gov (United States)

    Biazik, Joanna; Ylä-Anttila, Päivi; Vihinen, Helena; Jokitalo, Eija; Eskelinen, Eeva-Liisa

    2015-01-01

    Phagophore nucleates from a subdomain of the endoplasmic reticulum (ER) termed the omegasome and also makes contact with other organelles such as mitochondria, Golgi complex, plasma membrane and recycling endosomes during its formation. We have used serial block face scanning electron microscopy (SB-EM) and electron tomography (ET) to image phagophore biogenesis in 3 dimensions and to determine the relationship between the phagophore and surrounding organelles at high resolution. ET was performed to confirm whether membrane contact sites (MCSs) are evident between the phagophore and those surrounding organelles. In addition to the known contacts with the ER, we identified MCSs between the phagophore and membranes from putative ER exit sites, late endosomes or lysosomes, the Golgi complex and mitochondria. We also show that one phagophore can have simultaneous MCSs with more than one organelle. Future membrane flux experiments are needed to determine whether membrane contacts also signify lipid translocation.

  14. Proteomics of secretory and endocytic organelles in Giardia lamblia.

    Directory of Open Access Journals (Sweden)

    Petra B Wampfler

    Full Text Available Giardia lamblia is a flagellated protozoan enteroparasite transmitted as an environmentally resistant cyst. Trophozoites attach to the small intestine of vertebrate hosts and proliferate by binary fission. They access nutrients directly via uptake of bulk fluid phase material into specialized endocytic organelles termed peripheral vesicles (PVs, mainly on the exposed dorsal side. When trophozoites reach the G2/M restriction point in the cell cycle they can begin another round of cell division or encyst if they encounter specific environmental cues. They induce neogenesis of Golgi-like organelles, encystation-specific vesicles (ESVs, for regulated secretion of cyst wall material. PVs and ESVs are highly simplified and thus evolutionary diverged endocytic and exocytic organelle systems with key roles in proliferation and transmission to a new host, respectively. Both organelle systems physically and functionally intersect at the endoplasmic reticulum (ER which has catabolic as well as anabolic functions. However, the unusually high degree of sequence divergence in Giardia rapidly exhausts phylogenomic strategies to identify and characterize the molecular underpinnings of these streamlined organelles. To define the first proteome of ESVs and PVs we used a novel strategy combining flow cytometry-based organelle sorting with in silico filtration of mass spectrometry data. From the limited size datasets we retrieved many hypothetical but also known organelle-specific factors. In contrast to PVs, ESVs appear to maintain a strong physical and functional link to the ER including recruitment of ribosomes to organelle membranes. Overall the data provide further evidence for the formation of a cyst extracellular matrix with minimal complexity. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000694.

  15. Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses.

    OpenAIRE

    Ulgen, Ayse; Li, Wentian

    2005-01-01

    Abstract We compared linkage analysis results for an alcoholism trait, ALDX1 (DSM-III-R and Feigner criteria) using a nonparametric linkage analysis method, which takes into account allele sharing among several affected persons, for both microsatellite and single-nucleotide polymorphism (SNP) markers (Affymetrix and Illumina) in the Collaborative Study on the Genetics of Alcoholism (COGA) dataset provided to participants at the Genetic Analysis Workshop 14 (GAW14). The two sets of linkage res...

  16. Comprehensive analyses of core-shell InGaN/GaN single nanowire photodiodes

    Science.gov (United States)

    Zhang, H.; Guan, N.; Piazza, V.; Kapoor, A.; Bougerol, C.; Julien, F. H.; Babichev, A. V.; Cavassilas, N.; Bescond, M.; Michelini, F.; Foldyna, M.; Gautier, E.; Durand, C.; Eymery, J.; Tchernycheva, M.

    2017-12-01

    Single nitride nanowire core/shell n-p photodetectors are fabricated and analyzed. Nanowires consisting of an n-doped GaN stem, a radial InGaN/GaN multiple quantum well system and a p-doped GaN external shell were grown by catalyst-free metal-organic vapour phase epitaxy on sapphire substrates. Single nanowires were dispersed and the core and the shell regions were contacted with a metal and an ITO deposition, respectively, defined using electron beam lithography. The single wire photodiodes present a response in the visible to UV spectral range under zero external bias. The detector operation speed has been analyzed under different bias conditions. Under zero bias, the  -3 dB cut-off frequency is ~200 Hz for small light modulations. The current generation was modeled using non-equilibrium Green function formalism, which evidenced the importance of phonon scattering for carrier extraction from the quantum wells.

  17. Single-cell analyses identify bioengineered niches for enhanced maintenance of hematopoietic stem cells.

    Science.gov (United States)

    Roch, Aline; Giger, Sonja; Girotra, Mukul; Campos, Vasco; Vannini, Nicola; Naveiras, Olaia; Gobaa, Samy; Lutolf, Matthias P

    2017-08-09

    The in vitro expansion of long-term hematopoietic stem cells (HSCs) remains a substantial challenge, largely because of our limited understanding of the mechanisms that control HSC fate choices. Using single-cell multigene expression analysis and time-lapse microscopy, here we define gene expression signatures and cell cycle hallmarks of murine HSCs and the earliest multipotent progenitors (MPPs), and analyze systematically single HSC fate choices in culture. Our analysis revealed twelve differentially expressed genes marking the quiescent HSC state, including four genes encoding cell-cell interaction signals in the niche. Under basal culture conditions, most HSCs rapidly commit to become early MPPs. In contrast, when we present ligands of the identified niche components such as JamC or Esam within artificial niches, HSC cycling is reduced and long-term multipotency in vivo is maintained. Our approach to bioengineer artificial niches should be useful in other stem cell systems.Haematopoietic stem cell (HSC) self-renewal is not sufficiently understood to recapitulate in vitro. Here, the authors generate gene signature and cell cycle hallmarks of single murine HSCs, and use identified endothelial receptors Esam and JamC as substrates to enhance HSC growth in engineered niches.

  18. Creep fatigue analyses of a single wall redan according to the RCC-MR

    International Nuclear Information System (INIS)

    Blaix, J.C.; Buckthorpe, D.

    1989-01-01

    This paper deals with the validation of the single wall redan (inner vessel) option for the SUPERPHENIX 2 LMFBR project, according to the requirements of the RCC-MR Code. To complete this validation, an assessment against creep-fatigue damage has been carried out using elastic and inelastic methods. This paper presents the methods used and the results obtained. The approach has been to validate the design using elastic methods and support this with inelastic analysis to show the further safety margins that are available

  19. Reconstruction of the PETM onset from single specimen analyses of foraminiferal stable isotopes at Medford, NJ

    Science.gov (United States)

    Makarova, M.; Miller, K. G.; Wright, J. D.

    2017-12-01

    The Paleocene-Eocene transition ( 56 Ma) is marked by a global temperature increase of 4-8°C and the carbon isotope excursion (CIE) found ubiquitously in marine and terrestrial realms. However, the mechanisms of warming and overall changes in the ocean-atmosphere system during the Paleocene-Eocene thermal maximum (PETM) are uncertain. The timing of the PETM onset has been debated suggested by various studies between years to thousands of years and therefore is of particular interest to ascertain the trigger mechanism. One way to resolve this is to study thick cores on the continental margins that have higher sedimentation rates and thus resolution. Stratigraphically more complete in regard to the CIE onset marine PETM sections are found along the U.S. mid-Atlantic margin, New Jersey coastal plain (35-40°N paleolatitude). We present new carbon and oxygen isotopic data of planktonic and benthic foraminifera from the Medford 3A core, drilled on the New Jersey coastal plain in Summer 2016. Medford is the most proximal among the New Jersey coastal plain sites. The Medford 3A core has recovered 4 ft (1.2 m) of the Marlboro Formation, unit that contains the CIE "core" with low stable δ13C values and CIE recovery in other New Jersey cores. The top of the Marlboro Formation is truncated at Medford 3A, but the base is conformable with the underlaying Vincentown Formation. The sharp δ13C decrease appears within the Vincentown/Marlboro transitional lithological interval 1.5 ft (0.5 m) thick allowing a detailed study of the PETM onset. The Medford 3A core recovered sufficient well-preserved foraminifera to establish isotopic changes across the PETM onset. We measure δ13C and δ18O in single specimens of surface dwellers (Morozovella, Acarinina), thermocline dwellers (Subbotina), and benthic foraminifera (Anomalinoides, Cibicidoides) at high resolution to understand the nature of the PETM onset. We compliment previously published single specimen isotopic records from the

  20. Foraminiferal single chamber analyses of heavy metals as a tool for monitoring permanent and short term anthropogenic footprints.

    Science.gov (United States)

    Titelboim, Danna; Sadekov, Aleksey; Hyams-Kaphzan, Orit; Almogi-Labin, Ahuva; Herut, Barak; Kucera, Michal; Abramovich, Sigal

    2018-03-01

    In order to establish environmentally sustainable industries there is a need for high-resolution temporal and spatial monitoring of heavy metal pollutants even at low concentrations before they become hazardous for local ecosystems. Here we present single chamber records of Cu, Zn and Pb in shells of two benthic foraminifera species with different shell types from two shallow coastal stations in Israel: An area adjacent to an electrical power plant and desalination factory (Hadera) and an industrially free nature reserve (Nachsholim). Records of both foraminifera species show elevated metal concentrations in Hadera clearly identifying the footprint of the local industrial facilities. Moreover, short-term events of elevated Cu and Pb concentrations were detected by single chamber analyses. This study demonstrates the potential of using heavy metals anomalies in foraminiferal single chambers as a tool for detecting the industrial footprint of coastal facilities as well as short term events of elevated heavy metals. Copyright © 2018 Elsevier Ltd. All rights reserved.

  1. Single Ion transient-IBIC analyses of semiconductor devices using a cryogenic temperature stage

    International Nuclear Information System (INIS)

    Laird, J.S.; Bardos, R.; Legge, G.J.F.; Jagadish, C.

    1998-01-01

    A new Transient - IBIC data acquisition and analysis system at MARC is described. A discussion on the need for single ion control and temperature control is also given. The recorded signal is used as the trigger for beam pulsing. The new cryostatic temperature control stage is introduced. Data is presented on line profiles across the edge of a Au-Si junction collected over the temperature range of 25-300K using a developed C-V and I-V variable temperature stage incorporating a liquid helium cryostat. It demonstrates the potential improvements in spatial resolution in materials of long lifetime by mapping on timing windows around the prompt charge component in the charge transient

  2. Single Ion transient-IBIC analyses of semiconductor devices using a cryogenic temperature stage

    Energy Technology Data Exchange (ETDEWEB)

    Laird, J.S.; Bardos, R.; Legge, G.J.F. [Melbourne Univ., Parkville, VIC (Australia). School of Physics; Jagadish, C. [Australian National Univ., Canberra, ACT (Australia). School of Physics, Electronic Materials Engineering

    1998-06-01

    A new Transient - IBIC data acquisition and analysis system at MARC is described. A discussion on the need for single ion control and temperature control is also given. The recorded signal is used as the trigger for beam pulsing. The new cryostatic temperature control stage is introduced. Data is presented on line profiles across the edge of a Au-Si junction collected over the temperature range of 25-300K using a developed C-V and I-V variable temperature stage incorporating a liquid helium cryostat. It demonstrates the potential improvements in spatial resolution in materials of long lifetime by mapping on timing windows around the prompt charge component in the charge transient. 2 figs.

  3. Analyses of the energy-dependent single separable potential models for the NN scattering

    International Nuclear Information System (INIS)

    Ahmad, S.S.; Beghi, L.

    1981-08-01

    Starting from a systematic study of the salient features regarding the quantum-mechanical two-particle scattering off an energy-dependent (ED) single separable potential and its connection with the rank-2 energy-independent (EI) separable potential in the T-(K-) amplitude formulation, the present status of the ED single separable potential models due to Tabakin (M1), Garcilazo (M2) and Ahmad (M3) has been discussed. It turned out that the incorporation of a self-consistent optimization procedure improves considerably the results of the 1 S 0 and 3 S 1 scattering phase shifts for the models (M2) and (M3) up to the CM wave number q=2.5 fm -1 , although the extrapolation of the results up to q=10 fm -1 reveals that the two models follow the typical behaviour of the well-known super-soft core potentials. It has been found that a variant of (M3) - i.e. (M4) involving one more parameter - gives the phase shifts results which are generally in excellent agreement with the data up to q=2.5 fm -1 and the extrapolation of the results for the 1 S 0 case in the higher wave number range not only follows the corresponding data qualitatively but also reflects a behaviour similar to the Reid soft core and Hamada-Johnston potentials together with a good agreement with the recent [4/3] Pade fits. A brief discussion regarding the features resulting from the variations in the ED parts of all the four models under consideration and their correlations with the inverse scattering theory methodology concludes the paper. (author)

  4. Full-Scale Crash Tests and Analyses of Three High-Wing Single

    Science.gov (United States)

    Annett, Martin S.; Littell, Justin D.; Stimson, Chad M.; Jackson, Karen E.; Mason, Brian H.

    2015-01-01

    The NASA Emergency Locator Transmitter Survivability and Reliability (ELTSAR) project was initiated in 2014 to assess the crash performance standards for the next generation of ELT systems. Three Cessna 172 aircraft have been acquired to conduct crash testing at NASA Langley Research Center's Landing and Impact Research Facility. Testing is scheduled for the summer of 2015 and will simulate three crash conditions; a flare to stall while emergency landing, and two controlled flight into terrain scenarios. Instrumentation and video coverage, both onboard and external, will also provide valuable data of airframe response. Full-scale finite element analyses will be performed using two separate commercial explicit solvers. Calibration and validation of the models will be based on the airframe response under these varying crash conditions.

  5. A method for multiple sequential analyses of macrophage functions using a small single cell sample

    Directory of Open Access Journals (Sweden)

    F.R.F. Nascimento

    2003-09-01

    Full Text Available Microbial pathogens such as bacillus Calmette-Guérin (BCG induce the activation of macrophages. Activated macrophages can be characterized by the increased production of reactive oxygen and nitrogen metabolites, generated via NADPH oxidase and inducible nitric oxide synthase, respectively, and by the increased expression of major histocompatibility complex class II molecules (MHC II. Multiple microassays have been developed to measure these parameters. Usually each assay requires 2-5 x 10(5 cells per well. In some experimental conditions the number of cells is the limiting factor for the phenotypic characterization of macrophages. Here we describe a method whereby this limitation can be circumvented. Using a single 96-well microassay and a very small number of peritoneal cells obtained from C3H/HePas mice, containing as little as <=2 x 10(5 macrophages per well, we determined sequentially the oxidative burst (H2O2, nitric oxide production and MHC II (IAk expression of BCG-activated macrophages. More specifically, with 100 µl of cell suspension it was possible to quantify H2O2 release and nitric oxide production after 1 and 48 h, respectively, and IAk expression after 48 h of cell culture. In addition, this microassay is easy to perform, highly reproducible and more economical.

  6. Analysing Discursive Practices in Legal Research: How a Single Remark Implies a Paradigm

    Directory of Open Access Journals (Sweden)

    Paul van den Hoven

    2017-12-01

    Full Text Available Different linguistic theories of meaning (semantic theories imply different methods to discuss meaning. Discussing meaning is what legal practitioners frequently do to decide legal issues and, subsequently, legal scholars analyse in their studies these discursive practices of parties, judges and legal experts. Such scholarly analysis reveals a methodical choice on how to discuss meaning and therefore implies positioning oneself towards a semantic theory of meaning, whether the scholar is aware of this or not. Legal practitioners may not be bound to be consistent in their commitment to semantic theories, as their task is to decide legal issues. Legal scholars, however, should be consistent because commitment to a semantic theory implies a distinct position towards important legal theoretical doctrines. In this paper three examples are discussed that require an articulated position of the legal scholar because the discursive practices of legal practitioners show inconsistencies. For each of these examples it can be shown that a scholar’s methodic choice implies commitment to a specific semantic theory, and that adopting such a theory implies a distinct position towards the meaning of the Rule of Law, the separation of powers doctrine and the institutional position of the judge.

  7. Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair

    Energy Technology Data Exchange (ETDEWEB)

    Cappadocia, Laurent; Maréchal, Alexandre; Parent, Jean-Sébastien; Lepage, Étienne; Sygusch, Jurgen; Brisson, Normand (Montreal)

    2010-09-07

    DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial genome stability in plants, little is known about the mechanisms of DNA repair in these organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteins from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant organelle genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.

  8. Aggregations of organelles in meiotic cells of higher plants

    Directory of Open Access Journals (Sweden)

    Bohdan Rodkiewicz

    2014-01-01

    Full Text Available During early prophase I in microsporocytes and sporocytes of various plants all mitochondria and plastids aggregate in a group, where some plastids seem to undergo division. This group desintegrates by middle prophase I. Further aggregations of plastids and mitochondria occur in microsporogenesis and sporogenesis is of a simultaneous type. Organelles aggregate the second time at the end of prophase 1 and during or after telophase I they form a dense equatorial plate which lasts until telophase IL Since the phragmoplast is dismantled after telophase I and there is no cytokinesis, organelles aggregated in the plate apparently prevent merging of the nuclei and spindles of meiosis II, thus taking over a role of a phragmoplast and cell wall. In some plants after telophase II organelle aggregation changes shape and occupies the planes where cell walls will be built in simultaneous cytokinesis. Positioning of plastids and mitochondria along these planes may facilitate their equal apportionment among the postmeiotic cells.

  9. Visual CRO display of pulse height distribution including discriminator setting for a single channel X-ray analyser

    International Nuclear Information System (INIS)

    Shaw, S.E.

    1979-01-01

    An outline for a simple pulse spectroscope which attaches to a standard laboratory CRO is presented. The peak amplitude voltage of each pulse from the linear amplifier of a single channel X-ray analyser is stored for the duration of one oscilloscope trace. For each amplifier pulse, input from the discriminator is tested and if these is coincidence of pulses the oscilloscope beam is blanked for approximately the first 2 cm of its traverse across the screen. Repetition of pulses forms a pulse height distribution with a rectangular dark area marking the position of the discriminator window. (author)

  10. The Type and Impact of Evidence Review Group Exploratory Analyses in the NICE Single Technology Appraisal Process.

    Science.gov (United States)

    Carroll, Christopher; Kaltenthaler, Eva; Hill-McManus, Daniel; Scope, Alison; Holmes, Michael; Rice, Stephen; Rose, Micah; Tappenden, Paul; Woolacott, Nerys

    2017-06-01

    As part of the UK National Institute for Health and Care Excellence (NICE) single technology appraisal process, independent evidence review groups (ERGs) critically appraise a company's submission relating to a specific technology and indication. To explore the type of additional exploratory analyses conducted by ERGs and their impact on the recommendations made by NICE. The 100 most recently completed single technology appraisals with published guidance were selected for inclusion. A content analysis of relevant documents was undertaken to identify and extract relevant data, and narrative synthesis was used to rationalize and present these data. The types of exploratory analysis conducted in relation to companies' models were fixing errors, addressing violations, addressing matters of judgment, and the provision of a new, ERG-preferred base case. Ninety-three of the 100 ERG reports contained at least one of these analyses. The most frequently reported type of analysis in these 93 ERG reports related to the category "Matters of judgment," which was reported in 83 reports (89%). At least one of the exploratory analyses conducted and reported by an ERG is mentioned in 97% of NICE appraisal consultation documents and 94% of NICE final appraisal determinations, and had a clear influence on recommendations in 72% of appraisal consultation documents and 47% of final appraisal determinations. These results suggest that the additional analyses undertaken by ERGs in the appraisal of company submissions are highly influential in the policy-making and decision-making process. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

  11. The GC-Rich Mitochondrial and Plastid Genomes of the Green Alga Coccomyxa Give Insight into the Evolution of Organelle DNA Nucleotide Landscape

    Energy Technology Data Exchange (ETDEWEB)

    Smith, David Roy; Burki, Fabien; Yamada, Takashi; Grimwood, Jane; Grigoriev, Igor V.; Van Etten, James L.; Keeling, Patrick J.

    2011-05-13

    Most of the available mitochondrial and plastid genome sequences are biased towards adenine and thymine (AT) over guanine and cytosine (GC). Examples of GC-rich organelle DNAs are limited to a small but eclectic list of species, including certain green algae. Here, to gain insight in the evolution of organelle nucleotide landscape, we present the GC-rich mitochondrial and plastid DNAs from the trebouxiophyte green alga Coccomyxa sp. C-169. We compare these sequences with other GC-rich organelle DNAs and argue that the forces biasing them towards G and C are nonadaptive and linked to the metabolic and/or life history features of this species. The Coccomyxa organelle genomes are also used for phylogenetic analyses, which highlight the complexities in trying to resolve the interrelationships among the core chlorophyte green algae, but ultimately favour a sister relationship between the Ulvophyceae and Chlorophyceae, with the Trebouxiophyceae branching at the base of the chlorophyte crown.

  12. Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset

    Directory of Open Access Journals (Sweden)

    Jihye Kim

    2013-09-01

    Full Text Available Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05. Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

  13. Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signalling dynamics

    Science.gov (United States)

    Lee, Hong-Won; Kyung, Taeyoon; Yoo, Janghyun; Kim, Tackhoon; Chung, Chaeuk; Ryu, Ji Young; Lee, Hanki; Park, Kihyun; Lee, Sangkyu; Jones, Walton D.; Lim, Dae-Sik; Hyeon, Changbong; Do Heo, Won; Yoon, Tae-Young

    2013-01-01

    Co-immunoprecipitation (co-IP) has become a standard technique, but its protein-band output provides only static, qualitative information about protein–protein interactions. Here we demonstrate a real-time single-molecule co-IP technique that generates real-time videos of individual protein–protein interactions as they occur in unpurified cell extracts. By analysing single Ras–Raf interactions with a 50-ms time resolution, we have observed transient intermediates of the protein–protein interaction and determined all the essential kinetic rates. Using this technique, we have quantified the active fraction of native Ras proteins in xenograft tumours, normal tissue and cancer cell lines. We demonstrate that the oncogenic Ras mutations selectively increase the active-Ras fraction by one order of magnitude, without affecting total Ras levels or single-molecule signalling kinetics. Our approach allows us to probe the previously hidden, dynamic aspects of weak protein–protein interactions. It also suggests a path forward towards precision molecular diagnostics at the protein–protein interaction level. PMID:23422673

  14. Multimodal transport and dispersion of organelles in narrow tubular cells

    Science.gov (United States)

    Mogre, Saurabh S.; Koslover, Elena F.

    2018-04-01

    Intracellular components explore the cytoplasm via active motor-driven transport in conjunction with passive diffusion. We model the motion of organelles in narrow tubular cells using analytical techniques and numerical simulations to study the efficiency of different transport modes in achieving various cellular objectives. Our model describes length and time scales over which each transport mode dominates organelle motion, along with various metrics to quantify exploration of intracellular space. For organelles that search for a specific target, we obtain the average capture time for given transport parameters and show that diffusion and active motion contribute to target capture in the biologically relevant regime. Because many organelles have been found to tether to microtubules when not engaged in active motion, we study the interplay between immobilization due to tethering and increased probability of active transport. We derive parameter-dependent conditions under which tethering enhances long-range transport and improves the target capture time. These results shed light on the optimization of intracellular transport machinery and provide experimentally testable predictions for the effects of transport regulation mechanisms such as tethering.

  15. Review on recent advances in the analysis of isolated organelles

    Czech Academy of Sciences Publication Activity Database

    Satori, Ch. P.; Košťál, Vratislav; Arriaga, E. A.

    2012-01-01

    Roč. 753, NOV 13 (2012), s. 8-18 ISSN 0003-2670 R&D Projects: GA ČR(CZ) GBP206/12/G014 Institutional research plan: CEZ:AV0Z40310501 Keywords : organelle isolation * fluorescence * electrophoresis Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.387, year: 2012

  16. The endoplasmic reticulum exerts control over organelle streaming during cell expansion.

    Science.gov (United States)

    Stefano, Giovanni; Renna, Luciana; Brandizzi, Federica

    2014-03-01

    Cytoplasmic streaming is crucial for cell homeostasis and expansion but the precise driving forces are largely unknown. In plants, partial loss of cytoplasmic streaming due to chemical and genetic ablation of myosins supports the existence of yet-unknown motors for organelle movement. Here we tested a role of the endoplasmic reticulum (ER) as propelling force for cytoplasmic streaming during cell expansion. Through quantitative live-cell analyses in wild-type Arabidopsis thaliana cells and mutants with compromised ER structure and streaming, we demonstrate that cytoplasmic streaming undergoes profound changes during cell expansion and that it depends on motor forces co-exerted by the ER and the cytoskeleton.

  17. Dynein is the motor for retrograde axonal transport of organelles

    International Nuclear Information System (INIS)

    Schnapp, B.J.; Reese, T.S.

    1989-01-01

    Vesicular organelles in axons of nerve cells are transported along microtubules either toward their plus ends (fast anterograde transport) or toward their minus ends (retrograde transport). Two microtubule-based motors were previously identified by examining plastic beads induced to move along microtubules by cytosol fractions from the squid giant axon: (i) an anterograde motor, kinesin, and (ii) a retrograde motor, which is characterized here. The retrograde motor, a cytosolic protein previously termed HMW1, was purified from optic lobes and extruded axoplasm by nucleotide-dependent microtubule affinity and release; microtubule gliding was used as the assay of motor activity. The following properties of the retrograde motor suggest that it is cytoplasmic dynein: (i) sedimentation at 20-22 S with a heavy chain of Mr greater than 200,000 that coelectrophoreses with the alpha and beta subunits of axonemal dynein, (ii) cleavage by UV irradiation in the presence of ATP and vanadate, and (iii) a molecular structure resembling two-headed dynein from axonemes. Furthermore, bead movement toward the minus end of microtubules was blocked when axoplasmic supernatants were treated with UV/vanadate. Treatment of axoplasmic supernatant with UV/vanadate also blocks the retrograde movement of purified organelles in vitro without changing the number of anterograde moving organelles, indicating that dynein interacts specifically with a subgroup of organelles programmed to move toward the cell body. However, purified optic lobe dynein, like purified kinesin, does not by itself promote the movement of purified organelles along microtubules, suggesting that additional axoplasmic factors are necessary for retrograde as well as anterograde transport

  18. Mapping Invasive Tamarisk (Tamarix: A Comparison of Single-Scene and Time-Series Analyses of Remotely Sensed Data

    Directory of Open Access Journals (Sweden)

    Paul H. Evangelista

    2009-08-01

    Full Text Available In this study, we tested the Maximum Entropy model (Maxent for its application and performance in remotely sensing invasive Tamarix sp. Six Landsat 7 ETM+ satellite scenes and a suite of vegetation indices at different times of the growing season were selected for our study area along the Arkansas River in Colorado. Satellite scenes were selected for April, May, June, August, September, and October and tested in single-scene and time-series analyses. The best model was a time-series analysis fit with all spectral variables, which had an AUC = 0.96, overall accuracy = 0.90, and Kappa = 0.79. The top predictor variables were June tasselled cap wetness, September tasselled cap wetness, and October band 3. A second time-series analysis, where the variables that were highly correlated and demonstrated low predictive strengths were removed, was the second best model. The third best model was the October single-scene analysis. Our results may prove to be an effective approach for mapping Tamarix sp., which has been a challenge for resource managers. Of equal importance is the positive performance of the Maxent model in handling remotely sensed datasets.

  19. Updating our view of organelle genome nucleotide landscape

    Directory of Open Access Journals (Sweden)

    David Roy Smith

    2012-09-01

    Full Text Available Organelle genomes show remarkable variation in architecture and coding content, yet their nucleotide composition is relatively unvarying across the eukaryotic domain, with most having a high adenine and thymine (AT content. Recent studies, however, have uncovered guanine and cytosine (GC-rich mitochondrial and plastid genomes. These sequences come from a small but eclectic list of species, including certain green plants and animals. Here, I review GC-rich organelle DNAs and the insights they have provided into the evolution of nucleotide landscape. I emphasize that GC-biased mitochondrial and plastid DNAs are more widespread than once thought, sometimes occurring together in the same species, and suggest that the forces biasing their nucleotide content can differ both among and within lineages, and may be associated with specific genome architectural features and life history traits.

  20. Geometric modeling of subcellular structures, organelles, and multiprotein complexes

    OpenAIRE

    Feng, Xin; Xia, Kelin; Tong, Yiying; Wei, Guo-Wei

    2012-01-01

    Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multi-protein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric da...

  1. The nematocyst: a molecular map of the cnidarian stinging organelle.

    Science.gov (United States)

    Beckmann, Anna; Özbek, Suat

    2012-01-01

    Nematocysts or cnidocysts represent the common feature of all cnidarians. They are large organelles produced from the Golgi apparatus as a secretory product within a specialized cell, the nematocyte or cnidocyte. Nematocysts are predominantly used for prey capture and defense, but also for locomotion. In spite of large variations in size and morphology, nematocysts share a common build comprising a cylindrical capsule to which a long hollow thread is attached. The thread is inverted and coiled within the capsule and may be armed with spines in some nematocyst types. During the discharge of nematocysts following a chemical or mechanical stimulus, the thread is expelled from within the capsule matrix in a harpoon-like fashion. This process constitutes one of the fastest in biology and is accompanied by a release of toxins that are potentially harmful also for humans. The long history of research on Hydra as a model organism has been accompanied by the cellular, mechanistic and morphological analysis of its nematocyst repertoire. Although representing one of the most complex organelles of the animal kingdom, the evolutionary origin and molecular map of the nematocyst has remained largely unknown. Recent efforts in unraveling the molecular content of this fascinating organelle have revealed intriguing parallels to the extracellular matrix.

  2. Three-dimensional reconstruction of Trypanosoma cruzi epimastigotes and organelle distribution along the cell division cycle.

    Science.gov (United States)

    Ramos, Thiago Cesar Prata; Freymüller-Haapalainen, Edna; Schenkman, Sergio

    2011-07-01

    Trypanosoma cruzi is the protozoan that causes Chagas disease. It divides in the insect vector gut or in the cytosol of an infected mammalian cell. T. cruzi has one mitochondrion, one Golgi complex, one flagellum, and one cytostome. Here, we provide three-dimensional (3D) models of this protozoan based on images obtained from serial sections on electron microscopy at different stages of the cell cycle. Ultrathin serial sections were obtained from Epon™ embedded parasites, photographed in a transmission electron microscope, and 3D models were generated using Reconstruct and Blender 3D modeling softwares. The localization and distribution of organelles was evaluated and attributed to specific morphological patterns and deduced by distribution of specific markers by immunofluorescence analysis. The new features found in the 3D reconstructions are (1) the electron-dense chromatin is interconnected leaving an internal space for a centrally located nucleolus; (2) The kinetoplast is accommodated within a separated branch of the tubular and single mitochondrion; (3) The disk shaped kinetoplast, which is the mitochondrial DNA, duplicates from the interior in G2 phase; (4) The mitochondrion faces the external membrane and shrinks to accommodate an enlarged number of cytosolic vesicles from G1 to G2; (5) The cytostome progress from the parasite surface toward the posterior end contouring the kinetoplast and nucleus and retracts during cell cycle. These new observations might help understanding how organelles are formed and distributed in early divergent eukaryotic cells and provides a useful method to understand the organelle distribution in small eukaryotic cells. Copyright © 2011 International Society for Advancement of Cytometry.

  3. Neospora caninum Recruits Host Cell Structures to Its Parasitophorous Vacuole and Salvages Lipids from Organelles

    Science.gov (United States)

    Nolan, Sabrina J.; Luechtefeld, Thomas

    2015-01-01

    Toxoplasma gondii and Neospora caninum, which cause the diseases toxoplasmosis and neosporosis, respectively, are two closely related apicomplexan parasites. They have similar heteroxenous life cycles and conserved genomes and share many metabolic features. Despite these similarities, T. gondii and N. caninum differ in their transmission strategies and zoonotic potential. Comparative analyses of the two parasites are important to identify the unique biological features that underlie the basis of host preference and pathogenicity. T. gondii and N. caninum are obligate intravacuolar parasites; in contrast to T. gondii, events that occur during N. caninum infection remain largely uncharacterized. We examined the capability of N. caninum (Liverpool isolate) to interact with host organelles and scavenge nutrients in comparison to that of T. gondii (RH strain). N. caninum reorganizes the host microtubular cytoskeleton and attracts endoplasmic reticulum (ER), mitochondria, lysosomes, multivesicular bodies, and Golgi vesicles to its vacuole though with some notable differences from T. gondii. For example, the host ER gathers around the N. caninum parasitophorous vacuole (PV) but does not physically associate with the vacuolar membrane; the host Golgi apparatus surrounds the N. caninum PV but does not fragment into ministacks. N. caninum relies on plasma lipoproteins and scavenges cholesterol from NPC1-containing endocytic organelles. This parasite salvages sphingolipids from host Golgi Rab14 vesicles that it sequesters into its vacuole. Our data highlight a remarkable degree of conservation in the intracellular infection program of N. caninum and T. gondii. The minor differences between the two parasites related to the recruitment and rearrangement of host organelles around their vacuoles likely reflect divergent evolutionary paths. PMID:25750213

  4. Mycoplasma pneumoniae cytoskeletal protein HMW2 and the architecture of the terminal organelle.

    Science.gov (United States)

    Bose, Stephanie R; Balish, Mitchell F; Krause, Duncan C

    2009-11-01

    The terminal organelle of Mycoplasma pneumoniae mediates cytadherence and gliding motility and functions in cell division. The defining feature of this complex membrane-bound cell extension is an electron-dense core of two segmented rods oriented longitudinally and enlarging to form a bulb at the distal end. While the components of the core have not been comprehensively identified, previous evidence suggested that the cytoskeletal protein HMW2 forms parallel bundles oriented lengthwise to yield the major rod of the core. In the present study, we tested predictions emerging from that model by ultrastructural and immunoelectron microscopy analyses of cores from wild-type M. pneumoniae and mutants producing HMW2 derivatives. Antibodies specific for the N or C terminus of HMW2 labeled primarily peripheral to the core along its entire length. Furthermore, truncation of HMW2 did not correlate specifically with core length. However, mutant analysis correlated specific HMW2 domains with core assembly, and examination of core-enriched preparations confirmed that HMW2 was a major component of these fractions. Taken together, these findings yielded a revised model for HMW2 in terminal organelle architecture.

  5. Analyses of 32 Loci Clarify Phylogenetic Relationships among Trypanosoma cruzi Lineages and Support a Single Hybridization prior to Human Contact

    Science.gov (United States)

    Flores-López, Carlos A.; Machado, Carlos A.

    2011-01-01

    Background The genetic diversity of Trypanosoma cruzi, the etiological agent of Chagas disease, has been traditionally divided in two major groups, T. cruzi I and II, corresponding to discrete typing units TcI and TcII-VI under a recently proposed nomenclature. The two major groups of T. cruzi seem to differ in important biological characteristics, and are thus thought to represent a natural division relevant for epidemiological studies and development of prophylaxis. To understand the potential connection between the different manifestations of Chagas disease and variability of T. cruzi strains, it is essential to have a correct reconstruction of the evolutionary history of T. cruzi. Methodology/Principal Findings Nucleotide sequences from 32 unlinked loci (>26 Kilobases of aligned sequence) were used to reconstruct the evolutionary history of strains representing the known genetic variability of T. cruzi. Thorough phylogenetic analyses show that the original classification of T. cruzi in two major lineages does not reflect its evolutionary history and that there is only strong evidence for one major and recent hybridization event in the history of this species. Furthermore, estimates of divergence times using Bayesian methods show that current extant lineages of T. cruzi diverged very recently, within the last 3 million years, and that the major hybridization event leading to hybrid lineages TcV and TcVI occurred less than 1 million years ago, well before the contact of T. cruzi with humans in South America. Conclusions/Significance The described phylogenetic relationships among the six major genetic subdivisions of T. cruzi should serve as guidelines for targeted epidemiological and prophylaxis studies. We suggest that it is important to reconsider conclusions from previous studies that have attempted to uncover important biological differences between the two originally defined major lineages of T. cruzi especially if those conclusions were obtained from single

  6. Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh

    Directory of Open Access Journals (Sweden)

    Md. Rasel Uzzaman

    2014-10-01

    Full Text Available In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28 and a semi-domesticated population (gayal, n = 17. Overall, 95% and 58% of the total SNPs (69,804 showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (FIS in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33 was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

  7. Estimation of migration-time and mobility distributions in organelle capillary electrophoresis with statistical-overlap theory.

    Science.gov (United States)

    Davis, Joe M; Arriaga, Edgar A

    2010-01-01

    The separation of organelles by capillary electrophoresis (CE) produces large numbers of narrow peaks, which commonly are assumed to originate from single particles. In this paper, we show this is not always true. Here, we use established methods to partition simulated and real organelle CEs into regions of constant peak density and then use statistical-overlap theory to calculate the number of peaks (single particles) in each region. The only required measurements are the number of observed peaks (maxima) and peak standard deviation in the regions and the durations of the regions. Theory is developed for the precision of the estimated peak number and the threshold saturation above which the calculation is not advisable due to fluctuation of peak numbers. Theory shows that the relative precision is good when the saturation lies between 0.2 and 1.0 and is optimal when the saturation is slightly greater than 0.5. It also shows the threshold saturation depends on the peak standard deviation divided by the region's duration. The accuracy and precision of peak numbers estimated in different regions of organelle CEs are verified by computer simulations having both constant and nonuniform peak densities. The estimates are accurate to 6%. The estimated peak numbers in different regions are used to calculate migration-time and electrophoretic-mobility distributions. These distributions are less biased by peak overlap than ones determined by counting maxima and provide more correct measures of the organelle properties. The procedure is applied to a mitochondrial CE, in which over 20% of peaks are hidden by peak overlap.

  8. The Lipid Droplet – A Well-Connected Organelle

    Directory of Open Access Journals (Sweden)

    Qiang eGao

    2015-08-01

    Full Text Available Our knowledge of inter-organellar communication has grown exponentially in recent years. This review focuses on the interactions that cytoplasmic lipid droplets have with other organelles. Twenty-five years ago droplets were considered simply particles of coalesced fat. Ten years ago there were hints from proteomics studies that droplets might interact with other structures to share lipids and proteins. Now it is clear that the droplets interact with many if not most cellular structures to maintain cellular homeostasis and to buffer against insults such as starvation. The evidence for this statement, as well as probes to understand the nature and results of droplet interactions, are presented.

  9. Geometric modeling of subcellular structures, organelles, and multiprotein complexes.

    Science.gov (United States)

    Feng, Xin; Xia, Kelin; Tong, Yiying; Wei, Guo-Wei

    2012-12-01

    Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multiprotein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes. Copyright © 2012 John Wiley & Sons, Ltd.

  10. Prokaryotic cells: structural organisation of the cytoskeleton and organelles.

    Science.gov (United States)

    Souza, Wanderley de

    2012-05-01

    For many years, prokaryotic cells were distinguished from eukaryotic cells based on the simplicity of their cytoplasm, in which the presence of organelles and cytoskeletal structures had not been discovered. Based on current knowledge, this review describes the complex components of the prokaryotic cell cytoskeleton, including (i) tubulin homologues composed of FtsZ, BtuA, BtuB and several associated proteins, which play a fundamental role in cell division, (ii) actin-like homologues, such as MreB and Mb1, which are involved in controlling cell width and cell length, and (iii) intermediate filament homologues, including crescentin and CfpA, which localise on the concave side of a bacterium and along its inner curvature and associate with its membrane. Some prokaryotes exhibit specialised membrane-bound organelles in the cytoplasm, such as magnetosomes and acidocalcisomes, as well as protein complexes, such as carboxysomes. This review also examines recent data on the presence of nanotubes, which are structures that are well characterised in mammalian cells that allow direct contact and communication between cells.

  11. Analyses of significant features of L-Prolinium Picrate single crystal: An excellent material for non linear optical applications

    Energy Technology Data Exchange (ETDEWEB)

    Thukral, Kanika [Academy of Scientific and Innovative Research, CSIR- National Physical Laboratory, New Delhi, 110012 (India); CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi, 110 012 (India); Vijayan, N., E-mail: nvijayan@nplindia.org [CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi, 110 012 (India); Vij, Mahak [CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi, 110 012 (India); Nagaraja, C.M. [Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, 140001, Punjab (India); Jayaramakrishnan, V. [Centro De Investigations En Optica, Loma del Bosque 115, Colonia Lomas del Campestre, León, Guanajuato, Código Postal, 37150 (Mexico); Jayalakshmy, M.S. [International and Inter University Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kottayam, Kerala, 686560 (India); Kant, Rajni [Department of Physics and Electronics, University of Jammu, Jammu Tawi, 180006 (India)

    2017-06-15

    Today the fundamental aspect of the researchers is to explore maximum physical properties of the material for device fabrication. In the present article, single crystal X-ray diffraction has been carried out to verify the formation of the synthesized compound. In addition to that, powder X-ray diffraction has been performed to obtain diffraction pattern of L-Prolinium Picrate single crystal. The strain present inside the single crystal was measured using Hall-Williamson equation from PXRD measurements. The dark current and photon current was obtained from photoconductivity technique whose plot depicted that the sample was negative photoconducting material. Optical homogeneity of the single crystal was analyzed using birefringence technique. Its resistance towards Nd: YAG laser was scrutinized for L-Prolinium Picrate single crystal by applying 1 pulse per second. Different thermal parameters like thermal conductivity, thermal diffusivity, thermal effusivity and specific heat were computed using photo-pyroelectric technique. Solid state parameters were calculated from Clausius Mossotti relation by taking structural information of the title compound. Also, optical parameters like refractive index, reflectance etc were calculated through UV–Vis–NIR analysis. - Highlights: • An optically transparent L-Prolinium Picrate single crystal was harvested from slow evaporation solution growth technique. • The compound shows negative photoconducting nature. • Its optical homogeneity was analyzed using birefringence. • Single shot of laser was applied to sample to measure laser damage threshold value. • The thermal parameters were computed from Photopyroelectric technique.

  12. Coupling organelle inheritance with mitosis to balance growth and differentiation.

    Science.gov (United States)

    Asare, Amma; Levorse, John; Fuchs, Elaine

    2017-02-03

    Balancing growth and differentiation is essential to tissue morphogenesis and homeostasis. How imbalances arise in disease states is poorly understood. To address this issue, we identified transcripts differentially expressed in mouse basal epidermal progenitors versus their differentiating progeny and those altered in cancers. We used an in vivo RNA interference screen to unveil candidates that altered the equilibrium between the basal proliferative layer and suprabasal differentiating layers forming the skin barrier. We found that epidermal progenitors deficient in the peroxisome-associated protein Pex11b failed to segregate peroxisomes properly and entered a mitotic delay that perturbed polarized divisions and skewed daughter fates. Together, our findings unveil a role for organelle inheritance in mitosis, spindle alignment, and the choice of daughter progenitors to differentiate or remain stem-like. Copyright © 2017, American Association for the Advancement of Science.

  13. Physiological role of taurine - from organism to organelle

    DEFF Research Database (Denmark)

    Lambert, Ian Henry; Kristensen, David Møbjerg Boslev; Holm, Jacob Bak

    2015-01-01

    Taurine is often referred to as a semi-essential amino acid as newborn mammals have a limited ability to synthesize taurine and have to rely on dietary supply. Taurine is not thought to be incorporated into proteins as no aminoacyl tRNA synthetase has yet been identified and is not oxidized...... in mammalian cells. However, taurine contributes significantly to the cellular pool of organic osmolytes and has accordingly been acknowledged for its role in cell volume restoration following osmotic perturbation. This review describes taurine homeostasis in cells and organelles with emphasis on taurine...... biophysics/membrane dynamics, regulation of transport proteins involved in active taurine uptake and passive taurine release as well as physiological processes, for example, development, lung function, mitochondrial function, antioxidative defence and apoptosis which seem to be affected by a shift...

  14. Organelle targeting during bacterial infection: insights from Listeria.

    Science.gov (United States)

    Lebreton, Alice; Stavru, Fabrizia; Cossart, Pascale

    2015-06-01

    Listeria monocytogenes, a facultative intracellular bacterium responsible for severe foodborne infections, is now recognized as a multifaceted model in infection biology. Comprehensive studies of the molecular and cellular basis of the infection have unraveled how the bacterium crosses the intestinal and feto-placental barriers, invades several cell types in which it multiplies and moves, and spreads from cell to cell. Interestingly, although Listeria does not actively invade host cell organelles, it can interfere with their function. We discuss the effect of Listeria on the endoplasmic reticulum (ER) and the mechanisms leading to the fragmentation of the mitochondrial network and its consequences, and review the strategies used by Listeria to subvert nuclear functions, more precisely to control host gene expression at the chromatin level. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae

    Science.gov (United States)

    2013-01-01

    Background Microalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hindered by the paucity of phylogenetically closely-related finished genomes. Results Using the oleaginous eustigmatophyte Nannochloropsis as a model, we assessed current intragenus phylotyping strategies by producing the complete plastid (pt) and mitochondrial (mt) genomes of seven strains from six Nannochloropsis species. Genes on the pt and mt genomes have been highly conserved in content, size and order, strongly negatively selected and evolving at a rate 33% and 66% of nuclear genomes respectively. Pt genome diversification was driven by asymmetric evolution of two inverted repeats (IRa and IRb): psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. In the mt genomes, however, a single evolution hotspot varies in copy-number of a 3.5 Kb-long, cox1-harboring repeat. The organelle markers (e.g., cox1, cox2, psbA, rbcL and rrn16_mt) and nuclear markers (e.g., ITS2 and 18S) that are widely used for phylogenetic analysis obtained a divergent phylogeny for the seven strains, largely due to low SNP density. A new strategy for intragenus phylotyping of microalgae was thus proposed that includes (i) twelve sequence markers that are of higher sensitivity than ITS2 for interspecies phylogenetic analysis, (ii) multi-locus sequence typing based on rps11_mt-nad4, rps3_mt and cox2-rrn16_mt for intraspecies phylogenetic reconstruction and (iii) several SSR loci for identification of strains within a given species. Conclusion This first comprehensive dataset of organelle genomes for a microalgal genus enabled exhaustive assessment and searches of all candidate phylogenetic markers on the organelle genomes. A new strategy

  16. Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae.

    Science.gov (United States)

    Wei, Li; Xin, Yi; Wang, Dongmei; Jing, Xiaoyan; Zhou, Qian; Su, Xiaoquan; Jia, Jing; Ning, Kang; Chen, Feng; Hu, Qiang; Xu, Jian

    2013-08-05

    Microalgae are promising feedstock for production of lipids, sugars, bioactive compounds and in particular biofuels, yet development of sensitive and reliable phylotyping strategies for microalgae has been hindered by the paucity of phylogenetically closely-related finished genomes. Using the oleaginous eustigmatophyte Nannochloropsis as a model, we assessed current intragenus phylotyping strategies by producing the complete plastid (pt) and mitochondrial (mt) genomes of seven strains from six Nannochloropsis species. Genes on the pt and mt genomes have been highly conserved in content, size and order, strongly negatively selected and evolving at a rate 33% and 66% of nuclear genomes respectively. Pt genome diversification was driven by asymmetric evolution of two inverted repeats (IRa and IRb): psbV and clpC in IRb are highly conserved whereas their counterparts in IRa exhibit three lineage-associated types of structural polymorphism via duplication or disruption of whole or partial genes. In the mt genomes, however, a single evolution hotspot varies in copy-number of a 3.5 Kb-long, cox1-harboring repeat. The organelle markers (e.g., cox1, cox2, psbA, rbcL and rrn16_mt) and nuclear markers (e.g., ITS2 and 18S) that are widely used for phylogenetic analysis obtained a divergent phylogeny for the seven strains, largely due to low SNP density. A new strategy for intragenus phylotyping of microalgae was thus proposed that includes (i) twelve sequence markers that are of higher sensitivity than ITS2 for interspecies phylogenetic analysis, (ii) multi-locus sequence typing based on rps11_mt-nad4, rps3_mt and cox2-rrn16_mt for intraspecies phylogenetic reconstruction and (iii) several SSR loci for identification of strains within a given species. This first comprehensive dataset of organelle genomes for a microalgal genus enabled exhaustive assessment and searches of all candidate phylogenetic markers on the organelle genomes. A new strategy for intragenus phylotyping of

  17. Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids.

    Science.gov (United States)

    Park, Seongjun; Ruhlman, Tracey A; Sabir, Jamal S M; Mutwakil, Mohammed H Z; Baeshen, Mohammed N; Sabir, Meshaal J; Baeshen, Nabih A; Jansen, Robert K

    2014-05-28

    Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes. The 154,841 bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608 bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes. Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution

  18. The influence of the design matrix on treatment effect estimates in the quantitative analyses of single-subject experimental design research.

    Science.gov (United States)

    Moeyaert, Mariola; Ugille, Maaike; Ferron, John M; Beretvas, S Natasha; Van den Noortgate, Wim

    2014-09-01

    The quantitative methods for analyzing single-subject experimental data have expanded during the last decade, including the use of regression models to statistically analyze the data, but still a lot of questions remain. One question is how to specify predictors in a regression model to account for the specifics of the design and estimate the effect size of interest. These quantitative effect sizes are used in retrospective analyses and allow synthesis of single-subject experimental study results which is informative for evidence-based decision making, research and theory building, and policy discussions. We discuss different design matrices that can be used for the most common single-subject experimental designs (SSEDs), namely, the multiple-baseline designs, reversal designs, and alternating treatment designs, and provide empirical illustrations. The purpose of this article is to guide single-subject experimental data analysts interested in analyzing and meta-analyzing SSED data. © The Author(s) 2014.

  19. A mixed-methods approach for analysing social support and social anchorage of single mothers’ personal networks

    NARCIS (Netherlands)

    Lumino, Rosaria; Ragozini, Giancarlo; van Duijn, Marijtje; Vitale, Maria Prosperina

    2017-01-01

    The present paper analyses the relationship among social support and personal networks by focusing on social anchorage, which is a specific dimension of social support conveying to what extent people feel integrated into their personal networks. Specifying when, why, and how personal relationships

  20. Comparative Transcriptomic Analyses of Three Species of Placobdella (Rhynchobdellida: Glossiphoniidae) Confirms a Single Origin of Blood Feeding in Leeches.

    Science.gov (United States)

    Siddall, Mark E; Brugler, Mercer R; Kvist, Sebastian

    2016-02-01

    One of the recalcitrant questions regarding the evolutionary history of clitellate annelids involves the feeding preference of the common ancestor of extant rhynchobdellid (proboscis bearing) and arhynchobdellid (jaw bearing) leeches. Whereas early evidence, based on morphological data, pointed towards independent acquisitions of blood feeding in the 2 orders, molecular-based phylogenetic data suggest that the ancestor of modern leeches was a sanguivore. Here, we use a comparative transcriptomic approach in order to increase our understanding of the diversity of anticoagulation factors for 3 species of the genus Placobdella, for which comparative data have been lacking, and inspect these in light of archetypal anticoagulant data for both arhynchobdellid and other rhynchobdellid species. Notwithstanding the varying levels of host specificity displayed by the 3 different species of Placobdella, transcriptomic profiles with respect to anticoagulation factors were largely similar -this despite the fact that Placobdella kwetlumye only retains a single pair of salivary glands, as opposed to the 2 pairs more common in the genus. Results show that 9 different anticoagulant proteins and an additional 5 putative antihemostasis proteins are expressed in salivary secretions of the 3 species. In particular, an ortholog of the archetypal, single-copy, anticoagulant hirudin (not previously available as comparative data for rhynchobdellids) is present in at least 2 of 3 species examined, corroborating the notion of a single origin of blood feeding in the ancestral leech.

  1. Analyses of Short Channel Effects of Single-Gate and Double-Gate Graphene Nanoribbon Field Effect Transistors

    Directory of Open Access Journals (Sweden)

    Hojjatollah Sarvari

    2016-01-01

    Full Text Available Short channel effects of single-gate and double-gate graphene nanoribbon field effect transistors (GNRFETs are studied based on the atomistic pz orbital model for the Hamiltonian of graphene nanoribbon using the nonequilibrium Green’s function formalism. A tight-binding Hamiltonian with an atomistic pz orbital basis set is used to describe the atomistic details in the channel of the GNRFETs. We have investigated the vital short channel effect parameters such as Ion and Ioff, the threshold voltage, the subthreshold swing, and the drain induced barrier lowering versus the channel length and oxide thickness of the GNRFETs in detail. The gate capacitance and the transconductance of both devices are also computed in order to calculate the intrinsic cut-off frequency and switching delay of GNRFETs. Furthermore, the effects of doping of the channel on the threshold voltage and the frequency response of the double-gate GNRFET are discussed. We have shown that the single-gate GNRFET suffers more from short channel effects if compared with those of the double-gate structure; however, both devices have nearly the same cut-off frequency in the range of terahertz. This work provides a collection of data comparing different features of short channel effects of the single gate with those of the double gate GNRFETs. The results give a very good insight into the devices and are very useful for their digital applications.

  2. Characteristics of weak base-induced vacuoles formed around individual acidic organelles.

    Science.gov (United States)

    Hiruma, Hiromi; Kawakami, Tadashi

    2011-01-01

    We have previously found that the weak base 4-aminopyridine induces Brownian motion of acidic organelles around which vacuoles are formed, causing organelle traffic disorder in neurons. Our present study investigated the characteristics of vacuoles induced by weak bases (NH(4)Cl, aminopyridines, and chloroquine) using mouse cells. Individual vacuoles included acidic organelles identified by fluorescent protein expression. Mitochondria and actin filaments were extruded outside the vacuoles, composing the vacuole rim. Staining with amine-reactive fluorescence showed no protein/amino acid content in vacuoles. Thus, serous vacuolar contents are probably partitioned by viscous cytosol, other organelles, and cytoskeletons, but not membrane. The weak base (chloroquine) was immunochemically detected in intravacuolar organelles, but not in vacuoles. Early vacuolization was reversible, but long-term vacuolization caused cell death. The vacuolization and cell death were blocked by the vacuolar H(+)-ATPase inhibitor and Cl--free medium. Staining with LysoTracker or LysoSensor indicated that intravacuolar organelles were strongly acidic and vacuoles were slightly acidic. This suggests that vacuolization is caused by accumulation of weak base and H(+) in acidic organelles, driven by vacuolar H(+)-ATPase associated with Cl(-) entering, and probably by subsequent extrusion of H(+) and water from organelles to the surrounding cytoplasm.

  3. Recent Progress in Micro/Nanoreactors toward the Creation of Artificial Organelles

    DEFF Research Database (Denmark)

    Gallardo, Maria Godoy; York-Durán, María José; Hosta-Rigau, Leticia

    2017-01-01

    as nanoreactors to convert a prodrug into a drug inside the cells or as carriers encapsulating therapeutic enzymes to replace malfunctioning organelles in pathological conditions. For the design of artificial organelles, several requirements need to be fulfilled: a compartmentalized structure that can encapsulate...

  4. A review of modern advances in analyses and applications of single-phase natural circulation loop in nuclear thermal hydraulics

    International Nuclear Information System (INIS)

    Basu, Dipankar N.; Bhattacharyya, Souvik; Das, P.K.

    2014-01-01

    Highlights: • Comprehensive review of state-of-the-art on single-phase natural circulation loops. • Detailed discussion on growth in solar thermal system and nuclear thermal hydraulics. • Systematic development in scaling methodologies for fabrication of test facilities. • Importance of numerical modeling schemes for stability assessment using 1-D codes. • Appraisal of current trend of research and possible future directions. - Abstract: A comprehensive review of single-phase natural circulation loop (NCL) is presented here. Relevant literature reported since the later part of 1980s has been meticulously surveyed, with occasional obligatory reference to a few pioneering studies originating prior to that period, summarizing the key observations and the present trend of research. Development in the concept of buoyancy-induced flow is discussed, with introduction to flow initiation in an NCL due to instability. Detailed discussion on modern advancement in important application areas like solar thermal systems and nuclear thermal hydraulics are presented, with separate analysis for various reactor designs working on natural circulation. Identification of scaling criteria for designing lab-scale experimental facilities has gone through a series of modification. A systematic analysis of the same is presented, considering the state-of-the-art knowledge base. Different approaches have been followed for modeling single-phase NCLs, including simplified Lorenz system mostly for toroidal loops, 1-D computational modeling for both steady-state and stability characterization and 3-D commercial system codes to have a better flow visualization. Methodical review of the relevant studies is presented following a systematic approach, to assess the gradual progression in understanding of the practical system. Brief appraisal of current research interest is reported, including the use of nanofluids for fluid property augmentation, marine reactors subjected to rolling waves

  5. Analysing the effectiveness of vendor-managed inventory in a single-warehouse, multiple-retailer system

    Science.gov (United States)

    Rahim, Mohd Kamarul Irwan Abdul; Aghezzaf, El-Houssaine; Limère, Veronique; Raa, Birger

    2016-06-01

    This paper considers a two-stage supply chain, consisting of a single warehouse and multiple retailers facing deterministic demands, under a vendor-managed inventory (VMI) policy. It presents a two-phase optimisation approach for coordinating the shipments in this VMI system. The first phase uses direct shipping from the supplier to all retailers to minimise the overall inventory costs. Then, in the second phase, the retailers are clustered using a construction heuristic in order to optimise the transportation costs while satisfying some additional restrictions. The improvement of the system's performance through coordinated VMI replenishments against the system with direct shipping only is shown and discussed in the comparative analysis section.

  6. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations

    OpenAIRE

    Liang, Jingjing; Le, Thu H.; Edwards, Digna R. Velez; Tayo, Bamidele O.; Gaulton, Kyle J.; Smith, Jennifer A.; Lu, Yingchang; Jensen, Richard A.; Chen, Guanjie; Yanek, Lisa R.; Schwander, Karen; Tajuddin, Salman M.; Sofer, Tamar; Kim, Wonji; Kayima, James

    2017-01-01

    © 2017 Public Library of Science. All Rights Reserved. Hypertension is a leading cause of global disease, mortality, and disability. While individuals of African descent suffer a disproportionate burden of hypertension and its complications, they have been underrepresented in genetic studies. To identify novel susceptibility loci for blood pressure and hypertension in people of African ancestry, we performed both single and multiple-trait genome-wide association analyses. We analyzed 21 genom...

  7. Development of TUF-ELOCA - a software tool for integrated single-channel thermal-hydraulic and fuel element analyses

    International Nuclear Information System (INIS)

    Popescu, A.I.; Wu, E.; Yousef, W.W.; Pascoe, J.; Parlatan, Y.; Kwee, M.

    2006-01-01

    The TUF-ELOCA tool couples the TUF and ELOCA codes to enable an integrated thermal-hydraulic and fuel element analysis for a single channel during transient conditions. The coupled architecture is based on TUF as the parent process controlling multiple ELOCA executions that simulate the fuel elements behaviour and is scalable to different fuel channel designs. The coupling ensures a proper feedback between the coolant conditions and fuel elements response, eliminates model duplications, and constitutes an improvement from the prediction accuracy point of view. The communication interfaces are based on PVM and allow parallelization of the fuel element simulations. Developmental testing results are presented showing realistic predictions for the fuel channel behaviour during a transient. (author)

  8. The mitochondrial genome, a growing interest inside an organelle

    Directory of Open Access Journals (Sweden)

    Marco Crimi

    2008-03-01

    Full Text Available Marco Crimi1, Roberta Rigolio21National Institute of Molecular Genetics (INGM, Functional Genomics Unit, Milan, Italy; 2Department of Neurosciences and Biomedical Technologies, University of Milan Bicocca, Monza, ItalyAbstract: Mitochondria are semi-autonomously reproductive organelles within eukaryotic cells carrying their own genetic material, called the mitochondrial genome (mtDNA. Until some years ago, mtDNA had primarily been used as a tool in population genetics. As scientists began associating mtDNA mutations with dozens of mysterious disorders, as well as the aging process and a variety of chronic degenerative diseases, it became increasingly evident that the information contained in this genome had substantial potential applications to improve human health. Today, mitochondria research covers a wide range of disciplines, including clinical medicine, biochemistry, genetics, molecular cell biology, bioinformatics, plant sciences and physiology. The present review intends to present a summary of the most exiting fields of the mitochondrial research bringing together several contributes in terms of original prospective and future applications.Keywords: mtDNA, heteroplasmy, molecular diagnostics, mitochondriopathies, nanogenomics

  9. Estimation of pea (Pisum sativum L.) microsatellite mutation rate based on pedigree and single-seed descent analyses.

    Science.gov (United States)

    Cieslarová, Jaroslava; Hanáček, Pavel; Fialová, Eva; Hýbl, Miroslav; Smýkal, Petr

    2011-11-01

    Microsatellites, or simple sequence repeats (SSRs) are widespread class of repetitive DNA sequences, used in population genetics, genetic diversity and mapping studies. In spite of the SSR utility, the genetic and evolutionary mechanisms are not fully understood. We have investigated three microsatellite loci with different position in the pea (Pisum sativum L.) genome, the A9 locus residing in LTR region of abundant retrotransposon, AD270 as intergenic and AF016458 located in 5'untranslated region of expressed gene. Comparative analysis of a 35 pair samples from seven pea varieties propagated by single-seed descent for ten generations, revealed single 4 bp mutation in 10th generation sample at AD270 locus corresponding to stepwise increase in one additional ATCT repeat unit. The estimated mutation rate was 4.76 × 10(-3) per locus per generation, with a 95% confidence interval of 1.2 × 10(-4) to 2.7 × 10(-2). The comparison of cv. Bohatýr accessions retrieved from different collections, showed intra-, inter-accession variation and differences in flanking and repeat sequences. Fragment size and sequence alternations were also found in long term in vitro organogenic culture, established at 1983, indicative of somatic mutation process. The evidence of homoplasy was detected across of unrelated pea genotypes, which adversaly affects the reliability of diversity estimates not only for diverse germplasm but also highly bred material. The findings of this study have important implications for Pisum phylogeny studies, variety identification and registration process in pea breeding where mutation rate influences the genetic diversity and the effective population size estimates.

  10. Time Headway Modelling of Motorcycle-Dominated Traffic to Analyse Traffic Safety Performance and Road Link Capacity of Single Carriageways

    Directory of Open Access Journals (Sweden)

    D. M. Priyantha Wedagama

    2017-04-01

    Full Text Available This study aims to develop time headway distribution models to analyse traffic safety performance and road link capacities for motorcycle-dominated traffic in Denpasar, Bali. Three road links selected as the case study are Jl. Hayam Wuruk, Jl.Hang Tuah, and Jl. Padma. Data analysis showed that between 55%-80% of motorists in Denpasar during morning and evening peak hours paid less attention to the safe distance with the vehicles in front. The study found that Lognormal distribution models are best to fit time headway data during morning peak hours while either Weibull (3P or Pearson III distributions is for evening peak hours. Road link capacities for mixed traffic predominantly motorcycles are apparently affected by the behaviour of motorists in keeping safe distance with the vehicles in front. Theoretical road link capacities for Jl. Hayam Wuruk, Jl. Hang Tuah and Jl. Padma are 3,186 vehicles/hour, 3,077 vehicles/hour and 1935 vehicles/hour respectively.

  11. Single-particle Analyses of Compositions, Morphology, and Viscosity of Aerosol Particles Collected During GoAmazon2014

    Science.gov (United States)

    Adachi, K.; Gong, Z.; Bateman, A. P.; Martin, S. T.; Cirino, G. G.; Artaxo, P.; Sedlacek, A. J., III; Buseck, P. R.

    2014-12-01

    Single-particle analysis using transmission electron microscopy (TEM) shows composition and morphology of individual aerosol particles collected during the GoAmazon2014 campaign. These TEM results indicate aerosol types and mixing states, both of which are important for evaluating particle optical properties and cloud condensation nuclei activity. The samples were collected at the T3 site, which is located in the Amazon forest with influences from the urban pollution plume from Manaus. Samples were also collected from the T0 site, which is in the middle of the jungle with minimal to no influences of anthropogenic sources. The aerosol particles mainly originated from 1) anthropogenic pollution (e.g., nanosphere soot, sulfate), 2) biogenic emissions (e.g., primary biogenic particles, organic aerosols), and 3) long-range transport (e.g., sea salts). We found that the biogenic organic aerosol particles contain homogeneously distributed potassium. Particle viscosity is important for evaluating gas-particle interactions and atmospheric chemistry for the particles. Viscosity can be estimated from the rebounding behavior at controlled relative humidities, i.e., highly viscous particles display less rebound on a plate than low-viscosity particles. We collected 1) aerosol particles from a plate (non-rebounded), 2) those that had rebounded from the plate and were then captured onto an adjacent sampling plate, and 3) particles from ambient air using a separate impactor sampler. Preliminary results show that more than 90% of non-rebounded particles consisted of nanosphere soot with or without coatings. The coatings mostly consisted of organic matter. Although rebounded particles also contain nanosphere soot (number fraction 64-69%), they were mostly internally mixed with sulfate, organic matter, or their mixtures. TEM tilted images suggested that the rebounded particles were less deformed on the substrate, whereas the non-rebounded particles were more deformed, which could

  12. A method for analysing phosphatase activity in aquatic bacteria at the single cell level using flow cytometry.

    Science.gov (United States)

    Duhamel, Solange; Gregori, Gerald; Van Wambeke, France; Mauriac, Romain; Nedoma, Jirí

    2008-10-01

    It has been demonstrated that ELF97-phosphate (ELF-P) is a useful tool to detect and quantify phosphatase activity of phytoplankton populations at a single cell level. Recently, it has been successfully applied to marine heterotrophic bacteria in culture samples, the cells exhibiting phosphatase activity being detected using epifluorescence microscopy. Here, we describe a new protocol that enables the detection of ELF alcohol (ELFA), the product of ELF-P hydrolysis, allowing the detection of phosphatase positive bacteria, using flow cytometry. Bacteria from natural samples must be disaggregated and, in oligotrophic waters, concentrated before they can be analyzed by flow cytometry. The best efficiency for disaggregating/separating bacterial cell clumps was obtained by incubating the sample for 30 min with Tween 80 (10 mg l(-1), final concentration). A centrifugation step (20,000 g; 30 min) was required in order to recover all the cells in the pellet (only 7+/-2% of the cells were recovered from the supernatant). The cells and the ELFA precipitates were resistant to these treatments. ELFA-labelled samples were stored in liquid nitrogen for up to four months before counting without any significant loss in total or ELFA-labelled bacterial cell abundance or in the ELFA fluorescence intensity. We describe a new flow cytometry protocol for detecting and discriminating the signals from both ELFA and different counterstains (4',6-diamidino-2-phenylindole (DAPI) and propidium iodide (PI)) necessary to distinguish between ELFA-labelled and non ELFA-labelled heterotrophic bacteria. The method has been successfully applied in both freshwater and marine samples. This method promises to improve our understanding of the physiological response of heterotrophic bacteria to P limitation.

  13. Betting with single forams: Uncertainty constraints on El Niño Southern Oscillation reconstructions using individual foraminiferal analyses

    Science.gov (United States)

    Quinn, T. M.; Thirumalai, K.; Partin, J. W.; Jackson, C. S.

    2012-12-01

    Recent scientific investigations of sub-millennial paleoceanographic variability have attempted to use the population statistics of individual planktic foraminiferal δ18O to resolve high-frequency climate signals such as the El Niño Southern Oscillation (ENSO). However, this approach is complicated by the relatively short lifespan of individual foraminifera (~2-4 weeks) compared to the time represented by a typical marine sediment sample (decades to millennia). The resolving ability of individual foraminiferal analyses (IFA) is investigated through simulations on idealized virtual sediment samples constructed from the instrumental record. We focus on ENSO-related sea surface temperatures (SST) anomalies in the Niño3.4 region of the tropical Pacific Ocean. We constrain uncertainties on the range and standard deviation associated with the IFA technique using a bootstrap Monte Carlo approach. Sensitivity to changes in ENSO amplitude and frequency and the influence of the seasonal cycle on IFA are tested by constructing synthetic time series containing different characteristics of variability. We find that the standard deviation and range may be used to detect ENSO amplitude changes at particular thresholds (though the uncertainty in range is much larger than in standard deviation); however, it is improbable that IFA can resolve changes in ENSO frequency. We also determine that ENSO amplitude is the main driver of the IFA signal at Niño3.4 where the SST response to ENSO is large, and the seasonal cycle is relatively small. Our results suggest that rigorous uncertainty analysis should become a standard for IFA studies as it is crucial for accurate interpretation.

  14. The tannosome is an organelle forming condensed tannins in the chlorophyllous organs of Tracheophyta.

    Science.gov (United States)

    Brillouet, Jean-Marc; Romieu, Charles; Schoefs, Benoît; Solymosi, Katalin; Cheynier, Véronique; Fulcrand, Hélène; Verdeil, Jean-Luc; Conéjéro, Geneviève

    2013-10-01

    Condensed tannins (also called proanthocyanidins) are widespread polymers of catechins and are essential for the defence mechanisms of vascular plants (Tracheophyta). A large body of evidence argues for the synthesis of monomeric epicatechin on the cytosolic face of the endoplasmic reticulum and its transport to the vacuole, although the site of its polymerization into tannins remains to be elucidated. The aim of the study was to re-examine the cellular frame of tannin polymerization in various representatives of the Tracheophyta. Light microscopy epifluorescence, confocal microscopy, transmission electron microscopy (TEM), chemical analysis of tannins following cell fractionation, and immunocytochemistry were used as independent methods on tannin-rich samples from various organs from Cycadophyta, Ginkgophyta, Equisetophyta, Pteridophyta, Coniferophyta and Magnoliophyta. Tissues were fixed in a caffeine-glutaraldehyde mixture and examined by TEM. Other fresh samples were incubated with primary antibodies against proteins from both chloroplastic envelopes and a thylakoidal chlorophyll-carrying protein; they were also incubated with gelatin-Oregon Green, a fluorescent marker of condensed tannins. Coupled spectral analyses of chlorophyll and tannins were carried out by confocal microscopy on fresh tissues and tannin-rich accretions obtained through cell fractionation; chemical analyses of tannins and chlorophylls were also performed on the accretions. The presence of the three different chloroplast membranes inside vacuolar accretions that constitute the typical form of tannin storage in vascular plants was established in fresh tissues as well as in purified organelles, using several independent methods. Tannins are polymerized in a new chloroplast-derived organelle, the tannosome. These are formed by pearling of the thylakoids into 30 nm spheres, which are then encapsulated in a tannosome shuttle formed by budding from the chloroplast and bound by a membrane

  15. The CoRR hypothesis for genes in organelles.

    Science.gov (United States)

    Allen, John F

    2017-12-07

    Chloroplasts and mitochondria perform energy transduction in photosynthesis and respiration. These processes can be described in physico-chemical terms with no obvious requirement for co-located genetic systems, separat from those of the rest of the cell. Accordingly, biochemists once tended to regard endosymbiosis as untestable evolutionary speculation. Lynn Sagan's seminal 1967 paper "On the Origin of Mitosing Cells" outlined the evolution of eukaryotic cells by endosymbiosis of prokaryotes. The endosymbiont hypothesis is consistent with presence of DNA in chloroplasts and mitochondria, but does not assign it a function. Biochemistry and molecular biology now show that Sagan's proposal has an explanatory reach far beyond that originally envisaged. Prokaryotic origins of photosynthetic and respiratory mechanisms are apparent in protein structural insights into energy coupling. Genome sequencing confirms the underlying, prokaryotic architecture of chloroplasts and mitochondria and illustrates the profound influence of the original mergers of their ancestors' genes and proteins with those of their host cells. Peter Mitchell's 1961 chemiosmotic hypothesis applied the concept of vectorial catalysis that underlies biological energy transduction and cell structure, function, and origins. Continuity of electrical charge separation and membrane sidedness requires compartments within compartments, together with intricate mechanisms for transport within and between them. I suggest that the reason for the persistence of distinct genetic systems within bioenergetic organelles is the selective advantage of subcellular co-location of specific genes with their gene products. Co-location for Redox Regulation - CoRR - provides for a dialogue between chemical reduction-oxidation and the action of genes encoding its protein catalysts. These genes and their protein products are in intimate contact, and cannot be isolated from each other without loss of an essential mechanism of

  16. Crystallographic and single-particle analyses of native- and nucleotide-bound forms of the cystic fibrosis transmembrane conductance regulator (CFTR) protein.

    Science.gov (United States)

    Awayn, N H; Rosenberg, M F; Kamis, A B; Aleksandrov, L A; Riordan, J R; Ford, R C

    2005-11-01

    Cystic fibrosis, one of the major human inherited diseases, is caused by defects in the CFTR (cystic fibrosis transmembrane conductance regulator), a cell-membrane protein. CFTR acts as a chloride channel which can be opened by ATP. Low-resolution structural studies of purified recombinant human CFTR are described in the present paper. Localization of the C-terminal decahistidine tag in CFTR was achieved by Ni2+-nitriloacetate nanogold labelling, followed by electron microscopy and single-particle analysis. The presence of the gold label appears to improve the single-particle-alignment procedure. Projection structures of CFTR from two-dimensional crystals analysed by electron crystallography displayed two alternative conformational states in the presence of nucleotide and nanogold, but only one form of the protein was observed in the quiescent (nucleotide-free) state.

  17. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations.

    Directory of Open Access Journals (Sweden)

    Jingjing Liang

    2017-05-01

    Full Text Available Hypertension is a leading cause of global disease, mortality, and disability. While individuals of African descent suffer a disproportionate burden of hypertension and its complications, they have been underrepresented in genetic studies. To identify novel susceptibility loci for blood pressure and hypertension in people of African ancestry, we performed both single and multiple-trait genome-wide association analyses. We analyzed 21 genome-wide association studies comprised of 31,968 individuals of African ancestry, and validated our results with additional 54,395 individuals from multi-ethnic studies. These analyses identified nine loci with eleven independent variants which reached genome-wide significance (P < 1.25×10-8 for either systolic and diastolic blood pressure, hypertension, or for combined traits. Single-trait analyses identified two loci (TARID/TCF21 and LLPH/TMBIM4 and multiple-trait analyses identified one novel locus (FRMD3 for blood pressure. At these three loci, as well as at GRP20/CDH17, associated variants had alleles common only in African-ancestry populations. Functional annotation showed enrichment for genes expressed in immune and kidney cells, as well as in heart and vascular cells/tissues. Experiments driven by these findings and using angiotensin-II induced hypertension in mice showed altered kidney mRNA expression of six genes, suggesting their potential role in hypertension. Our study provides new evidence for genes related to hypertension susceptibility, and the need to study African-ancestry populations in order to identify biologic factors contributing to hypertension.

  18. Evaluation of peak overlap in migration-time distributions determined by organelle capillary electrophoresis: Type-II error analogy based on statistical-overlap theory.

    Science.gov (United States)

    Davis, Joe M; Arriaga, Edgar A

    2009-08-28

    Organelles commonly are separated by capillary electrophoresis (CE) with laser-induced-fluorescence detection. Usually, it is assumed that peaks observed in the CE originate from single organelles, with negligible occurrence of peak overlap. Under this assumption, migration-time and mobility distributions are obtained by partitioning the CE into different regions and counting the number of observed peaks in each region. In this paper, criteria based on statistical-overlap theory (SOT) are developed to test the assumption of negligible peak overlap and to predict conditions for its validity. For regions of the CE having constant peak density, the numbers of peaks (i.e., intensity profiles of single organelles) and observed peaks (i.e., maxima) are modeled by probability distributions. For minor peak overlap, the distributions partially merge, and their mergence is described by an analogy to the Type-II error of hypothesis testing. Criteria are developed for the amount of peak overlap, at which the number of observed peaks has an 85% or 90% probability of lying within the 95% confidence interval of the number of peaks of single organelles. For this or smaller amounts of peak overlap, the number of observed peaks is a good approximation to the number of peaks. A simple procedure is developed for evaluating peak overlap, requiring determination of only the peak standard deviation, the duration of the region occupied by peaks, and the number of observed peaks in the region. The procedure can be applied independently to each region of the partitioned CE. The procedure is applied to a mitochondrial CE.

  19. Photo and Nutritional Regulation of Euglena Organelle Development.

    Science.gov (United States)

    Schwartzbach, Steven D

    2017-01-01

    Euglena can use light and CO 2 , photosynthesis, as well as a large variety of organic molecules as the sole source of carbon and energy for growth. Light induces the enzymes, in this case an entire organelle, the chloroplast, that is required to use CO 2 as the sole source of carbon and energy for growth. Ethanol, but not malate, inhibits the photoinduction of chloroplast enzymes and induces the synthesis of the glyoxylate cycle enzymes that comprise the unique metabolic pathway leading to two carbon, ethanol and acetate, assimilation. In resting, carbon starved cells, light mobilizes the degradation of the storage carbohydrate paramylum and transiently induces the mitochondrial proteins required for the aerobic metabolism of paramylum to provide the carbon and energy required for chloroplast development. Other mitochondrial proteins are degraded upon light exposure providing the amino acids required for the synthesis of light induced proteins. Changes in protein levels are due to increased and decreased rates of synthesis rather than changes in degradation rates. Changes in protein synthesis rates occur in the absence of a concomitant increase in the levels of mRNAs encoding these proteins indicative of photo and metabolic control at the translational rather than the transcriptional level. The fraction of mRNA encoding a light induced protein such as the light harvesting chlorophyll a/b binding protein of photosystem II, (LHCPII) associated with polysomes in the dark is similar to the fraction associated with polysomes in the light indicative of photoregulation at the level of translational elongation. Ethanol, a carbon source whose assimilation requires carbon source specific enzymes, the glyoxylate cycle enzymes, represses the synthesis of chloroplast enzymes uniquely required to use light and CO 2 as the sole source of carbon and energy for growth. The catabolite sensitivity of chloroplast development provides a mechanism to prioritize carbon source

  20. Identification of Distinct Breast Cancer Stem Cell Populations Based on Single-Cell Analyses of Functionally Enriched Stem and Progenitor Pools

    Directory of Open Access Journals (Sweden)

    Nina Akrap

    2016-01-01

    Full Text Available The identification of breast cancer cell subpopulations featuring truly malignant stem cell qualities is a challenge due to the complexity of the disease and lack of general markers. By combining extensive single-cell gene expression profiling with three functional strategies for cancer stem cell enrichment including anchorage-independent culture, hypoxia, and analyses of low-proliferative, label-retaining cells derived from mammospheres, we identified distinct stem cell clusters in breast cancer. Estrogen receptor (ERα+ tumors featured a clear hierarchical organization with switch-like and gradual transitions between different clusters, illustrating how breast cancer cells transfer between discrete differentiation states in a sequential manner. ERα− breast cancer showed less prominent clustering but shared a quiescent cancer stem cell pool with ERα+ cancer. The cellular organization model was supported by single-cell data from primary tumors. The findings allow us to understand the organization of breast cancers at the single-cell level, thereby permitting better identification and targeting of cancer stem cells.

  1. B-jet and c-jet identification with Neural Networks as well as combination of multivariate analyses for the search for of multivariate analyses for the search for single top-quark production

    Energy Technology Data Exchange (ETDEWEB)

    Renz, Manuel; /Karlsruhe U., EKP

    2008-06-01

    In the first part of this diploma thesis, the current version of the KIT Flavor Separator, a neural network which is able to distinguish between tagged b-quark jets and tagged c/light-quark jets, is presented. In comparison with previous versions four new input variables are utilized and new Monte Carlo samples with a larger number of simulated events are used for the training of the neural network. It is illustrated that the output of the neural network is continuously distributed between 1 and -1, whereas b-quark jets accumulate at 1, however, c-quark jets and light-quark jets have outputs next to -1. To ensure that the network output describes observed events correctly, the shapes of all input variables are compared in simulation and data. Thus the mismodelling of any input variable is excluded. Moreover, the b jet and light jet output distributions are compared with the output of samples of observed events, which are enhanced in the particular flavor. In contrast to previous versions, no b-jet output correction function has to be calculated, because the agreement between simulation and collision data is excellent for b-quark jets. For the light-jet output, correction functions are developed. Different applications of the KIT Flavor Separator are mentioned. For example it provides a precious input to all three CDF single top quark analyses. Furthermore, it is shown that the KIT Flavor Separator is a universal tool, which can be used in every high-p{sub T} analysis that requires the identification of b-quark jets with high efficiency. As it is pointed out, a further application is the estimation of the flavor composition of a given sample of observed events. In addition a neural network, which is able to separate c-quark jets from light-quark jets, is trained. It is shown, that all three flavors can be separated in the c-net-Flavor Separator plane. As a result, the uncertainties on the estimation of the flavor composition in events with one tagged jet are cut

  2. B-jet and c-jet identification with Neural Networks as well as combination of multivariate analyses for the search for of multivariate analyses for the search for single top-quark production

    International Nuclear Information System (INIS)

    Renz, Manuel

    2008-01-01

    In the first part of this diploma thesis, the current version of the KIT Flavor Separator, a neural network which is able to distinguish between tagged b-quark jets and tagged c/light-quark jets, is presented. In comparison with previous versions four new input variables are utilized and new Monte Carlo samples with a larger number of simulated events are used for the training of the neural network. It is illustrated that the output of the neural network is continuously distributed between 1 and -1, whereas b-quark jets accumulate at 1, however, c-quark jets and light-quark jets have outputs next to -1. To ensure that the network output describes observed events correctly, the shapes of all input variables are compared in simulation and data. Thus the mismodelling of any input variable is excluded. Moreover, the b jet and light jet output distributions are compared with the output of samples of observed events, which are enhanced in the particular flavor. In contrast to previous versions, no b-jet output correction function has to be calculated, because the agreement between simulation and collision data is excellent for b-quark jets. For the light-jet output, correction functions are developed. Different applications of the KIT Flavor Separator are mentioned. For example it provides a precious input to all three CDF single top quark analyses. Furthermore, it is shown that the KIT Flavor Separator is a universal tool, which can be used in every high-p T analysis that requires the identification of b-quark jets with high efficiency. As it is pointed out, a further application is the estimation of the flavor composition of a given sample of observed events. In addition a neural network, which is able to separate c-quark jets from light-quark jets, is trained. It is shown, that all three flavors can be separated in the c-net-Flavor Separator plane. As a result, the uncertainties on the estimation of the flavor composition in events with one tagged jet are cut into

  3. Whole Genome and Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analyses of Listeria monocytogenes Isolates Associated with an Outbreak Linked to Cheese, United States, 2013

    Science.gov (United States)

    Luo, Yan; Carleton, Heather; Timme, Ruth; Melka, David; Muruvanda, Tim; Wang, Charles; Kastanis, George; Katz, Lee S.; Turner, Lauren; Fritzinger, Angela; Moore, Terence; Stones, Robert; Blankenship, Joseph; Salter, Monique; Parish, Mickey; Hammack, Thomas S.; Evans, Peter S.; Tarr, Cheryl L.; Allard, Marc W.; Strain, Errol A.; Brown, Eric W.

    2017-01-01

    ABSTRACT Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS 3 months later revealed that the equipment purchased by company B from company A yielded an environmental isolate highly similar to all outbreak isolates. The whole genome and core genome multilocus sequence typing and single nucleotide polymorphism (SNP) analyses results were compared to demonstrate the maximum discriminatory power obtained by using multiple analyses, which were needed to differentiate outbreak-associated isolates from a PFGE-indistinguishable isolate collected in a nonimplicated food source in 2012. This unrelated isolate differed from the outbreak isolates by only 7 to 14 SNPs, and as a result, the minimum spanning tree from the whole genome analyses and certain variant calling approach and phylogenetic algorithm for core genome-based analyses could not provide differentiation between unrelated isolates. Our data also suggest that SNP/allele counts should always be combined with WGS clustering analysis generated by phylogenetically meaningful algorithms on a sufficient number of isolates, and the SNP/allele threshold alone does not provide sufficient evidence to delineate an outbreak. The putative prophages were conserved across all the outbreak isolates. All outbreak isolates belonged to clonal complex 5 and serotype 1/2b and had an identical inlA sequence which did not have premature stop codons. IMPORTANCE In this outbreak, multiple analytical approaches were used for maximum discriminatory power. A PFGE-matched, epidemiologically unrelated isolate had high genetic similarity to the outbreak

  4. Single crystal structure analyses of scheelite-powellite CaW1-xMoxO4 solidsolutions and unique occurrence in Jisyakuyama skarn deposits

    Science.gov (United States)

    Yamashita, K.; Yoshiasa, A.; Miyazaki, H.; Tokuda, M.; Tobase, T.; Isobe, H.; Nishiyama, T.; Sugiyama, K.; Miyawaki, R.

    2017-12-01

    Jisyakuyama skarn deposit, Fukuchi, Fukuoka, Japan, shows a simple occurrenceformed by penetration of hot water into limestone cracks. A unique occurrence of scheelite-powellite CaW1-xMoxO4 minerals is observed in the skarn deposit. Many syntheticexperiments for scheelite-powellite solid solutions have been reported as research onfluorescent materials. In this system it is known that a complete continuous solid solution isformed even at room temperature. In this study, we have carried out the chemical analyses,crystal structural refinements and detail description of occurrence on scheelite-powelliteminerals. We have also attempted synthesis of single crystal of solid solution in a widecomposition range. The chemical compositions were determined by JEOL scanningelectron microscope and EDS, INCA system. We have performed the crystal structurerefinements of the scheelite-powellite CaW1-xMoxO4 solid solutions (x=0.0-1.0) byRIGAKU single-crystal structure analysis system RAPID. The R and S values are around0.0s and 1.03. As the result of structural refinements of natural products and many solidsolutions, we confirm that most large natural single crystals have compositions at bothendmembers, and large solid solution crystals are rare. The lattice constants, interatomicdistances and other crystallographic parameters for the solid solution change uniquely withcomposition and it was confirmed as a continuous solid solution. Single crystals of scheeliteendmember + powellite endmember + solid solution with various compositions form anaggregate in the deposit (Figure 1). Crystal shapes of powellite and scheelite arehypidiomorphic and allotriomorphic, respectively. Many solid solution crystals areaccompanied by scheelite endmember and a compositional gap is observed betweenpowellite and solid-solution crystals. The presence of several penetration solutions withsignificantly different W and Mo contents may be assumed. This research can be expectedto lead to giving restrictive

  5. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

    Science.gov (United States)

    Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

    2017-06-01

    Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  6. Quantitative analysis of organelle distribution and dynamics in Physcomitrella patens protonemal cells.

    Science.gov (United States)

    Furt, Fabienne; Lemoi, Kyle; Tüzel, Erkan; Vidali, Luis

    2012-05-17

    In the last decade, the moss Physcomitrella patens has emerged as a powerful plant model system, amenable for genetic manipulations not possible in any other plant. This moss is particularly well suited for plant polarized cell growth studies, as in its protonemal phase, expansion is restricted to the tip of its cells. Based on pollen tube and root hair studies, it is well known that tip growth requires active secretion and high polarization of the cellular components. However, such information is still missing in Physcomitrella patens. To gain insight into the mechanisms underlying the participation of organelle organization in tip growth, it is essential to determine the distribution and the dynamics of the organelles in moss cells. We used fluorescent protein fusions to visualize and track Golgi dictyosomes, mitochondria, and peroxisomes in live protonemal cells. We also visualized and tracked chloroplasts based on chlorophyll auto-fluorescence. We showed that in protonemata all four organelles are distributed in a gradient from the tip of the apical cell to the base of the sub-apical cell. For example, the density of Golgi dictyosomes is 4.7 and 3.4 times higher at the tip than at the base in caulonemata and chloronemata respectively. While Golgi stacks are concentrated at the extreme tip of the caulonemata, chloroplasts and peroxisomes are totally excluded. Interestingly, caulonemata, which grow faster than chloronemata, also contain significantly more Golgi dictyosomes and fewer chloroplasts than chloronemata. Moreover, the motility analysis revealed that organelles in protonemata move with low persistency and average instantaneous speeds ranging from 29 to 75 nm/s, which are at least three orders of magnitude slower than those of pollen tube or root hair organelles. To our knowledge, this study reports the first quantitative analysis of organelles in Physcomitrella patens and will make possible comparisons of the distribution and dynamics of organelles

  7. Manipulation and Motion of Organelles and Single Molecules in Living Cells

    DEFF Research Database (Denmark)

    Norregaard, Kamilla; Metzler, Ralf; Ritter, Christine M.

    2017-01-01

    used force spectroscopy techniques, namely optical tweezers, magnetic tweezers, and atomic force microscopy, are described in detail, and their strength and limitations related to in vivo experiments are discussed. Finally, recent exciting discoveries within the field of in vivo manipulation...

  8. A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv)*

    Science.gov (United States)

    Tu, Chao; Terraube, Virginie; Tam, Amy Sze Pui; Stochaj, Wayne; Fennell, Brian J.; Lin, Laura; Stahl, Mark; LaVallie, Edward R.; Somers, Will; Finlay, William J. J.; Mosyak, Lydia; Bard, Joel; Cunningham, Orla

    2016-01-01

    Fully-human single-chain Fv (scFv) proteins are key potential building blocks of bispecific therapeutic antibodies, but they often suffer from manufacturability and clinical development limitations such as instability and aggregation. The causes of these scFv instability problems, in proteins that should be theoretically stable, remains poorly understood. To inform the future development of such molecules, we carried out a comprehensive structural analysis of the highly stabilized anti-CXCL13 scFv E10. E10 was derived from the parental 3B4 using complementarity-determining region (CDR)-restricted mutagenesis and tailored selection and screening strategies, and carries four mutations in VL-CDR3. High-resolution crystal structures of parental 3B4 and optimized E10 scFvs were solved in the presence and absence of human CXCL13. In parallel, a series of scFv mutants was generated to interrogate the individual contribution of each of the four mutations to stability and affinity improvements. In combination, these analyses demonstrated that the optimization of E10 was primarily mediated by removing clashes between both the VL and the VH, and between the VL and CXCL13. Importantly, a single, germline-encoded VL-CDR3 residue mediated the key difference between the stable and unstable forms of the scFv. This work demonstrates that, aside from being the critical mediators of specificity and affinity, CDRs may also be the primary drivers of biotherapeutic developability. PMID:26515064

  9. Lipid droplet organelle distribution in populations of dividing cells studied by simulation

    International Nuclear Information System (INIS)

    Dalhaimer, Paul

    2013-01-01

    One of the key questions in cell biology is how organelles are passed from parent to daughter cells. To help address this question, I used Brownian dynamics to simulate lipid droplets as model organelles in populations of dividing cells. Lipid droplets are dynamic bodies that can form both de novo and by fission, they can also be depleted. The quantitative interplay among these three events is unknown but would seem crucial for controlling droplet distribution in populations of dividing cells. Surprisingly, of the three main events studied: biogenesis, fission, and depletion, the third played the key role in maintaining droplet organelle number—and to a lesser extent volume—in populations of dividing cells where formation events would have seemed paramount. In the case of lipid droplets, this provides computational evidence that they must be sustained, most likely through contacts with the endoplasmic reticulum. The findings also agree with video microscopy experiments over much shorter timescales where droplet depletion in fission yeast cells was not observed. In general, this work shows that organelle maintenance is invaluable and lack thereof cannot necessarily be compensated for by organelle formation. This study provides a time-accurate, physical-based template for long-term cell division studies. (paper)

  10. Lipid droplet organelle distribution in populations of dividing cells studied by simulation

    Science.gov (United States)

    Dalhaimer, Paul

    2013-06-01

    One of the key questions in cell biology is how organelles are passed from parent to daughter cells. To help address this question, I used Brownian dynamics to simulate lipid droplets as model organelles in populations of dividing cells. Lipid droplets are dynamic bodies that can form both de novo and by fission, they can also be depleted. The quantitative interplay among these three events is unknown but would seem crucial for controlling droplet distribution in populations of dividing cells. Surprisingly, of the three main events studied: biogenesis, fission, and depletion, the third played the key role in maintaining droplet organelle number—and to a lesser extent volume—in populations of dividing cells where formation events would have seemed paramount. In the case of lipid droplets, this provides computational evidence that they must be sustained, most likely through contacts with the endoplasmic reticulum. The findings also agree with video microscopy experiments over much shorter timescales where droplet depletion in fission yeast cells was not observed. In general, this work shows that organelle maintenance is invaluable and lack thereof cannot necessarily be compensated for by organelle formation. This study provides a time-accurate, physical-based template for long-term cell division studies.

  11. A Conserved, Mg2+-Dependent Exonuclease Degrades Organelle DNA during Arabidopsis Pollen Development[C][W

    Science.gov (United States)

    Matsushima, Ryo; Tang, Lay Yin; Zhang, Lingang; Yamada, Hiroshi; Twell, David; Sakamoto, Wataru

    2011-01-01

    In plant cells, mitochondria and plastids contain their own genomes derived from the ancestral bacteria endosymbiont. Despite their limited genetic capacity, these multicopy organelle genomes account for a substantial fraction of total cellular DNA, raising the question of whether organelle DNA quantity is controlled spatially or temporally. In this study, we genetically dissected the organelle DNA decrease in pollen, a phenomenon that appears to be common in most angiosperm species. By staining mature pollen grains with fluorescent DNA dye, we screened Arabidopsis thaliana for mutants in which extrachromosomal DNAs had accumulated. Such a recessive mutant, termed defective in pollen organelle DNA degradation1 (dpd1), showing elevated levels of DNAs in both plastids and mitochondria, was isolated and characterized. DPD1 encodes a protein belonging to the exonuclease family, whose homologs appear to be found in angiosperms. Indeed, DPD1 has Mg2+-dependent exonuclease activity when expressed as a fusion protein and when assayed in vitro and is highly active in developing pollen. Consistent with the dpd phenotype, DPD1 is dual-targeted to plastids and mitochondria. Therefore, we provide evidence of active organelle DNA degradation in the angiosperm male gametophyte, primarily independent of maternal inheritance; the biological function of organellar DNA degradation in pollen is currently unclear. PMID:21521697

  12. Role of centrins 2 and 3 in organelle segregation and cytokinesis in Trypanosoma brucei.

    Directory of Open Access Journals (Sweden)

    Angamuthu Selvapandiyan

    Full Text Available Centrins are calcium binding proteins involved in cell division in eukaryotes. Previously, we have shown that depletion of centrin1 in Trypanosoma brucei (T. brucei displayed arrested organelle segregation resulting in loss of cytokinesis. In this study we analyzed the role of T. brucei centrin2 (TbCen2 and T. brucei 3 (TbCen3 in the early events of T. brucei procyclic cell cycle. Both the immunofluorescence assay and electron microscopy showed that TbCen2 and 3-deficient cells were enlarged in size with duplicated basal bodies, multinuclei and new flagella that are detached along the length of the cell body. In both TbCen2 and TbCen3 depleted cells segregation of the organelles i.e. basal bodies, kinetoplast and nucleus was disrupted. Further analysis of the cells with defective organelle segregation identified three different sub configurations of organelle mis-segregations (Type 1-3. In addition, in majority of the TbCen2 depleted cells and in nearly half of the TbCen3 depleted cells, the kinetoplasts were enlarged and undivided. The abnormal segregations ultimately led to aborted cytokinesis and hence affected growth in these cells. Therefore, both centrin2 and 3 are involved in organelle segregation similar to centrin1 as was previously observed. In addition, we identified their role in kinetoplast division which may be also linked to overall mis-segregation.

  13. The force induced by organelles' weight in the microfilament is in the range of 0.1-1 pN

    Science.gov (United States)

    Yang, Chun; Wei, Dong; Zhuang, Feng Y.

    It has been well documented that a microgravity environment can bring about many changes in cell metabolism. Can mammalian cells feel the gravity directly? At present, arguments surrounding the problem are difficult to be answered through experiments. However, using finite element simulation to estimate the force exerted on the microfilament meshwork model, we demonstrated a possible way through which gravity acts on the cytoskeleton system. This system, which includes microfilaments, microtubules, and intermediate filaments, is responsible for the retention of cell shape and plays a role in many aspects related to cell proliferation and function. Many organelles, such as ribosomes and nucleus, are deposited, hinged, or attached on the cytoskeleton system. The weight of organelles can deform the cytoskeleton system and can induce force in it. Simulation results showed that the force induced by organelles' weight in the microfilament is in the range of 0.1-1 pN. The magnitude of the force is near the single Van der Waals bond force between the proteins, which is large enough to influence the hinge motion of proteins.

  14. Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms.

    Science.gov (United States)

    Chiang, Yu-Chung; Hung, Kuo-Hsiang; Moore, Shann-Jye; Ge, Xue-Jun; Huang, Shong; Hsu, Tsai-Wen; Schaal, Barbara A; Chiang, Ty

    2009-07-10

    This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China. The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atpB and rbcL genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA) about 327 (mt) and 204 MYA (cp), corresponding with the divergence of cycad sections in the Mesozoic. Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.

  15. The Walking Dead: sequential nuclear and organelle destruction during hair development.

    Science.gov (United States)

    Jones, L A; Harland, D P; Jarrold, B B; Connolly, J E; Davis, M G

    2017-11-27

    Transition of hair shaft keratinocytes from actively respiring, nucleated cells to structural cells devoid of nucleus and cytoplasm, is key to hair production. This form of cell "death", or cornification, requires cellular organelle removal to allow the cytoplasm to become packed with keratin filament bundles that further require cross-linking to create a strong hair fibre. Although these processes are well described in epidermal keratinocytes, there is a lack of understanding of such mechanisms specifically in the hair follicle. To gain insights into cornification mechanisms within the hair follicle and thus improve our understanding of normal hair physiology. Scalp biopsies and hair pluck samples were obtained from healthy human donors and analysed microscopically following immunohistochemical staining. A focal point of respiratory activity was evident in keratogenous zone cells within the hair shaft that also exhibited nuclear damage. Nuclear degradation occurred via both caspase-dependant and -independent pathways. Conversely, mitophagy was driven by Bnip3L and restricted to the boundary of the keratogenous zone at Adamson's Fringe. We propose a model of stepwise living-dead transition within the first 1 mm of hair formation, whereby fully functional, nucleated cells first consolidate required functions by degrading nuclear DNA, yet continue to respire and provide the source of ROS required for keratin cross-linking. Finally, as the cells become packed with keratin bundles, Bnip3L expression triggers mitophagy to rid the cells of the last remaining "living" characteristic thus completing the march from "living" to "dead" within the hair follicle. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  16. The mitochondrion-like organelle of Trimastix pyriformis contains the complete glycine cleavage system.

    Directory of Open Access Journals (Sweden)

    Zuzana Zubáčová

    Full Text Available All eukaryotic organisms contain mitochondria or organelles that evolved from the same endosymbiotic event like classical mitochondria. Organisms inhabiting low oxygen environments often contain mitochondrial derivates known as hydrogenosomes, mitosomes or neutrally as mitochondrion-like organelles. The detailed investigation has shown unexpected evolutionary plasticity in the biochemistry and protein composition of these organelles in various protists. We investigated the mitochondrion-like organelle in Trimastix pyriformis, a free-living member of one of the three lineages of anaerobic group Metamonada. Using 454 sequencing we have obtained 7 037 contigs from its transcriptome and on the basis of sequence homology and presence of N-terminal extensions we have selected contigs coding for proteins that putatively function in the organelle. Together with the results of a previous transcriptome survey, the list now consists of 23 proteins - mostly enzymes involved in amino acid metabolism, transporters and maturases of proteins and transporters of metabolites. We have no evidence of the production of ATP in the mitochondrion-like organelle of Trimastix but we have obtained experimental evidence for the presence of enzymes of the glycine cleavage system (GCS, which is part of amino acid metabolism. Using homologous antibody we have shown that H-protein of GCS localizes into vesicles in the cell of Trimastix. When overexpressed in yeast, H- and P-protein of GCS and cpn60 were transported into mitochondrion. In case of H-protein we have demonstrated that the first 16 amino acids are necessary for this transport. Glycine cleavage system is at the moment the only experimentally localized pathway in the mitochondrial derivate of Trimastix pyriformis.

  17. A workflow for the automatic segmentation of organelles in electron microscopy image stacks

    Directory of Open Access Journals (Sweden)

    Alex Joseph Perez

    2014-11-01

    Full Text Available Electron microscopy (EM facilitates analysis of the form, distribution, and functional status of key organelle systems in various pathological processes, including those associated with neurodegenerative disease. Such EM data often provide important new insights into the underlying disease mechanisms. The development of more accurate and efficient methods to quantify changes in subcellular microanatomy has already proven key to understanding the pathogenesis of Parkinson’s and Alzheimer’s diseases, as well as glaucoma. While our ability to acquire large volumes of 3D EM data is progressing rapidly, more advanced analysis tools are needed to assist in measuring precise three-dimensional morphologies of organelles within data sets that can include hundreds to thousands of whole cells. Although new imaging instrument throughputs can exceed teravoxels of data per day, image segmentation and analysis remain significant bottlenecks to achieving quantitative descriptions of whole cell structural organellomes. Here, we present a novel method for the automatic segmentation of organelles in 3D EM image stacks. Segmentations are generated using only 2D image information, making the method suitable for anisotropic imaging techniques such as serial block-face scanning electron microscopy (SBEM. Additionally, no assumptions about 3D organelle morphology are made, ensuring the method can be easily expanded to any number of structurally and functionally diverse organelles. Following the presentation of our algorithm, we validate its performance by assessing the segmentation accuracy of different organelle targets in an example SBEM dataset and demonstrate that it can be efficiently parallelized on supercomputing resources, resulting in a dramatic reduction in runtime.

  18. Single-molecule fluorescence microscopy in living Caenorhabditis elegans

    NARCIS (Netherlands)

    van Krugten, Jaap; Peterman, Erwin J.G.

    2018-01-01

    Transportation of organelles and biomolecules is vital for many cellular processes. Single-molecule (SM) fluorescence microscopy can expose molecular aspects of the dynamics that remain unresolved in ensemble experiments. For example, trajectories of individual, moving biomolecules can reveal

  19. Nanofiber scaffolds influence organelle structure and function in bone marrow stromal cells.

    Science.gov (United States)

    Tutak, Wojtek; Jyotsnendu, Giri; Bajcsy, Peter; Simon, Carl G

    2017-07-01

    Recent work demonstrates that osteoprogenitor cell culture on nanofiber scaffolds can promote differentiation. This response may be driven by changes in cell morphology caused by the three-dimensional (3D) structure of nanofibers. We hypothesized that nanofiber effects on cell behavior may be mediated by changes in organelle structure and function. To test this hypothesis, human bone marrow stromal cells (hBMSCs) were cultured on poly(ε-caprolactone) (PCL) nanofibers scaffolds and on PCL flat spuncoat films. After 1 day-culture, hBMSCs were stained for actin, nucleus, mitochondria, and peroxisomes, and then imaged using 3D confocal microscopy. Imaging revealed that the hBMSC cell body (actin) and peroxisomal volume were reduced during culture on nanofibers. In addition, the nucleus and peroxisomes occupied a larger fraction of cell volume during culture on nanofibers than on films, suggesting enhancement of the nuclear and peroxisomal functional capacity. Organelles adopted morphologies with greater 3D-character on nanofibers, where the Z-Depth (a measure of cell thickness) was increased. Comparisons of organelle positions indicated that the nucleus, mitochondria, and peroxisomes were closer to the cell center (actin) for nanofibers, suggesting that nanofiber culture induced active organelle positioning. The smaller cell volume and more centralized organelle positioning would reduce the energy cost of inter-organelle vesicular transport during culture on nanofibers. Finally, hBMSC bioassay measurements (DNA, peroxidase, bioreductive potential, lactate, and adenosine triphosphate (ATP)) indicated that peroxidase activity may be enhanced during nanofiber culture. These results demonstrate that culture of hBMSCs on nanofibers caused changes in organelle structure and positioning, which may affect organelle functional capacity and transport. Published 2016. This article is a U.S. Government work and is in the public domain in the USA. J Biomed Mater Res Part B: Appl

  20. Nanobiotechnology meets plant cell biology: Carbon nanotubes as organelle targeting nanocarriers

    KAUST Repository

    Serag, Maged F.

    2013-01-01

    For years, nanotechnology has shown great promise in the fields of biomedical and biotechnological sciences and medical research. In this review, we demonstrate its versatility and applicability in plant cell biology studies. Specifically, we discuss the ability of functionalized carbon nanotubes to penetrate the plant cell wall, target specific organelles, probe protein-carrier activity and induce organelle recycling in plant cells. We also, shed light on prospective applications of carbon nanomaterials in cell biology and plant cell transformation. © 2013 The Royal Society of Chemistry.

  1. Efficacy of the motile sperm organelle morphology examination (MSOME) in predicting pregnancy after intrauterine insemination

    Science.gov (United States)

    2011-01-01

    Background Although the motile sperm organelle morphology examination (MSOME) was developed merely as a selection criterion, its application as a method for classifying sperm morphology may represent an improvement in the evaluation of semen quality. The aim of this study was to determine the prognostic value of normal sperm morphology using MSOME with regard to clinical pregnancy (CP) after intrauterine insemination (IUI). Methods A total of 156 IUI cycles that were performed in 111 couples were prospectively analysed. Each subject received 75 IU of recombinant FSH every second day from the third day of the cycle. Beginning on the 10th day of the cycle, follicular development was monitored by vaginal ultrasound. When one or two follicles measuring at least 17 mm were observed, recombinant hCG was administered, and IUI was performed 12-14 h and 36-40 h after hCG treatment. Prior to the IUI procedure, sperm samples were analysed by MSOME at 8400× magnification using an inverted microscope that was equipped with DIC/Nomarski differential interference contrast optics. A minimum of 200 motile spermatozoa per semen sample were evaluated, and the percentage of normal spermatozoa in each sample was determined. Results Pregnancy occurred in 34 IUI cycles (CP rate per cycle: 21.8%, per patient: 30.6%). Based on the MSOME criteria, a significantly higher percentage of normal spermatozoa was found in the group of men in which the IUI cycles resulted in pregnancy (2.6+/-3.1%) compared to the group that did not achieve pregnancy (1.2+/-1.7%; P = 0.019). Logistic regression showed that the percentage of normal cells in the MSOME was a determining factor for the likelihood of clinical pregnancy (OR: 1.28; 95% CI: 1.08 to 1.51; P = 0.003). The ROC curve revealed an area under the curve of 0.63 and an optimum cut-off point of 2% of normal sperm morphology. At this cut-off threshold, using the percentage of normal sperm morphology by MSOME to predict pregnancy was 50% sensitive

  2. Efficacy of the motile sperm organelle morphology examination (MSOME in predicting pregnancy after intrauterine insemination

    Directory of Open Access Journals (Sweden)

    Mauri Ana L

    2011-08-01

    Full Text Available Abstract Background Although the motile sperm organelle morphology examination (MSOME was developed merely as a selection criterion, its application as a method for classifying sperm morphology may represent an improvement in the evaluation of semen quality. The aim of this study was to determine the prognostic value of normal sperm morphology using MSOME with regard to clinical pregnancy (CP after intrauterine insemination (IUI. Methods A total of 156 IUI cycles that were performed in 111 couples were prospectively analysed. Each subject received 75 IU of recombinant FSH every second day from the third day of the cycle. Beginning on the 10th day of the cycle, follicular development was monitored by vaginal ultrasound. When one or two follicles measuring at least 17 mm were observed, recombinant hCG was administered, and IUI was performed 12-14 h and 36-40 h after hCG treatment. Prior to the IUI procedure, sperm samples were analysed by MSOME at 8400× magnification using an inverted microscope that was equipped with DIC/Nomarski differential interference contrast optics. A minimum of 200 motile spermatozoa per semen sample were evaluated, and the percentage of normal spermatozoa in each sample was determined. Results Pregnancy occurred in 34 IUI cycles (CP rate per cycle: 21.8%, per patient: 30.6%. Based on the MSOME criteria, a significantly higher percentage of normal spermatozoa was found in the group of men in which the IUI cycles resulted in pregnancy (2.6+/-3.1% compared to the group that did not achieve pregnancy (1.2+/-1.7%; P = 0.019. Logistic regression showed that the percentage of normal cells in the MSOME was a determining factor for the likelihood of clinical pregnancy (OR: 1.28; 95% CI: 1.08 to 1.51; P = 0.003. The ROC curve revealed an area under the curve of 0.63 and an optimum cut-off point of 2% of normal sperm morphology. At this cut-off threshold, using the percentage of normal sperm morphology by MSOME to predict pregnancy

  3. A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv).

    Science.gov (United States)

    Tu, Chao; Terraube, Virginie; Tam, Amy Sze Pui; Stochaj, Wayne; Fennell, Brian J; Lin, Laura; Stahl, Mark; LaVallie, Edward R; Somers, Will; Finlay, William J J; Mosyak, Lydia; Bard, Joel; Cunningham, Orla

    2016-01-15

    Fully-human single-chain Fv (scFv) proteins are key potential building blocks of bispecific therapeutic antibodies, but they often suffer from manufacturability and clinical development limitations such as instability and aggregation. The causes of these scFv instability problems, in proteins that should be theoretically stable, remains poorly understood. To inform the future development of such molecules, we carried out a comprehensive structural analysis of the highly stabilized anti-CXCL13 scFv E10. E10 was derived from the parental 3B4 using complementarity-determining region (CDR)-restricted mutagenesis and tailored selection and screening strategies, and carries four mutations in VL-CDR3. High-resolution crystal structures of parental 3B4 and optimized E10 scFvs were solved in the presence and absence of human CXCL13. In parallel, a series of scFv mutants was generated to interrogate the individual contribution of each of the four mutations to stability and affinity improvements. In combination, these analyses demonstrated that the optimization of E10 was primarily mediated by removing clashes between both the VL and the VH, and between the VL and CXCL13. Importantly, a single, germline-encoded VL-CDR3 residue mediated the key difference between the stable and unstable forms of the scFv. This work demonstrates that, aside from being the critical mediators of specificity and affinity, CDRs may also be the primary drivers of biotherapeutic developability. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Implementation of a CO2 Laser Heating System for Paleomagnetic and Paleointensity Analyses of Single Silicate Crystals at Michigan Technological University

    Science.gov (United States)

    Barris, E. C.; Batzloff, R. M.; Smirnov, A. V.; Sergeev, A. V.; Kulakov, E.

    2011-12-01

    Data on the long-term changes of Earth's magnetic field strength are crucial for understanding the mechanisms of geomagnetic field generation and constraining models of planetary evolution. However, conventional paleointensity methods, based on thermal treatments of bulk rock samples, have low success rate due to heating-induced alteration of samples. In order to avoid this problem, a new technique has been recently developed at the University of Rochester that uses individual rock-forming crystals, heated by a laser, to measure paleointensity. Single crystals are less susceptible to natural and experimental alterations, which results in significantly higher experimental success rates. We report on the implementation of a laser-based system to be used for paleomagnetic and paleointensity analyses at the Michigan Tech's Earth Magnetism Laboratory. The system consists of a water-cooled 10W CO2 laser and a beam delivering system mounted on an optical bench, a field coil, and associated monitoring equipment. The system is integrated with a 2G Enterprises Superconducting Rock Magnetometer with automated sample handling and is located inside of a magnetically shielded room. Our preliminary experiments on several silicate crystals separated from recent and Precambrian rocks have indicated that the system provides a stable and repeatable thermal demagnetization of both natural and saturation isothermal remanent magnetization in the crystals. Pilot paleointensity experiments are in progress.

  5. Development of fine-resolution analyses and expanded large-scale forcing properties: 2. Scale awareness and application to single-column model experiments

    Science.gov (United States)

    Feng, Sha; Li, Zhijin; Liu, Yangang; Lin, Wuyin; Zhang, Minghua; Toto, Tami; Vogelmann, Andrew M.; Endo, Satoshi

    2015-01-01

    three-dimensional fields have been produced using the Community Gridpoint Statistical Interpolation (GSI) data assimilation system for the U.S. Department of Energy's Atmospheric Radiation Measurement Program (ARM) Southern Great Plains region. The GSI system is implemented in a multiscale data assimilation framework using the Weather Research and Forecasting model at a cloud-resolving resolution of 2 km. From the fine-resolution three-dimensional fields, large-scale forcing is derived explicitly at grid-scale resolution; a subgrid-scale dynamic component is derived separately, representing subgrid-scale horizontal dynamic processes. Analyses show that the subgrid-scale dynamic component is often a major component over the large-scale forcing for grid scales larger than 200 km. The single-column model (SCM) of the Community Atmospheric Model version 5 is used to examine the impact of the grid-scale and subgrid-scale dynamic components on simulated precipitation and cloud fields associated with a mesoscale convective system. It is found that grid-scale size impacts simulated precipitation, resulting in an overestimation for grid scales of about 200 km but an underestimation for smaller grids. The subgrid-scale dynamic component has an appreciable impact on the simulations, suggesting that grid-scale and subgrid-scale dynamic components should be considered in the interpretation of SCM simulations.

  6. The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.

    Science.gov (United States)

    Indio, Valentina; Martelli, Pier Luigi; Savojardo, Castrense; Fariselli, Piero; Casadio, Rita

    2013-04-15

    Targeting peptides are the most important signal controlling the import of nuclear encoded proteins into mitochondria and plastids. In the lack of experimental information, their prediction is an essential step when proteomes are annotated for inferring both the localization and the sequence of mature proteins. We developed TPpred a new predictor of organelle-targeting peptides based on Grammatical-Restrained Hidden Conditional Random Fields. TPpred is trained on a non-redundant dataset of proteins where the presence of a target peptide was experimentally validated, comprising 297 sequences. When tested on the 297 positive and some other 8010 negative examples, TPpred outperformed available methods in both accuracy and Matthews correlation index (96% and 0.58, respectively). Given its very low-false-positive rate (3.0%), TPpred is, therefore, well suited for large-scale analyses at the proteome level. We predicted that from ∼4 to 9% of the sequences of human, Arabidopsis thaliana and yeast proteomes contain targeting peptides and are, therefore, likely to be localized in mitochondria and plastids. TPpred predictions correlate to a good extent with the experimental annotation of the subcellular localization, when available. TPpred was also trained and tested to predict the cleavage site of the organelle-targeting peptide: on this task, the average error of TPpred on mitochondrial and plastidic proteins is 7 and 15 residues, respectively. This value is lower than the error reported by other methods currently available. The TPpred datasets are available at http://biocomp.unibo.it/valentina/TPpred/. TPpred is available on request from the authors. Supplementary data are available at Bioinformatics online.

  7. The mitochondrion-like organelle of Trimastix pyriformis contains the complete glycine cleavage system

    Czech Academy of Sciences Publication Activity Database

    Zubáčová, Z.; Novák, L.; Bublíková, J.; Vacek, V.; Fousek, Jan; Rídl, Jakub; Tachezy, J.; Doležal, P.; Vlček, Čestmír; Hampl, V.

    2013-01-01

    Roč. 8, č. 3 (2013), e55417 E-ISSN 1932-6203 R&D Projects: GA ČR GAP506/12/1010 Institutional support: RVO:68378050 Keywords : transcriptome sequencing * Trimastix * mitochondrion-like organelle * glycine cleavage complex Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.534, year: 2013

  8. Multiple vacuoles in impaired tonoplast trafficking3 mutants are independent organelles

    NARCIS (Netherlands)

    Zheng, J.; Han, S.W.; Munnik, T.; Rojas-Pierce, M.

    2014-01-01

    Plant vacuoles are essential and dynamic organelles, and mechanisms of vacuole biogenesis and fusion are not well characterized. We recently demonstrated that Wortmannin, an inhibitor of Phosphatidylinositol-3-Kinase (PI3K), induces the fusion of plant vacuoles both in roots of itt3/vti11 mutant

  9. Organelle proteomics by label-free and SILAC-based protein correlation profiling

    DEFF Research Database (Denmark)

    Dengjel, Joern; Jakobsen, Lis; Andersen, Jens S.

    2010-01-01

    The ability to purify cell organelles and protein complexes on a large scale, combined with advances in protein identification using mass spectrometry, has provided a wealth of information regarding protein localization and function. A major challenge in these studies has been the ability...

  10. TIG3 tumor suppressor-dependent organelle redistribution and apoptosis in skin cancer cells.

    Directory of Open Access Journals (Sweden)

    Tiffany M Scharadin

    Full Text Available TIG3 is a tumor suppressor protein that limits keratinocyte survival during normal differentiation. It is also important in cancer, as TIG3 level is reduced in tumors and in skin cancer cell lines, suggesting that loss of expression may be required for cancer cell survival. An important goal is identifying how TIG3 limits cell survival. In the present study we show that TIG3 expression in epidermal squamous cell carcinoma SCC-13 cells reduces cell proliferation and promotes morphological and biochemical apoptosis. To identify the mechanism that drives these changes, we demonstrate that TIG3 localizes near the centrosome and that pericentrosomal accumulation of TIG3 alters microtubule and microfilament organization and organelle distribution. Organelle accumulation at the centrosome is a hallmark of apoptosis and we demonstrate that TIG3 promotes pericentrosomal organelle accumulation. These changes are associated with reduced cyclin D1, cyclin E and cyclin A, and increased p21 level. In addition, Bax level is increased and Bcl-XL level is reduced, and cleavage of procaspase 3, procaspase 9 and PARP is enhanced. We propose that pericentrosomal localization of TIG3 is a key event that results in microtubule and microfilament redistribution and pericentrosomal organelle clustering and that leads to cancer cell apoptosis.

  11. Navigation through the Plasma Membrane Molecular Landscape Shapes Random Organelle Movement.

    Science.gov (United States)

    Dun, Alison R; Lord, Gabriel J; Wilson, Rhodri S; Kavanagh, Deirdre M; Cialowicz, Katarzyna I; Sugita, Shuzo; Park, Seungmee; Yang, Lei; Smyth, Annya M; Papadopulos, Andreas; Rickman, Colin; Duncan, Rory R

    2017-02-06

    Eukaryotic plasma membrane organization theory has long been controversial, in part due to a dearth of suitably high-resolution techniques to probe molecular architecture in situ and integrate information from diverse data streams [1]. Notably, clustered patterning of membrane proteins is a commonly conserved feature across diverse protein families (reviewed in [2]), including the SNAREs [3], SM proteins [4, 5], ion channels [6, 7], and receptors (e.g., [8]). Much effort has gone into analyzing the behavior of secretory organelles [9-13], and understanding the relationship between the membrane and proximal organelles [4, 5, 12, 14] is an essential goal for cell biology as broad concepts or rules may be established. Here we explore the generally accepted model that vesicles at the plasmalemma are guided by cytoskeletal tracks to specific sites on the membrane that have clustered molecular machinery for secretion [15], organized in part by the local lipid composition [16]. To increase our understanding of these fundamental processes, we integrated nanoscopy and spectroscopy of the secretory machinery with organelle tracking data in a mathematical model, iterating with knockdown cell models. We find that repeated routes followed by successive vesicles, the re-use of similar fusion sites, and the apparently distinct vesicle "pools" are all fashioned by the Brownian behavior of organelles overlaid on navigation between non-reactive secretory protein molecular depots patterned at the plasma membrane. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  12. Towards understanding the evolution and functional diversification of DNA-containing plant organelles

    DEFF Research Database (Denmark)

    Leister, Dario Michael

    2016-01-01

    of plant nuclear genomes that have emerged since 2000. Here I review the results of these attempts to reconstruct the evolution and functions of plant DNA-containing organelles, focusing in particular on data from nuclear genomes. In addition, I discuss proteomic approaches to the direct identification...

  13. Intracellular Microreactors as Artificial Organelles to Conduct Multiple Enzymatic Reactions Simultaneously

    DEFF Research Database (Denmark)

    Gallardo, Maria Godoy; Labay, Cédric Pierre; Jansman, Michelle M. T.

    2017-01-01

    of artificial organelles is advanced by reporting the assembly of a microreactor consisting of polymer capsules entrapping gold nanoclusters (AuNCs) and liposomes as sub-compartments. The fluorescence properties of AuNCs are employed to monitor the microreactors uptake by macrophages. Encapsulation...

  14. The age and provenance of metasedimentary rocks in the Quetico Subprovince, Ontario, from single zircon analyses: Implications for Archean sedimentation and tectonics in the Superior Province

    International Nuclear Information System (INIS)

    Davis, D.W.; Pezzutto, F.; Ojakangas, R.W.

    1990-01-01

    U-Pb isotopic analyses been performed on single detrital zircon grains from greywacke samples collected along the northern boundary of the Quetico Subprovince in northwest Ontario. Secondary lead loss was virtually eliminated by choosing crack-free grains and removing the outer surface using air abrasion. Thus, the 207 Pb/ 206 Pb age can be considered a good approximation to the age crystallization of each grain. Zircons in the Quetico metasediments show a range of ages from 2698 ± 3 Ma to 3009 ± 4 Ma. Deposition and metamorphism of the metasediments is bracketed within a 10 ± 5 Ma time span between crystallization of the youngest detritial zircon grain and a late-tectonic intrusion, the Blalock pluton, which cuts the sediments and has a zircon age of 2688 ± 4 Ma. The most easterly metasediment sample contains zircons with ages which cluster around 3007 ± 6 Ma which is within error of the age of a batholith dated in the adjacent Marmion Lake area of the Wabigoon Subprovince. This, along with the fact that most detrital zircons were only slightly abraded by sedimentary transport, suggests that the source of many zircons may have been proximal from the north. There is also a significant cluster of young zircon ages in a the range 2709-2698 Ma. Surprisingly, only a few ages correspond to the time of most intense arc-type felsic volcanism (2745-2710 Ma) in the main greenstone belt of the western Wabigoon Subprovince. Sedimentary deposition occurred at a time of extensive deformation in the adjacent Wabigoon Subprovince. The pattern of detrital grain ages indicates that this involved uplift of a complex older sialic landmass. Petrographic evidence for the presence of substantial felsic volcanic detritus as well as the fact that many of the zircons only slightly pre-date deposition indicates that much of the sediment was probably derived from erosion of active volcanic centers. (orig./WL)

  15. Characterization of isolates of Citrus tristeza virus by sequential analyses of enzyme immunoassays and capillary electrophoresis-single-strand conformation polymorphisms.

    Science.gov (United States)

    Licciardello, G; Raspagliesi, D; Bar-Joseph, M; Catara, A

    2012-05-01

    Citrus tristeza virus (CTV) is the causal agent of tristeza disease, which is one of the most devastating diseases of citrus crops worldwide. This paper describes a method for the rapid detection and genotyping of naturally spreading CTV isolates. This method uses ELISA or dot-blot immunological tests to detect trees infected with CTV. The reaction wells or membrane spots for which there is a positive reaction are sequentially treated by (i) washing and elution of viral RNA from the trapped samples, (ii) one-step synthesis of cDNA and PCR and (iii) automated fluorescence-based capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis of amplification products. Comparative CE-SSCP results are presented for CTV RNA extracted directly from infected leaves and ELISA plates or from membranes. In the analyses of all of these RNA samples, the p18, p27 and p23 CTV genes were targeted for amplification. Specific profiles of forward and reverse strands were obtained from a group of eight CTV isolates collected in Sicily, each with distinct biological characteristics, which were analyzed using the conventional two-step procedure (immunological detection followed by CE-SSCP molecular characterization after RNA isolation) or in a continuous process of ELISA/CE-SSCP or dot-blot/CE-SSCP starting from infected plant material. The combined method is simple, highly sensitive and reproducible, thus allowing the processing of numerous field samples for a variety of epidemiological needs. The sequential processing of an ELISA or dot-blot/ELISA followed by CE-SSCP is expected to allow the rapid detection of recent CTV infections along with the simultaneous characterization of the genetic diversity and structure of the population of newly invading CTV. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Smith, David R.; Lee, Robert W.; Cushman, John C.; Magnuson, Jon K.; Tran, Duc; Polle, Juergen E.

    2010-05-07

    Abstract Background: Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results: The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions: These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the development of a viable

  17. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    Directory of Open Access Journals (Sweden)

    Tran Duc

    2010-05-01

    Full Text Available Abstract Background Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the

  18. Methods Development for In Situ Laser-Ablation Pb and Sr Isotopic Analyses Using a Double-Focusing Single-Collector ICPMS

    Science.gov (United States)

    Pietruszka, A. J.; Neymark, L. A.

    2014-12-01

    Laser-ablation (LA) ICPMS isotopic analyses of Pb and Sr in geological materials have mostly used multi-collector instruments equipped with Faraday-type detectors (e.g., [1-3]). The main limitation of this approach is that samples with relatively high concentrations of Pb and Sr are typically required. Here we present the development of analytical methods for the accurate and precise in situ measurement of Pb and Sr isotope ratios in relatively low-concentration samples using a laser ablation system (193-nm excimer laser) with a double-focusing single-collector (SC) ICPMS (Nu AttoMTM). Our methods build on published techniques [4-6] that used different LA-SC-ICPMS instrumentation to demonstrate the benefits of fast-scanning ion-counting measurements combined with flat-top peaks. We have paid special attention to the characterization and correction of instrumental artifacts using solutions of the NIST SRM981 Pb and SRM987 Sr standards in "wet plasma" mode. For Pb, this includes correcting for the interference of 204Hg on 204Pb, characterizing the effects of tails from thallium (at masses 203 and 205) on the Pb peaks, evaluating the stability of the instrumental mass bias, and maintaining linearity of the detector response over the full dynamic range. For Sr, this includes correcting for the interference of 86Kr on 86Sr and 87Rb on 87Sr, verifying the accuracy of an internal correction for instrumental mass bias, and calibrating the ion optics scanning parameters. LA-SC-ICPMS results for Pb and Sr isotopic measurements of international glass standards and newly developed in-house mineral and glass reference materials will be presented. [1] Davidson et al. (2001) EPSL 184, 427-442. [2] Ramos et al. (2004) Chem. Geol. 211, 135-158. [3] Simon et al. (2007) GCA 71, 2014-2035. [4] Jochum et al. (2005) IJMS 242, 281-289. [5] Jochum et al. (2006) JAAS 21, 666-675. [6] Jochum et al. (2009) JAAS 24, 1237-1243.

  19. Multiple vacuoles in impaired tonoplast trafficking3 mutants are independent organelles.

    Science.gov (United States)

    Zheng, Jiameng; Han, Sang Won; Munnik, Teun; Rojas-Pierce, Marcela

    2014-01-01

    Plant vacuoles are essential and dynamic organelles, and mechanisms of vacuole biogenesis and fusion are not well characterized. We recently demonstrated that Wortmannin, an inhibitor of Phosphatidylinositol 3-Kinase (PI3K), induces the fusion of plant vacuoles both in roots of itt3/vti11 mutant alleles and in guard cells of wild type Arabidopsis and Fava bean. Here we used Fluorescence Recovery After Photobleaching (FRAP) to demonstrate that the vacuoles in itt3/vti11 are independent organelles. Furthermore, we used fluorescent protein reporters that bind specifically to Phosphatidylinositol 3-Phosphate (PtdIns(3)P) or PtdIns(4)P to show that Wortmannin treatments that induce the fusion of vti11 vacuoles result in the loss of PtdIns(3)P from cellular membranes. These results provided supporting evidence for a critical role of PtdIns(3)P in vacuole fusion in roots and guard cells.

  20. Direct comparison of soft x-ray images of organelles with optical fluorescence images

    International Nuclear Information System (INIS)

    Ishino, Masahiko; Kado, Masataka; Kishimoto, Maki; Nishikino, Masaharu; Ohba, Toshiyuki; Kaihori, Takeshi; Kawachi, Tetsuya; Tamotsu, Satoshi; Yasuda, Keiko; Mikata, Yuji; Shinohara, Kunio

    2011-01-01

    Soft x-ray microscopes operating in the water window region are capable of imaging living hydrated cells. Up to now, we have been able to take some soft x-ray images of living cells by the use of a contact x-ray microscope system with laser produced plasma soft x-ray source. Since the soft x-ray images are different from the optical images obtained with an ordinary microscope, it is very important to identify what is seen in the x-ray images. Hence, we have demonstrated the direct comparison between the images of organelles obtained with a fluorescence microscope and those with a soft x-ray microscope. Comparing the soft x-ray images to the fluorescence images, the fine structures of the organelles could be identified and observed. (author)

  1. Quantitatively Mapping Cellular Viscosity with Detailed Organelle Information via a Designed PET Fluorescent Probe

    Science.gov (United States)

    Liu, Tianyu; Liu, Xiaogang; Spring, David R.; Qian, Xuhong; Cui, Jingnan; Xu, Zhaochao

    2014-01-01

    Viscosity is a fundamental physical parameter that influences diffusion in biological processes. The distribution of intracellular viscosity is highly heterogeneous, and it is challenging to obtain a full map of cellular viscosity with detailed organelle information. In this work, we report 1 as the first fluorescent viscosity probe which is able to quantitatively map cellular viscosity with detailed organelle information based on the PET mechanism. This probe exhibited a significant ratiometric fluorescence intensity enhancement as solvent viscosity increases. The emission intensity increase was attributed to combined effects of the inhibition of PET due to restricted conformational access (favorable for FRET, but not for PET), and the decreased PET efficiency caused by viscosity-dependent twisted intramolecular charge transfer (TICT). A full map of subcellular viscosity was successfully constructed via fluorescent ratiometric detection and fluorescence lifetime imaging; it was found that lysosomal regions in a cell possess the highest viscosity, followed by mitochondrial regions. PMID:24957323

  2. Organelle-Specific Activity-Based Protein Profiling in Living Cells

    Energy Technology Data Exchange (ETDEWEB)

    Wiedner, Susan D.; Anderson, Lindsey N.; Sadler, Natalie C.; Chrisler, William B.; Kodali, Vamsi K.; Smith, Richard D.; Wright, Aaron T.

    2014-02-06

    A multimodal acidic organelle targeting activity-based probe was developed for analysis of subcellular native enzymatic activity of cells by fluorescent microscopy and mass spectrometry. A cathepsin reactive warhead was conjugated to an acidotropic amine, and a clickable alkyne for appendage of AlexaFluor 488 or biotin reporter tags. This probe accumulated in punctate vesicles surrounded by LAMP1, a lysosome marker, as observed by Structured Illumination Microscopy (SIM) in J774 mouse macrophage cells. Biotin conjugation, affinity purification, and analysis of in vivo labeled J774 by mass spectrometry showed that the probe was very selective for Cathepsins B and Z, two lysosomal cysteine proteases. Analysis of starvation induced autophagy, which is an increase in cell component catabolism involving lysosomes, showed a large increase in tagged protein number and an increase in cathepsin activity. Organelle targeting activity-based probes and subsequent analysis of resident proteins by mass spectrometry is enabled by tuning the physicochemical properties of the probe.

  3. Construction of an organelle-like nanodevice via supramolecular self-assembly for robust biocatalysts.

    Science.gov (United States)

    Li, Hongxia; Zheng, Guojun; Zhu, Shaozhou

    2018-02-20

    When using the microbial cell factories for green manufacturing, several important issues need to be addressed such as how to maintain the stability of biocatalysts used in the bioprocess and how to improve the synthetic efficiency of the biological system. One strategy widely used during natural evolution is the creation of organelles which can be used for regional control. This kind of compartmentalization strategy has inspired the design of artificial organelle-like nanodevice for synthetic biology and "green chemistry". Mimicking the natural concept of functional compartments, here we show that the engineered thermostable ketohydroxyglutarate aldolase from Thermotoga maritima could be developed as a general platform for nanoreactor design via supramolecular self-assembly. An industrial biocatalyst-(+)-γ-lactamase was selected as a model catalyst and successful encapsulated in the nanoreactor with high copies. These nanomaterials could easily be synthesized by Escherichia coli by heterologous expression and subsequently self-assembles into the target organelle-like nanoreactors both in vivo and in vitro. By probing their structural characteristics via transmission electronic microscopy and their catalytic activity under diverse conditions, we proved that these nanoreactors could confer a significant benefit to the cargo proteins. The encapsulated protein exhibits significantly improved stability under conditions such as in the presence of organic solvent or proteases, and shows better substrate tolerance than free enzyme. Our biodesign strategy provides new methods to develop new catalytically active protein-nanoreactors and could easily be applied into other biocatalysts. These artificial organelles could have widely application in sustainable catalysis, synthetic biology and could significantly improve the performance of microbial cell factories.

  4. Dual roles for ubiquitination in the processing of sperm organelles after fertilization.

    Science.gov (United States)

    Hajjar, Connie; Sampuda, Katherine M; Boyd, Lynn

    2014-02-15

    The process of fertilization involves a cell fusion event between the sperm and oocyte. Although sperm contain mitochondria when they fuse with the oocyte, paternal mitochondrial genomes do not persist in offspring and, thus, mitochondrial inheritance is maternal in most animals. Recent evidence suggests that paternal mitochondria may be eliminated via autophagy after fertilization. In C. elegans, sperm-specific organelles called membraneous organelles (MO) cluster together with paternal mitochondria immediately after fertilization. These MOs but not the mitochondria become polyubiquitinated and associated with proteasomes. The current model for the elimination of paternal mitochondria in C. elegans is that ubiquitination of the MOs induces the formation of autophagosomes which also capture the mitochondria and cause their degradation. Sperm-derived mitochondria and MOs show a sharp decrease in number during the time between sperm-oocyte fusion and the onset of mitosis. During this time, paternal mitochondria remain closely clustered with the MOs. Two types of polyubiquitin chains are observed on the MOs: K48-linked ubiquitin chains which are known to lead to proteasomal degradation and K63-linked ubiquitin chains which have been linked to autophagy. K48-linked ubiquitin chains and proteasomes show up on MOs very soon after sperm-oocyte fusion. These are present on MOs for only a short period of time. Maternal proteasomes localize to MOs and sperm proteasomes localize to structures that are at the periphery of the MO cluster suggesting that these two proteasome populations may have different roles in degrading paternal material. K63-linked ubiquitin chains appear on MOs early and remain throughout the first several cell divisions. Since there are two different types of polyubiquitin chains associated with sperm organelles and their timing differs, it suggests that ubiquitin has two or more roles in the processing of sperm components after fertilization. The K63

  5. Comparative proteomic analysis of lung lamellar bodies and lysosome-related organelles.

    Directory of Open Access Journals (Sweden)

    Ross Ridsdale

    2011-01-01

    Full Text Available Pulmonary surfactant is a complex mixture of lipids and proteins that is essential for postnatal function. Surfactant is synthesized in alveolar type II cells and stored as multi-bilayer membranes in a specialized secretory lysosome-related organelle (LRO, known as the lamellar body (LB, prior to secretion into the alveolar airspaces. Few LB proteins have been identified and the mechanisms regulating formation and trafficking of this organelle are poorly understood. Lamellar bodies were isolated from rat lungs, separated into limiting membrane and core populations, fractionated by SDS-PAGE and proteins identified by nanoLC-tandem mass spectrometry. In total 562 proteins were identified, significantly extending a previous study that identified 44 proteins in rat lung LB. The lung LB proteome reflects the dynamic interaction of this organelle with the biosynthetic, secretory and endocytic pathways of the type II epithelial cell. Comparison with other LRO proteomes indicated that 60% of LB proteins were detected in one or more of 8 other proteomes, confirming classification of the LB as a LRO. Remarkably the LB shared 37.8% of its proteins with the melanosome but only 9.9% with lamellar bodies from the skin. Of the 229 proteins not detected in other LRO proteomes, a subset of 34 proteins was enriched in lung relative to other tissues. Proteins with lipid-related functions comprised a significant proportion of the LB unique subset, consistent with the major function of this organelle in the organization, storage and secretion of surfactant lipid. The lung LB proteome will facilitate identification of molecular pathways involved in LB biogenesis, surfactant homeostasis and disease pathogenesis.

  6. Curvature of double-membrane organelles generated by changes in membrane size and composition.

    Directory of Open Access Journals (Sweden)

    Roland L Knorr

    Full Text Available Transient double-membrane organelles are key players in cellular processes such as autophagy, reproduction, and viral infection. These organelles are formed by the bending and closure of flat, double-membrane sheets. Proteins are believed to be important in these morphological transitions but the underlying mechanism of curvature generation is poorly understood. Here, we describe a novel mechanism for this curvature generation which depends primarily on three membrane properties: the lateral size of the double-membrane sheets, the molecular composition of their highly curved rims, and a possible asymmetry between the two flat faces of the sheets. This mechanism is evolutionary advantageous since it does not require active processes and is readily available even when resources within the cell are restricted as during starvation, which can induce autophagy and sporulation. We identify pathways for protein-assisted regulation of curvature generation, organelle size, direction of bending, and morphology. Our theory also provides a mechanism for the stabilization of large double-membrane sheet-like structures found in the endoplasmic reticulum and in the Golgi cisternae.

  7. Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways.

    Science.gov (United States)

    Bobik, Thomas A; Lehman, Brent P; Yeates, Todd O

    2015-10-01

    Prokaryotes use subcellular compartments for a variety of purposes. An intriguing example is a family of complex subcellular organelles known as bacterial microcompartments (MCPs). MCPs are widely distributed among bacteria and impact processes ranging from global carbon fixation to enteric pathogenesis. Overall, MCPs consist of metabolic enzymes encased within a protein shell, and their function is to optimize biochemical pathways by confining toxic or volatile metabolic intermediates. MCPs are fundamentally different from other organelles in having a complex protein shell rather than a lipid-based membrane as an outer barrier. This unusual feature raises basic questions about organelle assembly, protein targeting and metabolite transport. In this review, we discuss the three best-studied MCPs highlighting atomic-level models for shell assembly, targeting sequences that direct enzyme encapsulation, multivalent proteins that organize the lumen enzymes, the principles of metabolite movement across the shell, internal cofactor recycling, a potential system of allosteric regulation of metabolite transport and the mechanism and rationale behind the functional diversification of the proteins that form the shell. We also touch on some potential biotechnology applications of an unusual compartment designed by nature to optimize metabolic processes within a cellular context. © 2015 John Wiley & Sons Ltd.

  8. A quantitative assessment of the membrane-integral sub-proteome of a bacterial magnetic organelle.

    Science.gov (United States)

    Raschdorf, Oliver; Bonn, Florian; Zeytuni, Natalie; Zarivach, Raz; Becher, Dörte; Schüler, Dirk

    2018-02-10

    Magnetotactic bacteria produce chains of complex membrane-bound organelles that direct the biomineralization of magnetic nanoparticles and serve for magnetic field navigation. These magnetosome compartments have recently emerged as a model for studying the subcellular organization of prokaryotic organelles. Previous studies indicated the presence of specific proteins with various functions in magnetosome biosynthesis. However, the exact composition and stoichiometry of the magnetosome subproteome have remained unknown. In order to quantify and unambiguously identify all proteins specifically targeted to the magnetosome membrane of the Alphaproteobacterium Magnetospirillum gryphiswaldense, we analyzed the protein composition of several cellular fractions by semi-quantitative mass spectrometry. We found that nearly all genuine magnetosome membrane-integral proteins belong to a well-defined set of previously identified proteins encoded by gene clusters within a genomic island, indicating a highly controlled protein composition. Magnetosome proteins were present in different quantities with up to 120 copies per particle as estimated by correlating our results with available quantitative Western blot data. This high abundance suggests an unusually crowded protein composition of the membrane and a tight packing with transmembrane domains of integral proteins. Our findings will help to further define the structure of the organelle and contribute to the elucidation of magnetosome biogenesis. Magnetosomes are one of the most complex bacterial organelles and consist of membrane-bounded crystals of magnetic minerals. The exact composition and stoichiometry of the associated membrane integral proteins are of major interest for a deeper understanding of prokaryotic organelle assembly; however, previous proteomic studies failed to reveal meaningful estimations due to the lack of precise and quantitative data, and the inherently high degree of accumulated protein contaminants in

  9. Motile sperm organelle morphology examination (MSOME: intervariation study of normal sperm and sperm with large nuclear vacuoles

    Directory of Open Access Journals (Sweden)

    Baruffi Ricardo LR

    2010-06-01

    Full Text Available Abstract Background Although the motile sperm organelle morphology examination (MSOME was developed only as a selection criterion, its application as a method for classifying sperm morphology may represent an improvement in evaluation of semen quality, with potential clinical repercussions. The present study aimed to evaluate individual variations in the motile sperm organelle morphology examination (MSOME analysis after a time interval. Methods Two semen samples were obtained from 240 men from an unselected group of couples undergoing infertility investigation and treatment. Mean time interval between the two semen evaluations was 119 +/- 102 days. No clinical or surgical treatment was realized between the two observations. Spermatozoa were analyzed at greater than or equal to 8400× magnification by inverted microscope equipped with DIC/Nomarski differential interference contrast optics. At least 200 motile spermatozoa per semen sample were evaluated and percentages of normal spermatozoa and spermatozoa with large nuclear vacuoles (LNV/one or more vacuoles occupying >50% of the sperm nuclear area were determined. A spermatozoon was classified as morphologically normal when it exhibited a normal nucleus (smooth, symmetric and oval nucleus, width 3.28 +/- 0.20 μm, length 4.75 +/- 0.20 μm/absence of vacuoles occupying >4% of nuclear area as well as acrosome, post-acrosomal lamina, neck and tail, besides not presenting cytoplasm around the head. One examiner, blinded to subject identity, performed the entire study. Results Mean percentages of morphologically normal and LNV spermatozoa were identical in the two MSOME analyses (1.6 +/- 2.2% vs. 1.6 +/- 2.1% P = 0.83 and 25.2 +/- 19.2% vs. 26.1 +/- 19.0% P = 0.31, respectively. Regression analysis between the two samples revealed significant positive correlation for morphologically normal and for LNV spermatozoa (r = 0.57 95% CI:0.47-0.65 P P Conclusions The significant positive correlation and

  10. Involvement of sulphur nutrition in modulating iron deficiency responses in photosynthetic organelles of oilseed rape (Brassica napus L.).

    Science.gov (United States)

    Muneer, Sowbiya; Lee, Bok-Rye; Kim, Kil-Yong; Park, Sang-Hyun; Zhang, Qian; Kim, Tae-Hwan

    2014-03-01

    The aim of this study was to characterize the roles of sulphur (S) nutrition in modulating the responses to iron (Fe) deficiency in the photosynthetic organelles of oilseed rape. Eight-week-old plants grown hydroponically were fed with S-sufficient or S-deprived solution with or without Fe(III)-EDTA. Responses to four S and Fe combined treatments were analysed after 5 and 10 days. Leaf chlorosis was generated by either S- or Fe-deprivation, with a decrease in chlorophyll and carotenoid content. These negative effects were more severe in the absence of S. The expression of Fe²⁺ transporter (IRT1) and Fe(III) chelate reductase (FRO1) gene was induced for the first 5 days and decreased after 10 days in the S-deprived roots, but largely improved by S supply even in the absence of Fe. Lack of ferric chelate reducing activity in the Fe-deprived roots in the absence of S was largely improved by S supply. The activity of photosynthesis, RuBisCO and sucrose synthase was closely related to S status in leaves. Electron microscopic observation showed that the Fe-deficiency in the absence of S greatly resulted in a severe disorganisation of thylakoid lamellae with loss of grana. However, these impacts of Fe-deficiency were largely restored in the presence of S. The present results indicate that S nutrition has significant role in ameliorating the damages in photosynthetic apparatus caused by Fe-deficiency.

  11. Phylogenetic and Physicochemical Analyses Enhance the Classification of Rare Nonsynonymous Single Nucleotide Variants in Type 1 and 2 Long-QT Syndrome

    NARCIS (Netherlands)

    Giudicessi, John R.; Kapplinger, Jamie D.; Tester, David J.; Alders, Marielle; Salisbury, Benjamin A.; Wilde, Arthur A. M.; Ackerman, Michael J.

    2012-01-01

    Background-Hundreds of nonsynonymous single nucleotide variants (nsSNVs) have been identified in the 2 most common long-QT syndrome-susceptibility genes (KCNQ1 and KCNH2). Unfortunately, an approximate to 3% background rate of rare KCNQ1 and KCNH2 nsSNVs amongst healthy individuals complicates the

  12. A Ribbon-like Structure in the Ejective Organelle of the Green Microalga Pyramimonas parkeae (Prasinophyceae) Consists of Core Histones and Polymers Containing N-acetyl-glucosamine.

    Science.gov (United States)

    Yamagishi, Takahiro; Kurihara, Akira; Kawai, Hiroshi

    2015-11-01

    The green microalga, Pyramimonas parkeae (Prasinophyceae) has an ejective organelle containing a coiled ribbon structure resembling the ejectisome in Cryptophyta. This structure is discharged from the cell by a stimulus and extends to form a tube-like structure, but the molecular components of the structure have not been identified. Tricine-SDS-PAGE analysis indicated that the ribbon-like structure of P. parkeae contains some proteins and low molecular acidic polymers. Edman degradation, LC/MS/MS analyses and immunological studies demonstrated that their proteins are core histones (H3, H2A, H2B and H4). In addition, monosaccharide composition analysis of the ribbon-like structures and degradation by lysozyme strongly indicated that the ribbon-like structure consist of β (1-4) linked polymers containing N-acetyl-glucosamine. Purified polymers and recombinant histones formed glob-like or filamentous structures. Therefore we conclude that the ribbon-like structure of P. parkeae mainly consists of a complex of core histones (H3, H2A, H2B and H4) and polymers containing N-acetyl-glucosamine, and suggest to name the ejective organelle in P. parkeae the "histrosome" to distinguish it from the ejectisome in Cryptophyta. Copyright © 2015 Elsevier GmbH. All rights reserved.

  13. The Observation and Execution of Actions Share Motor and Somatosensory Voxels in all Tested Subjects : Single-Subject Analyses of Unsmoothed fMRI Data

    NARCIS (Netherlands)

    Gazzola, Valeria; Keysers, Christian

    Many neuroimaging studies of the mirror neuron system (MNS) examine if certain voxels in the brain are shared between action observation and execution (shared voxels, sVx). Unfortunately, finding sVx in standard group analyses is not a guarantee that sVx exist in individual subjects. Using

  14. Quantitative molecular and culture analyses of bacterial elimination in oval-shaped root canals by a single-file instrumentation technique.

    Science.gov (United States)

    Alves, F R F; Rôças, I N; Almeida, B M; Neves, M A S; Zoffoli, J; Siqueira, J F

    2012-09-01

    Bacterial reduction in oval-shaped root canals by a single-instrument technique was compared ex vivo with a conventional nickel-titanium rotary technique. Data obtained from two quantification methods, quantitative real-time polymerase chain reaction (qPCR) and culture, were also compared. Oval-shaped canals of extracted teeth contaminated with Enterococcus faecalis were instrumented using either a single Reciproc instrument or the BioRaCe instrument series. Bacteriological samples were taken before (S1) and after instrumentation (S2). Bacterial quantification was performed using qPCR and culture. Intragroup analysis showed that both protocols promoted a highly significant bacterial reduction (P 0.05). As for the quantification methods, qPCR revealed significantly higher counts of E. faecalis in S1 than culture (P 0.05). The single-file technique was comparable with the conventional technique in oval-shaped canals provided the width of apical preparation, volume of irrigants and duration of irrigation are kept similar. No significant difference was observed for qPCR and culture in post-instrumentation samples, indicating that both methods can be reliably used for studies of antibacterial effectiveness. © 2012 International Endodontic Journal.

  15. Myosin-Va and Dynamic Actin Oppose Microtubules to Drive Long-Range Organelle Transport

    Science.gov (United States)

    Evans, Richard D.; Robinson, Christopher; Briggs, Deborah A.; Tooth, David J.; Ramalho, Jose S.; Cantero, Marta; Montoliu, Lluis; Patel, Shyamal; Sviderskaya, Elena V.; Hume, Alistair N.

    2014-01-01

    Summary In animal cells, microtubule and actin tracks and their associated motors (dynein, kinesin, and myosin) are thought to regulate long- and short-range transport, respectively [1–8]. Consistent with this, microtubules extend from the perinuclear centrosome to the plasma membrane and allow bidirectional cargo transport over long distances (>1 μm). In contrast, actin often comprises a complex network of short randomly oriented filaments, suggesting that myosin motors move cargo short distances. These observations underpin the “highways and local roads” model for transport along microtubule and actin tracks [2]. The “cooperative capture” model exemplifies this view and suggests that melanosome distribution in melanocyte dendrites is maintained by long-range transport on microtubules followed by actin/myosin-Va-dependent tethering [5, 9]. In this study, we used cell normalization technology to quantitatively examine the contribution of microtubules and actin/myosin-Va to organelle distribution in melanocytes. Surprisingly, our results indicate that microtubules are essential for centripetal, but not centrifugal, transport. Instead, we find that microtubules retard a centrifugal transport process that is dependent on myosin-Va and a population of dynamic F-actin. Functional analysis of mutant proteins indicates that myosin-Va works as a transporter dispersing melanosomes along actin tracks whose +/barbed ends are oriented toward the plasma membrane. Overall, our data highlight the role of myosin-Va and actin in transport, and not tethering, and suggest a new model in which organelle distribution is determined by the balance between microtubule-dependent centripetal and myosin-Va/actin-dependent centrifugal transport. These observations appear to be consistent with evidence coming from other systems showing that actin/myosin networks can drive long-distance organelle transport and positioning [10, 11]. PMID:25065759

  16. Threshold-free method for three-dimensional segmentation of organelles

    Science.gov (United States)

    Chan, Yee-Hung M.; Marshall, Wallace F.

    2012-03-01

    An ongoing challenge in the field of cell biology is to how to quantify the size and shape of organelles within cells. Automated image analysis methods often utilize thresholding for segmentation, but the calculated surface of objects depends sensitively on the exact threshold value chosen, and this problem is generally worse at the upper and lower zboundaries because of the anisotropy of the point spread function. We present here a threshold-independent method for extracting the three-dimensional surface of vacuoles in budding yeast whose limiting membranes are labeled with a fluorescent fusion protein. These organelles typically exist as a clustered set of 1-10 sphere-like compartments. Vacuole compartments and center points are identified manually within z-stacks taken using a spinning disk confocal microscope. A set of rays is defined originating from each center point and radiating outwards in random directions. Intensity profiles are calculated at coordinates along these rays, and intensity maxima are taken as the points the rays cross the limiting membrane of the vacuole. These points are then fit with a weighted sum of basis functions to define the surface of the vacuole, and then parameters such as volume and surface area are calculated. This method is able to determine the volume and surface area of spherical beads (0.96 to 2 micron diameter) with less than 10% error, and validation using model convolution methods produce similar results. Thus, this method provides an accurate, automated method for measuring the size and morphology of organelles and can be generalized to measure cells and other objects on biologically relevant length-scales.

  17. Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction.

    Science.gov (United States)

    Xu, Ying-Ying; Yang, Fan; Shen, Hong-Bin

    2016-07-15

    Bioimages of subcellular protein distribution as a new data source have attracted much attention in the field of automated prediction of proteins subcellular localization. Performance of existing systems is significantly limited by the small number of high-quality images with explicit annotations, resulting in the small sample size learning problem. This limitation is more serious for the multi-location proteins that co-exist at two or more organelles, because it is difficult to accurately annotate those proteins by biological experiments or automated systems. In this study, we designed a new protein subcellular localization prediction pipeline aiming to deal with the small sample size learning and multi-location proteins annotation problems. Five semi-supervised algorithms that can make use of lower-quality data were integrated, and a new multi-label classification approach by incorporating the correlations among different organelles in cells was proposed. The organelle correlations were modeled by the Bayesian network, and the topology of the correlation graph was used to guide the order of binary classifiers training in the multi-label classification to reflect the label dependence relationship. The proposed protocol was applied on both immunohistochemistry and immunofluorescence images, and our experimental results demonstrated its efficiency. The datasets and code are available at: www.csbio.sjtu.edu.cn/bioinf/CorrASemiB CONTACT: hbshen@sjtu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. Analysis of Exocyst-Positive Organelle (EXPO)-Mediated Unconventional Protein Secretion (UPS) in Plant Cells.

    Science.gov (United States)

    Ding, Yu; Wang, Juan

    2017-01-01

    Unconventional protein secretion (UPS) together with conventional protein secretion (CPS) is responsible for protein secretion in plants. We have previously identified a novel UPS pathway in plants, which is mediated by exocyst-positive organelle-EXPO. Here, we describe detailed protocols to study UPS in plants by using Arabidopsis protoplasts or transgenic suspension cells, expressing the EXPO marker Exo70E2-XFP, as materials. Via drug and osmotic treatment plus secretion assay, we illustrate several major methods to analyze EXPO-mediated UPS in plant cells, which also supplys mining tools for similar study.

  19. Analysis of stray grain formation in single crystal CMSX-4 superalloy; Analyse der Bildung von Fehlkoernern in einer einkristallinen CMSX-4-Superlegierung

    Energy Technology Data Exchange (ETDEWEB)

    Chmiela, Bartosz; Sozanska, Maria; Cwajna, Jan [Silesian Univ. of Technology, Katowice (Poland). Dept. of Materials Science; Szeliga, Dariusz [Rzeszow Univ. of Technology (Poland). Dept. of Materials Science; Jarczyk, Jerzy [ALD Vacuum Technologies, Hanau (Germany)

    2013-08-01

    Modern single crystal (SX) turbine blades are fabricated by directional solidification using a grain selector. The grain selection process was investigated by numerical simulation and verified by the experiment. A coupled ProCAST and cellular automaton finite element (CAFE) model was used in this study. According to the latest literature data, we designed the grain selector. Simulation confirmed an optimal grain selection efficiency of the applied selector geometry. The obtained experimental results reveal the possibility of stray grain formation in SX castings with a designed selector, in contrast to the simulation results. (orig.)

  20. Single-nucleotide polymorphisms may cause erroneous results in primer-introduced restriction enzyme analyses: a case of molecular misdiagnosis of homozygous vs heterozygous familial hypercholesterolemia.

    Science.gov (United States)

    Vuorio, A F; Paulin, L; Saltevo, J; Kontula, K

    1999-12-01

    PCR amplification followed by a primer introduced restriction analysis PCR (PIRA-PCR) is a widely used method to detect point mutations. Usually the artificial RFLP is created by siting one nucleotide mismatch near the 3; end of the primer. This does not alter the hybrization of the primer to the target DNA sequence. Unfortunately, unexpected single nucleotide polymorphisms (SNPs) may lead to additional mismatches and result in no amplification of the allele having unexpected SNP. We describe a warning example in which heterozygous familial hypercholesterolemia patient had an unexpected SNP and this led to his misdiagnosis. Copyright 1999 Academic Press.

  1. Univariate and multiple linear regression analyses for 23 single nucleotide polymorphisms in 14 genes predisposing to chronic glomerular diseases and IgA nephropathy in Han Chinese.

    Science.gov (United States)

    Wang, Hui; Sui, Weiguo; Xue, Wen; Wu, Junyong; Chen, Jiejing; Dai, Yong

    2014-09-01

    Immunoglobulin A nephropathy (IgAN) is a complex trait regulated by the interaction among multiple physiologic regulatory systems and probably involving numerous genes, which leads to inconsistent findings in genetic studies. One possibility of failure to replicate some single-locus results is that the underlying genetics of IgAN nephropathy is based on multiple genes with minor effects. To learn the association between 23 single nucleotide polymorphisms (SNPs) in 14 genes predisposing to chronic glomerular diseases and IgAN in Han males, the 23 SNPs genotypes of 21 Han males were detected and analyzed with a BaiO gene chip, and their associations were analyzed with univariate analysis and multiple linear regression analysis. Analysis showed that CTLA4 rs231726 and CR2 rs1048971 revealed a significant association with IgAN. These findings support the multi-gene nature of the etiology of IgAN and propose a potential gene-gene interactive model for future studies.

  2. Transcriptomic responses of the aphid Myzus persicae nicotianae Blackman (Hemiptera: Aphididae to insecticides: Analyses in the single Chilean clone of the tobacco aphid

    Directory of Open Access Journals (Sweden)

    Marco Cabrera-Brandt

    2014-04-01

    Full Text Available The tobacco aphid Myzus persicae nicotianae Blackman is a subspecies of the highly polyphagous and agricultural pest Myzus persicae (Sulzer. For its control, insecticide applications are widely used, but resistance to numerous molecules has been reported, displaying at least three insecticide resistance mechanisms, including: (i elevated carboxylesterases (E-Carb, (ii modification of the acetylcholinesterase (MACE, and (iii kdr and super-kdr insensitivity mutations. In Chile, populations of the tobacco aphid are characterized by the presence of a single predominant clone, which is also present in high proportions in other countries of the Americas. This aphid clone exhibits low levels of carboxylesterase activity and is kdr susceptible, but the MACE mechanism of insecticide resistance has not been studied. In order to characterize the tobacco aphid in terms of the MACE mechanism and to identify a preliminary group of aphid genes putatively involved in insecticide resistance, a cDNA microarray was used to study the transcriptomic responses when aphids are sprayed with a carbamate insecticide. The single Chilean clone of the tobacco aphid was characterized as MACE susceptible, but we found 38 transcripts significantly regulated by insecticide exposure (13 up- and 25 down-regulated genes. The expression of six of them was validated by qRT-PCR experiments at several time points (6, 12, 18, 24, 30, 36, and 42 h after insecticide application. This mutational and transcriptomic characterization of the tobacco aphid responding to insecticide spray opens new hypotheses in the understanding of the molecular mechanisms underlying insecticide resistance.

  3. Immunolocalization of an enterotoxic glycoprotein exoantigen on the secretory organelles of Cryptosporidium parvum sporozoites

    Directory of Open Access Journals (Sweden)

    El-Shewy K.A.

    2004-06-01

    Full Text Available In this study, the fine ultrastructures of the secretory organelles of C. parvum sporozoites were demonstrated using transmission electron microscopy (TEM. Meanwhile, a previously identified enterotoxic 18-20 kDa copro-antigen (18-20 kDa CCA, associated with cryptosporidiosis in both human and calves, was isolated and immunolocalized on C. parvum sporozoites. Using immunoelectron microscopy and anti-18-20 kDa monospecific antibody demonstrated marked existence of the 18-20 kDa CCA on the apical organelles and at the trilaminar pellicles. An anterior extrusion of this protein was demonstrated around the excysted and released sporozoites. However, non excysted sporozoites did not show this protein. Affinity blotting, with biotinylated jacalin, demonstrated the O-linked oligosaccharide moiety of this protein. The potential role of this protein in the host cell invasion and/or gliding motility remains unelucidated. However, its enterotoxicity, location and secretory nature suggest that it may be a target for neutralization or invasion inhibition of Cryptosporidium.

  4. WASP-36b: A NEW TRANSITING PLANET AROUND A METAL-POOR G-DWARF, AND AN INVESTIGATION INTO ANALYSES BASED ON A SINGLE TRANSIT LIGHT CURVE

    Energy Technology Data Exchange (ETDEWEB)

    Smith, A. M. S.; Anderson, D. R.; Hellier, C.; Maxted, P. F. L.; Smalley, B.; Southworth, J. [Astrophysics Group, Keele University, Staffordshire, ST5 5BG (United Kingdom); Collier Cameron, A. [SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, Fife, KY16 9SS (United Kingdom); Gillon, M.; Jehin, E. [Institut d' Astrophysique et de Geophysique, Universite de Liege, Allee du 6 Aout, 17 Bat. B5C, Liege 1 (Belgium); Lendl, M.; Queloz, D.; Triaud, A. H. M. J.; Pepe, F.; Segransan, D.; Udry, S. [Observatoire de Geneve, Universite de Geneve, 51 Chemin des Maillettes, 1290 Sauverny (Switzerland); West, R. G. [Department of Physics and Astronomy, University of Leicester, Leicester, LE1 7RH (United Kingdom); Barros, S. C. C.; Pollacco, D. [Astrophysics Research Centre, School of Mathematics and Physics, Queen' s University, University Road, Belfast, BT7 1NN (United Kingdom); Street, R. A., E-mail: amss@astro.keele.ac.uk [Las Cumbres Observatory, 6740 Cortona Drive Suite 102, Goleta, CA 93117 (United States)

    2012-04-15

    We report the discovery, from WASP and CORALIE, of a transiting exoplanet in a 1.54 day orbit. The host star, WASP-36, is a magnitude V = 12.7, metal-poor G2 dwarf (T{sub eff} = 5959 {+-} 134 K), with [Fe/H] =-0.26 {+-} 0.10. We determine the planet to have mass and radius, respectively, 2.30 {+-} 0.07 and 1.28 {+-} 0.03 times that of Jupiter. We have eight partial or complete transit light curves, from four different observatories, which allow us to investigate the potential effects on the fitted system parameters of using only a single light curve. We find that the solutions obtained by analyzing each of these light curves independently are consistent with our global fit to all the data, despite the apparent presence of correlated noise in at least two of the light curves.

  5. Effects of memantine on cognition in patients with moderate to severe Alzheimer's disease: post-hoc analyses of ADAS-cog and SIB total and single-item scores from six randomized, double-blind, placebo-controlled studies.

    Science.gov (United States)

    Mecocci, Patrizia; Bladström, Anna; Stender, Karina

    2009-05-01

    The post-hoc analyses reported here evaluate the specific effects of memantine treatment on ADAS-cog single-items or SIB subscales for patients with moderate to severe AD. Data from six multicentre, randomised, placebo-controlled, parallel-group, double-blind, 6-month studies were used as the basis for these post-hoc analyses. All patients with a Mini-Mental State Examination (MMSE) score of less than 20 were included. Analyses of patients with moderate AD (MMSE: 10-19), evaluated with the Alzheimer's disease Assessment Scale (ADAS-cog) and analyses of patients with moderate to severe AD (MMSE: 3-14), evaluated using the Severe Impairment Battery (SIB), were performed separately. The mean change from baseline showed a significant benefit of memantine treatment on both the ADAS-cog (p ADAS-cog single-item analyses showed significant benefits of memantine treatment, compared to placebo, for mean change from baseline for commands (p < 0.001), ideational praxis (p < 0.05), orientation (p < 0.01), comprehension (p < 0.05), and remembering test instructions (p < 0.05) for observed cases (OC). The SIB subscale analyses showed significant benefits of memantine, compared to placebo, for mean change from baseline for language (p < 0.05), memory (p < 0.05), orientation (p < 0.01), praxis (p < 0.001), and visuospatial ability (p < 0.01) for OC. Memantine shows significant benefits on overall cognitive abilities as well as on specific key cognitive domains for patients with moderate to severe AD. (c) 2009 John Wiley & Sons, Ltd.

  6. Identification of Acan125 as a myosin-I-binding protein present with myosin-I on cellular organelles of Acanthamoeba.

    Science.gov (United States)

    Xu, P; Zot, A S; Zot, H G

    1995-10-27

    We have discovered the first protein to bind to a non-filamentous myosin, aside from actin. This protein, Acan125, is a 125-kDa protein from Acanthamoeba that associates with the SH3 domain of Acanthamoeba myosin-IC and not the SH3 domain of human fodrin. Antibodies raised against Acan125 recognize a single protein of 125 kDa from a whole cell lysate of Acanthamoeba; antibodies to myosin-I (M1.7 and M1.8) do not recognize Acan125 on the same blot. Double labeling of Acanthamoeba show Acan125 and myosin-I to be present on the same intracellular organelle, most likely amoebastomes. Immunoprecipitation with either anti-myosin-I or anti-Acan125 antibodies coprecipitates both Acan125 and myosin-I from a lysate of Acanthamoeba, demonstrating that Acan125 interacts with native myosin-I.

  7. Compartmentation of metals in foliage of Populus tremula grown on soils with mixed contamination. II. Zinc binding inside leaf cell organelles

    Energy Technology Data Exchange (ETDEWEB)

    Vollenweider, Pierre, E-mail: pierre.vollenweider@wsl.c [Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zuercherstrasse 111, 8903 Birmensdorf (Switzerland); Bernasconi, Petra [Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zuercherstrasse 111, 8903 Birmensdorf (Switzerland); Environmental Protection Office (AfU), Aabachstrasse 5, 6300 Zug (Switzerland); Gautschi, Hans-Peter [Centre for Microscopy and Image Analysis (CMI), University of Zurich, Gloriastrasse 30, 8006 Zuerich (Switzerland); Menard, Terry; Frey, Beat; Guenthardt-Goerg, Madeleine S. [Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zuercherstrasse 111, 8903 Birmensdorf (Switzerland)

    2011-01-15

    The phytoextraction potential of plants for removing heavy metals from polluted soils is determined by their capacity to store contaminants in aboveground organs and complex them safely. In this study, the metal compartmentation, elemental composition of zinc deposits and zinc complexation within leaves from poplars grown on soil with mixed metal contamination was analysed combining several histochemical and microanalytical approaches. Zinc was the only heavy metal detected and was stored in several organelles in the form of globoid deposits showing {beta}-metachromasy. It was associated to oxygen anions and different cations, noteworthy phosphorous. The deposit structure, elemental composition and element ratios indicated that zinc was chelated by phytic acid ligands. Maturation processes in vacuolar vs. cytoplasmic deposits were suggested by differences in size and amounts of complexed zinc. Hence, zinc complexation by phytate contributed to metal detoxification and accumulation in foliage but could not prevent toxicity reactions therein. - Zinc contaminants translocated to symplast of aged leaves were detoxified by phytic acid ligands.

  8. Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses

    Directory of Open Access Journals (Sweden)

    Adam C. Wilkinson

    2013-10-01

    Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2−/− Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.

  9. Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample.

    Science.gov (United States)

    Illeghems, Koen; Weckx, Stefan; De Vuyst, Luc

    2015-09-01

    A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Modeling single nucleotide polymorphisms in the human AKR1C1 and AKR1C2 genes: implications for functional and genotyping analyses.

    Directory of Open Access Journals (Sweden)

    Jonathan W Arthur

    2010-12-01

    Full Text Available Enzymes encoded by the AKR1C1 and AKR1C2 genes are responsible for the metabolism of progesterone and 5α-dihydrotestosterone (DHT, respectively. The effect of amino acid substitutions, resulting from single nucleotide polymorphisms (SNPs in the AKR1C2 gene, on the enzyme kinetics of the AKR1C2 gene product were determined experimentally by Takashi et al. In this paper, we used homology modeling to predict and analyze the structure of AKR1C1 and AKR1C2 genetic variants. The experimental reduction in enzyme activity in the AKR1C2 variants F46Y and L172Q, as determined by Takahashi et al., is predicted to be due to increased instability in cofactor binding, caused by disruptions to the hydrogen bonds between NADP and AKR1C2, resulting from the insertion of polar residues into largely non-polar environments near the site of cofactor binding. Other AKR1C2 variants were shown to involve either conservative substitutions or changes taking place on the surface of the molecule and distant from the active site, confirming the experimental finding of Takahashi et al. that these variants do not result in any statistically significant reduction in enzyme activity. The AKR1C1 R258C variant is predicted to have no effect on enzyme activity for similar reasons. Thus, we provide further insight into the molecular mechanism of the enzyme kinetics of these proteins. Our data also highlight previously reported difficulties with online databases.

  11. Use of genomic recursions and algorithm for proven and young animals for single-step genomic BLUP analyses--a simulation study.

    Science.gov (United States)

    Fragomeni, B O; Lourenco, D A L; Tsuruta, S; Masuda, Y; Aguilar, I; Misztal, I

    2015-10-01

    The purpose of this study was to examine accuracy of genomic selection via single-step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix (G) is replaced by an approximation of G(-1) based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G(-1) and the approximated G(-1) via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G(-1) and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method. © 2015 Blackwell Verlag GmbH.

  12. Chimeric green fluorescent protein as a tool for visualizing subcellular organelles in living cells.

    Science.gov (United States)

    Rizzuto, R; Brini, M; Pizzo, P; Murgia, M; Pozzan, T

    1995-06-01

    It has recently been demonstrated that the green fluorescent protein (GFP) of the jellyfish Aequorea victoria retains its fluorescent properties when recombinantly expressed in both prokaryotic (Escherichia coli) and eukaryotic (Caenorhabditis elegans and Drosophila melanogaster) living cells; it can therefore be used as a powerful marker of gene expression in vivo. The specific targeting of recombinant GFP within cells would allow it to be used for even more applications, but no information is yet available on the possibility of targeting GFP to intracellular organelles. In this study, we show that the GFP cDNA can be expressed at high levels in cultured mammalian cells; the recombinant polypeptide is highly fluorescent and is exclusively localized in the cytosol. Furthermore, we have modified the GFP cDNA to include a mitochondrial targeting sequence (and a strong immunological epitope at the amino terminus of the encoded polypeptide). When transiently transfected into mammalian cells, this construct drives the expression of a strongly fluorescent GFP chimera which selectively localizes to the mitochondria. We also describe two of the many possible applications of this recombinant GFP in physiological studies. The targeted chimera allows the visualization of mitochondrial movement in living cells. Also, unlike dyes such as rhodamine, it reveals morphological changes induced in mitochondria by drugs that collapse the organelle membrane potential. Moreover, when GFP is cotransfected with a membrane receptor, such as the alpha 1-adrenergic receptor, the fluorescence of the GFP in intact cells can be used in recognizing the transfected cells. Thus, specific changes in intracellular Ca2+ concentration that occur in cells expressing the recombinant receptor can be identified using a classical fluorescent Ca2+ indicator. GFP is an invaluable new tool for studies of molecular biology and cell physiology. As a marker of transfection in vivo, it provides a simple means of

  13. Statistical organelle dissection of Arabidopsis guard cells using image database LIPS.

    Science.gov (United States)

    Higaki, Takumi; Kutsuna, Natsumaro; Hosokawa, Yoichiroh; Akita, Kae; Ebine, Kazuo; Ueda, Takashi; Kondo, Noriaki; Hasezawa, Seiichiro

    2012-01-01

    To comprehensively grasp cell biological events in plant stomatal movement, we have captured microscopic images of guard cells with various organelles markers. The 28,530 serial optical sections of 930 pairs of Arabidopsis guard cells have been released as a new image database, named Live Images of Plant Stomata (LIPS). We visualized the average organellar distributions in guard cells using probabilistic mapping and image clustering techniques. The results indicated that actin microfilaments and endoplasmic reticulum (ER) are mainly localized to the dorsal side and connection regions of guard cells. Subtractive images of open and closed stomata showed distribution changes in intracellular structures, including the ER, during stomatal movement. Time-lapse imaging showed that similar ER distribution changes occurred during stomatal opening induced by light irradiation or femtosecond laser shots on neighboring epidermal cells, indicating that our image analysis approach has identified a novel ER relocation in stomatal opening.

  14. Organelle-specific injury to melanin-containing cells in human skin by pulsed laser irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, G.F.; Shepard, R.S.; Paul, B.S.; Menkes, A.; Anderson, R.R.; Parrish, J.A.

    1983-12-01

    Physical models predict that ultraviolet laser radiation of appropriately brief pulses can selectively alter melanin-containing cellular targets in human skin. Skin of normal human volunteers was exposed to brief (20 nanosecond) 351-nm wave length pulses from a XeF excimer laser, predicting that those cells containing the greatest quantities of melanized melanosomes (lower half of the epidermis) would be selectively damaged. Transmission electron microscopy revealed the earliest cellular alteration to be immediate disruption of melanosomes, both within melanocytes and basal keratinocytes. This disruption was dose dependent and culminated in striking degenerative changes in these cells. Superficial keratinocytes and Langerhans cells were not affected. It was concluded that the XeF excimer laser is capable of organelle-specific injury to melanosomes. These findings may have important clinical implications in the treatment of both benign and malignant pigmented lesions by laser radiations of defined wave lengths and pulse durations.

  15. Confinement to organelle-associated inclusion structures mediates asymmetric inheritance of aggregated protein in budding yeast.

    Science.gov (United States)

    Spokoini, Rachel; Moldavski, Ofer; Nahmias, Yaakov; England, Jeremy L; Schuldiner, Maya; Kaganovich, Daniel

    2012-10-25

    The division of the S. cerevisiae budding yeast, which produces one mother cell and one daughter cell, is asymmetric with respect to aging. Remarkably, the asymmetry of yeast aging coincides with asymmetric inheritance of damaged and aggregated proteins by the mother cell. Here, we show that misfolded proteins are retained in the mother cell by being sequestered in juxtanuclear quality control compartment (JUNQ) and insoluble protein deposit (IPOD) inclusions, which are attached to organelles. Upon exposure to stress, misfolded proteins accumulate in stress foci that must be disaggregated by Hsp104 in order to be degraded or processed to JUNQ and IPOD. Cells that fail to deliver aggregates to an inclusion pass on aggregates to subsequent generations. Copyright © 2012 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Confinement to Organelle-Associated Inclusion Structures Mediates Asymmetric Inheritance of Aggregated Protein in Budding Yeast

    Directory of Open Access Journals (Sweden)

    Rachel Spokoini

    2012-10-01

    Full Text Available The division of the S. cerevisiae budding yeast, which produces one mother cell and one daughter cell, is asymmetric with respect to aging. Remarkably, the asymmetry of yeast aging coincides with asymmetric inheritance of damaged and aggregated proteins by the mother cell. Here, we show that misfolded proteins are retained in the mother cell by being sequestered in juxtanuclear quality control compartment (JUNQ and insoluble protein deposit (IPOD inclusions, which are attached to organelles. Upon exposure to stress, misfolded proteins accumulate in stress foci that must be disaggregated by Hsp104 in order to be degraded or processed to JUNQ and IPOD. Cells that fail to deliver aggregates to an inclusion pass on aggregates to subsequent generations.

  17. Microtubule-Based Transport and the Distribution, Tethering, and Organization of Organelles.

    Science.gov (United States)

    Barlan, Kari; Gelfand, Vladimir I

    2017-05-01

    SUMMARYMicrotubules provide long tracks along which a broad range of organelles and vesicles are transported by kinesin and dynein motors. Motor protein complexes also tether cargoes to cytoskeletal filaments, helping facilitate their interaction and communication. The generation of biochemically distinct microtubule subpopulations allows subsets of motors to recognize a given microtubule identity, allowing further organization within the cytoplasm. Both transport and tethering are spatiotemporally regulated through multiple modes, including acute modification of both motor-cargo and motor-track associations by various physiological signals. Strict regulation of intracellular transport is particularly important in specialized cell types such as neurons. Here, we review general mechanisms by which cargo transport is controlled and also highlight examples of transport regulated by multiple mechanisms. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  18. A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle.

    Science.gov (United States)

    Mackinder, Luke C M; Meyer, Moritz T; Mettler-Altmann, Tabea; Chen, Vivian K; Mitchell, Madeline C; Caspari, Oliver; Freeman Rosenzweig, Elizabeth S; Pallesen, Leif; Reeves, Gregory; Itakura, Alan; Roth, Robyn; Sommer, Frederik; Geimer, Stefan; Mühlhaus, Timo; Schroda, Michael; Goodenough, Ursula; Stitt, Mark; Griffiths, Howard; Jonikas, Martin C

    2016-05-24

    Biological carbon fixation is a key step in the global carbon cycle that regulates the atmosphere's composition while producing the food we eat and the fuels we burn. Approximately one-third of global carbon fixation occurs in an overlooked algal organelle called the pyrenoid. The pyrenoid contains the CO2-fixing enzyme Rubisco and enhances carbon fixation by supplying Rubisco with a high concentration of CO2 Since the discovery of the pyrenoid more that 130 y ago, the molecular structure and biogenesis of this ecologically fundamental organelle have remained enigmatic. Here we use the model green alga Chlamydomonas reinhardtii to discover that a low-complexity repeat protein, Essential Pyrenoid Component 1 (EPYC1), links Rubisco to form the pyrenoid. We find that EPYC1 is of comparable abundance to Rubisco and colocalizes with Rubisco throughout the pyrenoid. We show that EPYC1 is essential for normal pyrenoid size, number, morphology, Rubisco content, and efficient carbon fixation at low CO2 We explain the central role of EPYC1 in pyrenoid biogenesis by the finding that EPYC1 binds Rubisco to form the pyrenoid matrix. We propose two models in which EPYC1's four repeats could produce the observed lattice arrangement of Rubisco in the Chlamydomonas pyrenoid. Our results suggest a surprisingly simple molecular mechanism for how Rubisco can be packaged to form the pyrenoid matrix, potentially explaining how Rubisco packaging into a pyrenoid could have evolved across a broad range of photosynthetic eukaryotes through convergent evolution. In addition, our findings represent a key step toward engineering a pyrenoid into crops to enhance their carbon fixation efficiency.

  19. The core components of organelle biogenesis and membrane transport in the hydrogenosomes of Trichomonas vaginalis.

    Directory of Open Access Journals (Sweden)

    Petr Rada

    Full Text Available Trichomonas vaginalis is a parasitic protist of the Excavata group. It contains an anaerobic form of mitochondria called hydrogenosomes, which produce hydrogen and ATP; the majority of mitochondrial pathways and the organellar genome were lost during the mitochondrion-to-hydrogenosome transition. Consequently, all hydrogenosomal proteins are encoded in the nucleus and imported into the organelles. However, little is known about the membrane machineries required for biogenesis of the organelle and metabolite exchange. Using a combination of mass spectrometry, immunofluorescence microscopy, in vitro import assays and reverse genetics, we characterized the membrane proteins of the hydrogenosome. We identified components of the outer membrane (TOM and inner membrane (TIM protein translocases include multiple paralogs of the core Tom40-type porins and Tim17/22/23 channel proteins, respectively, and uniquely modified small Tim chaperones. The inner membrane proteins TvTim17/22/23-1 and Pam18 were shown to possess conserved information for targeting to mitochondrial inner membranes, but too divergent in sequence to support the growth of yeast strains lacking Tim17, Tim22, Tim23 or Pam18. Full complementation was seen only when the J-domain of hydrogenosomal Pam18 was fused with N-terminal region and transmembrane segment of the yeast homolog. Candidates for metabolite exchange across the outer membrane were identified including multiple isoforms of the β-barrel proteins, Hmp35 and Hmp36; inner membrane MCF-type metabolite carriers were limited to five homologs of the ATP/ADP carrier, Hmp31. Lastly, hydrogenosomes possess a pathway for the assembly of C-tail-anchored proteins into their outer membrane with several new tail-anchored proteins being identified. These results show that hydrogenosomes and mitochondria share common core membrane components required for protein import and metabolite exchange; however, they also reveal remarkable differences

  20. Developmental changes and organelle biogenesis in the reproductive organs of thermogenic skunk cabbage (Symplocarpus renifolius).

    Science.gov (United States)

    Ito-Inaba, Yasuko; Sato, Mayuko; Masuko, Hiromi; Hida, Yamato; Toyooka, Kiminori; Watanabe, Masao; Inaba, Takehito

    2009-01-01

    Sex-dependent thermogenesis during reproductive organ development in the inflorescence is a characteristic feature of some of the protogynous arum species. One such plant, skunk cabbage (Symplocarpus renifolius), can produce massive heat during the female stage but not during the subsequent male stage in which the stamen completes development, the anthers dehisce, and pollen is released. Unlike other thermogenic species, skunk cabbage belongs to the bisexual flower group. Although recent studies have identified the spadix as the thermogenic organ, it remains unclear how individual tissues or intracellular structures are involved in thermogenesis. In this study, reproductive organ development and organelle biogenesis were examined during the transition from the female to the male stage. During the female stage, the stamens exhibit extensive structural changes including changes in organelle structure and density. They accumulate high levels of mitochondrial proteins, including possible thermogenic factors, alternative oxidase, and uncoupling protein. By contrast, the petals and pistils do not undergo extensive changes during the female stage. However, they contain a larger number of mitochondria than during the male stage in which they develop large cytoplasmic vacuoles. Comparison between female and male spadices suggests that mitochondrial number rather than their level of activity correlates with thermogenesis. Their spadices, even in the male, contain a larger amount of mitochondria that had greater oxygen consumption, compared with non-thermogenic plants. Taken together, our data suggest that the extensive maturation process in stamens produces massive heat through increased metabolic activities. The possible mechanisms by which petal and pistil metabolism may affect thermogenesis are also discussed.

  1. Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health.

    Science.gov (United States)

    Hazkani-Covo, Einat; Martin, William F

    2017-05-01

    Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy. Because numts and nupts are typically identified through sequence comparison tools such as BLAST, disruption of insertions into smaller fragments can lead to systematic overestimation of numt and nupt frequencies. Accurate identification of numts and nupts is important, however, both for better understanding of their role during evolution, and for monitoring their increasingly evident role in human disease. Human populations are polymorphic for 141 numt loci, five numts are causal to genetic disease, and cancer genomic studies are revealing an abundance of numts associated with tumor progression. Here, we report investigation of salient parameters involved in obtaining accurate estimates of numt and nupt numbers in genome sequence data. Numts and nupts from 44 sequenced eukaryotic genomes reveal lineage-specific differences in the number, relative age and frequency of insertional events as well as lineage-specific dynamics of their postinsertional fragmentation. Our findings outline the main technical parameters influencing accurate identification and frequency estimation of numts in genomic studies pertinent to both evolution and human health. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Organelles contribute differentially to reactive oxygen species-related events during extended darkness.

    Science.gov (United States)

    Rosenwasser, Shilo; Rot, Ilona; Sollner, Evelyn; Meyer, Andreas J; Smith, Yoav; Leviatan, Noam; Fluhr, Robert; Friedman, Haya

    2011-05-01

    Treatment of Arabidopsis (Arabidopsis thaliana) leaves by extended darkness generates a genetically activated senescence program that culminates in cell death. The transcriptome of leaves subjected to extended darkness was found to contain a variety of reactive oxygen species (ROS)-specific signatures. The levels of transcripts constituting the transcriptome footprints of chloroplasts and cytoplasm ROS stresses decreased in leaves, as early as the second day of darkness. In contrast, an increase was detected in transcripts associated with mitochondrial and peroxisomal ROS stresses. The sequential changes in the redox state of the organelles during darkness were examined by redox-sensitive green fluorescent protein probes (roGFP) that were targeted to specific organelles. In plastids, roGFP showed a decreased level of oxidation as early as the first day of darkness, followed by a gradual increase to starting levels. However, in mitochondria, the level of oxidation of roGFP rapidly increased as early as the first day of darkness, followed by an increase in the peroxisomal level of oxidation of roGFP on the second day. No changes in the probe oxidation were observed in the cytoplasm until the third day. The increase in mitochondrial roGFP degree of oxidation was abolished by sucrose treatment, implying that oxidation is caused by energy deprivation. The dynamic redox state visualized by roGFP probes and the analysis of microarray results are consistent with a scenario in which ROS stresses emanating from the mitochondria and peroxisomes occur early during darkness at a presymptomatic stage and jointly contribute to the senescence program.

  3. Membrane-bound organelles versus membrane-less compartments and their control of anabolic pathways in Drosophila

    NARCIS (Netherlands)

    Aguilera-Gomez, Angelica; Rabouille, Catherine

    2017-01-01

    Classically, we think of cell compartmentalization as being achieved by membrane-bound organelles. It has nevertheless emerged that membrane-less assemblies also largely contribute to this compartmentalization. Here, we compare the characteristics of both types of compartmentalization in term of

  4. Dual targeting of a processing peptidase into both endosymbiotic organelles mediated by a transport signal of unusual architecture.

    Science.gov (United States)

    Baudisch, Bianca; Klösgen, Ralf Bernd

    2012-03-01

    As a result of the endosymbiotic gene transfer, the majority of proteins of mitochondria and chloroplasts are encoded in the nucleus and synthesized in the cytosol as precursor proteins carrying N-terminal transport signals for the 're-import' into the respective target organelle. Most of these transport signals are monospecific, although some of them have dual targeting properties, that is, they are recognized both by mitochondria and by chloroplasts as target organelles. We have identified alpha-MPP2, one of the two isoforms of the substrate binding subunit of mitochondrial processing peptidase of Arabidopsis thaliana, as a novel member of this class of nuclear-encoded organelle proteins. As demonstrated by in organello transport experiments with isolated organelles and by in vivo localization studies employing fluorescent chimeric reporter proteins, the N-terminal region of the alpha-MPP2 precursor comprises transport signals for the import into mitochondria as well as into chloroplasts. Both signals are found within the N-terminal 79 residues of the precursor protein, where they occupy partly separated and partly overlapping regions. Deletion mapping combined with in organello and in vivo protein transport studies demonstrate an unusual architecture of this transport signal, suggesting a composition of three functionally separated domains.

  5. Not All the Organelles of Living Cells Are Equal! Or Are They? Engaging Students in Deep Learning and Conceptual Change

    Science.gov (United States)

    Cherif, Abour H.; Siuda, JoElla Eaglin; Jedlicka, Dianne M.; Bondoc, Jasper Marc; Movahedzadeh, Farahnaz

    2016-01-01

    The cell is the fundamental basis for understanding biology much like the atom is the fundamental basis for understanding physics. Understanding biology requires the understanding of the fundamental functions performed by components within each cell. These components, or organelles, responsible for both maintenance and functioning of the cell…

  6. A divergent ADP/ATP carrier in the hydrogenosomes of Trichomonas gallinae argues for an independent origin of these organelles.

    NARCIS (Netherlands)

    Tjaden, J.; Haferkamp, I.; Boxma, B.; Tielens, A.G.; Huynen, M.A.; Hackstein, J.H.P.

    2004-01-01

    The evolution of mitochondrial ADP and ATP exchanging proteins (AACs) highlights a key event in the evolution of the eukaryotic cell, as ATP exporting carriers were indispensable in establishing the role of mitochondria as ATP-generating cellular organelles. Hydrogenosomes, i.e. ATP- and

  7. Formation of organelle-like N2-fixing symbiosomes in legume root nodules is controlled by DMI2

    NARCIS (Netherlands)

    Limpens, E.H.M.; Mirabella, R.; Fedorova, E.; Franken, C.; Franssen, H.; Bisseling, T.; Geurts, R.

    2005-01-01

    In most legume nodules, the N2-fixing rhizobia are present as organelle-like structures inside their host cells. These structures, named symbiosomes, contain one or a few rhizobia surrounded by a plant membrane. Symbiosome formation requires the release of bacteria from cell-wall-bound infection

  8. Structure-Guided Mutations in the Terminal Organelle Protein MG491 Cause Major Motility and Morphologic Alterations on Mycoplasma genitalium

    NARCIS (Netherlands)

    Martinelli, Luca; García-Morales, Luis; Querol, Enrique; Piñol, Jaume; Fita, Ignacio; Calisto, Bárbara M.

    2016-01-01

    The emergent human pathogen Mycoplasma genitalium, with one of the smallest genomes among cells capable of growing in axenic cultures, presents a flask-shaped morphology due to a protrusion of the cell membrane, known as the terminal organelle, that is involved in cell adhesion and motility and is

  9. Chemical rescue of malaria parasites lacking an apicoplast defines organelle function in blood-stage Plasmodium falciparum.

    Science.gov (United States)

    Yeh, Ellen; DeRisi, Joseph L

    2011-08-01

    Plasmodium spp parasites harbor an unusual plastid organelle called the apicoplast. Due to its prokaryotic origin and essential function, the apicoplast is a key target for development of new anti-malarials. Over 500 proteins are predicted to localize to this organelle and several prokaryotic biochemical pathways have been annotated, yet the essential role of the apicoplast during human infection remains a mystery. Previous work showed that treatment with fosmidomycin, an inhibitor of non-mevalonate isoprenoid precursor biosynthesis in the apicoplast, inhibits the growth of blood-stage P. falciparum. Herein, we demonstrate that fosmidomycin inhibition can be chemically rescued by supplementation with isopentenyl pyrophosphate (IPP), the pathway product. Surprisingly, IPP supplementation also completely reverses death following treatment with antibiotics that cause loss of the apicoplast. We show that antibiotic-treated parasites rescued with IPP over multiple cycles specifically lose their apicoplast genome and fail to process or localize organelle proteins, rendering them functionally apicoplast-minus. Despite the loss of this essential organelle, these apicoplast-minus auxotrophs can be grown indefinitely in asexual blood stage culture but are entirely dependent on exogenous IPP for survival. These findings indicate that isoprenoid precursor biosynthesis is the only essential function of the apicoplast during blood-stage growth. Moreover, apicoplast-minus P. falciparum strains will be a powerful tool for further investigation of apicoplast biology as well as drug and vaccine development.

  10. Single organelle fret-based analysis of intracellular calcium: different effects of presinilis carrying Familial Alzheimer's Disease mutations

    OpenAIRE

    wong, andrea kuan cie

    2014-01-01

    Calcium (Ca2+) is one of the major intracellular messengers that impacts nearly every aspect of cell life. In particular, it plays essential roles in neuronal development, synaptic transmission and plasticity, as well as in the regulation of metabolic pathways and cell fate decisions. The first goal of my work was to study more in details the Golgi apparatus (GA), as an intracellular Ca2+ store. The Golgi complex may store up to 5% of the total cellular Ca2+ at higher concentrations an...

  11. Mitochondria are the main target organelle for trivalent monomethylarsonous acid (MMA(III))-induced cytotoxicity.

    Science.gov (United States)

    Naranmandura, Hua; Xu, Shi; Sawata, Takashi; Hao, Wen Hui; Liu, Huan; Bu, Na; Ogra, Yasumitsu; Lou, Yi Jia; Suzuki, Noriyuki

    2011-07-18

    Excessive generation of reactive oxygen species (ROS) is considered to play an important role in arsenic-induced carcinogenicity in the liver, lungs, and urinary bladder. However, little is known about the mechanism of ROS-based carcinogenicity, including where the ROS are generated, and which arsenic species are the most effective ROS inducers. In order to better understand the mechanism of arsenic toxicity, rat liver RLC-16 cells were exposed to arsenite (iAs(III)) and its intermediate metabolites [i.e., monomethylarsonous acid (MMA(III)) and dimethylarsinous acid (DMA(III))]. MMA(III) (IC(50) = 1 μM) was found to be the most toxic form, followed by DMA(III) (IC(50) = 2 μM) and iAs(III) (IC(50) = 18 μM). Following exposure to MMA(III), ROS were found to be generated primarily in the mitochondria. DMA(III) exposure resulted in ROS generation in other organelles, while no ROS generation was seen following exposures to low levels of iAs(III). This suggests the mechanisms of induction of ROS are different among the three arsenicals. The effects of iAs(III), MMA(III), and DMA(III) on activities of complexes I-IV in the electron transport chain (ETC) of rat liver submitochondrial particles and on the stimulation of ROS production in intact mitochondria were also studied. Activities of complexes II and IV were significantly inhibited by MMA(III), but only the activity of complexes II was inhibited by DMA(III). Incubation with iAs(III) had no inhibitory effects on any of the four complexes. Generation of ROS in intact mitochondria was significantly increased following incubation with MMA(III), while low levels of ROS generation were observed following incubation with DMA(III). ROS was not produced in mitochondria following exposure to iAs(III). The mechanism underlying cell death is different among As(III), MMA(III), and DMA(III), with mitochondria being one of the primary target organelles for MMA(III)-induced cytotoxicity. © 2011 American Chemical Society

  12. Ontogenetic changes in the ultrastructure of rat hepatocyte organelles after prenatal x irradiation

    International Nuclear Information System (INIS)

    Chedid, A.; Nair, V.

    1975-01-01

    The effects of prenatal x irradiation on the development of hepatocyte organelles have been studied in Sprague-Dawley rats. Pregnant rats received 50 R to the pelvic region on the 13th gestation day (g.d.). Animals were sacrificed on g.d.'s 15 and 20, day of birth, and 5th postnatal day. The fetal and neonatal livers were obtained and processed for electron-microscopic examination. The most striking discernible change after irradiation involves the appearance of cytoplasmic ''polyribosomal aggregates'' in the hepatocyte specimens of 15th and 20th g.d.'s. In the control rat, smooth endoplasmic reticulum (SER) appears for the first time on 20th g.d., while no SER could be detected in the hepatocytes from the irradiated animals at this period nor on day of birth. In the irradiated animals, SER was observed on the 5th postnatal day. Our results are consistent with the hypothesis that lipid peroxidation membrane alteration, delayed appearance of SER, and ''polyribosomal aggregation'' may be sequentially linked events after prenatal x irradiation. (U.S.)

  13. Shifts in oxidation states of cerium oxide nanoparticles detected inside intact hydrated cells and organelles

    Energy Technology Data Exchange (ETDEWEB)

    Szymanski, Craig J.; Munusamy, Prabhakaran; Mihai, Cosmin; Xie, Yumei; Hu, Dehong; Gilles, Marry K.; Tyliszczak, T.; Thevuthasan, Suntharampillai; Baer, Donald R.; Orr, Galya

    2015-09-01

    Cerium oxide nanoparticles (CNPs) have been shown to induce diverse biological effects, ranging from toxic to beneficial. The beneficial effects have been attributed to the potential antioxidant activity of CNPs via certain redox reactions, depending on their oxidation state or Ce3+/Ce4+ ratio. However, this ratio is strongly dependent on the environment and age of the nanoparticles and it is unclear whether and how the complex intracellular environment impacts this ratio and the possible redox reactions of CNPs. To identify any changes in the oxidation state of CNPs in the intracellular environment and better understand their intracellular reactions, we directly quantified the oxidation states of CNPs outside and inside intact hydrated cells and organelles using correlated scanning transmission x-ray and super resolution fluorescence microscopies. By analyzing hundreds of small CNP aggregates, we detected a shift to a higher Ce3+/Ce4+ ratio in CNPs inside versus outside the cells, indicating a net reduction of CNPs in the intracellular environment. We further found a similar ratio in the cytoplasm and in the lysosomes, indicating that the net reduction occurs earlier in the internalization pathway. Together with oxidative stress and toxicity measurements, our observations identify a net reduction of CNPs in the intracellular environment, which is consistent with their involvement in potentially beneficial oxidation reactions, but also point to interactions that can negatively impact the health of cells.

  14. Motile sperm organelle morphology examination (MSOME) and sperm head vacuoles: state of the art in 2013.

    Science.gov (United States)

    Perdrix, Anne; Rives, Nathalie

    2013-01-01

    BACKGROUND Approximately 10 years after the first publication introducing the motile sperm organelle morphology examination (MSOME), many questions remained about sperm vacuoles: frequency, size, localization, mode of occurrence, biological significance and impact on male fertility potential. Many studies have tried to characterize sperm vacuoles, to determine the sperm abnormalities possibly associated with vacuoles, to test the diagnostic value of MSOME for male infertility or to question the benefits of intracytoplasmic morphologically selected sperm injection (IMSI). METHODS We searched PubMed for articles in the English language published in 2001-2012 regarding human sperm head vacuoles, MSOME and IMSI. RESULTS A bibliographic analysis revealed consensus for the following findings: (i) sperm vacuoles appeared frequently, often multiple and preferentially anterior; (ii) sperm vacuoles and sperm chromatin immaturity have been associated, particularly in the case of large vacuoles; (iii) teratozoospermia was a preferred indication of MSOME and IMSI. CONCLUSION The high-magnification system appears to be a powerful method to improve our understanding of human spermatozoa. However, its clinical use remains unclear in the fields of male infertility diagnosis and assisted reproduction techniques (ARTs).

  15. Organelle Size Scaling of the Budding Yeast Vacuole Is Tuned by Membrane Trafficking Rates

    Science.gov (United States)

    Chan, Yee-Hung Mark; Marshall, Wallace F.

    2014-01-01

    Organelles serve as biochemical reactors in the cell, and often display characteristic scaling trends with cell size, suggesting mechanisms that coordinate their sizes. In this study, we measure the vacuole-cell size scaling trends in budding yeast using optical microscopy and a novel, to our knowledge, image analysis algorithm. Vacuole volume and surface area both show characteristic scaling trends with respect to cell size that are consistent among different strains. Rapamycin treatment was found to increase vacuole-cell size scaling trends for both volume and surface area. Unexpectedly, these increases did not depend on macroautophagy, as similar increases in vacuole size were observed in the autophagy deficient mutants atg1Δ and atg5Δ. Rather, rapamycin appears to act on vacuole size by inhibiting retrograde membrane trafficking, as the atg18Δ mutant, which is defective in retrograde trafficking, shows similar vacuole size scaling to rapamycin-treated cells and is itself insensitive to rapamycin treatment. Disruption of anterograde membrane trafficking in the apl5Δ mutant leads to complementary changes in vacuole size scaling. These quantitative results lead to a simple model for vacuole size scaling based on proportionality between cell growth rates and vacuole growth rates. PMID:24806931

  16. Stimulated emission depletion (STED) nanoscopy of a fluorescent protein-labeled organelle inside a living cell.

    Science.gov (United States)

    Hein, Birka; Willig, Katrin I; Hell, Stefan W

    2008-09-23

    We demonstrate far-field optical imaging with subdiffraction resolution of the endoplasmic reticulum (ER) in the interior of a living mammalian cell. The diffraction barrier is overcome by applying stimulated emission depletion (STED) on a yellow fluorescent protein tag. Imaging individual structural elements of the ER revealed a focal plane (x, y) resolution of <50 nm inside the living cell, corresponding to a 4-fold improvement over that of a confocal microscope and a 16-fold reduction in the focal-spot cross-sectional area. A similar gain in resolution is realized with both pulsed- and continuous-wave laser illumination. Images of highly convoluted parts of the ER reveal a similar resolution improvement in 3D optical sectioning by a factor of 3 along the optic axis (z). Time-lapse STED recordings document morphological changes of the ER over time. Thus, nanoscale 3D imaging of organelles in the interior of living cells greatly expands the scope of light microscopy in cell biology.

  17. Structure and Mechanisms of a Protein-Based Organelle in Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, Shiho; Sawaya, Michael R.; Yeates, Todd O. (UCLA)

    2010-08-18

    Many bacterial cells contain proteinaceous microcompartments that act as simple organelles by sequestering specific metabolic processes involving volatile or toxic metabolites. Here we report the three-dimensional (3D) crystal structures, with resolutions between 1.65 and 2.5 angstroms, of the four homologous proteins (EutS, EutL, EutK, and EutM) that are thought to be the major shell constituents of a functionally complex ethanolamine utilization (Eut) microcompartment. The Eut microcompartment is used to sequester the metabolism of ethanolamine in bacteria such as Escherichia coli and Salmonella enterica. The four Eut shell proteins share an overall similar 3D fold, but they have distinguishing structural features that help explain the specific roles they play in the microcompartment. For example, EutL undergoes a conformational change that is probably involved in gating molecular transport through shell protein pores, whereas structural evidence suggests that EutK might bind a nucleic acid component. Together these structures give mechanistic insight into bacterial microcompartments.

  18. Identification of novel proteins in Neospora caninum using an organelle purification and monoclonal antibody approach.

    Directory of Open Access Journals (Sweden)

    Catherine S Sohn

    2011-04-01

    Full Text Available Neospora caninum is an important veterinary pathogen that causes abortion in cattle and neuromuscular disease in dogs. Neospora has also generated substantial interest because it is an extremely close relative of the human pathogen Toxoplasma gondii, yet does not appear to infect humans. While for Toxoplasma there are a wide array of molecular tools and reagents available for experimental investigation, relatively few reagents exist for Neospora. To investigate the unique biological features of this parasite and exploit the recent sequencing of its genome, we have used an organelle isolation and monoclonal antibody approach to identify novel organellar proteins and develop a wide array of probes for subcellular localization. We raised a panel of forty-six monoclonal antibodies that detect proteins from the rhoptries, micronemes, dense granules, inner membrane complex, apicoplast, mitochondrion and parasite surface. A subset of the proteins was identified by immunoprecipitation and mass spectrometry and reveal that we have identified and localized many of the key proteins involved in invasion and host interaction in Neospora. In addition, we identified novel secretory proteins not previously studied in any apicomplexan parasite. Thus, this organellar monoclonal antibody approach not only greatly enhances the tools available for Neospora cell biology, but also identifies novel components of the unique biological characteristics of this important veterinary pathogen.

  19. Identification of Novel Proteins in Neospora caninum Using an Organelle Purification and Monoclonal Antibody Approach

    Science.gov (United States)

    Sohn, Catherine S.; Cheng, Tim T.; Drummond, Michael L.; Peng, Eric D.; Vermont, Sarah J.; Xia, Dong; Cheng, Stephen J.; Wastling, Jonathan M.; Bradley, Peter J.

    2011-01-01

    Neospora caninum is an important veterinary pathogen that causes abortion in cattle and neuromuscular disease in dogs. Neospora has also generated substantial interest because it is an extremely close relative of the human pathogen Toxoplasma gondii, yet does not appear to infect humans. While for Toxoplasma there are a wide array of molecular tools and reagents available for experimental investigation, relatively few reagents exist for Neospora. To investigate the unique biological features of this parasite and exploit the recent sequencing of its genome, we have used an organelle isolation and monoclonal antibody approach to identify novel organellar proteins and develop a wide array of probes for subcellular localization. We raised a panel of forty-six monoclonal antibodies that detect proteins from the rhoptries, micronemes, dense granules, inner membrane complex, apicoplast, mitochondrion and parasite surface. A subset of the proteins was identified by immunoprecipitation and mass spectrometry and reveal that we have identified and localized many of the key proteins involved in invasion and host interaction in Neospora. In addition, we identified novel secretory proteins not previously studied in any apicomplexan parasite. Thus, this organellar monoclonal antibody approach not only greatly enhances the tools available for Neospora cell biology, but also identifies novel components of the unique biological characteristics of this important veterinary pathogen. PMID:21483743

  20. Alzheimer's disease-related misfolded proteins and dysfunctional organelles on autophagy menu.

    Science.gov (United States)

    Correia, Sónia C; Resende, Rosa; Moreira, Paula I; Pereira, Cláudia M

    2015-04-01

    Autophagy is a housekeeping process responsible for the bulk degradation of misfolded protein aggregates and damaged organelles through the lysosomal machinery. Given its key role as a cellular quality control mechanism, autophagy is now a focus of intense scrutiny in Alzheimer's disease (AD). The hallmarks of this devastating neurodegenerative disease are the accumulation of misfolded amyloid-β (Aβ) peptide and hyperphosphorylated tau protein and neuronal loss, which are accompanied by mitochondrial dysfunction and endoplasmic reticulum (ER) stress, suggesting that faulty autophagy is a contributing factor to AD pathology. Indeed, the AD brain is characterized by a massive accumulation of autophagic vacuoles within large swellings along dystrophic neurites and defects at different steps of the autophagic-lysosomal pathway. In this sense, this review provides an overview on the role of autophagy on Aβ metabolism, tau processing and clearance, and the contribution of ER-phagy and mitophagy to AD pathology. From a therapeutic perspective, this review also intends to clarify whether, when, and how autophagy can be targeted to efficaciously counteract AD-related symptomatic and neuropathological features.

  1. Organelle-cytoskeleton relationships in fibroblasts: mitochondria, Golgi apparatus, and endoplasmic reticulum in phases of movement and growth

    DEFF Research Database (Denmark)

    Couchman, J R; Rees, D A

    1982-01-01

    previously - including the development of pronounced microfilament bundles and of stable and well-defined focal adhesions - and appears to be related to changes in the motility status of the cells rather than to alterations in growth or synthetic capability. Mitochondrial mobility is strongly reduced...... the phenotypic conversion, although the locomotory cells are characterized by a zone close to the leading lamella, which is completely free from these organelles. The form and distribution of the Golgi apparatus, but not the endoplasmic reticulum, was sensitive to microtubule disruption but was also shown...... to have direct functional associations with the centriolar region. The relative distributions of the three types of organelle during the phases of cell movements and cell growth, are consistent with their biochemical functions in cellular activity....

  2. Live-cell Microscopy and Fluorescence-based Measurement of Luminal pH in Intracellular Organelles

    Directory of Open Access Journals (Sweden)

    Li Ma

    2017-08-01

    Full Text Available Luminal pH is an important functional feature of intracellular organelles. Acidification of the lumen of organelles such as endosomes, lysosomes, and the Golgi apparatus plays a critical role in fundamental cellular processes. As such, measurement of the luminal pH of these organelles has relevance to both basic research and translational research. At the same time, accurate measurement of intraorganellar pH in living cells can be challenging and may be a limiting hurdle for research in some areas. Here, we describe three powerful methods to measure rigorously the luminal pH of different intracellular organelles, focusing on endosomes, lysosomes, and the Golgi apparatus. The described methods are based on live imaging of pH-sensitive fluorescent probes and include: (1 A protocol based on quantitative, ratiometric measurement of endocytosis of pH-sensitive and pH-insensitive fluorescent conjugates of transferrin; (2 A protocol for the use of proteins tagged with a ratiometric variant of the pH-sensitive intrinsically fluorescent protein pHluorin; and (3 A protocol using the fluorescent dye LysoSensor™. We describe necessary reagents, key procedures, and methods and equipment for data acquisition and analysis. Examples of implementation of the protocols are provided for cultured cells derived from a cancer cell line and for primary cultures of mouse hippocampal neurons. In addition, we present strengths and weaknesses of the different described intraorganellar pH measurement methods. These protocols are likely to be of benefit to many researchers, from basic scientists to those conducting translational research with a focus on diseases in patient-derived cells.

  3. Dynactin binding to tyrosinated microtubules promotes centrosome centration in C. elegans by enhancing dynein-mediated organelle transport

    OpenAIRE

    Barbosa, Daniel J.; Duro, Joana; Prevo, Bram; Cheerambathur, Dhanya K.; Carvalho, Ana X.; Gassmann, Reto

    2017-01-01

    Author summary Animal cells rely on molecular motor proteins to distribute intracellular components and organize their cytoplasmic content. The motor cytoplasmic dynein 1 (dynein) uses microtubule filaments as tracks to transport cargo from the cell periphery to the cell center, where the microtubule minus ends are embedded at the centrosome. Conversely, when dynein is anchored at the cell cortex or on organelles in the cytoplasm, the motor can pull on microtubules to position centrosomes wit...

  4. Actin cytoskeleton and organelle movement in the sporangiophore of the zygomycete Phycomyces blakesleeanus.

    Science.gov (United States)

    Grolig, F; Moch, J; Schneider, A; Galland, P

    2014-01-01

    Growth, photo- and gravitropism of sporangiophores of the zygomycete Phycomyces blakesleeanus occur within the apical growing zone, a cylindrical structure (diameter about 100 μm) that reaches about 1.5-2.5 mm below the tip and has growth rates up to 50 μm·min(-1) . To better understand morphogenesis and growth of the giant aerial hypha, we investigated with confocal microscopy and inhibitors the actin cytoskeleton and by in-vivo particle tracking the associated organelle movement. We found stage-1 sporangiophores (without sporangium) possess an actin cytoskeleton with polar zonation. (i) In the apex, abundant microfilaments without preferential orientation entangled numerous nuclei as well as a conspicious complex of some 200 lipid globules. Microfilament patches (≈ 1.6-μm diameter) are clustered in the tip and were found in the apical cortex, whereas short, curved microfilament bundles (≈ 2.3-μm long) prevailed in the subapex. (ii) In a transition zone downwards to the shaft, the microfilaments rearranged into a dense mat of longitudinal microfilaments that was parallel close to the periphery but more random towards the cell centre. Numerous microfilament patches were found near the cortex (≈ 10/100 μm(2) ); their number decreased rapidly in the subcortex. In contrast, the short, curved microfilament bundles were found only in the subcortex. (iii) The basal shaft segment of the sporangiophore (with central vacuole) exhibited bidirectional particle movement over long distances (velocity ≈ 2 μm·s(-1) ) along massive longitudinal, subcortical microfilament cables. The zonation of the cytoskeleton density correlated well with the local growth rates at the tip of the sporangiophore, and appears thus as a structural prerequisite for growth and bending. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  5. Ricinosomes: an organelle for developmentally regulated programmed cell death in senescing plant tissues

    Science.gov (United States)

    Gietl, C.; Schmid, M.

    2001-02-01

    This review describes aspects of programmed cell death (PCD). Present research maps the enzymes involved and explores the signal transduction pathways involved in their synthesis. A special organelle (the ricinosome) has been discovered in the senescing endosperm of germinating castor beans (Ricinus communis) that develops at the beginning of PCD and delivers large amounts of a papain-type cysteine endopeptidase (CysEP) in the final stages of cellular disintegration. Castor beans store oil and proteins in a living endosperm surrounding the cotyledons. These stores are mobilized during germination and transferred into the cotyledons. PCD is initiated after this transfer is complete. The CysEP is synthesized in the lumen of the endoplasmic reticulum (ER) where it is retained by its C-terminal KDEL peptide as a rather inactive pro-enzyme. Large number of ricinosomes bud from the ER at the same time as the nuclear DNA is characteristically fragmented during PCD. The mitochondria, glyoxysomes and ribosomes are degraded in autophagic vacuoles, while the endopeptidase is activated by removal of the propeptide and the KDEL tail and enters the cytosol. The endosperm dries and detaches from the cotyledons. A homologous KDEL-tailed cysteine endopeptidase has been found in several senescing tissues; it has been localized in ricinosomes of withering day-lily petals and dying seed coats. Three genes for a KDEL-tailed cysteine endopeptidase have been identified in Arabidopsis. One is expressed in senescing ovules, the second in the vascular vessels and the third in maturing siliques. These genes open the way to exploring PCD in plants.

  6. A morphometric analysis of the redistribution of organelles in columella cells of horizontally-oriented roots of Zea mays

    Science.gov (United States)

    Moore, R.

    1986-01-01

    In order to determine what structural changes in graviperceptive cells are associated with onset of root gravicurvature, the redistribution of organelles in columella cells of horizontally-oriented, graviresponding roots of Zea mays has been quantified. Root gravicurvature began by 15 min after reorientation, and did not involve significant changes in the (i) volume of individual columella cells or amyloplasts, (ii) relative volume of any cellular organelle, (iii) number of amyloplasts per columella cell, or (iv) surface area of cellular location of endoplasmic reticulum. Sedimentation of amyloplasts began within 1 to 2 min after reorientation, and was characterized by an intensely staining area of cytoplasm adjacent to the sedimenting amyloplasts. By 5 min after reorientation, amyloplasts were located in the lower distal corner of columella cells, and, by 15 min after reorientation, overlaid the entire length of the lower cell wall. No consistent contact between amyloplasts and any cellular structure was detected at any stage of gravicurvature. Centrally-located nuclei initially migrated upward in columella cells of horizontally-oriented roots, after which they moved to the proximal ends of the cells by 15 min after reorientation. No significant pattern of redistribution of vacuoles, mitochondria, dictyosomes, or hyaloplasm was detected that correlated with the onset of gravicurvature. These results indicate that amyloplasts and nuclei are the only organelles whose movements correlate positively with the onset of gravicurvature by primary roots of this cultivar of Zea mays.

  7. Toxoplasma DJ-1 Regulates Organelle Secretion by a Direct Interaction with Calcium-Dependent Protein Kinase 1.

    Science.gov (United States)

    Child, Matthew A; Garland, Megan; Foe, Ian; Madzelan, Peter; Treeck, Moritz; van der Linden, Wouter A; Oresic Bender, Kristina; Weerapana, Eranthie; Wilson, Mark A; Boothroyd, John C; Reese, Michael L; Bogyo, Matthew

    2017-02-28

    Human DJ-1 is a highly conserved and yet functionally enigmatic protein associated with a heritable form of Parkinson's disease. It has been suggested to be a redox-dependent regulatory scaffold, binding to proteins to modulate their function. Here we present the X-ray crystal structure of the Toxoplasma orthologue Toxoplasma gondii DJ-1 (TgDJ-1) at 2.1-Å resolution and show that it directly associates with calcium-dependent protein kinase 1 (CDPK1). The TgDJ-1 structure identifies an orthologously conserved arginine dyad that acts as a phospho-gatekeeper motif to control complex formation. We determined that the binding of TgDJ-1 to CDPK1 is sensitive to oxidation and calcium, and that this interaction potentiates CDPK1 kinase activity. Finally, we show that genetic deletion of TgDJ-1 results in upregulation of CDPK1 expression and that disruption of the CDPK1/TgDJ-1 complex in vivo prevents normal exocytosis of parasite virulence-associated organelles called micronemes. Overall, our data suggest that TgDJ-1 functions as a noncanonical kinase-regulatory scaffold that integrates multiple intracellular signals to tune microneme exocytosis in T. gondii IMPORTANCE Apicomplexan parasites such as Toxoplasma and Plasmodium are obligate intracellular parasites that require the protective environment of a host cell in order to replicate and survive within a host organism. These parasites secrete effector proteins from specialized apical organelles to select and invade a chosen host cell. The secretion of these organelles is a tightly regulated process coordinated by endogenous small molecules and calcium-dependent protein kinases. We previously identified the Toxoplasma orthologue of the highly conserved protein DJ-1 as a regulator of microneme secretion, but the molecular basis for this was not known. We have now identified the molecular mechanism for how TgDJ-1 regulates microneme secretion. TgDJ-1 interacts with the kinase responsible for the secretion of these

  8. Hole Burning Imaging Studies of Cancerous and Analogous Normal Ovarian Tissues Utilizing Organelle Specific Dyes

    Energy Technology Data Exchange (ETDEWEB)

    Matsuzaki, Satoshi [Iowa State Univ., Ames, IA (United States)

    2004-01-01

    Presented in this dissertation is the successful demonstration that nonphotochemical hole burning (NPWB) imaging can be used to study in vitro tissue cellular systems for discerning differences in cellular ultrastructures due to cancer development. This has been accomplished with the surgically removed cancerous ovarian and analogous normal peritoneal tissues from the same patient and the application of a fluorescent mitochondrion specific dye, Molecular Probe MitoFluor Far Red 680 (MF680), commonly known as rhodamine 800, that has been proven to exhibit efficient NPHB. From the results presented in Chapters 4 and 5 , and Appendix B, the following conclusions were made: (1) fluorescence excitation spectra of MF680 and confocal microscopy images of thin sliced tissues incubated with MF680 confirm the site-specificity of the probe molecules in the cellular systems. (2) Tunneling parameters, {lambda}{sub 0} and σΛ, as well as the standard hole burning parameters (namely, γ and S), have been determined for the tissue samples by hole growth kinetics (HGK) analyses. Unlike the preliminary cultured cell studies, these parameters have not shown the ability to distinguish tissue cellular matrices surrounding the chromophores. (3) Effects of an external electric (Stark) field on the nonphotochemical holes have been used to determine the changes in permanent dipole moment (fΔμ) for MF680 in tissue samples when burn laser polarization is parallel to the Stark field. Differences are detected between fΔμs in the two tissue samples, with the cancerous tissue exhibiting a more pronounced change (1.35-fold increase) in permanent dipole moment change relative to the normal analogs. It is speculated that the difference may be related to differences in mitochondrial membrane potentials in these tissue samples. (4) In the HGK mode, hole burning imaging (HBI) of cells adhered to coverslips and cooled to liquid helium temperatures in the complete absence of

  9. A divergent ADP/ATP carrier in the hydrogenosomes of Trichomonas gallinae argues for an independent origin of these organelles.

    Science.gov (United States)

    Tjaden, Joachim; Haferkamp, Ilka; Boxma, Brigitte; Tielens, Aloysius G M; Huynen, Martijn; Hackstein, Johannes H P

    2004-03-01

    The evolution of mitochondrial ADP and ATP exchanging proteins (AACs) highlights a key event in the evolution of the eukaryotic cell, as ATP exporting carriers were indispensable in establishing the role of mitochondria as ATP-generating cellular organelles. Hydrogenosomes, i.e. ATP- and hydrogen-generating organelles of certain anaerobic unicellular eukaryotes, are believed to have evolved from the same ancestral endosymbiont that gave rise to present day mitochondria. Notably, the hydrogenosomes of the parasitic anaerobic flagellate Trichomonas seemed to be deficient in mitochondrial-type AACs. Instead, HMP 31, a different member of the mitochondrial carrier family (MCF) with a hitherto unknown function, is abundant in the hydrogenosomal membranes of Trichomonas vaginalis. Here we show that the homologous HMP 31 of closely related Trichomonas gallinae specifically transports ADP and ATP with high efficiency, as do genuine mitochondrial AACs. However, phylogenetic analysis and its resistance against bongkrekic acid (BKA, an efficient inhibitor of mitochondrial-type AACs) identify HMP 31 as a member of the mitochondrial carrier family that is distinct from all mitochondrial and hydrogenosomal AACs studied so far. Thus, our data support the hypothesis that the various hydrogenosomes evolved repeatedly and independently.

  10. Protein transport in organelles: The composition, function and regulation of the Tic complex in chloroplast protein import.

    Science.gov (United States)

    Benz, J Philipp; Soll, Jürgen; Bölter, Bettina

    2009-03-01

    It is widely accepted that chloroplasts derived from an endosymbiotic event in which an early eukaryotic cell engulfed an ancient cyanobacterial prokaryote. During subsequent evolution, this new organelle lost its autonomy by transferring most of its genetic information to the host cell nucleus and therefore became dependent on protein import from the cytoplasm. The so-called 'general import pathway' makes use of two multisubunit protein translocases located in the two envelope membranes: the Toc and Tic complexes (translocon at the outer/inner envelope membrane of chloroplasts). The main function of both complexes, which are thought to work in parallel, is to provide a protein-selective channel through the envelope membrane and to exert the necessary driving force for the translocation. To achieve high efficiency of protein import, additional regulatory subunits have been developed that sense, and quickly react to, signals giving information about the status and demand of the organelle. These include calcium-mediated signals, most likely through a potential plastidic calmodulin, as well as redox sensing (e.g. via the stromal NADP(+)/NADPH pool). In this minireview, we briefly summarize the present knowledge of how the Tic complex adapted to the tasks outlined above, focusing more on the recent advances in the field, which have brought substantial progress concerning the motor function as well as the regulatory potential of this protein translocation system.

  11. Co-ordinate synthesis and protein localization in a bacterial organelle by the action of a penicillin-binding-protein.

    Science.gov (United States)

    Hughes, H Velocity; Lisher, John P; Hardy, Gail G; Kysela, David T; Arnold, Randy J; Giedroc, David P; Brun, Yves V

    2013-12-01

    Organelles with specialized form and function occur in diverse bacteria. Within the Alphaproteobacteria, several species extrude thin cellular appendages known as stalks, which function in nutrient uptake, buoyancy and reproduction. Consistent with their specialization, stalks maintain a unique molecular composition compared with the cell body, but how this is achieved remains to be fully elucidated. Here we dissect the mechanism of localization of StpX, a stalk-specific protein in Caulobacter crescentus. Using a forward genetics approach, we identify a penicillin-binding-protein, PbpC, which is required for the localization of StpX in the stalk. We show that PbpC acts at the stalked cell pole to anchor StpX to rigid components of the outer membrane of the elongating stalk, concurrent with stalk synthesis. Stalk-localized StpX in turn functions in cellular responses to copper and zinc, suggesting that the stalk may contribute to metal homeostasis in Caulobacter. Together, these results identify a novel role for a penicillin-binding-protein in compartmentalizing a bacterial organelle it itself helps create, raising the possibility that cell wall-synthetic enzymes may broadly serve not only to synthesize the diverse shapes of bacteria, but also to functionalize them at the molecular level. © 2013 John Wiley & Sons Ltd.

  12. Oncoprotein AEG-1 is an Endoplasmic Reticulum RNA Binding Protein Whose Interactome is Enriched In Organelle Resident Protein-Encoding mRNAs.

    Science.gov (United States)

    Hsu, Jack C-C; Reid, David W; Hoffman, Alyson M; Sarkar, Devanand; Nicchitta, Christopher V

    2018-02-07

    Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs. Cluster mapping of the AEG-1/RNA interaction sites demonstrated a normalized rank order interaction of coding sequence > 5' untranslated region, with 3' untranslated region interactions only weakly represented. Intriguingly, AEG-1/membrane protein mRNA interaction sites clustered downstream of encoded transmembrane domains, suggestive of a role in membrane protein biogenesis. Secretory and cytosolic protein-encoding mRNAs were also represented in the AEG-1 RNA interactome, with the latter category notably enriched in genes functioning in mRNA localization, translational regulation, and RNA quality control. Bioinformatic analyses of RNA binding motifs and predicted secondary structure characteristics indicate that AEG-1 lacks established RNA binding sites though shares the property of high intrinsic disorder commonly seen in RBPs. These data implicate AEG-1 in the localization and regulation of secretory and membrane protein-encoding mRNAs and provide a framework for understanding AEG-1 function in health and disease. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  13. Reciprocal exchange of minor components of type 1 and F1C fimbriae results in hybrid organelles with changed receptor specificities

    DEFF Research Database (Denmark)

    Klemm, P; Christiansen, Gunna; Kreft, B

    1994-01-01

    recognition proteins present in the organelles as minor structural elements. The organization of the fim and foc gene clusters encoding these fimbriae, as well as the structures of the organelles, are very similar, although the actual sequence homology of the structural elements is not remarkable; notably...... to epithelial cells in the collecting ducts of the human kidney as well as to cells of various cell lines. This report addresses the question of fimbrial promiscuity. Our data indicate that minor fimbrial structural elements can be exchanged between the two fimbrial systems, resulting in hybrid organelles...... with changed receptor specificity. This is the first study on reciprocal exchange of structural components from two different fimbrial systems....

  14. Organelles Contribute Differentially to Reactive Oxygen Species-Related Events during Extended Darkness1[C][W][OA

    Science.gov (United States)

    Rosenwasser, Shilo; Rot, Ilona; Sollner, Evelyn; Meyer, Andreas J.; Smith, Yoav; Leviatan, Noam; Fluhr, Robert; Friedman, Haya

    2011-01-01

    Treatment of Arabidopsis (Arabidopsis thaliana) leaves by extended darkness generates a genetically activated senescence program that culminates in cell death. The transcriptome of leaves subjected to extended darkness was found to contain a variety of reactive oxygen species (ROS)-specific signatures. The levels of transcripts constituting the transcriptome footprints of chloroplasts and cytoplasm ROS stresses decreased in leaves, as early as the second day of darkness. In contrast, an increase was detected in transcripts associated with mitochondrial and peroxisomal ROS stresses. The sequential changes in the redox state of the organelles during darkness were examined by redox-sensitive green fluorescent protein probes (roGFP) that were targeted to specific organelles. In plastids, roGFP showed a decreased level of oxidation as early as the first day of darkness, followed by a gradual increase to starting levels. However, in mitochondria, the level of oxidation of roGFP rapidly increased as early as the first day of darkness, followed by an increase in the peroxisomal level of oxidation of roGFP on the second day. No changes in the probe oxidation were observed in the cytoplasm until the third day. The increase in mitochondrial roGFP degree of oxidation was abolished by sucrose treatment, implying that oxidation is caused by energy deprivation. The dynamic redox state visualized by roGFP probes and the analysis of microarray results are consistent with a scenario in which ROS stresses emanating from the mitochondria and peroxisomes occur early during darkness at a presymptomatic stage and jointly contribute to the senescence program. PMID:21372201

  15. Organelle-Specific Triggered Release of Immunostimulatory Oligonucleotides from Intrinsically Coordinated DNA-Metal-Organic Frameworks with Soluble Exoskeleton.

    Science.gov (United States)

    Wang, Zejun; Fu, Yao; Kang, Zhengzhong; Liu, Xiaoguo; Chen, Nan; Wang, Qi; Tu, Yaoquan; Wang, Lihua; Song, Shiping; Ling, Daishun; Song, Haiyun; Kong, Xueqian; Fan, Chunhai

    2017-11-08

    DNA has proven of high utility to modulate the surface functionality of metal-organic frameworks (MOFs) for various biomedical applications. Nevertheless, current methods for preparing DNA-MOF nanoparticles rely on either inefficient covalent conjugation or specific modification of oligonucleotides. In this work, we report that unmodified oligonucleotides can be loaded on MOFs with high density (∼2500 strands/particle) via intrinsic, multivalent coordination between DNA backbone phosphate and unsaturated zirconium sites on MOFs. More significantly, surface-bound DNA can be efficiently released in either bulk solution or specific organelles in live cells when free phosphate ions are present. As a proof-of-concept for using this novel type of DNA-MOFs in immunotherapy, we prepared a construct of immunostimulatory DNA-MOFs (isMOFs) by intrinsically coordinating cytosine-phosphate-guanosine (CpG) oligonucleotides on biocompatible zirconium MOF nanoparticles, which was further armed by a protection shell of calcium phosphate (CaP) exoskeleton. We demonstrated that isMOFs exhibited high cellular uptake, organelle specificity, and spatiotemporal control of Toll-like receptors (TLR)-triggered immune responses. When isMOF reached endolysosomes via microtubule-mediated trafficking, the CaP exoskeleton dissolved in the acidic environment and in situ generated free phosphate ions. As a result, CpG was released from isMOFs and stimulated potent immunostimulation in living macrophage cells. Compared with naked CpG-MOF, isMOFs exhibited 83-fold up-regulation in stimulated secretion of cytokines. We thus expect this isMOF design with soluble CaP exoskeleton and an embedded sequential "protect-release" program provides a highly generic approach for intracellular delivery of therapeutic nucleic acids.

  16. Laser microbeam abalation of GFP-labeled nuclear organelles in a living cell.

    Science.gov (United States)

    LaMorte, Vickie J.; Krasieva, Tatiana B.; Evans, Ronald M.; Berns, Michael W.; Tromberg, Bruce J.

    1997-05-01

    Cancer, development, cellular growth and differentiation are governed by gene expression. Recent molecular and cellular advances to visualize and perturb the pathways of transcriptional regulation, nascent RNA processing, and protein trafficking at the single cell level have been developed. More recently, applications utilizing the green fluorescent marker (GFP) from Aequorea victoria have facilitated visualization of these molecular events in a living cell. Specifically, we will describe a novel approach to perturb cellular processes by labeling discrete cellular components of interest with GFP and subsequently altering/ablating them with a laser microbeam.

  17. Recent advances in the development of single cell analysis--a review.

    Science.gov (United States)

    Klepárník, Karel; Foret, František

    2013-10-24

    Development of techniques for the analysis of the content of individual cells represents an important direction in modern bioanalytical chemistry. While the analysis of chromosomes, organelles, or location of selected proteins has been traditionally the domain of microscopic techniques, the advances in miniaturized analytical systems bring new possibilities for separations and detections of molecules inside the individual cells including smaller molecules such as hormones or metabolites. It should be stressed that the field of single cell analysis is very broad, covering advanced optical, electrochemical and mass spectrometry instrumentation, sensor technology and separation techniques. The number of papers published on single cell analysis has reached several hundred in recent years. Thus a complete literature coverage is beyond the limits of a journal article. The following text provides a critical overview of some of the latest developments with the main focus on mass spectrometry, microseparation methods, electrophoresis in capillaries and microfluidic devices and respective detection techniques for performing single cell analyses. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Efficient behavior of photosynthetic organelles via Pareto optimality, identifiability, and sensitivity analysis.

    Science.gov (United States)

    Carapezza, Giovanni; Umeton, Renato; Costanza, Jole; Angione, Claudio; Stracquadanio, Giovanni; Papini, Alessio; Lió, Pietro; Nicosia, Giuseppe

    2013-05-17

    In this work, we develop methodologies for analyzing and cross comparing metabolic models. We investigate three important metabolic networks to discuss the complexity of biological organization of organisms, modeling, and system properties. In particular, we analyze these metabolic networks because of their biotechnological and basic science importance: the photosynthetic carbon metabolism in a general leaf, the Rhodobacter spheroides bacterium, and the Chlamydomonas reinhardtii alga. We adopt single- and multi-objective optimization algorithms to maximize the CO 2 uptake rate and the production of metabolites of industrial interest or for ecological purposes. We focus both on the level of genes (e.g., finding genetic manipulations to increase the production of one or more metabolites) and on finding concentration enzymes for improving the CO 2 consumption. We find that R. spheroides is able to absorb an amount of CO 2 until 57.452 mmol h (-1) gDW (-1) , while C. reinhardtii obtains a maximum of 6.7331. We report that the Pareto front analysis proves extremely useful to compare different organisms, as well as providing the possibility to investigate them with the same framework. By using the sensitivity and robustness analysis, our framework identifies the most sensitive and fragile components of the biological systems we take into account, allowing us to compare their models. We adopt the identifiability analysis to detect functional relations among enzymes; we observe that RuBisCO, GAPDH, and FBPase belong to the same functional group, as suggested also by the sensitivity analysis.

  19. Origin of Oryza sativa in China Inferred by Nucleotide Polymorphisms of Organelle DNA

    Science.gov (United States)

    Wei, Xin; Wang, Rongsheng; Cao, Lirong; Yuan, Nannan; Huang, Juan; Qiao, Weihua; Zhang, Wanxia; Zeng, Hanlai; Yang, Qingwen

    2012-01-01

    China is rich of germplasm resources of common wild rice (Oryza rufipogon Griff.) and Asian cultivated rice (O. sativa L.) which consists of two subspecies, indica and japonica. Previous studies have shown that China is one of the domestication centers of O. sativa. However, the geographic origin and the domestication times of O. sativa in China are still under debate. To settle these disputes, six chloroplast loci and four mitochondrial loci were selected to examine the relationships between 50 accessions of Asian cultivated rice and 119 accessions of common wild rice from China based on DNA sequence analysis in the present study. The results indicated that Southern China is the genetic diversity center of O. rufipogon and it might be the primary domestication region of O. sativa. Molecular dating suggested that the two subspecies had diverged 0.1 million years ago, much earlier than the beginning of rice domestication. Genetic differentiations and phylogeography analyses indicated that indica was domesticated from tropical O. rufipogon while japonica was domesticated from O. rufipogon which located in higher latitude. These results provided molecular evidences for the hypotheses of (i) Southern China is the origin center of O. sativa in China and (ii) the two subspecies of O. sativa were domesticated multiple times. PMID:23166706

  20. Assembly of Robust Bacterial Microcompartment Shells Using Building Blocks from an Organelle of Unknown Function

    Energy Technology Data Exchange (ETDEWEB)

    Lassila, JK; Bernstein, SL; Kinney, JN; Axen, SD; Kerfeld, CA

    2014-05-29

    Bacterial microconnpartnnents (BMCs) sequester enzymes from the cytoplasmic environment by encapsulation inside a selectively permeable protein shell. Bioinformatic analyses indicate that many bacteria encode BMC clusters of unknown function and with diverse combinations of shell proteins. The genome of the halophilic myxobacterium Haliangium ochraceum encodes one of the most atypical sets of shell proteins in terms of composition and primary structure. We found that microconnpartnnent shells could be purified in high yield when all seven H. ochraceum BMC shell genes were expressed from a synthetic operon in Escherichia coll. These shells differ substantially from previously isolated shell systems in that they are considerably smaller and more homogeneous, with measured diameters of 39 2 nm. The size and nearly uniform geometry allowed the development of a structural model for the shells composed of 260 hexagonal units and 13 hexagons per icosahedral face. We found that new proteins could be recruited to the shells by fusion to a predicted targeting peptide sequence, setting the stage for the use of these remarkably homogeneous shells for applications such as three-dimensional scaffolding and the construction of synthetic BMCs. Our results demonstrate the value of selecting from the diversity of BMC shell building blocks found in genomic sequence data for the construction of novel compartments. (C) 2014 Elsevier Ltd. All rights reserved.

  1. Network class superposition analyses.

    Directory of Open Access Journals (Sweden)

    Carl A B Pearson

    Full Text Available Networks are often used to understand a whole system by modeling the interactions among its pieces. Examples include biomolecules in a cell interacting to provide some primary function, or species in an environment forming a stable community. However, these interactions are often unknown; instead, the pieces' dynamic states are known, and network structure must be inferred. Because observed function may be explained by many different networks (e.g., ≈ 10(30 for the yeast cell cycle process, considering dynamics beyond this primary function means picking a single network or suitable sample: measuring over all networks exhibiting the primary function is computationally infeasible. We circumvent that obstacle by calculating the network class ensemble. We represent the ensemble by a stochastic matrix T, which is a transition-by-transition superposition of the system dynamics for each member of the class. We present concrete results for T derived from boolean time series dynamics on networks obeying the Strong Inhibition rule, by applying T to several traditional questions about network dynamics. We show that the distribution of the number of point attractors can be accurately estimated with T. We show how to generate Derrida plots based on T. We show that T-based Shannon entropy outperforms other methods at selecting experiments to further narrow the network structure. We also outline an experimental test of predictions based on T. We motivate all of these results in terms of a popular molecular biology boolean network model for the yeast cell cycle, but the methods and analyses we introduce are general. We conclude with open questions for T, for example, application to other models, computational considerations when scaling up to larger systems, and other potential analyses.

  2. Watching single molecules dance

    Science.gov (United States)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  3. Uncertainty Analyses and Strategy

    International Nuclear Information System (INIS)

    Kevin Coppersmith

    2001-01-01

    The DOE identified a variety of uncertainties, arising from different sources, during its assessment of the performance of a potential geologic repository at the Yucca Mountain site. In general, the number and detail of process models developed for the Yucca Mountain site, and the complex coupling among those models, make the direct incorporation of all uncertainties difficult. The DOE has addressed these issues in a number of ways using an approach to uncertainties that is focused on producing a defensible evaluation of the performance of a potential repository. The treatment of uncertainties oriented toward defensible assessments has led to analyses and models with so-called ''conservative'' assumptions and parameter bounds, where conservative implies lower performance than might be demonstrated with a more realistic representation. The varying maturity of the analyses and models, and uneven level of data availability, result in total system level analyses with a mix of realistic and conservative estimates (for both probabilistic representations and single values). That is, some inputs have realistically represented uncertainties, and others are conservatively estimated or bounded. However, this approach is consistent with the ''reasonable assurance'' approach to compliance demonstration, which was called for in the U.S. Nuclear Regulatory Commission's (NRC) proposed 10 CFR Part 63 regulation (64 FR 8640 [DIRS 101680]). A risk analysis that includes conservatism in the inputs will result in conservative risk estimates. Therefore, the approach taken for the Total System Performance Assessment for the Site Recommendation (TSPA-SR) provides a reasonable representation of processes and conservatism for purposes of site recommendation. However, mixing unknown degrees of conservatism in models and parameter representations reduces the transparency of the analysis and makes the development of coherent and consistent probability statements about projected repository

  4. Brachmann-Cornelia de Lange syndrome with a papilloma of the choroid plexus: analyses of molecular genetic characteristics of the patient and the tumor. A single-case study.

    Science.gov (United States)

    de León, Fernando Chico-Ponce; Gordillo-Domínguez, Luis F; González-Carranza, Vicente; Torres-García, Samuel; García-Delgado, Constanza; Sánchez-Boiso, Adriana; Arenas-Huertero, Francisco; Perezpeña-Diazconti, Mario; Eguía-Aguilar, Pilar; Baqueiro-Hernández, César; Buenrostro-Márquez, Guillermo; Martínez-Rodríguez, Sonia; Dhellemmes, Patrick; Castro-Sierra, Eduardo

    2015-01-01

    A 10-month-old girl with a Brachmann-Cornelia de Lange syndrome and a choroid plexus papilloma of the brain was studied at the Hospital Infantil de México Federico Gómez (HIMFG) in Mexico City. Presumptive papilloma of the third ventricle was evidenced on CT and MR images and removed. Pathological analysis confirmed its origin. A posterior radiosurgery was required due to a tumor relapse. Karyotypes (GTG bands) of the patient and her parents undertaken at HIMFG were normal. Array comparative genomic hybridization (array CGH) analyses of blood DNA of the patient and her parents carried out at BlueGnome's Laboratory in Cambridge, UK, set in evidence amplification of genes SPNS2, GGT6, SMTNL2, PELP1, MYBBP1A, and ALOX15 in chromosome 17p of the patient. Since MYBBP1A is a proto-oncogene and ALOX15 participates in the development of cancer and metastases of tumors, further fluorescent in situ hybridization (FISH) analyses of these two genes were implemented at HIMFG. Amplification of the two genes was found in the tumor of the case under study but not in an unrelated papilloma of the choroid plexus. Further analyses of the association of choroid plexus papillomas with disorders of psycho-neural development and its relationship to molecular genetic modifications at chromosome 17p are now under way at HIMFG.

  5. AMPHIDINIUM REVISITED. I. REDEFINITION OF AMPHIDINIUM (DINOPHYCEAE) BASED ON CLADISTIC AND MOLECULAR PHYLOGENETIC ANALYSES

    DEFF Research Database (Denmark)

    Jørgensen, Mårten Flø; Murray, Shauna; Daugbjerg, Niels

    2004-01-01

    -deflected epicones formed a monophyletic clade that included the type species. Amphidinium species with other epicone types were found to be unrelated to this clade. The type species A. operculatum was identified based on general cell shape and size, position of a dark organelle previously defined as a stigma......, and origin of the sulcus. The description of A. elegans by Grell and Wohlfarth-Bottermann was found to be identical to it. A species fitting the original description of A. operculatum was cultured and included in the analyses. Based on cladistic and molecular analyses, it grouped together with all other...

  6. Inhibitor-induced oxidation of the nucleus and cytosol in Arabidopsis thaliana: implications for organelle to nucleus retrograde signalling.

    Science.gov (United States)

    Karpinska, Barbara; Alomrani, Sarah Owdah; Foyer, Christine H

    2017-09-26

    Concepts of organelle-to-nucleus signalling pathways are largely based on genetic screens involving inhibitors of chloroplast and mitochondrial functions such as norflurazon, lincomycin (LINC), antimycin A (ANT) and salicylhydroxamic acid. These inhibitors favour enhanced cellular oxidation, but their precise effects on the cellular redox state are unknown. Using the in vivo reduction-oxidation (redox) reporter, roGFP2, inhibitor-induced changes in the glutathione redox potentials of the nuclei and cytosol were measured in Arabidopsis thaliana root, epidermal and stomatal guard cells, together with the expression of nuclear-encoded chloroplast and mitochondrial marker genes. All the chloroplast and mitochondrial inhibitors increased the degree of oxidation in the nuclei and cytosol. However, inhibitor-induced oxidation was less marked in stomatal guard cells than in epidermal or root cells. Moreover, LINC and ANT caused a greater oxidation of guard cell nuclei than the cytosol. Chloroplast and mitochondrial inhibitors significantly decreased the abundance of LHCA1 and LHCB1 transcripts. The levels of WHY1 , WHY3 and LEA5 transcripts were increased in the presence of inhibitors. Chloroplast inhibitors decreased AOXA1 mRNA levels, while mitochondrial inhibitors had the opposite effect. Inhibitors that are used to characterize retrograde signalling pathways therefore have similar general effects on cellular redox state and gene expression.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'. © 2017 The Authors.

  7. Malaria parasite cGMP-dependent protein kinase regulates blood stage merozoite secretory organelle discharge and egress.

    Directory of Open Access Journals (Sweden)

    Christine R Collins

    2013-05-01

    Full Text Available The malaria parasite replicates within an intraerythrocytic parasitophorous vacuole (PV. Eventually, in a tightly regulated process called egress, proteins of the PV and intracellular merozoite surface are modified by an essential parasite serine protease called PfSUB1, whilst the enclosing PV and erythrocyte membranes rupture, releasing merozoites to invade fresh erythrocytes. Inhibition of the Plasmodium falciparum cGMP-dependent protein kinase (PfPKG prevents egress, but the underlying mechanism is unknown. Here we show that PfPKG activity is required for PfSUB1 discharge into the PV, as well as for release of distinct merozoite organelles called micronemes. Stimulation of PfPKG by inhibiting parasite phosphodiesterase activity induces premature PfSUB1 discharge and egress of developmentally immature, non-invasive parasites. Our findings identify the signalling pathway that regulates PfSUB1 function and egress, and raise the possibility of targeting PfPKG or parasite phosphodiesterases in therapeutic approaches to dysregulate critical protease-mediated steps in the parasite life cycle.

  8. Cytoplasmic membrane is the target organelle for transition metal mediated damage induced by paraquat in Escherichia coli

    International Nuclear Information System (INIS)

    Kohen, R.; Chevion, M.

    1988-01-01

    Bacterial survival indicates that copper or iron is an essential mediator in paraquat toxicity in Escherichia coli. In this study the authors have identified the cytoplasmic membrane as a target organelle in metal-mediated paraquat toxicity and have demonstrated the complete correlation of the membrane damage with the levels of adventitious copper (or iron). The extent of membrane damage was related by use of four parameters: (a) the level of cellular ATP, (b) the level of cellular potassium, (c) the cellular capacity to accumulate and retain radiolabeled leucine, and (d) the cellular integrity as reflected by transmission electron microscopy (TEM). Exposure of bacterial cells to a combination of paraquat and copper caused a marked decline in parameters a, b, and c. This decline was found to occur in parallel with, or even to precede, the sharp loss of survival of E. coli under the same conditions. Likewise, TEM micrographs clearly indicated alternations in cellular structure that possibly reflect sites of detachment of the cytoplasmic membrane from the bacterial capsule. In contradistinction, copper alone or paraquat alone could not bring about similar changes in cellular structure. These findings are in accord with the suggested site-specific metal-mediated Haber-Weiss mechanism for paraquat toxicity and support our notion that specific chelators of transition metals could reduce or prevent the biological deleterious effects of this herbicide

  9. How to get more from less. Comments on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

    Science.gov (United States)

    Sachs, Frederick; Flomenbom, Ophir

    2015-06-01

    Measuring individual entities at room temperature has become routine due to improvements in technology. We can study ion channels (since the 70s), quantum dots (since the 80s), and receptors, molecular engines and enzymes (since the 90s). The inherent nature of these small systems is that the standard deviation of the measurement is comparable to the mean - the definition of a small system [1]. Individual probes are detected, measured, and the trajectories are then analyzed to extract the mean properties of the system. The review [2] provides links to many examples of single molecule studies, mostly those using optical probes.

  10. Head-neck domain of Arabidopsis myosin XI, MYA2, fused with GFP produces F-actin patterns that coincide with fast organelle streaming in different plant cells

    Directory of Open Access Journals (Sweden)

    Holweg Carola L

    2008-07-01

    Full Text Available Abstract Background The cytoskeletal mechanisms that underlie organelle transport in plants are intimately linked to acto-myosin function. This function is mediated by the attachment of myosin heads to F-actin and the binding of cargo to the tails. Acto-myosin also powers vigorous cytoplasmic streaming in plant cells. Class XI myosins exhibit strikingly fast velocities and may have extraordinary roles in cellular motility. Studies of the structural basis of organelle transport have focused on the cargo-binding tails of myosin XI, revealing a close relationship with the transport of peroxisomes, mitochondria, and Golgi-vesicles. Links between myosin heads and F-actin-based motility have been less investigated. To address this function, we performed localization studies using the head-neck domain of AtMYA2, a myosin XI from Arabidopsis. Results We expressed the GFP-fused head-neck domain of MYA2 in epidermal cells of various plant species and found that it associated with F-actin. By comparison to other markers such as fimbrin and talin, we revealed that the myosin-labeled F-actin was of a lower quality and absent from the fine microfilament arrays at the cell cortex. However, it colocalized with cytoplasmic (transvacuolar F-actin in areas coinciding with the tracks of fast organelles. This observation correlates well with the proposed function of myosin XI in organelle trafficking. The fact that organelle streaming was reduced in cells expressing the GFP-MYA2-head6IQ indicated that the functionless motor protein inhibits endogenous myosins. Furthermore, co-expression of the GFP-MYA2-head6IQ with other F-actin markers disrupted its attachment to F-actin. In nuclei, the GFP-myosin associated with short bundles of F-actin. Conclusion The localization of the head of MYA2 in living plant cells, as investigated here for the first time, suggests a close linkage between this myosin XI and cytoplasmic microfilaments that support the rapid streaming of

  11. Effects of post-Kyoto policy on the Swiss national economy - Analysis using a single-country equilibrium model; Volkswirtschaftliche Auswirkungen der Schweizer Post-Kyoto-Politik - Analyse mit einem dynamischen Gleichgewichtsmodell fuer die Schweiz

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2009-08-15

    This final report elaborated for the Swiss Federal Office for the Environment (FOEN) deals with questions concerning Swiss climate policy after 2012. In 2012, existing climate legislation as defined in CO{sub 2} emission legislation is to be revised and brought in line with European legislation on greenhouse gases. The paper presents and discusses the proposals of the Swiss government that are to make Switzerland climate-neutral. These questions include how high a steering-tax must be in order to provide a 20% reduction in CO{sub 2} emissions, which effects on the economy in general (BIP) and on particular sectors are to be expected, how households will be affected and how large the positive secondary side-effects are. The methods used in the study and their limitations are examined. In particular, a dynamic, single-country equilibrium model is introduced and various scenarios are discussed

  12. Efficacy and tolerability of a single-pill combination of telmisartan 80 mg and hydrochlorothiazide 25 mg according to age, gender, race, hypertension severity, and previous antihypertensive use: planned analyses of a randomized trial

    Directory of Open Access Journals (Sweden)

    Zhu D

    2013-04-01

    Full Text Available Dingliang Zhu,1 Harold Bays,2 Pingjin Gao,1 Michaela Mattheus,3 Birgit Voelker,3 Luis M Ruilope4 1Shanghai Ruijin Hospital, Shanghai, People’s Republic of China; 2Louisville Metabolic and Atherosclerosis Research Center Inc, Louisville, KY, USA; 3Boehringer Ingelheim International GmbH, Ingelheim, Germany; 4Hospital 12 de Octubre, Madrid, Spain Background: The purpose of this work was to describe the efficacy and safety of a telmisartan 80 mg + hydrochlorothiazide 25 mg (T80/H25 single-pill combination therapy in patients with moderate-severe hypertension (mean seated trough cuff systolic blood pressure [BP] ≥ 160 mmHg and diastolic BP ≥ 100 mmHg in specific patient subpopulations. Methods: This was a planned analysis of a double-blind, multicenter, parallel-group trial that demonstrated the superiority of a single-pill combination of T80/H25 versus T80 monotherapy in terms of systolic BP change from baseline to week 7. Subpopulations included older (aged ≥ 65 years versus younger, gender, race, hypertension severity, and prior antihypertensive therapy. Endpoints were change from baseline in mean seated trough cuff systolic and diastolic BP, proportion of patients achieving their BP goal (systolic/diastolic BP 30 mmHg and >40 mmHg. Results: Across all subgroups, the T80/H25 single-pill combination provided consistently greater systolic and diastolic BP reductions than T80 and more patients had systolic BP reductions of >30 mmHg. In the T80 and T80/H25 groups, BP control was achieved in 34.1% and 48.8% of men, 35.5% and 62.7% of women, 34.5% and 56.6% of Asians, 22.6% and 38.6% of blacks, 36.7% and 57.8% of whites, 36.9% and 57.5% of patients < 65 years, 29.3% and 49.3% ≥65 years, 44.2% and 66.2% of those with grade 2 hypertension, 20.4% and 39.4% of those with grade 3 hypertension, 38.9% and 53.2% of previously untreated patients, 38.1% and 62.5% of patients previously treated with one antihypertensive, and 29.7% and 48.9% of patients

  13. Transformations of membrane-bound organelles in sec 14 mutants of the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica.

    Science.gov (United States)

    Rambourg, A; Clermont, Y; Nicaud, J M; Gaillardin, C; Kepes, F

    1996-07-01

    In early descriptions of ultrastructural alterations of secretory (sec) mutants of the yeast Saccharomyces cerevisiae, two mutants, sec7 and sec14, were shown to produce cell structures, the so-called Berkeley bodies thought at first to correspond to Golgi structures. In sec7 mutants grown at restrictive temperature, secretion granules soon dis-appeared, whereas networks of Golgi tubules increased in size and transformed into stacks of seven to eight flattened elements. At these time intervals, structures resembling Berkeley bodies appeared to be extensions of the endoplasmic reticulum (Rambourg et al., 1993). It is the purpose of the present study to examine by electron microscopy S. cerevisiae sec14 mutants and to compare the modifications along their secretory pathway with those occurring in a homologous mutant of Yarrowia lipolytica. S. cerevisiae sec 14 mutant cells coming from exponentially growing cultures were examined either at 24 degrees C or after shifting at 37 degrees C for 0, 2, 5, 10, 15, 20, 30, 45, 60, 90, and 120 min. Y. lipolytica mutant cells were first cultured in YNB in 5000 medium and then transferred for 0, 6, 8, 12, 20, and 24 hr, in a phosphate-buffered YPD medium, which allows wild cells to differentiate from yeast to mycelian form. In both cases, cells were fixed in 2% glutaraldehyde, treated for 15 min in 1% sodium metaperiodate, post-fixed in reduced osmium, and embedded in Epon. To visualize the three-dimensional configuration of cell organelles, stereopairs were prepared from section stained with lead citrate and tilted at +/- 15 degrees from the 0 degree position of the goniometric stage of the electron microscope. In S. cerevisiae mutant cells shifted for 2 min at the restrictive temperature, faintly stained networks of thin anastomosed tubules were located at close proximity and often continuous with faintly stained ER cisternae. More intensely stained tubular networks with nodular dilations having the size of secretion granules

  14. Interplay between Two Bacterial Actin Homologs, MamK and MamK-Like, Is Required for the Alignment of Magnetosome Organelles in Magnetospirillum magneticum AMB-1

    OpenAIRE

    Abreu, Nicole; Mannoubi, Soumaya; Ozyamak, Ertan; Pignol, David; Ginet, Nicolas; Komeili, Arash

    2014-01-01

    Many bacterial species contain multiple actin-like proteins tasked with the execution of crucial cell biological functions. MamK, an actin-like protein found in magnetotactic bacteria, is important in organizing magnetosome organelles into chains that are used for navigation along geomagnetic fields. MamK and numerous other magnetosome formation factors are encoded by a genetic island termed the magnetosome island. Unlike most magnetotactic bacteria, Magnetospirillum magneticum AMB-1 (AMB-1) ...

  15. Graphene nanoplatelets spontaneously translocate into the cytosol and physically interact with cellular organelles in the fish cell line PLHC-1

    Energy Technology Data Exchange (ETDEWEB)

    Lammel, Tobias; Navas, José M., E-mail: jmnavas@inia.es

    2014-05-01

    Highlights: • We assessed the cytotoxicity and uptake of graphene nanomaterials in PLHC-1 cells. • GO and CXYG nanoplatelets caused physical injury of the plasma membrane. • GO and CXYG accumulated in the cytosol and interacted with cellular organelles. • PLHC-1 cells exposed to GO/CXYG demonstrated high ROS levels but low cytotoxicity. • ROS formation was related with GO/CXYG-induced structural damage of mitochondria. - Abstract: Graphene and graphene derivatives constitute a novel class of carbon-based nanomaterials being increasingly produced and used in technical and consumer applications. Release of graphene nanoplatelets during the life cycle of these applications may result in human and environmental exposure calling for assessment of their potential to cause harm to humans and wildlife. This study aimed to assess the toxicity of graphene oxide (GO) and carboxyl graphene (CXYG) nanoplatelets to non-mammalian species using the fish cell line PLHC-1 as in vitro model. The cytotoxicity of GO and CXYG was assessed using different assays measuring alterations in plasma membrane integrity, metabolic activity, and lysosomal and mitochondrial function. The induction of oxidative stress was assessed by measuring intracellular reactive oxygen species (ROS) levels. Interaction with the plasma membrane and internalization of nanoplatelets were investigated by electron microscopy. Graphene nanoplatelets spontaneously penetrated through the plasma membrane and accumulated in the cytosol, where they further interacted with mitochondrial and nuclear membranes. PLHC-1 cells demonstrated significantly reduced mitochondrial membrane potential (MMP) and increased ROS levels at 16 μg/ml GO and CXYG (72 h), but barely any decrease in cell viability. The observation of intracellular graphene accumulations not enclosed by membranes suggests that GO and CXYG internalization in fish hepatoma cells occurs through an endocytosis-independent mechanism.

  16. Mitofusin 2-containing Mitochondrial-Reticular Microdomains Direct Rapid Cardiomyocyte Bioenergetic Responses via Inter-Organelle Ca2+ Crosstalk

    Science.gov (United States)

    Chen, Yun; Csordás, György; Jowdy, Casey; Schneider, Timothy G.; Csordás, Norbert; Wang, Wei; Liu, Yingqiu; Kohlhaas, Michael; Meiser, Maxie; Bergem, Stefanie; Nerbonne, Jeanne M.; Dorn, Gerald W.; Maack, Christoph

    2012-01-01

    Rationale Mitochondrial Ca2+ uptake is essential for the bioenergetic feedback response through stimulation of Krebs cycle dehydrogenases. Close association of mitochondria to the sarcoplasmic reticulum (SR) may explain efficient mitochondrial Ca2+ uptake despite low Ca2+ affinity of the mitochondrial Ca2+ uniporter. However, the existence of such mitochondrial Ca2+ microdomains and their functional role are presently unresolved. Mitofusin (Mfn) 1 and 2 mediate mitochondrial outer membrane fusion, while Mfn2, but not Mfn1, tethers endoplasmic reticulum to mitochondria in non-cardiac cells. Objective To elucidate roles for Mfn1 and 2 in SR-mitochondrial tethering, Ca2+ signaling and bioenergetic regulation in cardiac myocytes. Methods and Results Fruit fly heart tubes deficient of the Drosophila Mfn ortholog, MARF, had increased contraction-associated and caffeine-sensitive Ca2+ release, suggesting a role for Mfn in SR Ca2+ handling. While cardiac-specific Mfn1 ablation had no effects on murine heart function or Ca2+ cycling, Mfn2 deficiency decreased cardiomyocyte SR-mitochondrial contact length by 30% and reduced the content of SR-associated proteins in mitochondria-associated membranes. This was associated with decreased mitochondrial Ca2+ uptake (despite unchanged mitochondrial membrane potential) but increased steady-state and caffeine-induced SR Ca2+ release. Accordingly, Ca2+-induced stimulation of Krebs cycle dehydrogenases during β-adrenergic stimulation was hampered in Mfn2-, but not Mfn1-KO myocytes, evidenced by oxidation of the redox states of NAD(P)H/NAD(P)+ and FADH2/FAD. Conclusions Physical tethering of SR and mitochondria via Mfn2 is essential for normal inter-organelle Ca2+ signaling in the myocardium, consistent with a requirement for SR-mitochondrial Ca2+ signaling through microdomains in the cardiomyocyte bioenergetic feedback response to physiological stress. PMID:22777004

  17. Bioanalysis of eukaryotic organelles

    Czech Academy of Sciences Publication Activity Database

    Satori, Ch. P.; Henderson, M. M.; Krautkramer, E. A.; Košťál, Vratislav; Distefano, M. M.; Arriaga, E. A.

    2013-01-01

    Roč. 113, č. 4 (2013), s. 2733-2811 ISSN 0009-2665 R&D Projects: GA ČR(CZ) GBP206/12/G014 Grant - others:GA AV ČR(CZ) M200311201 Institutional support: RVO:68081715 Keywords : green fluorescent protein * atomic-force microscopy * capillary electrophoretic analysis Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 45.661, year: 2013

  18. Clinical significance of previously cryptic copy number alterations and loss of heterozygosity in pediatric acute myeloid leukemia and myelodysplastic syndrome determined using combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray analyses.

    Science.gov (United States)

    Koh, Kyung-Nam; Lee, Jin Ok; Seo, Eul Ju; Lee, Seong Wook; Suh, Jin Kyung; Im, Ho Joon; Seo, Jong Jin

    2014-07-01

    The combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray (CGH+SNP microarray) platform can simultaneously detect copy number alterations (CNA) and copy-neutral loss of heterozygosity (LOH). Eighteen children with acute myeloid leukemia (AML) (n=15) or myelodysplastic syndrome (MDS) (n=3) were studied using CGH+SNP microarray to evaluate the clinical significance of submicroscopic chromosomal aberrations. CGH+SNP microarray revealed CNAs at 14 regions in 9 patients, while metaphase cytogenetic (MC) analysis detected CNAs in 11 regions in 8 patients. Using CGH+SNP microarray, LOHs>10 Mb involving terminal regions or the whole chromosome were detected in 3 of 18 patients (17%). CGH+SNP microarray revealed cryptic LOHs with or without CNAs in 3 of 5 patients with normal karyotypes. CGH+SNP microarray detected additional cryptic CNAs (n=2) and LOHs (n=5) in 6 of 13 patients with abnormal MC. In total, 9 patients demonstrated additional aberrations, including CNAs (n=3) and/or LOHs (n=8). Three of 15 patients with AML and terminal LOH>10 Mb demonstrated a significantly inferior relapse-free survival rate (P=0.041). This study demonstrates that CGH+SNP microarray can simultaneously detect previously cryptic CNAs and LOH, which may demonstrate prognostic implications.

  19. Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer.

    Science.gov (United States)

    Disciglio, Vittoria; Devecchi, Andrea; Palumbo, Orazio; Carella, Massimo; Penso, Donata; Milione, Massimo; Valle, Giorgio; Pierotti, Marco Alessandro; Vitellaro, Marco; Bertario, Lucio; Canevari, Silvana; Signoroni, Stefano; De Cecco, Loris

    2016-06-07

    Androgen insensitivity syndrome (AIS), a disorder of sexual development in 46, XY individuals, is caused by loss-of-function mutations in the androgen receptor (AR) gene. A variety of tumors have been reported in association with AIS, but no cases with colorectal cancer (CRC) have been described. Here, we present a male patient with AIS who developed multiple early-onset CRCs and his pedigree. His first cousin was diagnosed with AIS and harbored the same AR gene mutation, but with no signs of CRC. The difference in clinical management for the two patients was that testosterone treatment was given to the proband for a much longer time compared with the cousin. The CRC family history was negative, and no germline mutations in well-known CRC-related genes were identified. A single nucleotide polymorphism array revealed a microduplication on chromosome 22q11.22 that encompassed a microRNA potentially related to CRC pathogenesis. In the proband, whole exome sequencing identified a polymorphism in an oncogene and 13 rare loss-of-function variants, of which two were in CRC-related genes and four were in genes associated with other human cancers. By pathway analysis, all inherited germline genetic events were connected in a unique network whose alteration in the proband, together with continuous testosterone stimulation, may have played a role in CRC pathogenesis.

  20. Historical and Current Perspectives on the Systematics of the 'Enigmatic' Diatom Genus Rhoicosphenia (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of 'Monoraphid' Diatoms.

    Science.gov (United States)

    Thomas, Evan W; Stepanek, Joshua G; Kociolek, J Patrick

    2016-01-01

    This study seeks to determine the phylogenetic position of the diatom genus Rhoicosphenia. Currently, four hypotheses based on the morphology of the siliceous valve and its various ultrastructural components, sexual reproduction, and chloroplasts have been proposed. Two previous morphological studies have tentatively placed Rhoicosphenia near members of the Achnanthidiaceae and Gomphonemataceae, and no molecular studies have been completed. The position of Rhoicosphenia as sister to 'monoraphid' diatoms is problematic due to the apparent non-monophyly of that group, so hypotheses of 'monoraphid' monophyly are also tested. Using an analysis of morphological and cytological features, as well as sequences from three genes, SSU, LSU, and rbcL, recovered from several freshwater Rhoicosphenia populations that have similar morphology to Rhoicosphenia abbreviata (Agardh) Lange-Bertalot, we have analyzed the phylogenetic position of Rhoicosphenia in the context of raphid diatoms. Further, we have used topology testing to determine the statistical likelihoods of these relationships. The hypothesis that Rhoicosphenia is a member of the Achnanthidiaceae cannot be rejected, while the hypothesis that it is a member of the Gomphonemataceae can be rejected. In our analyses, members of the Achnanthidiaceae are basal to Rhoicosphenia, and Rhoicosphenia is basal to the Cymbellales, or a basal member of the Cymbellales, which includes the Gomphonemataceae. Hypothesis testing rejects the monophyly of 'monoraphid' diatoms.

  1. Historical and Current Perspectives on the Systematics of the ‘Enigmatic’ Diatom Genus Rhoicosphenia (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of ‘Monoraphid’ Diatoms

    Science.gov (United States)

    Thomas, Evan W.; Stepanek, Joshua G.; Kociolek, J. Patrick

    2016-01-01

    This study seeks to determine the phylogenetic position of the diatom genus Rhoicosphenia. Currently, four hypotheses based on the morphology of the siliceous valve and its various ultrastructural components, sexual reproduction, and chloroplasts have been proposed. Two previous morphological studies have tentatively placed Rhoicosphenia near members of the Achnanthidiaceae and Gomphonemataceae, and no molecular studies have been completed. The position of Rhoicosphenia as sister to ‘monoraphid’ diatoms is problematic due to the apparent non-monophyly of that group, so hypotheses of ‘monoraphid’ monophyly are also tested. Using an analysis of morphological and cytological features, as well as sequences from three genes, SSU, LSU, and rbcL, recovered from several freshwater Rhoicosphenia populations that have similar morphology to Rhoicosphenia abbreviata (Agardh) Lange-Bertalot, we have analyzed the phylogenetic position of Rhoicosphenia in the context of raphid diatoms. Further, we have used topology testing to determine the statistical likelihoods of these relationships. The hypothesis that Rhoicosphenia is a member of the Achnanthidiaceae cannot be rejected, while the hypothesis that it is a member of the Gomphonemataceae can be rejected. In our analyses, members of the Achnanthidiaceae are basal to Rhoicosphenia, and Rhoicosphenia is basal to the Cymbellales, or a basal member of the Cymbellales, which includes the Gomphonemataceae. Hypothesis testing rejects the monophyly of ‘monoraphid’ diatoms. PMID:27045763

  2. Analytical Bias Exceeding Desirable Quality Goal in 4 out of 5 Common Immunoassays: Results of a Native Single Serum Sample External Quality Assessment Program for Cobalamin, Folate, Ferritin, Thyroid-Stimulating Hormone, and Free T4 Analyses.

    Science.gov (United States)

    Kristensen, Gunn B B; Rustad, Pål; Berg, Jens P; Aakre, Kristin M

    2016-09-01

    We undertook this study to evaluate method differences for 5 components analyzed by immunoassays, to explore whether the use of method-dependent reference intervals may compensate for method differences, and to investigate commutability of external quality assessment (EQA) materials. Twenty fresh native single serum samples, a fresh native serum pool, Nordic Federation of Clinical Chemistry Reference Serum X (serum X) (serum pool), and 2 EQA materials were sent to 38 laboratories for measurement of cobalamin, folate, ferritin, free T4, and thyroid-stimulating hormone (TSH) by 5 different measurement procedures [Roche Cobas (n = 15), Roche Modular (n = 4), Abbott Architect (n = 8), Beckman Coulter Unicel (n = 2), and Siemens ADVIA Centaur (n = 9)]. The target value for each component was calculated based on the mean of method means or measured by a reference measurement procedure (free T4). Quality specifications were based on biological variation. Local reference intervals were reported from all laboratories. Method differences that exceeded acceptable bias were found for all components except folate. Free T4 differences from the uncommonly used reference measurement procedure were large. Reference intervals differed between measurement procedures but also within 1 measurement procedure. The serum X material was commutable for all components and measurement procedures, whereas the EQA materials were noncommutable in 13 of 50 occasions (5 components, 5 methods, 2 EQA materials). The bias between the measurement procedures was unacceptably large in 4/5 tested components. Traceability to reference materials as claimed by the manufacturers did not lead to acceptable harmonization. Adjustment of reference intervals in accordance with method differences and use of commutable EQA samples are not implemented commonly. © 2016 American Association for Clinical Chemistry.

  3. Quantitative Imaging of Single, Unstained Viruses with Coherent X Rays

    International Nuclear Information System (INIS)

    Song Changyong; Jiang Huaidong; Mancuso, Adrian; Amirbekian, Bagrat; Miao Jianwei; Peng Li; Sun Ren; Shah, Sanket S.; Zhou, Z. Hong; Ishikawa, Tetsuya

    2008-01-01

    We report the recording and reconstruction of x-ray diffraction patterns from single, unstained viruses, for the first time. By separating the diffraction pattern of the virus particles from that of their surroundings, we performed quantitative and high-contrast imaging of a single virion. The structure of the viral capsid inside a virion was visualized. This work opens the door for quantitative x-ray imaging of a broad range of specimens from protein machineries and viruses to cellular organelles. Moreover, our experiment is directly transferable to the use of x-ray free electron lasers, and represents an experimental milestone towards the x-ray imaging of large protein complexes

  4. Responsive hetero-organelle partition conferred fluorogenic sensing of mitochondrial depolarization† †Electronic supplementary information (ESI) available: Biodistribution of RC; cytotoxicity of RC-TPP; and analysis spectra of RC-TPP and RC. See DOI: 10.1039/c6sc04158b Click here for additional data file.

    Science.gov (United States)

    Xue, Zhongwei; Zhao, Hu; Liu, Jian; Han, Jiahuai

    2017-01-01

    Malfunctioning organelles are often difficult to probe with classical organelle-homing sensors owing to disruption of physiological organelle-probe affinity. We herein report the use of a responsive hetero-organelle partition and signal activable probe (RC-TPP) for detecting mitochondrial depolarization, a pathologically relevant event featuring loss of the electrical potentials across the mitochondrial membrane (ΔΨ m). Partitioned in mitochondria to give blue fluorescence, RC-TPP relocates into lysosomes upon mitochondrial depolarization and exhibits red fluorescence triggered by lysosomal acidity, enabling determination of autophagy relevant mitochondrial depolarization and the chronological sequence of mitochondrial depolarization and lysosomal neutralization in distinct cell death signalling pathways. As an alternative to classic homo-organelle specific molecular systems, this hetero-organelle responsive approach provides a new perspective from which to study dysfunctional organelles. PMID:28451305

  5. The enteropathogenic Escherichia coli (EPEC) Map effector is imported into the mitochondrial matrix by the TOM/Hsp70 system and alters organelle morphology.

    Science.gov (United States)

    Papatheodorou, Panagiotis; Domańska, Grazyna; Oxle, Marius; Mathieu, Johannes; Selchow, Olaf; Kenny, Brendan; Rassow, Joachim

    2006-04-01

    Enteropathogenic Escherichia coli (EPEC) is a human intestinal pathogen and a major cause of diarrhoea, particularly among infants in developing countries. EPEC target the Map and EspF multifunctional effector proteins to host mitochondria - organelles that play crucial roles in regulating cellular processes such as programmed cell death (apoptosis). While both molecules interfere with the organelles ability to maintain a membrane potential, EspF plays the predominant role and is responsible for triggering cell death. To learn more about the Map-mitochondria interaction, we studied Map localization to mitochondria with purified mitochondria (from mammalian and yeast cells) and within intact yeast. This revealed that (i) Map targeting is dependent on the predicted N-terminal mitochondrial targeting sequence, (ii) the N-terminal 44 residues are sufficient to target proteins to mitochondria and (iii) Map import involves the mitochondrial outer membrane translocase (Tom22 and Tom40), the mitochondrial membrane potential, and the matrix chaperone, mtHsp70. These results are consistent with Map import into the mitochondria matrix via the classical import mechanism. As all known, Map-associated phenotypes in mammalian cells are independent of mitochondrial targeting, this may indicate that import serves as a mechanism to remove Map from the cytoplasm thereby regulating cytoplasmic function. Intriguingly, Map, but not EspF, alters mitochondrial morphology with deletion analysis revealing important roles for residues 101-152. Changes in mitochondrial morphology have been linked to alterations in the ability of these organelles to regulate cellular processes providing a possible additional role for Map import into mitochondria.

  6. Using FRAP or FRAPA to Visualize the Movement of Fluorescently Labeled Proteins or Cellular Organelles in Live Cultured Neurons Transformed with Adeno-Associated Viruses.

    Science.gov (United States)

    Tevet, Yaara; Gitler, Daniel

    2016-01-01

    Fluorescence recovery after photobleaching (FRAP) and fluorescence redistribution after photoactivation (FRAPA) are complementary methods used to gauge the movement of proteins or sub-resolution organelles within cells. Using these methods we can determine the nature of the movement of labeled particles, whether it is random, constrained, or active, the coefficient of diffusion if applicable, binding and unbinding constants, and the direction of active transport. These two techniques have been extensively utilized to probe the cell biology of neurons. A practical outline of FRAP and FRAPA in cultured neurons is presented, including the preparation of the neurons and their infection with adeno-associated viral vectors. Considerations in planning such experiments are provided.

  7. Periodic safety analyses

    International Nuclear Information System (INIS)

    Gouffon, A.; Zermizoglou, R.

    1990-12-01

    The IAEA Safety Guide 50-SG-S8 devoted to 'Safety Aspects of Foundations of Nuclear Power Plants' indicates that operator of a NPP should establish a program for inspection of safe operation during construction, start-up and service life of the plant for obtaining data needed for estimating the life time of structures and components. At the same time the program should ensure that the safety margins are appropriate. Periodic safety analysis are an important part of the safety inspection program. Periodic safety reports is a method for testing the whole system or a part of the safety system following the precise criteria. Periodic safety analyses are not meant for qualification of the plant components. Separate analyses are devoted to: start-up, qualification of components and materials, and aging. All these analyses are described in this presentation. The last chapter describes the experience obtained for PWR-900 and PWR-1300 units from 1986-1989

  8. Laser Beam Focus Analyser

    DEFF Research Database (Denmark)

    Nielsen, Peter Carøe; Hansen, Hans Nørgaard; Olsen, Flemming Ove

    2007-01-01

    the obtainable features in direct laser machining as well as heat affected zones in welding processes. This paper describes the development of a measuring unit capable of analysing beam shape and diameter of lasers to be used in manufacturing processes. The analyser is based on the principle of a rotating...... mechanical wire being swept through the laser beam at varying Z-heights. The reflected signal is analysed and the resulting beam profile determined. The development comprised the design of a flexible fixture capable of providing both rotation and Z-axis movement, control software including data capture...... and finally data analysis based on the ISO approach. The device was calibrated and tested on commercially available laser systems. It showed good reproducibility. It was the target to be able to measure CW lasers with a power up to 200 W, focused down to spot diameters in the range of 10µm. In order...

  9. Contesting Citizenship: Comparative Analyses

    DEFF Research Database (Denmark)

    Siim, Birte; Squires, Judith

    2007-01-01

    importance of particularized experiences and multiple ineequality agendas). These developments shape the way citizenship is both practiced and analysed. Mapping neat citizenship modles onto distinct nation-states and evaluating these in relation to formal equality is no longer an adequate approach....... Comparative citizenship analyses need to be considered in relation to multipleinequalities and their intersections and to multiple governance and trans-national organisinf. This, in turn, suggests that comparative citizenship analysis needs to consider new spaces in which struggles for equal citizenship occur...

  10. Dialogisk kommunikationsteoretisk analyse

    DEFF Research Database (Denmark)

    Phillips, Louise Jane

    2018-01-01

    analysemetode, der er blevet udviklet inden for dialogisk kommunikationsforskning - The Integrated Framework for Analysing Dialogic Knowledge Production and Communication (IFADIA). IFADIA-metoden bygger på en kombination af Bakhtins dialogteori og Foucaults teori om magt/viden og diskurs. Metoden er beregnet...

  11. Probabilistic safety analyses (PSA)

    International Nuclear Information System (INIS)

    1997-01-01

    The guide shows how the probabilistic safety analyses (PSA) are used in the design, construction and operation of light water reactor plants in order for their part to ensure that the safety of the plant is good enough in all plant operational states

  12. Meta-analyses

    NARCIS (Netherlands)

    Hendriks, Maria A.; Luyten, Johannes W.; Scheerens, Jaap; Sleegers, P.J.C.; Scheerens, J

    2014-01-01

    In this chapter results of a research synthesis and quantitative meta-analyses of three facets of time effects in education are presented, namely time at school during regular lesson hours, homework, and extended learning time. The number of studies for these three facets of time that could be used

  13. Analysing Access Control Specifications

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, René Rydhof

    2009-01-01

    . Recent events have revealed intimate knowledge of surveillance and control systems on the side of the attacker, making it often impossible to deduce the identity of an inside attacker from logged data. In this work we present an approach that analyses the access control configuration to identify the set...

  14. Wavelet Analyses and Applications

    Science.gov (United States)

    Bordeianu, Cristian C.; Landau, Rubin H.; Paez, Manuel J.

    2009-01-01

    It is shown how a modern extension of Fourier analysis known as wavelet analysis is applied to signals containing multiscale information. First, a continuous wavelet transform is used to analyse the spectrum of a nonstationary signal (one whose form changes in time). The spectral analysis of such a signal gives the strength of the signal in each…

  15. Filmstil - teori og analyse

    DEFF Research Database (Denmark)

    Hansen, Lennard Højbjerg

    Filmstil påvirker på afgørende vis vores oplevelse af film. Men filmstil, måden, de levende billeder organiserer fortællingen på fylder noget mindre end filmens handling, når vi taler om film. Filmstil - teori og analyse er en rigt eksemplificeret præsentation, kritik og videreudvikling af...

  16. Risico-analyse brandstofpontons

    NARCIS (Netherlands)

    Uijt de Haag P; Post J; LSO

    2001-01-01

    Voor het bepalen van de risico's van brandstofpontons in een jachthaven is een generieke risico-analyse uitgevoerd. Er is een referentiesysteem gedefinieerd, bestaande uit een betonnen brandstofponton met een relatief grote inhoud en doorzet. Aangenomen is dat de ponton gelegen is in een

  17. Phenol homeostasis is ensured in vanilla fruit by storage under solid form in a new chloroplast-derived organelle, the phenyloplast.

    Science.gov (United States)

    Brillouet, Jean-Marc; Verdeil, Jean-Luc; Odoux, Eric; Lartaud, Marc; Grisoni, Michel; Conéjéro, Geneviève

    2014-06-01

    A multiple cell imaging approach combining immunofluorescence by confocal microscopy, fluorescence spectral analysis by multiphotonic microscopy, and transmission electron microscopy identified the site of accumulation of 4-O-(3-methoxybenzaldehyde) β-d-glucoside, a phenol glucoside massively stockpiled by vanilla fruit. The glucoside is sufficiently abundant to be detected by spectral analysis of its autofluorescence. The convergent results obtained by these different techniques demonstrated that the phenol glucoside accumulates in the inner volume of redifferentiating chloroplasts as solid amorphous deposits, thus ensuring phenylglucoside cell homeostasis. Redifferentiation starts with the generation of loculi between thylakoid membranes which are progressively filled with the glucoside until a fully matured organelle is obtained. This peculiar mode of storage of a phenolic secondary metabolite is suspected to occur in other plants and its generalization in the Plantae could be considered. This new chloroplast-derived organelle is referred to as a 'phenyloplast'. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  18. Recent Trends on Micro/Nanofluidic Single Cell Electroporation

    Directory of Open Access Journals (Sweden)

    Tuhin Subhra Santra

    2013-09-01

    Full Text Available The behaviors of cell to cell or cell to environment with their organelles and their intracellular physical or biochemical effects are still not fully understood. Analyzing millions of cells together cannot provide detailed information, such as cell proliferation, differentiation or different responses to external stimuli and intracellular reaction. Thus, single cell level research is becoming a pioneering research area that unveils the interaction details in high temporal and spatial resolution among cells. To analyze the cellular function, single cell electroporation can be conducted by employing a miniaturized device, whose dimension should be similar to that of a single cell. Micro/nanofluidic devices can fulfill this requirement for single cell electroporation. This device is not only useful for cell lysis, cell to cell fusion or separation, insertion of drug, DNA and antibodies inside single cell, but also it can control biochemical, electrical and mechanical parameters using electroporation technique. This device provides better performance such as high transfection efficiency, high cell viability, lower Joule heating effect, less sample contamination, lower toxicity during electroporation experiment when compared to bulk electroporation process. In addition, single organelles within a cell can be analyzed selectively by reducing the electrode size and gap at nanoscale level. This advanced technique can deliver (in/out biomolecules precisely through a small membrane area (micro to nanoscale area of the single cell, known as localized single cell membrane electroporation (LSCMEP. These articles emphasize the recent progress in micro/nanofluidic single cell electroporation, which is potentially beneficial for high-efficient therapeutic and delivery applications or understanding cell to cell interaction.

  19. Biomass feedstock analyses

    Energy Technology Data Exchange (ETDEWEB)

    Wilen, C.; Moilanen, A.; Kurkela, E. [VTT Energy, Espoo (Finland). Energy Production Technologies

    1996-12-31

    The overall objectives of the project `Feasibility of electricity production from biomass by pressurized gasification systems` within the EC Research Programme JOULE II were to evaluate the potential of advanced power production systems based on biomass gasification and to study the technical and economic feasibility of these new processes with different type of biomass feed stocks. This report was prepared as part of this R and D project. The objectives of this task were to perform fuel analyses of potential woody and herbaceous biomasses with specific regard to the gasification properties of the selected feed stocks. The analyses of 15 Scandinavian and European biomass feed stock included density, proximate and ultimate analyses, trace compounds, ash composition and fusion behaviour in oxidizing and reducing atmospheres. The wood-derived fuels, such as whole-tree chips, forest residues, bark and to some extent willow, can be expected to have good gasification properties. Difficulties caused by ash fusion and sintering in straw combustion and gasification are generally known. The ash and alkali metal contents of the European biomasses harvested in Italy resembled those of the Nordic straws, and it is expected that they behave to a great extent as straw in gasification. Any direct relation between the ash fusion behavior (determined according to the standard method) and, for instance, the alkali metal content was not found in the laboratory determinations. A more profound characterisation of the fuels would require gasification experiments in a thermobalance and a PDU (Process development Unit) rig. (orig.) (10 refs.)

  20. Possible future HERA analyses

    International Nuclear Information System (INIS)

    Geiser, Achim

    2015-12-01

    A variety of possible future analyses of HERA data in the context of the HERA data preservation programme is collected, motivated, and commented. The focus is placed on possible future analyses of the existing ep collider data and their physics scope. Comparisons to the original scope of the HERA pro- gramme are made, and cross references to topics also covered by other participants of the workshop are given. This includes topics on QCD, proton structure, diffraction, jets, hadronic final states, heavy flavours, electroweak physics, and the application of related theory and phenomenology topics like NNLO QCD calculations, low-x related models, nonperturbative QCD aspects, and electroweak radiative corrections. Synergies with other collider programmes are also addressed. In summary, the range of physics topics which can still be uniquely covered using the existing data is very broad and of considerable physics interest, often matching the interest of results from colliders currently in operation. Due to well-established data and MC sets, calibrations, and analysis procedures the manpower and expertise needed for a particular analysis is often very much smaller than that needed for an ongoing experiment. Since centrally funded manpower to carry out such analyses is not available any longer, this contribution not only targets experienced self-funded experimentalists, but also theorists and master-level students who might wish to carry out such an analysis.

  1. Always single and single again women: a qualitative study.

    Science.gov (United States)

    Lewis, K G; Moon, S

    1997-04-01

    What is it like to be a single woman today? Are the experiences of women who have always been single different from those who find themselves single again after having been married? How can family therapists promote the development of single women both individually and relationally? The purpose of this phenomenological, multiple-case study was to investigate perceptions of being single among heterosexual single women between the ages of 30 and 65. Nine focus group interviews and a semistructured, mailed questionnaire were used to collect the data. Constant comparative analyses were used to develop the findings. The findings were organized around the most salient theme that emerged from the analyses: single women have unresolved or unrecognized ambivalences about being single. This overarching theme was supported by three subassertions: (a) single women are aware of both the advantages and the drawbacks of being single; (b) single women are ambivalent about the reasons for their singleness; (c) although content with being single, many women simultaneously experience feelings of loss and grief. Implications for the clinical practice of family therapy and future research on single women are discussed.

  2. Single Nanoparticle Plasmonic Sensors

    Directory of Open Access Journals (Sweden)

    Manish Sriram

    2015-10-01

    Full Text Available The adoption of plasmonic nanomaterials in optical sensors, coupled with the advances in detection techniques, has opened the way for biosensing with single plasmonic particles. Single nanoparticle sensors offer the potential to analyse biochemical interactions at a single-molecule level, thereby allowing us to capture even more information than ensemble measurements. We introduce the concepts behind single nanoparticle sensing and how the localised surface plasmon resonances of these nanoparticles are dependent upon their materials, shape and size. Then we outline the different synthetic approaches, like citrate reduction, seed-mediated and seedless growth, that enable the synthesis of gold and silver nanospheres, nanorods, nanostars, nanoprisms and other nanostructures with tunable sizes. Further, we go into the aspects related to purification and functionalisation of nanoparticles, prior to the fabrication of sensing surfaces. Finally, the recent developments in single nanoparticle detection, spectroscopy and sensing applications are discussed.

  3. AMS analyses at ANSTO

    International Nuclear Information System (INIS)

    Lawson, E.M.

    1998-01-01

    The major use of ANTARES is Accelerator Mass Spectrometry (AMS) with 14 C being the most commonly analysed radioisotope - presently about 35 % of the available beam time on ANTARES is used for 14 C measurements. The accelerator measurements are supported by, and dependent on, a strong sample preparation section. The ANTARES AMS facility supports a wide range of investigations into fields such as global climate change, ice cores, oceanography, dendrochronology, anthropology, and classical and Australian archaeology. Described here are some examples of the ways in which AMS has been applied to support research into the archaeology, prehistory and culture of this continent's indigenous Aboriginal peoples. (author)

  4. EEG analyses with SOBI.

    Energy Technology Data Exchange (ETDEWEB)

    Glickman, Matthew R.; Tang, Akaysha (University of New Mexico, Albuquerque, NM)

    2009-02-01

    The motivating vision behind Sandia's MENTOR/PAL LDRD project has been that of systems which use real-time psychophysiological data to support and enhance human performance, both individually and of groups. Relevant and significant psychophysiological data being a necessary prerequisite to such systems, this LDRD has focused on identifying and refining such signals. The project has focused in particular on EEG (electroencephalogram) data as a promising candidate signal because it (potentially) provides a broad window on brain activity with relatively low cost and logistical constraints. We report here on two analyses performed on EEG data collected in this project using the SOBI (Second Order Blind Identification) algorithm to identify two independent sources of brain activity: one in the frontal lobe and one in the occipital. The first study looks at directional influences between the two components, while the second study looks at inferring gender based upon the frontal component.

  5. A simple beam analyser

    International Nuclear Information System (INIS)

    Lemarchand, G.

    1977-01-01

    (ee'p) experiments allow to measure the missing energy distribution as well as the momentum distribution of the extracted proton in the nucleus versus the missing energy. Such experiments are presently conducted on SACLAY's A.L.S. 300 Linac. Electrons and protons are respectively analysed by two spectrometers and detected in their focal planes. Counting rates are usually low and include time coincidences and accidentals. Signal-to-noise ratio is dependent on the physics of the experiment and the resolution of the coincidence, therefore it is mandatory to get a beam current distribution as flat as possible. Using new technologies has allowed to monitor in real time the behavior of the beam pulse and determine when the duty cycle can be considered as being good with respect to a numerical basis

  6. Analyse af elbilers forbrug

    DEFF Research Database (Denmark)

    Andersen, Ove; Krogh, Benjamin Bjerre; Torp, Kristian

    2014-01-01

    Denne rapport undersøger GPS og CAN bus datagrundlaget opsamlet ved kørsel med elbiler og analysere på elbilers forbrug. Analyserne er baseret på godt 133 millioner GPS og CAN bus målinger opsamlet fra 164 elbiler (Citroen C-Zero, Mitsubishi iMiev og Peugeot Ion) i kalenderåret 2012....... For datagrundlaget kan det konstateres, at der er behov for væsentlige, men simple opstramninger for fremadrettet at gøre det nemmere at anvende GPS/CAN bus data fra elbiler i andre analyser. Brugen af elbiler er sammenlignet med brændstofbiler og konklusionen er, at elbiler generelt kører 10-15 km/t langsommere på...

  7. Analyse de "La banlieue"

    Directory of Open Access Journals (Sweden)

    Nelly Morais

    2006-11-01

    Full Text Available 1. Préambule - Conditions de réalisation de la présente analyse Un groupe d'étudiants de master 1 de FLE de l'université Paris 3 (donc des étudiants en didactique des langues se destinant à l'enseignement du FLE a observé le produit au cours d'un module sur les TIC (Technologies de l'Information et de la Communication et la didactique des langues. Une discussion s'est ensuite engagée sur le forum d'une plate-forme de formation à distance à partir de quelques questions posées par l'enseigna...

  8. Methotrexate administration induces differential and selective protein tyrosine nitration and cysteine nitrosylation in the subcellular organelles of the small intestinal mucosa of rats.

    Science.gov (United States)

    Natarajan, Kasthuri; Abraham, Premila

    2016-05-05

    Gastrointestinal toxicity is one of the most frequent dose limiting side effects of methotrexate (MTX), a commonly used chemotherapeutic drug. Peroxynitrite (PON) overproduction is reported to contribute to MTX induced gastrointestinal mucositis. However, the consequence of PON overproduction i.e. protein tyrosine nitration and protein cysteine nitrosylation, the subcellular distribution of these modified proteins and their molecular weights have not been investigated yet. Mucositis was induced in Wistar rats by the administration of 3 consecutive i.p. injections of MTX. Tyrosine nitrated proteins and cysteine nitrosylated proteins were determined in the subcellular organelles fractions of mucosa using immunoprecipitation and western blot. The proteins in the subcellular fractions were separated by 1D electrophoresis, and probed with anti -nitrotyrosine antibody and anti-nitrosocysteine antibody. After MTX treatment, a general increase in protein tyrosine nitration as well as a change in the spectrum of proteins that underwent nitration was observed. The relative densities of the 3 nitrotyrosine protein adducts were as follows: Mitochondria > cytosol > microsomes > nucleus. In the mitochondrial fraction increased nitration of 12 kDa, 25 kDa 29Kda, 47 kDa, and 62Kda proteins, in the cytosol increased nitration of 12 kDa, 19 kDa, 45 kDa, and 60 kDa proteins and in the nuclear fraction increased nitration of 17 kDa, 35 kDa, and 58 kDa proteins was observed. On the other hand, MTX treatment resulted to a general decrease in protein cysteine nitrosylation in all the subcellular fractions. These results suggest that MTX induced, PON mediated small intestinal injury is mediated by differential nitration and nitrosylation of proteins in the subcellular organelles with increased protein tyrosine nitration and decreased cysteine nitrosylation. In addition MTX treatment results in selective nitration and nitrosylation of proteins in the intestinal mucosa. This differential

  9. Seismic fragility analyses

    International Nuclear Information System (INIS)

    Kostov, Marin

    2000-01-01

    In the last two decades there is increasing number of probabilistic seismic risk assessments performed. The basic ideas of the procedure for performing a Probabilistic Safety Analysis (PSA) of critical structures (NUREG/CR-2300, 1983) could be used also for normal industrial and residential buildings, dams or other structures. The general formulation of the risk assessment procedure applied in this investigation is presented in Franzini, et al., 1984. The probability of failure of a structure for an expected lifetime (for example 50 years) can be obtained from the annual frequency of failure, β E determined by the relation: β E ∫[d[β(x)]/dx]P(flx)dx. β(x) is the annual frequency of exceedance of load level x (for example, the variable x may be peak ground acceleration), P(fI x) is the conditional probability of structure failure at a given seismic load level x. The problem leads to the assessment of the seismic hazard β(x) and the fragility P(fl x). The seismic hazard curves are obtained by the probabilistic seismic hazard analysis. The fragility curves are obtained after the response of the structure is defined as probabilistic and its capacity and the associated uncertainties are assessed. Finally the fragility curves are combined with the seismic loading to estimate the frequency of failure for each critical scenario. The frequency of failure due to seismic event is presented by the scenario with the highest frequency. The tools usually applied for probabilistic safety analyses of critical structures could relatively easily be adopted to ordinary structures. The key problems are the seismic hazard definitions and the fragility analyses. The fragility could be derived either based on scaling procedures or on the base of generation. Both approaches have been presented in the paper. After the seismic risk (in terms of failure probability) is assessed there are several approaches for risk reduction. Generally the methods could be classified in two groups. The

  10. Analysing health outcomes.

    Science.gov (United States)

    Dowie, J

    2001-08-01

    If we cross-classify the absolutist-consequentialist distinction with an intuitive-analytical one we can see that economists probably attract the hostility of those in the other three cells as a result of being analytical consequentialists, as much as because of their concern with "costs". Suggesting that some sources of utility (either "outcome" or "process" in origin) are to be regarded as rights cannot, says the analytical consequentialist, overcome the fact that fulfilling and respecting rights is a resource-consuming activity, one that will inevitably have consequences, in resource-constrained situations, for the fulfillment of the rights of others. Within the analytical consequentialist framework QALY-type measures of health outcome have the unique advantage of allowing technical and allocative efficiency to be addressed simultaneously, while differential weighting of QALYs accruing to different groups means that efficiency and equity can be merged into the necessary single maximand. But what if such key concepts of the analytical consequentialist are not part of the discursive equipment of others? Are they to be disqualified from using them on this ground? Is it ethical for intuition to be privileged in ethical discourse, or is the analyst entitled to "equal opportunities" in the face of "analysisism", the cognitive equivalent of "racism" and "sexism"?

  11. Website-analyse

    DEFF Research Database (Denmark)

    Thorlacius, Lisbeth

    2009-01-01

    eller blindgyder, når han/hun besøger sitet. Studier i design og analyse af de visuelle og æstetiske aspekter i planlægning og brug af websites har imidlertid kun i et begrænset omfang været under reflektorisk behandling. Det er baggrunden for dette kapitel, som indleder med en gennemgang af æstetikkens......Websitet er i stigende grad det foretrukne medie inden for informationssøgning,virksomhedspræsentation, e-handel, underholdning, undervisning og social kontakt. I takt med denne voksende mangfoldighed af kommunikationsaktiviteter på nettet, er der kommet mere fokus på at optimere design og...... planlægning af de funktionelle og indholdsmæssige aspekter ved websites. Der findes en stor mængde teori- og metodebøger, som har specialiseret sig i de tekniske problemstillinger i forbindelse med interaktion og navigation, samt det sproglige indhold på websites. Den danske HCI (Human Computer Interaction...

  12. A channel profile analyser

    International Nuclear Information System (INIS)

    Gobbur, S.G.

    1983-01-01

    It is well understood that due to the wide band noise present in a nuclear analog-to-digital converter, events at the boundaries of adjacent channels are shared. It is a difficult and laborious process to exactly find out the shape of the channels at the boundaries. A simple scheme has been developed for the direct display of channel shape of any type of ADC on a cathode ray oscilliscope display. This has been accomplished by sequentially incrementing the reference voltage of a precision pulse generator by a fraction of a channel and storing ADC data in alternative memory locations of a multichannel pulse height analyser. Alternative channels are needed due to the sharing at the boundaries of channels. In the flat region of the profile alternate memory locations are channels with zero counts and channels with the full scale counts. At the boundaries all memory locations will have counts. The shape of this is a direct display of the channel boundaries. (orig.)

  13. Digital image analyser for autoradiography

    International Nuclear Information System (INIS)

    Muth, R.A.; Plotnick, J.

    1985-01-01

    The most critical parameter in quantitative autoradiography for assay of tissue concentrations of tracers is the ability to obtain precise and accurate measurements of optical density of the images. Existing high precision systems for image analysis, rotating drum densitometers, are expensive, suffer from mechanical problems and are slow. More moderately priced and reliable video camera based systems are available, but their outputs generally do not have the uniformity and stability necessary for high resolution quantitative autoradiography. The authors have designed and constructed an image analyser optimized for quantitative single and multiple tracer autoradiography which the authors refer to as a memory-mapped charged-coupled device scanner (MM-CCD). The input is from a linear array of CCD's which is used to optically scan the autoradiograph. Images are digitized into 512 x 512 picture elements with 256 gray levels and the data is stored in buffer video memory in less than two seconds. Images can then be transferred to RAM memory by direct memory-mapping for further processing. Arterial blood curve data and optical density-calibrated standards data can be entered and the optical density images can be converted automatically to tracer concentration or functional images. In double tracer studies, images produced from both exposures can be stored and processed in RAM to yield ''pure'' individual tracer concentration or functional images. Any processed image can be transmitted back to the buffer memory to be viewed on a monitor and processed for region of interest analysis

  14. Analyses of cavitation instabilities in ductile metals

    DEFF Research Database (Denmark)

    Tvergaard, Viggo

    2007-01-01

    , and also tests for a thin ductile metal layer bonding two ceramic blocks have indicated rapid void growth. Analyses for these material configurations are discussed here. When the void radius is very small, a nonlocal plasticity model is needed to account for observed size-effects, and recent analyses......Cavitation instabilities have been predicted for a single void in a ductile metal stressed under high triaxiality conditions. In experiments for a ceramic reinforced by metal particles a single dominant void has been observed on the fracture surface of some of the metal particles bridging a crack...... for the influence of such size-effects on cavitation instabilities are presented. When a metal contains a distribution of micro voids, and the void spacing compared to void size is not extremely large, the surrounding voids may affect the occurrence of a cavitation instability at one of the voids. This has been...

  15. Micromechanical Analyses of Sturzstroms

    Science.gov (United States)

    Imre, Bernd; Laue, Jan; Springman, Sarah M.

    2010-05-01

    Sturzstroms are very fast landslides of very large initial volume. As type features they display extreme run out, pared with intensive fragmentation of the involved blocks of rock within a collisional flow. The inherent danger to the growing communities in alpine valleys below future potential sites of sturzstroms must be examined and results of predictions of endangered zones allow to impact upon the planning processes in these areas. This calls for the ability to make Type A predictions, according to Lambe (1973), which are done before an event. But Type A predictions are only possible if sufficient understanding of the mechanisms involved in a process is available. The motivation of the doctoral thesis research project presented is therefore to reveal the mechanics of sturzstroms in more detail in order to contribute to the development of a Type A run out prediction model. It is obvious that a sturzstrom represents a highly dynamic collisional granular regime. Thus particles do not only collide but will eventually crush each other. Erismann and Abele (2001) describe this process as dynamic disintegration, where kinetic energy is the main driver for fragmenting the rock mass. In this case an approach combining the type features long run out and fragmentation within a single hypothesis is represented by the dynamic fragmentation-spreading model (Davies and McSaveney, 2009; McSaveney and Davies, 2009). Unfortunately, sturzstroms, and fragmentation within sturzstroms, can not be observed directly in a real event because of their long "reoccurrence time" and the obvious difficulties in placing measuring devices within such a rock flow. Therefore, rigorous modelling is required in particular of the transition from static to dynamic behaviour to achieve better knowledge of the mechanics of sturzstroms, and to provide empirical evidence to confirm the dynamic fragmentation-spreading model. Within this study fragmentation and their effects on the mobility of sturzstroms

  16. Methods for analysing cardiovascular studies with repeated measures

    NARCIS (Netherlands)

    Cleophas, T. J.; Zwinderman, A. H.; van Ouwerkerk, B. M.

    2009-01-01

    Background. Repeated measurements in a single subject are generally more similar than unrepeated measurements in different subjects. Unrepeated analyses of repeated data cause underestimation of the treatment effects. Objective. To review methods adequate for the analysis of cardiovascular studies

  17. A hydrophobic organelle probe based on aggregation-induced emission: Nanosuspension preparation and direct use for endoplasmic reticulum imaging in living cells

    Science.gov (United States)

    Zheng, Sichao; Huang, Cuihong; Zhao, Xuyan; Zhang, Yong; Liu, Shuwen; Zhu, Qiuhua

    2018-01-01

    Organic fluorophores have a wide range of biological uses and are usually needed to be prepared as water-soluble compounds or nanoparticles for applications in aqueous biosystems owing to their hydrophobic properties, which often is a complex, time-consuming and high-cost process. Here, the nanoparticle preparation of hydrophobic fluorophores and their application in cell imaging have been investigated. It was found: a) fetal bovine serum (FBS) shows an excellent dispersion effect on hydrophobic small-molecule organic compounds; b) a hydrophobic C6-unsubstituted tetrahydropyrimidine (Me-THP-Naph) can be prepared as nanosuspensions utilizing cell culture medium with 10% FBS and directly be used as a specific real-time imaging probe for the endoplasmic reticulum (ER), a dynamic organelle playing a crucial role in many cellular processes. Compared with existing ER-targeted organic fluorescent probes, Me-THP-Naph, a product of an efficient five-component reaction that we developed, has unconventional aggregation-induced emission characteristics and shows advantages of low cost, long-term staining, good photostability, high signal-to-noise ratio and excellent biocompatibility, which make it a potential specific probe for real-time ER imaging. More importantly, this work affords a simple strategy for direct application of hydrophobic organic compounds in aqueous biological systems.

  18. An organelle-free assay for pea chloroplast Mg-chelatase: Resolution of the activity into soluble and membrane bound fractions

    Energy Technology Data Exchange (ETDEWEB)

    Walker, C.J.; Weinstein, J.D. (Clemson Univ, SC (United States))

    1991-05-01

    Mg-chelatase, which catalyzes the insertion of magnesium into protoporphyrin, lies at the branchpoint of heme and chlorophyll biosynthesis in chloroplasts. Since magnesium chelation is the first step unique to chlorophyll synthesis, one would expect this step to be highly regulated. However, to date little is known about the enzymology or regulation of Mg-chelatase due mostly to an inability to assay it's activity outside of the intact plastid. Here the authors report the first truly in vitro i.e. organelle-free, assay for Mg-chelatase. Mg-chelatase activity in intact pea chloroplasts which is 3 to 4 fold higher than in cucumber chloroplasts, survived chloroplast lysis and could be fractionated, by centrifugation, into supernatant and pellet components. Both of these fractions were required to reconstitute Mg-chelatase activity and both were inactivated by boiling; indicating that the enzyme is composed of soluble and membrane bound protein(s). The specific activity of the reconstituted system was typically 1 nmol Mg-Deuteroporphyrin/h/mg protein and activity was linear for at least 60 min under our assay conditions. ATP and magnesium were required for Mg-chelatase activity. The soluble component could be fractionated with ammonium sulfate. The product of the reaction was confirmed fluorometrically as the magnesium chelate of the porphyrin substrate. Crude separation of chloroplast membranes into thylakoids and envelopes, suggested that the membrane-bound component of Mg-chelatase is probably located in the envelope.

  19. Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling.

    Directory of Open Access Journals (Sweden)

    Wei Li

    2008-01-01

    Full Text Available Specificity of protein ubiquitylation is conferred by E3 ubiquitin (Ub ligases. We have annotated approximately 617 putative E3s and substrate-recognition subunits of E3 complexes encoded in the human genome. The limited knowledge of the function of members of the large E3 superfamily prompted us to generate genome-wide E3 cDNA and RNAi expression libraries designed for functional screening. An imaging-based screen using these libraries to identify E3s that regulate mitochondrial dynamics uncovered MULAN/FLJ12875, a RING finger protein whose ectopic expression and knockdown both interfered with mitochondrial trafficking and morphology. We found that MULAN is a mitochondrial protein - two transmembrane domains mediate its localization to the organelle's outer membrane. MULAN is oriented such that its E3-active, C-terminal RING finger is exposed to the cytosol, where it has access to other components of the Ub system. Both an intact RING finger and the correct subcellular localization were required for regulation of mitochondrial dynamics, suggesting that MULAN's downstream effectors are proteins that are either integral to, or associated with, mitochondria and that become modified with Ub. Interestingly, MULAN had previously been identified as an activator of NF-kappaB, thus providing a link between mitochondrial dynamics and mitochondria-to-nucleus signaling. These findings suggest the existence of a new, Ub-mediated mechanism responsible for integration of mitochondria into the cellular environment.

  20. Effect of Content of Sulfate Groups in Seaweed Polysaccharides on Antioxidant Activity and Repair Effect of Subcellular Organelles in Injured HK-2 Cells

    Directory of Open Access Journals (Sweden)

    Xiao-Tao Ma

    2017-01-01

    Full Text Available This study aims to investigate the repair effect of subcellular structure injuries of the HK-2 cells of four degraded seaweed polysaccharides (DSPs, namely, the degraded Porphyra yezoensis, Gracilaria lemaneiformis, Sargassum fusiform, and Undaria pinnatifida polysaccharides. The four DSPs have similar molecular weight, but with different content of sulfate groups (i.e., 17.9%, 13.3%, 8.2%, and 5.5%, resp.. The damaged model was established using 2.8 mmol/L oxalate to injure HK-2 cells, and 60 μg/mL of various DSPs was used to repair the damaged cells. With the increase of sulfate group content in DSPs, the scavenging activity of radicals and their reducing power were all improved. Four kinds of DSPs have repair effect on the subcellular organelles of damaged HK-2 cells. After being repaired by DSPs, the release amount of lactate dehydrogenase was decreased, the integrity of cell membrane and lysosome increased, the Δψm increased, the cell of G1 phase arrest was inhibited, the proportion of S phase increased, and cell apoptotic and necrosis rates were significantly reduced. The greater the content of sulfate group is, the stronger is the repair ability of the polysaccharide. These DSPs, particularly the polysaccharide with higher sulfate group content, may be a potential drug for the prevention and cure of kidney stones.

  1. Proteomic Analyses Reveal a Role of Cytoplasmic Droplets as an Energy Source during Epididymal Sperm Maturation

    Science.gov (United States)

    Yuan, Shuiqiao; Zheng, Huili; Zheng, Zhihong; Yan, Wei

    2013-01-01

    A small portion of cytoplasm is generally retained as the cytoplasmic droplet (CD) on the flagellum of spermatozoa after spermiation in mice. CDs are believed to play a role in osmoadaptation by allowing water entrance or exit. However, many lines of evidence suggest that CDs may have roles beyond osmoregulation. To gain more insights, we purified CDs from murine epididymal spermatozoa and conducted proteomic analyses on proteins highly enriched in CDs. Among 105 proteins identified, 71 (68%) were enzymes involved in energy metabolism. We also found that sperm mitochondria underwent a reactivation process and glycolytic enzymes were further distributed and incorporated into different regions of the flagellum during epididymal sperm maturation. Both processes appeared to require CDs. Our data suggest that the CD represents a transient organelle that serves as an energy source essential for epididymal sperm maturation. PMID:24155961

  2. Cell Biology of Prokaryotic Organelles

    OpenAIRE

    Murat, Dorothee; Byrne, Meghan; Komeili, Arash

    2010-01-01

    Mounting evidence in recent years has challenged the dogma that prokaryotes are simple and undefined cells devoid of an organized subcellular architecture. In fact, proteins once thought to be the purely eukaryotic inventions, including relatives of actin and tubulin control prokaryotic cell shape, DNA segregation, and cytokinesis. Similarly, compartmentalization, commonly noted as a distinguishing feature of eukaryotic cells, is also prevalent in the prokaryotic world in the form of protein-...

  3. Multiple Imputation for Network Analyses

    NARCIS (Netherlands)

    Krause, Robert; Huisman, Mark; Steglich, Christian; Snijders, Thomas

    2016-01-01

    Missing data on network ties is a fundamental problem for network analyses. The biases induced by missing edge data, even when missing completely at random (MCAR), are widely acknowledged and problematic for network analyses (Kossinets, 2006; Huisman & Steglich, 2008; Huisman, 2009). Although

  4. Do single women value early retirement more than single men?

    DEFF Research Database (Denmark)

    Danø, Anne Møller; Ejrnæs, Mette; Husted, Leif

    2005-01-01

    The focus of this paper is to analyse why a large fraction of single elderly people choose to retire early. A structural model directly based on the individual decision of labour supply is estimated on a sample of singles, where singles are defined as those who are living alone. We find that inco...... are willing to reduce the income to 81%. Men's retirement decision is mainly influenced by income and health, whereas women's retirement decision is also affected by education and unemployment experience...... and health are important determinants of the retirement decision. Furthermore, we find substantial gender differences in the retirement pattern. Healthy single women value retirement more than healthy single men and are willing to reduce their disposable income to 74% of their previous income while men...

  5. Radiation Protection Using Single-Wall Carbon Nanotube Derivatives

    Science.gov (United States)

    Tour, James M.; Lu, Meng; Lucente-Schultz, Rebecca; Leonard, Ashley; Doyle, Condell Dewayne; Kosynkin, Dimitry V.; Price, Brandi Katherine

    2011-01-01

    This invention is a means of radiation protection, or cellular oxidative stress mitigation, via a sequence of quenching radical species using nano-engineered scaffolds, specifically single-wall carbon nanotubes (SWNTs) and their derivatives. The material can be used as a means of radiation protection by reducing the number of free radicals within, or nearby, organelles, cells, tissue, organs, or living organisms, thereby reducing the risk of damage to DNA and other cellular components (i.e., RNA, mitochondria, membranes, etc.) that can lead to chronic and/or acute pathologies, including but not limited to cancer, cardiovascular disease, immuno-suppression, and disorders of the central nervous system. In addition, this innovation could be used as a prophylactic or antidote for accidental radiation exposure, during high-altitude or space travel where exposure to radiation is anticipated, or to protect from exposure from deliberate terrorist or wartime use of radiation- containing weapons.

  6. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

    Directory of Open Access Journals (Sweden)

    Ma Hong

    2010-02-01

    Full Text Available Abstract Background Although the overwhelming majority of genes found in angiosperms are members of gene families, and both gene- and genome-duplication are pervasive forces in plant genomes, some genes are sufficiently distinct from all other genes in a genome that they can be operationally defined as 'single copy'. Using the gene clustering algorithm MCL-tribe, we have identified a set of 959 single copy genes that are shared single copy genes in the genomes of Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa. To characterize these genes, we have performed a number of analyses examining GO annotations, coding sequence length, number of exons, number of domains, presence in distant lineages, such as Selaginella and Physcomitrella, and phylogenetic analysis to estimate copy number in other seed plants and to demonstrate their phylogenetic utility. We then provide examples of how these genes may be used in phylogenetic analyses to reconstruct organismal history, both by using extant coverage in EST databases for seed plants and de novo amplification via RT-PCR in the family Brassicaceae. Results There are 959 single copy nuclear genes shared in Arabidopsis, Populus, Vitis and Oryza ["APVO SSC genes"]. The majority of these genes are also present in the Selaginella and Physcomitrella genomes. Public EST sets for 197 species suggest that most of these genes are present across a diverse collection of seed plants, and appear to exist as single or very low copy genes, though exceptions are seen in recently polyploid taxa and in lineages where there is significant evidence for a shared large-scale duplication event. Genes encoding proteins localized in organelles are more commonly single copy than expected by chance, but the evolutionary forces responsible for this bias are unknown. Regardless of the evolutionary mechanisms responsible for the large number of shared single copy genes in diverse flowering plant lineages, these

  7. An extensible analysable system model

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, Rene Rydhof

    2008-01-01

    Analysing real-world systems for vulnerabilities with respect to security and safety threats is a difficult undertaking, not least due to a lack of availability of formalisations for those systems. While both formalisations and analyses can be found for artificial systems such as software......, this does not hold for real physical systems. Approaches such as threat modelling try to target the formalisation of the real-world domain, but still are far from the rigid techniques available in security research. Many currently available approaches to assurance of critical infrastructure security...... are based on (quite successful) ad-hoc techniques. We believe they can be significantly improved beyond the state-of-the-art by pairing them with static analyses techniques. In this paper we present an approach to both formalising those real-world systems, as well as providing an underlying semantics, which...

  8. Sample preparation in foodomic analyses.

    Science.gov (United States)

    Martinović, Tamara; Šrajer Gajdošik, Martina; Josić, Djuro

    2018-04-16

    Representative sampling and adequate sample preparation are key factors for successful performance of further steps in foodomic analyses, as well as for correct data interpretation. Incorrect sampling and improper sample preparation can be sources of severe bias in foodomic analyses. It is well known that both wrong sampling and sample treatment cannot be corrected anymore. These, in the past frequently neglected facts, are now taken into consideration, and the progress in sampling and sample preparation in foodomics is reviewed here. We report the use of highly sophisticated instruments for both high-performance and high-throughput analyses, as well as miniaturization and the use of laboratory robotics in metabolomics, proteomics, peptidomics and genomics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  9. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

    Paijmans, Johanna L. A.; Gilbert, Tom; Hofreiter, Michael

    2013-01-01

    The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA...... analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences...... (mitogenomes). Such studies were initially limited to analyses of extant organisms, but developments in both DNA sequencing technologies and general methodological aspects related to working with degraded DNA have resulted in complete mitogenomes becoming increasingly popular for ancient DNA studies as well...

  10. Single Top Physics at ATLAS and CMS

    CERN Document Server

    zur Nedden, Martin; The ATLAS collaboration

    2016-01-01

    A summary over the single top analyses in the ATLAS and CMS experiments is given. In this talk, the measurements of the single top cross sections in the t-channel, the Wt-channel and the s-channel are shown as the basis for a rich physics program with single top quarks. After discussing also the differential and fiducial cross sections and the V_tb properties, the single-top analyses are used as the bases for searches for physics beyond the Standard Model. Searches for Mono-tops, Flavour Changing Neutral Currents and anomalous couplings are discussed.

  11. Doubly Latent Multilevel Analyses of Classroom Climate: An Illustration

    Science.gov (United States)

    Morin, Alexandre J. S.; Marsh, Herbert W.; Nagengast, Benjamin; Scalas, L. Francesca

    2014-01-01

    Many classroom climate studies suffer from 2 critical problems: They (a) treat climate as a student-level (L1) variable in single-level analyses instead of a classroom-level (L2) construct in multilevel analyses; and (b) rely on manifest-variable models rather than on latent-variable models that control measurement error at L1 and L2, and sampling…

  12. Single-Cell Genomic Analysis in Plants

    Directory of Open Access Journals (Sweden)

    Yuxuan Yuan

    2018-01-01

    Full Text Available Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis.

  13. Analysing and Comparing Encodability Criteria

    Directory of Open Access Journals (Sweden)

    Kirstin Peters

    2015-08-01

    Full Text Available Encodings or the proof of their absence are the main way to compare process calculi. To analyse the quality of encodings and to rule out trivial or meaningless encodings, they are augmented with quality criteria. There exists a bunch of different criteria and different variants of criteria in order to reason in different settings. This leads to incomparable results. Moreover it is not always clear whether the criteria used to obtain a result in a particular setting do indeed fit to this setting. We show how to formally reason about and compare encodability criteria by mapping them on requirements on a relation between source and target terms that is induced by the encoding function. In particular we analyse the common criteria full abstraction, operational correspondence, divergence reflection, success sensitiveness, and respect of barbs; e.g. we analyse the exact nature of the simulation relation (coupled simulation versus bisimulation that is induced by different variants of operational correspondence. This way we reduce the problem of analysing or comparing encodability criteria to the better understood problem of comparing relations on processes.

  14. Descriptive Analyses of Mechanical Systems

    DEFF Research Database (Denmark)

    Andreasen, Mogens Myrup; Hansen, Claus Thorp

    2003-01-01

    Forord Produktanalyse og teknologianalyse kan gennmføres med et bredt socio-teknisk sigte med henblik på at forstå kulturelle, sociologiske, designmæssige, forretningsmæssige og mange andre forhold. Et delområde heri er systemisk analyse og beskrivelse af produkter og systemer. Nærværende kompend...

  15. Millifluidic droplet analyser for microbiology

    NARCIS (Netherlands)

    Baraban, L.; Bertholle, F.; Salverda, M.L.M.; Bremond, N.; Panizza, P.; Baudry, J.; Visser, de J.A.G.M.; Bibette, J.

    2011-01-01

    We present a novel millifluidic droplet analyser (MDA) for precisely monitoring the dynamics of microbial populations over multiple generations in numerous (=103) aqueous emulsion droplets (100 nL). As a first application, we measure the growth rate of a bacterial strain and determine the minimal

  16. Genetic Analyses of Sorting of Paternally Transmitted Mitochondrial DNA

    Science.gov (United States)

    The organelles are maternally transmitted in the vast majority of eukaryotes. However paternal transmission of plastids and mitochondria occurs rarely in plants. Cucumber is a unique model plant for organellar genetics because its three genomes show differential transmission: maternal for chlorop...

  17. Comprehensive immunoproteogenomic analyses of malignant pleural mesothelioma.

    Science.gov (United States)

    Lee, Hyun-Sung; Jang, Hee-Jin; Choi, Jong Min; Zhang, Jun; de Rosen, Veronica Lenge; Wheeler, Thomas M; Lee, Ju-Seog; Tu, Thuydung; Jindra, Peter T; Kerman, Ronald H; Jung, Sung Yun; Kheradmand, Farrah; Sugarbaker, David J; Burt, Bryan M

    2018-04-05

    We generated a comprehensive atlas of the immunologic cellular networks within human malignant pleural mesothelioma (MPM) using mass cytometry. Data-driven analyses of these high-resolution single-cell data identified 2 distinct immunologic subtypes of MPM with vastly different cellular composition, activation states, and immunologic function; mass spectrometry demonstrated differential abundance of MHC-I and -II neopeptides directly identified between these subtypes. The clinical relevance of this immunologic subtyping was investigated with a discriminatory molecular signature derived through comparison of the proteomes and transcriptomes of these 2 immunologic MPM subtypes. This molecular signature, representative of a favorable intratumoral cell network, was independently associated with improved survival in MPM and predicted response to immune checkpoint inhibitors in patients with MPM and melanoma. These data additionally suggest a potentially novel mechanism of response to checkpoint blockade: requirement for high measured abundance of neopeptides in the presence of high expression of MHC proteins specific for these neopeptides.

  18. Analyse der Wohnungsbewertungen von Airbnb

    OpenAIRE

    Schlesinger, Daniel; Zarnekow, Rüdiger; Repschläger, Jonas

    2016-01-01

    With millions of registered users Airbnb conciliates rooms from C2C in the share economy. To get landlords and tenants together it is crucial that they trust each other. Therefore, users can verify their personality, write comments about each other and the tenants can rate the rooms they rented. With a dataset of more than one million profiles we evaluate statistically how to distinguish between ratings in detail. Therefore, we analyze frequency distributions of single judging criteria and...

  19. Workload analyse of assembling process

    Science.gov (United States)

    Ghenghea, L. D.

    2015-11-01

    The workload is the most important indicator for managers responsible of industrial technological processes no matter if these are automated, mechanized or simply manual in each case, machines or workers will be in the focus of workload measurements. The paper deals with workload analyses made to a most part manual assembling technology for roller bearings assembling process, executed in a big company, with integrated bearings manufacturing processes. In this analyses the delay sample technique have been used to identify and divide all bearing assemblers activities, to get information about time parts from 480 minutes day work time that workers allow to each activity. The developed study shows some ways to increase the process productivity without supplementary investments and also indicated the process automation could be the solution to gain maximum productivity.

  20. Single Top-Quark Production at CDF

    CERN Multimedia

    CERN. Geneva

    2008-01-01

    The main challenge of the single top-quark search at the Tevatron is the huge background from W+jets events and QCD events, which makes the use of advanced multivariate techniques essential. The recent single top analyses using either the matrix element method, neural networks, likelihood discriminants or boosted decision trees as well as the combination of the former three analyses will be presented...

  1. Safety analyses of surface facilities

    International Nuclear Information System (INIS)

    Anspach, W.; Baran, A.; Dorst, H.J.; Eifert, B.; Gruen, M.; Behrendt, V.; Berkhan, W.; Dincklage, R.D. v.; Doehler, J.; Bruecher, H.

    1981-01-01

    The investigations were carried out using the example of the Gorleben waste disposal center and the planning documents established for this center. The safety analyses refer to the transport of spent fuel elements, the water-cooled interin storage and the reprocessing stage. Regarding the risk analysis of the technical systems the dynamics of the courses of incidents can be better taken into account by doing a methodical development. (DG) [de

  2. Technical center for transportation analyses

    International Nuclear Information System (INIS)

    Foley, J.T.

    1978-01-01

    A description is presented of an information search/retrieval/research activity of Sandia Laboratories which provides technical environmental information which may be used in transportation risk analyses, environmental impact statements, development of design and test criteria for packaging of energy materials, and transportation mode research studies. General activities described are: (1) history of center development; (2) environmental information storage/retrieval system; (3) information searches; (4) data needs identification; and (5) field data acquisition system and applications

  3. Methodology of cost benefit analyses

    International Nuclear Information System (INIS)

    Patrik, M.; Babic, P.

    2000-10-01

    The report addresses financial aspects of proposed investments and other steps which are intended to contribute to nuclear safety. The aim is to provide introductory insight into the procedures and potential of cost-benefit analyses as a routine guide when making decisions on costly provisions as one of the tools to assess whether a particular provision is reasonable. The topic is applied to the nuclear power sector. (P.A.)

  4. Statistical power analyses using G*Power 3.1: tests for correlation and regression analyses.

    Science.gov (United States)

    Faul, Franz; Erdfelder, Edgar; Buchner, Axel; Lang, Albert-Georg

    2009-11-01

    G*Power is a free power analysis program for a variety of statistical tests. We present extensions and improvements of the version introduced by Faul, Erdfelder, Lang, and Buchner (2007) in the domain of correlation and regression analyses. In the new version, we have added procedures to analyze the power of tests based on (1) single-sample tetrachoric correlations, (2) comparisons of dependent correlations, (3) bivariate linear regression, (4) multiple linear regression based on the random predictor model, (5) logistic regression, and (6) Poisson regression. We describe these new features and provide a brief introduction to their scope and handling.

  5. Uncertainty in Operational Atmospheric Analyses and Re-Analyses

    Science.gov (United States)

    Langland, R.; Maue, R. N.

    2016-12-01

    This talk will describe uncertainty in atmospheric analyses of wind and temperature produced by operational forecast models and in re-analysis products. Because the "true" atmospheric state cannot be precisely quantified, there is necessarily error in every atmospheric analysis, and this error can be estimated by computing differences ( variance and bias) between analysis products produced at various centers (e.g., ECMWF, NCEP, U.S Navy, etc.) that use independent data assimilation procedures, somewhat different sets of atmospheric observations and forecast models with different resolutions, dynamical equations, and physical parameterizations. These estimates of analysis uncertainty provide a useful proxy to actual analysis error. For this study, we use a unique multi-year and multi-model data archive developed at NRL-Monterey. It will be shown that current uncertainty in atmospheric analyses is closely correlated with the geographic distribution of assimilated in-situ atmospheric observations, especially those provided by high-accuracy radiosonde and commercial aircraft observations. The lowest atmospheric analysis uncertainty is found over North America, Europe and Eastern Asia, which have the largest numbers of radiosonde and commercial aircraft observations. Analysis uncertainty is substantially larger (by factors of two to three times) in most of the Southern hemisphere, the North Pacific ocean, and under-developed nations of Africa and South America where there are few radiosonde or commercial aircraft data. It appears that in regions where atmospheric analyses depend primarily on satellite radiance observations, analysis uncertainty of both temperature and wind remains relatively high compared to values found over North America and Europe.

  6. [AO distribution and fluorescence spectra in myoblasts and single muscle fibres].

    Science.gov (United States)

    Beliaeva, T N; Krolenko, S A; Leont'eva, E A; Mozhenok, T P; Salova, A V; Faddeeva, M D

    2009-01-01

    Using spectral scanning regime of Leica TCS SL confocal microscope, acridine orange (AO) fluorescence spectra in nuclei and cytoplasms of living myoblasts L6J1 and frog single muscle fibres have been studied. AO fluorescence spectra in salt solutions dependent on free AO concentrations and in AO complexes with DNA have also been obtained for comparison. Myoblasts nuclei fluoresced in green spectral region with maximum at approximately 530 nm (corresponding AO monomers fluorescence), nucleoli fluoresced most brightly. Nuclear chromatin fluoresced not uniformly in these cells. We saw similar to myoblasts AO emission in nucleoli and nuclei of frog single muscle fibres. The uniformed weak green fluorescence was observed for myoblast cytoplasm. As to the muscle fibres sarcoplasm, we saw also AO green fluorescence in A-discs. In myoblasts and muscle fibre cytoplasm we saw the fluorescent red, yellow and green granules which were acidic organelles. The comparison of AO fluorescence spectra in living cells with fluorescence spectra of different AO concentrations and complexes of AO with DNA in buffer solutions allows estimation of AO concentration in acidic granules which is of interest in the investigation of cellular organelles functions in the processes of intracellular transport, adaptation, apoptosis and a number of pathological conditions.

  7. Providing traceability for neuroimaging analyses.

    Science.gov (United States)

    McClatchey, Richard; Branson, Andrew; Anjum, Ashiq; Bloodsworth, Peter; Habib, Irfan; Munir, Kamran; Shamdasani, Jetendr; Soomro, Kamran

    2013-09-01

    With the increasingly digital nature of biomedical data and as the complexity of analyses in medical research increases, the need for accurate information capture, traceability and accessibility has become crucial to medical researchers in the pursuance of their research goals. Grid- or Cloud-based technologies, often based on so-called Service Oriented Architectures (SOA), are increasingly being seen as viable solutions for managing distributed data and algorithms in the bio-medical domain. For neuroscientific analyses, especially those centred on complex image analysis, traceability of processes and datasets is essential but up to now this has not been captured in a manner that facilitates collaborative study. Few examples exist, of deployed medical systems based on Grids that provide the traceability of research data needed to facilitate complex analyses and none have been evaluated in practice. Over the past decade, we have been working with mammographers, paediatricians and neuroscientists in three generations of projects to provide the data management and provenance services now required for 21st century medical research. This paper outlines the finding of a requirements study and a resulting system architecture for the production of services to support neuroscientific studies of biomarkers for Alzheimer's disease. The paper proposes a software infrastructure and services that provide the foundation for such support. It introduces the use of the CRISTAL software to provide provenance management as one of a number of services delivered on a SOA, deployed to manage neuroimaging projects that have been studying biomarkers for Alzheimer's disease. In the neuGRID and N4U projects a Provenance Service has been delivered that captures and reconstructs the workflow information needed to facilitate researchers in conducting neuroimaging analyses. The software enables neuroscientists to track the evolution of workflows and datasets. It also tracks the outcomes of

  8. Systematic derivation of correct variability-aware program analyses

    DEFF Research Database (Denmark)

    Midtgaard, Jan; Dimovski, Aleksandar S.; Brabrand, Claus

    2015-01-01

    A recent line of work lifts particular verification and analysis methods to Software Product Lines (SPL). In an effort to generalize such case-by-case approaches, we develop a systematic methodology for lifting single-program analyses to SPLs using abstract interpretation. Abstract interpretation...

  9. Single-Level and Multilevel Mediation Analysis

    Science.gov (United States)

    Tofighi, Davood; Thoemmes, Felix

    2014-01-01

    Mediation analysis is a statistical approach used to examine how the effect of an independent variable on an outcome is transmitted through an intervening variable (mediator). In this article, we provide a gentle introduction to single-level and multilevel mediation analyses. Using single-level data, we demonstrate an application of structural…

  10. Computational approaches to analyse and predict small molecule transport and distribution at cellular and subcellular levels.

    Science.gov (United States)

    Min, Kyoung Ah; Zhang, Xinyuan; Yu, Jing-yu; Rosania, Gus R

    2014-01-01

    Quantitative structure-activity relationship (QSAR) studies and mechanistic mathematical modeling approaches have been independently employed for analysing and predicting the transport and distribution of small molecule chemical agents in living organisms. Both of these computational approaches have been useful for interpreting experiments measuring the transport properties of small molecule chemical agents, in vitro and in vivo. Nevertheless, mechanistic cell-based pharmacokinetic models have been especially useful to guide the design of experiments probing the molecular pathways underlying small molecule transport phenomena. Unlike QSAR models, mechanistic models can be integrated from microscopic to macroscopic levels, to analyse the spatiotemporal dynamics of small molecule chemical agents from intracellular organelles to whole organs, well beyond the experiments and training data sets upon which the models are based. Based on differential equations, mechanistic models can also be integrated with other differential equations-based systems biology models of biochemical networks or signaling pathways. Although the origin and evolution of mathematical modeling approaches aimed at predicting drug transport and distribution has occurred independently from systems biology, we propose that the incorporation of mechanistic cell-based computational models of drug transport and distribution into a systems biology modeling framework is a logical next step for the advancement of systems pharmacology research. Copyright © 2013 John Wiley & Sons, Ltd.

  11. Methodological challenges in carbohydrate analyses

    Directory of Open Access Journals (Sweden)

    Mary Beth Hall

    2007-07-01

    Full Text Available Carbohydrates can provide up to 80% of the dry matter in animal diets, yet their specific evaluation for research and diet formulation is only now becoming a focus in the animal sciences. Partitioning of dietary carbohydrates for nutritional purposes should reflect differences in digestion and fermentation characteristics and effects on animal performance. Key challenges to designating nutritionally important carbohydrate fractions include classifying the carbohydrates in terms of nutritional characteristics, and selecting analytical methods that describe the desired fraction. The relative lack of information on digestion characteristics of various carbohydrates and their interactions with other fractions in diets means that fractions will not soon be perfectly established. Developing a system of carbohydrate analysis that could be used across animal species could enhance the utility of analyses and amount of data we can obtain on dietary effects of carbohydrates. Based on quantities present in diets and apparent effects on animal performance, some nutritionally important classes of carbohydrates that may be valuable to measure include sugars, starch, fructans, insoluble fiber, and soluble fiber. Essential to selection of methods for these fractions is agreement on precisely what carbohydrates should be included in each. Each of these fractions has analyses that could potentially be used to measure them, but most of the available methods have weaknesses that must be evaluated to see if they are fatal and the assay is unusable, or if the assay still may be made workable. Factors we must consider as we seek to analyze carbohydrates to describe diets: Does the assay accurately measure the desired fraction? Is the assay for research, regulatory, or field use (affects considerations of acceptable costs and throughput? What are acceptable accuracy and variability of measures? Is the assay robust (enhances accuracy of values? For some carbohydrates, we

  12. Health Insurance without Single Crossing

    DEFF Research Database (Denmark)

    Boone, Jan; Schottmüller, Christoph

    2017-01-01

    Standard insurance models predict that people with high risks have high insurance coverage. It is empirically documented that people with high income have lower health risks and are better insured. We show that income differences between risk types lead to a violation of single crossing...... in an insurance model where people choose treatment intensity. We analyse different market structures and show the following: If insurers have market power, the violation of single crossing caused by income differences and endogenous treatment choice can explain the empirically observed outcome. Our results do...

  13. Theorising and Analysing Academic Labour

    Directory of Open Access Journals (Sweden)

    Thomas Allmer

    2018-01-01

    Full Text Available The aim of this article is to contextualise universities historically within capitalism and to analyse academic labour and the deployment of digital media theoretically and critically. It argues that the post-war expansion of the university can be considered as medium and outcome of informational capitalism and as a dialectical development of social achievement and advanced commodification. The article strives to identify the class position of academic workers, introduces the distinction between academic work and labour, discusses the connection between academic, information and cultural work, and suggests a broad definition of university labour. It presents a theoretical model of working conditions that helps to systematically analyse the academic labour process and to provide an overview of working conditions at universities. The paper furthermore argues for the need to consider the development of education technologies as a dialectics of continuity and discontinuity, discusses the changing nature of the forces and relations of production, and the impact on the working conditions of academics in the digital university. Based on Erik Olin Wright’s inclusive approach of social transformation, the article concludes with the need to bring together anarchist, social democratic and revolutionary strategies for establishing a socialist university in a commons-based information society.

  14. Incorporating nonlinearity into mediation analyses.

    Science.gov (United States)

    Knafl, George J; Knafl, Kathleen A; Grey, Margaret; Dixon, Jane; Deatrick, Janet A; Gallo, Agatha M

    2017-03-21

    Mediation is an important issue considered in the behavioral, medical, and social sciences. It addresses situations where the effect of a predictor variable X on an outcome variable Y is explained to some extent by an intervening, mediator variable M. Methods for addressing mediation have been available for some time. While these methods continue to undergo refinement, the relationships underlying mediation are commonly treated as linear in the outcome Y, the predictor X, and the mediator M. These relationships, however, can be nonlinear. Methods are needed for assessing when mediation relationships can be treated as linear and for estimating them when they are nonlinear. Existing adaptive regression methods based on fractional polynomials are extended here to address nonlinearity in mediation relationships, but assuming those relationships are monotonic as would be consistent with theories about directionality of such relationships. Example monotonic mediation analyses are provided assessing linear and monotonic mediation of the effect of family functioning (X) on a child's adaptation (Y) to a chronic condition by the difficulty (M) for the family in managing the child's condition. Example moderated monotonic mediation and simulation analyses are also presented. Adaptive methods provide an effective way to incorporate possibly nonlinear monotonicity into mediation relationships.

  15. Incorporating nonlinearity into mediation analyses

    Directory of Open Access Journals (Sweden)

    George J. Knafl

    2017-03-01

    Full Text Available Abstract Background Mediation is an important issue considered in the behavioral, medical, and social sciences. It addresses situations where the effect of a predictor variable X on an outcome variable Y is explained to some extent by an intervening, mediator variable M. Methods for addressing mediation have been available for some time. While these methods continue to undergo refinement, the relationships underlying mediation are commonly treated as linear in the outcome Y, the predictor X, and the mediator M. These relationships, however, can be nonlinear. Methods are needed for assessing when mediation relationships can be treated as linear and for estimating them when they are nonlinear. Methods Existing adaptive regression methods based on fractional polynomials are extended here to address nonlinearity in mediation relationships, but assuming those relationships are monotonic as would be consistent with theories about directionality of such relationships. Results Example monotonic mediation analyses are provided assessing linear and monotonic mediation of the effect of family functioning (X on a child’s adaptation (Y to a chronic condition by the difficulty (M for the family in managing the child's condition. Example moderated monotonic mediation and simulation analyses are also presented. Conclusions Adaptive methods provide an effective way to incorporate possibly nonlinear monotonicity into mediation relationships.

  16. WE-H-206-01: Photoacoustic Tomography: Multiscale Imaging From Organelles to Patients by Ultrasonically Beating the Optical Diffusion Limit

    Energy Technology Data Exchange (ETDEWEB)

    Wang, L. [Washington University (United States)

    2016-06-15

    Lihong V. Wang: Photoacoustic tomography (PAT), combining non-ionizing optical and ultrasonic waves via the photoacoustic effect, provides in vivo multiscale functional, metabolic, and molecular imaging. Broad applications include imaging of the breast, brain, skin, esophagus, colon, vascular system, and lymphatic system in humans or animals. Light offers rich contrast but does not penetrate biological tissue in straight paths as x-rays do. Consequently, high-resolution pure optical imaging (e.g., confocal microscopy, two-photon microscopy, and optical coherence tomography) is limited to penetration within the optical diffusion limit (∼1 mm in the skin). Ultrasonic imaging, on the contrary, provides fine spatial resolution but suffers from both poor contrast in early-stage tumors and strong speckle artifacts. In PAT, pulsed laser light penetrates tissue and generates a small but rapid temperature rise, which induces emission of ultrasonic waves due to thermoelastic expansion. The ultrasonic waves, orders of magnitude less scattering than optical waves, are then detected to form high-resolution images of optical absorption at depths up to 7 cm, conquering the optical diffusion limit. PAT is the only modality capable of imaging across the length scales of organelles, cells, tissues, and organs (up to whole-body small animals) with consistent contrast. This rapidly growing technology promises to enable multiscale biological research and accelerate translation from microscopic laboratory discoveries to macroscopic clinical practice. PAT may also hold the key to label-free early detection of cancer by in vivo quantification of hypermetabolism, the quintessential hallmark of malignancy. Learning Objectives: To understand the contrast mechanism of PAT To understand the multiscale applications of PAT Benjamin M. W. Tsui: Multi-modality molecular imaging instrumentation and techniques have been major developments in small animal imaging that has contributed significantly

  17. WE-H-206-01: Photoacoustic Tomography: Multiscale Imaging From Organelles to Patients by Ultrasonically Beating the Optical Diffusion Limit

    International Nuclear Information System (INIS)

    Wang, L.

    2016-01-01

    Lihong V. Wang: Photoacoustic tomography (PAT), combining non-ionizing optical and ultrasonic waves via the photoacoustic effect, provides in vivo multiscale functional, metabolic, and molecular imaging. Broad applications include imaging of the breast, brain, skin, esophagus, colon, vascular system, and lymphatic system in humans or animals. Light offers rich contrast but does not penetrate biological tissue in straight paths as x-rays do. Consequently, high-resolution pure optical imaging (e.g., confocal microscopy, two-photon microscopy, and optical coherence tomography) is limited to penetration within the optical diffusion limit (∼1 mm in the skin). Ultrasonic imaging, on the contrary, provides fine spatial resolution but suffers from both poor contrast in early-stage tumors and strong speckle artifacts. In PAT, pulsed laser light penetrates tissue and generates a small but rapid temperature rise, which induces emission of ultrasonic waves due to thermoelastic expansion. The ultrasonic waves, orders of magnitude less scattering than optical waves, are then detected to form high-resolution images of optical absorption at depths up to 7 cm, conquering the optical diffusion limit. PAT is the only modality capable of imaging across the length scales of organelles, cells, tissues, and organs (up to whole-body small animals) with consistent contrast. This rapidly growing technology promises to enable multiscale biological research and accelerate translation from microscopic laboratory discoveries to macroscopic clinical practice. PAT may also hold the key to label-free early detection of cancer by in vivo quantification of hypermetabolism, the quintessential hallmark of malignancy. Learning Objectives: To understand the contrast mechanism of PAT To understand the multiscale applications of PAT Benjamin M. W. Tsui: Multi-modality molecular imaging instrumentation and techniques have been major developments in small animal imaging that has contributed significantly

  18. Automated single particle detection and tracking for large microscopy datasets.

    Science.gov (United States)

    Wilson, Rhodri S; Yang, Lei; Dun, Alison; Smyth, Annya M; Duncan, Rory R; Rickman, Colin; Lu, Weiping

    2016-05-01

    Recent advances in optical microscopy have enabled the acquisition of very large datasets from living cells with unprecedented spatial and temporal resolutions. Our ability to process these datasets now plays an essential role in order to understand many biological processes. In this paper, we present an automated particle detection algorithm capable of operating in low signal-to-noise fluorescence microscopy environments and handling large datasets. When combined with our particle linking framework, it can provide hitherto intractable quantitative measurements describing the dynamics of large cohorts of cellular components from organelles to single molecules. We begin with validating the performance of our method on synthetic image data, and then extend the validation to include experiment images with ground truth. Finally, we apply the algorithm to two single-particle-tracking photo-activated localization microscopy biological datasets, acquired from living primary cells with very high temporal rates. Our analysis of the dynamics of very large cohorts of 10 000 s of membrane-associated protein molecules show that they behave as if caged in nanodomains. We show that the robustness and efficiency of our method provides a tool for the examination of single-molecule behaviour with unprecedented spatial detail and high acquisition rates.

  19. Analysing long term discursive processes

    DEFF Research Database (Denmark)

    Horsbøl, Anders

    What do timescales - the notion that processes take place or can be viewed within a shorter or longer temporal range (Lemke 2005) - mean for the analysis of discourse? What are the methodological consequences of analyzing discourse at different timescales? It may be argued that discourse analysis...... in general has favored either the analysis of short term processes such as interviews, discussions, and lessons, or the analysis of non-processual entities such as (multimodal) texts, arguments, discursive repertoires, and discourses (in a Foucaultian sense). In contrast, analysis of long term processes...... which extend beyond the single interaction, for instance negotiations or planning processes, seems to have played a less important role, with studies such as Iedema 2001 and Wodak 2000 as exceptions. These long term processes, however, are central to the constitution and workings of organizations...

  20. Uncertainty and Sensitivity Analyses Plan

    International Nuclear Information System (INIS)

    Simpson, J.C.; Ramsdell, J.V. Jr.

    1993-04-01

    Hanford Environmental Dose Reconstruction (HEDR) Project staff are developing mathematical models to be used to estimate the radiation dose that individuals may have received as a result of emissions since 1944 from the US Department of Energy's (DOE) Hanford Site near Richland, Washington. An uncertainty and sensitivity analyses plan is essential to understand and interpret the predictions from these mathematical models. This is especially true in the case of the HEDR models where the values of many parameters are unknown. This plan gives a thorough documentation of the uncertainty and hierarchical sensitivity analysis methods recommended for use on all HEDR mathematical models. The documentation includes both technical definitions and examples. In addition, an extensive demonstration of the uncertainty and sensitivity analysis process is provided using actual results from the Hanford Environmental Dose Reconstruction Integrated Codes (HEDRIC). This demonstration shows how the approaches used in the recommended plan can be adapted for all dose predictions in the HEDR Project

  1. Hydrogen Analyses in the EPR

    International Nuclear Information System (INIS)

    Worapittayaporn, S.; Eyink, J.; Movahed, M.

    2008-01-01

    In severe accidents with core melting large amounts of hydrogen may be released into the containment. The EPR provides a combustible gas control system to prevent hydrogen combustion modes with the potential to challenge the containment integrity due to excessive pressure and temperature loads. This paper outlines the approach for the verification of the effectiveness and efficiency of this system. Specifically, the justification is a multi-step approach. It involves the deployment of integral codes, lumped parameter containment codes and CFD codes and the use of the sigma criterion, which provides the link to the broad experimental data base for flame acceleration (FA) and deflagration to detonation transition (DDT). The procedure is illustrated with an example. The performed analyses show that hydrogen combustion at any time does not lead to pressure or temperature loads that threaten the containment integrity of the EPR. (authors)

  2. Analysing performance through value creation

    Directory of Open Access Journals (Sweden)

    Adrian TRIFAN

    2015-12-01

    Full Text Available This paper draws a parallel between measuring financial performance in 2 variants: the first one using data offered by accounting, which lays emphasis on maximizing profit, and the second one which aims to create value. The traditional approach to performance is based on some indicators from accounting data: ROI, ROE, EPS. The traditional management, based on analysing the data from accounting, has shown its limits, and a new approach is needed, based on creating value. The evaluation of value based performance tries to avoid the errors due to accounting data, by using other specific indicators: EVA, MVA, TSR, CVA. The main objective is shifted from maximizing the income to maximizing the value created for shareholders. The theoretical part is accompanied by a practical analysis regarding the creation of value and an analysis of the main indicators which evaluate this concept.

  3. HGCal Simulation Analyses for CMS

    CERN Document Server

    Bruno, Sarah Marie

    2015-01-01

    This summer, I approached the topic of fast-timing detection of photons from Higgs decays via simulation analyses, working under the supervision of Dr. Adolf Bornheim of the California Institute of Technology. My specific project focused on simulating the high granularity calorimeter for the Compact Muon Solenoid (CMS) experiment. CMS detects particles using calorimeters. The Electromagnetic Calorimeter (ECal) is arranged cylindrically to form a barrel section and two “endcaps.” Previously, both the barrel and endcap have employed lead tungstate crystal detectors, known as the “shashlik” design. The crystal detectors, however, rapidly degrade from exposure to radiation. This effect is most pronounced in the endcaps. To avoid the high expense of frequently replacing degraded detectors, it was recently decided to eliminate the endcap crystals in favor of an arrangement of silicon detectors known as the “High Granularity Calorimeter” (HGCal), while leaving the barrel detector technology unchanged. T...

  4. Isotopic signatures by bulk analyses

    International Nuclear Information System (INIS)

    Efurd, D.W.; Rokop, D.J.

    1997-01-01

    Los Alamos National Laboratory has developed a series of measurement techniques for identification of nuclear signatures by analyzing bulk samples. Two specific applications for isotopic fingerprinting to identify the origin of anthropogenic radioactivity in bulk samples are presented. The first example is the analyses of environmental samples collected in the US Arctic to determine the impact of dumping of radionuclides in this polar region. Analyses of sediment and biota samples indicate that for the areas sampled the anthropogenic radionuclide content of sediments was predominantly the result of the deposition of global fallout. The anthropogenic radionuclide concentrations in fish, birds and mammals were very low. It can be surmised that marine food chains are presently not significantly affected. The second example is isotopic fingerprinting of water and sediment samples from the Rocky Flats Facility (RFP). The largest source of anthropogenic radioactivity presently affecting surface-waters at RFP is the sediments that are currently residing in the holding ponds. One gram of sediment from a holding pond contains approximately 50 times more plutonium than 1 liter of water from the pond. Essentially 100% of the uranium in Ponds A-1 and A-2 originated as depleted uranium. The largest source of radioactivity in the terminal Ponds A-4, B-5 and C-2 was naturally occurring uranium and its decay product radium. The uranium concentrations in the waters collected from the terminal ponds contained 0.05% or less of the interim standard calculated derived concentration guide for uranium in waters available to the public. All of the radioactivity observed in soil, sediment and water samples collected at RFP was naturally occurring, the result of processes at RFP or the result of global fallout. No extraneous anthropogenic alpha, beta or gamma activities were detected. The plutonium concentrations in Pond C-2 appear to vary seasonally

  5. From joint to single audits

    DEFF Research Database (Denmark)

    Holm, Claus; Thinggaard, Frank

    2018-01-01

    This study analyses audit quality differences between audits by a single big audit firm and joint audits with either one or two big audit firms. We exploit the unique situation in Denmark beginning on 1 January 2005, at which time a long-standing mandatory joint audit system for listed companies...... was replaced by a voluntary joint audit system. First, we report the results of a survey of Danish CFOs’ views on and their experiences with the choice of single or joint audits and their perceptions of audit quality. Second, based on data from the mandatory joint audit abolition year and the following two...... years, we test the audit quality differences using abnormal accruals. Most CFOs perceive that audit quality by a single big four audit firm is the same as it is in joint audits with either one or two big four audit firms. The results of our empirical analysis are in line with the perceptions. We find...

  6. Proteins analysed as virtual knots

    Science.gov (United States)

    Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

    2017-02-01

    Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.

  7. Severe Accident Recriticality Analyses (SARA)

    Energy Technology Data Exchange (ETDEWEB)

    Frid, W. [Swedish Nuclear Power Inspectorate, Stockholm (Sweden); Hoejerup, F. [Risoe National Lab. (Denmark); Lindholm, I.; Miettinen, J.; Puska, E.K. [VTT Energy, Helsinki (Finland); Nilsson, Lars [Studsvik Eco and Safety AB, Nykoeping (Sweden); Sjoevall, H. [Teoliisuuden Voima Oy (Finland)

    1999-11-01

    Recriticality in a BWR has been studied for a total loss of electric power accident scenario. In a BWR, the B{sub 4}C control rods would melt and relocate from the core before the fuel during core uncovery and heat-up. If electric power returns during this time-window unborated water from ECCS systems will start to reflood the partly control rod free core. Recriticality might take place for which the only mitigating mechanisms are the Doppler effect and void formation. In order to assess the impact of recriticality on reactor safety, including accident management measures, the following issues have been investigated in the SARA project: 1. the energy deposition in the fuel during super-prompt power burst, 2. the quasi steady-state reactor power following the initial power burst and 3. containment response to elevated quasi steady-state reactor power. The approach was to use three computer codes and to further develop and adapt them for the task. The codes were SIMULATE-3K, APROS and RECRIT. Recriticality analyses were carried out for a number of selected reflooding transients for the Oskarshamn 3 plant in Sweden with SIMULATE-3K and for the Olkiluoto 1 plant in Finland with all three codes. The core state initial and boundary conditions prior to recriticality have been studied with the severe accident codes SCDAP/RELAP5, MELCOR and MAAP4. The results of the analyses show that all three codes predict recriticality - both superprompt power bursts and quasi steady-state power generation - for the studied range of parameters, i. e. with core uncovery and heat-up to maximum core temperatures around 1800 K and water flow rates of 45 kg/s to 2000 kg/s injected into the downcomer. Since the recriticality takes place in a small fraction of the core the power densities are high which results in large energy deposition in the fuel during power burst in some accident scenarios. The highest value, 418 cal/g, was obtained with SIMULATE-3K for an Oskarshamn 3 case with reflooding

  8. Ergonomic analyses of downhill skiing.

    Science.gov (United States)

    Clarys, J P; Publie, J; Zinzen, E

    1994-06-01

    The purpose of this study was to provide electromyographic feedback for (1) pedagogical advice in motor learning, (2) the ergonomics of materials choice and (3) competition. For these purposes: (1) EMG data were collected for the Stem Christie, the Stem Turn and the Parallel Christie (three basic ski initiation drills) and verified for the complexity of patterns; (2) integrated EMG (iEMG) and linear envelopes (LEs) were analysed from standardized positions, motions and slopes using compact, soft and competition skis; (3) in a simulated 'parallel special slalom', the muscular activity pattern and intensity of excavated and flat snow conditions were compared. The EMG data from the three studies were collected on location in the French Alps (Tignes). The analog raw EMG was recorded on the slopes with a portable seven-channel FM recorder (TEAC MR30) and with pre-amplified bipolar surface electrodes supplied with a precision instrumentation amplifier (AD 524, Analog Devices, Norwood, USA). The raw signal was full-wave rectified and enveloped using a moving average principle. This linear envelope was normalized according to the highest peak amplitude procedure per subject and was integrated in order to obtain a reference of muscular intensity. In the three studies and for all subjects (elite skiers: n = 25 in studies 1 and 2, n = 6 in study 3), we found a high level of co-contractions in the lower limb extensors and flexors, especially during the extension phase of the ski movement. The Stem Christie and the Parallel Christie showed higher levels of rhythmic movement (92 and 84%, respectively).(ABSTRACT TRUNCATED AT 250 WORDS)

  9. Network-Based and Binless Frequency Analyses.

    Directory of Open Access Journals (Sweden)

    Sybil Derrible

    Full Text Available We introduce and develop a new network-based and binless methodology to perform frequency analyses and produce histograms. In contrast with traditional frequency analysis techniques that use fixed intervals to bin values, we place a range ±ζ around each individual value in a data set and count the number of values within that range, which allows us to compare every single value of a data set with one another. In essence, the methodology is identical to the construction of a network, where two values are connected if they lie within a given a range (±ζ. The value with the highest degree (i.e., most connections is therefore assimilated to the mode of the distribution. To select an optimal range, we look at the stability of the proportion of nodes in the largest cluster. The methodology is validated by sampling 12 typical distributions, and it is applied to a number of real-world data sets with both spatial and temporal components. The methodology can be applied to any data set and provides a robust means to uncover meaningful patterns and trends. A free python script and a tutorial are also made available to facilitate the application of the method.

  10. Interim Basis for PCB Sampling and Analyses

    International Nuclear Information System (INIS)

    BANNING, D.L.

    2001-01-01

    This document was developed as an interim basis for sampling and analysis of polychlorinated biphenyls (PCBs) and will be used until a formal data quality objective (DQO) document is prepared and approved. On August 31, 2000, the Framework Agreement for Management of Polychlorinated Biphenyls (PCBs) in Hanford Tank Waste was signed by the US. Department of Energy (DOE), the Environmental Protection Agency (EPA), and the Washington State Department of Ecology (Ecology) (Ecology et al. 2000). This agreement outlines the management of double shell tank (DST) waste as Toxic Substance Control Act (TSCA) PCB remediation waste based on a risk-based disposal approval option per Title 40 of the Code of Federal Regulations 761.61 (c). The agreement calls for ''Quantification of PCBs in DSTs, single shell tanks (SSTs), and incoming waste to ensure that the vitrification plant and other ancillary facilities PCB waste acceptance limits and the requirements of the anticipated risk-based disposal approval are met.'' Waste samples will be analyzed for PCBs to satisfy this requirement. This document describes the DQO process undertaken to assure appropriate data will be collected to support management of PCBs and is presented in a DQO format. The DQO process was implemented in accordance with the U.S. Environmental Protection Agency EPA QAlG4, Guidance for the Data Quality Objectives Process (EPA 1994) and the Data Quality Objectives for Sampling and Analyses, HNF-IP-0842/Rev.1 A, Vol. IV, Section 4.16 (Banning 1999)

  11. Reproducibility of neuroimaging analyses across operating systems.

    Science.gov (United States)

    Glatard, Tristan; Lewis, Lindsay B; Ferreira da Silva, Rafael; Adalat, Reza; Beck, Natacha; Lepage, Claude; Rioux, Pierre; Rousseau, Marc-Etienne; Sherif, Tarek; Deelman, Ewa; Khalili-Mahani, Najmeh; Evans, Alan C

    2015-01-01

    Neuroimaging pipelines are known to generate different results depending on the computing platform where they are compiled and executed. We quantify these differences for brain tissue classification, fMRI analysis, and cortical thickness (CT) extraction, using three of the main neuroimaging packages (FSL, Freesurfer and CIVET) and different versions of GNU/Linux. We also identify some causes of these differences using library and system call interception. We find that these packages use mathematical functions based on single-precision floating-point arithmetic whose implementations in operating systems continue to evolve. While these differences have little or no impact on simple analysis pipelines such as brain extraction and cortical tissue classification, their accumulation creates important differences in longer pipelines such as subcortical tissue classification, fMRI analysis, and cortical thickness extraction. With FSL, most Dice coefficients between subcortical classifications obtained on different operating systems remain above 0.9, but values as low as 0.59 are observed. Independent component analyses (ICA) of fMRI data differ between operating systems in one third of the tested subjects, due to differences in motion correction. With Freesurfer and CIVET, in some brain regions we find an effect of build or operating system on cortical thickness. A first step to correct these reproducibility issues would be to use more precise representations of floating-point numbers in the critical sections of the pipelines. The numerical stability of pipelines should also be reviewed.

  12. In-Depth Temporal Transcriptome Profiling Reveals a Crucial Developmental Switch with Roles for RNA Processing and Organelle Metabolism That Are Essential for Germination in Arabidopsis1[W][OA

    Science.gov (United States)

    Narsai, Reena; Law, Simon R.; Carrie, Chris; Xu, Lin; Whelan, James

    2011-01-01

    Germination represents a rapid transition from dormancy to a high level of metabolic activity. In-depth transcriptomic profiling at 10 time points in Arabidopsis (Arabidopsis thaliana), including fresh seed, ripened seed, during stratification, germination, and postgermination per se, revealed specific temporal expression patterns that to our knowledge have not previously been identified. Over 10,000 transcripts were differentially expressed during cold stratification, with subequal numbers up-regulated as down-regulated, revealing an active period in preparing seeds for germination, where transcription and RNA degradation both play important roles in regulating the molecular sequence of events. A previously unidentified transient expression pattern was observed for a group of genes, whereby a significant rise in expression was observed at the end of stratification and significantly lower expression was observed 6 h later. These genes were further defined as germination specific, as they were most highly expressed at this time in germination, in comparison with all developmental tissues in the AtGenExpress data set. Functional analysis of these genes using genetic inactivation revealed that they displayed a significant enrichment for embryo-defective or -arrested phenotype. This group was enriched in genes encoding mitochondrial and nuclear RNA-processing proteins, including more than 45% of all pentatricopeptide domain-containing proteins expressed during germination. The presence of mitochondrial DNA replication factors and RNA-processing functions in this germination-specific subset represents the earliest events in organelle biogenesis, preceding any changes associated with energy metabolism. Green fluorescent protein analysis also confirmed organellar localization for 65 proteins, largely showing germination-specific expression. These results suggest that mitochondrial biogenesis involves a two-step process to produce energetically active organelles: an

  13. Automatic incrementalization of Prolog based static analyses

    DEFF Research Database (Denmark)

    Eichberg, Michael; Kahl, Matthias; Saha, Diptikalyan

    2007-01-01

    Modem development environments integrate various static analyses into the build process. Analyses that analyze the whole project whenever the project changes are impractical in this context. We present an approach to automatic incrementalization of analyses that are specified as tabled logic...... incrementalizing a broad range of static analyses....

  14. Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana

    KAUST Repository

    Bigeard, Jean

    2014-07-10

    The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.

  15. Genetic biosensors for imaging nitric oxide in single cells.

    Science.gov (United States)

    Eroglu, Emrah; Charoensin, Suphachai; Bischof, Helmut; Ramadani, Jeta; Gottschalk, Benjamin; Depaoli, Maria R; Waldeck-Weiermair, Markus; Graier, Wolfgang F; Malli, Roland

    2018-02-01

    Over the last decades a broad collection of sophisticated fluorescent protein-based probes was engineered with the aim to specifically monitor nitric oxide (NO), one of the most important signaling molecules in biology. Here we report and discuss the characteristics and fields of applications of currently available genetically encoded fluorescent sensors for the detection of NO and its metabolites in different cell types. Because of its radical nature and short half-life, real-time imaging of NO on the level of single cells is challenging. Herein we review state-of-the-art genetically encoded fluorescent sensors for NO and its byproducts such as peroxynitrite, nitrite and nitrate. Such probes enable the real-time visualization of NO signals directly or indirectly on the level of single cells and cellular organelles and, hence, extend our understanding of the spatiotemporal dynamics of NO formation, diffusion and degradation. Here, we discuss the significance of NO detection in individual cells and on subcellular level with genetic biosensors. Currently available genetically encoded fluorescent probes for NO and nitrogen species are critically discussed in order to provide insights in the functionality and applicability of these promising tools. As an outlook we provide ideas for novel approaches for the design and application of improved NO probes and fluorescence imaging protocols. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  16. Pawnee Nation Energy Option Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Matlock, M.; Kersey, K.; Riding In, C.

    2009-07-21

    Pawnee Nation of Oklahoma Energy Option Analyses In 2003, the Pawnee Nation leadership identified the need for the tribe to comprehensively address its energy issues. During a strategic energy planning workshop a general framework was laid out and the Pawnee Nation Energy Task Force was created to work toward further development of the tribe’s energy vision. The overarching goals of the “first steps” project were to identify the most appropriate focus for its strategic energy initiatives going forward, and to provide information necessary to take the next steps in pursuit of the “best fit” energy options. Description of Activities Performed The research team reviewed existing data pertaining to the availability of biomass (focusing on woody biomass, agricultural biomass/bio-energy crops, and methane capture), solar, wind and hydropower resources on the Pawnee-owned lands. Using these data, combined with assumptions about costs and revenue streams, the research team performed preliminary feasibility assessments for each resource category. The research team also reviewed available funding resources and made recommendations to Pawnee Nation highlighting those resources with the greatest potential for financially-viable development, both in the near-term and over a longer time horizon. Findings and Recommendations Due to a lack of financial incentives for renewable energy, particularly at the state level, combined mediocre renewable energy resources, renewable energy development opportunities are limited for Pawnee Nation. However, near-term potential exists for development of solar hot water at the gym, and an exterior wood-fired boiler system at the tribe’s main administrative building. Pawnee Nation should also explore options for developing LFGTE resources in collaboration with the City of Pawnee. Significant potential may also exist for development of bio-energy resources within the next decade. Pawnee Nation representatives should closely monitor

  17. The paths of mortality: how understanding the biology of aging can help explain systems behavior of single cells.

    Science.gov (United States)

    Crane, Matthew M; Kaeberlein, Matt

    2018-04-01

    Aging is a fundamental aspect of life, yet also one of the most confounding. In individual cells, aging results in a progressive decline which affects all organelles and reduces a cell's ability to maintain homeostasis. Because of the interconnected nature of cellular systems, the failure of even a single organelle can have cascading effects. We are just beginning to understand the dramatic physiological changes that occur during aging. Because most aging research has focused on population dynamics, or differences between wild-type and mutant populations, single-cell behavior has been largely overlooked. An open question is whether aging cells are defined by predictable sequences of physiological changes, or whether they proceed along divergent aging trajectories defined by whichever system begins to fail first. Can aging be best characterized by a cell-cycle like model with stereotyped states all cells progress through, or a Waddington landscape with divergent trajectories? Here we present work on understanding the changing physiological states of aging cells, why it will impact systems and synthetic biologists, and how the systems community can contribute significantly to the study of aging.

  18. Chloroplast genes in Chlamydomonas affecting organelle ribosomes. Genetic and biochemical analysis of analysis of antibiotic-resistant mutants at several gene loci.

    Science.gov (United States)

    Conde, M F; Boynton, J E; Gillham, N W; Harris, E H; Tingle, C L; Wang, W L

    1975-10-03

    Six chloroplast gene mutants of Chlamydomonas reinhardtii resistant to spectinomycin, erythromycin, or streptomycin have been assessed for antibiotic resistance of their chloroplast ribosomes. Four of these mutations clearly confer high levels of antibiotic resistance on the chloroplast ribosomes both in vivo. Although one mutant resistant to streptomycin and one resistant to spectinomycin have chloroplast ribosomes as sensitive to antibiotics as those of wild type in vivo, these mutations can be shown to alter the wildtype sensitivity of chloroplast ribosomes in polynucleotide-directed amino acid incorporation in vitro. Genetic analysis of these six chloroplast mutants and three similar mutants (Sager, 1972), two of which have been shown to affect chloroplast ribosomes (Mets and Bogorad, 1972; Schlanger and Sager, 1974), indicates that in Chlamydomonas at least three chloroplast gene loci can affect streptomycin resistance of chloroplast ribosomes and that two can affect erythromycin resistance. The three spectinomycin-resistant mutants examined appear to be alleles at a single chloroplast gene locus, but may represent mutations at two different sites within the same gene. Unlike wild type, the streptomycin and spectinomycin resistant mutants which have chloroplast ribosomes sensitive to antibiotics in vivo, grow well in the presence of antibiotic by respiring exogenously supplied acetate as a carbon source, and have normal levels of cytochrome oxidase activity and cyanide-sensitive respiration. We conclude that mitochondrial protein synthesis in these mutants is resistant to these antibiotics, whereas in wild type it is sensitive. To explain the behavior of these two chloroplast gene mutants as well as other one-step mutants which are resistant both photosynthetically and when respiring acetate in the dark, we have postulated that a mutation in a single chloroplast gene may result in alteration of both chloroplast and mitochondrial ribosomes. Mitochondrial

  19. Genome-Facilitated Analyses of Geomicrobial Processes

    Energy Technology Data Exchange (ETDEWEB)

    Kenneth H. Nealson

    2012-05-02

    This project had the goal(s) of understanding the mechanism(s) of extracellular electron transport (EET) in the microbe Shewanella oneidensis MR-1, and a number of other strains and species in the genus Shewanella. The major accomplishments included sequencing, annotation, and analysis of more than 20 Shewanella genomes. The comparative genomics enabled the beginning of a systems biology approach to this genus. Another major contribution involved the study of gene regulation, primarily in the model organism, MR-1. As part of this work, we took advantage of special facilities at the DOE: e.g., the synchrotron radiation facility at ANL, where we successfully used this system for elemental characterization of single cells in different metabolic states (1). We began work with purified enzymes, and identification of partially purified enzymes, leading to initial characterization of several of the 42 c-type cytochromes from MR-1 (2). As the genome became annotated, we began experiments on transcriptome analysis under different conditions of growth, the first step towards systems biology (3,4). Conductive appendages of Shewanella, called bacterial nanowires were identified and characterized during this work (5, 11, 20,21). For the first time, it was possible to measure the electron transfer rate between single cells and a solid substrate (20), a rate that has been confirmed by several other laboratories. We also showed that MR-1 cells preferentially attach to cells at a given charge, and are not attracted, or even repelled by other charges. The interaction with the charged surfaces begins with a stimulation of motility (called electrokinesis), and eventually leads to attachment and growth. One of the things that genomics allows is the comparative analysis of the various Shewanella strains, which led to several important insights. First, while the genomes predicted that none of the strains looked like they should be able to degrade N-acetyl glucosamine (NAG), the monomer

  20. Techniques for Analysing Problems in Engineering Projects

    DEFF Research Database (Denmark)

    Thorsteinsson, Uffe

    1998-01-01

    Description of how CPM network can be used for analysing complex problems in engineering projects.......Description of how CPM network can be used for analysing complex problems in engineering projects....

  1. Loss of a doublecortin (DCX)-domain protein causes structural defects in a tubulin-based organelle of Toxoplasma gondii and impairs host-cell invasion

    Science.gov (United States)

    Nagayasu, Eiji; Hwang, Yu-Chen; Liu, Jun; Murray, John M.; Hu, Ke

    2017-01-01

    The ∼6000 species in phylum Apicomplexa are single-celled obligate intracellular parasites. Their defining characteristic is the apical complex—membranous and cytoskeletal elements at the apical end of the cell that participate in host-cell invasion. The apical complex of Toxoplasma gondii and some other apicomplexans includes a cone-shaped assembly, the conoid, which in T. gondii comprises 14 spirally arranged fibers that are nontubular polymers of tubulin. The tubulin dimers of the conoid fibers make canonical microtubules elsewhere in the same cell, suggesting that nontubulin protein dictates their special arrangement in the conoid fibers. One candidate for this role is TgDCX, which has a doublecortin (DCX) domain and a TPPP/P25-α domain, both of which are known modulators of tubulin polymer structure. Loss of TgDCX radically disrupts the structure of the conoid, severely impairs host-cell invasion, and slows growth. Both the conoid structural defects and the impaired invasion of TgDCX-null parasites are corrected by reintroduction of a TgDCX coding sequence. The nontubular polymeric form of tubulin found in the conoid is not found in the host cell, suggesting that TgDCX may be an attractive target for new parasite-specific chemotherapeutic agents. PMID:27932494

  2. Single Audit: Single Audit Act Effectiveness Issues

    National Research Council Canada - National Science Library

    Thompson, Sally

    2002-01-01

    As discussed in the report we are releasing today, our work to review agency actions to ensure that recipients take timely and appropriate corrective actions to fix audit findings contained in single...

  3. Single photon from a single trapped atom

    International Nuclear Information System (INIS)

    Dingjan, J.; Jones, M.P.A.; Beugnon, J.; Darquiee, B.; Bergamini, S.; Browaeys, A.; Messin, G.; Grangier, P.

    2005-01-01

    Full text: A quantum treatment of the interaction between atoms and light usually begins with the simplest model system: a two-level atom interacting with a monochromatic light wave. Here we demonstrate an elegant experimental realization of this system using an optically trapped single rubidium atom illuminated by resonant light pulses. We observe Rabi oscillations, and show that this system can be used as a highly efficient triggered source of single photons with a well-defined polarisation. In contrast to other sources based on neutral atoms and trapped ions, no optical cavity is required. We achieved a flux of single photons of about 10 4 s -1 at the detector, and observe complete antibunching. This source has potential applications for distributed atom-atom entanglement using single photons. (author)

  4. Improving word coverage using unsupervised morphological analyser

    Indian Academy of Sciences (India)

    Institute of Information Technology (IIIT), Hyderabad. The study was made in various direc- tions to compare the results our system developed with the out put of Hindi Analyser developed by IIIT, Hyderabad. 3.1 Comparison of rule-based morphological analyser with unsupervised morphological analyser. 3.1a Calculation of ...

  5. Prospects of Single Tax Payers

    Directory of Open Access Journals (Sweden)

    Tofan Ivan M.

    2014-03-01

    Full Text Available The article speaks about problem aspects of taxation, which were set by the state for the single tax administering due to permanent and system changes in the tax legislation. It shows the necessity of search for alternative methods of administering in the process of taxation of single tax payers by fiscal services. The goal of the article is the study of prospects of further taxation of entrepreneurs – single tax payers on the basis of analysis of conditions and principles created by the state for the business. The article used methods of system analysis, comparison, forecasting and modelling. It analyses the process of evolution of the simplified taxation system, accounting and reporting from the moment of its adoption until today. The article presents the structure of the quantitative composition of single tax payers depending on the selected groups. It marks out and characterises administrative and fiscal factors that do not facilitate further development of entrepreneurship in Ukraine. In the result of the conducted studies the article outlines problem aspects of organisation of taxation of the small business and offers specific and real ways of their overcoming or partial solution.

  6. Single-molecule nanopore enzymology

    Science.gov (United States)

    Wloka, Carsten; Maglia, Giovanni

    2017-01-01

    Biological nanopores are a class of membrane proteins that open nanoscale water-conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. More recently, proteins and enzymes have started being analysed with nanopores. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here we describe the approaches and challenges in nanopore enzymology. PMID:28630164

  7. High perfomance liquid chromatography in pharmaceutical analyses.

    Science.gov (United States)

    Nikolin, Branko; Imamović, Belma; Medanhodzić-Vuk, Saira; Sober, Miroslav

    2004-05-01

    compounds often present in concentrations much greater than those of analyte. Analiyte concentrations are often low, and in the case of drugs, the endogenous compounds are sometimes structurally very similar to the drug to be measured. The binding of drugs to the plasma protein also may occur which decreases the amount of free compound that is measured. To undertake the analyses of drugs and metabolites in body fluids the analyst is facet with several problems. The first problem is due to the complex nature of the body fluid, the drugs must be isolated by an extraction technique, which ideally should provide a relatively clean extract, and the separation system must be capable of resolving the drugs of interest from co extractives. All mentioned when we are using high performance liquid chromatography require good selections of detectors, good stationary phase, eluents and adequate program during separation. UV/VIS detector is the most versatile detector used in high performance liquid chromatography it is not always ideal since it is lack of specificity means high resolution of the analyte that may be required. UV detection is preferred since it offers excellent linearity and rapid quantitative analyses can be performed against a single standard of the drug being determined. Diode array and rapid scanning detector are useful for peak identification and monitoring peak purity but they are somewhat less sensitive then single wavelength detectors. In liquid chromatography some components may have a poor UV chromophores if UV detection is being used or be completely retained on the liquid chromatography column. Fluorescence and electrochemical detector are not only considerably more sensitive towed appropriate analytes but also more selective than UV detectors for many compounds. If at all possible fluorescence detectors are sensitive, stable, selective and easy to operate. It is selectivity shows itself in the lack of frontal components observed in plasma extract whereas

  8. Vps15p regulates the distribution of cup-shaped organelles containing the major eisosome protein Pil1p to the extracellular fraction required for endocytosis of extracellular vesicles carrying metabolic enzymes.

    Science.gov (United States)

    Stein, Kathryn; Winters, Chelsea; Chiang, Hui-Ling

    2017-05-01

    Exosomes are small vesicles secreted from virtually every cell from bacteria to humans. Saccharomyces cerevisiae is a model system to study trafficking of small vesicles in response to changes in the environment. When yeast cells are grown in low glucose, vesicles carrying gluconeogenic enzymes are present as free vesicles and aggregated clusters in the cytoplasm. These vesicles are also secreted into the periplasm and account for more than 90% of total extracellular organelles, while less than 10% are larger 100-300 nm structures with unknown functions. When glucose is added to glucose-starved cells, secreted vesicles are endocytosed and then targeted to the vacuole. Recent secretomic studies indicated that more than 300 proteins involved in diverse biological functions are secreted during glucose starvation and endocytosed during glucose re-feeding. We hypothesised that extracellular vesicles are internalised using novel mechanisms independent of clathrin-mediated endocytosis. Our results showed that vesicles carrying metabolic enzymes were endocytosed at a fast rate, whereas vesicles carrying the heat shock protein Ssa1p were endocytosed at a slow rate. The PI3K regulator Vps15p is critical for the fast internalisation of extracellular vesicles. VPS15 regulates the distribution of the 100-300 nm organelles that contain the major eisosome protein Pil1p to the extracellular fraction. These Pil1p-containing structures were purified and showed unique cup-shape with their centres deeper than the peripheries. In the absence of VPS15, PIL1 or when PIL1 was mutated, the 100-300 nm structures were not observed in the extracellular fraction and the rapid internalisation of vesicles was impaired. We conclude that VPS15 regulates the distribution of the 100-300 nm Pil1p-containing organelles to the extracellular fraction required for fast endocytosis of vesicles carrying metabolic enzymes. This work provides the first evidence showing that Pil1p displayed unique

  9. Automated Single Cell Data Decontamination Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Tennessen, Kristin [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Pati, Amrita [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

    2014-03-21

    Recent technological advancements in single-cell genomics have encouraged the classification and functional assessment of microorganisms from a wide span of the biospheres phylogeny.1,2 Environmental processes of interest to the DOE, such as bioremediation and carbon cycling, can be elucidated through the genomic lens of these unculturable microbes. However, contamination can occur at various stages of the single-cell sequencing process. Contaminated data can lead to wasted time and effort on meaningless analyses, inaccurate or erroneous conclusions, and pollution of public databases. A fully automated decontamination tool is necessary to prevent these instances and increase the throughput of the single-cell sequencing process

  10. Single-cell technologies in environmental omics

    KAUST Repository

    Kodzius, Rimantas

    2015-10-22

    Environmental studies are primarily done by culturing isolated microorganisms or by amplifying and sequencing conserved genes. Difficulties understanding the complexity of large numbers of various microorganisms in an environment led to the development of techniques to enrich specific microorganisms for upstream analysis, ultimately leading to single-cell isolation and analyses. We discuss the significance of single-cell technologies in omics studies with focus on metagenomics and metatranscriptomics. We propose that by reducing sample heterogeneity using single-cell genomics, metaomic studies can be simplified.

  11. Single frequency intracavity SRO

    DEFF Research Database (Denmark)

    Abitan, Haim; Buchhave, Preben

    2000-01-01

    Summary form only given. A single resonance optical parametric oscillator (SRO) is inserted intracavity to a CW high power, single frequency, and ring Nd:YVO4 laser. We obtain a stable single frequency CW SRO with output at 1.7-1.9 μm (idler) and a resonating signal at 2.3-2.6 μm. The behavior...

  12. HLA region excluded by linkage analyses of early onset periodontitis

    Energy Technology Data Exchange (ETDEWEB)

    Sun, C.; Wang, S.; Lopez, N.

    1994-09-01

    Previous studies suggested that HLA genes may influence susceptibility to early-onset periodontitis (EOP). Segregation analyses indicate that EOP may be due to a single major gene. We conducted linkage analyses to assess possible HLA effects on EOP. Fifty families with two or more close relatives affected by EOP were ascertained in Virginia and Chile. A microsatellite polymorphism within the HLA region (at the tumor necrosis factor beta locus) was typed using PCR. Linkage analyses used a donimant model most strongly supported by previous studies. Assuming locus homogeneity, our results exclude a susceptibility gene within 10 cM on either side of our marker locus. This encompasses all of the HLA region. Analyses assuming alternative models gave qualitatively similar results. Allowing for locus heterogeneity, our data still provide no support for HLA-region involvement. However, our data do not statistically exclude (LOD <-2.0) hypotheses of disease-locus heterogeneity, including models where up to half of our families could contain an EOP disease gene located in the HLA region. This is due to the limited power of even our relatively large collection of families and the inherent difficulties of mapping genes for disorders that have complex and heterogeneous etiologies. Additional statistical analyses, recruitment of families, and typing of flanking DNA markers are planned to more conclusively address these issues with respect to the HLA region and other candidate locations in the human genome. Additional results for markers covering most of the human genome will also be presented.

  13. Analyses of single nucleotide polymorphisms in selected nutrient-sensitive genes in weight-regain prevention

    DEFF Research Database (Denmark)

    Larsen, Lesli Hingstrup; Ängquist, Lars Henrik; Vimaleswaran, Karani S

    2012-01-01

    Differences in the interindividual response to dietary intervention could be modified by genetic variation in nutrient-sensitive genes.......Differences in the interindividual response to dietary intervention could be modified by genetic variation in nutrient-sensitive genes....

  14. [Anne Arold. Kontrastive Analyse...] / Paul Alvre

    Index Scriptorium Estoniae

    Alvre, Paul, 1921-2008

    2001-01-01

    Arvustus: Arold, Anne. Kontrastive analyse der Wortbildungsmuster im Deutschen und im Estnischen (am Beispiel der Aussehensadjektive). Tartu, 2000. (Dissertationes philologiae germanicae Universitatis Tartuensis)

  15. 3D analyses of cavitation instabilities accounting for plastic anisotropy

    DEFF Research Database (Denmark)

    Legarth, Brian Nyvang; Tvergaard, Viggo

    2010-01-01

    Full three dimensional cell model analyses are carried out for a solid containing a single small void, in order to determine the critical stress levels for the occurrence of cavitation instabilities. The material models applied are elastic‐viscoplastic, with a small rate‐hardening exponent...... that the quasi‐static solution is well approximated. A special procedure is used to strongly reduce the loading rate a little before the instability occurs. It is found that plastic anisotropy has a significant effect on the level of the critical stress for cavitation instabilities....

  16. Approximate analyses of inelastic effects in pipework

    International Nuclear Information System (INIS)

    Jobson, D.A.

    1983-01-01

    This presentation shows figures concerned with analyses of inelastic effects in pipework as follows: comparison of experimental and calculated simplified analyses results for free end rotation and for circumferential strain; interrupted stress relaxation; regenerated relaxation caused by reversed yield; buckling of straight pipe under combined bending and torsion; results of fatigues test of pipe bend

  17. Roux 105 PHONETIC DATA AND PHONOLOGICAL ANALYSES ...

    African Journals Online (AJOL)

    This paper is basically concerned with the relationship between phonetic data and phonological analyses. I) It will be shown that phonological analyses based on unverified phonetic data tend to accommodate ad hoc, unmotivated, and even phonetically implausible phonological rules. On the other hand, it will be ...

  18. Diversity of primary care systems analysed.

    NARCIS (Netherlands)

    Kringos, D.; Boerma, W.; Bourgueil, Y.; Cartier, T.; Dedeu, T.; Hasvold, T.; Hutchinson, A.; Lember, M.; Oleszczyk, M.; Pavlick, D.R.

    2015-01-01

    This chapter analyses differences between countries and explains why countries differ regarding the structure and process of primary care. The components of primary care strength that are used in the analyses are health policy-making, workforce development and in the care process itself (see Fig.

  19. Random error in cardiovascular meta-analyses

    DEFF Research Database (Denmark)

    Albalawi, Zaina; McAlister, Finlay A; Thorlund, Kristian

    2013-01-01

    BACKGROUND: Cochrane reviews are viewed as the gold standard in meta-analyses given their efforts to identify and limit systematic error which could cause spurious conclusions. The potential for random error to cause spurious conclusions in meta-analyses is less well appreciated. METHODS: We exam...

  20. Novel Algorithms for Astronomical Plate Analyses

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... Powerful computers and dedicated software allow effective data mining and scientific analyses in astronomical plate archives. We give and discuss examples of newly developed algorithms for astronomical plate analyses, e.g., searches for optical transients, as well as for major spectral and brightness ...

  1. A review of bioinformatic methods for forensic DNA analyses.

    Science.gov (United States)

    Liu, Yao-Yuan; Harbison, SallyAnn

    2018-03-01

    Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Creation of a knowledge management system for QT analyses.

    Science.gov (United States)

    Tornøe, Christoffer W; Garnett, Christine E; Wang, Yaning; Florian, Jeffry; Li, Michael; Gobburu, Jogarao V

    2011-07-01

    An increasing number of thorough QT (TQT) reports are being submitted to the US Food and Drug Administration's interdisciplinary review team for QT (IRT-QT), requiring time-intensive quantitative analyses by a multidisciplinary review team within 45 days. This calls for systematic learning to guide future trials and policies by standardizing and automating the QT analyses to improve review efficiency, provide consistent advice, and enable pooled data analyses to answer key regulatory questions. The QT interval represents the time from initiation of ventricular depolarization to completion of ventricular repolarization recorded by electrocardiograph (ECG) and is used in the proarrhythmic risk assessment. The developed QT knowledge management system is implemented in the R package "QT." Data from 11 crossover TQT studies including time-matched ECGs and pharmacokinetic measurements following single doses of 400 to 1200 mg moxifloxacin were used for the QT analysis example. The automated workflow was divided into 3 components (data management, analysis, and archival). The generated data sets, scripts, tables, and graphs are automatically stored in a queryable repository and summarized in an analysis report. More than 100 TQT studies have been analyzed using the system since 2007. This has dramatically reduced the time needed to review TQT studies and has made the IRT-QT reviews consistent across reviewers. Furthermore, the system enables leveraging prior knowledge through pooled data analyses to answer policy-related questions and to understand the various effects that influence study results.

  3. Single ventricle cardiac defect

    International Nuclear Information System (INIS)

    Eren, B.; Turkmen, N.; Fedakar, R.; Cetin, V.

    2010-01-01

    Single ventricle heart is defined as a rare cardiac abnormality with a single ventricle chamber involving diverse functional and physiological defects. Our case is of a ten month-old baby boy who died shortly after admission to the hospital due to vomiting and diarrhoea. Autopsy findings revealed cyanosis of finger nails and ears. Internal examination revealed; large heart, weighing 60 grams, single ventricle, without a septum and upper membranous part. Single ventricle is a rare pathology, hence, this paper aims to discuss this case from a medico-legal point of view. (author)

  4. Cost-Benefit Analyses of Transportation Investments

    DEFF Research Database (Denmark)

    Næss, Petter

    2006-01-01

    -to-pay investigations. Accepting the ontological and epistemological assumptions of cost-benefit analysis involves an implicit acceptance of the ethical and political values favoured by these assumptions. Cost-benefit analyses of transportation investment projects tend to neglect long-term environmental consequences...... and needs among population groups with a low ability to pay. Instead of cost-benefit analyses, impact analyses evaluating the likely effects of project alternatives against a wide range of societal goals is recommended, with quantification and economic valorisation only for impact categories where this can......This paper discusses the practice of cost-benefit analyses of transportation infrastructure investment projects from the meta-theoretical perspective of critical realism. Such analyses are based on a number of untenable ontological assumptions about social value, human nature and the natural...

  5. Single-level resonance parameters fit nuclear cross-sections

    Science.gov (United States)

    Drawbaugh, D. W.; Gibson, G.; Miller, M.; Page, S. L.

    1970-01-01

    Least squares analyses of experimental differential cross-section data for the U-235 nucleus have yielded single level Breit-Wigner resonance parameters that fit, simultaneously, three nuclear cross sections of capture, fission, and total.

  6. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    GENERAL ARTICLE. Single-Molecule Spectroscopy. Every Molecule is Different! Kankan Bhattacharyya. Keywords. Single-molecule spectroscopy. (SMS), confocal microscopy,. FCS, sm-FRET, FLIM. 1 High-resolution spectrum re- fers to a spectrum consisting of very sharp lines. The sharp lines clearly display transitions to ...

  7. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    RESONANCE. February 2015. GENERAL ARTICLE. Single-Molecule Spectroscopy. Every Molecule is Different! Kankan Bhattacharyya. Keywords. Single-molecule ..... Resonance Energy. Transfer (FRET) is an elegant technique to measure the distance between a donor and an acceptor molecule. FRET refers to the.

  8. Single photon and nonlocality

    Indian Academy of Sciences (India)

    critical analysis of the concept of hidden variable used by the authors of [1] shows that the reasoning is not correct. Keywords. Nonlocality; single particle; hidden variables. PACS Nos 03.67.Ba; 03.65.Ta; 32.80.Lg; 07.79.Fc. 1. Introduction. Quantum nonlocality [2] for single particle is a subject of debate since the origin.

  9. Single gaze gestures

    DEFF Research Database (Denmark)

    Møllenbach, Emilie; Lilholm, Martin; Gail, Alastair

    2010-01-01

    This paper examines gaze gestures and their applicability as a generic selection method for gaze-only controlled interfaces. The method explored here is the Single Gaze Gesture (SGG), i.e. gestures consisting of a single point-to-point eye movement. Horizontal and vertical, long and short SGGs were...

  10. Understanding Single Adulthood.

    Science.gov (United States)

    Stein, Peter J.

    The life styles and life chances of the unmarried include elements of choices. Singles may be grouped and characterized according to whether their status may be considered stable or temporary. A life cycle, or continuum model of singlehood is reviewed, including its different factors, or phases. A new model for singles is proposed--a life spiral…

  11. Single-sided NMR

    CERN Document Server

    Casanova, Federico; Blümich, Bernhard

    2011-01-01

    Single-Sided NMR describes the design of the first functioning single-sided tomograph, the related measurement methods, and a number of applications. One of the key advantages to this method is the speed at which the images are obtained.

  12. Single molecules and nanotechnology

    CERN Document Server

    Vogel, Horst

    2007-01-01

    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  13. Single-photon imaging

    CERN Document Server

    Seitz, Peter

    2011-01-01

    The acquisition and interpretation of images is a central capability in almost all scientific and technological domains. In particular, the acquisition of electromagnetic radiation, in the form of visible light, UV, infrared, X-ray, etc. is of enormous practical importance. The ultimate sensitivity in electronic imaging is the detection of individual photons. With this book, the first comprehensive review of all aspects of single-photon electronic imaging has been created. Topics include theoretical basics, semiconductor fabrication, single-photon detection principles, imager design and applications of different spectral domains. Today, the solid-state fabrication capabilities for several types of image sensors has advanced to a point, where uncoooled single-photon electronic imaging will soon become a consumer product. This book is giving a specialist´s view from different domains to the forthcoming “single-photon imaging” revolution. The various aspects of single-photon imaging are treated by internati...

  14. Single-Phase PLLs

    DEFF Research Database (Denmark)

    Golestan, Saeed; Guerrero, Josep M.; Quintero, Juan Carlos Vasquez

    2017-01-01

    Single-phase phase-locked loops (PLLs) are popular for the synchronization and control of single-phase gridconnected converters. They are also widely used for monitoring and diagnostic purposes in the power and energy areas. In recent years, a large number of single-phase PLLs with different...... structures and properties have been proposed in the literature. The main aim of this paper is to provide a review of these PLLs. To this end, the single-phase PLLs are first classified into two major categories: 1) power-based PLLs (pPLLs), and 2) quadrature signal generation-based PLLs (QSG......-PLLs). The members of each category are then described and their pros and cons are discussed. This work provides a deep insight into characteristics of different single-phase PLLs and, therefore, can be considered as a reference for researchers and engineers....

  15. Epigenetics reloaded: the single-cell revolution.

    Science.gov (United States)

    Bheda, Poonam; Schneider, Robert

    2014-11-01

    Mechanistically, how epigenetic states are inherited through cellular divisions remains an important open question in the chromatin field and beyond. Defining the heritability of epigenetic states and the underlying chromatin-based mechanisms within a population of cells is complicated due to cell heterogeneity combined with varying levels of stability of these states; thus, efforts must be focused toward single-cell analyses. The approaches presented here constitute the forefront of epigenetics research at the single-cell level using classic and innovative methods to dissect epigenetics mechanisms from the limited material available in a single cell. This review further outlines exciting future avenues of research to address the significance of epigenetic heterogeneity and the contributions of microfluidics technologies to single-cell isolation and analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Automatic incrementalization of Prolog based static analyses

    DEFF Research Database (Denmark)

    Eichberg, Michael; Kahl, Matthias; Saha, Diptikalyan

    2007-01-01

    Modem development environments integrate various static analyses into the build process. Analyses that analyze the whole project whenever the project changes are impractical in this context. We present an approach to automatic incrementalization of analyses that are specified as tabled logic...... programs and evaluated using incremental tabled evaluation, a technique for efficiently updating memo tables in response to changes in facts and rules. The approach has been implemented and integrated into the Eclipse IDE. Our measurements show that this technique is effective for automatically...

  17. Anthocyanin analyses of Vaccinium fruit dietary supplements

    Science.gov (United States)

    Vaccinium fruit ingredients within dietary supplements were identified by comparisons with anthocyanin analyses of known Vaccinium profiles (demonstration of anthocyanin fingerprinting). Available Vaccinium supplements were purchased and analyzed; their anthocyanin profiles (based on HPLC separation...

  18. Understanding Human Error Based on Automated Analyses

    Data.gov (United States)

    National Aeronautics and Space Administration — This is a report on a continuing study of automated analyses of experiential textual reports to gain insight into the causal factors of human errors in aviation...

  19. Analyse of Maintenance Cost in ST

    CERN Document Server

    Jenssen, B W

    2001-01-01

    An analyse has been carried out in ST concerning the total costs for the division. Even though the target was the maintenance costs in ST, the global budget over has been analysed. This has been done since there is close relation between investments & consolidation and the required level for maintenance. The purpose of the analyse was to focus on maintenance cost in ST as a ratio of total maintenance costs over the replacement value of the equipment, and to make some comparisons with other industries and laboratories. Families of equipment have been defined and their corresponding ratios calculated. This first approach gives us some "quantitative" measurements. This analyse should be combined with performance indicators (more "qualitative" measurements) that are telling us how well we are performing. This will help us in defending our budget, make better priorities, and we will satisfy the requirements from our external auditors.

  20. 7 CFR 94.102 - Analyses available.

    Science.gov (United States)

    2010-01-01

    ... analyses for total ash, fat by acid hydrolysis, moisture, salt, protein, beta-carotene, catalase... glycol, SLS, and zeolex. There are also be tests for starch, total sugars, sugar profile, whey, standard...

  1. Transport of Lysosome-Related Organelles

    NARCIS (Netherlands)

    Jordens, Ingrid

    2005-01-01

    Many intracellular compartments, including (MHC class II-containing) lysosomes, melanosomes and phagosomes, move along microtubules in a bi-directional manner due to the alternating activities of the plus-end directed kinesin motor and the minus-end directed dynein-dynactin motor. However, it is

  2. Chlorosomes: antenna organelles in photosynthetic green bacteria

    DEFF Research Database (Denmark)

    Frigaard, N.-U.; Bryant, D. A.

    2006-01-01

    The new series "Microbiology Monographs" begins with two volumes on intracellular components in prokaryotes. In this second volume, "Complex Intracellular Structures in Prokaryotes", the components, labelled complex intracellular structures, encompass a multitude of important cellular functions. ...

  3. The golgi apparatus: two organelles in tandem.

    Science.gov (United States)

    Rothman, J E

    1981-09-11

    The Golgi apparatus consists of distinct cis and trans compartments that may act sequentially to refine the protein export of the endoplasmic reticulum by removing escaped endoplasmic reticulum proteins. Refinement may be a multistage process akin to fractional distillation; the stack of cisternae comprising the cis Golgi may be the plates in this distillation tower. The trans Golgi, consisting of the last one or two cisternae, may be the receiver that collects from the cis Golgi only its most refined fraction for later distribution to specific locations throughout the cell.

  4. Maintaining ancient organelles: mitochondrial biogenesis and maturation.

    Science.gov (United States)

    Vega, Rick B; Horton, Julie L; Kelly, Daniel P

    2015-05-22

    The ultrastructure of the cardiac myocyte is remarkable for the high density of mitochondria tightly packed between sarcomeres. This structural organization is designed to provide energy in the form of ATP to fuel normal pump function of the heart. A complex system comprised of regulatory factors and energy metabolic machinery, encoded by both mitochondrial and nuclear genomes, is required for the coordinate control of cardiac mitochondrial biogenesis, maturation, and high-capacity function. This process involves the action of a transcriptional regulatory network that builds and maintains the mitochondrial genome and drives the expression of the energy transduction machinery. This finely tuned system is responsive to developmental and physiological cues, as well as changes in fuel substrate availability. Deficiency of components critical for mitochondrial energy production frequently manifests as a cardiomyopathic phenotype, underscoring the requirement to maintain high respiration rates in the heart. Although a precise causative role is not clear, there is increasing evidence that perturbations in this regulatory system occur in the hypertrophied and failing heart. This review summarizes current knowledge and highlights recent advances in our understanding of the transcriptional regulatory factors and signaling networks that serve to regulate mitochondrial biogenesis and function in the mammalian heart. © 2015 American Heart Association, Inc.

  5. The Centrosome, a Multitalented Renaissance Organelle.

    Science.gov (United States)

    Vertii, Anastassiia; Hehnly, Heidi; Doxsey, Stephen

    2016-12-01

    The centrosome acts as a microtubule-organizing center (MTOC) from the G 1 to G 2 phases of the cell cycle; it can mature into a spindle pole during mitosis and/or transition into a cilium by elongating microtubules (MTs) from the basal body on cell differentiation or cell cycle arrest. New studies hint that the centrosome functions in more than MT organization. For instance, it has recently been shown that a specific substructure of the centrosome-the mother centriole appendages-are required for the recycling of endosomes back to the plasma membrane. This alone could have important implications for a renaissance in our understanding of the development of primary cilia, endosome recycling, and the immune response. Here, we review newly identified roles for the centrosome in directing membrane traffic, the immunological synapse, and the stress response. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

  6. A Eukaryote without a Mitochondrial Organelle

    Czech Academy of Sciences Publication Activity Database

    Karnkowska, A.; Vacek, V.; Zubáčová, Z.; Treitli, S.C.; Petrzelkova, R.; Eme, L.; Novák, L.; Žárský, V.; Barlow, L.D.; Herman, E.K.; Soukal, P.; Hroudová, Miluše; Doležal, P.; Stairs, C.W.; Roger, A. J.; Eliaš, M.; Dacks, J.B.; Vlček, Čestmír; Hampl, V.

    2016-01-01

    Roč. 26, č. 10 (2016), s. 1274-1284 ISSN 0960-9822 R&D Projects: GA MŠk(CZ) LQ1604; GA MŠk(CZ) ED1.1.00/02.0109; GA ČR GAP506/12/1010 Institutional support: RVO:68378050 Keywords : arginine dihydrolase pathway * tail-anchored proteins * fe-s cluster * trichomonas-vaginalis * entamoeba-histolytica * giardia-intestinalis * tritrichomonas-fetus * genome annotation * energy-metabolism * gene-transfer Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Developmental biology Impact factor: 8.851, year: 2016

  7. Risk analyses of nuclear power plants

    International Nuclear Information System (INIS)

    Jehee, J.N.T.; Seebregts, A.J.

    1991-02-01

    Probabilistic risk analyses of nuclear power plants are carried out by systematically analyzing the possible consequences of a broad spectrum of causes of accidents. The risk can be expressed in the probabilities for melt down, radioactive releases, or harmful effects for the environment. Following risk policies for chemical installations as expressed in the mandatory nature of External Safety Reports (EVRs) or, e.g., the publication ''How to deal with risks'', probabilistic risk analyses are required for nuclear power plants

  8. A History of Rotorcraft Comprehensive Analyses

    Science.gov (United States)

    Johnson, Wayne

    2013-01-01

    A history of the development of rotorcraft comprehensive analyses is presented. Comprehensive analyses are digital computer programs that calculate the aeromechanical behavior of the rotor and aircraft, bringing together the most advanced models of the geometry, structure, dynamics, and aerodynamics available in rotary wing technology. The development of the major codes of the last five decades from industry, government, and universities is described. A number of common themes observed in this history are discussed.

  9. Thermal Analyse sof Cross-Linked Polyethylene

    Directory of Open Access Journals (Sweden)

    Radek Polansky

    2007-01-01

    Full Text Available The paper summarizes results obtained during the structural analyses measurements (Differential Scanning Calorimetry DSC, Thermogravimetry TG, Thermomechanical analysis TMA and Fourier transform infrared spectroscopy FT-IR. The samples of cross-linked polyethylene cable insulation were tested via these analyses. The DSC and TG were carried out using simultaneous thermal analyzer TA Instruments SDT Q600 with connection of Fourier transform infrared spectrometer Nicolet 380. Thermomechanical analysis was carried out by TMA Q400EM TA Instruments apparatus.

  10. Single Policy Study

    DEFF Research Database (Denmark)

    Kronsell, Annica; Manners, Ian James

    2015-01-01

    Single policy studies are the most common form of European Union (EU) research. Single policy studies are widely used to understand the role of the EU in a wide variety of sectors, together with their development over time, and often offer public policy prescriptions. This chapter discusses the r...... Policy (CSDP). The examples are illustrative of how single policy studies can be designed to use different approaches in the analysis: multiple streams approach to policy-making; a comparative hypothesis testing; and feminist institutional theory.......Single policy studies are the most common form of European Union (EU) research. Single policy studies are widely used to understand the role of the EU in a wide variety of sectors, together with their development over time, and often offer public policy prescriptions. This chapter discusses...... the relevance of single policy studies in EU research and give examples of how such research can be designed and carried out. The chapter reviews three examples of single policy studies using different methods based on EU environmental policy, the EU biofuels directive, and the EU Common Security and Defence...

  11. Single neuron computation

    CERN Document Server

    McKenna, Thomas M; Zornetzer, Steven F

    1992-01-01

    This book contains twenty-two original contributions that provide a comprehensive overview of computational approaches to understanding a single neuron structure. The focus on cellular-level processes is twofold. From a computational neuroscience perspective, a thorough understanding of the information processing performed by single neurons leads to an understanding of circuit- and systems-level activity. From the standpoint of artificial neural networks (ANNs), a single real neuron is as complex an operational unit as an entire ANN, and formalizing the complex computations performed by real n

  12. Single photon ECT

    International Nuclear Information System (INIS)

    Maeda, Toshio; Matsuda, Hiroshi; Tada, Akira; Bunko, Hisashi; Koizumi, Kiyoshi

    1982-01-01

    The detectability of lesions located deep in a body or overlapped with a physiologically increased activity improve with the help of single photon ECT. In some cases, the ECT is superior to the conventional gamma camera images and X-ray CT scans in the evaluation of the location and size of lesion. The single photon ECT of the brain compares favorably with the contrast enhansed X-ray CT scans. The most important adaptation of the single photon ECT are the detection of recurrent brain tumors after craniotomy and the evaluation of ischemic heart diseases. (author)

  13. Single Electron Tunneling

    International Nuclear Information System (INIS)

    Ruggiero, Steven T.

    2005-01-01

    Financial support for this project has led to advances in the science of single-electron phenomena. Our group reported the first observation of the so-called ''Coulomb Staircase'', which was produced by tunneling into ultra-small metal particles. This work showed well-defined tunneling voltage steps of width e/C and height e/RC, demonstrating tunneling quantized on the single-electron level. This work was published in a now well-cited Physical Review Letter. Single-electron physics is now a major sub-field of condensed-matter physics, and fundamental work in the area continues to be conducted by tunneling in ultra-small metal particles. In addition, there are now single-electron transistors that add a controlling gate to modulate the charge on ultra-small photolithographically defined capacitive elements. Single-electron transistors are now at the heart of at least one experimental quantum-computer element, and single-electron transistor pumps may soon be used to define fundamental quantities such as the farad (capacitance) and the ampere (current). Novel computer technology based on single-electron quantum dots is also being developed. In related work, our group played the leading role in the explanation of experimental results observed during the initial phases of tunneling experiments with the high-temperature superconductors. When so-called ''multiple-gap'' tunneling was reported, the phenomenon was correctly identified by our group as single-electron tunneling in small grains in the material. The main focus throughout this project has been to explore single electron phenomena both in traditional tunneling formats of the type metal/insulator/particles/insulator/metal and using scanning tunneling microscopy to probe few-particle systems. This has been done under varying conditions of temperature, applied magnetic field, and with different materials systems. These have included metals, semi-metals, and superconductors. Amongst a number of results, we have

  14. Stresses of Single Parenting

    Science.gov (United States)

    ... Text Size Email Print Share Stresses of Single Parenting Page Content Article Body What are some ways ... way. Check your local library for books on parenting. Local hospitals, the YMCA, and church groups often ...

  15. A Single Atom Antenna

    International Nuclear Information System (INIS)

    Trinter, Florian; Williams, Joshua B; Weller, Miriam; Waitz, Markus; Pitzer, Martin; Voigtsberger, Jörg; Schober, Carl; Kastirke, Gregor; Müller, Christian; Goihl, Christoph; Burzynski, Phillip; Wiegandt, Florian; Wallauer, Robert; Kalinin, Anton; Schmidt, Lothar Ph H; Schöffler, Markus S; Jahnke, Till; Dörner, Reinhard; Chiang, Ying-Chih; Gokhberg, Kirill

    2015-01-01

    Here we demonstrate the smallest possible implementation of an antenna-receiver complex which consists of a single (helium) atom acting as the antenna and a second (neon) atom acting as a receiver. (paper)

  16. Single Beam Holography.

    Science.gov (United States)

    Chen, Hsuan; Ruterbusch, Paul H.

    1979-01-01

    Discusses how holography can be used as part of undergraduate physics laboratories. The authors propose a single beam technique of holography, which will reduce the recording scheme as well as relax the isolation requirements. (HM)

  17. Controlled generation of a single Trichel pulse and a series of single Trichel pulses in air

    Science.gov (United States)

    Mizeraczyk, Jerzy; Berendt, Artur; Akishev, Yuri

    2018-04-01

    In this paper, a simple method for the controlled generation of a single Trichel pulse or a series of single Trichel pulses of a regulated repetition frequency in air is proposed. The concept of triggering a single Trichel pulse or a series of such pulses is based on the precise controlling the voltage inception of the negative corona, which can be accomplished through the use of a ramp voltage pulse or a series of such pulses with properly chosen ramp voltage pulse parameters (rise and fall times, and ramp voltage pulse repetition frequency). The proposal has been tested in experiments using a needle-to-plate electrode arrangement in air, and reproducible Trichel pulses (single or in a series) were obtained by triggering them with an appropriately designed voltage waveform. The proposed method and results obtained have been qualitatively analysed. The analysis provides guidance for designing the voltage ramp pulse in respect of the generation of a single Trichel pulse or a series of single Trichel pulses. The controlled generation of a single Trichel pulse or a series of such pulses would be a helpful research tool for the refined studies of the fundamental processes in a negative corona discharge in a single- (air is an example) and multi-phase gaseous fluids. The controlled generation of a single Trichel pulse or a series of Trichel pulses can also be attractive for those corona treatments which need manipulation of the electric charge and heat portions delivered by the Trichel pulses to the object.

  18. Sequential interim analyses of survival data in DNA microarray experiments

    Directory of Open Access Journals (Sweden)

    Jung Klaus

    2011-04-01

    Full Text Available Abstract Background Discovery of biomarkers that are correlated with therapy response and thus with survival is an important goal of medical research on severe diseases, e.g. cancer. Frequently, microarray studies are performed to identify genes of which the expression levels in pretherapeutic tissue samples are correlated to survival times of patients. Typically, such a study can take several years until the full planned sample size is available. Therefore, interim analyses are desirable, offering the possibility of stopping the study earlier, or of performing additional laboratory experiments to validate the role of the detected genes. While many methods correcting the multiple testing bias introduced by interim analyses have been proposed for studies of one single feature, there are still open questions about interim analyses of multiple features, particularly of high-dimensional microarray data, where the number of features clearly exceeds the number of samples. Therefore, we examine false discovery rates and power rates in microarray experiments performed during interim analyses of survival studies. In addition, the early stopping based on interim results of such studies is evaluated. As stop criterion we employ the achieved average power rate, i.e. the proportion of detected true positives, for which a new estimator is derived and compared to existing estimators. Results In a simulation study, pre-specified levels of the false discovery rate are maintained in each interim analysis, where reduced levels as used in classical group sequential designs of one single feature are not necessary. Average power rates increase with each interim analysis, and many studies can be stopped prior to their planned end when a certain pre-specified power rate is achieved. The new estimator for the power rate slightly deviates from the true power rate but is comparable to other estimators. Conclusions Interim analyses of microarray experiments can provide

  19. A theoretical framework for analysing preschool teaching

    DEFF Research Database (Denmark)

    Chaiklin, Seth

    2014-01-01

    This article introduces a theoretical framework for analysing preschool teaching as a historically-grounded societal practice. The aim is to present a unified framework that can be used to analyse and compare both historical and contemporary examples of preschool teaching practice within and across...... national traditions. The framework has two main components, an analysis of preschool teaching as a practice, formed in relation to societal needs, and an analysis of the categorical relations which necessarily must be addressed in preschool teaching activity. The framework is introduced and illustrated...... through the analysis of one of the earliest recorded examples of preschool education (initiated by J. F. Oberlin in northeastern France in 1767). The general idea of societal need is elaborated as a way of analysing practices, and a general analytic schema is presented for characterising preschool...

  20. Advanced toroidal facility vaccuum vessel stress analyses

    International Nuclear Information System (INIS)

    Hammonds, C.J.; Mayhall, J.A.

    1987-01-01

    The complex geometry of the Advance Toroidal Facility (ATF) vacuum vessel required special analysis techniques in investigating the structural behavior of the design. The response of a large-scale finite element model was found for transportation and operational loading. Several computer codes and systems, including the National Magnetic Fusion Energy Computer Center Cray machines, were implemented in accomplishing these analyses. The work combined complex methods that taxed the limits of both the codes and the computer systems involved. Using MSC/NASTRAN cyclic-symmetry solutions permitted using only 1/12 of the vessel geometry to mathematically analyze the entire vessel. This allowed the greater detail and accuracy demanded by the complex geometry of the vessel. Critical buckling-pressure analyses were performed with the same model. The development, results, and problems encountered in performing these analyses are described. 5 refs., 3 figs

  1. Advanced Toroidal Facility vacuum vessel stress analyses

    International Nuclear Information System (INIS)

    Hammonds, C.J.; Mayhall, J.A.

    1987-01-01

    The complex geometry of the Advanced Toroidal Facility (ATF) vacuum vessel required special analysis techniques in investigating the structural behavior of the design. The response of a large-scale finite element model was found for transportation and operational loading. Several computer codes and systems, including the National Magnetic Fusion Energy Computer Center Cray machines, were implemented in accomplishing these analyses. The work combined complex methods that taxed the limits of both the codes and the computer systems involved. Using MSC/NASTRAN cyclic-symmetry solutions permitted using only 1/12 of the vessel geometry to mathematically analyze the entire vessel. This allowed the greater detail and accuracy demanded by the complex geometry of the vessel. Critical buckling-pressure analyses were performed with the same model. The development, results, and problems encountered in performing these analyses are described

  2. Proteomic Analyses of the Vitreous Humour

    Directory of Open Access Journals (Sweden)

    Martina Angi

    2012-01-01

    Full Text Available The human vitreous humour (VH is a transparent, highly hydrated gel, which occupies the posterior segment of the eye between the lens and the retina. Physiological and pathological conditions of the retina are reflected in the protein composition of the VH, which can be sampled as part of routine surgical procedures. Historically, many studies have investigated levels of individual proteins in VH from healthy and diseased eyes. In the last decade, proteomics analyses have been performed to characterise the proteome of the human VH and explore networks of functionally related proteins, providing insight into the aetiology of diabetic retinopathy and proliferative vitreoretinopathy. Recent proteomic studies on the VH from animal models of autoimmune uveitis have identified new signalling pathways associated to autoimmune triggers and intravitreal inflammation. This paper aims to guide biological scientists through the different proteomic techniques that have been used to analyse the VH and present future perspectives for the study of intravitreal inflammation using proteomic analyses.

  3. Microchambers with Solid-State Phosphorescent Sensor for Measuring Single Mitochondrial Respiration.

    Science.gov (United States)

    Pham, Ted D; Wallace, Douglas C; Burke, Peter J

    2016-07-09

    It is now well established that, even within a single cell, multiple copies of the mitochondrial genome may be present (genetic heteroplasmy). It would be interesting to develop techniques to determine if and to what extent this genetic variation results in functional variation from one mitochondrion to the next (functional heteroplasmy). Measuring mitochondrial respiration can reveal the organelles' functional capacity for Adenosine triphosphate (ATP) production and determine mitochondrial damage that may arise from genetic or age related defects. However, available technologies require significant quantities of mitochondria. Here, we develop a technology to assay the respiration of a single mitochondrion. Our "micro-respirometer" consists of micron sized chambers etched out of borofloat glass substrates and coated with an oxygen sensitive phosphorescent dye Pt(II) meso-tetra(pentafluorophenyl)porphine (PtTFPP) mixed with polystyrene. The chambers are sealed with a polydimethylsiloxane layer coated with oxygen impermeable Viton rubber to prevent diffusion of oxygen from the environment. As the mitochondria consume oxygen in the chamber, the phosphorescence signal increases, allowing direct determination of the respiration rate. Experiments with coupled vs. uncoupled mitochondria showed a substantial difference in respiration, confirming the validity of the microchambers as single mitochondrial respirometers. This demonstration could enable future high-throughput assays of mitochondrial respiration and benefit the study of mitochondrial functional heterogeneity, and its role in health and disease.

  4. A 256-channel pulse-height analyser

    International Nuclear Information System (INIS)

    Berset, J.C.; Delavallade, G.; Lindsay, J.

    1975-01-01

    The design, construction, and testing of a small, low-cost 256-channel pulse-height analyser is briefly discussed. The analyser, intended for use in the setting up of experiments in high-energy physics, is fully compatible with the CERN/NIM nucleonic instrumentation. It has a digital display of channel and content as well as outputs for printing, plotting, and binary transfer. The logic circuitry is made with TTL integrated circuits and has a static random-access MOS memory. Logic and timing diagrams are given. Detailed specifications are also included. (Author)

  5. Power System Oscillatory Behaviors: Sources, Characteristics, & Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Follum, James D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Tuffner, Francis K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dosiek, Luke A. [Union College, Schenectady, NY (United States); Pierre, John W. [Univ. of Wyoming, Laramie, WY (United States)

    2017-05-17

    This document is intended to provide a broad overview of the sources, characteristics, and analyses of natural and forced oscillatory behaviors in power systems. These aspects are necessarily linked. Oscillations appear in measurements with distinguishing characteristics derived from the oscillation’s source. These characteristics determine which analysis methods can be appropriately applied, and the results from these analyses can only be interpreted correctly with an understanding of the oscillation’s origin. To describe oscillations both at their source within a physical power system and within measurements, a perspective from the boundary between power system and signal processing theory has been adopted.

  6. Fundamental data analyses for measurement control

    International Nuclear Information System (INIS)

    Campbell, K.; Barlich, G.L.; Fazal, B.; Strittmatter, R.B.

    1987-02-01

    A set of measurment control data analyses was selected for use by analysts responsible for maintaining measurement quality of nuclear materials accounting instrumentation. The analyses consist of control charts for bias and precision and statistical tests used as analytic supplements to the control charts. They provide the desired detection sensitivity and yet can be interpreted locally, quickly, and easily. The control charts provide for visual inspection of data and enable an alert reviewer to spot problems possibly before statistical tests detect them. The statistical tests are useful for automating the detection of departures from the controlled state or from the underlying assumptions (such as normality). 8 refs., 3 figs., 5 tabs

  7. Human oocyte chromosome analyses need a standardized ...

    Indian Academy of Sciences (India)

    karyotyping (Sandalinas et al. 2002), centromere-specific multiplex fluorescence in situ hybridization (cenM-FISH). (Gutiérrez-Mateo et al. 2005) and single cell comparative genomic hybridization (CGH) (Fragouli et al. 2006) have re- cently been applied to human oocytes. It is to be expected that such studies comprising an ...

  8. Consistent Visual Analyses of Intrasubject Data

    Science.gov (United States)

    Kahng, SungWoo; Chung, Kyong-Mee; Gutshall, Katharine; Pitts, Steven C.; Kao, Joyce; Girolami, Kelli

    2010-01-01

    Visual inspection of single-case data is the primary method of interpretation of the effects of an independent variable on a dependent variable in applied behavior analysis. The purpose of the current study was to replicate and extend the results of DeProspero and Cohen (1979) by reexamining the consistency of visual analysis across raters. We…

  9. Single-Mode VCSELs

    Science.gov (United States)

    Larsson, Anders; Gustavsson, Johan S.

    The only active transverse mode in a truly single-mode VCSEL is the fundamental mode with a near Gaussian field distribution. A single-mode VCSEL produces a light beam of higher spectral purity, higher degree of coherence and lower divergence than a multimode VCSEL and the beam can be more precisely shaped and focused to a smaller spot. Such beam properties are required in many applications. In this chapter, after discussing applications of single-mode VCSELs, we introduce the basics of fields and modes in VCSELs and review designs implemented for single-mode emission from VCSELs in different materials and at different wavelengths. This includes VCSELs that are inherently single-mode as well as inherently multimode VCSELs where higher-order modes are suppressed by mode selective gain or loss. In each case we present the current state-of-the-art and discuss pros and cons. At the end, a specific example with experimental results is provided and, as a summary, the most promising designs based on current technologies are identified.

  10. Meta-analyses on viral hepatitis

    DEFF Research Database (Denmark)

    Gluud, Lise L; Gluud, Christian

    2009-01-01

    This article summarizes the meta-analyses of interventions for viral hepatitis A, B, and C. Some of the interventions assessed are described in small trials with unclear bias control. Other interventions are supported by large, high-quality trials. Although attempts have been made to adjust...

  11. Good Governance Analysing Performance of Economic Community ...

    African Journals Online (AJOL)

    Good Governance Analysing Performance of Economic Community of West African States and Southern African Development Community Members on Mo Ibrahim Index of ... The Index is important, significant and appropriate because it outlines criteria and conditions deemed essential for Africans to live meaningful lives.

  12. Regression og geometrisk data analyse (2. del)

    DEFF Research Database (Denmark)

    Brinkkjær, Ulf

    2010-01-01

    Artiklen søger at vise, hvordan regressionsanalyse og geometrisk data analyse kan integreres. Det er interessant, fordi disse metoder ofte opstilles som modsætninger f.eks. som en modsætning mellem beskrivende og forklarende metoder. Artiklens første del bragtes i Praktiske Grunde 3-4 / 2007....

  13. Heritability estimates derived from threshold analyses for ...

    African Journals Online (AJOL)

    Unknown

    Abstract. The object of this study was to estimate heritabilities and sire breeding values for stayability and reproductive traits in a composite multibreed beef cattle herd using a threshold model. A GFCAT set of programmes was used to analyse reproductive data. Heritabilities and product-moment correlations between.

  14. Phonetic data and phonological analyses | Roux | Stellenbosch ...

    African Journals Online (AJOL)

    Stellenbosch Papers in Linguistics. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 1 (1978) >. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register. Phonetic data and phonological analyses. JC Roux. Abstract.

  15. En kvantitativ metode til analyse af radio

    Directory of Open Access Journals (Sweden)

    Christine Lejre

    2014-06-01

    Full Text Available I den danske såvel som den internationale radiolitteratur er bud på metoder til analyse af radiomediet sparsomme. Det skyldes formentlig, at radiomediet er svært at analysere, fordi det er et medie, der ikke er visualiseret i form af billeder eller understøttet af printet tekst. Denne artikel har til formål at beskrive en ny kvantitativ metode til analyse af radio, der tager særligt hensyn til radiomediets modalitet – lyd struktureret som et lineært forløb i tid. Metoden understøtter dermed både radiomediet som et medie i tid og som et blindt medie. Metoden er udviklet i forbindelse med en komparativ analyse af kulturprogrammer på P1 og Radio24syv lavet for Danmarks Radio. Artiklen peger på, at metoden er velegnet til analyse af ikke kun radio, men også andre medieplatforme samt forskellige journalistiske stofområder.

  16. Cosmetology: Task Analyses. Competency-Based Education.

    Science.gov (United States)

    Henrico County Public Schools, Glen Allen, VA. Virginia Vocational Curriculum Center.

    These task analyses are designed to be used in combination with the "Trade and Industrial Education Service Area Resource" in order to implement competency-based education in the cosmetology program in Virginia. The task analysis document contains the task inventory, suggested task sequence lists, and content outlines for the secondary…

  17. Some Tools for Robustifying Econometric Analyses

    NARCIS (Netherlands)

    V. Hoornweg (Victor)

    2013-01-01

    markdownabstract__Abstract__ We use automated algorithms to update and evaluate ad hoc judgments that are made in applied econometrics. Such an application of automated algorithms robustifies empirical econometric analyses, it achieves lower and more consistent prediction errors, and it helps to

  18. Chromosomal evolution and phylogenetic analyses in Tayassu ...

    Indian Academy of Sciences (India)

    The phylogenetic relationships among the tayassuids are unclear and have insti- gated debate over the ... [Adega F., Chaves R. and Guedes-Pinto H. 2007 Chromosomal evolution and phylogenetic analyses in Tayassu pecari and Pecari tajacu. (Tayassuidae): tales ..... Chromosome banding in Amphibia. XXV. Karyotype ...

  19. Analyses of hydraulic performance of velocity caps

    DEFF Research Database (Denmark)

    Christensen, Erik Damgaard; Degn Eskesen, Mark Chr.; Buhrkall, Jeppe

    2014-01-01

    The hydraulic performance of a velocity cap has been investigated. Velocity caps are often used in connection with offshore intakes. CFD (computational fluid dynamics) examined the flow through the cap openings and further down into the intake pipes. This was combined with dimension analyses...

  20. Quantitative analyses of shrinkage characteristics of neem ...

    African Journals Online (AJOL)

    Quantitative analyses of shrinkage characteristics of neem (Azadirachta indica A. Juss.) wood were carried out. Forty five wood specimens were prepared from the three ecological zones of north eastern Nigeria, viz: sahel savanna, sudan savanna and guinea savanna for the research. The results indicated that the wood ...

  1. Analysing User Lifetime in Voluntary Online Collaboration

    DEFF Research Database (Denmark)

    McHugh, Ronan; Larsen, Birger

    2010-01-01

    This paper analyses persuasion in online collaboration projects. It introduces a set of heuristics that can be applied to such projects and combines these with a quantitative analysis of user activity over time. Two example sites are studies, Open Street Map and The Pirate Bay. Results show...

  2. 10 CFR 61.13 - Technical analyses.

    Science.gov (United States)

    2010-01-01

    ... must clearly identify and differentiate between the roles performed by the natural disposal site... and segregation requirements will be met and that adequate barriers to inadvertent intrusion will be... need for ongoing active maintenance after closure must be based upon analyses of active natural...

  3. Chemical Analyses of Silicon Aerogel Samples

    Energy Technology Data Exchange (ETDEWEB)

    van der Werf, I.; Palmisano, F.; De Leo, Raffaele; Marrone, Stefano

    2008-04-01

    After five years of operating, two Aerogel counters: A1 and A2, taking data in Hall A at Jefferson Lab, suffered a loss of performance. In this note possible causes of degradation have been studied. In particular, various chemical and physical analyses have been carried out on several Aerogel tiles and on adhesive tape in order to reveal the presence of contaminants.

  4. Uncertainty quantification approaches for advanced reactor analyses.

    Energy Technology Data Exchange (ETDEWEB)

    Briggs, L. L.; Nuclear Engineering Division

    2009-03-24

    The original approach to nuclear reactor design or safety analyses was to make very conservative modeling assumptions so as to ensure meeting the required safety margins. Traditional regulation, as established by the U. S. Nuclear Regulatory Commission required conservatisms which have subsequently been shown to be excessive. The commission has therefore moved away from excessively conservative evaluations and has determined best-estimate calculations to be an acceptable alternative to conservative models, provided the best-estimate results are accompanied by an uncertainty evaluation which can demonstrate that, when a set of analysis cases which statistically account for uncertainties of all types are generated, there is a 95% probability that at least 95% of the cases meet the safety margins. To date, nearly all published work addressing uncertainty evaluations of nuclear power plant calculations has focused on light water reactors and on large-break loss-of-coolant accident (LBLOCA) analyses. However, there is nothing in the uncertainty evaluation methodologies that is limited to a specific type of reactor or to specific types of plant scenarios. These same methodologies can be equally well applied to analyses for high-temperature gas-cooled reactors and to liquid metal reactors, and they can be applied to steady-state calculations, operational transients, or severe accident scenarios. This report reviews and compares both statistical and deterministic uncertainty evaluation approaches. Recommendations are given for selection of an uncertainty methodology and for considerations to be factored into the process of evaluating uncertainties for advanced reactor best-estimate analyses.

  5. Secundaire analyses organisatiebeleid psychosociale arbeidsbelasting (PSA)

    NARCIS (Netherlands)

    Kraan, K.O.; Houtman, I.L.D.

    2016-01-01

    Hoe het organisatiebeleid rond psychosociale arbeidsbelasting (PSA) eruit ziet anno 2014 en welke samenhang er is met ander beleid en uitkomstmaten, zijn de centrale vragen in dit onderzoek. De resultaten van deze verdiepende analyses kunnen ten goede komen aan de lopende campagne ‘Check je

  6. Hybrid Logical Analyses of the Ambient Calculus

    DEFF Research Database (Denmark)

    Bolander, Thomas; Hansen, Rene Rydhof

    2010-01-01

    In this paper, hybrid logic is used to formulate three control flow analyses for Mobile Ambients, a process calculus designed for modelling mobility. We show that hybrid logic is very well-suited to express the semantic structure of the ambient calculus and how features of hybrid logic can...

  7. Comparison of elastic and inelastic analyses

    International Nuclear Information System (INIS)

    Ammerman, D.J.; Heinstein, M.W.; Wellman, G.W.

    1993-01-01

    In this paper, comparisons between elastic and inelastic analyses are made for a simple ring structure and for a package to transport a large quantity of RAM by rail (rail cask) with lead gamma shielding to illustrate the differences in the two analysis techniques. (J.P.N.)

  8. Microbiological And Physicochemical Analyses Of Oil Contaminated ...

    African Journals Online (AJOL)

    Michael Horsfall

    The physicochemical properties of the soil samples analysed shows the pH ... Keywords: Oil contaminated soil, microbial isolates, mechanical workshops and physicochemical parameters. Pollution of the environment by petroleum ... strains capable of degrading Poly aromatic hydrocarbons have been isolated from soil and.

  9. Pecheries maritimes artisanales Togolaises : analyse des ...

    African Journals Online (AJOL)

    Pecheries maritimes artisanales Togolaises : analyse des debarquements et de la valeur commerciale des captures. K.M. Sedzro, E.D. Fiogbe, E.B. Guerra. Abstract. Description du sujet : La connaissance scientifique de la pression des pêcheries artisanales sur les ressources marines togolaises s'avère nécessaire pour ...

  10. Multivariate differential analyses of adolescents' experiences of ...

    African Journals Online (AJOL)

    Aggression is reasoned to be dependent on aspects such as self-concept, moral reasoning, communication, frustration tolerance and family relationships. To analyse the data from questionnaires of 101 families (95 adolescents, 95 mothers and 91 fathers) Cronbach Alpha, various consecutive first and second order factor ...

  11. The Economic Cost of Homosexuality: Multilevel Analyses

    Science.gov (United States)

    Baumle, Amanda K.; Poston, Dudley, Jr.

    2011-01-01

    This article builds on earlier studies that have examined "the economic cost of homosexuality," by using data from the 2000 U.S. Census and by employing multilevel analyses. Our findings indicate that partnered gay men experience a 12.5 percent earnings penalty compared to married heterosexual men, and a statistically insignificant earnings…

  12. Incidence of Abcd1 level on the induction of cell death and organelle dysfunctions triggered by very long chain fatty acids and TNF-α on oligodendrocytes and astrocytes.

    Science.gov (United States)

    Baarine, Mauhamad; Ragot, Kévin; Athias, Anne; Nury, Thomas; Kattan, Zilal; Genin, Emmanuelle C; Andreoletti, Pierre; Ménétrier, Franck; Riedinger, Jean-Marc; Bardou, Marc; Lizard, Gérard

    2012-03-01

    , in our experimental conditions, plasmatic concentrations of these fatty acids were unable to induce cell death, and organelle dysfunctions on oligodendrocytes and astrocytes, and additional intrinsic and environmental factors, such as reduced Abcd1 level and/or TNF-α, were ineffective to potentiate their side effects. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. Grey literature in meta-analyses.

    Science.gov (United States)

    Conn, Vicki S; Valentine, Jeffrey C; Cooper, Harris M; Rantz, Marilyn J

    2003-01-01

    In meta-analysis, researchers combine the results of individual studies to arrive at cumulative conclusions. Meta-analysts sometimes include "grey literature" in their evidential base, which includes unpublished studies and studies published outside widely available journals. Because grey literature is a source of data that might not employ peer review, critics have questioned the validity of its data and the results of meta-analyses that include it. To examine evidence regarding whether grey literature should be included in meta-analyses and strategies to manage grey literature in quantitative synthesis. This article reviews evidence on whether the results of studies published in peer-reviewed journals are representative of results from broader samplings of research on a topic as a rationale for inclusion of grey literature. Strategies to enhance access to grey literature are addressed. The most consistent and robust difference between published and grey literature is that published research is more likely to contain results that are statistically significant. Effect size estimates of published research are about one-third larger than those of unpublished studies. Unfunded and small sample studies are less likely to be published. Yet, importantly, methodological rigor does not differ between published and grey literature. Meta-analyses that exclude grey literature likely (a) over-represent studies with statistically significant findings, (b) inflate effect size estimates, and (c) provide less precise effect size estimates than meta-analyses including grey literature. Meta-analyses should include grey literature to fully reflect the existing evidential base and should assess the impact of methodological variations through moderator analysis.

  14. SINGLE HEATER TEST FINAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    J.B. Cho

    1999-05-01

    The Single Heater Test is the first of the in-situ thermal tests conducted by the U.S. Department of Energy as part of its program of characterizing Yucca Mountain in Nevada as the potential site for a proposed deep geologic repository for the disposal of spent nuclear fuel and high-level nuclear waste. The Site Characterization Plan (DOE 1988) contained an extensive plan of in-situ thermal tests aimed at understanding specific aspects of the response of the local rock-mass around the potential repository to the heat from the radioactive decay of the emplaced waste. With the refocusing of the Site Characterization Plan by the ''Civilian Radioactive Waste Management Program Plan'' (DOE 1994), a consolidated thermal testing program emerged by 1995 as documented in the reports ''In-Situ Thermal Testing Program Strategy'' (DOE 1995) and ''Updated In-Situ Thermal Testing Program Strategy'' (CRWMS M&O 1997a). The concept of the Single Heater Test took shape in the summer of 1995 and detailed planning and design of the test started with the beginning fiscal year 1996. The overall objective of the Single Heater Test was to gain an understanding of the coupled thermal, mechanical, hydrological, and chemical processes that are anticipated to occur in the local rock-mass in the potential repository as a result of heat from radioactive decay of the emplaced waste. This included making a priori predictions of the test results using existing models and subsequently refining or modifying the models, on the basis of comparative and interpretive analyses of the measurements and predictions. A second, no less important, objective was to try out, in a full-scale field setting, the various instruments and equipment to be employed in the future on a much larger, more complex, thermal test of longer duration, such as the Drift Scale Test. This ''shake down'' or trial aspect of the Single Heater Test applied

  15. SINGLE HEATER TEST FINAL REPORT

    International Nuclear Information System (INIS)

    J.B. Cho

    1999-01-01

    The Single Heater Test is the first of the in-situ thermal tests conducted by the U.S. Department of Energy as part of its program of characterizing Yucca Mountain in Nevada as the potential site for a proposed deep geologic repository for the disposal of spent nuclear fuel and high-level nuclear waste. The Site Characterization Plan (DOE 1988) contained an extensive plan of in-situ thermal tests aimed at understanding specific aspects of the response of the local rock-mass around the potential repository to the heat from the radioactive decay of the emplaced waste. With the refocusing of the Site Characterization Plan by the ''Civilian Radioactive Waste Management Program Plan'' (DOE 1994), a consolidated thermal testing program emerged by 1995 as documented in the reports ''In-Situ Thermal Testing Program Strategy'' (DOE 1995) and ''Updated In-Situ Thermal Testing Program Strategy'' (CRWMS M and O 1997a). The concept of the Single Heater Test took shape in the summer of 1995 and detailed planning and design of the test started with the beginning fiscal year 1996. The overall objective of the Single Heater Test was to gain an understanding of the coupled thermal, mechanical, hydrological, and chemical processes that are anticipated to occur in the local rock-mass in the potential repository as a result of heat from radioactive decay of the emplaced waste. This included making a priori predictions of the test results using existing models and subsequently refining or modifying the models, on the basis of comparative and interpretive analyses of the measurements and predictions. A second, no less important, objective was to try out, in a full-scale field setting, the various instruments and equipment to be employed in the future on a much larger, more complex, thermal test of longer duration, such as the Drift Scale Test. This ''shake down'' or trial aspect of the Single Heater Test applied not just to the hardware, but also to the teamwork and cooperation between

  16. Single-Photon Optomechanics

    Science.gov (United States)

    Nunnenkamp, A.; Børkje, K.; Girvin, S. M.

    2011-08-01

    Optomechanics experiments are rapidly approaching the regime where the radiation pressure of a single photon displaces the mechanical oscillator by more than its zero-point uncertainty. We show that in this limit the power spectrum has multiple sidebands and that the cavity response has several resonances in the resolved-sideband limit. Using master-equation simulations, we also study the crossover from the weak-coupling many-photon to the single-photon strong-coupling regime. Finally, we find non-Gaussian steady states of the mechanical oscillator when multiphoton transitions are resonant. Our study provides the tools to detect and take advantage of this novel regime of optomechanics.

  17. Single well techniques

    International Nuclear Information System (INIS)

    Drost, W.

    1983-01-01

    The single well technique method includes measurement of parameters of groundwater flow in saturated rock. For determination of filtration velocity the dilution of radioactive tracer is measured, for direction logging the collimeter is rotated in the probe linked with the compass. The limiting factor for measurement of high filtration velocities is the occurrence of turbulent flow. The single well technique is used in civil engineering projects, water works and subsurface drainage of liquid waste from disposal sites. The radioactive tracer method for logging the vertical fluid movement in bore-holes is broadly used in groundwater survey and exploitation. (author)

  18. Biocatalytic Single Enzyme Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Grate, Jay W.; Kim, Jungbae

    2004-03-31

    As an innovative way of enzyme stabilization, we recently developed a new enzyme composite of nano-meter scale that we call "single-enzyme nanoparticles (SENs)" (9). Each enzyme molecule is surrounded with a porous composite organic/inorganic network of less than a few nanometers think. This approach represents a new type of enzyme-containing nanostructure. In experiments with perotease (chymotrypsin, CT), the activity of single enzyme nanoparticle form of the enzyme was greatly stabilized compared to the free form, without imposing a serious mass transfer limitation of substrates. In this chapter we will describe the synthesis, characterization and catalytic activity of the new SENs.

  19. Single port laparoscopic surgery

    DEFF Research Database (Denmark)

    Springborg, Henrik; Istre, Olav

    2012-01-01

    potential benefits. Theoretically, cosmetic outcomes, postoperative pain and complication rates could be improved with use of single site surgery. This study describes introduction of the method in a private hospital in Denmark, in which 40 patients have been treated for benign gynecologic conditions......LESS, or laparo-endoscopic single site surgery, is a promising new method in minimally invasive surgery. An increasing number of surgical procedures are being performed using this technique, however, its large-scale adoption awaits results of prospective randomized controlled studies confirming...

  20. Whole-Genome Analyses of lung function, height and smoking

    DEFF Research Database (Denmark)

    Janss, Luc; Sigsgaard, Torben; Sorensen, Daniel

    2014-01-01

    A joint analysis of FEV1 (forced expiratory volume after one second) and height is reported using novel methodology, as well as a single-trait analysis of smoking status. A first goal of the study was to incorporate dense genetic marker information in a random regression (Bayesian) model...... to quantify the relative contributions of genomic and environmental factors to the relationship between FEV1 and height. Smoking status was analysed using a probit random regression model and a second goal of the study was to estimate the genomic heritability of smoking status. Estimates of genomic...... heritabilities for height and FEV1 are equal to 0.47 and to 0.30, respectively. The estimates of the genomic and environmental correlations between height and FEV1 are 0.78 and 0.34, respectively. The posterior mean of the genomic heritability of smoking status is equal to 0.14 and provides evidence...

  1. Toward a unified method for analysing and teaching Human Robot Interaction

    DEFF Research Database (Denmark)

    Dinesen, Jens Vilhelm

    This abstract aims to present key aspect of a future paper, which outlines the ongoing development ofa unified method for analysing and teaching Human-Robot-Interaction. The paper will propose a novel method for analysing both HRI, interaction with other forms of technologies and fellow humans......, drawing on key theories and methods from both communications- and interaction-theory. The aim is to provide a single unified method for analysing interaction, through means of video analysis and then applying theories, with proven mutual compatibility, to reach a desired granularity of study....

  2. Important discoveries from analysing bacterial phenotypes

    OpenAIRE

    Bochner, Barry R; Giovannetti, Luciana; Viti, Carlo

    2008-01-01

    The ability to test hundreds to thousands of cellular phenotypes in a single experiment has opened up new avenues of investigation and exploration and led to important discoveries in very diverse applications of microbiological research and development. The information provided by global phenotyping is complementary to, and often more easily interpretable than information provided by global molecular analytical methods such as gene chips and proteomics. This report summarizes advances present...

  3. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! Kankan Bhattacharyya. General Article Volume 20 Issue 2 February 2015 pp 151-164. Fulltext. Click here to view fulltext PDF. Permanent link:

  4. Single Item Inventory Models

    NARCIS (Netherlands)

    E.M. Bazsa-Oldenkamp; P. den Iseger

    2001-01-01

    textabstractThis paper extends a fundamental result about single-item inventory systems. This approach allows more general performance measures, demand processes and order policies, and leads to easier analysis and implementation, than prior research. We obtain closed form expressions for the

  5. Single Nucleotide Polymorphism

    DEFF Research Database (Denmark)

    Børsting, Claus; Pereira, Vania; Andersen, Jeppe Dyrberg

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations in the genome. They have been studied extensively in the last decade with various purposes in mind. In this chapter, we will discuss the advantages and disadvantages of using SNPs for human identification...

  6. Single Value Devices

    NARCIS (Netherlands)

    Mader, Angelika H.; Dertien, Edwin Christian; Reidsma, Dennis

    2011-01-01

    We live in a world of continuous information overflow, but the quality of information and communication is suffering. Single value devices contribute to the information and communication quality by fo- cussing on one explicit, relevant piece of information. The information is decoupled from a

  7. Single Value Devices

    NARCIS (Netherlands)

    Mader, Angelika H.; Dertien, Edwin Christian; Reidsma, Dennis; Camurri, Antonio; Costa, Cristina

    We live in a world of continuous information overflow, but the quality of information and communication is suffering. Single value devices contribute to information and communication quality by focussing on one explicit, relevant piece of information. The information is decoupled from a computer and

  8. Single Value Devices

    NARCIS (Netherlands)

    Mader, Angelika H.; Reidsma, Dennis; Dertien, Edwin Christian; Volpe, G; Kolkmeier, Jan; Camurri, A.; Kolkmeier, Jan; Nijholt, Antinus

    2015-01-01

    We live in a world of continuous information overflow, but the quality of information and communication is suffering. Single value devices contribute to the information and communication quality by focussing on one explicit, relevant piece of information. The information is decoupled from a computer

  9. Beware the single hit!

    CERN Multimedia

    2008-01-01

    The first time that single particle effects from cosmic rays on electronics were observed was in 1991, when one of the instruments aboard an ESA satellite broke down after only five days in space. On 5 July, the TS-LEA group will have completed the installation of monitors that will help to reduce similar dangerous effects on LHC electronics.

  10. Single reusable spacecraft

    Data.gov (United States)

    National Aeronautics and Space Administration — Design of a my single person reusable spacecraft. It can carry one person and it has to be dropped from an aircraft at an altitude of 40,000 - 45,000 feet. Can be...

  11. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! ... Author Affiliations. Kankan Bhattacharyya1. Department of Physical Chemistry, Indian Association for the Cultivation of Science Jadavpur, Kolkata 700 032 India.

  12. Single photon and nonlocality

    Indian Academy of Sciences (India)

    In a paper by Home and Agarwal [1], it is claimed that quantum nonlocality can be revealed in a simple interferometry experiment using only single particles. A critical analysis of the concept of hidden variable used by the authors of [1] shows that the reasoning is not correct.

  13. Beyond the Single Story

    Science.gov (United States)

    McKenney, Yekaterina

    2016-01-01

    Teachers of world literature have the opportunity to help students explore the more complex reality behind the stereotypes that they often see in the media. If we don't encourage students to challenge one-dimensional "single stories" that characterize an entire people--whether Muslims, Russians, Mexicans, African Americans, Chinese,…

  14. Sorption analyses in materials science: selected oxides

    International Nuclear Information System (INIS)

    Fuller, E.L. Jr.; Condon, J.B.; Eager, M.H.; Jones, L.L.

    1981-01-01

    Physical adsorption studies have been shown to be extremely valuable in studying the chemistry and structure of dispersed materials. Many processes rely on the access to the large amount of surface made available by the high degree of dispersion. Conversely, there are many applications where consolidation of the dispersed solids is required. Several systems (silica gel, alumina catalysts, mineralogic alumino-silicates, and yttrium oxide plasters) have been studied to show the type and amount of chemical and structural information that can be obtained. Some review of current theories is given and additional concepts are developed based on statistical and thermodynamic arguments. The results are applied to sorption data to show that detailed sorption analyses are extremely useful and can provide valuable information that is difficult to obtain by any other means. Considerable emphasis has been placed on data analyses and interpretation of a nonclassical nature to show the potential of such studies that is often not recognized nor utilized

  15. DCH analyses using the CONTAIN code

    International Nuclear Information System (INIS)

    Hong, Sung Wan; Kim, Hee Dong

    1996-08-01

    This report describes CONTAIN analyses performed during participation in the project of 'DCH issue resolution for ice condenser plants' which is sponsored by NRC at SNL. Even though the calculations were performed for the Ice Condenser plant, CONTAIN code has been used for analyses of many phenomena in the PWR containment and the DCH module can be commonly applied to any plant types. The present ice condenser issue resolution effort intended to provide guidance as to what might be needed to resolve DCH for ice condenser plants. It includes both a screening analysis and a scoping study if the screening analysis cannot provide an complete resolution. The followings are the results concerning DCH loads in descending order. 1. Availability of ignition sources prior to vessel breach 2. availability and effectiveness of ice in the ice condenser 3. Loads modeling uncertainties related to co-ejected RPV water 4. Other loads modeling uncertainties 10 tabs., 3 figs., 14 refs. (Author)

  16. DCH analyses using the CONTAIN code

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Sung Wan; Kim, Hee Dong [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1996-08-01

    This report describes CONTAIN analyses performed during participation in the project of `DCH issue resolution for ice condenser plants` which is sponsored by NRC at SNL. Even though the calculations were performed for the Ice Condenser plant, CONTAIN code has been used for analyses of many phenomena in the PWR containment and the DCH module can be commonly applied to any plant types. The present ice condenser issue resolution effort intended to provide guidance as to what might be needed to resolve DCH for ice condenser plants. It includes both a screening analysis and a scoping study if the screening analysis cannot provide an complete resolution. The followings are the results concerning DCH loads in descending order. 1. Availability of ignition sources prior to vessel breach 2. availability and effectiveness of ice in the ice condenser 3. Loads modeling uncertainties related to co-ejected RPV water 4. Other loads modeling uncertainties 10 tabs., 3 figs., 14 refs. (Author).

  17. Analysing organic transistors based on interface approximation

    International Nuclear Information System (INIS)

    Akiyama, Yuto; Mori, Takehiko

    2014-01-01

    Temperature-dependent characteristics of organic transistors are analysed thoroughly using interface approximation. In contrast to amorphous silicon transistors, it is characteristic of organic transistors that the accumulation layer is concentrated on the first monolayer, and it is appropriate to consider interface charge rather than band bending. On the basis of this model, observed characteristics of hexamethylenetetrathiafulvalene (HMTTF) and dibenzotetrathiafulvalene (DBTTF) transistors with various surface treatments are analysed, and the trap distribution is extracted. In turn, starting from a simple exponential distribution, we can reproduce the temperature-dependent transistor characteristics as well as the gate voltage dependence of the activation energy, so we can investigate various aspects of organic transistors self-consistently under the interface approximation. Small deviation from such an ideal transistor operation is discussed assuming the presence of an energetically discrete trap level, which leads to a hump in the transfer characteristics. The contact resistance is estimated by measuring the transfer characteristics up to the linear region

  18. Introduction à l'analyse fonctionnelle

    CERN Document Server

    Reischer, Corina; Hengartner, Walter

    1981-01-01

    Fruit de la collaboration des professeur Walter Hengarther de l'Université Laval, Marcel Lambert et Corina Reischer de l'Université du Québec à Trois-Rivières, Introduction à l'analyse fonctionnelle se distingue tant par l'étendue de son contenu que par l'accessibilité de sa présentation. Sans céder quoi que ce soit sur la rigueur, il est parfaitement adapté à un premier cours d'analyse fonctionnelle. Tout en étant d'abord destiné aux étudiants en mathématiques, il pourra certes être utile aux étudiants de second cycle en sciences et en génie.

  19. Analyses and characterization of double shell tank

    International Nuclear Information System (INIS)

    1994-01-01

    Evaporator candidate feed from tank 241-AP-108 (108-AP) was sampled under prescribed protocol. Physical, inorganic, and radiochemical analyses were performed on tank 108-AP. Characterization of evaporator feed tank waste is needed primarily for an evaluation of its suitability to be safely processed through the evaporator. Such analyses should provide sufficient information regarding the waste composition to confidently determine whether constituent concentrations are within not only safe operating limits, but should also be relevant to functional limits for operation of the evaporator. Characterization of tank constituent concentrations should provide data which enable a prediction of where the types and amounts of environmentally hazardous waste are likely to occur in the evaporator product streams

  20. Pratique de l'analyse fonctionelle

    CERN Document Server

    Tassinari, Robert

    1997-01-01

    Mettre au point un produit ou un service qui soit parfaitement adapté aux besoins et aux exigences du client est indispensable pour l'entreprise. Pour ne rien laisser au hasard, il s'agit de suivre une méthodologie rigoureuse : celle de l'analyse fonctionnelle. Cet ouvrage définit précisément cette méthode ainsi que ses champs d'application. Il décrit les méthodes les plus performantes en termes de conception de produit et de recherche de qualité et introduit la notion d'analyse fonctionnelle interne. Un ouvrage clé pour optimiser les processus de conception de produit dans son entreprise. -- Idées clés, par Business Digest

  1. New environmental metabarcodes for analysing soil DNA

    DEFF Research Database (Denmark)

    Epp, Laura S.; Boessenkool, Sanne; Bellemain, Eva P.

    2012-01-01

    was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late......Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized...... for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups...

  2. BWR core melt progression phenomena: Experimental analyses

    International Nuclear Information System (INIS)

    Ott, L.J.

    1992-01-01

    In the BWR Core Melt in Progression Phenomena Program, experimental results concerning severe fuel damage and core melt progression in BWR core geometry are used to evaluate existing models of the governing phenomena. These include control blade eutectic liquefaction and the subsequent relocation and attack on the channel box structure; oxidation heating and hydrogen generation; Zircaloy melting and relocation; and the continuing oxidation of zirconium with metallic blockage formation. Integral data have been obtained from the BWR DF-4 experiment in the ACRR and from BWR tests in the German CORA exreactor fuel-damage test facility. Additional integral data will be obtained from new CORA BWR test, the full-length FLHT-6 BWR test in the NRU test reactor, and the new program of exreactor experiments at Sandia National Laboratories (SNL) on metallic melt relocation and blockage formation. an essential part of this activity is interpretation and use of the results of the BWR tests. The Oak Ridge National Laboratory (ORNL) has developed experiment-specific models for analysis of the BWR experiments; to date, these models have permitted far more precise analyses of the conditions in these experiments than has previously been available. These analyses have provided a basis for more accurate interpretation of the phenomena that the experiments are intended to investigate. The results of posttest analyses of BWR experiments are discussed and significant findings from these analyses are explained. The ORNL control blade/canister models with materials interaction, relocation and blockage models are currently being implemented in SCDAP/RELAP5 as an optional structural component

  3. Analysing qualitative research data using computer software.

    Science.gov (United States)

    McLafferty, Ella; Farley, Alistair H

    An increasing number of clinical nurses are choosing to undertake qualitative research. A number of computer software packages are available designed for the management and analysis of qualitative data. However, while it is claimed that the use of these programs is also increasing, this claim is not supported by a search of recent publications. This paper discusses the advantages and disadvantages of using computer software packages to manage and analyse qualitative data.

  4. En Billig GPS Data Analyse Platform

    DEFF Research Database (Denmark)

    Andersen, Ove; Christiansen, Nick; Larsen, Niels T.

    2011-01-01

    Denne artikel præsenterer en komplet software platform til analyse af GPS data. Platformen er bygget udelukkende vha. open-source komponenter. De enkelte komponenter i platformen beskrives i detaljer. Fordele og ulemper ved at bruge open-source diskuteres herunder hvilke IT politiske tiltage, der...... organisationer med et digitalt vejkort og GPS data begynde at lave trafikanalyser på disse data. Det er et krav, at der er passende IT kompetencer tilstede i organisationen....

  5. Analysing customer behaviour in mobile app usage

    OpenAIRE

    Chen, Qianling; Zhang, Min; Zhao, Xiande

    2017-01-01

    Purpose – Big data produced by mobile apps contains valuable knowledge about customers and markets and has been viewed as productive resources. This study proposes a multiple methods approach to elicit intelligence and value from big data by analysing customer behaviour in mobile app usage. Design/methodology/approach – The big data analytical approach is developed using three data mining techniques: RFM (Recency, Frequency, Monetary) analysis, link analysis, and association rule learning. We...

  6. Modelling and analysing oriented fibrous structures

    International Nuclear Information System (INIS)

    Rantala, M; Lassas, M; Siltanen, S; Sampo, J; Takalo, J; Timonen, J

    2014-01-01

    A mathematical model for fibrous structures using a direction dependent scaling law is presented. The orientation of fibrous nets (e.g. paper) is analysed with a method based on the curvelet transform. The curvelet-based orientation analysis has been tested successfully on real data from paper samples: the major directions of fibrefibre orientation can apparently be recovered. Similar results are achieved in tests on data simulated by the new model, allowing a comparison with ground truth

  7. Microfluidic single sperm analysis

    NARCIS (Netherlands)

    de Wagenaar, B.

    2016-01-01

    Samenvatting Microfluїdische technologie wordt steeds frequenter toegepast voor de analyse en scheiding van spermacellen. Verschillende onderzoeken hebben laten zien dat deze technologie zeer geschikt is voor het sorteren van spermacellen op basis van hun motiliteit. Met de beschreven en gebruikte

  8. Comparative genomic analyses of the Taylorellae.

    Science.gov (United States)

    Hauser, Heidi; Richter, Daniel C; van Tonder, Andries; Clark, Louise; Preston, Andrew

    2012-09-14

    Contagious equine metritis (CEM) is an important venereal disease of horses that is of concern to the thoroughbred industry. Taylorella equigenitalis is a causative agent of CEM but very little is known about it or its close relative Taylorella asinigenitalis. To reveal novel information about Taylorella biology, comparative genomic analyses were undertaken. Whole genome sequencing was performed for the T. equigenitalis type strain, NCTC11184. Draft genome sequences were produced for a second T. equigenitalis strain and for a strain of T. asinigenitalis. These genome sequences were analysed and compared to each other and the recently released genome sequence of T. equigenitalis MCE9. These analyses revealed that T. equigenitalis strains appear to be very similar to each other with relatively little strain-specific DNA content. A number of genes were identified that encode putative toxins and adhesins that are possibly involved in infection. Analysis of T. asinigenitalis revealed that it has a very similar gene repertoire to that of T. equigenitalis but shares surprisingly little DNA sequence identity with it. The generation of genome sequence information greatly increases knowledge of these poorly characterised bacteria and greatly facilitates study of them. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. An analyser for power plant operations

    International Nuclear Information System (INIS)

    Rogers, A.E.; Wulff, W.

    1990-01-01

    Safe and reliable operation of power plants is essential. Power plant operators need a forecast of what the plant will do when its current state is disturbed. The in-line plant analyser provides precisely this information at relatively low cost. The plant analyser scheme uses a mathematical model of the dynamic behaviour of the plant to establish a numerical simulation. Over a period of time, the simulation is calibrated with measurements from the particular plant in which it is used. The analyser then provides a reference against which to evaluate the plant's current behaviour. It can be used to alert the operator to any atypical excursions or combinations of readings that indicate malfunction or off-normal conditions that, as the Three Mile Island event suggests, are not easily recognised by operators. In a look-ahead mode, it can forecast the behaviour resulting from an intended change in settings or operating conditions. Then, when such changes are made, the plant's behaviour can be tracked against the forecast in order to assure that the plant is behaving as expected. It can be used to investigate malfunctions that have occurred and test possible adjustments in operating procedures. Finally, it can be used to consider how far from the limits of performance the elements of the plant are operating. Then by adjusting settings, the required power can be generated with as little stress as possible on the equipment. (6 figures) (Author)

  10. Rotational distortion in conventional allometric analyses.

    Science.gov (United States)

    Packard, Gary C

    2011-08-01

    Three data sets from the recent literature were submitted to new analyses to illustrate the rotational distortion that commonly accompanies traditional allometric analyses and that often causes allometric equations to be inaccurate and misleading. The first investigation focused on the scaling of evaporative water loss to body mass in passerine birds; the second was concerned with the influence of body size on field metabolic rates of rodents; and the third addressed interspecific variation in kidney mass among primates. Straight lines were fitted to logarithmic transformations by Ordinary Least Squares and Generalized Linear Models, and the resulting equations then were re-expressed as two-parameter power functions in the original arithmetic scales. The re-expressed models were displayed on bivariate graphs together with tracings for equations fitted directly to untransformed data by nonlinear regression. In all instances, models estimated by back-transformation failed to describe major features of the arithmetic distribution whereas equations fitted by nonlinear regression performed quite well. The poor performance of equations based on models fitted to logarithms can be traced to the increased weight and leverage exerted in those analyses by observations for small species and to the decreased weight and leverage exerted by large ones. The problem of rotational distortion can be avoided by performing exploratory analysis on untransformed values and by validating fitted models in the scale of measurement. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. Integration efficiency for model reduction in micro-mechanical analyses

    Science.gov (United States)

    van Tuijl, Rody A.; Remmers, Joris J. C.; Geers, Marc G. D.

    2017-11-01

    Micro-structural analyses are an important tool to understand material behavior on a macroscopic scale. The analysis of a microstructure is usually computationally very demanding and there are several reduced order modeling techniques available in literature to limit the computational costs of repetitive analyses of a single representative volume element. These techniques to speed up the integration at the micro-scale can be roughly divided into two classes; methods interpolating the integrand and cubature methods. The empirical interpolation method (high-performance reduced order modeling) and the empirical cubature method are assessed in terms of their accuracy in approximating the full-order result. A micro-structural volume element is therefore considered, subjected to four load-cases, including cyclic and path-dependent loading. The differences in approximating the micro- and macroscopic quantities of interest are highlighted, e.g. micro-fluctuations and stresses. Algorithmic speed-ups for both methods with respect to the full-order micro-structural model are quantified. The pros and cons of both classes are thereby clearly identified.

  12. Biopolymer gel swelling analysed with scaling laws and Flory-Rehner theory

    NARCIS (Netherlands)

    Sman, van der R.G.M.

    2015-01-01

    The swelling of biopolymer gels is analysed with scaling laws from polymer physics, as an alternative for the classical Flory-Rehner theory. With these scaling laws, holding for polymer concentrations in the semi-dilute regime, experimental data on deswelling of gels can be collapsed to a single

  13. Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure

    Directory of Open Access Journals (Sweden)

    Takumi Katsuhisa

    2012-08-01

    Full Text Available Abstract Background Giardia duodenalis is a common protozoan parasite of humans and animals. Genetic characterization of single loci indicates the existence of eight groups called assemblages, which differ in their host distribution. Molecular analyses challenged the idea that G. duodenalis is a strictly clonal diplomonad by providing evidence of recombination within and between assemblages. Particularly, inter-assemblage recombination events would complicate the interpretation of multi-locus genotyping data from field isolates: where is a host infected with multiple Giardia genotypes or with a single, recombined Giardia genotype. Methods Population genetic analyses on the single and multiple-locus level on an extensive dataset of G. duodenalis isolates from humans and animals were performed. Results Our analyses indicate that recombination between isolates from different assemblages are apparently very rare or absent in the natural population of Giardia duodenalis. At the multi-locus level, our statistical analyses are more congruent with clonal reproduction and can equally well be explained with the presence of multiple G. duodenalis genotypes within one field isolate. Conclusions We conclude that recombination between G. duodenalis assemblages is either very rare or absent. Recombination between genotypes from the same assemblage and genetic exchange between the nuclei of a single cyst needs further investigation.

  14. New Blood Pressure-Associated Loci Identified in Meta-Analyses of 475 000 Individuals

    NARCIS (Netherlands)

    Kraja, Aldi T; Cook, James P; Warren, Helen R; Surendran, Praveen; Liu, Chunyu; Evangelou, Evangelos; Manning, Alisa K; Grarup, Niels; Drenos, Fotios; Sim, Xueling; Smith, Albert Vernon; Amin, Najaf; Blakemore, Alexandra I F; Bork-Jensen, Jette; Brandslund, Ivan; Farmaki, Aliki-Eleni; Fava, Cristiano; Ferreira, Teresa; Herzig, Karl-Heinz; Giri, Ayush; Giulianini, Franco; Grove, Megan L; Guo, Xiuqing; Harris, Sarah E; Have, Christian T; Havulinna, Aki S; Zhang, He; Jørgensen, Marit E; Käräjämäki, AnneMari; Kooperberg, Charles; Linneberg, Allan; Little, Louis; Liu, Yongmei; Bonnycastle, Lori L; Lu, Yingchang; Mägi, Reedik; Mahajan, Anubha; Malerba, Giovanni; Marioni, Riccardo E; Mei, Hao; Menni, Cristina; Morrison, Alanna C; Padmanabhan, Sandosh; Palmas, Walter; Poveda, Alaitz; Rauramaa, Rainer; Rayner, Nigel William; Riaz, Muhammad; Rice, Ken; Richard, Melissa A; Smith, Jennifer A; Southam, Lorraine; Stančáková, Alena; Stirrups, Kathleen E; Tragante, Vinicius; Tuomi, Tiinamaija; Tzoulaki, Ioanna; Varga, Tibor V; Weiss, Stefan; Yiorkas, Andrianos M; Young, Robin; Zhang, Weihua; Barnes, Michael R; Cabrera, Claudia P; Gao, He; Boehnke, Michael; Boerwinkle, Eric; Chambers, John C; Connell, John M; Christensen, Cramer K; de Boer, Rudolf A; Deary, Ian J; Dedoussis, George; Deloukas, Panos; Dominiczak, Anna F; Dörr, Marcus; Joehanes, Roby; Edwards, Todd L; Esko, Tõnu; Fornage, Myriam; Franceschini, Nora; Franks, Paul W; Gambaro, Giovanni; Groop, Leif; Hallmans, Göran; Hansen, Torben; Hayward, Caroline; Heikki, Oksa; Ingelsson, Erik; Tuomilehto, Jaakko; Jarvelin, Marjo-Riitta; Kardia, Sharon L R; Karpe, Fredrik; Kooner, Jaspal S; Lakka, Timo A; Langenberg, Claudia; Lind, Lars; Loos, Ruth J F; Laakso, Markku; McCarthy, Mark I; Melander, Olle; Mohlke, Karen L; Morris, Andrew P; Palmer, Colin N A; Pedersen, Oluf; Polasek, Ozren; Poulter, Neil R; Province, Michael A; Psaty, Bruce M; Ridker, Paul M; Rotter, Jerome I; Rudan, Igor; Salomaa, Veikko; Samani, Nilesh J; Sever, Peter J; Skaaby, Tea; Stafford, Jeanette M; Starr, John M; van der Harst, Pim; van der Meer, Peter; van Duijn, Cornelia M; Vergnaud, Anne-Claire; Gudnason, Vilmundur; Wareham, Nicholas J; Wilson, James G; Willer, Cristen J; Witte, Daniel R; Zeggini, Eleftheria; Saleheen, Danish; Butterworth, Adam S; Danesh, John; Asselbergs, Folkert W; Wain, Louise V; Ehret, Georg B; Chasman, Daniel I; Caulfield, Mark J; Elliott, Paul; Lindgren, Cecilia M; Levy, Daniel; Newton-Cheh, Christopher; Munroe, Patricia B; Howson, Joanna M M

    2017-01-01

    BACKGROUND: Genome-wide association studies have recently identified >400 loci that harbor DNA sequence variants that influence blood pressure (BP). Our earlier studies identified and validated 56 single nucleotide variants (SNVs) associated with BP from meta-analyses of exome chip genotype data. An

  15. Comparison of plasma input and reference tissue models for analysing [(11)C]flumazenil studies

    NARCIS (Netherlands)

    Klumpers, Ursula M. H.; Veltman, Dick J.; Boellaard, Ronald; Comans, Emile F.; Zuketto, Cassandra; Yaqub, Maqsood; Mourik, Jurgen E. M.; Lubberink, Mark; Hoogendijk, Witte J. G.; Lammertsma, Adriaan A.

    2008-01-01

    A single-tissue compartment model with plasma input is the established method for analysing [(11)C]flumazenil ([(11)C]FMZ) studies. However, arterial cannulation and measurement of metabolites are time-consuming. Therefore, a reference tissue approach is appealing, but this approach has not been

  16. Chlorophyll fluorescence and X-ray analyses to characterise and improve paddy rice seed quality

    NARCIS (Netherlands)

    Costa, D.S.; Kodde, J.; Groot, S.P.C.

    2014-01-01

    The presence of less-mature seeds or seeds with cracks in a paddy rice seed lot may result in lower seed quality. The potential of chlorophyll fluorescence to provide information on the maturity of single seeds and X-ray analyses to identify seeds with cracks was evaluated in relation to paddy rice

  17. On the Use of Roche Equipotentials in Analysing the Problems of ...

    Indian Academy of Sciences (India)

    obtained by approximating its inner structure with Roche model. This expression for the potential has been used in subsequent analysis by var- ious authors to analyse the problems of structures and oscillations of synchronous and nonsynchronus binary stars as well as single rotating stars. Occasionally, doubts have been ...

  18. A Protocol for Better Design, Application, and Communication of Population Viability Analyses

    NARCIS (Netherlands)

    Pe'er, G.; Matsinos, Y.G.; Johst, K.; Franz, K.W.; Turlure, C.; Radchuk, V.; Malinowska, A.H.; Curtis, J.M.R.; Naujokaitis-Lewis, I.; Wintle, B.A.; Henle, K.

    2013-01-01

    Population viability analyses (PVAs) contribute to conservation theory, policy, and management. Most PVAs focus on single species within a given landscape and address a specific problem. This specificity often is reflected in the organization of published PVA descriptions. Many lack structure,

  19. Physical chemistry in a single live cell: confocal microscopy.

    Science.gov (United States)

    Amin, Md Asif; Nandi, Somen; Mondal, Prasenjit; Mahata, Tanushree; Ghosh, Surajit; Bhattacharyya, Kankan

    2017-05-24

    A live cell is a complex, yet extremely important container. Understanding the dynamics in a selected intracellular component is a challenging task. We have recently made significant progress in this direction using a confocal microscope as a tool. The smallest size of the focused spot in a confocal microscope is ∼0.2 μm (200 nm). This is nearly one hundred times smaller than the size of a live cell. Thus, one can selectively study different intracellular components/organelles in a live cell. In this paper, we discuss how one can image different intracellular components/organelles, record fluorescence spectra and decay at different locations, ascertain local polarity and viscosity, and monitor the dynamics of solvation, proton transfer, red-ox and other phenomena at specified locations/organelles inside a cell. We will highlight how this knowledge enriched us in differentiating between cancer and non-cancer cells, 3D tumor spheroids and towards drug delivery.

  20. ANDES: Statistical tools for the ANalyses of DEep Sequencing

    Directory of Open Access Journals (Sweden)

    Denison Mark R

    2010-07-01

    Full Text Available Abstract Background The advancements in DNA sequencing technologies have allowed researchers to progress from the analyses of a single organism towards the deep sequencing of a sample of organisms. With sufficient sequencing depth, it is now possible to detect subtle variations between members of the same species, or between mixed species with shared biomarkers, such as the 16S rRNA gene. However, traditional sequencing analyses of samples from largely homogeneous populations are often still based on multiple sequence alignments (MSA, where each sequence is placed along a separate row and similarities between aligned bases can be followed down each column. While this visual format is intuitive for a small set of aligned sequences, the representation quickly becomes cumbersome as sequencing depths cover loci hundreds or thousands of reads deep. Findings We have developed ANDES, a software library and a suite of applications, written in Perl and R, for the statistical ANalyses of DEep Sequencing. The fundamental data structure underlying ANDES is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment (MSA. Tools include the root mean square deviation (RMSD plot, which allows for the visual comparison of multiple samples on a position-by-position basis, and the computation of base conversion frequencies (transition/transversion rates, variation (Shannon entropy, inter-sample clustering and visualization (dendrogram and multidimensional scaling (MDS plot, threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values. Conclusions As new sequencing technologies evolve, deep sequencing will become increasingly cost-efficient and the inter and intra-sample comparisons of largely homogeneous sequences will become more common. We have provided a software package and demonstrated its