The big and intricate dreams of little organelles: Embracing complexity in the study of membrane traffic.

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Liu, Allen P; Botelho, Roberto J; Antonescu, Costin N

2017-09-01

Compartmentalization of eukaryotic cells into dynamic organelles that exchange material through regulated membrane traffic governs virtually every aspect of cellular physiology including signal transduction, metabolism and transcription. Much has been revealed about the molecular mechanisms that control organelle dynamics and membrane traffic and how these processes are regulated by metabolic, physical and chemical cues. From this emerges the understanding of the integration of specific organellar phenomena within complex, multiscale and nonlinear regulatory networks. In this review, we discuss systematic approaches that revealed remarkable insight into the complexity of these phenomena, including the use of proximity-based proteomics, high-throughput imaging, transcriptomics and computational modeling. We discuss how these methods offer insights to further understand molecular versatility and organelle heterogeneity, phenomena that allow a single organelle population to serve a range of physiological functions. We also detail on how transcriptional circuits drive organelle adaptation, such that organelles may shift their function to better serve distinct differentiation and stress conditions. Thus, organelle dynamics and membrane traffic are functionally heterogeneous and adaptable processes that coordinate with higher-order system behavior to optimize cell function under a range of contexts. Obtaining a comprehensive understanding of organellar phenomena will increasingly require combined use of reductionist and system-based approaches. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The (in)complete organelle genome: exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes.

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Sanitá Lima, Matheus; Woods, Laura C; Cartwright, Matthew W; Smith, David Roy

2016-11-01

Not long ago, scientists paid dearly in time, money and skill for every nucleotide that they sequenced. Today, DNA sequencing technologies epitomize the slogan 'faster, easier, cheaper and more', and in many ways, sequencing an entire genome has become routine, even for the smallest laboratory groups. This is especially true for mitochondrial and plastid genomes. Given their relatively small sizes and high copy numbers per cell, organelle DNAs are currently among the most highly sequenced kind of chromosome. But accurately characterizing an organelle genome and the information it encodes can require much more than DNA sequencing and bioinformatics analyses. Organelle genomes can be surprisingly complex and can exhibit convoluted and unconventional modes of gene expression. Unravelling this complexity can demand a wide assortment of experiments, from pulsed-field gel electrophoresis to Southern and Northern blots to RNA analyses. Here, we show that it is exactly these types of 'complementary' analyses that are often lacking from contemporary organelle genome papers, particularly short 'genome announcement' articles. Consequently, crucial and interesting features of organelle chromosomes are going undescribed, which could ultimately lead to a poor understanding and even a misrepresentation of these genomes and the genes they express. High-throughput sequencing and bioinformatics have made it easy to sequence and assemble entire chromosomes, but they should not be used as a substitute for or at the expense of other types of genomic characterization methods. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Mind the Organelle Gap - Peroxisome Contact Sites in Disease.

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Castro, Inês Gomes; Schuldiner, Maya; Zalckvar, Einat

2018-03-01

The eukaryotic cell is organized as a complex grid system where membrane-bound cellular compartments, organelles, must be localized to the right place at the right time. One way to facilitate correct organelle localization and organelle cooperation is through membrane contact sites, areas of close proximity between two organelles that are bridged by protein/lipid complexes. It is now clear that all organelles physically contact each other. The main focus of this review is contact sites of peroxisomes, central metabolic hubs whose defects lead to a variety of diseases. New peroxisome contacts, their tethering complexes and functions have been recently discovered. However, if and how peroxisome contacts contribute to the development of peroxisome-related diseases is still a mystery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evolving a photosynthetic organelle

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Nakayama Takuro

2012-04-01

Full Text Available Abstract The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles. The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis - the conversion of solar energy into chemical energy - and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

Evolving a photosynthetic organelle.

Science.gov (United States)

Nakayama, Takuro; Archibald, John M

2012-04-24

The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles.The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis--the conversion of solar energy into chemical energy--and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

Organelle-localized potassium transport systems in plants.

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Hamamoto, Shin; Uozumi, Nobuyuki

2014-05-15

Some intracellular organelles found in eukaryotes such as plants have arisen through the endocytotic engulfment of prokaryotic cells. This accounts for the presence of plant membrane intrinsic proteins that have homologs in prokaryotic cells. Other organelles, such as those of the endomembrane system, are thought to have evolved through infolding of the plasma membrane. Acquisition of intracellular components (organelles) in the cells supplied additional functions for survival in various natural environments. The organelles are surrounded by biological membranes, which contain membrane-embedded K(+) transport systems allowing K(+) to move across the membrane. K(+) transport systems in plant organelles act coordinately with the plasma membrane intrinsic K(+) transport systems to maintain cytosolic K(+) concentrations. Since it is sometimes difficult to perform direct studies of organellar membrane proteins in plant cells, heterologous expression in yeast and Escherichia coli has been used to elucidate the function of plant vacuole K(+) channels and other membrane transporters. The vacuole is the largest organelle in plant cells; it has an important task in the K(+) homeostasis of the cytoplasm. The initial electrophysiological measurements of K(+) transport have categorized three classes of plant vacuolar cation channels, and since then molecular cloning approaches have led to the isolation of genes for a number of K(+) transport systems. Plants contain chloroplasts, derived from photoautotrophic cyanobacteria. A novel K(+) transport system has been isolated from cyanobacteria, which may add to our understanding of K(+) flux across the thylakoid membrane and the inner membrane of the chloroplast. This chapter will provide an overview of recent findings regarding plant organellar K(+) transport proteins. Copyright © 2014 Elsevier GmbH. All rights reserved.

Microbial arms race: Ballistic "nematocysts" in dinoflagellates represent a new extreme in organelle complexity.

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Gavelis, Gregory S; Wakeman, Kevin C; Tillmann, Urban; Ripken, Christina; Mitarai, Satoshi; Herranz, Maria; Özbek, Suat; Holstein, Thomas; Keeling, Patrick J; Leander, Brian S

2017-03-01

We examine the origin of harpoon-like secretory organelles (nematocysts) in dinoflagellate protists. These ballistic organelles have been hypothesized to be homologous to similarly complex structures in animals (cnidarians); but we show, using structural, functional, and phylogenomic data, that nematocysts evolved independently in both lineages. We also recorded the first high-resolution videos of nematocyst discharge in dinoflagellates. Unexpectedly, our data suggest that different types of dinoflagellate nematocysts use two fundamentally different types of ballistic mechanisms: one type relies on a single pressurized capsule for propulsion, whereas the other type launches 11 to 15 projectiles from an arrangement similar to a Gatling gun. Despite their radical structural differences, these nematocysts share a single origin within dinoflagellates and both potentially use a contraction-based mechanism to generate ballistic force. The diversity of traits in dinoflagellate nematocysts demonstrates a stepwise route by which simple secretory structures diversified to yield elaborate subcellular weaponry.

The Biogenesis of Lysosomes and Lysosome-Related Organelles

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Luzio, J. Paul; Hackmann, Yvonne; Dieckmann, Nele M.G.; Griffiths, Gillian M.

2014-01-01

Lysosomes were once considered the end point of endocytosis, simply used for macromolecule degradation. They are now recognized to be dynamic organelles, able to fuse with a variety of targets and to be re-formed after fusion events. They are also now known to be the site of nutrient sensing and signaling to the cell nucleus. In addition, lysosomes are secretory organelles, with specialized machinery for regulated secretion of proteins in some cell types. The biogenesis of lysosomes and lysosome-related organelles is discussed, taking into account their dynamic nature and multiple roles. PMID:25183830

Ultrastructural relationship of the phagophore with surrounding organelles.

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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.

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

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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.

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

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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.

Physiology and pathophysiology of cell organelles

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J. J. Theron

1998-07-01

Full Text Available Mitochondria are found in all eucaryotic cells except mature red blood cells. The structural components of these organelles are briefly described. The primary function of mitochondria, i.e. transduction of energy with formation of ATP through a process of oxidative phosphorylation (OXPHOS occurs in six protein complexes arranged in sequence on the mitochondrial cristae formed by infoldings of the internal membrane. Mitochondrial DNA and ribosomes are found in mitochondria and protein synthesis can therefore occur in these organelles. However, most mitochondrial proteins and practically all lipids are imported from the cytoplasm.

Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists

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Matheus Sanitá Lima

2017-11-01

Full Text Available Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq data. Little is known about organelle transcription in nonmodel species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts. Here, we use publicly available RNA-seq experiments to investigate organelle transcription in 30 diverse plastid-bearing protists with varying organelle genomic architectures. Mapping RNA-seq data to organelle genomes revealed pervasive, genome-wide transcription, regardless of the taxonomic grouping, gene organization, or noncoding content. For every species analyzed, transcripts covered ≥85% of the mitochondrial and/or plastid genomes (all of which were ≤105 kb, indicating that most of the organelle DNA—coding and noncoding—is transcriptionally active. These results follow earlier studies of model species showing that organellar transcription is coupled and ubiquitous across the genome, requiring significant downstream processing of polycistronic transcripts. Our findings suggest that noncoding organelle DNA can be transcriptionally active, raising questions about the underlying function of these transcripts and underscoring the utility of publicly available RNA-seq data for recovering complete genome sequences. If pervasive transcription is also found in bigger organelle genomes (>105 kb and across a broader range of eukaryotes, this could indicate that noncoding organelle RNAs are regulating fundamental processes within eukaryotic cells.

AQUATIC PLANT SPECIATION AFFECTED BY DIVERSIFYING SELECTION OF ORGANELLE DNA REGIONS(1).

Science.gov (United States)

Kato, Syou; Misawa, Kazuharu; Takahashi, Fumio; Sakayama, Hidetoshi; Sano, Satomi; Kosuge, Keiko; Kasai, Fumie; Watanabe, Makoto M; Tanaka, Jiro; Nozaki, Hisayoshi

2011-10-01

Many of the genes that control photosynthesis are carried in the chloroplast. These genes differ among species. However, evidence has yet to be reported revealing the involvement of organelle genes in the initial stages of plant speciation. To elucidate the molecular basis of aquatic plant speciation, we focused on the unique plant species Chara braunii C. C. Gmel. that inhabits both shallow and deep freshwater habitats and exhibits habitat-based dimorphism of chloroplast DNA (cpDNA). Here, we examined the "shallow" and "deep" subpopulations of C. braunii using two nuclear DNA (nDNA) markers and cpDNA. Genetic differentiation between the two subpopulations was measured in both nDNA and cpDNA regions, although phylogenetic analyses suggested nuclear gene flow between subpopulations. Neutrality tests based on Tajima's D demonstrated diversifying selection acting on organelle DNA regions. Furthermore, both "shallow" and "deep" haplotypes of cpDNA detected in cultures originating from bottom soils of three deep environments suggested that migration of oospores (dormant zygotes) between the two habitats occurs irrespective of the complete habitat-based dimorphism of cpDNA from field-collected vegetative thalli. Therefore, the two subpopulations are highly selected by their different aquatic habitats and show prezygotic isolation, which represents an initial process of speciation affected by ecologically based divergent selection of organelle genes. © 2011 Phycological Society of America.

Cytoplasmic Flow Enhances Organelle Dispersion in Eukaryotic Cells

Science.gov (United States)

Koslover, Elena; Mogre, Saurabh; Chan, Caleb; Theriot, Julie

The cytoplasm of a living cell is an active environment through which intracellular components move and mix. We explore, using theoretical modeling coupled with microrheological measurements, the efficiency of particle dispersion via different modes of transport within this active environment. In particular, we focus on the role of cytoplasmic flow over different scales in contributing to organelle transport within two different cell types. In motile neutrophil cells, we show that bulk fluid flow associated with rapid cell deformation enhances particle transport to and from the cell periphery. In narrow fungal hyphae, localized flows due to hydrodynamic entrainment are shown to contribute to optimally efficient organelle dispersion. Our results highlight the importance of non-traditional modes of transport associated with flow of the cytoplasmic fluid in the distribution of organelles throughout eukaryotic cells.

Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists.

Science.gov (United States)

Sanitá Lima, Matheus; Smith, David Roy

2017-11-06

Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq) data. Little is known about organelle transcription in nonmodel species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts. Here, we use publicly available RNA-seq experiments to investigate organelle transcription in 30 diverse plastid-bearing protists with varying organelle genomic architectures. Mapping RNA-seq data to organelle genomes revealed pervasive, genome-wide transcription, regardless of the taxonomic grouping, gene organization, or noncoding content. For every species analyzed, transcripts covered ≥85% of the mitochondrial and/or plastid genomes (all of which were ≤105 kb), indicating that most of the organelle DNA-coding and noncoding-is transcriptionally active. These results follow earlier studies of model species showing that organellar transcription is coupled and ubiquitous across the genome, requiring significant downstream processing of polycistronic transcripts. Our findings suggest that noncoding organelle DNA can be transcriptionally active, raising questions about the underlying function of these transcripts and underscoring the utility of publicly available RNA-seq data for recovering complete genome sequences. If pervasive transcription is also found in bigger organelle genomes (>105 kb) and across a broader range of eukaryotes, this could indicate that noncoding organelle RNAs are regulating fundamental processes within eukaryotic cells. Copyright © 2017 Sanitá Lima and Smith.

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,

Trans-membrane area asymmetry controls the shape of cellular organelles

NARCIS (Netherlands)

Beznoussenko, Galina V; Pilyugin, Sergei S; Geerts, Willie J C; Kozlov, Michael M; Burger, Koert N J; Luini, Alberto; Derganc, Jure; Mironov, Alexander A

2015-01-01

Membrane organelles often have complicated shapes and differ in their volume, surface area and membrane curvature. The ratio between the surface area of the cytosolic and luminal leaflets (trans-membrane area asymmetry (TAA)) determines the membrane curvature within different sites of the organelle.

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.

Deleterious mutation accumulation in organelle genomes.

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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.

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

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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.

Paulinella chromatophora – rethinking the transition from endosymbiont to organelle

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Eva C.M. Nowack

2014-12-01

Full Text Available Eukaryotes co-opted photosynthetic carbon fixation from prokaryotes by engulfing a cyanobacterium and stably integrating it as a photosynthetic organelle (plastid in a process known as primary endosymbiosis. The sheer complexity of interactions between a plastid and the surrounding cell that started to evolve over 1 billion years ago, make it challenging to reconstruct intermediate steps in organelle evolution by studying extant plastids. Recently, the photosynthetic amoeba Paulinella chromatophora was identified as a much sought-after intermediate stage in the evolution of a photosynthetic organelle. This article reviews the current knowledge on this unique organism. In particular it describes how the interplay of reductive genome evolution, gene transfers, and trafficking of host-encoded proteins into the cyanobacterial endosymbiont contributed to transform the symbiont into a nascent photosynthetic organelle. Together with recent results from various other endosymbiotic associations a picture emerges that lets the targeting of host-encoded proteins into bacterial endosymbionts appear as an early step in the establishment of an endosymbiotic relationship that enables the host to gain control over the endosymbiont.

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

The creation of artificial organelles is a new paradigm in medical therapy that aims to substitute for missing cellular function by replenishing a specific cellular task. Artificial organelles tackle the challenge of mimicking metabolism, which is the set of chemical reactions that occur within a...

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

[Methods of substances and organelles introduction in living cell for cell engineering technologies].

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Nikitin, V A

2007-01-01

We have presented the classification of more than 40 methods of genetic material, substances and organelles introduction into a living cell. Each of them has its characteristic advantages, disadvantages and limitations with respect to cell viability, transfer efficiency, general applicability, and technical requirements. It this article we have enlarged on the description of our developments of several new and improved approaches, methods and devices of the direct microinjection into a single cell and cell microsurgery with the help of glass micropipettes. The problem of low efficiency of mammalian cloning is discussed with emphasis on the necessity of expertizing of each step of single cell reconstruction to begin with microsurgical manipulations and necessity of the development of such methods of single cell resonstruction that could minimize the possible damage of the cell.

Limited distal organelles and synaptic function in extensive monoaminergic innervation.

Science.gov (United States)

Tao, Juan; Bulgari, Dinara; Deitcher, David L; Levitan, Edwin S

2017-08-01

Organelles such as neuropeptide-containing dense-core vesicles (DCVs) and mitochondria travel down axons to supply synaptic boutons. DCV distribution among en passant boutons in small axonal arbors is mediated by circulation with bidirectional capture. However, it is not known how organelles are distributed in extensive arbors associated with mammalian dopamine neuron vulnerability, and with volume transmission and neuromodulation by monoamines and neuropeptides. Therefore, we studied presynaptic organelle distribution in Drosophila octopamine neurons that innervate ∼20 muscles with ∼1500 boutons. Unlike in smaller arbors, distal boutons in these arbors contain fewer DCVs and mitochondria, although active zones are present. Absence of vesicle circulation is evident by proximal nascent DCV delivery, limited impact of retrograde transport and older distal DCVs. Traffic studies show that DCV axonal transport and synaptic capture are not scaled for extensive innervation, thus limiting distal delivery. Activity-induced synaptic endocytosis and synaptic neuropeptide release are also reduced distally. We propose that limits in organelle transport and synaptic capture compromise distal synapse maintenance and function in extensive axonal arbors, thereby affecting development, plasticity and vulnerability to neurodegenerative disease. © 2017. Published by The Company of Biologists Ltd.

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

2018-01-01

Artificial organelles created from a bottom up approach are a new type of engineered materials, which are not designed to be living but, instead, to mimic some specific functions inside cells. By doing so, artificial organelles are expected to become a powerful tool in biomedicine. They can act a...

Lipid droplets as ubiquitous fat storage organelles in C. elegans

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Guo Fengli

2010-12-01

Full Text Available Abstract Background Lipid droplets are a class of eukaryotic cell organelles for storage of neutral fat such as triacylglycerol (TAG and cholesterol ester (CE. We and others have recently reported that lysosome-related organelles (LROs are not fat storage structures in the nematode C. elegans. We also reported the formation of enlarged lipid droplets in a class of peroxisomal fatty acid β-oxidation mutants. In the present study, we seek to provide further evidence on the organelle nature and biophysical properties of fat storage structures in wild-type and mutant C. elegans. Results In this study, we provide biochemical, histological and ultrastructural evidence of lipid droplets in wild-type and mutant C. elegans that lack lysosome related organelles (LROs. The formation of lipid droplets and the targeting of BODIPY fatty acid analogs to lipid droplets in live animals are not dependent on lysosomal trafficking or peroxisome dysfunction. However, the targeting of Nile Red to lipid droplets in live animals occurs only in mutants with defective peroxisomes. Nile Red labelled-lipid droplets are characterized by a fluorescence emission spectrum distinct from that of Nile Red labelled-LROs. Moreover, we show that the recently developed post-fix Nile Red staining method labels lipid droplets exclusively. Conclusions Our results demonstrate lipid droplets as ubiquitous fat storage organelles and provide a unified explanation for previous studies on fat labelling methods in C. elegans. These results have important applications to the studies of fat storage and lipid droplet regulation in the powerful genetic system, C. elegans.

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

Scanning ion images; analysis of pharmaceutical drugs at organelle levels

Science.gov (United States)

Larras-Regard, E.; Mony, M.-C.

1995-05-01

With the ion analyser IMS 4F used in microprobe mode, it is possible to obtain images of fields of 10 × 10 [mu]m2, corresponding to an effective magnification of 7000 with lateral resolution of 250 nm, technical characteristics that are appropriate for the size of cell organelles. It is possible to characterize organelles by their relative CN-, P- and S- intensities when the tissues are prepared by freeze fixation and freeze substitution. The recognition of organelles enables correlation of the tissue distribution of ebselen, a pharmaceutical drug containing selenium. The various metabolites characterized in plasma, bile and urine during biotransformation of ebselen all contain selenium, so the presence of the drug and its metabolites can be followed by images of Se. We were also able to detect the endogenous content of Se in tissue, due to the increased sensitivity of ion analysis in microprobe mode. Our results show a natural occurrence of Se in the border corresponding to the basal lamina of cells of proximal but not distal tubules of the kidney. After treatment of rats with ebselen, an additional site of Se is found in the lysosomes. We suggest that in addition to direct elimination of ebselen and its metabolites by glomerular filtration and urinary elimination, a second process of elimination may occur: Se compounds reaching the epithelial cells via the basal lamina accumulate in lysosomes prior to excretion into the tubular fluid. The technical developments of using the IMS 4F instrument in the microprobe mode and the improvement in preparation of samples by freeze fixation and substitution further extend the limit of ion analysis in biology. Direct imaging of trace elements and molecules marked with a tracer make it possible to determine their targets by comparison with images of subcellular structures. This is a promising advance in the study of pathways of compounds within tissues, cells and the whole organism.

Analyzing Lysosome-Related Organelles by Electron Microscopy

KAUST Repository

Hurbain, Ilse; Romao, Maryse; Bergam, Ptissam; Heiligenstein, Xavier; Raposo, Graç a

2017-01-01

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

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.

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)

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.

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.

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...

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.

Reduction of Cr (VI) into Cr (III) by organelles of Chlorella vulgaris in aqueous solution: An organelle-level attempt.

Science.gov (United States)

Chen, Zunwei; Song, Shufang; Wen, Yuezhong

2016-12-01

The priority pollutant chromium (Cr) was ubiquitous and great efforts have been made to reduce Cr (VI) into less-toxic Cr (III) by alga for the convenient availability and low expense. However, the functional role of organelle inside the algal cell in Cr (VI) reduction was poorly understood. In this study, organelles in green algae Chlorella vulgaris were extracted and further decorated for Cr (VI) reduction tests. Results showed that the chloroplast exhibited not only adsorption ability of total Cr (21.18% comparing to control) but also reduction potential of Cr (VI) (almost 70% comparing to control), whose most suitable working concentration was at 17μg/mL. Furtherly, the isolated thylakoid membrane (ITM) showed better Cr (VI) reduction potential with the presence of sodium alginate (SA), even though the Hill reaction activity (HRA) was inhibited. As for photosystem II (PSII), the addition of mesoporous silica SBA-15 enhanced the reduction ability through improving the light-harvesting complex (LHC) II efficiency and electron transport rate. On the whole, the reduction ability order of the three kinds of materials based on chloroplast in C. vulgaris was PSII@SBA-15>Chloroplast>ITM@SA. The attempt made in this study to reduce the Cr (VI) with C. vulgaris organelles might not only offer basement to detect the potential action mechanism of Cr (VI) reduction by C. vulgaris but also provide a new sight for the scavenge of heavy metal with biological materials. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

Perez, Alex J.; Seyedhosseini, Mojtaba; Deerinck, Thomas J.; Bushong, Eric A.; Panda, Satchidananda; Tasdizen, Tolga; Ellisman, Mark H.

2014-01-01

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. PMID:25426032

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.

From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism

NARCIS (Netherlands)

Gabaldon, T.; Huynen, M.A.

2007-01-01

Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the transition from a free-living cell to a specialized organelle, we compared a reconstructed ancestral

From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.

NARCIS (Netherlands)

Gabaldon, T.; Huynen, M.A.

2007-01-01

Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the transition from a free-living cell to a specialized organelle, we compared a reconstructed ancestral

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

KAUST Repository

Serag, Maged F.; Kaji, Noritada; Habuchi, Satoshi; Bianco, Alberto; Baba, Yoshinobu

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.

Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules.

Science.gov (United States)

Valach, Matus; Burger, Gertraud; Gray, Michael W; Lang, B Franz

2014-12-16

5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Organelles genome stability of wheat plantlets produced by anther ...

African Journals Online (AJOL)

Yomi

2012-03-15

Mar 15, 2012 ... 1Department of Biotechnology, Faculty of Agricultural Technology, Al-Balqa' Applied University, ... genetic stability of wheat organelles genomes for plantlets produced by anther culture using restriction ..... of transgenic plants.

Novel quantitative autophagy analysis by organelle flow cytometry after cell sonication.

Directory of Open Access Journals (Sweden)

Michael Degtyarev

Full Text Available Autophagy is a dynamic process of bulk degradation of cellular proteins and organelles in lysosomes. Current methods of autophagy measurement include microscopy-based counting of autophagic vacuoles (AVs in cells. We have developed a novel method to quantitatively analyze individual AVs using flow cytometry. This method, OFACS (organelle flow after cell sonication, takes advantage of efficient cell disruption with a brief sonication, generating cell homogenates with fluorescently labeled AVs that retain their integrity as confirmed with light and electron microscopy analysis. These AVs could be detected directly in the sonicated cell homogenates on a flow cytometer as a distinct population of expected organelle size on a cytometry plot. Treatment of cells with inhibitors of autophagic flux, such as chloroquine or lysosomal protease inhibitors, increased the number of particles in this population under autophagy inducing conditions, while inhibition of autophagy induction with 3-methyladenine or knockdown of ATG proteins prevented this accumulation. This assay can be easily performed in a high-throughput format and opens up previously unexplored avenues for autophagy analysis.

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.

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

Beta-Poisson model for single-cell RNA-seq data analyses.

Science.gov (United States)

Vu, Trung Nghia; Wills, Quin F; Kalari, Krishna R; Niu, Nifang; Wang, Liewei; Rantalainen, Mattias; Pawitan, Yudi

2016-07-15

Single-cell RNA-sequencing technology allows detection of gene expression at the single-cell level. One typical feature of the data is a bimodality in the cellular distribution even for highly expressed genes, primarily caused by a proportion of non-expressing cells. The standard and the over-dispersed gamma-Poisson models that are commonly used in bulk-cell RNA-sequencing are not able to capture this property. We introduce a beta-Poisson mixture model that can capture the bimodality of the single-cell gene expression distribution. We further integrate the model into the generalized linear model framework in order to perform differential expression analyses. The whole analytical procedure is called BPSC. The results from several real single-cell RNA-seq datasets indicate that ∼90% of the transcripts are well characterized by the beta-Poisson model; the model-fit from BPSC is better than the fit of the standard gamma-Poisson model in > 80% of the transcripts. Moreover, in differential expression analyses of simulated and real datasets, BPSC performs well against edgeR, a conventional method widely used in bulk-cell RNA-sequencing data, and against scde and MAST, two recent methods specifically designed for single-cell RNA-seq data. An R package BPSC for model fitting and differential expression analyses of single-cell RNA-seq data is available under GPL-3 license at https://github.com/nghiavtr/BPSC CONTACT: yudi.pawitan@ki.se or mattias.rantalainen@ki.se 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.

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

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

Organelle-targeting surface-enhanced Raman scattering (SERS) nanosensors for subcellular pH sensing.

Science.gov (United States)

Shen, Yanting; Liang, Lijia; Zhang, Shuqin; Huang, Dianshuai; Zhang, Jing; Xu, Shuping; Liang, Chongyang; Xu, Weiqing

2018-01-25

The pH value of subcellular organelles in living cells is a significant parameter in the physiological activities of cells. Its abnormal fluctuations are commonly believed to be associated with cancers and other diseases. Herein, a series of surface-enhanced Raman scattering (SERS) nanosensors with high sensitivity and targeting function was prepared for the quantification and monitoring of pH values in mitochondria, nucleus, and lysosome. The nanosensors were composed of gold nanorods (AuNRs) functionalized with a pH-responsive molecule (4-mercaptopyridine, MPy) and peptides that could specifically deliver the AuNRs to the targeting subcellular organelles. The localization of our prepared nanoprobes in specific organelles was confirmed by super-high resolution fluorescence imaging and bio-transmission electron microscopy (TEM) methods. By the targeting ability, the pH values of the specific organelles can be determined by monitoring the vibrational spectral changes of MPy with different pH values. Compared to the cases of reported lysosome and cytoplasm SERS pH sensors, more accurate pH values of mitochondria and nucleus, which could be two additional intracellular tracers for subcellular microenvironments, were disclosed by this SERS approach, further improving the accuracy of discrimination of related diseases. Our sensitive SERS strategy can also be employed to explore crucial physiological and biological processes that are related to subcellular pH fluctuations.

Targeting mammalian organelles with internalizing phage (iPhage) libraries

Science.gov (United States)

Rangel, Roberto; Dobroff, Andrey S.; Guzman-Rojas, Liliana; Salmeron, Carolina C.; Gelovani, Juri G.; Sidman, Richard L.; Pasqualini, Renata; Arap, Wadih

2015-01-01

Techniques largely used for protein interaction studies and discovery of intracellular receptors, such as affinity capture complex purification and yeast two-hybrid, may produce inaccurate datasets due to protein insolubility, transient or weak protein interactions, or irrelevant intracellular context. A versatile tool to overcome these limitations as well as to potentially create vaccines and engineer peptides and antibodies as targeted diagnostic and therapeutic agents, is the phage display technique. We have recently developed a new technology for screening internalizing phage (iPhage) vectors and libraries utilizing a ligand/receptor-independent mechanism to penetrate eukaryotic cells. iPhage particles provide a unique discovery platform for combinatorial intracellular targeting of organelle ligands along with their corresponding receptors and to fingerprint functional protein domains in living cells. Here we explain the design, cloning, construction, and production of iPhage-based vectors and libraries, along with basic ligand-receptor identification and validation methodologies for organelle receptors. An iPhage library screening can be performed in ~8 weeks. PMID:24030441

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.

Effects of 4-aminopyridine on organelle movement in cultured mouse dorsal root ganglion neurites.

Science.gov (United States)

Hiruma, Hiromi; Kawakami, Tadashi

2010-03-01

Aminopyridines, widely used as a K(+) channel blocker, are membrane-permeable weak bases and have the ability to form vacuoles in the cytoplasm. The vacuoles originate from acidic organelles such as lysosomes. Here, we investigated the effects of 4-aminopyridine (4-AP) on organelle movement in neurites of cultured mouse dorsal root ganglion (DRG) neurons by using video-enhanced microscopy. Some experiments were carried out using fluorescent dyes for lysosomes and mitochondria and confocal microscopy. Treatment of DRG neurons with 4 mM 4-AP caused Brownian movement of some lysosomes within 5 min. The Brownian movement gradually became rapid and vacuoles were formed around individual lysosomes 10-20 min after the start of treatment. Axonal transport of organelles was inhibited by 4-AP. Lysosomes showing Brownian movement were not transported in longitudinal direction of the neurite and the transport of mitochondria was interrupted by vacuoles. The 4-AP-induced Brownian movement of lysosomes with vacuole formation and inhibition of axonal transport were prevented by the simultaneous treatment with vacuolar H(+) ATPase inhibitor bafilomycin A1 or in Cl(-)-free SO(4)(2-) medium. These results indicate that changes in organelle movement by 4-AP are related to vacuole formation and the vacuolar H(+) ATPase and Cl(-) are required for the effects of 4-AP.

Organization of organelles within hyphae of Ashbya gossypii revealed by electron tomography.

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Gibeaux, Romain; Hoepfner, Dominic; Schlatter, Ivan; Antony, Claude; Philippsen, Peter

2013-11-01

Ashbya gossypii grows as multinucleated and constantly elongating hyphae. Nuclei are in continuous forward and backward motion, also move during mitosis, and frequently bypass each other. Whereas these nuclear movements are well documented, comparatively little is known about the density and morphology of organelles which very likely influence these movements. To understand the three-dimensional subcellular organization of hyphae at high resolution, we performed large-scale electron tomography of the tip regions in A. gossypii. Here, we present a comprehensive space-filling model in which most membrane-limited organelles including nuclei, mitochondria, endosomes, multivesicular bodies, vacuoles, autophagosomes, peroxisomes, and vesicles are modeled. Nuclei revealed different morphologies and protrusions filled by the nucleolus. Mitochondria are very abundant and form a tubular network with a polarized spherical fraction. The organelles of the degradative pathways show a clustered organization. By analyzing vesicle-like bodies, we identified three size classes of electron-dense vesicles (∼200, ∼150, and ∼100 nm) homogeneously distributed in the cytoplasm which most likely represent peroxisomes. Finally, coated and uncoated vesicles with approximately 40-nm diameters show a polarized distribution toward the hyphal tip with the coated vesicles preferentially localizing at the hyphal periphery.

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).

Leading-process actomyosin coordinates organelle positioning and adhesion receptor dynamics in radially migrating cerebellar granule neurons.

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Trivedi, Niraj; Ramahi, Joseph S; Karakaya, Mahmut; Howell, Danielle; Kerekes, Ryan A; Solecki, David J

2014-12-02

During brain development, neurons migrate from germinal zones to their final positions to assemble neural circuits. A unique saltatory cadence involving cyclical organelle movement (e.g., centrosome motility) and leading-process actomyosin enrichment prior to nucleokinesis organizes neuronal migration. While functional evidence suggests that leading-process actomyosin is essential for centrosome motility, the role of the actin-enriched leading process in globally organizing organelle transport or traction forces remains unexplored. We show that myosin ii motors and F-actin dynamics are required for Golgi apparatus positioning before nucleokinesis in cerebellar granule neurons (CGNs) migrating along glial fibers. Moreover, we show that primary cilia are motile organelles, localized to the leading-process F-actin-rich domain and immobilized by pharmacological inhibition of myosin ii and F-actin dynamics. Finally, leading process adhesion dynamics are dependent on myosin ii and F-actin. We propose that actomyosin coordinates the overall polarity of migrating CGNs by controlling asymmetric organelle positioning and cell-cell contacts as these cells move along their glial guides.

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.

Prokaryotic cells: structural organisation of the cytoskeleton and organelles

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Wanderley de Souza

2012-05-01

Full Text Available 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.

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

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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

Organelle targeting: third level of drug targeting

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Sakhrani NM

2013-07-01

Full Text Available Niraj M Sakhrani, Harish PadhDepartment of Cell and Molecular Biology, BV Patel Pharmaceutical Education and Research Development (PERD Centre, Gujarat, IndiaAbstract: Drug discovery and drug delivery are two main aspects for treatment of a variety of disorders. However, the real bottleneck associated with systemic drug administration is the lack of target-specific affinity toward a pathological site, resulting in systemic toxicity and innumerable other side effects as well as higher dosage requirement for efficacy. An attractive strategy to increase the therapeutic index of a drug is to specifically deliver the therapeutic molecule in its active form, not only into target tissue, nor even to target cells, but more importantly, into the targeted organelle, ie, to its intracellular therapeutic active site. This would ensure improved efficacy and minimize toxicity. Cancer chemotherapy today faces the major challenge of delivering chemotherapeutic drugs exclusively to tumor cells, while sparing normal proliferating cells. Nanoparticles play a crucial role by acting as a vehicle for delivery of drugs to target sites inside tumor cells. In this review, we spotlight active and passive targeting, followed by discussion of the importance of targeting to specific cell organelles and the potential role of cell-penetrating peptides. Finally, the discussion will address the strategies for drug/DNA targeting to lysosomes, mitochondria, nuclei and Golgi/endoplasmic reticulum.Keywords: intracellular drug delivery, cancer chemotherapy, therapeutic index, cell penetrating peptides

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

Investigating the effect of poly-l-lactic acid nanoparticles carrying hypericin on the flow-biased diffusive motion of HeLa cell organelles.

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Penjweini, Rozhin; Deville, Sarah; Haji Maghsoudi, Omid; Notelaers, Kristof; Ethirajan, Anitha; Ameloot, Marcel

2017-07-19

In this study, we investigate in human cervical epithelial HeLa cells the intracellular dynamics and the mutual interaction with the organelles of the poly-l-lactic acid nanoparticles (PLLA NPs) carrying the naturally occurring hydrophobic photosensitizer hypericin. Temporal and spatiotemporal image correlation spectroscopy was used for the assessment of the intracellular diffusion and directed motion of the nanocarriers by tracking the hypericin fluorescence. Using image cross-correlation spectroscopy and specific fluorescent labelling of endosomes, lysosomes and mitochondria, the NPs dynamics in association with the cell organelles was studied. Static colocalization experiments were interpreted according to the Manders' overlap coefficient. Nanoparticles associate with a small fraction of the whole-organelle population. The organelles moving with NPs exhibit higher directed motion compared to those moving without them. The rate of the directed motion drops substantially after the application of nocodazole. The random component of the organelle motions is not influenced by the NPs. Image correlation and cross-correlation spectroscopy are most appropriate to unravel the motion of the PLLA nanocarrier and to demonstrate that the rate of the directed motion of organelles is influenced by their interaction with the nanocarriers. Not all PLLA-hypericin NPs are associated with organelles. © 2017 Royal Pharmaceutical Society.

Cholesterol transfer at endosomal-organelle membrane contact sites.

Science.gov (United States)

Ridgway, Neale D; Zhao, Kexin

2018-06-01

Cholesterol is delivered to the limiting membrane of late endosomes by Niemann-Pick Type C1 and C2 proteins. This review summarizes recent evidence that cholesterol transfer from endosomes to the endoplasmic reticulum and other organelles is mediated by lipid-binding proteins that localize to membrane contact sites (MCS). LDL-cholesterol in the late endosomal/lysosomes is exported to the plasma membrane, where most cholesterol resides, and the endoplasmic reticulum, which harbors the regulatory complexes and enzymes that control the synthesis and esterification of cholesterol. A major advance in dissecting these cholesterol transport pathways was identification of frequent and dynamic MCS between endosomes and the endoplasmic reticulum, peroxisomes and plasma membrane. Positioned at these MCS are members of the oxysterol-binding protein (OSBP) and steroidogenic acute regulatory protein-related lipid-transfer family of lipid transfer proteins that bridge the opposing membranes and directly or indirectly mediate cholesterol transfer. OSBP-related protein 1L (ORP1L), ORP5 and ORP6 mediate cholesterol transfer to the endoplasmic reticulum that regulates cholesterol homeostasis. ORP1L and STARD3 also move cholesterol from the endoplasmic reticulum-to-late endosomal/lysosomes under low-cholesterol conditions to facilitate intraluminal vesicle formation. Cholesterol transport also occurs at MCS with peroxisomes and possibly the plasma membrane. Frequent contacts between organelles and the endo-lysosomal vesicles are sites for bidirectional transfer of cholesterol.

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

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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.

Notochord vacuoles are lysosome-related organelles that function in axis and spine morphogenesis.

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Ellis, Kathryn; Bagwell, Jennifer; Bagnat, Michel

2013-03-04

The notochord plays critical structural and signaling roles during vertebrate development. At the center of the vertebrate notochord is a large fluid-filled organelle, the notochord vacuole. Although these highly conserved intracellular structures have been described for decades, little is known about the molecular mechanisms involved in their biogenesis and maintenance. Here we show that zebrafish notochord vacuoles are specialized lysosome-related organelles whose formation and maintenance requires late endosomal trafficking regulated by the vacuole-specific Rab32a and H(+)-ATPase-dependent acidification. We establish that notochord vacuoles are required for body axis elongation during embryonic development and identify a novel role in spine morphogenesis. Thus, the vertebrate notochord plays important structural roles beyond early development.

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

DEFF Research Database (Denmark)

Leister, Dario Michael

2016-01-01

direct way to reconstruct the evolutionary history of plastids and mitochondria is to sequence and analyze their relatively small genomes. However, understanding the functional diversification of these organelles requires the identification of their complete protein repertoires - which is the ultimate...

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

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)

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...... 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...

Propeptides are sufficient to regulate organelle-specific pH-dependent activation of furin and proprotein convertase 1/3.

Science.gov (United States)

Dillon, Stephanie L; Williamson, Danielle M; Elferich, Johannes; Radler, David; Joshi, Rajendra; Thomas, Gary; Shinde, Ujwal

2012-10-12

The proprotein convertases (PCs) furin and proprotein convertase 1/3 (PC1) cleave substrates at dibasic residues along the eukaryotic secretory/endocytic pathway. PCs are evolutionarily related to bacterial subtilisin and are synthesized as zymogens. They contain N-terminal propeptides (PRO) that function as dedicated catalysts that facilitate folding and regulate activation of cognate proteases through multiple-ordered cleavages. Previous studies identified a histidine residue (His69) that functions as a pH sensor in the propeptide of furin (PRO(FUR)), which regulates furin activation at pH~6.5 within the trans-Golgi network. Although this residue is conserved in the PC1 propeptide (PRO(PC1)), PC1 nonetheless activates at pH~5.5 within the dense core secretory granules. Here, we analyze the mechanism by which PRO(FUR) regulates furin activation and examine why PRO(FUR) and PRO(PC1) differ in their pH-dependent activation. Sequence analyses establish that while both PRO(FUR) and PRO(PC1) are enriched in histidines when compared with cognate catalytic domains and prokaryotic orthologs, histidine content in PRO(FUR) is ~2-fold greater than that in PRO(PC1), which may augment its pH sensitivity. Spectroscopy and molecular dynamics establish that histidine protonation significantly unfolds PRO(FUR) when compared to PRO(PC1) to enhance autoproteolysis. We further demonstrate that PRO(FUR) and PRO(PC1) are sufficient to confer organelle sensing on folding and activation of their cognate proteases. Swapping propeptides between furin and PC1 transfers pH-dependent protease activation in a propeptide-dictated manner in vitro and in cells. Since prokaryotes lack organelles and eukaryotic PCs evolved from propeptide-dependent, not propeptide-independent prokaryotic subtilases, our results suggest that histidine enrichment may have enabled propeptides to evolve to exploit pH gradients to activate within specific organelles. Copyright © 2012 Elsevier Ltd. All rights reserved.

High resolution light-sheet based high-throughput imaging cytometry system enables visualization of intra-cellular organelles

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Regmi, Raju; Mohan, Kavya; Mondal, Partha Pratim

2014-09-01

Visualization of intracellular organelles is achieved using a newly developed high throughput imaging cytometry system. This system interrogates the microfluidic channel using a sheet of light rather than the existing point-based scanning techniques. The advantages of the developed system are many, including, single-shot scanning of specimens flowing through the microfluidic channel at flow rate ranging from micro- to nano- lit./min. Moreover, this opens-up in-vivo imaging of sub-cellular structures and simultaneous cell counting in an imaging cytometry system. We recorded a maximum count of 2400 cells/min at a flow-rate of 700 nl/min, and simultaneous visualization of fluorescently-labeled mitochondrial network in HeLa cells during flow. The developed imaging cytometry system may find immediate application in biotechnology, fluorescence microscopy and nano-medicine.

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.

The Lipid Droplet – A Well-Connected Organelle

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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.

Nonspecific Organelle-Targeting Strategy with Core-Shell Nanoparticles of Varied Lipid Components/Ratios.

Science.gov (United States)

Zhang, Lu; Sun, Jiashu; Wang, Yilian; Wang, Jiancheng; Shi, Xinghua; Hu, Guoqing

2016-07-19

We report a nonspecific organelle-targeting strategy through one-step microfluidic fabrication and screening of a library of surface charge- and lipid components/ratios-varied lipid shell-polymer core nanoparticles. Different from the common strategy relying on the use of organelle-targeted moieties conjugated onto the surface of nanoparticles, here, we program the distribution of hybrid nanoparticles in lysosomes or mitochondria by tuning the lipid components/ratios in shell. Hybrid nanoparticles with 60% 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and 20% 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) can intracellularly target mitochondria in both in vitro and in vivo models. While replacing DOPE with the same amount of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), the nanoparticles do not show mitochondrial targeting, indicating an incremental effect of cationic and fusogenic lipids on lysosomal escape which is further studied by molecular dynamics simulations. This work unveils the lipid-regulated subcellular distribution of hybrid nanoparticles in which target moieties and complex synthetic steps are avoided.

The autophagoproteasome a novel cell clearing organelle in baseline and stimulated conditions

Directory of Open Access Journals (Sweden)

Paola Lenzi

2016-07-01

to be anatomically segregated co-exist and they are likely to interact at molecular level. In fact, LC3 and P20S co-immunoprecipitate, suggesting a specific binding and functional interplay, which may be altered by inhibiting mTOR. In summary, ATG and UP often represent two facets of a single organelle, in which unexpected amount of enzymatic activity should be available. Thus, autophagoproteasome may represent a sophisticated ultimate clearing apparatus.

The Autophagoproteasome a Novel Cell Clearing Organelle in Baseline and Stimulated Conditions.

Science.gov (United States)

Lenzi, Paola; Lazzeri, Gloria; Biagioni, Francesca; Busceti, Carla L; Gambardella, Stefano; Salvetti, Alessandra; Fornai, Francesco

2016-01-01

anatomically segregated) co-exist and they are likely to interact at molecular level. In fact, LC3 and P20S co-immunoprecipitate, suggesting a specific binding and functional interplay, which may be altered by inhibiting mTOR. In summary, ATG and UP often represent two facets of a single organelle, in which unexpected amount of enzymatic activity should be available. Thus, autophagoproteasome may represent a sophisticated ultimate clearing apparatus.

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

Mapping organelle motion reveals a vesicular conveyor belt spatially replenishing secretory vesicles in stimulated chromaffin cells.

Science.gov (United States)

Maucort, Guillaume; Kasula, Ravikiran; Papadopulos, Andreas; Nieminen, Timo A; Rubinsztein-Dunlop, Halina; Meunier, Frederic A

2014-01-01

How neurosecretory cells spatially adjust their secretory vesicle pools to replenish those that have fused and released their hormonal content is currently unknown. Here we designed a novel set of image analyses to map the probability of tracked organelles undergoing a specific type of movement (free, caged or directed). We then applied our analysis to time-lapse z-stack confocal imaging of secretory vesicles from bovine Chromaffin cells to map the global changes in vesicle motion and directionality occurring upon secretagogue stimulation. We report a defined region abutting the cortical actin network that actively transports secretory vesicles and is dissipated by actin and microtubule depolymerizing drugs. The directionality of this "conveyor belt" towards the cell surface is activated by stimulation. Actin and microtubule networks therefore cooperatively probe the microenvironment to transport secretory vesicles to the periphery, providing a mechanism whereby cells globally adjust their vesicle pools in response to secretagogue stimulation.

Student creativity in creating cell organelles as media for learning

Science.gov (United States)

Fatmawati, B.

2018-04-01

Creativity is not formed by itself but it is influenced by some others factors. Creativity is a . person’s ability to create / generate an idea embodied in the form of a product to solve problems which is accepted socially, spiritually, artificially, scientifically, and technologically. Learning media is a means of communication to deliver learning materials. There are three kinds of learning media produced by students such as books story, playdough, and the utilization of inorganic waste. The focus of this research is to know the students’ creativity in producing learnning media to understand an Abstract material especially on topic of cell organelles of animal and plant cell. Data analysis is using two ways that calculate the score of mastery in terms of concepts and creativity. The results showed the score of students’ understanding was increasing from 15 (average score of pre-test) to 31.1 (average score of post-test). It was categorized into three level, that are, high level with 21.4% of participants, medium with 64.3%, and low with 14.3%). Seven groups of students make learning media made of waste, playdough, and waste made in story form. The assessment of creativity involved four aspects, namely, color combinations, stringing, tidiness, and make (the accuracy of the concept with the form). Thus, it can be argued that self-created learning media helps in understanding the Abstract concepts of cell organelles.

Ligand-directed profiling of organelles with internalizing phage libraries

Science.gov (United States)

Dobroff, Andrey S.; Rangel, Roberto; Guzman-Roja, Liliana; Salmeron, Carolina C.; Gelovani, Juri G.; Sidman, Richard L.; Bologa, Cristian G.; Oprea, Tudor I.; Brinker, C. Jeffrey; Pasqualini, Renata; Arap, Wadih

2015-01-01

Phage display is a resourceful tool to, in an unbiased manner, discover and characterize functional protein-protein interactions, to create vaccines, and to engineer peptides, antibodies, and other proteins as targeted diagnostic and/or therapeutic agents. Recently, our group has developed a new class of internalizing phage (iPhage) for ligand-directed targeting of organelles and/or to identify molecular pathways within live cells. This unique technology is suitable for applications ranging from fundamental cell biology to drug development. Here we describe the method for generating and screening the iPhage display system, and explain how to select and validate candidate internalizing homing peptide. PMID:25640897

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...... 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...

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.

Elucidating polyploidization of bermudagrasses as assessed by organelle and nuclear DNA markers.

Science.gov (United States)

Gulsen, Osman; Ceylan, Ahmet

2011-12-01

Clarification of relationships among ploidy series of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to elucidate polyploidization among Cynodon accessions with different ploidy series collected from Turkey based on chloroplast and nuclear DNA. Forty Cynodon accessions including 7 diploids, 3 triploids, 10 tetraploids, 11 pentaploids, and 9 hexaploids were analyzed using chloroplast DNA restriction fragment-length polymorphism (cpDNA RFLP), chloroplast DNA simple sequence repeat (cpDNA SSR), and nuclear DNA markers based on neighbor-joining (NJ) and principle component analyses (PCA). All three-marker systems with two statistical algorithms clustered the diploids apart from the other ploidy levels. Assuming autopolyploidy, spontaneous polyploidization followed by rapid diversification among the higher ploidy levels than the diploids is likely in Cynodon's evolution. Few tetraploid and hexaploid accessions were clustered with or closely to the group of diploids, supporting the hypothesis above. Eleven haplotypes as estimated by cpDNA RFLP and SSR markers were detected. This study indicated that the diploids had different organelle genome from the rest of the ploidy series and provided valuable insight into relationships among ploidy series of Cynodon accessions based on cp and nuclear DNAs.

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

Fluorogenic Substrates for Visualizing Acidic Organelle Enzyme Activities.

Directory of Open Access Journals (Sweden)

Fiona Karen Harlan

Full Text Available Lysosomes are acidic cytoplasmic organelles that are present in all nucleated mammalian cells and are involved in a variety of cellular processes including repair of the plasma membrane, defense against pathogens, cholesterol homeostasis, bone remodeling, metabolism, apoptosis and cell signaling. Defects in lysosomal enzyme activity have been associated with a variety of neurological diseases including Parkinson's Disease, Lysosomal Storage Diseases, Alzheimer's disease and Huntington's disease. Fluorogenic lysosomal staining probes were synthesized for labeling lysosomes and other acidic organelles in a live-cell format and were shown to be capable of monitoring lysosomal metabolic activity. The new targeted substrates were prepared from fluorescent dyes having a low pKa value for optimum fluorescence at the lower physiological pH found in lysosomes. They were modified to contain targeting groups to direct their accumulation in lysosomes as well as enzyme-cleavable functions for monitoring specific enzyme activities using a live-cell staining format. Application to the staining of cells derived from blood and skin samples of patients with Metachromatic Leukodystrophy, Krabbe and Gaucher Diseases as well as healthy human fibroblast and leukocyte control cells exhibited localization to the lysosome when compared with known lysosomal stain LysoTracker® Red DND-99 as well as with anti-LAMP1 Antibody staining. When cell metabolism was inhibited with chloroquine, staining with an esterase substrate was reduced, demonstrating that the substrates can be used to measure cell metabolism. When applied to diseased cells, the intensity of staining was reflective of lysosomal enzyme levels found in diseased cells. Substrates specific to the enzyme deficiencies in Gaucher or Krabbe disease patient cell lines exhibited reduced staining compared to that in non-diseased cells. The new lysosome-targeted fluorogenic substrates should be useful for research

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...

Mitochondria: Target organelles for estrogen action

Directory of Open Access Journals (Sweden)

Małgorzata Chmielewska

2017-06-01

Full Text Available Estrogens belong to a group of sex hormones, which have been shown to act in multidirectional way. Estrogenic effects are mediated by two types of intracellular receptors: estrogen receptor 1 (ESR1 and estrogen receptor 2 (ESR2. There are two basic mechanisms of estrogen action: 1 classical-genomic, in which the ligand-receptor complex acts as a transcriptional factor and 2 a nongenomic one, which is still not fully understood, but has been seen to lead to distinct biological effects, depending on tissue and ligand type. It is postulated that nongenomic effects may be associated with membrane signaling and the presence of classical nuclear receptors within the cell membrane. Estrogens act in a multidirectional way also within cell organelles. It is assumed that there is a mechanism which manages the migration of ESR into the mitochondrial membrane, wherein the exogenous estrogen affect the morphology of mitochondria. Estrogen, through its receptor, can directly modulate mitochondrial gene expression. Moreover, by regulating the level of reactive oxygen species, estrogens affect the biology of mitochondria. The considerations presented in this paper indicate the pleiotropic effects of estrogens, which represent a multidirectional pathway of signal transduction.

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

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

The shells of BMC-type microcompartment organelles in bacteria.

Science.gov (United States)

Yeates, Todd O; Jorda, Julien; Bobik, Thomas A

2013-01-01

Bacterial microcompartments are large proteinaceous structures that act as metabolic organelles in many bacterial cells. A shell or capsid, which is composed of a few thousand protein subunits, surrounds a series of sequentially acting enzymes and controls the diffusion of substrates and products into and out of the lumen. The carboxysome and the propanediol utilization microcompartment represent two well-studied systems among seven or more distinct types that can be delineated presently. Recent structural studies have highlighted a number of sophisticated mechanisms that underlie the function of bacterial microcompartment shell proteins. This review updates our understanding of bacterial microcompartment shells, how they are assembled, and how they carry out their functions in molecular transport and enzyme organization. Copyright © 2013 S. Karger AG, Basel.

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.

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.

Parametric analyses of single-zone thorium-fueled molten salt reactor fuel cycle options

International Nuclear Information System (INIS)

Powers, J.J.; Worrall, A.; Gehin, J.C.; Harrison, T.J.; Sunny, E.E.

2013-01-01

Analyses of fuel cycle options based on thorium-fueled Molten Salt Reactors (MSRs) have been performed in support of fuel cycle screening and evaluation activities for the United States Department of Energy. The MSR options considered are based on thermal spectrum MSRs with 3 different separations levels: full recycling, limited recycling, and 'once-through' operation without active separations. A single-fluid, single-zone 2250 MWth (1000 MWe) MSR concept consisting of a fuel-bearing molten salt with graphite moderator and reflectors was used as the basis for this study. Radiation transport and isotopic depletion calculations were performed using SCALE 6.1 with ENDF/B-VII nuclear data. New methodology developed at Oak Ridge National Laboratory (ORNL) enables MSR analysis using SCALE, modeling material feed and removal by taking user-specified parameters and performing multiple SCALE/TRITON simulations to determine the resulting equilibrium operating conditions. Parametric analyses examined the sensitivity of the performance of a thorium MSR to variations in the separations efficiency for protactinium and fission products. Results indicate that self-sustained operation is possible with full or limited recycling but once-through operation would require an external neutron source. (authors)

Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing.

Science.gov (United States)

Zhang, Jin; Ruhlman, Tracey A; Mower, Jeffrey P; Jansen, Robert K

2013-12-29

, results indicated no major improvements in breadth of coverage with data sets larger than six billion nucleotides or when sampling RNA from four tissue types rather than from a single tissue. Finally, this work demonstrates the power of cross-compartmental genomic analyses to deepen our understanding of the correlated evolution of the nuclear, plastid, and mitochondrial genomes in plants.

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

Silencing of RpATG6 impaired the yolk accumulation and the biogenesis of the yolk organelles in the insect vector R. prolixus.

Directory of Open Access Journals (Sweden)

Priscila H Vieira

2018-05-01

Full Text Available In oviparous animals, the egg yolk is synthesized by the mother in a major metabolic challenge, where the different yolk components are secreted to the hemolymph and delivered to the oocytes mostly by endocytosis. The yolk macromolecules are then stored in a wide range of endocytic-originated vesicles which are collectively referred to as yolk organelles and occupy most of the mature oocytes cytoplasm. After fertilization, the contents of these organelles are degraded in a regulated manner to supply the embryo cells with fundamental molecules for de novo synthesis. Yolk accumulation and its regulated degradation are therefore crucial for successful development, however, most of the molecular mechanisms involved in the biogenesis, sorting and degradation of targeted yolk organelles are still poorly understood. ATG6 is part of two PI3P-kinase complexes that can regulate the recruitment of the endocytic or the autophagy machineries. Here, we investigate the role of RpATG6 in the endocytosis of the yolk macromolecules and in the biogenesis of the yolk organelles in the insect vector Rhodnius prolixus. We found that vitellogenic females express high levels of RpATG6 in the ovaries, when compared to the levels detected in the midgut and fat body. RNAi silencing of RpATG6 resulted in yolk proteins accumulated in the vitellogenic hemolymph, as a consequence of poor uptake by the oocytes. Accordingly, the silenced oocytes are unviable, white (contrasting to the control pink oocytes, smaller (62% of the control oocyte volume and accumulate only 40% of the yolk proteins, 80% of the TAG and 50% of the polymer polyphosphate quantified in control oocytes. The cortex of silenced oocytes present atypical smaller vesicles indicating that the yolk organelles were not properly formed and/or sorted, which was supported by the lack of endocytic vesicles near the plasma membrane of silenced oocytes as seen by TEM. Altogether, we found that RpATG6 is central for the

Biased Brownian motion mechanism for processivity and directionality of single-headed myosin-VI.

Science.gov (United States)

Iwaki, Mitsuhiro; Iwane, Atsuko Hikikoshi; Ikebe, Mitsuo; Yanagida, Toshio

2008-01-01

Conventional form to function as a vesicle transporter is not a 'single molecule' but a coordinated 'two molecules'. The coordinated two molecules make it complicated to reveal its mechanism. To overcome the difficulty, we adopted a single-headed myosin-VI as a model protein. Myosin-VI is an intracellular vesicle and organelle transporter that moves along actin filaments in a direction opposite to most other known myosin classes. The myosin-VI was expected to form a dimer to move processively along actin filaments with a hand-over-hand mechanism like other myosin organelle transporters. However, wild-type myosin-VI was demonstrated to be monomer and single-headed, casting doubt on its processivity. Using single molecule techniques, we show that green fluorescent protein (GFP)-fused single-headed myosin-VI does not move processively. However, when coupled to a 200 nm polystyrene bead (comparable to an intracellular vesicle in size) at a ratio of one head per bead, single-headed myosin-VI moves processively with large (40 nm) steps. Furthermore, we found that a single-headed myosin-VI-bead complex moved more processively in a high-viscous solution (40-fold higher than water) similar to cellular environment. Because diffusion of the bead is 60-fold slower than myosin-VI heads alone in water, we propose a model in which the bead acts as a diffusional anchor for the myosin-VI, enhancing the head's rebinding following detachment and supporting processive movement of the bead-monomer complex. This investigation will help us understand how molecular motors utilize Brownian motion in cells.

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.

Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data.

Science.gov (United States)

Kustatscher, Georg; Grabowski, Piotr; Rappsilber, Juri

2016-02-01

Subcellular localization is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterized. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here, we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a structure of interest biochemically, we target it by machine learning. This becomes possible by taking data obtained for one organelle and searching it for traces of another organelle. As an extreme example and proof-of-concept we predict mitochondrial proteins based on their covariation in published interphase chromatin data. We detect about ⅓ of the known mitochondrial proteins in our chromatin data, presumably most as contaminants. However, these proteins are not present at random. We show covariation of mitochondrial proteins in chromatin proteomics data. We then exploit this covariation by multiclassifier combinatorial proteomics to define a list of mitochondrial proteins. This list agrees well with different databases on mitochondrial composition. This benchmark test raises the possibility that, in principle, covariation proteomics may also be applicable to structures for which no biochemical isolation procedures are available. © 2015 The Authors. Proteomics Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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...

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

Directory of Open Access Journals (Sweden)

Dmitri Papatsenko

2015-08-01

Full Text Available Analyses of gene expression in single mouse embryonic stem cells (mESCs cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM. In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

Changes in protein metabolism after irradiation. Pt. 1. Protease activity, protease pattern, protein and free amino acids in cytoplasm and cell organelles of the rat spleen after 600 R whole body x irradiation

Energy Technology Data Exchange (ETDEWEB)

Valet, G [Max-Planck-Institut fuer Biochemie, Muenchen (F.R. Germany). Abt. fuer Experimentelle Medizin

1975-12-01

The protease activity of cytoplasm and cell organelles of the rat spleen against spleen protein and hemoglobin as a substrate increases during a initial reaction phase of the organism on the first day after 600 R whole body X-irradiation. The alkaline protease in the cytoplasm and the acid protease in the cell organelles increase, whereas the protease activity against externally added hemoglobin as substrate decreases below the initial values. The protein, the protease activity and the free amino acids of the cytoplasm and the cell organelles decrease during the disease phase on day 3 and 4 after irradiation. The protein loss of the spleen is therefore not explained by an increased protease activity. Acid proteases appear in the cytoplasm which derive probably from the cell organelles. The protease activity and the free amino acids are increased in the cytoplasm and the cell organelles during the regeneration phase of the organism between day 15 and 18 after irradiation.

Sterol composition of yeast organelle membranes and subcellular distribution of enzymes involved in sterol metabolism.

OpenAIRE

Zinser, E; Paltauf, F; Daum, G

1993-01-01

Organelles of the yeast Saccharomyces cerevisiae were isolated and analyzed for sterol composition and the activity of three enzymes involved in sterol metabolism. The plasma membrane and secretory vesicles, the fractions with the highest sterol contents, contain ergosterol as the major sterol. In other subcellular membranes, which exhibit lower sterol contents, intermediates of the sterol biosynthetic pathway were found at higher percentages. Lipid particles contain, in addition to ergostero...

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

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

Science.gov (United States)

Vollenweider, Pierre; Bernasconi, Petra; Gautschi, Hans-Peter; Menard, Terry; Frey, Beat; Günthardt-Goerg, Madeleine S

2011-01-01

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 β-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. Copyright © 2010 Elsevier Ltd. All rights reserved.

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.

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

International Nuclear Information System (INIS)

Vollenweider, Pierre; Bernasconi, Petra; Gautschi, Hans-Peter; Menard, Terry; Frey, Beat; Guenthardt-Goerg, Madeleine S.

2011-01-01

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 β-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.

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

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.

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

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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.

Single- and multi-frequency bioelectrical impedance analyses to analyse body composition in maintenance haemodialysis patients: comparison with dual-energy x-ray absorptiometry

International Nuclear Information System (INIS)

Donadio, C; Halim, A Ben; Caprio, F; Grassi, G; Khedr, B; Mazzantini, M

2008-01-01

The aim of this study was to evaluate the adequacy of single-frequency (sf-BIA) and multi-frequency bioelectrical impedance analyses (mf-BIA), in comparison with dual-energy x-ray absorptiometry (DXA), to evaluate body composition in maintenance haemodialysis (MHD) patients. Body composition of 27 adult MHD patients (9 f, 18 m), BMI 17.5–34.4 kg m −2 , was examined with DXA and BIA, with two different sf-BIA and 1 mf-BIA analysers. Biochemical markers of nutritional status and adequacy of dialytic treatment were also determined. Fat mass (FM) estimated by the different BIA analysers was found to be slightly but significantly higher than FM measured by DXA. In contrast, fat-free mass (FFM) obtained with BIA was found to be slightly but significantly lower than FFM DXA. No significant differences were found between LBM-DXA (that is FFM-DXA minus bone mass) and the different FFM BIA. The lowest mean prediction error versus DXA values was found with sf1BIA. In any case, a close correlation was found between all BIA values and DXA values, particularly for FFM. Furthermore, FFM and LBM results were significantly correlated with serum creatinine, which in MHD patients is an indicator of muscle mass. These results indicate that BIA can be used to evaluate body composition in MHD patients

Regulation of traffic and organelle architecture of the ER-Golgi interface by signal transduction.

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Tillmann, Kerstin D; Millarte, Valentina; Farhan, Hesso

2013-09-01

The components that control trafficking between organelles of the secretory pathway as well as their architecture were uncovered to a reasonable extent in the past decades. However, only recently did we begin to explore the regulation of the secretory pathway by cellular signaling. In the current review, we focus on trafficking between the endoplasmic reticulum and the Golgi apparatus. We highlight recent advances that have been made toward a better understanding of how the secretory pathway is regulated by signaling and discuss how this knowledge is important to obtain an integrative view of secretion in the context of other homeostatic processes such as growth and proliferation.

Cell shape and organelle modification in apoptotic U937 cells

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MR Montinari

2009-12-01

Full Text Available U937 cells induced to apoptosis, progressively and dramatically modified their cell shape by intense blebbing formation, leading to the production of apoptotic bodies. The blebs evolved with time; milder forms of blebbing involving only a region or just the cortical part of the cytoplasm were observed within the first hour of incubation with puromycin; blebbing involving the whole cell body with very deep constrictions is the most frequent event observed during late times of incubation. The ultrastructural analysis of apoptotic cells revealed characteristic features of nuclear fragmentation (budding and cleavage mode and cytoplasmatic modifications. The cytoplasm of blebs does not contain organelles, such as ribosomes or mitochondria. Scarce presence of endoplasmic reticulum can be observed at the site of bleb detachment. However, blebbing is a dispensable event as evaluated by using inhibitor of actin polymerization. In the present study, the progressive modifications of the nucleus, mitochondria, nuclear fragmentation, cytoplasmic blebs formation and production of apoptotic bodies in U937 monocytic cells induced to apoptosis by puromycin (an inhibitor of protein synthesis were simultaneously analyzed.

Changes in protein metabolism after irradiation. Pt. 2. Protease activity, protease pattern, protein and free amino acids in cytoplasm and cell organelles of the rat liver after 600 R whole body X-irradiation

Energy Technology Data Exchange (ETDEWEB)

Valet, G [Max-Planck-Institut fuer Biochemie, Muenchen (F.R. Germany). Abt. fuer Experimentelle Medizin

1976-01-01

The protease activity of cytoplasm and cell organelles of the rat liver against liver protein and hemoglobin as a substrate increases during an initial reaction phase on the first day after 600 R whole body x irradiation. This is probably a consequence of the degradation of cellular debris. The protein, the protease activity and the free amino acids of the cytoplasm and the cell organelles decrease during the disease phase on day 3 and 4 after irradiation. The protein loss of the liver is therefore not explained by an increased protease activity. The protease activity and the free amino acids are increased in the cytoplasm and the cell organelles during the regeneration phase of the organism between day 15 and 18 after irradiation.

Muscle intermediate filaments and their links to membranes and membranous organelles

International Nuclear Information System (INIS)

Capetanaki, Yassemi; Bloch, Robert J.; Kouloumenta, Asimina; Mavroidis, Manolis; Psarras, Stelios

2007-01-01

Intermediate filaments (IFs) play a key role in the integration of structure and function of striated muscle, primarily by mediating mechanochemical links between the contractile apparatus and mitochondria, myonuclei, the sarcolemma and potentially the vesicle trafficking apparatus. Linkage of all these membranous structures to the contractile apparatus, mainly through the Z-disks, supports the integration and coordination of growth and energy demands of the working myocyte, not only with force transmission, but also with de novo gene expression, energy production and efficient protein and lipid trafficking and targeting. Desmin, the most abundant and intensively studied muscle intermediate filament protein, is linked to proper costamere organization, myoblast and stem cell fusion and differentiation, nuclear shape and positioning, as well as mitochondrial shape, structure, positioning and function. Similar links have been established for lysosomes and lysosome-related organelles, consistent with the presence of widespread links between IFs and membranous structures and the regulation of their fusion, morphology and stabilization necessary for cell survival

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

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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.

Metabolic Interplay between Peroxisomes and Other Subcellular Organelles Including Mitochondria and the Endoplasmic Reticulum

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Wanders, Ronald J. A.; Waterham, Hans R.; Ferdinandusse, Sacha

2016-01-01

Peroxisomes are unique subcellular organelles which play an indispensable role in several key metabolic pathways which include: (1.) etherphospholipid biosynthesis; (2.) fatty acid beta-oxidation; (3.) bile acid synthesis; (4.) docosahexaenoic acid (DHA) synthesis; (5.) fatty acid alpha-oxidation; (6.) glyoxylate metabolism; (7.) amino acid degradation, and (8.) ROS/RNS metabolism. The importance of peroxisomes for human health and development is exemplified by the existence of a large number of inborn errors of peroxisome metabolism in which there is an impairment in one or more of the metabolic functions of peroxisomes. Although the clinical signs and symptoms of affected patients differ depending upon the enzyme which is deficient and the extent of the deficiency, the disorders involved are usually (very) severe diseases with neurological dysfunction and early death in many of them. With respect to the role of peroxisomes in metabolism it is clear that peroxisomes are dependent on the functional interplay with other subcellular organelles to sustain their role in metabolism. Indeed, whereas mitochondria can oxidize fatty acids all the way to CO2 and H2O, peroxisomes are only able to chain-shorten fatty acids and the end products of peroxisomal beta-oxidation need to be shuttled to mitochondria for full oxidation to CO2 and H2O. Furthermore, NADH is generated during beta-oxidation in peroxisomes and beta-oxidation can only continue if peroxisomes are equipped with a mechanism to reoxidize NADH back to NAD+, which is now known to be mediated by specific NAD(H)-redox shuttles. In this paper we describe the current state of knowledge about the functional interplay between peroxisomes and other subcellular compartments notably the mitochondria and endoplasmic reticulum for each of the metabolic pathways in which peroxisomes are involved. PMID:26858947

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

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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.

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

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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

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

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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

Mitochondria: An Organelle of Bacterial Origin Controlling Inflammation

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Alain Meyer

2018-04-01

Full Text Available Inflammation is a cellular and molecular response to infection and/or tissues injury. While a suited inflammatory response in intensity and time allows for killing pathogens, clearing necrotic tissue, and healing injury; an excessive inflammatory response drives various diseases in which inflammation and tissues damages/stress self-sustain each other. Microbes have been poorly implied in non-resolving inflammation, emphasizing the importance of endogenous regulation of inflammation. Mitochondria have been historically identified as the main source of cellular energy, by coupling the oxidation of fatty acids and pyruvate with the production of high amount of adenosine triphosphate by the electron transport chain. Mitochondria are also the main source of reactive oxygen species. Interestingly, research in the last decade has highlighted that since its integration in eukaryote cells, this organelle of bacterial origin has not only been tolerated by immunity, but has also been placed as a central regulator of cell defense. In intact cells, mitochondria regulate cell responses to critical innate immune receptors engagement. Downstream intracellular signaling pathways interact with mitochondrial proteins and are tuned by mitochondrial functioning. Moreover, upon cell stress or damages, mitochondrial components are released into the cytoplasm or the extra cellular milieu, where they act as danger signals when recognized by innate immune receptors. Finally, by regulating the energetic state of immunological synapse between dendritic cells and lymphocytes, mitochondria regulate the inflammation fate toward immunotolerance or immunogenicity. As dysregulations of these processes have been recently involved in various diseases, the identification of the underlying mechanisms might open new avenues to modulate inflammation.

Protein Expression Analyses at the Single Cell Level

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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.

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

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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.

Cadmium Disrupts Subcellular Organelles, Including Chloroplasts, Resulting in Melatonin Induction in Plants

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Hyoung-Yool Lee

2017-10-01

Full Text Available Cadmium is a well-known elicitor of melatonin synthesis in plants, including rice. However, the mechanisms by which cadmium induces melatonin induction remain elusive. To investigate whether cadmium influences physical integrities in subcellular organelles, we treated tobacco leaves with either CdCl2 or AlCl3 and monitored the structures of subcellular organelles—such as chloroplasts, mitochondria, and the endoplasmic reticulum (ER—using confocal microscopic analysis. Unlike AlCl3 treatment, CdCl2 (0.5 mM treatment significantly disrupted chloroplasts, mitochondria, and ER. In theory, the disruption of chloroplasts enabled chloroplast-expressed serotonin N-acetyltransferase (SNAT to encounter serotonin in the cytoplasm, leading to the synthesis of N-acetylserotonin followed by melatonin synthesis. In fact, the disruption of chloroplasts by cadmium, not by aluminum, gave rise to a huge induction of melatonin in rice leaves, which suggests that cadmium-treated chloroplast disruption plays an important role in inducing melatonin in plants by removing physical barriers, such as chloroplast double membranes, allowing SNAT to gain access to the serotonin substrate enriched in the cytoplasm.

The Role of Organelle Stresses in Diabetes Mellitus and Obesity: Implication for Treatment

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Chang, Yi-Cheng; Hee, Siow-Wey; Hsieh, Meng-Lun; Chuang, Lee-Ming

2015-01-01

The type 2 diabetes pandemic in recent decades is a huge global health threat. This pandemic is primarily attributed to the surplus of nutrients and the increased prevalence of obesity worldwide. In contrast, calorie restriction and weight reduction can drastically prevent type 2 diabetes, indicating a central role of nutrient excess in the development of diabetes. Recently, the molecular links between excessive nutrients, organelle stress, and development of metabolic disease have been extensively studied. Specifically, excessive nutrients trigger endoplasmic reticulum stress and increase the production of mitochondrial reactive oxygen species, leading to activation of stress signaling pathway, inflammatory response, lipogenesis, and pancreatic beta-cell death. Autophagy is required for clearance of hepatic lipid clearance, alleviation of pancreatic beta-cell stress, and white adipocyte differentiation. ROS scavengers, chemical chaperones, and autophagy activators have demonstrated promising effects for the treatment of insulin resistance and diabetes in preclinical models. Further results from clinical trials are eagerly awaited. PMID:26613076

The effects of male age on sperm analysis by motile sperm organelle morphology examination (MSOME

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Silva Liliane FI

2012-03-01

Full Text Available Abstract Background This study aimed to investigate the influence of age on sperm quality, as analysed by motile sperm organelle morphology examination (MSOME. Methods Semen samples were collected from 975 men undergoing evaluation or treatment for infertility. Sperm cells were evaluated at 8400× magnification using an inverted microscope equipped with Nomarski (differential interference contrast optics. Two forms of spermatozoa were considered: normal spermatozoa and spermatozoa with large nuclear vacuoles (LNV, defined as vacuoles occupying > 50% of the sperm nuclear area. At least 200 spermatozoa per sample were evaluated, and the percentages of normal and LNV spermatozoa were determined. The subjects were divided into three groups according to age: Group I, less than or equal to 35 years; Group II, 36-40 years; and Group III, greater than or equal to 41 years. Results There was no difference in the percentages of normal sperm between the two younger (I and II groups (P >0.05. The percentage of normal sperm in the older group (III was significantly lower than that in the younger (I and II groups (P P >0.05. The percentage of LNV spermatozoa was significantly higher in the older group (III than in the younger (I and II groups (P P P Conclusion The results demonstrated a consistent decline in semen quality, as reflected by morphological evaluation by MSOME, with increased age. Considering the relationship between nuclear vacuoles and DNA damage, these age-related changes predict that increased paternal age should be associated with unsuccessful or abnormal pregnancy as a consequence of fertilisation with damaged spermatozoa. Given that sperm nuclear vacuoles can be evaluated more precisely at high magnification, these results support the routine use of MSOME for ICSI as a criterion for semen analysis.

Preliminary Analyses Showed Short-Term Mental Health Improvements after a Single-Day Manager Training.

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Boysen, Elena; Schiller, Birgitta; Mörtl, Kathrin; Gündel, Harald; Hölzer, Michael

2018-01-10

Psychosocial working conditions attract more and more attention when it comes to mental health in the workplace. Trying to support managers to deal with their own as well as their employees' psychological risk factors, we conducted a specific manager training. Within this investigation, we wanted to learn about the training's effects and acceptance. A single-day manager training was provided in a large industrial company in Germany. The participants were asked to fill out questionnaires regarding their own physical and mental health condition as well as their working situation. Questionnaires were distributed at baseline, 3-month, and 12-month follow-up. At this point of time the investigation is still ongoing. The current article focuses on short-term preliminary effects. Analyses only included participants that already completed baseline and three months follow-up. Preliminary results from three-month follow-up survey ( n = 33, nmale = 30, Mage = 47.5) indicated positive changes in the manager's mental health condition measured by the Patient Health Questionnaire for depression (PHQ-9: Mt1 = 3.82, Mt2 = 3.15). Training managers about common mental disorders and risk factors at the workplace within a single-day workshop seems to promote positive effects on their own mental health. Especially working with the managers on their own early stress symptoms might have been an important element.

Hypoxia signaling pathways: modulators of oxygen-related organelles

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Schönenberger, Miriam J.; Kovacs, Werner J.

2015-01-01

Oxygen (O2) is an essential substrate in cellular metabolism, bioenergetics, and signaling and as such linked to the survival and normal function of all metazoans. Low O2 tension (hypoxia) is a fundamental feature of physiological processes as well as pathophysiological conditions such as cancer and ischemic diseases. Central to the molecular mechanisms underlying O2 homeostasis are the hypoxia-inducible factors-1 and -2 alpha (HIF-1α and EPAS1/HIF-2α) that function as master regulators of the adaptive response to hypoxia. HIF-induced genes promote characteristic tumor behaviors, including angiogenesis and metabolic reprogramming. The aim of this review is to critically explore current knowledge of how HIF-α signaling regulates the abundance and function of major O2-consuming organelles. Abundant evidence suggests key roles for HIF-1α in the regulation of mitochondrial homeostasis. An essential adaptation to sustained hypoxia is repression of mitochondrial respiration and induction of glycolysis. HIF-1α activates several genes that trigger mitophagy and represses regulators of mitochondrial biogenesis. Several lines of evidence point to a strong relationship between hypoxia, the accumulation of misfolded proteins in the endoplasmic reticulum, and activation of the unfolded protein response. Surprisingly, although peroxisomes depend highly on molecular O2 for their function, there has been no evidence linking HIF signaling to peroxisomes. We discuss our recent findings that establish HIF-2α as a negative regulator of peroxisome abundance and suggest a mechanism by which cells attune peroxisomal function with O2 availability. HIF-2α activation augments peroxisome turnover by pexophagy and thereby changes lipid composition reminiscent of peroxisomal disorders. We discuss potential mechanisms by which HIF-2α might trigger pexophagy and place special emphasis on the potential pathological implications of HIF-2α-mediated pexophagy for human health. PMID:26258123

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...

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.

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

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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.

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)

Bidirectional transport of organelles: unity and struggle of opposing motors.

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Bryantseva, Sofiya A; Zhapparova, Olga N

2012-01-01

Bidirectional transport along microtubules is ensured by opposing motor proteins: cytoplasmic dynein that drives cargo to the minus-ends and various kinesins that generally move to the plus-ends of microtubules. Regulation of motor proteins that are simultaneously bound to the same organelle is required to maintain directional transport and prevent pausing of cargo pulled away by motors of opposite polarity. Debates of the recent decade have been focused on two possible mechanisms of such regulation: (i) coordination, which implies that only one type of motors is active at a given time, and (ii) tug-of-war, which assumes that both motors are active at the same time and that direction of transport depends on the outcome of motor's confrontation. The initial idea of coordination has been challenged by observations of simultaneous activity of plus- and minus-end-directed motors applied to the same cargo. Analysis of the available data indicates that coordination and tug-of-war theories rather complement than contradict each other: cargo interacts with two teams of active motors, the resulting direction and the winner team are determined by coordination complexes, but the activity of the loser team is never completely inhibited and remains at some background level. Such persisting activity might enhance the overall efficiency of transport by increasing processivity or helping to overcome the obstacles on microtubule track. © The Author(s) Journal compilation © 2012 Portland Press Limited

Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination

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Hsiu-Fang Fan

2018-05-01

Full Text Available Tethered particle motion/microscopy (TPM is a biophysical tool used to analyze changes in the effective length of a polymer, tethered at one end, under changing conditions. The tether length is measured indirectly by recording the Brownian motion amplitude of a bead attached to the other end. In the biological realm, DNA, whose interactions with proteins are often accompanied by apparent or real changes in length, has almost exclusively been the subject of TPM studies. TPM has been employed to study DNA bending, looping and wrapping, DNA compaction, high-order DNA–protein assembly, and protein translocation along DNA. Our TPM analyses have focused on tyrosine and serine site-specific recombinases. Their pre-chemical interactions with DNA cause reversible changes in DNA length, detectable by TPM. The chemical steps of recombination, depending on the substrate and the type of recombinase, may result in a permanent length change. Single molecule TPM time traces provide thermodynamic and kinetic information on each step of the recombination pathway. They reveal how mechanistically related recombinases may differ in their early commitment to recombination, reversibility of individual steps, and in the rate-limiting step of the reaction. They shed light on the pre-chemical roles of catalytic residues, and on the mechanisms by which accessory proteins regulate recombination directionality.

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.)

A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium

Science.gov (United States)

Ramsay, Joshua P.; Williamson, Neil R.; Spring, David R.; Salmond, George P. C.

2011-01-01

Gas vesicles are hollow intracellular proteinaceous organelles produced by aquatic Eubacteria and Archaea, including cyanobacteria and halobacteria. Gas vesicles increase buoyancy and allow taxis toward air–liquid interfaces, enabling subsequent niche colonization. Here we report a unique example of gas vesicle-mediated flotation in an enterobacterium; Serratia sp. strain ATCC39006. This strain is a member of the Enterobacteriaceae previously studied for its production of prodigiosin and carbapenem antibiotics. Genes required for gas vesicle synthesis mapped to a 16.6-kb gene cluster encoding three distinct homologs of the main structural protein, GvpA. Heterologous expression of this locus in Escherichia coli induced copious vesicle production and efficient cell buoyancy. Gas vesicle morphogenesis in Serratia enabled formation of a pellicle-like layer of highly vacuolated cells, which was dependent on oxygen limitation and the expression of ntrB/C and cheY-like regulatory genes within the gas-vesicle gene cluster. Gas vesicle biogenesis was strictly controlled by intercellular chemical signaling, through an N-acyl homoserine lactone, indicating that in this system the quorum-sensing molecule acts as a morphogen initiating organelle development. Flagella-based motility and gas vesicle morphogenesis were also oppositely regulated by the small RNA-binding protein, RsmA, suggesting environmental adaptation through physiological control of the choice between motility and flotation as alternative taxis modes. We propose that gas vesicle biogenesis in this strain represents a distinct mechanism of mobility, regulated by oxygen availability, nutritional status, the RsmA global regulatory system, and the quorum-sensing morphogen. PMID:21873216

A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium.

Science.gov (United States)

Ramsay, Joshua P; Williamson, Neil R; Spring, David R; Salmond, George P C

2011-09-06

Gas vesicles are hollow intracellular proteinaceous organelles produced by aquatic Eubacteria and Archaea, including cyanobacteria and halobacteria. Gas vesicles increase buoyancy and allow taxis toward air-liquid interfaces, enabling subsequent niche colonization. Here we report a unique example of gas vesicle-mediated flotation in an enterobacterium; Serratia sp. strain ATCC39006. This strain is a member of the Enterobacteriaceae previously studied for its production of prodigiosin and carbapenem antibiotics. Genes required for gas vesicle synthesis mapped to a 16.6-kb gene cluster encoding three distinct homologs of the main structural protein, GvpA. Heterologous expression of this locus in Escherichia coli induced copious vesicle production and efficient cell buoyancy. Gas vesicle morphogenesis in Serratia enabled formation of a pellicle-like layer of highly vacuolated cells, which was dependent on oxygen limitation and the expression of ntrB/C and cheY-like regulatory genes within the gas-vesicle gene cluster. Gas vesicle biogenesis was strictly controlled by intercellular chemical signaling, through an N-acyl homoserine lactone, indicating that in this system the quorum-sensing molecule acts as a morphogen initiating organelle development. Flagella-based motility and gas vesicle morphogenesis were also oppositely regulated by the small RNA-binding protein, RsmA, suggesting environmental adaptation through physiological control of the choice between motility and flotation as alternative taxis modes. We propose that gas vesicle biogenesis in this strain represents a distinct mechanism of mobility, regulated by oxygen availability, nutritional status, the RsmA global regulatory system, and the quorum-sensing morphogen.

The endoplasmic reticulum is a target organelle for trivalent dimethylarsinic acid (DMA{sup III})-induced cytotoxicity

Energy Technology Data Exchange (ETDEWEB)

Naranmandura, Hua, E-mail: narenman@zju.edu.cn [Department of Pharmacology, Toxicology, and Biochemical Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China); Xu, Shi [Department of Pharmacology, Toxicology, and Biochemical Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China); Koike, Shota [Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675 (Japan); Pan, Li Qiang [Department of Pharmacology, Toxicology, and Biochemical Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China); Chen, Bin [Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030 (China); Wang, Yan Wei; Rehman, Kanwal; Wu, Bin [Department of Pharmacology, Toxicology, and Biochemical Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 (China); Chen, Zhe [Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou (China); Suzuki, Noriyuki, E-mail: n-suzuki@p.chiba-u.ac.jp [Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675 (Japan)

2012-05-01

The purpose of present study was to characterize the endoplasmic reticulum stress and generation of ROS in rat liver RLC-16 cells by exposing to trivalent dimethylarsinous acid (DMA{sup III}) and compared with that of trivalent arsenite (iAs{sup III}) and monomethylarsonous acid (MMA{sup III}). Protein kinase-like endoplasmic reticulum kinase (PERK) phosphorylation was significantly induced in cells exposed to DMA{sup III}, while there was no change in phosphorylated PERK (P-PERK) detected in cells after exposure to iAs{sup III} or MMA{sup III}. The generation of reactive oxygen species (ROS) after DMA{sup III} exposure was found to take place specifically in the endoplasmic reticulum (ER), while previous reports showed that ROS was generated in mitochondria following exposure to MMA{sup III}. Meanwhile, cycloheximide (CHX) which is an inhibitor of protein biosynthesis strongly inhibited the DMA{sup III}-induced intracellular ROS generation in the ER and the phosphorylation of PERK, suggesting the induction of ER stress probably occurs through the inhibition of the protein folding process. Activating transcription factor 4 (ATF4) and C/EBP homologous protein (CHOP) mRNA were induced by all three arsenic species, however, evidence suggested that they might be induced by different pathways in the case of iAs{sup III} and MMA{sup III}. In addition, ER resident molecular chaperone glucose-regulated protein78 (GRP78) was not affected by trivalent arsenicals, while it was induced in positive control only at high concentration (Thapsigargin;Tg), suggesting the GRP78 is less sensitive to low levels of ER stress. In summary, our findings demonstrate that the endoplasmic reticulum is a target organelle for DMA{sup III}-induced cytotoxicity. Highlights: ►ER is a target organelle for trivalent DMA{sup III}-induced cytotoxicity. ►Generation of ROS in ER can be induced specially by trivalent DMA{sup III}. ►ER-stress and generation of ROS are caused by the increase in

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

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

Issues Related to the Frequency of Exploratory Analyses by Evidence Review Groups in the NICE Single Technology Appraisal Process.

Science.gov (United States)

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

2017-06-01

Evidence Review Groups (ERGs) critically appraise company submissions as part of the National Institute for Health and Care Excellence (NICE) Single Technology Appraisal (STA) process. As part of their critique of the evidence submitted by companies, the ERGs undertake exploratory analyses to explore uncertainties in the company's model. The aim of this study was to explore pre-defined factors that might influence or predict the extent of ERG exploratory analyses. The aim of this study was to explore predefined factors that might influence or predict the extent of ERG exploratory analyses. We undertook content analysis of over 400 documents, including ERG reports and related documentation for the 100 most recent STAs (2009-2014) for which guidance has been published. Relevant data were extracted from the documents and narrative synthesis was used to summarise the extracted data. All data were extracted and checked by two researchers. Forty different companies submitted documents as part of the NICE STA process. The most common disease area covered by the STAs was cancer (44%), and most ERG reports (n = 93) contained at least one exploratory analysis. The incidence and frequency of ERG exploratory analyses does not appear to be related to any developments in the appraisal process, the disease area covered by the STA, or the company's base-case incremental cost-effectiveness ratio (ICER). However, there does appear to be a pattern in the mean number of analyses conducted by particular ERGs, but the reasons for this are unclear and potentially complex. No clear patterns were identified regarding the presence or frequency of exploratory analyses, apart from the mean number conducted by individual ERGs. More research is needed to understand this relationship.

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.

Cadmium induced changes in cell organelles: An ultrastructural study using cadmium sensitive and resistant muntjac fibroblast cell lines

Energy Technology Data Exchange (ETDEWEB)

Ord, M.J.; Chibber, R.; Bouffler, S.D.

1988-09-01

A detailed electron microscopy study of cadmium sensitive and resistant muntjac fibroblast cell lines has identified a wide range of intracellular damage following exposure to cadmium. Damaged organelles included cell membrane, mitochondria, Golgi cisternae and tubular network, chromatin, nucleoli, microfilaments and ribosomes. Although cell membrane damage was generally the earliest indication of adverse cadmium action, particularly with continuous cadmium exposures, cells could tolerate extensive membrane loss. Mitochondrial distortion and some damage to Golgi was also tolerated. The turning point at which cadmium became lethal was generally marked by a cascade of events which included damage to both nuclear and cytoplasmic components. These results for fibroblasts are discussed and compared with damage reported in other types of cells.

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.

Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles

Science.gov (United States)

Wei, Ming-Tzo; Elbaum-Garfinkle, Shana; Holehouse, Alex S.; Chen, Carlos Chih-Hsiung; Feric, Marina; Arnold, Craig B.; Priestley, Rodney D.; Pappu, Rohit V.; Brangwynne, Clifford P.

2017-11-01

Many intracellular membraneless organelles form via phase separation of intrinsically disordered proteins (IDPs) or regions (IDRs). These include the Caenorhabditis elegans protein LAF-1, which forms P granule-like droplets in vitro. However, the role of protein disorder in phase separation and the macromolecular organization within droplets remain elusive. Here, we utilize a novel technique, ultrafast-scanning fluorescence correlation spectroscopy, to measure the molecular interactions and full coexistence curves (binodals), which quantify the protein concentration within LAF-1 droplets. The binodals of LAF-1 and its IDR display a number of unusual features, including 'high concentration' binodal arms that correspond to remarkably dilute droplets. We find that LAF-1 and other in vitro and intracellular droplets are characterized by an effective mesh size of ∼3-8 nm, which determines the size scale at which droplet properties impact molecular diffusion and permeability. These findings reveal how specific IDPs can phase separate to form permeable, low-density (semi-dilute) liquids, whose structural features are likely to strongly impact biological function.

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.

DNA Checkpoint and Repair Factors Are Nuclear Sensors for Intracellular Organelle Stresses—Inflammations and Cancers Can Have High Genomic Risks

Directory of Open Access Journals (Sweden)

Huihong Zeng

2018-05-01

Full Text Available Under inflammatory conditions, inflammatory cells release reactive oxygen species (ROS and reactive nitrogen species (RNS which cause DNA damage. If not appropriately repaired, DNA damage leads to gene mutations and genomic instability. DNA damage checkpoint factors (DDCF and DNA damage repair factors (DDRF play a vital role in maintaining genomic integrity. However, how DDCFs and DDRFs are modulated under physiological and pathological conditions are not fully known. We took an experimental database analysis to determine the expression of 26 DNA DDCFs and 42 DNA DDRFs in 21 human and 20 mouse tissues in physiological/pathological conditions. We made the following significant findings: (1 Few DDCFs and DDRFs are ubiquitously expressed in tissues while many are differentially regulated.; (2 the expression of DDCFs and DDRFs are modulated not only in cancers but also in sterile inflammatory disorders and metabolic diseases; (3 tissue methylation status, pro-inflammatory cytokines, hypoxia regulating factors and tissue angiogenic potential can determine the expression of DDCFs and DDRFs; (4 intracellular organelles can transmit the stress signals to the nucleus, which may modulate the cell death by regulating the DDCF and DDRF expression. Our results shows that sterile inflammatory disorders and cancers increase genomic instability, therefore can be classified as pathologies with a high genomic risk. We also propose a new concept that as parts of cellular sensor cross-talking network, DNA checkpoint and repair factors serve as nuclear sensors for intracellular organelle stresses. Further, this work would lead to identification of novel therapeutic targets and new biomarkers for diagnosis and prognosis of metabolic diseases, inflammation, tissue damage and cancers.

Short length transmembrane domains having voluminous exoplasmic halves determine retention of Type II membrane proteins in the Golgi complex

OpenAIRE

Quiroga, Rodrigo; Trenchi, Alejandra; Gonzalez Montoro, Ayelén; Valdez, Javier Esteban; Maccioni, Hugo Jose Fernando

2017-01-01

It is still unclear why some proteins that travel along the secretory pathway are retained in the Golgi complex whereas others make their way to the plasma membrane. Recent bioinformatic analyses on a large number of single-spanning membrane proteins support the hypothesis that specific features of the transmembrane domain (TMD) are relevant to the sorting of these proteins to particular organelles. Here we experimentally test this hypothesis for Golgi and plasma membrane proteins. Using the ...

Model tests and numerical analyses on horizontal impedance functions of inclined single piles embedded in cohesionless soil

Science.gov (United States)

Goit, Chandra Shekhar; Saitoh, Masato

2013-03-01

Horizontal impedance functions of inclined single piles are measured experimentally for model soil-pile systems with both the effects of local soil nonlinearity and resonant characteristics. Two practical pile inclinations of 5° and 10° in addition to a vertical pile embedded in cohesionless soil and subjected to lateral harmonic pile head loadings for a wide range of frequencies are considered. Results obtained with low-to-high amplitude of lateral loadings on model soil-pile systems encased in a laminar shear box show that the local nonlinearities have a profound impact on the horizontal impedance functions of piles. Horizontal impedance functions of inclined piles are found to be smaller than the vertical pile and the values decrease as the angle of pile inclination increases. Distinct values of horizontal impedance functions are obtained for the `positive' and `negative' cycles of harmonic loadings, leading to asymmetric force-displacement relationships for the inclined piles. Validation of these experimental results is carried out through three-dimensional nonlinear finite element analyses, and the results from the numerical models are in good agreement with the experimental data. Sensitivity analyses conducted on the numerical models suggest that the consideration of local nonlinearity at the vicinity of the soil-pile interface influence the response of the soil-pile systems.

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.

Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana

KAUST Repository

Bigeard, Jean; Rayapuram, Naganand; Bonhomme, Ludovic; Hirt, Heribert; Pflieger, Delphine

2014-01-01

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.

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.

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

Purification of intact chloroplasts from marine plant Posidonia oceanica suitable for organelle proteomics.

Science.gov (United States)

Piro, Amalia; Serra, Ilia Anna; Spadafora, Antonia; Cardilio, Monica; Bianco, Linda; Perrotta, Gaetano; Santos, Rui; Mazzuca, Silvia

2015-12-01

Posidonia oceanica is a marine angiosperm, or seagrass, adapted to grow to the underwater life from shallow waters to 50 m depth. This raises questions of how their photosynthesis adapted to the attenuation of light through the water column and leads to the assumption that biochemistry and metabolism of the chloroplast are the basis of adaptive capacity. In the present study, we described a protocol that was adapted from those optimized for terrestrial plants, to extract chloroplasts from as minimal tissue as possible. We obtained the best balance between tissue amount/intact chloroplasts yield using one leaf from one plant. After isopynic separations, the chloroplasts purity and integrity were evaluated by biochemical assay and using a proteomic approach. Chloroplast proteins were extracted from highly purified organelles and resolved by 1DE SDS-PAGE. Proteins were sequenced by nLC-ESI-IT-MS/MS of 1DE gel bands and identified against NCBInr green plant databases, Dr. Zompo database for seagrasses in a local customized dataset. The curated localization of proteins in sub-plastidial compartments (i.e. envelope, stroma and thylakoids) was retrieved in the AT_CHLORO database. This purification protocol and the validation of compartment markers may serve as basis for sub-cellular proteomics in P. oceanica and other seagrasses. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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)

Growth of Bi doped cadmium zinc telluride single crystals by Bridgman oscillation method and its structural, optical, and electrical analyses

International Nuclear Information System (INIS)

Carcelen, V.; Rodriguez-Fernandez, J.; Dieguez, E.; Hidalgo, P.

2010-01-01

The II-VI compound semiconductor cadmium zinc telluride (CZT) is very useful for room temperature radiation detection applications. In the present research, we have successfully grown Bi doped CZT single crystals with two different zinc concentrations (8 and 14 at. %) by the Bridgman oscillation method, in which one experiment has been carried out with a platinum (Pt) tube as the ampoule support. Pt also acts as a cold finger and reduces the growth velocity and enhances crystalline perfection. The grown single crystals have been studied with different analysis methods. The stoichiometry was confirmed by energy dispersive by x-ray and inductively coupled plasma mass spectroscopy analyses and it was found there is no incorporation of impurities in the grown crystal. The presence of Cd and Te vacancies was determined by cathodoluminescence studies. Electrical properties were assessed by I-V analysis and indicated higher resistive value (8.53x10 8 Ω cm) for the crystal grown with higher zinc concentration (with Cd excess) compare to the other (3.71x10 5 Ω cm).

Advances and New Concepts in Alcohol-Induced Organelle Stress, Unfolded Protein Responses and Organ Damage

Directory of Open Access Journals (Sweden)

Cheng Ji

2015-06-01

Full Text Available Alcohol is a simple and consumable biomolecule yet its excessive consumption disturbs numerous biological pathways damaging nearly all organs of the human body. One of the essential biological processes affected by the harmful effects of alcohol is proteostasis, which regulates the balance between biogenesis and turnover of proteins within and outside the cell. A significant amount of published evidence indicates that alcohol and its metabolites directly or indirectly interfere with protein homeostasis in the endoplasmic reticulum (ER causing an accumulation of unfolded or misfolded proteins, which triggers the unfolded protein response (UPR leading to either restoration of homeostasis or cell death, inflammation and other pathologies under severe and chronic alcohol conditions. The UPR senses the abnormal protein accumulation and activates transcription factors that regulate nuclear transcription of genes related to ER function. Similarly, this kind of protein stress response can occur in other cellular organelles, which is an evolving field of interest. Here, I review recent advances in the alcohol-induced ER stress response as well as discuss new concepts on alcohol-induced mitochondrial, Golgi and lysosomal stress responses and injuries.

Metabolic flux ratio analysis and cell staining suggest the existence of C4 photosynthesis in Phaeodactylum tricornutum.

Science.gov (United States)

Huang, A; Liu, L; Zhao, P; Yang, C; Wang, G C

2016-03-01

Mechanisms for carbon fixation via photosynthesis in the diatom Phaeodactylum tricornutum Bohlin were studied recently but there remains a long-standing debate concerning the occurrence of C4 photosynthesis in this species. A thorough investigation of carbon metabolism and the evidence for C4 photosynthesis based on organelle partitioning was needed. In this study, we identified the flux ratios between C3 and C4 compounds in P. tricornutum using (13)C-labelling metabolic flux ratio analysis, and stained cells with various cell-permeant fluorescent probes to investigate the likely organelle partitioning required for single-cell C4 photosynthesis. Metabolic flux ratio analysis indicated the C3/C4 exchange ratios were high. Cell staining indicated organelle partitioning required for single-cell C4 photosynthesis might exist in P. tricornutum. The results of (13)C-labelling metabolic flux ratio analysis and cell staining suggest single-cell C4 photosynthesis exists in P. tricornutum. This study provides insights into photosynthesis patterns of P. tricornutum and the evidence for C4 photosynthesis based on (13)C-labelling metabolic flux ratio analysis and organelle partitioning. © 2015 The Society for Applied Microbiology.

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

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.

Analyses of cavitation instabilities in ductile metals

DEFF Research Database (Denmark)

Tvergaard, Viggo

2007-01-01

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......, 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......, while the surrounding voids are represented by a porous ductile material model in terms of a field quantity that specifies the variation of the void volume fraction in the surrounding metal....

Electromyographic analyses of muscle pre-activation induced by single joint exercise.

Science.gov (United States)

Júnior, Valdinar A R; Bottaro, Martim; Pereira, Maria C C; Andrade, Marcelino M; P Júnior, Paulo R W; Carmo, Jake C

2010-01-01

To investigate whether performing a low-intensity, single-joint exercises for knee extensors was an efficient strategy for increasing the number of motor units recruited in the vastus lateralis muscle during a subsequent multi-joint exercises. Nine healthy male participants (23.33+/-3.46 yrs) underwent bouts of exercise in which knee extension and 45 degrees , and leg press exercises were performed in sequence. In the low-intensity bout (R30), 15 unilateral knee extensions were performed, followed by 15 repetitions of the leg presses at 30% and 60% of one maximum repetition load (1-MR), respectively. In the high-intensity bout (R60), the same sequence was performed, but the applied load was 60% of 1-MR for both exercises. A single set of 15 repetitions of the leg press at 60% of 1-MR was performed as a control exercise (CR). The surface electromyographic signals of the vastus lateralis muscle were recorded by means of a linear electrode array. The root mean square (RMS) values were determined for each repetition of the leg press, and linear regressions were calculated from these results. The slopes of the straight lines obtained were then normalized using the linear coefficients of the regression equations and compared using one-way ANOVAs for repeated measures. The slopes observed in the CR were significantly lower than those in the R30 and R60 (precruitment of motor units was more effective when a single-joint exercise preceded the multi-joint exercise. Article registered in the Australian New Zealand Clinical Trials Registry (ANZCTR) under the number ACTRN12609000413224.

Integrative analysis of the mitochondrial proteome in yeast.

Directory of Open Access Journals (Sweden)

Holger Prokisch

2004-06-01

Full Text Available In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans.

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...

Fiscal 2000 research report on the technology for utilizing intracellular protein transport; 2000 nendo saibonai tanpakushitsu yuso kino riyo gijutsu chosa hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-03-01

Research was conducted for the establishment of 'intracellular transport engineering' for collecting eucaryotic proteins having cytotoxicity and activated proteins having escaped decomposition into an appropriate intracellular organelle by artificially manipulating the intracellular transport system for proteins in eucaryotes. In this fiscal year, element technologies and tasks necessary for the transport and activation of intracellular proteins in eucaryotes are extracted, and research was conducted on relevant patents. In a survey of the latest trends of research and development, attention was directed mainly at cells or organelles, and the details of progress in the last one year were investigated and reported, which were related to the functions of single membrane organelles excluding for double membrane bound organelles, e.g., mitochondria and chloroplast, etc., that have unique DNA (deoxyribonucleic acid) and to the molecular mechanism of transport of protein to each organelle. Furthermore, relative to each organelle, deployment of protein transport function application technology was taken up. (NEDO)

Do single women value early retirement more than single men?

DEFF Research Database (Denmark)

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

2005-01-01

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......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 income...... 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...

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.

2017-01-01

ABSTRACT 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. PMID:28246362

Ultrastructural observations on giardiasis in a mouse model. II. Endosymbiosis and organelle distribution in Giardia muris and Giardia lamblia.

Science.gov (United States)

Nemanic, P C; Owen, R L; Stevens, D P; Mueller, J C

1979-08-01

Ultrastructural observations of Giardia muris in a mouse model revealed endosymbiotic microbes not previously reported in Giardia. Endosymbionts 240--360 nm wide, 600--1,400 nm long, and with an internal structure similar to that of bacilli were not seen entering Giardia but were found and appeared to divide within Giardia. No evidence was found of digestion of the endosymbionts by the giardia host in either the trophozoite or the cyst form. Endosymbionts were concentrated centrally around the nuclear area and were uncommon in peripheral feeding regions. The same cellular organelles seen in G. muris were found in Giardia lamblia from human jejunal biopsy material, but no endosymbionts were identified in G. lamblia trophozoites from the seven patients examined. Endosymbionts within Giardia may be found to alter trophozoite pathogenicity, metabolism, range of infectivity, antigenic surface characteristics, and host specificity, as they do in other protozoa.

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.

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.

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.

Fusion of lysosomes with secretory organelles leads to uncontrolled exocytosis in the lysosomal storage disease mucolipidosis type IV.

Science.gov (United States)

Park, Soonhong; Ahuja, Malini; Kim, Min Seuk; Brailoiu, G Cristina; Jha, Archana; Zeng, Mei; Baydyuk, Maryna; Wu, Ling-Gang; Wassif, Christopher A; Porter, Forbes D; Zerfas, Patricia M; Eckhaus, Michael A; Brailoiu, Eugen; Shin, Dong Min; Muallem, Shmuel

2016-02-01

Mutations in TRPML1 cause the lysosomal storage disease mucolipidosis type IV (MLIV). The role of TRPML1 in cell function and how the mutations cause the disease are not well understood. Most studies focus on the role of TRPML1 in constitutive membrane trafficking to and from the lysosomes. However, this cannot explain impaired neuromuscular and secretory cells' functions that mediate regulated exocytosis. Here, we analyzed several forms of regulated exocytosis in a mouse model of MLIV and, opposite to expectations, we found enhanced exocytosis in secretory glands due to enlargement of secretory granules in part due to fusion with lysosomes. Preliminary exploration of synaptic vesicle size, spontaneous mEPSCs, and glutamate secretion in neurons provided further evidence for enhanced exocytosis that was rescued by re-expression of TRPML1 in neurons. These features were not observed in Niemann-Pick type C1. These findings suggest that TRPML1 may guard against pathological fusion of lysosomes with secretory organelles and suggest a new approach toward developing treatment for MLIV. © 2015 The Authors.

Eye-like ocelloids are built from different endosymbiotically acquired components

KAUST Repository

Gavelis, Gregory S.; Hayakawa, Shiho; White, Richard A.; Gojobori, Takashi; Suttle, Curtis A.; Keeling, Patrick J.; Leander, Brian S.

2015-01-01

Multicellularity is often considered a prerequisite for morphological complexity, as seen in the camera-type eyes found in several groups of animals. A notable exception exists in single-celled eukaryotes called dinoflagellates, some of which have an eye-like 'ocelloid' consisting of subcellular analogues to a cornea, lens, iris, and retina. These planktonic cells are uncultivated and rarely encountered in environmental samples, obscuring the function and evolutionary origin of the ocelloid. Here we show, using a combination of electron microscopy, tomography, isolated-organelle genomics, and single-cell genomics, that ocelloids are built from pre-existing organelles, including a cornea-like layer made of mitochondria and a retinal body made of anastomosing plastids. We find that the retinal body forms the central core of a network of peridinin-type plastids, which in dinoflagellates and their relatives originated through an ancient endosymbiosis with a red alga. As such, the ocelloid is a chimaeric structure, incorporating organelles with different endosymbiotic histories. The anatomical complexity of single-celled organisms may be limited by the components available for differentiation, but the ocelloid shows that pre-existing organelles can be assembled into a structure so complex that it was initially mistaken for a multicellular eye. Although mitochondria and plastids are acknowledged chiefly for their metabolic roles, they can also be building blocks for greater structural complexity.

Eye-like ocelloids are built from different endosymbiotically acquired components

KAUST Repository

Gavelis, Gregory S.

2015-07-01

Multicellularity is often considered a prerequisite for morphological complexity, as seen in the camera-type eyes found in several groups of animals. A notable exception exists in single-celled eukaryotes called dinoflagellates, some of which have an eye-like \\'ocelloid\\' consisting of subcellular analogues to a cornea, lens, iris, and retina. These planktonic cells are uncultivated and rarely encountered in environmental samples, obscuring the function and evolutionary origin of the ocelloid. Here we show, using a combination of electron microscopy, tomography, isolated-organelle genomics, and single-cell genomics, that ocelloids are built from pre-existing organelles, including a cornea-like layer made of mitochondria and a retinal body made of anastomosing plastids. We find that the retinal body forms the central core of a network of peridinin-type plastids, which in dinoflagellates and their relatives originated through an ancient endosymbiosis with a red alga. As such, the ocelloid is a chimaeric structure, incorporating organelles with different endosymbiotic histories. The anatomical complexity of single-celled organisms may be limited by the components available for differentiation, but the ocelloid shows that pre-existing organelles can be assembled into a structure so complex that it was initially mistaken for a multicellular eye. Although mitochondria and plastids are acknowledged chiefly for their metabolic roles, they can also be building blocks for greater structural complexity.

The use of exploratory analyses within the National Institute for Health and Care Excellence single technology appraisal process: an evaluation and qualitative analysis.

Science.gov (United States)

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

2016-04-01

As part of the National Institute for Health and Care Excellence (NICE) single technology appraisal (STA) process, independent Evidence Review Groups (ERGs) critically appraise the company submission. During the critical appraisal process the ERG may undertake analyses to explore uncertainties around the company's model and their implications for decision-making. The ERG reports are a central component of the evidence considered by the NICE Technology Appraisal Committees (ACs) in their deliberations. The aim of this research was to develop an understanding of the number and type of exploratory analyses undertaken by the ERGs within the STA process and to understand how these analyses are used by the NICE ACs in their decision-making. The 100 most recently completed STAs with published guidance were selected for inclusion in the analysis. The documents considered were ERG reports, clarification letters, the first appraisal consultation document and the final appraisal determination. Over 400 documents were assessed in this study. The categories of types of exploratory analyses included fixing errors, fixing violations, addressing matters of judgement and the ERG-preferred base case. A content analysis of documents (documentary analysis) was undertaken to identify and extract relevant data, and narrative synthesis was then used to rationalise and present these data. The level and type of detail in ERG reports and clarification letters varied considerably. The vast majority (93%) of ERG reports reported one or more exploratory analyses. The most frequently reported type of analysis in these 93 ERG reports related to the category 'matters of judgement', which was reported in 83 (89%) reports. The category 'ERG base-case/preferred analysis' was reported in 45 (48%) reports, the category 'fixing errors' was reported in 33 (35%) reports and the category 'fixing violations' was reported in 17 (18%) reports. The exploratory analyses performed were the result of issues

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

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

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.

Apparently conclusive meta-analyses may be inconclusive--Trial sequential analysis adjustment of random error risk due to repetitive testing of accumulating data in apparently conclusive neonatal meta-analyses

DEFF Research Database (Denmark)

Brok, Jesper; Thorlund, Kristian; Wetterslev, Jørn

2008-01-01

BACKGROUND: Random error may cause misleading evidence in meta-analyses. The required number of participants in a meta-analysis (i.e. information size) should be at least as large as an adequately powered single trial. Trial sequential analysis (TSA) may reduce risk of random errors due to repeti......BACKGROUND: Random error may cause misleading evidence in meta-analyses. The required number of participants in a meta-analysis (i.e. information size) should be at least as large as an adequately powered single trial. Trial sequential analysis (TSA) may reduce risk of random errors due...

An experimental study of americium-241 biokinetics in the Lobster Homarus Gammarus. Analysis of the accumulation/storage and detoxification processes at the subcellular level; Etude experimentale des biocinetiques de l`americium-241 chez le homard homarus gammarus. Analyse des mecanismes d`accumulation et de detoxication au niveau subcellulaire

Energy Technology Data Exchange (ETDEWEB)

Paquet, F

1993-01-01

An experimental study of americium-241 kinetics has been conducted in the lobster Homarus gammmarus. The investigations were conducted at all the levels from the whole body to the subcellular and molecular levels. The animals were contaminated by a single or chronic ingestion of {sup 241} Am labelled mussels. Assessments of accumulation, elimination and distribution of the radionuclide were established on organisms kept in the laboratory; they made it possible to demonstrate the importance of the digestive gland in the radionuclide transfer pathways. The preliminary results led to structural then ultrastructural investigations of the digestive gland in association with radioautographic studies and cellular extractions methods. Four cellular types were demonstrated, only two of them being implied in the radionuclide retention, the former being responsible for americium intake and the latter for its long-term retention. By means of biochemical techniques, subcellular accumulation was studied and the organelles implied in the nuclide retention were specified. Finally, a method of cellular nuclei dissociation was developed; it made it possible to analyse the molecular nature of americium ligands and to demonstrate the function of the protein nuclear matrix in the nuclide retention.

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…

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

Plant Systems Biology at the Single-Cell Level.

Science.gov (United States)

Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

2017-11-01

Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

The UIC 406 capacity method used on single track sections

DEFF Research Database (Denmark)

Landex, Alex; Kaas, Anders H.; Jacobsen, Erik M.

2007-01-01

This paper describes the relatively new UIC 406 capacity method which is an easy and effective way of calculating capacity consumption on railway lines. However, it is possible to expound the method in different ways which can lead to different capacity consumptions. This paper describes the UIC...... 406 method for single track lines and how it is expounded in Denmark. Many capacity analyses using the UIC 406 capacity method for double track lines have been carried out and presented internationally but only few capacity analyses using the UIC 406 capacity method on single track lines have been...... presented. Therefore, the differences between capacity analysis for double track lines and single track lines are discussed in the beginning of this paper. Many of the principles of the UIC 406 capacity analyses on double track lines can be used on single track lines – at least when more than one train...

Acoustic effects of single electrostatic discharges

International Nuclear Information System (INIS)

Orzech, Łukasz

2015-01-01

Electric discharges, depending on their character, can emit different types of energy, resulting in different effects. Single electrostatic discharges besides generation of electromagnetic pulses are also the source of N acoustic waves. Their specified parameters depending on amount of discharging charge enable determination of value of released charge in a function of acoustic descriptor (e.g. acoustic pressure). Presented approach is the basics of acoustic method for measurement of single electrostatic discharges, enabling direct and contactless measurement of value of charge released during ESD. Method for measurement of acoustic effect of impact of a single electrostatic discharge on the environment in a form of pressure shock wave and examples of acoustic descriptors in a form of equation Q=f(p a ) are described. The properties of measuring system as well as the results of regression static analyses used to determine the described relationships are analysed in details. (paper)

A Structural Basis for Sustained Bacterial Adhesion – Biomechanical Properties of CFA/I Pili

OpenAIRE

Andersson, Magnus; Björnham, Oscar; Svantesson, Mats; Badahdah, Arwa; Uhlin, Bernt Eric; Bullitt, Esther

2011-01-01

Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrheal disease worldwide. Adhesion pili (or fimbriae), such as the CFA/I (colonization factor antigen I) organelles that enable ETEC to attach efficiently to the host intestinal tract epithelium, are critical virulence factors for initiation of infection. We characterized at single organelle level the intrinsic biomechanical properties and kinetics of individual CFA/I pili, demonstrating that weak external forces (7.5 pN) are suf...

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.

Single-cell technologies in environmental omics

KAUST Repository

Kodzius, Rimantas; Gojobori, Takashi

2015-01-01

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.

Evidence for an All-Or-None Perceptual Response: Single-Trial Analyses of Magnetoencephalography Signals Indicate an Abrupt Transition Between Visual Perception and Its Absence

Science.gov (United States)

Sekar, Krithiga; Findley, William M.; Llinás, Rodolfo R.

2014-01-01

Whether consciousness is an all-or-none or graded phenomenon is an area of inquiry that has received considerable interest in neuroscience and is as of yet, still debated. In this magnetoencephalography (MEG) study we used a single stimulus paradigm with sub-threshold, threshold and supra-threshold duration inputs to assess whether stimulus perception is continuous with or abruptly differentiated from unconscious stimulus processing in the brain. By grouping epochs according to stimulus identification accuracy and exposure duration, we were able to investigate whether a high-amplitude perception-related cortical event was (1) only evoked for conditions where perception was most probable (2) had invariant amplitude once evoked and (3) was largely absent for conditions where perception was least probable (criteria satisfying an all-on-none hypothesis). We found that averaged evoked responses showed a gradual increase in amplitude with increasing perceptual strength. However, single trial analyses demonstrated that stimulus perception was correlated with an all-or-none response, the temporal precision of which increased systematically as perception transitioned from ambiguous to robust states. Due to poor signal-to-noise resolution of single trial data, whether perception-related responses, whenever present, were invariant in amplitude could not be unambiguously demonstrated. However, our findings strongly suggest that visual perception of simple stimuli is associated with an all-or-none cortical evoked response the temporal precision of which varies as a function of perceptual strength. PMID:22020091

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.

Extremely thin layer plastification for focused-ion beam scanning electron microscopy: an improved method to study cell surfaces and organelles of cultured cells.

Science.gov (United States)

VAN Donselaar, E G; Dorresteijn, B; Popov-Čeleketić, D; VAN DE Wetering, W J; Verrips, T C; Boekhout, T; Schneijdenberg, C T W M; Xenaki, A T; VAN DER Krift, T P; Müller, W H

2018-03-25

Since the recent boost in the usage of electron microscopy in life-science research, there is a great need for new methods. Recently minimal resin embedding methods have been successfully introduced in the sample preparation for focused-ion beam scanning electron microscopy (FIB-SEM). In these methods several possibilities are given to remove as much resin as possible from the surface of cultured cells or multicellular organisms. Here we introduce an alternative way in the minimal resin embedding method to remove excess of resin from two widely different cell types by the use of Mascotte filter paper. Our goal in correlative light and electron microscopic studies of immunogold-labelled breast cancer SKBR3 cells was to visualise gold-labelled HER2 plasma membrane proteins as well as the intracellular structures of flat and round cells. We found a significant difference (p flat cell contained 2.46 ± 1.98 gold particles, and a round cell 5.66 ± 2.92 gold particles. Moreover, there was a clear difference in the subcellular organisation of these two cells. The round SKBR3 cell contained many organelles, such as mitochondria, Golgi and endoplasmic reticulum, when compared with flat SKBR3 cells. Our next goal was to visualise crosswall associated organelles, septal pore caps, of Rhizoctonia solani fungal cells by the combined use of a heavy metal staining and our extremely thin layer plastification (ETLP) method. At low magnifications this resulted into easily finding septa which appeared as bright crosswalls in the back-scattered electron mode in the scanning electron microscope. Then, a septum was selected for FIB-SEM. Cross-sectioned views clearly revealed the perforate septal pore cap of R. solani next to other structures, such as mitochondria, endoplasmic reticulum, lipid bodies, dolipore septum, and the pore channel. As the ETLP method was applied on two widely different cell types, the use of the ETLP method will be beneficial to correlative studies of other cell

Creating single-subject design graphs in Microsoft Excel 2007.

Science.gov (United States)

Dixon, Mark R; Jackson, James W; Small, Stacey L; Horner-King, Mollie J; Lik, Nicholas Mui Ker; Garcia, Yors; Rosales, Rocio

2009-01-01

Over 10 years have passed since the publication of Carr and Burkholder's (1998) technical article on how to construct single-subject graphs using Microsoft Excel. Over the course of the past decade, the Excel program has undergone a series of revisions that make the Carr and Burkholder paper somewhat difficult to follow with newer versions. The present article provides task analyses for constructing various types of commonly used single-subject design graphs in Microsoft Excel 2007. The task analyses were evaluated using a between-subjects design that compared the graphing skills of 22 behavior-analytic graduate students using Excel 2007 and either the Carr and Burkholder or newly developed task analyses. Results indicate that the new task analyses yielded more accurate and faster graph construction than the Carr and Burkholder instructions.

Toward a unified method for analysing and teaching Human Robot Interaction

DEFF Research Database (Denmark)

Dinesen, Jens Vilhelm

, 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.......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...

From Single Microparticles to Microfluidic Emulsification

DEFF Research Database (Denmark)

Kinoshita, K.; Ortiz, Elisa Parra; Hussein, Abdirazak

2016-01-01

The micropipette manipulation technique is capable of making fundamental single particle measurements and analyses. This information is critical for establishing processing parameters in systems such as microfluidics and homogenization. To demonstrate what can be achieved at the single particle l...... a very useful tool for understanding microsphere-processes and hence can help to establish process conditions without resorting to expensive and material-consuming bulk particle runs....

Single and multi-frequency impedance characterization of symmetric activated carbon single capacitor cells

Directory of Open Access Journals (Sweden)

Suzana Sopčić

2018-05-01

Full Text Available Electrochemical impedance spectroscopy (EIS technique is used for characterization of single cell symmetric capacitors having different mass loadings of activated carbon (AC. Relevant values of charge storage capacitance (CT and internal resistance (ESR were evaluated by the single frequency and multi-frequency analyses of measured impedance spectra. Curve fittings were based on the non-ideal R-C model that takes into account the parasitic inductance, contributions from electrode materials/contacts and the effects of AC porosity. Higher CT and lower ESR values were obtained not only for the cell with higher mass of AC, but also using the single vs. multi-frequency approach. Lower CT and higher values of ESR that are generally obtained using the multi-frequency method and curve fittings should be related to the not ideal capacitive response of porous AC material and too high frequency chosen in applying the single frequency analysis.

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.

Real-Time Intracellular Measurements of ROS and RNS in Living Cells with Single Core-Shell Nanowire Electrodes.

Science.gov (United States)

Zhang, Xin-Wei; Qiu, Quan-Fa; Jiang, Hong; Zhang, Fu-Li; Liu, Yan-Lin; Amatore, Christian; Huang, Wei-Hua

2017-10-09

Nanoelectrodes allow precise and quantitative measurements of important biological processes at the single living-cell level in real time. Cylindrical nanowire electrodes (NWEs) required for intracellular measurements create a great challenge for achieving excellent electrochemical and mechanical performances. Herein, we present a facile and robust solution to this problem based on a unique SiC-core-shell design to produce cylindrical NWEs with superior mechanical toughness provided by the SiC nano-core and an excellent electrochemical performance provided by the ultrathin carbon shell that can be used as such or platinized. The use of such NWEs for biological applications is illustrated by the first quantitative measurements of ROS/RNS in individual phagolysosomes of living macrophages. As the shell material can be varied to meet any specific detection purpose, this work opens up new opportunities to monitor quantitatively biological functions occurring inside cells and their organelles. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single-cell analysis of pyroptosis dynamics reveals conserved GSDMD-mediated subcellular events that precede plasma membrane rupture.

Science.gov (United States)

de Vasconcelos, Nathalia M; Van Opdenbosch, Nina; Van Gorp, Hanne; Parthoens, Eef; Lamkanfi, Mohamed

2018-04-17

Pyroptosis is rapidly emerging as a mechanism of anti-microbial host defense, and of extracellular release of the inflammasome-dependent cytokines interleukin (IL)-1β and IL-18, which contributes to autoinflammatory pathology. Caspases 1, 4, 5 and 11 trigger this regulated form of necrosis by cleaving the pyroptosis effector gasdermin D (GSDMD), causing its pore-forming amino-terminal domain to oligomerize and perforate the plasma membrane. However, the subcellular events that precede pyroptotic cell lysis are ill defined. In this study, we triggered primary macrophages to undergo pyroptosis from three inflammasome types and recorded their dynamics and morphology using high-resolution live-cell spinning disk confocal laser microscopy. Based on quantitative analysis of single-cell subcellular events, we propose a model of pyroptotic cell disintegration that is initiated by opening of GSDMD-dependent ion channels or pores that are more restrictive than recently proposed GSDMD pores, followed by osmotic cell swelling, commitment of mitochondria and other membrane-bound organelles prior to sudden rupture of the plasma membrane and full permeability to intracellular proteins. This study provides a dynamic framework for understanding cellular changes that occur during pyroptosis, and charts a chronological sequence of GSDMD-mediated subcellular events that define pyroptotic cell death at the single-cell level.

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...

Single Parenthood and Children's Reading Performance in Asia

Science.gov (United States)

Park, Hyunjoon

2007-01-01

Using the data from Program for International Student Assessment, I examine the gap in reading performance between 15-year-old students in single-parent and intact families in 5 Asian countries in comparison to the United States. The ordinary least square regression analyses show negligible disadvantages of students with a single parent in Hong…

Dissociation of single-strand DNA: single-walled carbon nanotube hybrids by Watson-Crick base-pairing.

Science.gov (United States)

Jung, Seungwon; Cha, Misun; Park, Jiyong; Jeong, Namjo; Kim, Gunn; Park, Changwon; Ihm, Jisoon; Lee, Junghoon

2010-08-18

It has been known that single-strand DNA wraps around a single-walled carbon nanotube (SWNT) by pi-stacking. In this paper it is demonstrated that such DNA is dissociated from the SWNT by Watson-Crick base-pairing with a complementary sequence. Measurement of field effect transistor characteristics indicates a shift of the electrical properties as a result of this "unwrapping" event. We further confirm the suggested process through Raman spectroscopy and gel electrophoresis. Experimental results are verified in view of atomistic mechanisms with molecular dynamics simulations and binding energy analyses.

Addressable droplet microarrays for single cell protein analysis.

Science.gov (United States)

Salehi-Reyhani, Ali; Burgin, Edward; Ces, Oscar; Willison, Keith R; Klug, David R

2014-11-07

Addressable droplet microarrays are potentially attractive as a way to achieve miniaturised, reduced volume, high sensitivity analyses without the need to fabricate microfluidic devices or small volume chambers. We report a practical method for producing oil-encapsulated addressable droplet microarrays which can be used for such analyses. To demonstrate their utility, we undertake a series of single cell analyses, to determine the variation in copy number of p53 proteins in cells of a human cancer cell line.

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

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 ...

The Mental Health Status of Single-Parent Community College Students in California.

Science.gov (United States)

Shenoy, Divya P; Lee, Christine; Trieu, Sang Leng

2016-01-01

Single-parenting students face unique challenges that may adversely affect their mental health, which have not been explored in community college settings. The authors conducted secondary analysis of Spring 2013 data from the American College Health Association-National College Health Assessment to examine difficulties facing single-parent community college students and the association between single parenting and negative mental health (depression, self-injury, suicide attempt). Participants were 6,832 California community college students, of whom 309 were single parents. Demographic and mental health data were characterized using univariate descriptive analyses. Bivariate analyses determined whether single parents differed from other students regarding negative mental health or traumatic/difficult events. Finances, family, and relationship difficulties disproportionally affected single parents, who reported nearly twice as many suicide attempts as their counterparts (5.3% vs. 2.7%; p students face a higher prevalence of mental health stressors than other community college students.

Pathway-based analyses.

Science.gov (United States)

Kent, Jack W

2016-02-03

New technologies for acquisition of genomic data, while offering unprecedented opportunities for genetic discovery, also impose severe burdens of interpretation and penalties for multiple testing. The Pathway-based Analyses Group of the Genetic Analysis Workshop 19 (GAW19) sought reduction of multiple-testing burden through various approaches to aggregation of highdimensional data in pathways informed by prior biological knowledge. Experimental methods testedincluded the use of "synthetic pathways" (random sets of genes) to estimate power and false-positive error rate of methods applied to simulated data; data reduction via independent components analysis, single-nucleotide polymorphism (SNP)-SNP interaction, and use of gene sets to estimate genetic similarity; and general assessment of the efficacy of prior biological knowledge to reduce the dimensionality of complex genomic data. The work of this group explored several promising approaches to managing high-dimensional data, with the caveat that these methods are necessarily constrained by the quality of external bioinformatic annotation.

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.

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.

Effect of fluoride on the cell viability, cell organelle potential, and photosynthetic capacity of freshwater and soil algae.

Science.gov (United States)

Chae, Yooeun; Kim, Dokyung; An, Youn-Joo

2016-12-01

Although fluoride occurs naturally in the environment, excessive amounts of fluoride in freshwater and terrestrial ecosystems can be harmful. We evaluated the toxicity of fluoride compounds on the growth, viability, and photosynthetic capacity of freshwater (Chlamydomonas reinhardtii and Pseudokirchneriella subcapitata) and terrestrial (Chlorococcum infusionum) algae. To measure algal growth inhibition, a flow cytometric method was adopted (i.e., cell size, granularity, and auto-fluorescence measurements), and algal yield was calculated to assess cell viability. Rhodamine123 and fluorescein diacetate were used to evaluate mitochondrial membrane potential (MMA, ΔΨ m ) and cell permeability. Nine parameters related to the photosynthetic capacity of algae were also evaluated. The results indicated that high concentrations of fluoride compounds affected cell viability, cell organelle potential, and photosynthetic functions. The cell viability measurements of the three algal species decreased, but apoptosis was only observed in C. infusionum. The MMA (ΔΨ m ) of cells exposed to fluoride varied among species, and the cell permeability of the three species generally decreased. The decrease in the photosynthetic activity of algae may be attributable to the combination of fluoride ions (F - ) with magnesium ions (Mg 2+ ) in chlorophyll. Our results therefore provide strong evidence for the potential risks of fluoride compounds to microflora and microfauna in freshwater and terrestrial ecosystems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Protein determination in single corns

International Nuclear Information System (INIS)

Knorr, J.; Schiekel, M.; Franke, W.; Focke, F.

1994-01-01

Determination of protein content in food materials is usually done by analyzing the nitrogen amount by wet chemical Kjeldahl method. An improved accuracy accompanied by smaller analyzing intervals can be achieved using nondestructive neutron activation. Analyses have been performed using 14 MeV neutrons to determine the content of N and P in single wheat corns. Irradiation parameters have been optimized to prevent serious radiation damage in grains. About 200 single corns have been investigated with total net weights ranging from 30 to 70 mg. The tested arrangement allows determination of nitrogen amount in a single corn down to 0.3 mg with an accuracy of better than 4 %. Mean nitrogen concentrations in the range from 9 to 19% per corn have been detected. (author) 5 refs.; 6 figs

Elemental abundance analyses with coadded DAO spectrograms: Pt. 4

International Nuclear Information System (INIS)

Adelman, S.J.

1988-01-01

The analyses presented in the first three papers of this series are revised to include more accurate gf-values and damping constants. The largest changes are in the chromium, manganese, and nickel abundances derived from singly ionized lines. The agreement with the values from neutral lines of the same element is improved. The microturbulent velocities determined from neutral and singly ionized lines by demanding that the derived abundances not be a function of equivalent width were checked by performing similar calculations on lines of selected atomic species and by studying the rms scatter of individual line values as a function of assumed microturbulence. On the whole the adopted values of microturbulence appear to be well determined. (author)

Freeze-fracture study of Trichomonas vaginalis

Directory of Open Access Journals (Sweden)

Marlene Benchimol

1990-12-01

Full Text Available The freeze-fracture technique was used to analyse the organization of the plasma membrane, as well as membranes of cytoplasmic organelles, of the pathogenic protozoan Trichomonas vaginalis. Rosettes formed by 4 to 14 intramembranous particles were seen on the fracture faces of the membrane lining the anterior flagella as well as in fracture faces of the plasma membrane enclosing the anterior region of the protozoan and in cytoplasmic organelles. Special organization of the membrane particles were also seen in the region of association of the recurrent flagellum to the cell body.

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

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)

Single camera analyses in studying pattern forming dynamics of player interactions in team sports.

OpenAIRE

Duarte, Ricardo; Fernandes, Orlando; Folgado, Hugo; Araújo, Duarte

2013-01-01

A network of patterned interactions between players characterises team ball sports. Thus, interpersonal coordination patterns are an important topic in the study of performance in such sports. A very useful method has been the study of inter-individual interactions captured by a single camera filming an extended performance area. The appropriate collection of positional data allows investigating the pattern forming dynamics emerging in different performance sub-phases of team ball sports. Thi...

ECSPECT prospective multicentre registry for single-port laparoscopic colorectal procedures

DEFF Research Database (Denmark)

Weiss, Helmut; Zorron, R; Vestweber, K-H

2017-01-01

BACKGROUND: The international multicentre registry ECSPECT (European Consensus of Single Port Expertise in Colorectal Treatment) was established to evaluate the general feasibility and safety of single-port colorectal surgery with regard to preoperative risk assessment. METHODS: Consecutive...... patients undergoing single-port colorectal surgery were enrolled from 11 European centres between March 2010 and March 2014. Data were analysed to assess patient-, technique- and procedure-dependent parameters. A validated sex-adjusted risk chart was developed for prediction of single-port colorectal...

Aligning of single and multiple wavelength chromatographic

DEFF Research Database (Denmark)

Nielsen, Niels-Peter Vest; Carstensen, Jens Michael; Smedsgaard, Jørn

1998-01-01

optimised warping (COW) using two input parameters which can be estimated from the observed peak width. COW is demonstrated on constructed single trace chromatograms and on single and multiple wavelength chromatograms obtained from HPLC diode detection analyses of fungal extractsA copy of the C program......The use of chemometric data processing is becoming an important part of modern chromatography. Most chemometric analyses are performed on reduced data sets using areas of selected peaks detected in the chromatograms, which means a loss of data and introduces the problem of extracting peak data from...... to utilise the entire data matrix or rely on peak detection, thus having the same limitations as the commonly used chemometric procedures. The method presented uses the entire chromatographic data matrices and does not require any preprocessing e.g., peak detection. It relies on piecewise linear correlation...

Single-molecule dynamics in nanofabricated traps

Science.gov (United States)

Cohen, Adam

2009-03-01

The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

Economic Analyses in Anterior Cruciate Ligament Reconstruction: A Qualitative and Systematic Review.

Science.gov (United States)

Saltzman, Bryan M; Cvetanovich, Gregory L; Nwachukwu, Benedict U; Mall, Nathan A; Bush-Joseph, Charles A; Bach, Bernard R

2016-05-01

As the health care system in the United States (US) transitions toward value-based care, there is an increased emphasis on understanding the cost drivers and high-value procedures within orthopaedics. To date, there has been no systematic review of the economic literature on anterior cruciate ligament reconstruction (ACLR). To evaluate the overall evidence base for economic studies published on ACLR in the orthopaedic literature. Data available on the economics of ACLR are summarized and cost drivers associated with the procedure are identified. Systematic review. All economic studies (including US-based and non-US-based) published between inception of the MEDLINE database and October 3, 2014, were identified. Given the heterogeneity of the existing evidence base, a qualitative, descriptive approach was used to assess the collective results from the economic studies on ACLR. When applicable, comparisons were made for the following cost-related variables associated with the procedure for economic implications: outpatient versus inpatient surgery (or outpatient vs overnight hospital stay vs >1-night stay); bone-patellar tendon-bone (BPTB) graft versus hamstring (HS) graft source; autograft versus allograft source; staged unilateral ACLR versus bilateral ACLR in a single setting; single- versus double-bundle technique; ACLR versus nonoperative treatment; and other unique comparisons reported in single studies, including computer-assisted navigation surgery (CANS) versus traditional surgery, early versus delayed ACLR, single- versus double-incision technique, and finally the costs of ACLR without comparison of variables. A total of 24 studies were identified and included; of these, 17 included studies were cost identification studies. The remaining 7 studies were cost utility analyses that used economic models to investigate the effect of variables such as the cost of allograft tissue, fixation devices, and physical therapy, the percentage and timing of revision

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

Design considerations for a Space Shuttle Main Engine turbine blade made of single crystal material

Science.gov (United States)

Abdul-Aziz, A.; August, R.; Nagpal, V.

1993-01-01

Nonlinear finite-element structural analyses were performed on the first stage high-pressure fuel turbopump blade of the Space Shuttle Main Engine. The analyses examined the structural response and the dynamic characteristics at typical operating conditions. Single crystal material PWA-1480 was considered for the analyses. Structural response and the blade natural frequencies with respect to the crystal orientation were investigated. The analyses were conducted based on typical test stand engine cycle. Influence of combined thermal, aerodynamic, and centrifugal loadings was considered. Results obtained showed that the single crystal secondary orientation effects on the maximum principal stresses are not highly significant.

Single-particle motion in large-amplitude quadrupole shape transition

International Nuclear Information System (INIS)

Yamada, Kazuya

1991-01-01

The microscopic structure of the single-particle motion for the spherical-deformed transitional nuclei is analysed by using the self-consistent collective-coordinate method (SCC method). The single-particle motion in the moving-frame of reference called the collective vibrating coordinate frame is introduced by the generalized Bogoliubov transformation depending on the collective coordinate. The numerical calculations of the single-particle (quasi-particle) energy level diagrams and their occupation probabilities for the static deformation are carried out for the Sm isotopes. A clear change of the single-particle distribution structure appears in the course of deformation. (author)

Quantifying Golgi structure using EM: combining volume-SEM and stereology for higher throughput.

Science.gov (United States)

Ferguson, Sophie; Steyer, Anna M; Mayhew, Terry M; Schwab, Yannick; Lucocq, John Milton

2017-06-01

Investigating organelles such as the Golgi complex depends increasingly on high-throughput quantitative morphological analyses from multiple experimental or genetic conditions. Light microscopy (LM) has been an effective tool for screening but fails to reveal fine details of Golgi structures such as vesicles, tubules and cisternae. Electron microscopy (EM) has sufficient resolution but traditional transmission EM (TEM) methods are slow and inefficient. Newer volume scanning EM (volume-SEM) methods now have the potential to speed up 3D analysis by automated sectioning and imaging. However, they produce large arrays of sections and/or images, which require labour-intensive 3D reconstruction for quantitation on limited cell numbers. Here, we show that the information storage, digital waste and workload involved in using volume-SEM can be reduced substantially using sampling-based stereology. Using the Golgi as an example, we describe how Golgi populations can be sensed quantitatively using single random slices and how accurate quantitative structural data on Golgi organelles of individual cells can be obtained using only 5-10 sections/images taken from a volume-SEM series (thereby sensing population parameters and cell-cell variability). The approach will be useful in techniques such as correlative LM and EM (CLEM) where small samples of cells are treated and where there may be variable responses. For Golgi study, we outline a series of stereological estimators that are suited to these analyses and suggest workflows, which have the potential to enhance the speed and relevance of data acquisition in volume-SEM.

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.

Validation of chemical analyses of atmospheric deposition in forested European sites

Directory of Open Access Journals (Sweden)

Erwin ULRICH

2005-08-01

Full Text Available Within the activities of the Integrated Co-operative Programme on Assessment and Monitoring of Air Pollution Effects on Forests (ICP Forests and of the EU Regulation 2152/2003, a Working Group on Quality Assurance/Quality Control of analyses has been created to assist the participating laboratories in the analysis of atmospheric deposition, soil and soil solution, and leaves/needles. As part of the activity of the WG, this study is a statistical analysis in the field of water analysis of chemical concentrations and relationships between ions, and between conductivity and ions for different types of samples (bulk or wet-only samples, throughfall, stemflow considered in forest studies. About 5000 analyses from seven laboratories were used to establish relationships representative of different European geographic and climatic situations, from northern Finland to southern Italy. Statistically significant differences between the relationships obtained from different types of solutions, interacting with different types of vegetation (throughfall and stemflow samples, broad-leaved trees and conifers and with varying influence of marine salt were tested. The ultimate aim is to establish general relationships between ions, and between conductivity and ions, with relative confidence limits, which can be used as a comparison with those established in single laboratories. The use of such techniques is strongly encouraged in the ICPF laboratories to validate single chemical analyses, to be performed when it is still possible to replicate the analysis, and as a general overview of the whole set of analyses, to obtain an indication of the laboratory performance on a long-term basis.

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.

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.

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.

Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

Science.gov (United States)

Gu, Liangcai; Li, Chao; Aach, John; Hill, David E; Vidal, Marc; Church, George M

2014-11-27

In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by the number of spectrally non-overlapping chromophores. Here we introduce a single-molecular-interaction sequencing (SMI-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide thin film to construct a random single-molecule array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies) and analysed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimetre. Furthermore, protein interactions can be measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor and antibody-binding profiling, are demonstrated. SMI-seq enables 'library versus library' screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity.

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.

Arabidopsis peroxisome proteomics

Directory of Open Access Journals (Sweden)

John D. Bussell

2013-04-01

Full Text Available The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. This is primarily due to the difficulties associated with isolating and obtaining purified samples of peroxisomes from Arabidopsis. So far only a handful of research groups have been successful in obtaining such fractions. To make things worse, enriched peroxisome fractions frequently suffer from significant organellar contamination, lowering confidence in localization assignment of the identified proteins. As with other cellular compartments, identification of peroxisomal proteins forms the basis for investigations of the dynamics of the peroxisomal proteome. It is therefore not surprising that, in terms of functional analyses by proteomic means, there remains a considerable gap between peroxisomes and chloroplasts or mitochondria. Alternative strategies are needed to overcome the obstacle of hard-to-obtain organellar fractions. This will help to close the knowledge gap between peroxisomes and other organelles and provide a full picture of the physiological pathways shared between organelles. In this review we briefly summarize the status quo and discuss some of the methodological alternatives to classic organelle proteomic approaches.

Microarray analyses of glucocorticoid and vitamin D3 target genes in differentiating cultured human podocytes.

Directory of Open Access Journals (Sweden)

Xiwen Cheng

Full Text Available Glomerular podocytes are highly differentiated epithelial cells that are key components of the kidney filtration units. Podocyte damage or loss is the hallmark of nephritic diseases characterized by severe proteinuria. Recent studies implicate that hormones including glucocorticoids (ligand for glucocorticoid receptor and vitamin D3 (ligand for vitamin D receptor protect or promote repair of podocytes from injury. In order to elucidate the mechanisms underlying hormone-mediated podocyte-protecting activity from injury, we carried out microarray gene expression studies to identify the target genes and corresponding pathways in response to these hormones during podocyte differentiation. We used immortalized human cultured podocytes (HPCs as a model system and carried out in vitro differentiation assays followed by dexamethasone (Dex or vitamin D3 (VD3 treatment. Upon the induction of differentiation, multiple functional categories including cell cycle, organelle dynamics, mitochondrion, apoptosis and cytoskeleton organization were among the most significantly affected. Interestingly, while Dex and VD3 are capable of protecting podocytes from injury, they only share limited target genes and affected pathways. Compared to VD3 treatment, Dex had a broader and greater impact on gene expression profiles. In-depth analyses of Dex altered genes indicate that Dex crosstalks with a broad spectrum of signaling pathways, of which inflammatory responses, cell migration, angiogenesis, NF-κB and TGFβ pathways are predominantly altered. Together, our study provides new information and identifies several new avenues for future investigation of hormone signaling in podocytes.

Single Motherhood, Alcohol Dependence, and Smoking During Pregnancy: A Propensity Score Analysis.

Science.gov (United States)

Waldron, Mary; Bucholz, Kathleen K; Lian, Min; Lessov-Schlaggar, Christina N; Miller, Ruth Huang; Lynskey, Michael T; Knopik, Valerie S; Madden, Pamela A F; Heath, Andrew C

2017-09-01

Few studies linking single motherhood and maternal smoking during pregnancy consider correlated risk from problem substance use beyond history of smoking and concurrent use of alcohol. In the present study, we used propensity score methods to examine whether the risk of smoking during pregnancy associated with single motherhood is the result of potential confounders, including alcohol dependence. Data were drawn from mothers participating in a birth cohort study of their female like-sex twin offspring (n = 257 African ancestry; n = 1,711 European or other ancestry). We conducted standard logistic regression models predicting smoking during pregnancy from single motherhood at twins' birth, followed by propensity score analyses comparing single-mother and two-parent families stratified by predicted probability of single motherhood. In standard models, single motherhood predicted increased risk of smoking during pregnancy in European ancestry but not African ancestry families. In propensity score analyses, rates of smoking during pregnancy were elevated in single-mother relative to two-parent European ancestry families across much of the spectrum a priori risk of single motherhood. Among African ancestry families, within-strata comparisons of smoking during pregnancy by single-mother status were nonsignificant. These findings highlight single motherhood as a unique risk factor for smoking during pregnancy in European ancestry mothers, over and above alcohol dependence. Additional research is needed to identify risks, beyond single motherhood, associated with smoking during pregnancy in African ancestry mothers.

Accidents and transients analyses of a super fast reactor with single flow pass core

International Nuclear Information System (INIS)

Sutanto,; Oka, Yoshiaki

2014-01-01

Highlights: • Safety analysis of a Super FR with single flow pass core is conducted. • Loss of feed water flow leads to a direct effect on the loss of fuel channel flow. • The core pressure is sensitive to LOCA accidents due to the direct effect. • Small LOCA introduces a critical break. • The safety criteria for all selected events are satisfied. - Abstract: The supercritical water cooled fast reactor with single flow pass core has been designed to simplify refueling and the structures of upper and lower mixing plenums. To evaluate the safety performance, safety analysis has been conducted with regard to LOCA and non-LOCA accidents including transient events. Safety analysis results show that the safety criteria are satisfied for all selected events. The total loss of feed water flow is the most important accident which the maximum cladding surface temperature (MCST) is high due to a direct effect of the accident on the total loss of flow in all fuel assemblies. However, actuation of the ADS can mitigate the accident. Small LOCA also introduces a critical break at 7.8% break which results high MCST at BOC because the scram and ADS are not actuated. Early ADS actuation is effective to mitigate the accident. In large LOCA, 100% break LOCA results a high MCST of flooding phase at BOC due to high power peaking at the bottom part. Use of high injection flow rate by 2 LPCI units is effective to decrease the MCST

New Blood Pressure-Associated Loci Identified in Meta-Analyses of 475 000 Individuals

DEFF Research Database (Denmark)

Kraja, Aldi T.; Cook, James P.; Warren, Helen R.

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...

Single ovalbumin molecules exploring nucleoplasm and nucleoli of living cell nuclei.

Science.gov (United States)

Speil, Jasmin; Kubitscheck, Ulrich

2010-03-01

The nucleus is the center of direction and coordination of the cell's metabolic and reproductive activities and contains numerous functionally specialized domains. These subnuclear structures are not delimited by membranes like cytoplasmic organelles and their function is only poorly understood. Here, we studied the most prominent nuclear domains, nucleoli and the remaining nucleoplasm. We used fluorescently labeled ovalbumin-ATTO647N, an inert protein, to examine their physical properties. This inert tracer was microinjected into the cytoplasm of HeLa cells, and after diffusion into the nucleus the tracer distribution and mobility in the two nuclear compartments was examined. Like many macromolecular probes ovalbumin was significantly less abundant in nucleoli compared to the nucleoplasm. High-speed fluorescence microscopy allowed visualizing and analyzing single tracer molecule trajectories within nucleoli and nucleoplasm. In accordance with previous studies we found that the viscosity of the nucleus is sevenfold higher than that of aqueous buffer. Notably, nucleoplasm and nucleoli did not significantly differ in viscosity, however, the fraction of slow or trapped molecules was higher in the nucleoplasm than in nucleoli (6% versus 0.2%). Surprisingly, even a completely inert molecule like ovalbumin showed at times short-lived binding events with a decay time of 8 ms in the nucleoplasm and even shorter-6.3 ms-within the nucleoli. Copyright 2009 Elsevier B.V. All rights reserved.

The mechanism distinguishability problem in biochemical kinetics: the single-enzyme, single-substrate reaction as a case study.

Science.gov (United States)

Schnell, Santiago; Chappell, Michael J; Evans, Neil D; Roussel, Marc R

2006-01-01

A theoretical analysis of the distinguishability problem of two rival models of the single enzyme-single substrate reaction, the Michaelis-Menten and Henri mechanisms, is presented. We also outline a general approach for analysing the structural indistinguishability between two mechanisms. The approach involves constructing, if possible, a smooth mapping between the two candidate models. Evans et al. [N.D. Evans, M.J. Chappell, M.J. Chapman, K.R. Godfrey, Structural indistinguishability between uncontrolled (autonomous) nonlinear analytic systems, Automatica 40 (2004) 1947-1953] have shown that if, in addition, either of the mechanisms satisfies a particular criterion then such a transformation always exists when the models are indistinguishable from their experimentally observable outputs. The approach is applied to the single enzyme-single substrate reaction mechanism. In principle, mechanisms can be distinguished using this analysis, but we show that our ability to distinguish mechanistic models depends both on the precise measurements made, and on our knowledge of the system prior to performing the kinetics experiments.

A new support measure to quantify the impact of local optima in phylogenetic analyses.

KAUST Repository

Brammer, Grant; Sul, Seung-Jin; Williams, Tiffani L

2011-01-01

Phylogentic analyses are often incorrectly assumed to have stabilized to a single optimum. However, a set of trees from a phylogenetic analysis may contain multiple distinct local optima with each optimum providing different levels of support

RoboSCell: An automated single cell arraying and analysis instrument

KAUST Repository

Sakaki, Kelly

2009-09-09

Single cell research has the potential to revolutionize experimental methods in biomedical sciences and contribute to clinical practices. Recent studies suggest analysis of single cells reveals novel features of intracellular processes, cell-to-cell interactions and cell structure. The methods of single cell analysis require mechanical resolution and accuracy that is not possible using conventional techniques. Robotic instruments and novel microdevices can achieve higher throughput and repeatability; however, the development of such instrumentation is a formidable task. A void exists in the state-of-the-art for automated analysis of single cells. With the increase in interest in single cell analyses in stem cell and cancer research the ability to facilitate higher throughput and repeatable procedures is necessary. In this paper, a high-throughput, single cell microarray-based robotic instrument, called the RoboSCell, is described. The proposed instrument employs a partially transparent single cell microarray (SCM) integrated with a robotic biomanipulator for in vitro analyses of live single cells trapped at the array sites. Cells, labeled with immunomagnetic particles, are captured at the array sites by channeling magnetic fields through encapsulated permalloy channels in the SCM. The RoboSCell is capable of systematically scanning the captured cells temporarily immobilized at the array sites and using optical methods to repeatedly measure extracellular and intracellular characteristics over time. The instrument\\'s capabilities are demonstrated by arraying human T lymphocytes and measuring the uptake dynamics of calcein acetoxymethylester-all in a fully automated fashion. © 2009 Springer Science+Business Media, LLC.

Biochemical and single-molecule analyses of the RNA silencing suppressing activity of CrPV-1A.

Science.gov (United States)

Watanabe, Mariko; Iwakawa, Hiro-Oki; Tadakuma, Hisashi; Tomari, Yukihide

2017-10-13

Viruses often encode viral silencing suppressors (VSSs) to counteract the hosts' RNA silencing activity. The cricket paralysis virus 1A protein (CrPV-1A) is a unique VSS that binds to a specific Argonaute protein (Ago)-the core of the RNA-induced silencing complex (RISC)-in insects to suppress its target cleavage reaction. However, the precise molecular mechanism of CrPV-1A action remains unclear. Here we utilized biochemical and single-molecule imaging approaches to analyze the effect of CrPV-1A during target recognition and cleavage by Drosophila Ago2-RISC. Our results suggest that CrPV-1A obstructs the initial target searching by Ago2-RISC via base pairing in the seed region. The combination of biochemistry and single-molecule imaging may help to pave the way for mechanistic understanding of VSSs with diverse functions. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

Single-fiber myosin heavy chain polymorphism during postnatal development: modulation by hypothyroidism

Science.gov (United States)

di Maso, N. A.; Caiozzo, V. J.; Baldwin, K. M.

2000-01-01

The primary objective of this study was to follow the developmental time course of myosin heavy chain (MHC) isoform transitions in single fibers of the rodent plantaris muscle. Hypothyroidism was used in conjunction with single-fiber analyses to better describe a possible linkage between the neonatal and fast type IIB MHC isoforms during development. In contrast to the general concept that developmental MHC isoform transitions give rise to muscle fibers that express only a single MHC isoform, the single-fiber analyses revealed a very high degree of MHC polymorphism throughout postnatal development. In the adult state, MHC polymorphism was so pervasive that the rodent plantaris muscles contained approximately 12-15 different pools of fibers (i.e., fiber types). The degree of polymorphism observed at the single-fiber level made it difficult to determine specific developmental schemes analogous to those observed previously for the rodent soleus muscle. However, hypothyroidism was useful in that it confirmed a possible link between the developmental regulation of the neonatal and fast type IIB MHC isoforms.

The novel protein BboRhop68 is expressed by intraerytrhocytic stages of Babesia bovis

Science.gov (United States)

The apical complex of intracellular hemoparasites contains organelles like micronemes and rhoptries, specialized structures required for adherence and invasion of host cells. Several molecules discharged from rhoptries have been identified from Plasmodium spp., but only a single rhoptry associated p...

CFD analyses in regulatory practice

International Nuclear Information System (INIS)

Bloemeling, F.; Pandazis, P.; Schaffrath, A.

2012-01-01

Numerical software is used in nuclear regulatory procedures for many problems in the fields of neutron physics, structural mechanics, thermal hydraulics etc. Among other things, the software is employed in dimensioning and designing systems and components and in simulating transients and accidents. In nuclear technology, analyses of this kind must meet strict requirements. Computational Fluid Dynamics (CFD) codes were developed for computing multidimensional flow processes of the type occurring in reactor cooling systems or in containments. Extensive experience has been accumulated by now in selected single-phase flow phenomena. At the present time, there is a need for development and validation with respect to the simulation of multi-phase and multi-component flows. As insufficient input by the user can lead to faulty results, the validity of the results and an assessment of uncertainties are guaranteed only through consistent application of so-called Best Practice Guidelines. The authors present the possibilities now available to CFD analyses in nuclear regulatory practice. This includes a discussion of the fundamental requirements to be met by numerical software, especially the demands upon computational analysis made by nuclear rules and regulations. In conclusion, 2 examples are presented of applications of CFD analysis to nuclear problems: Determining deboration in the condenser reflux mode of operation, and protection of the reactor pressure vessel (RPV) against brittle failure. (orig.)

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.

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.

IDEA: Interactive Display for Evolutionary Analyses.

Science.gov (United States)

Egan, Amy; Mahurkar, Anup; Crabtree, Jonathan; Badger, Jonathan H; Carlton, Jane M; Silva, Joana C

2008-12-08

The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

Spectrally Resolved and Functional Super-resolution Microscopy via Ultrahigh-Throughput Single-Molecule Spectroscopy.

Science.gov (United States)

Yan, Rui; Moon, Seonah; Kenny, Samuel J; Xu, Ke

2018-03-20

SMLM was next utilized to achieve f-SRM. By encoding functional information into the spectral responses of environment-sensing fluorescent probes, f-SRM transcends the structural information provided by typical SRM techniques and reveals the spatiotemporal distribution of physicochemical parameters with single-molecule sensitivity and nanoscale spatial resolution. As one example, by employing the solvatochromic dye Nile Red to sense local chemical polarity, we revealed nanoscale heterogeneity in the membranes of live mammalian cells. This enabled us to unveil substantial polarity differences between the plasma membrane and the membranes of nanoscale intracellular organelles, a result we determined to be due to differences in local cholesterol levels. With the addition of cholesterol or cholera toxin, we further observed the formation of low-polarity, raftlike nanodomains in the plasma membrane. In another study, we generalized SR-SMLM to fluorogenic single-molecule reactions. As a wide-field technique, SR-SMLM readily captures the emission spectra of individual product fluorescent molecules that are stochastically produced from nonfluorescent reactants at random locations over large sample areas, and therefore, it provides the unique possibility to spectrally identify and characterize single product molecules in a high-throughput fashion. Using the ring-opening reaction of a photochromic spiropyran as an example, we demonstrated that the capability to resolve the emission spectra of single product molecules could unveil rich, multipath reaction pathways. In summary, by integrating the spatial, temporal, and spectral dimensions of single-molecule fluorescence, SR-SMLM and f-SRM add rich spectral and functional dimensions to SRM and thus open up new ways of probing biological and chemical systems at the single-molecule and nanoscale levels.

Analyser for fast single events; Analyseur d'evenements rapides simples; Analizator bystrykh odnokratnykh yavlenij; Analizador de sucesos rapidos no recurrentes

Energy Technology Data Exchange (ETDEWEB)

Sedlmeyer, J W; Patten, R B; Fussell, L Jr [Edgerton, Germeshausen And Grier, Inc., Las Vegas, NV (United States)

1962-04-15

An electronic analyser has been designed and constructed for use with single non-recurring transient signals. The signal, during passage along a coaxial line, is sampled instantaneously at a number of tap-off points, by means of a single short-duration gate pulse. Multipoint time-dissection is accomplished using a gate-duration and a time-interval between samples, which are independently adjustable from about 4 ns. The time-intervals may be programmed in non-linear array, and jitter is less than 0.5 ns. The speed of response is at present limited by diode characteristics. Each sampled voltage is stretched in a circuit which retains the voltage amplitude. A time-stretch by a factor of 10{sup 8} has been realized, with good stability. These data points may be commutated and transmitted over open-wire to low-frequency recording systems ; they may be converted to digital form for rapid data-processing, using conventional equipment; and/or they may be presented visually. The analyser is advantageous, compared with high-speed oscilloscopy, when large numbers of single-transients require individual analysis; such requirements exist for investigations into fluctuations in the response of systems, or for production-testing of components. The analyser is advantageous when the data-analysis must be accomplished quickly after the signal event occurs; it is not necessary to develop films or to read them. The analyser is also advantageous when the analysis-computation centre is located remotely from the event. Applications of this technique in the nuclear field are many. Fluctuation studies of reactors and subcritical assemblies may be carried out rapidly by pulsed neutron techniques. The build-up and decay characteristics of detectors may be determined, together with analysis of statistics and fluctuations. The pulse shape of the radiation wave from nuclear accelerators may be measured. Neutron-spectrometry using the time-of-flight method may be facilitated. Isomeric studies

The significance of peroxisomes in secondary metabolite biosynthesis in filamentous fungi

NARCIS (Netherlands)

Bartoszewska, Magdalena; Opalinski, Lukasz; Veenhuis, Marten; van der Klei, Ida J.

2011-01-01

Peroxisomes are ubiquitous organelles characterized by a protein-rich matrix surrounded by a single membrane. In filamentous fungi, peroxisomes are crucial for the primary metabolism of several unusual carbon sources used for growth (e. g. fatty acids), but increasing evidence is presented that

Experiment and density functional theory analyses of GdTaO4 single crystal

Science.gov (United States)

Ding, Shoujun; Kinross, Ashlie; Wang, Xiaofei; Yang, Huajun; Zhang, Qingli; Liu, Wenpeng; Sun, Dunlu

2018-05-01

GdTaO4 is a type of excellent materials that can be used as scintillation, laser matrix as well as self-activated phosphor has generated significant interest. Whereas its band structure, electronic structure and optical properties are still need elucidation. To solve this intriguing problem, high-quality GdTaO4 single crystal (M-type) was grown successfully using Czochralski method. Its structure as well as optical properties was determined in experiment. Moreover, a systematic theoretical calculation based on the density function theory methods were performed on M-type and M‧-type GdTaO4 and their band structure, density of state as well as optical properties were obtained. Combine with the performed experiment results, the calculated results were proved with high reliability. Hence, the calculated results obtained in this work could provide a deep understanding of GdTaO4 material, which also useful for the further investigation on GdTaO4 material.

Combined analyses of costs, market value and eco-costs in circular business models : eco-efficient value creation in remanufacturing

NARCIS (Netherlands)

Vogtländer, J.G.; Scheepens, A.E.; Bocken, N.M.P.; Peck, D.P.

2017-01-01

Eco-efficient Value Creation is a method to analyse innovative product and service design together with circular business strategies. The method is based on combined analyses of the costs, market value (perceived customer value) and eco-costs. This provides a prevention-based single indicator for

Single-hit mechanism of tumour cell killing by radiation.

Science.gov (United States)

Chapman, J D

2003-02-01

To review the relative importance of the single-hit mechanism of radiation killing for tumour response to 1.8-2.0 Gy day(-1) fractions and to low dose-rate brachytherapy. Tumour cell killing by ionizing radiation is well described by the linear-quadratic equation that contains two independent components distinguished by dose kinetics. Analyses of tumour cell survival curves that contain six or more dose points usually provide good estimates of the alpha- and beta-inactivation coefficients. Superior estimates of tumour cell intrinsic radiosensitivity are obtained when synchronized populations are employed. The characteristics of single-hit inactivation of tumour cells are reviewed and compared with the characteristics of beta-inactivation. Potential molecular targets associated with single-hit inactivation are discussed along with strategies for potentiating cell killing by this mechanism. The single-hit mechanism of tumour cell killing shows no dependence on dose-rate and, consequently, no evidence of sublethal damage repair. It is uniquely potentiated by high linear-energy-transfer radiation, exhibits a smaller oxygen enhancement ratio and exhibits a larger indirect effect by hydroxyl radicals than the beta-mechanism. alpha-inactivation coefficients vary slightly throughout interphase but mitotic cells exhibit extremely high alpha-coefficients in the range of those observed for lymphocytes and some repair-deficient cells. Evidence is accumulating to suggest that chromatin in compacted form could be a radiation-hypersensitive target associated with single-hit radiation killing. Analyses of tumour cell survival curves demonstrate that it is the single-hit mechanism (alpha) that determines the majority of cell killing after doses of 2Gy and that this mechanism is highly variable between tumour cell lines. The characteristics of single-hit inactivation are qualitatively and quantitatively distinct from those of beta-inactivation. Compacted chromatin in tumour cells

Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms

Science.gov (United States)

Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to show the distribution of these 2 important incompatible cultivated pepper species. Estimated mean nucleotide...

THE BERTRAND MODEL OF THE SINGLE MARKET

Directory of Open Access Journals (Sweden)

Vadasan Ioana

2010-12-01

Full Text Available Starting with the signification of the rationality hypothesis when the agent’s contentment is directly affected by the other agents’ decisions, the theory of games defines solutions for solving different situations of conflict. The economic actors have different behaviours of the Single Market. Oligopoly strategic behaviours were analysed by the Bertrand model. The two types revealed in the work show that strategic interactions are sensitive to the companies’ features, products and markets. Regarding the situation when we have an oligopoly competition, the companies make interdependent decisions in the environment affected by risk and uncertainty of the Single Market. For this reason it is an opportunity to study the structure of oligopoly type of of the Single Market with the aid of non – cooperative games.

Cloning of Plasmodium falciparum by single-cell sorting.

Science.gov (United States)

Miao, Jun; Li, Xiaolian; Cui, Liwang

2010-10-01

Malaria parasite cloning is traditionally carried out mainly by using the limiting dilution method, which is laborious, imprecise, and unable to distinguish multiply-infected RBCs. In this study, we used a parasite engineered to express green fluorescent protein (GFP) to evaluate a single-cell sorting method for rapidly cloning Plasmodium falciparum. By dividing a two-dimensional scattergram from a cell sorter into 17 gates, we determined the parameters for isolating singly-infected erythrocytes and sorted them into individual cultures. Pre-gating of the engineered parasites for GFP allowed the isolation of almost 100% GFP-positive clones. Compared with the limiting dilution method, the number of parasite clones obtained by single-cell sorting was much higher. Molecular analyses showed that parasite isolates obtained by single-cell sorting were highly homogenous. This highly efficient single-cell sorting method should prove very useful for cloning both P. falciparum laboratory populations from genetic manipulation experiments and clinical samples. Copyright 2010 Elsevier Inc. All rights reserved.

Cloning of Plasmodium falciparum by single-cell sorting

Science.gov (United States)

Miao, Jun; Li, Xiaolian; Cui, Liwang

2010-01-01

Malaria parasite cloning is traditionally carried out mainly by using the limiting dilution method, which is laborious, imprecise, and unable to distinguish multiply-infected RBCs. In this study, we used a parasite engineered to express green fluorescent protein (GFP) to evaluate a single-cell sorting method for rapidly cloning Plasmodium falciparum. By dividing a two dimensional scattergram from a cell sorter into 17 gates, we determined the parameters for isolating singly-infected erythrocytes and sorted them into individual cultures. Pre-gating of the engineered parasites for GFP allowed the isolation of almost 100% GFP-positive clones. Compared with the limiting dilution method, the number of parasite clones obtained by single-cell sorting was much higher. Molecular analyses showed that parasite isolates obtained by single-cell sorting were highly homogenous. This highly efficient single-cell sorting method should prove very useful for cloning both P. falciparum laboratory populations from genetic manipulation experiments and clinical samples. PMID:20435038

Automatic settlement analysis of single-layer armour layers

NARCIS (Netherlands)

Hofland, B.; van gent, Marcel

2016-01-01

A method to quantify, analyse, and present the settlement of single-layer concrete armour layers of coastal structures is presented. The use of the image processing technique for settlement analysis is discussed based on various modelling
studies performed over the years. The accuracy of the

Scenario sensitivity analyses performed on the PRESTO-EPA LLW risk assessment models

International Nuclear Information System (INIS)

Bandrowski, M.S.

1988-01-01

The US Environmental Protection Agency (EPA) is currently developing standards for the land disposal of low-level radioactive waste. As part of the standard development, EPA has performed risk assessments using the PRESTO-EPA codes. A program of sensitivity analysis was conducted on the PRESTO-EPA codes, consisting of single parameter sensitivity analysis and scenario sensitivity analysis. The results of the single parameter sensitivity analysis were discussed at the 1987 DOE LLW Management Conference. Specific scenario sensitivity analyses have been completed and evaluated. Scenario assumptions that were analyzed include: site location, disposal method, form of waste, waste volume, analysis time horizon, critical radionuclides, use of buffer zones, and global health effects

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

Determinants for membrane association and permeabilization of the coxsackievirus 2B protein and the identification of the Golgi complex as the target organelle.

Science.gov (United States)

de Jong, Arjan S; Wessels, Els; Dijkman, Henri B P M; Galama, Jochem M D; Melchers, Willem J G; Willems, Peter H G M; van Kuppeveld, Frank J M

2003-01-10

The 2B protein of enterovirus is responsible for the alterations in the permeability of secretory membranes and the plasma membrane in infected cells. The structural requirements for the membrane association and the subcellular localization of this essential virus protein, however, have not been defined. Here, we provide evidence that the 2B protein is an integral membrane protein in vivo that is predominantly localized at the Golgi complex upon individual expression. Addition of organelle-specific targeting signals to the 2B protein revealed that the Golgi localization is an absolute prerequisite for the ability of the protein to modify plasma membrane permeability. Expression of deletion mutants and heterologous proteins containing specific domains of the 2B protein demonstrated that each of the two hydrophobic regions could mediate membrane binding individually. However, the presence of both hydrophobic regions was required for the correct membrane association, efficient Golgi targeting, and the membrane-permeabilizing activity of the 2B protein, suggesting that the two hydrophobic regions are cooperatively involved in the formation of a membrane-integral complex. The formation of membrane-integral pores by the 2B protein in the Golgi complex and the possible mechanism by which a Golgi-localized virus protein modifies plasma membrane permeability are discussed.

Acidocalcisomes as calcium- and polyphosphate-storage compartments during embryogenesis of the insect Rhodnius prolixus Stahl.

Directory of Open Access Journals (Sweden)

Isabela Ramos

Full Text Available BACKGROUND: The yolk of insect eggs is a cellular domain specialized in the storage of reserve components for embryo development. The reserve macromolecules are stored in different organelles and their interactions with the embryo cells are mostly unknown. Acidocalcisomes are lysosome-related organelles characterized by their acidic nature, high electron density and large content of polyphosphate bound to several cations. In this work, we report the presence of acidocalcisome-like organelles in eggs of the insect vector Rhodnius prolixus. METHODOLOGY/PRINCIPAL FINDINGS: Characterization of the elemental composition of electron-dense vesicles by electron probe X-ray microanalysis revealed a composition similar to that previously described for acidocalcisomes. Following subcellular fractionation experiments, fractions enriched in acidocalcisomes were obtained and characterized. Immunofluorescence showed that polyphosphate polymers and the vacuolar proton translocating pyrophosphatase (V-H(+-PPase, considered as a marker for acidocalcisomes are found in the same vesicles and that these organelles are mainly localized in the egg cortex. Polyphosphate quantification showed that acidocalcisomes contain a significant amount of polyphosphate detected at day-0 eggs. Elemental analyses of the egg fractions showed that 24.5±0.65% of the egg calcium are also stored in such organelles. During embryogenesis, incubation of acidocalcisomes with acridine orange showed that these organelles are acidified at day-3 (coinciding with the period of yolk mobilization and polyphosphate quantification showed that the levels of polyphosphate tend to decrease during early embryogenesis, being approximately 30% lower at day-3 compared to day-0 eggs. CONCLUSIONS: We found that acidocalcisomes are present in the eggs and are the main storage compartments of polyphosphate and calcium in the egg yolk. As such components have been shown to be involved in a series of dynamic

Impact of covariate models on the assessment of the air pollution-mortality association in a single- and multipollutant context.

Science.gov (United States)

Sacks, Jason D; Ito, Kazuhiko; Wilson, William E; Neas, Lucas M

2012-10-01

With the advent of multicity studies, uniform statistical approaches have been developed to examine air pollution-mortality associations across cities. To assess the sensitivity of the air pollution-mortality association to different model specifications in a single and multipollutant context, the authors applied various regression models developed in previous multicity time-series studies of air pollution and mortality to data from Philadelphia, Pennsylvania (May 1992-September 1995). Single-pollutant analyses used daily cardiovascular mortality, fine particulate matter (particles with an aerodynamic diameter ≤2.5 µm; PM(2.5)), speciated PM(2.5), and gaseous pollutant data, while multipollutant analyses used source factors identified through principal component analysis. In single-pollutant analyses, risk estimates were relatively consistent across models for most PM(2.5) components and gaseous pollutants. However, risk estimates were inconsistent for ozone in all-year and warm-season analyses. Principal component analysis yielded factors with species associated with traffic, crustal material, residual oil, and coal. Risk estimates for these factors exhibited less sensitivity to alternative regression models compared with single-pollutant models. Factors associated with traffic and crustal material showed consistently positive associations in the warm season, while the coal combustion factor showed consistently positive associations in the cold season. Overall, mortality risk estimates examined using a source-oriented approach yielded more stable and precise risk estimates, compared with single-pollutant analyses.

IDEA: Interactive Display for Evolutionary Analyses

Directory of Open Access Journals (Sweden)

Carlton Jane M

2008-12-01

Full Text Available Abstract Background The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency. Results We have developed IDEA (Interactive Display for Evolutionary Analyses, an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly. Conclusion IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

Synthesis, Hirshfeld surface analyses and magnetism of a 1D Mn(II ...

African Journals Online (AJOL)

A new Mn-based complex of {[Mn(L)2(mi)]·H2O}n (1) (HL = p-hydroxy phenylacetic acid; mi = 1,1'-(1,4-butanediyl)bis(imidazole)), has been synthesized and structurally characterized. Single-crystal X-ray analyses reveal that compound 1 has a dinuclear Mn(II) unit linking by four carboxylate groups. The bridging N-donor ...

Determination of trace elements in BCR single cell protein via destructive neutron activation analyses

International Nuclear Information System (INIS)

Tjioe, P.S.; Goeij, J.J.M. de; Nooijen, J.L.; Kroon, J.J.

1978-10-01

The amount of some trace elements in single cell protein (SCP), a product of BP Research Centre at Sunbury-at-Thames, England, was determined by neutron activation analysis. The SCP-samples were irradiated in the reactor of the Interuniversity Reactor Institute at Delft in a neutron flux of 1.0x10 13 n/cm 2 s for 12 hours. Samples of Bowen's Kale were used as reference material. After a decay of two or three days the samples were chemically destroyed, and the trace elements were separated. The quantity of the following elements was determined by measuring the γ-activity by means of a scintillation counter: antimony, cadmium, mercury, arsenic and selenium. The amounts of these elements in the SCP and in the reference material were tabled

Quantitative high-resolution genomic analysis of single cancer cells.

Science.gov (United States)

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns.

Science.gov (United States)

Shepherd, Lara D; Holland, Barbara R; Perrie, Leon R

2008-07-01

A previous study of the relationships amongst three subgroups of the Austral Asplenium ferns found conflicting signal between the two chloroplast loci investigated. Because organelle genomes like those of chloroplasts and mitochondria are thought to be non-recombining, with a single evolutionary history, we sequenced four additional chloroplast loci with the expectation that this would resolve these relationships. Instead, the conflict was only magnified. Although tree-building analyses favoured one of the three possible trees, one of the alternative trees actually had one more supporting site (six versus five) and received greater support in spectral and neighbor-net analyses. Simulations suggested that chance alone was unlikely to produce strong support for two of the possible trees and none for the third. Likelihood permutation tests indicated that the concatenated chloroplast sequence data appeared to have experienced recombination. However, recombination between the chloroplast genomes of different species would be highly atypical, and corollary supporting observations, like chloroplast heteroplasmy, are lacking. Wider taxon sampling clarified the composition of the Austral group, but the conflicting signal meant analyses (e.g., morphological evolution, biogeographic) conditional on a well-supported phylogeny could not be performed.

Dynamic contrast-enhanced MR imaging of the rectum: Correlations between single-section and whole-tumor histogram analyses.

Science.gov (United States)

Choi, M H; Oh, S N; Park, G E; Yeo, D-M; Jung, S E

2018-05-10

To evaluate the interobserver and intermethod correlations of histogram metrics of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) parameters acquired by multiple readers using the single-section and whole-tumor volume methods. Four DCE parameters (K trans , K ep , V e , V p ) were evaluated in 45 patients (31 men and 14 women; mean age, 61±11 years [range, 29-83 years]) with locally advanced rectal cancer using pre-chemoradiotherapy (CRT) MRI. Ten histogram metrics were extracted using two methods of lesion selection performed by three radiologists: the whole-tumor volume method for the whole tumor on axial section-by-section images and the single-section method for the entire area of the tumor on one axial image. The interobserver and intermethod correlations were evaluated using the intraclass correlation coefficients (ICCs). The ICCs showed excellent interobserver and intermethod correlations in most of histogram metrics of the DCE parameters. The ICCs among the three readers were > 0.7 (Phistogram metrics, except for the minimum and maximum. The intermethod correlations for most of the histogram metrics were excellent for each radiologist, regardless of the differences in the radiologists' experience. The interobserver and intermethod correlations for most of the histogram metrics of the DCE parameters are excellent in rectal cancer. Therefore, the single-section method may be a potential alternative to the whole-tumor volume method using pre-CRT MRI, despite the fact that the high agreement between the two methods cannot be extrapolated to post-CRT MRI. Copyright © 2018 Société française de radiologie. Published by Elsevier Masson SAS. All rights reserved.

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.

Doping control analyses in horseracing: a clinician's guide.

Science.gov (United States)

Wong, Jenny K Y; Wan, Terence S M

2014-04-01

Doping(1) in sports is highly detrimental, not only to the athletes involved but to the sport itself as well as to the confidence of the spectators and other participants. To protect the integrity of any sport, there must be in place an effective doping control program. In human sports, a 'top-down' and generally unified approach is taken where the rules and regulations against doping for the majority of elite sport events held in any country are governed by the World Anti-Doping Agency (WADA). However, in horseracing, there is no single organisation regulating this form of equestrian sport; instead, the rules and regulations are provided by individual racing authorities and so huge variations exist in the doping control programs currently in force around the world. This review summarises the current status of doping control analyses in horseracing, from sample collection, to the analyses of the samples, and to the need for harmonisation as well as exploring some of the difficulties currently faced by racing authorities, racing chemists and regulatory veterinarians worldwide. Copyright © 2014 Elsevier Ltd. All rights reserved.

Indian Point 2 steam generator tube rupture analyses

International Nuclear Information System (INIS)

Dayan, A.

1985-01-01

Analyses were conducted with RETRAN-02 to study consequences of steam generator tube rupture (SGTR) events. The Indian Point, Unit 2, power plant (IP2, PWR) was modeled as a two asymmetric loops, consisting of 27 volumes and 37 junctions. The break section was modeled once, conservatively, as a 150% flow area opening at the wall of the steam generator cold leg plenum, and once as a 200% double-ended tube break. Results revealed 60% overprediction of breakflow rates by the traditional conservative model. Two SGTR transients were studied, one with low-pressure reactor trip and one with an earlier reactor trip via over temperature ΔT. The former is more typical to a plant with low reactor average temperature such as IP2. Transient analyses for a single tube break event over 500 seconds indicated continued primary subcooling and no need for steam line pressure relief. In addition, SGTR transients with reactor trip while the pressurizer still contains water were found to favorably reduce depressurization rates. Comparison of the conservative results with independent LOFTRAN predictions showed good agreement

Metabolic Energy Generation In Hydrogenosomes Of The Anaerobic Fungus Neocallimastix - Evidence For A Functional-relationship With Mitochondria

NARCIS (Netherlands)

Marvin-Sikkema, F. D.; Driessen, A. J. M.; Gottschal, J. C.; Prins, R. A.

Anaerobic eukaryotes are often devoid of mitochondria but contain special organelles separated from the cytosol by a single (in fungi) or a double (in protozoa) membrane. Hydrogenosomes from the anaerobic fungus Neocallimastix sp. L2 are thought to catalyse the enzymic steps in the ATP-yielding

Equitable Prices of Single-Source Drugs in Thailand.

Science.gov (United States)

Ngorsuraches, Surachat; Chaiyakan, Kanokkan

2015-08-01

In Thailand, total drug expenditure has grown rapidly. Recently, the Thai government has addressed the issue of drug pricing, but the prices of single-source drugs remain a major challenge. To examine equitable prices of single-source drugs in Thailand. A total of 98 single-source and high-expenditure drugs were examined. Unit prices from the Drug and Medical Supplies Information Center (DMSIC) and National Average Drug Acquisition Cost (NADAC) were used to represent drug prices at the provider level in Thailand and the U.S., respectively. Data for measuring drug affordability, e.g., dose and poverty line, were obtained from Micromedex online and the National Statistical Office (NSO). The U.S. drug prices were adjusted by the Human Development Index (HDI) to be equitable prices for Thailand. Purchasing Power Parity (PPP) was used to convert US currency into Thai baht. All prices in this study were based on the year 2012. Catastrophic, Impoverishment, and WHO/Health Action International (HAI) approaches were used to determine Thai citizens' ability to afford the study drugs. Finally, uncertainty analyses were conducted. From all study drugs, 55 single-source drugs were priced higher than their equitable prices, ranging from 0.38 to 422.36% higher. Among these, 28 items were antineoplastic drugs. The prices of drugs outside the National List of Essential Medicines (NLEM), as well as the country's newer drugs, tended to be higher than their calculated equitable prices. The majority of drugs in Thailand priced higher than equitable prices were unaffordable for most Thai citizens. The uncertainty analyses revealed that almost all results were relatively robust. Most single-source drug prices in Thailand were higher than their equitable prices, and were likely to be unaffordable to Thai citizens.

Group-Level EEG-Processing Pipeline for Flexible Single Trial-Based Analyses Including Linear Mixed Models.

Science.gov (United States)

Frömer, Romy; Maier, Martin; Abdel Rahman, Rasha

2018-01-01

Here we present an application of an EEG processing pipeline customizing EEGLAB and FieldTrip functions, specifically optimized to flexibly analyze EEG data based on single trial information. The key component of our approach is to create a comprehensive 3-D EEG data structure including all trials and all participants maintaining the original order of recording. This allows straightforward access to subsets of the data based on any information available in a behavioral data structure matched with the EEG data (experimental conditions, but also performance indicators, such accuracy or RTs of single trials). In the present study we exploit this structure to compute linear mixed models (LMMs, using lmer in R) including random intercepts and slopes for items. This information can easily be read out from the matched behavioral data, whereas it might not be accessible in traditional ERP approaches without substantial effort. We further provide easily adaptable scripts for performing cluster-based permutation tests (as implemented in FieldTrip), as a more robust alternative to traditional omnibus ANOVAs. Our approach is particularly advantageous for data with parametric within-subject covariates (e.g., performance) and/or multiple complex stimuli (such as words, faces or objects) that vary in features affecting cognitive processes and ERPs (such as word frequency, salience or familiarity), which are sometimes hard to control experimentally or might themselves constitute variables of interest. The present dataset was recorded from 40 participants who performed a visual search task on previously unfamiliar objects, presented either visually intact or blurred. MATLAB as well as R scripts are provided that can be adapted to different datasets.

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.

Static internal pressure capacity of Hanford Single-Shell Waste Tanks

Energy Technology Data Exchange (ETDEWEB)

Julyk, L.J.

1994-07-19

Underground single-shell waste storage tanks located at the Hanford Site in Richland, Washington, generate gaseous mixtures that could be ignited, challenging the structural integrity of the tanks. The structural capacity of the single-shell tanks to internal pressure is estimated through nonlinear finite-element structural analyses of the reinforced concrete tank. To determine their internal pressure capacity, designs for both the million-gallon and the half-million-gallon tank are evaluated on the basis of gross structural instability.

Static internal pressure capacity of Hanford Single-Shell Waste Tanks

International Nuclear Information System (INIS)

Julyk, L.J.

1994-01-01

Underground single-shell waste storage tanks located at the Hanford Site in Richland, Washington, generate gaseous mixtures that could be ignited, challenging the structural integrity of the tanks. The structural capacity of the single-shell tanks to internal pressure is estimated through nonlinear finite-element structural analyses of the reinforced concrete tank. To determine their internal pressure capacity, designs for both the million-gallon and the half-million-gallon tank are evaluated on the basis of gross structural instability

Unconscious analyses of visual scenes based on feature conjunctions.

Science.gov (United States)

Tachibana, Ryosuke; Noguchi, Yasuki

2015-06-01

To efficiently process a cluttered scene, the visual system analyzes statistical properties or regularities of visual elements embedded in the scene. It is controversial, however, whether those scene analyses could also work for stimuli unconsciously perceived. Here we show that our brain performs the unconscious scene analyses not only using a single featural cue (e.g., orientation) but also based on conjunctions of multiple visual features (e.g., combinations of color and orientation information). Subjects foveally viewed a stimulus array (duration: 50 ms) where 4 types of bars (red-horizontal, red-vertical, green-horizontal, and green-vertical) were intermixed. Although a conscious perception of those bars was inhibited by a subsequent mask stimulus, the brain correctly analyzed the information about color, orientation, and color-orientation conjunctions of those invisible bars. The information of those features was then used for the unconscious configuration analysis (statistical processing) of the central bars, which induced a perceptual bias and illusory feature binding in visible stimuli at peripheral locations. While statistical analyses and feature binding are normally 2 key functions of the visual system to construct coherent percepts of visual scenes, our results show that a high-level analysis combining those 2 functions is correctly performed by unconscious computations in the brain. (c) 2015 APA, all rights reserved).

Total Internal Reflection Fluorescence Microscopy Imaging-Guided Confocal Single-Molecule Fluorescence Spectroscopy

OpenAIRE

Zheng, Desheng; Kaldaras, Leonora; Lu, H. Peter

2013-01-01

We have developed an integrated spectroscopy system combining total internal reflection fluorescence microscopy imaging with confocal single-molecule fluorescence spectroscopy for two-dimensional interfaces. This spectroscopy approach is capable of both multiple molecules simultaneously sampling and in situ confocal fluorescence dynamics analyses of individual molecules of interest. We have demonstrated the calibration with fluorescent microspheres, and carried out single-molecule spectroscop...

Candidate gene association analyses for ketosis resistance in Holsteins.

Science.gov (United States)

Kroezen, V; Schenkel, F S; Miglior, F; Baes, C F; Squires, E J

2018-06-01

High-yielding dairy cattle are susceptible to ketosis, a metabolic disease that negatively affects the health, fertility, and milk production of the cow. Interest in breeding for more robust dairy cattle with improved resistance to disease is global; however, genetic evaluations for ketosis would benefit from the additional information provided by genetic markers. Candidate genes that are proposed to have a biological role in the pathogenesis of ketosis were investigated in silico and a custom panel of 998 putative single nucleotide polymorphism (SNP) markers was developed. The objective of this study was to test the associations of these new markers with deregressed estimated breeding values (EBV) for ketosis. A sample of 653 Canadian Holstein cows that had been previously genotyped with a medium-density SNP chip were regenotyped with the custom panel. The EBV for ketosis in first and later lactations were obtained for each animal and deregressed for use as pseudo-phenotypes for association analyses. Results of the mixed inheritance model for single SNP association analyses suggested 15 markers in 6 unique candidate genes were associated with the studied trait. Genes encoding proteins involved in metabolic processes, including the synthesis and degradation of fatty acids and ketone bodies, gluconeogenesis, lipid mobilization, and the citric acid cycle, were identified to contain SNP associated with ketosis resistance. This work confirmed the presence of previously described quantitative trait loci for dairy cattle, suggested novel markers for ketosis-resistance, and provided insight into the underlying biology of this disease. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Expanding Single Particle Mass Spectrometer Analyses for the Identification of Microbe Signatures in Sea Spray Aerosol.

Science.gov (United States)

Sultana, Camille M; Al-Mashat, Hashim; Prather, Kimberly A

2017-10-03

Ocean-derived microbes in sea spray aersosol (SSA) have the potential to influence climate and weather by acting as ice nucleating particles in clouds. Single particle mass spectrometers (SPMSs), which generate in situ single particle composition data, are excellent tools for characterizing aerosols under changing environmental conditions as they can provide high temporal resolution and require no sample preparation. While SPMSs have proven capable of detecting microbes, these instruments have never been utilized to definitively identify aerosolized microbes in ambient sea spray aersosol. In this study, an aerosol time-of-flight mass spectrometer was used to analyze laboratory generated SSA produced from natural seawater in a marine aerosol reference tank. We present the first description of a population of biological SSA mass spectra (BioSS), which closely match the ion signatures observed in previous terrestrial microbe studies. The fraction of BioSS dramatically increased in the largest supermicron particles, consistent with field and laboratory measurements of microbes ejected by bubble bursting, further supporting the assignment of BioSS mass spectra as microbes. Finally, as supported by analysis of inorganic ion signals, we propose that dry BioSS particles have heterogeneous structures, with microbes adhered to sodium chloride nodules surrounded by magnesium-enriched coatings. Consistent with this structure, chlorine-containing ion markers were ubiquitous in BioSS spectra and identified as possible tracers for distinguishing recently aerosolized marine from terrestrial microbes.

Quantitative high-resolution genomic analysis of single cancer cells.

Directory of Open Access Journals (Sweden)

Juliane Hannemann

Full Text Available During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

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.

Oxidative metabolism of 5-o-caffeoylquinic acid (chlorogenic acid), a bioactive natural product, by metalloporphyrin and rat liver mitochondria.

Science.gov (United States)

dos Santos, Michel D; Martins, Patrícia R; dos Santos, Pierre A; Bortocan, Renato; Iamamoto, Y; Lopes, Norberto P

2005-09-01

Synthetic metalloporphyrins, in the presence of monooxygen donors, are known to mimic the various reactions of cytochrome P450 enzymes systems in the oxidation and oxygenation of various drugs and biologically active compounds. This paper reports an HPLC-MS-MS investigation of chlorogenic acid (CGA) oxidation by iodosylbenzene using iron(III) tetraphenylporphyrin chloride as catalyst. The oxidation products have been detected by sequential MS analyses. In addition, CGA was submitted to an in vitro metabolism assay employing isolated rat liver mitochondria. The single oxidized product obtained from mitochondrial metabolism corresponds to the major product formed by the metalloporphyrin-catalyzed reaction. These results indicate that biomimetic oxidation reactions, in addition to in vitro metabolism assays employing isolated organs/organelles, could replace some in vivo metabolism studies, thus minimizing the problems related to the use of a large number of living animals in experimental research.

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.

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

Pricing and ordering policies for price-dependent demand in a supply chain of a single retailer and a single manufacturer

Science.gov (United States)

Kim, Jungkyu; Hong, Yushin; Kim, Taebok

2011-01-01

This article discusses joint pricing and ordering policies for price-dependent demand in a supply chain consisting of a single retailer and a single manufacturer. The retailer places orders for products according to an EOQ policy and the manufacturer produces them on a lot-for-lot basis. Four mechanisms with differing levels of coordination are presented. Mathematical models are formulated and solution procedures are developed to determine the optimal retail prices and order quantities. Through extensive numerical experiments, we analyse and compare the behaviours and characteristics of the proposed mechanisms, and find that enhancing the level of coordination has important benefits for the supply chain.

K-West and K-East basin thermal analyses for dry conditions

International Nuclear Information System (INIS)

Beaver, T.R.; Cramer, E.R.; Hinman, C.A.

1994-01-01

Detailed 3 dimensional thermal analyses of the 100K East and 100 K West basins were conducted to determine the peak fuel temperature for intact fuel in the event of a complete loss of water from the basins. Thermal models for the building, an array of fuel encapsulation canisters on the basin floor, and the fuel within a single canister are described along with conservative predictions for the maximum expected temperatures for the loss of water event

Enzymes involved in organellar DNA replication in photosynthetic eukaryotes.

Science.gov (United States)

Moriyama, Takashi; Sato, Naoki

2014-01-01

Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.

A single amino acid substitution in the core protein of West Nile virus increases resistance to acidotropic compounds.

Directory of Open Access Journals (Sweden)

Miguel A Martín-Acebes

Full Text Available West Nile virus (WNV is a worldwide distributed mosquito-borne flavivirus that naturally cycles between birds and mosquitoes, although it can infect multiple vertebrate hosts including horses and humans. This virus is responsible for recurrent epidemics of febrile illness and encephalitis, and has recently become a global concern. WNV requires to transit through intracellular acidic compartments at two different steps to complete its infectious cycle. These include fusion between the viral envelope and the membrane of endosomes during viral entry, and virus maturation in the trans-Golgi network. In this study, we followed a genetic approach to study the connections between viral components and acidic pH. A WNV mutant with increased resistance to the acidotropic compound NH4Cl, which blocks organelle acidification and inhibits WNV infection, was selected. Nucleotide sequencing revealed that this mutant displayed a single amino acid substitution (Lys 3 to Glu on the highly basic internal capsid or core (C protein. The functional role of this replacement was confirmed by its introduction into a WNV infectious clone. This single amino acid substitution also increased resistance to other acidification inhibitor (concanamycin A and induced a reduction of the neurovirulence in mice. Interestingly, a naturally occurring accompanying mutation found on prM protein abolished the resistant phenotype, supporting the idea of a genetic crosstalk between the internal C protein and the external glycoproteins of the virion. The findings here reported unveil a non-previously assessed connection between the C viral protein and the acidic pH necessary for entry and proper exit of flaviviruses.

A single amino acid substitution in the core protein of West Nile virus increases resistance to acidotropic compounds.

Science.gov (United States)

Martín-Acebes, Miguel A; Blázquez, Ana-Belén; de Oya, Nereida Jiménez; Escribano-Romero, Estela; Shi, Pei-Yong; Saiz, Juan-Carlos

2013-01-01

West Nile virus (WNV) is a worldwide distributed mosquito-borne flavivirus that naturally cycles between birds and mosquitoes, although it can infect multiple vertebrate hosts including horses and humans. This virus is responsible for recurrent epidemics of febrile illness and encephalitis, and has recently become a global concern. WNV requires to transit through intracellular acidic compartments at two different steps to complete its infectious cycle. These include fusion between the viral envelope and the membrane of endosomes during viral entry, and virus maturation in the trans-Golgi network. In this study, we followed a genetic approach to study the connections between viral components and acidic pH. A WNV mutant with increased resistance to the acidotropic compound NH4Cl, which blocks organelle acidification and inhibits WNV infection, was selected. Nucleotide sequencing revealed that this mutant displayed a single amino acid substitution (Lys 3 to Glu) on the highly basic internal capsid or core (C) protein. The functional role of this replacement was confirmed by its introduction into a WNV infectious clone. This single amino acid substitution also increased resistance to other acidification inhibitor (concanamycin A) and induced a reduction of the neurovirulence in mice. Interestingly, a naturally occurring accompanying mutation found on prM protein abolished the resistant phenotype, supporting the idea of a genetic crosstalk between the internal C protein and the external glycoproteins of the virion. The findings here reported unveil a non-previously assessed connection between the C viral protein and the acidic pH necessary for entry and proper exit of flaviviruses.

Unravelling biology and shifting paradigms in cancer with single-cell sequencing.

Science.gov (United States)

Baslan, Timour; Hicks, James

2017-08-24

The fundamental operative unit of a cancer is the genetically and epigenetically innovative single cell. Whether proliferating or quiescent, in the primary tumour mass or disseminated elsewhere, single cells govern the parameters that dictate all facets of the biology of cancer. Thus, single-cell analyses provide the ultimate level of resolution in our quest for a fundamental understanding of this disease. Historically, this quest has been hampered by technological shortcomings. In this Opinion article, we argue that the rapidly evolving field of single-cell sequencing has unshackled the cancer research community of these shortcomings. From furthering an elemental understanding of intra-tumoural genetic heterogeneity and cancer genome evolution to illuminating the governing principles of disease relapse and metastasis, we posit that single-cell sequencing promises to unravel the biology of all facets of this disease.

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

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....

Trial sequential analysis reveals insufficient information size and potentially false positive results in many meta-analyses

DEFF Research Database (Denmark)

Brok, J.; Thorlund, K.; Gluud, C.

2008-01-01

in 80% (insufficient information size). TSA(15%) and TSA(LBHIS) found that 95% and 91% had absence of evidence. The remaining nonsignificant meta-analyses had evidence of lack of effect. CONCLUSION: TSA reveals insufficient information size and potentially false positive results in many meta......OBJECTIVES: To evaluate meta-analyses with trial sequential analysis (TSA). TSA adjusts for random error risk and provides the required number of participants (information size) in a meta-analysis. Meta-analyses not reaching information size are analyzed with trial sequential monitoring boundaries...... analogous to interim monitoring boundaries in a single trial. STUDY DESIGN AND SETTING: We applied TSA on meta-analyses performed in Cochrane Neonatal reviews. We calculated information sizes and monitoring boundaries with three different anticipated intervention effects of 30% relative risk reduction (TSA...

CORSEN, a new software dedicated to microscope-based 3D distance measurements: mRNA-mitochondria distance, from single-cell to population analyses.

Science.gov (United States)

Jourdren, Laurent; Delaveau, Thierry; Marquenet, Emelie; Jacq, Claude; Garcia, Mathilde

2010-07-01

Recent improvements in microscopy technology allow detection of single molecules of RNA, but tools for large-scale automatic analyses of particle distributions are lacking. An increasing number of imaging studies emphasize the importance of mRNA localization in the definition of cell territory or the biogenesis of cell compartments. CORSEN is a new tool dedicated to three-dimensional (3D) distance measurements from imaging experiments especially developed to access the minimal distance between RNA molecules and cellular compartment markers. CORSEN includes a 3D segmentation algorithm allowing the extraction and the characterization of the cellular objects to be processed--surface determination, aggregate decomposition--for minimal distance calculations. CORSEN's main contribution lies in exploratory statistical analysis, cell population characterization, and high-throughput assays that are made possible by the implementation of a batch process analysis. We highlighted CORSEN's utility for the study of relative positions of mRNA molecules and mitochondria: CORSEN clearly discriminates mRNA localized to the vicinity of mitochondria from those that are translated on free cytoplasmic polysomes. Moreover, it quantifies the cell-to-cell variations of mRNA localization and emphasizes the necessity for statistical approaches. This method can be extended to assess the evolution of the distance between specific mRNAs and other cellular structures in different cellular contexts. CORSEN was designed for the biologist community with the concern to provide an easy-to-use and highly flexible tool that can be applied for diverse distance quantification issues.

Three-Input Single-Output Voltage-Mode Multifunction Filter with Electronic Controllability Based on Single Commercially Available IC

Directory of Open Access Journals (Sweden)

Supachai Klungtong

2017-01-01

Full Text Available This paper presents a second-order voltage-mode filter with three inputs and single-output voltage using single commercially available IC, one resistor, and two capacitors. The used commercially available IC, called LT1228, is manufactured by Linear Technology Corporation. The proposed filter is based on parallel RLC circuit. The filter provides five output filter responses, namely, band-pass (BP, band-reject (BR, low-pass (LP, high-pass (HP, and all-pass (AP functions. The selection of each filter response can be done without the requirement of active and passive component matching condition. Furthermore, the natural frequency and quality factor are electronically controlled. Besides, the nonideal case is also investigated. The output voltage node exhibits low impedance. The experimental results can validate the theoretical analyses.

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 σ_Λ, 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

General-purpose chemical analyzer for on-line analyses of radioactive solutions

International Nuclear Information System (INIS)

Spencer, W.A.; Kronberg, J.W.

1983-01-01

An automated analyzer is being developed to perform analytical measurements on radioactive solutions on-line in a hostile environment. This General Purpose Chemical Analyzer (GPCA) samples a process stream, adds reagents, measures solution absorbances or electrode potentials, and automatically calculates the results. The use of modular components, under microprocessor control, permits a single analyzer design to carry out many types of analyses. This paper discusses the more important design criteria for the GPCA, and describes the equipment being tested in a prototype unit

Elevated CO2 can modify the response to a water status gradient in a steppe grass: from cell organelles to photosynthetic capacity to plant growth.

Science.gov (United States)

Jiang, Yanling; Xu, Zhenzhu; Zhou, Guangsheng; Liu, Tao

2016-07-12

The atmospheric CO2 concentration is rising continuously, and abnormal precipitation may occur more frequently in the future. Although the effects of elevated CO2 and drought on plants have been well reported individually, little is known about their interaction, particularly over a water status gradient. Here, we aimed to characterize the effects of elevated CO2 and a water status gradient on the growth, photosynthetic capacity, and mesophyll cell ultrastructure of a dominant grass from a degraded grassland. Elevated CO2 stimulated plant biomass to a greater extent under moderate changes in water status than under either extreme drought or over-watering conditions. Photosynthetic capacity and stomatal conductance were also enhanced by elevated CO2 under moderate drought, but inhibited with over-watering. Severe drought distorted mesophyll cell organelles, but CO2 enrichment partly alleviated this effect. Intrinsic water use efficiency (WUEi) and total biomass water use efficiency (WUEt) were increased by elevated CO2, regardless of water status. Plant structural traits were also found to be tightly associated with photosynthetic potentials. The results indicated that CO2 enrichment alleviated severe and moderate drought stress, and highlighted that CO2 fertilization's dependency on water status should be considered when projecting key species' responses to climate change in dry ecosystems.

The sequence of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus genome

NARCIS (Netherlands)

Chen, X.; IJkel, W.F.J.; Tarchini, R.; Sun, X.; Sandbrink, H.; Wang, H.; Peters, S.; Zuidema, D.; Klein Lankhorst, R.; Vlak, J.M.; Hu, Z.

2001-01-01

The nucleotide sequence of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HaSNPV) DNA genome was determined and analysed. The circular genome encompasses 131 403 bp, has a G C content of 39.1 molnd contains five homologous regions with a unique pattern of repeats.

Laparoendoscopic single site surgery in urology: A single centre experience

Directory of Open Access Journals (Sweden)

Arvind P Ganpule

2012-01-01

Full Text Available Objective : To analyze our experience of 87 cases with single port surgery, which is also known as laparoendoscopic single site surgery (LESS. Materials and Methods: Case records of all LESS procedures performed between December 2007 and June 2010 were analysed. The procedures performed were donor nephrectomy (n=45, simple nephrectomy (n=27, radical nephrectomy (n=5, pyeloplasty (n=9, and ureteroneocystostomy (n=1. Parameters analysed were operating room (OR time, estimated blood loss (EBL, visual analogue score (VAS, and complications in all patients undergoing LESS procedure and additionally, warm ischaemia time (WIT and graft outcome in patients undergoing LESS donor nephrectomy. In reconstructive procedures, the functional assessment was performed with a diuretic renogram at 6 months. Results: In LESS donor nephrectomy, the mean WIT was 6.9 ± 1.9 min. Mean serum creatinine in recipients at 1 month was 0.96 ± 0.21 mg%. We encountered one instance each of renal artery injury, renal vein injury, large bowel injury, minor cortical laceration at the upper pole and two instances of diaphragmatic injury. In LESS simple nephrectomy, the average OR time was 148.7 ± 52.2 min and hospital stay was 3.7 ± 1.2 days. There was one instance of large bowel injury during specimen retrieval. In LESS radical nephrectomy, the average OR time was 202.5 ± 35.7 min and average hospital stay was 4.2 ± 1.3 days. 6 patients of LESS pyeloplasty completed follow up with a diuretic renogram showing a good drainage. LESS ureteroneocystostomy could also be performed successfully without any complications. Conclusion: LESS surgery can be accomplished safely in nephrectomy and reconstructive procedures such as pyeloplasty and ureteroneocystostomy with equivalent outcomes as standard laparoscopy and with added benefits of cosmesis and quicker convalescence. LESS donor nephrectomy is a technically feasible procedure; current status of procedure needs to be proved with

Barriers to guideline-compliant psoriasis care: analyses and concepts.

Science.gov (United States)

Eissing, L; Radtke, M A; Zander, N; Augustin, M

2016-04-01

Despite the availability of effective therapeutics and evidence-based treatment guidelines, a substantial proportion of patients with moderate-to-severe psoriasis does not receive appropriate care. This under-provision of health care may cause further worsening of health, remarkable limitations of the patient's quality of life, and indirect costs for the health care system. In order to provide guideline-compliant care for every psoriasis patient, it is important to identify barriers obstructing optimal care. Studies have identified various barriers on the physician's and on the patient's side; however, respective studies approached only single barriers, and not all of them in the context of psoriasis. Other publications that describe barriers systematically did not focus on psoriasis either. The objective of this literature review was to identify barriers and facilitators, based on studies analysing quality of care and single barriers, resulting in a comprehensive model of causal factors. Our analyses revealed three categories of barriers - patient-related, physician-related and external factors: On the patient side, we found non-adherence to therapies to be an important barrier, often in close association with psychiatric factors. Barriers on the physician's side predominantly are incomplete knowledge of the guidelines as well as the complexity of psoriasis comorbidity. In some countries, payment for patients with complex disease status is poor and inconsistent reimbursement regulations potentially interfere with optimal care. The current analysis indicates that most barriers are interdependent. Thus, measures approaching related barriers simultaneously are required. To improve care for psoriasis patients, further studies systematically addressing all potentially relevant barriers in conjoint are needed. © 2015 European Academy of Dermatology and Venereology.

Simulation and analysis of single-ribosome translation

International Nuclear Information System (INIS)

Tinoco, Ignacio Jr; Wen, Jin-Der

2009-01-01

In the cell, proteins are synthesized by ribosomes in a multi-step process called translation. The ribosome translocates along the messenger RNA to read the codons that encode the amino acid sequence of a protein. Elongation factors, including EF-G and EF-Tu, are used to catalyze the process. Recently, we have shown that translation can be followed at the single-molecule level using optical tweezers; this technique allows us to study the kinetics of translation by measuring the lifetime the ribosome spends at each codon. Here, we analyze the data from single-molecule experiments and fit the data with simple kinetic models. We also simulate the translation kinetics based on a multi-step mechanism from ensemble kinetic measurements. The mean lifetimes from the simulation were consistent with our experimental single-molecule measurements. We found that the calculated lifetime distributions were fit in general by equations with up to five rate-determining steps. Two rate-determining steps were only obtained at low concentrations of elongation factors. These analyses can be used to design new single-molecule experiments to better understand the kinetics and mechanism of translation

Isotachophoresis for fractionation and recovery of cytoplasmic RNA and nucleus from single cells.

Science.gov (United States)

Kuriyama, Kentaro; Shintaku, Hirofumi; Santiago, Juan G

2015-07-01

There is a substantial need for simultaneous analyses of RNA and DNA from individual single cells. Such analysis provides unique evidence of cell-to-cell differences and the correlation between gene expression and genomic mutation in highly heterogeneous cell populations. We present a novel microfluidic system that leverages isotachophoresis to fractionate and isolate cytoplasmic RNA and genomic DNA (gDNA) from single cells. The system uniquely enables independent, sequence-specific analyses of these critical markers. Our system uses a microfluidic chip with a simple geometry and four end-channel electrodes, and completes the entire process in RNA output reservoirs, each containing high quality and purity aliquots with no measurable cross-contamination of cytoplasmic RNA versus gDNA. We demonstrate our system with simultaneous, sequence-specific quantitation using off-chip RT-qPCR and qPCR for simultaneous cytoplasmic RNA and gDNA analyses, respectively. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single-molecule imaging and manipulation of biomolecular machines and systems.

Science.gov (United States)

Iino, Ryota; Iida, Tatsuya; Nakamura, Akihiko; Saita, Ei-Ichiro; You, Huijuan; Sako, Yasushi

2018-02-01

Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Single-Cell Memory Regulates a Neural Circuit for Sensory Behavior.

Science.gov (United States)

Kobayashi, Kyogo; Nakano, Shunji; Amano, Mutsuki; Tsuboi, Daisuke; Nishioka, Tomoki; Ikeda, Shingo; Yokoyama, Genta; Kaibuchi, Kozo; Mori, Ikue

2016-01-05

Unveiling the molecular and cellular mechanisms underlying memory has been a challenge for the past few decades. Although synaptic plasticity is proven to be essential for memory formation, the significance of "single-cell memory" still remains elusive. Here, we exploited a primary culture system for the analysis of C. elegans neurons and show that a single thermosensory neuron has an ability to form, retain, and reset a temperature memory. Genetic and proteomic analyses found that the expression of the single-cell memory exhibits inter-individual variability, which is controlled by the evolutionarily conserved CaMKI/IV and Raf pathway. The variable responses of a sensory neuron influenced the neural activity of downstream interneurons, suggesting that modulation of the sensory neurons ultimately determines the behavioral output in C. elegans. Our results provide proof of single-cell memory and suggest that the individual differences in neural responses at the single-cell level can confer individuality. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Single Top quark production cross section using ATLAS detector at the LHC

CERN Document Server

Estrada Pastor, Oscar; The ATLAS collaboration

2018-01-01

Measurements of single top-quark production in proton-proton collisions are presented based on the 8 TeV and 13 TeV ATLAS datasets. In the leading order process, a W boson is exchanged in the t-channel. The cross-section for the production of single top-quarks and single anti-top-quarks, their ratio, as well as differential cross-section measurements are also reported. These analyses include limits on anomalous contributions to the Wtb vertex and measurement of the top quark polarization. Measurements of the inclusive and differential cross-sections for the production of a single top quark in association with a W boson, the second largest single-top production mode, are also presented. Finally, evidence for s-channel single-top production in the 8 TeV ATLAS dataset is presented. All measurements are compared to state-of-the-art theoretical calculations.

Analysis on Single Point Vulnerabilities of Plant Control System

International Nuclear Information System (INIS)

Chi, Moon Goo; Lee, Eun Chan; Bae, Yeon Kyoung

2011-01-01

The Plant Control System (PCS) is a system that controls pumps, valves, dampers, etc. in nuclear power plants with an OPR-1000 design. When there is a failure or spurious actuation of the critical components in the PCS, it can result in unexpected plant trips or transients. From this viewpoint, single point vulnerabilities are evaluated in detail using failure mode effect analyses (FMEA) and fault tree analyses (FTA). This evaluation demonstrates that the PCS has many vulnerable components and the analysis results are provided for OPR-1000 plants for reliability improvements that can reduce their vulnerabilities

Analysis on Single Point Vulnerabilities of Plant Control System

Energy Technology Data Exchange (ETDEWEB)

Chi, Moon Goo; Lee, Eun Chan; Bae, Yeon Kyoung [Korea Hydro and Nuclear Power Co., Daejeon (Korea, Republic of)

2011-08-15

The Plant Control System (PCS) is a system that controls pumps, valves, dampers, etc. in nuclear power plants with an OPR-1000 design. When there is a failure or spurious actuation of the critical components in the PCS, it can result in unexpected plant trips or transients. From this viewpoint, single point vulnerabilities are evaluated in detail using failure mode effect analyses (FMEA) and fault tree analyses (FTA). This evaluation demonstrates that the PCS has many vulnerable components and the analysis results are provided for OPR-1000 plants for reliability improvements that can reduce their vulnerabilities.

Japanese standard method for safety evaluation using best estimate code based on uncertainty and scaling analyses with statistical approach

International Nuclear Information System (INIS)

Mizokami, Shinya; Hotta, Akitoshi; Kudo, Yoshiro; Yonehara, Tadashi; Watada, Masayuki; Sakaba, Hiroshi

2009-01-01

Current licensing practice in Japan consists of using conservative boundary and initial conditions(BIC), assumptions and analytical codes. The safety analyses for licensing purpose are inherently deterministic. Therefore, conservative BIC and assumptions, such as single failure, must be employed for the analyses. However, using conservative analytical codes are not considered essential. The standard committee of Atomic Energy Society of Japan(AESJ) has drawn up the standard for using best estimate codes for safety analyses in 2008 after three-years of discussions reflecting domestic and international recent findings. (author)

Investigating single molecule adhesion by atomic force spectroscopy.

Science.gov (United States)

Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

2015-02-27

Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

Septin-Containing Barriers Control the Differential Inheritance of Cytoplasmic Elements

Directory of Open Access Journals (Sweden)

Alan Michael Tartakoff

2013-01-01

Full Text Available Fusion of haploid cells of Saccharomyces cerevisiae generates zygotes. We observe that the zygote midzone includes a septin annulus and differentially affects redistribution of supramolecular complexes and organelles. Redistribution across the midzone of supramolecular complexes (polysomes and Sup35p-GFP [PSI+] is unexpectedly delayed relative to soluble proteins; however, in [psi-] × [PSI+] crosses, all buds eventually receive Sup35p-GFP [PSI+]. Encounter between parental mitochondria is further delayed until septins relocate to the bud site, where they are required for repolarization of the actin cytoskeleton. This delay allows rationalization of the longstanding observation that terminal zygotic buds preferentially inherit a single mitochondrial genotype. The rate of redistribution of complexes and organelles determines whether their inheritance will be uniform.

Lysosome Transport as a Function of Lysosome Diameter

Science.gov (United States)

Bandyopadhyay, Debjyoti; Cyphersmith, Austin; Zapata, Jairo A.; Kim, Y. Joseph; Payne, Christine K.

2014-01-01

Lysosomes are membrane-bound organelles responsible for the transport and degradation of intracellular and extracellular cargo. The intracellular motion of lysosomes is both diffusive and active, mediated by motor proteins moving lysosomes along microtubules. We sought to determine how lysosome diameter influences lysosome transport. We used osmotic swelling to double the diameter of lysosomes, creating a population of enlarged lysosomes. This allowed us to directly examine the intracellular transport of the same organelle as a function of diameter. Lysosome transport was measured using live cell fluorescence microscopy and single particle tracking. We find, as expected, the diffusive component of intracellular transport is decreased proportional to the increased lysosome diameter. Active transport of the enlarged lysosomes is not affected by the increased lysosome diameter. PMID:24497985

Kinematics of electroweak single top quark production

International Nuclear Information System (INIS)

Lueck, Jan; Karlsruhe U., EKP

2006-01-01

In this thesis, the t-channel matching procedure of two single-top signal Monte Carlo samples is optimized. The s- and matched t-channel samples, generated by MadEvent, are validated by comparing to ZTOP next-to-leading-order calculations. We find good agreement for all kinematic distributions we investigate, except for softer light quark jets due to gluon radiation. Since this has only minor impact on the s-channel, the corresponding MadEvent sample performs its task as expected. For the t-channel, we can conclude that the applied matching procedure leads to a MadEvent sample that successfully describes the kinematic distributions and rates of the 2nd-b quark. However, small differences remain. The discrepancy in the p T -ordered 2nd-leading light jets is mainly due to the absence of initial state gluon splitting and initial and final state gluon radiation matrix elements in the MadEvent sample production. The subsequent PYTHIA showering of the partons is apparently inappropriate for modeling those contributions and not intended for this purpose. The proper way would be to produce all relevant NLO matrix elements and match them as proposed in reference [15]. At present, an NLO-MC-generator for single-top is in preparation [41]. Probably it will be available for future iterations of single-top analyses and will redundantize further matching procedures. We estimate the systematic uncertainty on the single-top acceptance due to the Monte Carlo modeling and find an uncertainty of about 1% on the t-channel acceptance. We obtain a negligible uncertainty well below 1% on the s-channel acceptance. These acceptance uncertainties are very well acceptable for the single-top analyses that are currently under way. A sensitivity study of the simultaneous cross section measurement of the s- and t-channel single-top production modes is conducted. For this purpose, only statistical uncertainties are included. For a future integrated luminosity of 1 fb -1 , we expect to obtain an s

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

Directory of Open Access Journals (Sweden)

Tamar Hashimshony

2012-09-01

Full Text Available High-throughput sequencing has allowed for unprecedented detail in gene expression analyses, yet its efficient application to single cells is challenged by the small starting amounts of RNA. We have developed CEL-Seq, a method for overcoming this limitation by barcoding and pooling samples before linearly amplifying mRNA with the use of one round of in vitro transcription. We show that CEL-Seq gives more reproducible, linear, and sensitive results than a PCR-based amplification method. We demonstrate the power of this method by studying early C. elegans embryonic development at single-cell resolution. Differential distribution of transcripts between sister cells is seen as early as the two-cell stage embryo, and zygotic expression in the somatic cell lineages is enriched for transcription factors. The robust transcriptome quantifications enabled by CEL-Seq will be useful for transcriptomic analyses of complex tissues containing populations of diverse cell types.

Effects of single parenthood on educational aspiration and student disengagement in Korea

Directory of Open Access Journals (Sweden)

Hyunjoon Park

2008-05-01

Full Text Available The recent rapid increase in divorce, along with its distinctive cultural and welfare environments for single-parent families, makes Korea an interesting case for examining effects of single parenthood on children's education. Using data from Korean 9th and 12th graders, I compare the levels of educational aspiration and student disengagement between students with two parents and those with a single parent, distinguishing divorced single fathers, widowed single fathers, divorced single mothers, and widowed single mothers. Logistic regression analyses show that students with a divorced single parent, regardless of gender of the parent, are much less likely to aspire to four-year university education and more likely to be disengaged than their counterparts with two parents. The effects of widowhood disappear once control variables are held constant. Lower household income among single-parent families explains in part the poorer educational outcomes of their children. Parent-child interaction is another important mediating factor for the effect of single fatherhood but not for single motherhood. The relevance of the extended family system and distinctive features of post-divorce living arrangements in Korea is discussed to understand the effects of single parenthood.

Precise analysis of the metal package photomultiplier single photoelectron spectra

International Nuclear Information System (INIS)

Chirikov-Zorin, I.E.; Fedorko, I.; Sykora, I.; Tokar, S.; Menzione, A.

2000-01-01

A deconvolution method based on a sophisticated photomultiplier response function was used to analyse the compact metal package photomultiplier spectra taken in single photoelectron mode. The spectra taken by Hamamtsu R5600 and R5900 photomultipliers have been analysed. The detailed analysis shows that the method appropriately describes the process of charge multiplication in these photomultipliers in a wide range of working regimes and the deconvoluted parameters are established with about 1% accuracy. The method can be used for a detailed analysis of photomultiplier noise and for calibration purposes

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.

Fourier Transform Near Infrared Microspectroscopy, Infrared Chemical Imaging, High-Resolution Nuclear Magnetic Resonance and Fluorescence Microspectroscopy Detection of Single Cancer Cells and Single Viral Particles

CERN Document Server

Baianu,I C; Hofmann, N E; Korban, S S; Lozano, P; You, T

2004-01-01

Single Cancer Cells from Human tumors are being detected and imaged by Fourier Transform Infrared (FT-IR), Fourier Transform Near Infrared (FT-NIR)Hyperspectral Imaging and Fluorescence Correlation Microspectroscopy. The first FT-NIR chemical, microscopic images of biological systems approaching one micron resolution are here reported. Chemical images obtained by FT-NIR and FT-IR Microspectroscopy are also presented for oil in soybean seeds and somatic embryos under physiological conditions. FT-NIR spectra of oil and proteins were obtained for volumes as small as two cubic microns. Related, HR-NMR analyses of oil contents in somatic embryos as well as 99% accurate calibrations are also presented here with nanoliter precision. Such high-resolution, 400 MHz H-1 NMR analyses allowed the selection of mutagenized embryos with higher oil content (e.g. >~20%) compared to the average levels in non-mutagenized control embryos. Moreover, developmental changes in single soybean seeds and/or somatic embryos may be monito...

Single-case research design in pediatric psychology: considerations regarding data analysis.

Science.gov (United States)

Cohen, Lindsey L; Feinstein, Amanda; Masuda, Akihiko; Vowles, Kevin E

2014-03-01

Single-case research allows for an examination of behavior and can demonstrate the functional relation between intervention and outcome in pediatric psychology. This review highlights key assumptions, methodological and design considerations, and options for data analysis. Single-case methodology and guidelines are reviewed with an in-depth focus on visual and statistical analyses. Guidelines allow for the careful evaluation of design quality and visual analysis. A number of statistical techniques have been introduced to supplement visual analysis, but to date, there is no consensus on their recommended use in single-case research design. Single-case methodology is invaluable for advancing pediatric psychology science and practice, and guidelines have been introduced to enhance the consistency, validity, and reliability of these studies. Experts generally agree that visual inspection is the optimal method of analysis in single-case design; however, statistical approaches are becoming increasingly evaluated and used to augment data interpretation.

Ascorbate peroxidase-related (APx-R) is not a duplicable gene.

Science.gov (United States)

Dunand, Christophe; Mathé, Catherine; Lazzarotto, Fernanda; Margis, Rogério; Margis-Pinheiro, Marcia

2011-12-01

Phylogenetic, genomic and functional analyses have allowed the identification of a new class of putative heme peroxidases, so called APx-R (APx-Related). These new class, mainly present in the green lineage (including green algae and land plants), can also be detected in other unicellular chloroplastic organisms. Except for recent polyploid organisms, only single-copy of APx-R gene was detected in each genome, suggesting that the majority of the APx-R extra-copies were lost after chromosomal or segmental duplications. In a similar way, most APx-R co-expressed genes in Arabidopsis genome do not have conserved extra-copies after chromosomal duplications and are predicted to be localized in organelles, as are the APx-R. The member of this gene network can be considered as unique gene, well conserved through the evolution due to a strong negative selection pressure and a low evolution rate. © 2011 Landes Bioscience

Non-destructive XRF analyses of fine-grained basalts from Eiao, Marquesas Islands

International Nuclear Information System (INIS)

Charleux, M.; McAlister, A.; Mills, P.R.; Lundblad, S.P.

2014-01-01

The Marquesan island of Eiao was an important source of fine-grained basalt in Central East Polynesia, with examples being identified in archaeological assemblages throughout the region. However, compared to many other large-scale Polynesian basalt sources, little has been published about the physical extent and geochemical variability of tool-quality basalt on Eiao; prior to our study, only a single site with evidence of stone extraction had been identified and geochemical information was limited to less than two dozen samples. In this paper we report geochemical data for 225 additional basalt specimens collected on Eiao. Our analyses were conducted non-destructively using three EDXRF instruments: one lab-based unit and two portable analysers. The majority of our sample, identified here as Group 1, possesses geochemical and physical characteristics similar to those reported in previous studies. Group 1 samples were collected from various locations on Eiao suggesting that, rather than being limited to a single quarry site, fine-grained basalt was extracted from multiple sources throughout the island. In addition, we identified a second group (Group 2), which possesses a distinct geochemistry, a coarser grain and often an unusual reddish colour. Evidence from Eiao indicates that Group 2 stone was regularly utilised and our analysis of an adze collected on Hiva Oa Island suggests that this material was distributed at least as far as the southern Marquesas. (author)

Single-tube library preparation for degraded DNA

DEFF Research Database (Denmark)

Carøe, Christian; Gopalakrishnan, Shyam; Vinner, Lasse

2018-01-01

these obstacles and enable higher throughput are therefore of interest to researchers working with degraded DNA. 2.In this study, we compare four Illumina library preparation protocols, including two “single-tube” methods developed for this study with the explicit aim of improving data quality and reducing...... of chemically damaged and highly fragmented DNA molecules. In particular, the enzymatic reactions and DNA purification steps during library preparation can result in DNA template loss and sequencing biases, affecting downstream analyses. The development of library preparation methods that circumvent...... preparation time and expenses. The methods are tested on grey wolf (Canis lupus) museum specimens. 3.We found single-tube protocols increase library complexity, yield more reads that map uniquely to the reference genome, reduce processing time, and may decrease laboratory costs by 90%. 4.Given the advantages...

Multiple single-centered attractors

International Nuclear Information System (INIS)

Dominic, Pramod; Mandal, Taniya; Tripathy, Prasanta K.

2014-01-01

In this paper we study spherically symmetric single-centered attractors in N=2 supergravity in four dimensions. The attractor points are obtained by extremising the effective black hole potential in the moduli space. Both supersymmetric as well as non-supersymmetric attractors exist in mutually exclusive domains of the charge lattice. We construct axion free supersymmetric as well as non-supersymmetric multiple attractors in a simple two parameter model. We further obtain explicit examples of two distinct non-supersymmetric attractors in type IIA string theory compactified on K3×T"2 carrying D0−D4−D6 charges. We compute the entropy of these attractors and analyse their stability in detail.

Native human serum amyloid P component is a single pentamer

DEFF Research Database (Denmark)

Sørensen, Inge Juul; Andersen, Ove; Nielsen, EH

1995-01-01

and ELISA, and SAP peak fractions were analysed by use of SDS-PAGE, Western blotting, and electron microscopy. The results indicate that native SAP circulates as a single pentamer, a part of which forms complexes with C4b-binding protein. The properties of SAP changed during purification as indicated...

Imaging and controlling intracellular reactions: Lysosome transport as a function of diameter and the intracellular synthesis of conducting polymers

Science.gov (United States)

Payne, Christine

2014-03-01

Eukaryotic cells are the ultimate complex environment with intracellular chemical reactions regulated by the local cellular environment. For example, reactants are sequestered into specific organelles to control local concentration and pH, motor proteins transport reactants within the cell, and intracellular vesicles undergo fusion to bring reactants together. Current research in the Payne Lab in the School of Chemistry and Biochemistry at Georgia Tech is aimed at understanding and utilizing this complex environment to control intracellular chemical reactions. This will be illustrated using two examples, intracellular transport as a function of organelle diameter and the intracellular synthesis of conducting polymers. Using single particle tracking fluorescence microscopy, we measured the intracellular transport of lysosomes, membrane-bound organelles, as a function of diameter as they underwent transport in living cells. Both ATP-dependent active transport and diffusion were examined. As expected, diffusion scales with the diameter of the lysosome. However, active transport is unaffected suggesting that motor proteins are insensitive to cytosolic drag. In a second example, we utilize intracellular complexity, specifically the distinct micro-environments of different organelles, to carry out chemical reactions. We show that catalase, found in the peroxisomes of cells, can be used to catalyze the polymerization of the conducting polymer PEDOT:PSS. More importantly, we have found that a range of iron-containing biomolecules are suitable catalysts with different iron-containing biomolecules leading to different polymer properties. These experiments illustrate the advantage of intracellular complexity for the synthesis of novel materials.

The Double-Edged Sword in Pathogenic Trypanosomatids: The Pivotal Role of Mitochondria in Oxidative Stress and Bioenergetics

Directory of Open Access Journals (Sweden)

Rubem Figueiredo Sadok Menna-Barreto

2014-01-01

Full Text Available The pathogenic trypanosomatids Trypanosoma brucei, Trypanosoma cruzi, and Leishmania spp. are the causative agents of African trypanosomiasis, Chagas disease, and leishmaniasis, respectively. These diseases are considered to be neglected tropical illnesses that persist under conditions of poverty and are concentrated in impoverished populations in the developing world. Novel efficient and nontoxic drugs are urgently needed as substitutes for the currently limited chemotherapy. Trypanosomatids display a single mitochondrion with several peculiar features, such as the presence of different energetic and antioxidant enzymes and a specific arrangement of mitochondrial DNA (kinetoplast DNA. Due to mitochondrial differences between mammals and trypanosomatids, this organelle is an excellent candidate for drug intervention. Additionally, during trypanosomatids’ life cycle, the shape and functional plasticity of their single mitochondrion undergo profound alterations, reflecting adaptation to different environments. In an uncoupling situation, the organelle produces high amounts of reactive oxygen species. However, these species role in parasite biology is still controversial, involving parasite death, cell signalling, or even proliferation. Novel perspectives on trypanosomatid-targeting chemotherapy could be developed based on better comprehension of mitochondrial oxidative regulation processes.

The function of single containment and double containment of PWR nuclear power plant

International Nuclear Information System (INIS)

Chen Weijing.

1985-01-01

The function and structures of single containment and double containment of PWR nuclear power plant were described briefiy. The dissimilarites of diffent type of containments, which effects the impact of environment are discused. The impact of environment, effected by 'source term', containment gas leak rate and diffusion pattern of the released gas, under different operating condition is analysed. Especially, the impact of environment under LOCA accident is fully analysed

ARP2/3 localization in Arabidopsis leaf pavement cells: a diversity of intracellular pools and cytoskeletal interactions.

Science.gov (United States)

Zhang, Chunhua; Mallery, Eileen L; Szymanski, Daniel B

2013-01-01

In plant cells the actin cytoskeleton adopts many configurations, but is best understood as an unstable, interconnected track that rearranges to define the patterns of long distance transport of organelles during growth. Actin filaments do not form spontaneously; instead filament nucleators, such as the evolutionarily conserved actin-related protein (ARP) 2/3 complex, can efficiently generate new actin filament networks when in a fully activated state. A growing number of genetic experiments have shown that ARP2/3 is necessary for morphogenesis in processes that range from tip growth during root nodule formation to the diffuse polarized growth of leaf trichomes and pavement cells. Although progress has been rapid in the identification of proteins that function in series to positively regulate ARP2/3, less has been learned about the actual function of ARP2/3 in cells. In this paper, we analyze the localization of ARP2/3 in Arabidopsis leaf pavement cells. We detect a pool of ARP2/3 in the nucleus, and also find that ARP2/3 is efficiently and specifically clustered on multiple organelle surfaces and associates with both the actin filament and microtubule cytoskeletons. Our mutant analyses and ARP2/3 and actin double labeling experiments indicate that the clustering of ARP2/3 on organelle surfaces and an association with actin bundles does not necessarily reflect an active pool of ARP2/3, and instead most of the complex appears to exist as a latent organelle-associated pool.

Statistical approaches to assessing single and multiple outcome measures in dry eye therapy and diagnosis.

Science.gov (United States)

Tomlinson, Alan; Hair, Mario; McFadyen, Angus

2013-10-01

Dry eye is a multifactorial disease which would require a broad spectrum of test measures in the monitoring of its treatment and diagnosis. However, studies have typically reported improvements in individual measures with treatment. Alternative approaches involve multiple, combined outcomes being assessed by different statistical analyses. In order to assess the effect of various statistical approaches to the use of single and combined test measures in dry eye, this review reanalyzed measures from two previous studies (osmolarity, evaporation, tear turnover rate, and lipid film quality). These analyses assessed the measures as single variables within groups, pre- and post-intervention with a lubricant supplement, by creating combinations of these variables and by validating these combinations with the combined sample of data from all groups of dry eye subjects. The effectiveness of single measures and combinations in diagnosis of dry eye was also considered. Copyright © 2013. Published by Elsevier Inc.

Inner Surface Chirality of Single-Handed Twisted Carbonaceous Tubular Nanoribbons.

Science.gov (United States)

Liu, Dan; Li, Baozong; Guo, Yongmin; Li, Yi; Yang, Yonggang

2015-11-01

Single-handed twisted 4,4'-biphenylene-bridged polybissilsesquioxane tubular nanoribbons and single-layered nanoribbons were prepared by tuning the water/ethanol volume ratio in the reaction mixture at pH = 11.6 through a supramolecular templating approach. The single-layered nanoribbons were formed by shrinking tubular nanoribbons after the removal of the templates. In addition, solvent-induced handedness inversion was achieved. The handedness of the polybissilsesquioxanes could be controlled by changing the ethanol/water volume ratio in the reaction mixture. After carbonization at 900 °C for 4.0 h and removal of silica, single-handed twisted carbonaceous tubular nanoribbons and single-layered nanoribbons with micropores in the walls were obtained. X-ray diffraction and Raman spectroscopy analyses indicated that the carbon is predominantly amorphous. The circular dichroism spectra show that the twisted tubular nanoribbons exhibit optical activity, while the twisted single-layered nanoribbons do not. The results shown here indicate that chirality is transferred from the organic self-assemblies to the inner surfaces of the 4,4'-biphenylene-bridged polybissilsesquioxane tubular nanoribbons and subsequently to those of the carbonaceous tubular nanoribbons. © 2015 Wiley Periodicals, Inc.

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization.

Science.gov (United States)

Zhao, Shanrong; Xi, Li; Quan, Jie; Xi, Hualin; Zhang, Ying; von Schack, David; Vincent, Michael; Zhang, Baohong

2016-01-08

RNA sequencing (RNA-seq), a next-generation sequencing technique for transcriptome profiling, is being increasingly used, in part driven by the decreasing cost of sequencing. Nevertheless, the analysis of the massive amounts of data generated by large-scale RNA-seq remains a challenge. Multiple algorithms pertinent to basic analyses have been developed, and there is an increasing need to automate the use of these tools so as to obtain results in an efficient and user friendly manner. Increased automation and improved visualization of the results will help make the results and findings of the analyses readily available to experimental scientists. By combing the best open source tools developed for RNA-seq data analyses and the most advanced web 2.0 technologies, we have implemented QuickRNASeq, a pipeline for large-scale RNA-seq data analyses and visualization. The QuickRNASeq workflow consists of three main steps. In Step #1, each individual sample is processed, including mapping RNA-seq reads to a reference genome, counting the numbers of mapped reads, quality control of the aligned reads, and SNP (single nucleotide polymorphism) calling. Step #1 is computationally intensive, and can be processed in parallel. In Step #2, the results from individual samples are merged, and an integrated and interactive project report is generated. All analyses results in the report are accessible via a single HTML entry webpage. Step #3 is the data interpretation and presentation step. The rich visualization features implemented here allow end users to interactively explore the results of RNA-seq data analyses, and to gain more insights into RNA-seq datasets. In addition, we used a real world dataset to demonstrate the simplicity and efficiency of QuickRNASeq in RNA-seq data analyses and interactive visualizations. The seamless integration of automated capabilites with interactive visualizations in QuickRNASeq is not available in other published RNA-seq pipelines. The high degree

Pathogenic mechanisms in lysosomal disease: a reappraisal of the role of the lysosome.

Science.gov (United States)

Walkley, Steven U

2007-04-01

The view that lysosomes simply represent end organelles in the serial degradation of polymeric molecules derived from the cell surface and its interior has led to major misconceptions about the nature of lysosomal storage diseases and the pathogenic cascades that characterize them. Accordingly, lysosomal storage bodies are often considered 'inert', inducing cell dysfunction and death primarily through mechanical overcrowding of normal organelles or by other non-specific means leading to generalized cytotoxicity. However, modern studies of lysosomes and their component proteins provide evidence to support a far greater role for these organelles in cell metabolism. In intimate association with endosomal, autophagosomal and related vesicular systems, the greater lysosomal system can be conceptualized as a vital recycling centre that serves as a central metabolic coordinator, influencing literally every aspect of the cell, from signal transduction to regulation of gene expression. This broader view of the role of lysosomes in cells not only provides insight into how single gene defects impacting on lysosomal function can result in the plethora of complex cellular transformations characteristic of these diseases, but also suggests new and innovative therapies that may hold considerable promise for ameliorating disease progression.

Automatic storage of single gamma spectra on magnetic tape. Programs Longo, Dire

International Nuclear Information System (INIS)

Los Arcos Merino, J.M.

1978-01-01

The program Longo provides the block size and the black number in a binary file on magnetic tape. It has been applied to analyse the structure of the nine-track magnetic tapes storing single or coincidence gamma spectra files, recorded in octet form by a Multi-8 minicomputer in the Nuclear Spectrometry Laboratory of J.E.N. Then the program Dire has been written to transform the single gamma spectra into a new Fastrand disk file, storing the information in 36 bit words. A copy of this file is obtained on magnetic tape and the single gamma spectra are then availables by standard Fortran V reading sentences. (author)

Automatic storing of single gamma spectra on magnetic tape. Programs LONGO, DIRE

International Nuclear Information System (INIS)

Los Arcos Merino, J. M.

1978-01-01

The program LONGO provides the block size and the block number in a binary file on magnetic tape. It has been applied to analyse the structure of the nine-track magnetic tapes storing single or coincidence gamma spectra files, recorded in octet form by a MULTI-8 minicomputer in the Nuclear Spectrometry Laboratory of J.E.N. Then the program DIRE has been written to transform the single gamma spectra into a new FASTRAND disk file, storing the information in-36 bit words. A copy of this file is obtained on magnetic tape and the single gamma spectra are then available by standard FORTRAN V reading sentences. (Author) 3 refs

Discussions On Worst-Case Test Condition For Single Event Burnout

Science.gov (United States)

Liu, Sandra; Zafrani, Max; Sherman, Phillip

2011-10-01

This paper discusses the failure characteristics of single- event burnout (SEB) on power MOSFETs based on analyzing the quasi-stationary avalanche simulation curves. The analyses show the worst-case test condition for SEB would be using the ion that has the highest mass that would result in the highest transient current due to charge deposition and displacement damage. The analyses also show it is possible to build power MOSFETs that will not exhibit SEB even when tested with the heaviest ion, which have been verified by heavy ion test data on SEB sensitive and SEB immune devices.

Discussion on stochastic braking for a single-rail rope-driven lifter

Energy Technology Data Exchange (ETDEWEB)

1987-02-01

This paper discusses the braking and control of a A-2/73 clip type friction brake system made in FRG - a clamp type brake system made in USSR and an eccentric wheel type brake system made in Poland. Then it analyses a ZGZ auto increasing force type braking system of a single-rail rope driven lifter. The braking principle of the ZGZ system is that the braking blocks insert along the brake base and contact with the ribs of the single-rail. Then the braking would be realized as a function of increasing frictional force.

Availability and costs of single cigarettes in Guatemala.

Science.gov (United States)

de Ojeda, Ana; Barnoya, Joaquin; Thrasher, James F

2013-01-01

Single-cigarette sales have been associated with increased cigarette accessibility to less educated, lower-income populations, and minors; lower immediate cost, and increased smoking cues. Since 1997, Guatemalan Law bans the sale of single cigarettes and packs with fewer than 20 cigarettes. In 2005, Guatemala ratified the World Health Organization Framework Convention on Tobacco Control (WHO FCTC); it is therefore obliged to "prohibit sale of cigarettes individually or in small packets." Blocks were numbered and randomly selected in Guatemala City and 3 neighboring towns. All stores in each block were surveyed. Single-cigarette and fewer than 20-cigarette pack sales were assessed by observation and purchase attempts. Cigarette brands and manufacturers (Philip Morris, PM or British American Tobacco, BAT) were also recorded. Percentages and means were used to describe data. Analyses were done using STATA 11.0. Of 398 stores and street vendors surveyed, 75.6% (301) sold cigarettes. Of these, 91% (275) sold single cigarettes and none sold fewer than 20-cigarette packs. Only informal economic sectors sold singles. There was no difference on sales between Guatemala City and neighboring towns and by store type. Buying 20 single cigarettes was US$ 0.83 more expensive than buying a 20-cigarette pack. The most prevalent brands were Rubios (PM), Marlboro (PM), Payasos (BAT), and After Hours (BAT). Single-cigarettes sales are highly prevalent among informal economic sectors in Guatemala City and its neighboring towns. Our data should prove useful to advocate for FCTC Article 16 enforcement in Guatemala.

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.

Single-case synthesis tools II: Comparing quantitative outcome measures.

Science.gov (United States)

Zimmerman, Kathleen N; Pustejovsky, James E; Ledford, Jennifer R; Barton, Erin E; Severini, Katherine E; Lloyd, Blair P

2018-03-07

Varying methods for evaluating the outcomes of single case research designs (SCD) are currently used in reviews and meta-analyses of interventions. Quantitative effect size measures are often presented alongside visual analysis conclusions. Six measures across two classes-overlap measures (percentage non-overlapping data, improvement rate difference, and Tau) and parametric within-case effect sizes (standardized mean difference and log response ratio [increasing and decreasing])-were compared to determine if choice of synthesis method within and across classes impacts conclusions regarding effectiveness. The effectiveness of sensory-based interventions (SBI), a commonly used class of treatments for young children, was evaluated. Separately from evaluations of rigor and quality, authors evaluated behavior change between baseline and SBI conditions. SBI were unlikely to result in positive behavior change across all measures except IRD. However, subgroup analyses resulted in variable conclusions, indicating that the choice of measures for SCD meta-analyses can impact conclusions. Suggestions for using the log response ratio in SCD meta-analyses and considerations for understanding variability in SCD meta-analysis conclusions are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

DNA analysis by single molecule stretching in nanofluidic biochips

DEFF Research Database (Denmark)

Abad, E.; Juarros, A.; Retolaza, A.

2011-01-01

Imprint Lithography (NIL) technology combined with a conventional anodic bonding of the silicon base and Pyrex cover. Using this chip, we have performed single molecule imaging on a bench-top fluorescent microscope system. Lambda phage DNA was used as a model sample to characterize the chip. Single molecules of λ-DNA......Stretching single DNA molecules by confinement in nanofluidic channels has attracted a great interest during the last few years as a DNA analysis tool. We have designed and fabricated a sealed micro/nanofluidic device for DNA stretching applications, based on the use of the high throughput Nano...... stained with the fluorescent dye YOYO-1 were stretched in the nanochannel array and the experimental results were analysed to determine the extension factor of the DNA in the chip and the geometrical average of the nanochannel inner diameter. The determination of the extension ratio of the chip provides...

Measurement of Single-top Quark Production with ATLAS Data

CERN Document Server

Holzbauer, J L

2011-01-01

Single-top production processes have been studied using 0.7 fb-1 of data from 7 TeV center-of-mass energy proton-proton collisions collected with the ATLAS detector at the LHC. Single-top is electroweak top production and the standard model includes three production modes. Each contains a Wtb vertex, allowing the possibility of a direct measurement of the CKM matrix element |Vtb|. Single-top could also be sensitive to new physics, such as flavor changing neutral currents or heavy W' bosons. Using cut-based selections, a limit of < 39.1 pb is set for dilepton Wt production and < 26.5 pb for s-channel production. For the t-channel measurement, both cut-based and neural network analyses are performed and the cross-section is measured to be 90 +32 -22 pb, where 65 +28 -19 pb is expected according to standard model.

[Considerations on the use of meta-analyses in the orientation of knowledge and decisions in Occupational Medicine].

Science.gov (United States)

Catalani, Simona; Berra, Alessandro; Tomasi, Cesare; Romano, Canzio; Pira, Enrico; Garzaro, Giacomo; Apostoli, Pietro

2015-01-01

In recent years, due to the need to elaborate the amount of information available from the scientific literature, the meta-analyses and systematic reviews have become very numerous. The meta-analyses are carried out to evaluate the association between two events when single researches haven't provided comprehensive data. On the other hand, a good meta-analysis must satisfy certain criteria, from the selection of the studies until the evaluation of the outcomes; to this purpose, the application of methods for quality assessment is a crucial point to obtain data of adequate reliability. The aim of this review is to give some introductory tools for a critical approach to meta-analyses and systematic reviews, which have become useful instruments also in occupational medicine.

Hydrometeorological and statistical analyses of heavy rainfall in Midwestern USA

Science.gov (United States)

Thorndahl, S.; Smith, J. A.; Krajewski, W. F.

2012-04-01

During the last two decades the mid-western states of the United States of America has been largely afflicted by heavy flood producing rainfall. Several of these storms seem to have similar hydrometeorological properties in terms of pattern, track, evolution, life cycle, clustering, etc. which raise the question if it is possible to derive general characteristics of the space-time structures of these heavy storms. This is important in order to understand hydrometeorological features, e.g. how storms evolve and with what frequency we can expect extreme storms to occur. In the literature, most studies of extreme rainfall are based on point measurements (rain gauges). However, with high resolution and quality radar observation periods exceeding more than two decades, it is possible to do long-term spatio-temporal statistical analyses of extremes. This makes it possible to link return periods to distributed rainfall estimates and to study precipitation structures which cause floods. However, doing these statistical frequency analyses of rainfall based on radar observations introduces some different challenges, converting radar reflectivity observations to "true" rainfall, which are not problematic doing traditional analyses on rain gauge data. It is for example difficult to distinguish reflectivity from high intensity rain from reflectivity from other hydrometeors such as hail, especially using single polarization radars which are used in this study. Furthermore, reflectivity from bright band (melting layer) should be discarded and anomalous propagation should be corrected in order to produce valid statistics of extreme radar rainfall. Other challenges include combining observations from several radars to one mosaic, bias correction against rain gauges, range correction, ZR-relationships, etc. The present study analyzes radar rainfall observations from 1996 to 2011 based the American NEXRAD network of radars over an area covering parts of Iowa, Wisconsin, Illinois, and

Precursor uptake assays and metabolic analyses in isolated tomato fruit chromoplasts

Directory of Open Access Journals (Sweden)

Angaman Djédoux

2012-01-01

Full Text Available Abstract Background Carotenoids are the most widespread group of pigments found in nature. In addition to their role in the physiology of the plant, carotenoids also have nutritional relevance as their incorporation in the human diet provides health benefits. In non-photosynthetic tissues, carotenoids are synthesized and stored in specialized plastids called chromoplasts. At present very little is known about the origin of the metabolic precursors and cofactors required to sustain the high rate of carotenoid biosynthesis in these plastids. Recent proteomic data have revealed a number of biochemical and metabolic processes potentially operating in fruit chromoplasts. However, considering that chloroplast to chromoplast differentiation is a very rapid process during fruit ripening, there is the possibility that some of the proteins identified in the proteomic analysis could represent remnants no longer having a functional role in chromoplasts. Therefore, experimental validation is necessary to prove whether these predicted processes are actually operative in chromoplasts. Results A method has been established for high-yield purification of tomato fruit chromoplasts suitable for metabolic studies. Radiolabeled precursors were efficiently incorporated and further metabolized in isolated chromoplast. Analysis of labeled lipophilic compounds has revealed that lipid biosynthesis is a very efficient process in chromoplasts, while the relatively low incorporation levels found in carotenoids suggest that lipid production may represent a competing pathway for carotenoid biosynthesis. Malate and pyruvate are efficiently converted into acetyl-CoA, in agreement with the active operation of the malic enzyme and the pyruvate dehydrogenase complex in the chromoplast. Our results have also shown that isolated chromoplasts can actively sustain anabolic processes without the exogenous supply of ATP, thus suggesting that these organelles may generate this energetic

Precursor uptake assays and metabolic analyses in isolated tomato fruit chromoplasts.

Science.gov (United States)

Angaman, Djédoux Maxime; Petrizzo, Rocco; Hernández-Gras, Francesc; Romero-Segura, Carmen; Pateraki, Irene; Busquets, Montserrat; Boronat, Albert

2012-01-13

Carotenoids are the most widespread group of pigments found in nature. In addition to their role in the physiology of the plant, carotenoids also have nutritional relevance as their incorporation in the human diet provides health benefits. In non-photosynthetic tissues, carotenoids are synthesized and stored in specialized plastids called chromoplasts. At present very little is known about the origin of the metabolic precursors and cofactors required to sustain the high rate of carotenoid biosynthesis in these plastids. Recent proteomic data have revealed a number of biochemical and metabolic processes potentially operating in fruit chromoplasts. However, considering that chloroplast to chromoplast differentiation is a very rapid process during fruit ripening, there is the possibility that some of the proteins identified in the proteomic analysis could represent remnants no longer having a functional role in chromoplasts. Therefore, experimental validation is necessary to prove whether these predicted processes are actually operative in chromoplasts. A method has been established for high-yield purification of tomato fruit chromoplasts suitable for metabolic studies. Radiolabeled precursors were efficiently incorporated and further metabolized in isolated chromoplast. Analysis of labeled lipophilic compounds has revealed that lipid biosynthesis is a very efficient process in chromoplasts, while the relatively low incorporation levels found in carotenoids suggest that lipid production may represent a competing pathway for carotenoid biosynthesis. Malate and pyruvate are efficiently converted into acetyl-CoA, in agreement with the active operation of the malic enzyme and the pyruvate dehydrogenase complex in the chromoplast. Our results have also shown that isolated chromoplasts can actively sustain anabolic processes without the exogenous supply of ATP, thus suggesting that these organelles may generate this energetic cofactor in an autonomous way. We have set up a

Comparative biochemical analyses of venous blood and peritoneal fluid from horses with colic using a portable analyser and an in-house analyser.

Science.gov (United States)

Saulez, M N; Cebra, C K; Dailey, M

2005-08-20

Fifty-six horses with colic were examined over a period of three months. The concentrations of glucose, lactate, sodium, potassium and chloride, and the pH of samples of blood and peritoneal fluid, were determined with a portable clinical analyser and with an in-house analyser and the results were compared. Compared with the in-house analyser, the portable analyser gave higher pH values for blood and peritoneal fluid with greater variability in the alkaline range, and lower pH values in the acidic range, lower concentrations of glucose in the range below 8.3 mmol/l, and lower concentrations of lactate in venous blood in the range below 5 mmol/l and in peritoneal fluid in the range below 2 mmol/l, with less variability. On average, the portable analyser underestimated the concentrations of lactate and glucose in peritoneal fluid in comparison with the in-house analyser. Its measurements of the concentrations of sodium and chloride in peritoneal fluid had a higher bias and were more variable than the measurements in venous blood, and its measurements of potassium in venous blood and peritoneal fluid had a smaller bias and less variability than the measurements made with the in-house analyser.

Proteomic characterization of golgi membranes enriched from Arabidopsis suspension cell cultures

DEFF Research Database (Denmark)

Hansen, Sara Fasmer; Ebert, Berit; Rautengarten, Carsten

2016-01-01

The plant Golgi apparatus has a central role in the secretory pathway and is the principal site within the cell for the assembly and processing of macromolecules. The stacked membrane structure of the Golgi apparatus along with its interactions with the cytoskeleton and endoplasmic reticulum has...... historically made the isolation and purification of this organelle difficult. Density centrifugation has typically been used to enrich Golgi membranes from plant microsomal preparations, and aside from minor adaptations, the approach is still widely employed. Here we outline the enrichment of Golgi membranes...... from an Arabidopsis cell suspension culture that can be used to investigate the proteome of this organelle. We also provide a useful workflow for the examination of proteomic data as the result of multiple analyses. Finally, we highlight a simple technique to validate the subcellular localization...

Hematopoietic stem cell fate through metabolic control.

Science.gov (United States)

Ito, Kyoko; Ito, Keisuke

2018-05-25

Hematopoietic stem cells (HSCs) maintain a quiescent state in the bone marrow to preserve their self-renewal capacity, but also undergo cell divisions as required. Organelles such as the mitochondria sustain cumulative damage during these cell divisions, and this damage may eventually compromise the cells' self-renewal capacity. HSC divisions result in either self-renewal or differentiation, with the balance between the two directly impacting hematopoietic homeostasis; but the heterogeneity of available HSC-enriched fractions, together with the technical challenges of observing HSC behavior, has long hindered the analysis of individual HSCs, and prevented the elucidation of this process. However, recent advances in genetic models, metabolomics analyses and single-cell approaches have revealed the contributions made to HSC self-renewal by metabolic cues, mitochondrial biogenesis, and autophagy/mitophagy, which have highlighted mitochondrial quality as a key control factor in the equilibrium of HSCs. A deeper understanding of precisely how specific modes of metabolism control HSC fate at the single cell level is therefore not only of great biological interest, but will have clear clinical implications for the development of therapies for hematological disease. Copyright © 2018. Published by Elsevier Inc.

Castor-1C spent fuel storage cask decay heat, heat transfer, and shielding analyses

International Nuclear Information System (INIS)

Rector, D.R.; McCann, R.A.; Jenquin, U.P.; Heeb, C.M.; Creer, J.M.; Wheeler, C.L.

1986-12-01

This report documents the decay heat, heat transfer, and shielding analyses of the Gesellschaft fuer Nuklear Services (GNS) CASTOR-1C cask used in a spent fuel storage demonstration performed at Preussen Elektra's Wurgassen nuclear power plant. The demonstration was performed between March 1982 and January 1984, and resulted in cask and fuel temperature data and cask exterior surface gamma-ray and neutron radiation dose rate measurements. The purpose of the analyses reported here was to evaluate decay heat, heat transfer, and shielding computer codes. The analyses consisted of (1) performing pre-look predictions (predictions performed before the analysts were provided the test data), (2) comparing ORIGEN2 (decay heat), COBRA-SFS and HYDRA (heat transfer), and QAD and DOT (shielding) results to data, and (3) performing post-test analyses if appropriate. Even though two heat transfer codes were used to predict CASTOR-1C cask test data, no attempt was made to compare the two codes. The codes are being evaluated with other test data (single-assembly data and other cask data), and to compare the codes based on one set of data may be premature and lead to erroneous conclusions

STATUS OF THE LINUX PC CLUSTER FOR BETWEEN-PULSE DATA ANALYSES AT DIII-D

International Nuclear Information System (INIS)

PENG, Q; GROEBNER, R.J; LAO, L.L; SCHACHTER, J.; SCHISSEL, D.P; WADE, M.R.

2001-08-01

OAK-B135 Some analyses that survey experimental data are carried out at a sparse sample rate between pulses during tokamak operation and/or completed as a batch job overnight because the complete analysis on a single fast workstation cannot fit in the narrow time window between two pulses. Scientists therefore miss the opportunity to use these results to guide experiments quickly. With a dedicated Beowulf type cluster at a cost less than that of a workstation, these analyses can be accomplished between pulses and the analyzed data made available for the research team during the tokamak operation. A Linux PC cluster comprises of 12 processors was installed at DIII-D National Fusion Facility in CY00 and expanded to 24 processors in CY01 to automatically perform between-pulse magnetic equilibrium reconstructions using the EFIT code written in Fortran, CER analyses using CERQUICK code written in IDL and full profile fitting analyses (n e , T e , T i , V r , Z eff ) using IDL code ZIPFIT. This paper reports the current status of the system and discusses some problems and concerns raised during the implementation and expansion of the system

When ab ≠ c - c': published errors in the reports of single-mediator models.

Science.gov (United States)

Petrocelli, John V; Clarkson, Joshua J; Whitmire, Melanie B; Moon, Paul E

2013-06-01

Accurate reports of mediation analyses are critical to the assessment of inferences related to causality, since these inferences are consequential for both the evaluation of previous research (e.g., meta-analyses) and the progression of future research. However, upon reexamination, approximately 15% of published articles in psychology contain at least one incorrect statistical conclusion (Bakker & Wicherts, Behavior research methods, 43, 666-678 2011), disparities that beget the question of inaccuracy in mediation reports. To quantify this question of inaccuracy, articles reporting standard use of single-mediator models in three high-impact journals in personality and social psychology during 2011 were examined. More than 24% of the 156 models coded failed an equivalence test (i.e., ab = c - c'), suggesting that one or more regression coefficients in mediation analyses are frequently misreported. The authors cite common sources of errors, provide recommendations for enhanced accuracy in reports of single-mediator models, and discuss implications for alternative methods.

Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses.

Science.gov (United States)

Yan, Liying; Huang, Lei; Xu, Liya; Huang, Jin; Ma, Fei; Zhu, Xiaohui; Tang, Yaqiong; Liu, Mingshan; Lian, Ying; Liu, Ping; Li, Rong; Lu, Sijia; Tang, Fuchou; Qiao, Jie; Xie, X Sunney

2015-12-29

In vitro fertilization (IVF), preimplantation genetic diagnosis (PGD), and preimplantation genetic screening (PGS) help patients to select embryos free of monogenic diseases and aneuploidy (chromosome abnormality). Next-generation sequencing (NGS) methods, while experiencing a rapid cost reduction, have improved the precision of PGD/PGS. However, the precision of PGD has been limited by the false-positive and false-negative single-nucleotide variations (SNVs), which are not acceptable in IVF and can be circumvented by linkage analyses, such as short tandem repeats or karyomapping. It is noteworthy that existing methods of detecting SNV/copy number variation (CNV) and linkage analysis often require separate procedures for the same embryo. Here we report an NGS-based PGD/PGS procedure that can simultaneously detect a single-gene disorder and aneuploidy and is capable of linkage analysis in a cost-effective way. This method, called "mutated allele revealed by sequencing with aneuploidy and linkage analyses" (MARSALA), involves multiple annealing and looping-based amplification cycles (MALBAC) for single-cell whole-genome amplification. Aneuploidy is determined by CNVs, whereas SNVs associated with the monogenic diseases are detected by PCR amplification of the MALBAC product. The false-positive and -negative SNVs are avoided by an NGS-based linkage analysis. Two healthy babies, free of the monogenic diseases of their parents, were born after such embryo selection. The monogenic diseases originated from a single base mutation on the autosome and the X-chromosome of the disease-carrying father and mother, respectively.

The use of mass spectrometry for analysing metabolite biomarkers in epidemiology

DEFF Research Database (Denmark)

Lind, Mads Vendelbo; Savolainen, Otto I; Ross, Alastair B

2016-01-01

measurement tools. One tool that is increasingly being used for measuring biomarkers in epidemiological cohorts is mass spectrometry (MS), because of the high specificity and sensitivity of MS-based methods and the expanding range of biomarkers that can be measured. Further, the ability of MS to quantify many...... biomarkers simultaneously is advantageously compared to single biomarker methods. However, as with all methods used to measure biomarkers, there are a number of pitfalls to consider which may have an impact on results when used in epidemiology. In this review we discuss the use of MS for biomarker analyses...

Integrating Risk Analyses and Tools at the DOE Hanford Site

International Nuclear Information System (INIS)

LOBER, R.W.

2002-01-01

Risk assessment and environmental impact analysis at the U.S. Department of Energy (DOE) Hanford Site in Washington State has made significant progress in refining the strategy for using risk analysis to support closing of several hundred waste sites plus 149 single-shell tanks at the Hanford Site. A Single-Shell Tank System Closure Work Plan outlines the current basis for closing the single-shell tank systems. An analogous site approach has been developed to address closure of aggregated groups of similar waste sites. Because of the complexity, decision time frames, proximity of non-tank farm waste sites to tank farms, scale, and regulatory considerations, various projects are providing integrated assessments to support risk analyses and decision-making. Projects and the tools that are being developed and applied at Hanford to support retrieval and cleanup decisions include: (1) Life Cycle Model (LCM) and Risk Receptor Model (RRM)--A site-level set of tools to support strategic analyses through scoping level risk management to assess different alternatives and options for tank closure. (2) Systems Assessment Capability for Integrated Groundwater Nadose Zone (SAC) and the Site-Wide Groundwater Model (SWGM)--A site-wide groundwater modeling system coupled with a risk-based uncertainty analysis of inventory, vadose zone, groundwater, and river interactions for evaluating cumulative impacts from individual and aggregate waste sites. (3) Retrieval Performance Evaluation (RPE)--A site-specific, risk-based methodology developed to evaluate performance of waste retrieval, leak detection and closure on a tank-specific basis as a function of past tank Leaks, potential leakage during retrieval operations, and remaining residual waste inventories following completion of retrieval operations. (4) Field Investigation Report (FIR)--A corrective action program to investigate the nature and extent of past tank leaks through characterization activities and assess future impacts to

Quantification of abscisic acid in a single maize root

International Nuclear Information System (INIS)

Reymond, P.; Saugy, M.; Pilet, P.E.

1987-01-01

Quantitative analyses of abscisic acid in the elongating zone of a single maize root (Zea mays L. cv LG 11) were performed by gas chromatography-mass spectrometry using negative chemical ion ionization. Data showed that the more abscisic acid, the slower the growth, but a large dispersion of individual values was observed. We assume that abscisic acid is perhaps not correlated only to the growth rate. (author)

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

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

Energy Technology Data Exchange (ETDEWEB)

Basu, Dipankar N., E-mail: dipankar.n.basu@gmail.com [Department of Mechanical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039 (India); Bhattacharyya, Souvik; Das, P.K. [Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302 (India)

2014-12-15

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

Analysing Terrorism from a Systems Thinking Perspective

Directory of Open Access Journals (Sweden)

Lukas Schoenenberger

2014-02-01

Full Text Available Given the complexity of terrorism, solutions based on single factors are destined to fail. Systems thinking offers various tools for helping researchers and policy makers comprehend terrorism in its entirety. We have developed a semi-quantitative systems thinking approach for characterising relationships between variables critical to terrorism and their impact on the system as a whole. For a better understanding of the mechanisms underlying terrorism, we present a 16-variable model characterising the critical components of terrorism and perform a series of highly focused analyses. We show how to determine which variables are best suited for government intervention, describing in detail their effects on the key variable—the political influence of a terrorist network. We also offer insights into how to elicit variables that destabilise and ultimately break down these networks. Because we clarify our novel approach with fictional data, the primary importance of this paper lies in the new framework for reasoning that it provides.

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.

Neutron beam applications - Development of single crystal structure analysis technique using the HANARO neutron four circle diffractometer

Energy Technology Data Exchange (ETDEWEB)

Suh, Il Hwan; Kim, Moon Jib; Kim, Jin Gyu [Chungnam National University, Taejon (Korea)

2000-04-01

As the four circle diffractometer (FCD) has been set up in HANARO, it has become possible to study the single crystal structures by means of the neutron diffraction. Taking account of the geometry of the FCD, a program for the control of te FCD and neutron data acquisition operating under Windows' circumstance has been accomplished. Also, a computer program which can automatically measure the diffraction intensity data has been developed. All data obtained from the FCD are processed automatically for further work and a software for the single crystal structure analyses has been prepared. A KC1 single crystal was selected as first test sample for a structure analysis had been successfully performed on the FCD using in-house developed program and accordingly their functionings with precision were confirmed. For regular single crystal diffraction experiments, the structure analyses of chrysoberyl and Zr(Y)0{sub 1.87} single crystals were performed using both neutron and X-ray diffraction methods, and the result showed that the neutron diffraction work is superior to the X-ray one from the viewpoint of certain crystallographic information obtainable only from the former one. 24 refs., 15 figs., 15 tabs. (Author)

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

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

A review of computer tools for analysing the integration of renewable energy into various energy systems

DEFF Research Database (Denmark)

Connolly, D.; Lund, Henrik; Mathiesen, Brian Vad

2010-01-01

to integrating renewable energy, but instead the ‘ideal’ energy tool is highly dependent on the specific objectives that must be fulfilled. The typical applications for the 37 tools reviewed (from analysing single-building systems to national energy-systems), combined with numerous other factors......This paper includes a review of the different computer tools that can be used to analyse the integration of renewable energy. Initially 68 tools were considered, but 37 were included in the final analysis which was carried out in collaboration with the tool developers or recommended points...... of contact. The results in this paper provide the information necessary to identify a suitable energy tool for analysing the integration of renewable energy into various energy-systems under different objectives. It is evident from this paper that there is no energy tool that addresses all issues related...

Cell biochemistry studied by single-molecule imaging.

Science.gov (United States)

Mashanov, G I; Nenasheva, T A; Peckham, M; Molloy, J E

2006-11-01

Over the last decade, there have been remarkable developments in live-cell imaging. We can now readily observe individual protein molecules within living cells and this should contribute to a systems level understanding of biological pathways. Direct observation of single fluorophores enables several types of molecular information to be gathered. Temporal and spatial trajectories enable diffusion constants and binding kinetics to be deduced, while analyses of fluorescence lifetime, intensity, polarization or spectra give chemical and conformational information about molecules in their cellular context. By recording the spatial trajectories of pairs of interacting molecules, formation of larger molecular complexes can be studied. In the future, multicolour and multiparameter imaging of single molecules in live cells will be a powerful analytical tool for systems biology. Here, we discuss measurements of single-molecule mobility and residency at the plasma membrane of live cells. Analysis of diffusional paths at the plasma membrane gives information about its physical properties and measurement of temporal trajectories enables rates of binding and dissociation to be derived. Meanwhile, close scrutiny of individual fluorophore trajectories enables ideas about molecular dimerization and oligomerization related to function to be tested directly.

Single top quark production cross section using the ATLAS detector at the LHC

CERN Document Server

Cioara, Irina Antonela; The ATLAS collaboration

2017-01-01

Measurements of single top-quark production in proton-proton collisions are presented based on the 8 TeV and 13 TeV ATLAS datasets. In the leading order process, a W boson is exchanged in the t-channel. The cross-section for the production of single top-quarks and single anti-top-quarks total production cross sections, their ratio, as well as a measurement of the inclusive production cross section is presented. At 8 TeV, differential cross-section measurements of the t-channel process are also reported, these analyses include limits on anomalous contributions to the Wtb vertex and measurement of the top quark polarization. A measurement of the production cross section of a single top quark in association with a W boson, the second largest single-top production mode, is also presented. Finally, evidence for s-channel single-top production in the 8 TeV ATLAS dataset is presented. All measurements are compared to state-of-the-art theoretical calculations.

Single Photon Counting Performance and Noise Analysis of CMOS SPAD-Based Image Sensors

Science.gov (United States)

Dutton, Neale A. W.; Gyongy, Istvan; Parmesan, Luca; Henderson, Robert K.

2016-01-01

SPAD-based solid state CMOS image sensors utilising analogue integrators have attained deep sub-electron read noise (DSERN) permitting single photon counting (SPC) imaging. A new method is proposed to determine the read noise in DSERN image sensors by evaluating the peak separation and width (PSW) of single photon peaks in a photon counting histogram (PCH). The technique is used to identify and analyse cumulative noise in analogue integrating SPC SPAD-based pixels. The DSERN of our SPAD image sensor is exploited to confirm recent multi-photon threshold quanta image sensor (QIS) theory. Finally, various single and multiple photon spatio-temporal oversampling techniques are reviewed. PMID:27447643

Detection and direction discrimination of single vortex rings by harbour seals (Phoca vitulina).

Science.gov (United States)

Krüger, Yvonne; Hanke, Wolf; Miersch, Lars; Dehnhardt, Guido

2018-04-25

Harbour seals possess highly sensitive vibrissae that enable them to track hydrodynamic trails left behind by a swimming fish. Most of these trails contain vortex rings as a main hydrodynamic component. They may reveal information about their generator as the trails differ depending on the fish species, the fish's body shape, size and swimming style. In addition, fish generate single vortex rings in diverse natural situations. In this study, the ability of blindfolded stationary harbour seals to detect and analyse single vortex rings regarding directional information has been investigated. In three different behavioural experiments, the animals were trained to respond to single artificially generated vortex rings. The results show that harbour seals are able to respond to a variety of different vortex rings upon vibrissal stimulation. The investigation of the minimum hydrodynamically perceivable angle revealed that it is at least as small as 5.7 deg, which was the smallest adjustable angle. Moreover, harbour seals are capable of analysing the travel direction of a vortex ring perceived by the mystacial vibrissae irrespective of whether the vibrissae were stimulated ipsilaterally or contralaterally. In situations in which no complex hydrodynamic trail is available, it is advantageous for a hunting seal to be able to extract information from a single vortex ring. © 2018. Published by The Company of Biologists Ltd.

Multi-photon absorption limits to heralded single photon sources

Science.gov (United States)

Husko, Chad A.; Clark, Alex S.; Collins, Matthew J.; De Rossi, Alfredo; Combrié, Sylvain; Lehoucq, Gaëlle; Rey, Isabella H.; Krauss, Thomas F.; Xiong, Chunle; Eggleton, Benjamin J.

2013-01-01

Single photons are of paramount importance to future quantum technologies, including quantum communication and computation. Nonlinear photonic devices using parametric processes offer a straightforward route to generating photons, however additional nonlinear processes may come into play and interfere with these sources. Here we analyse spontaneous four-wave mixing (SFWM) sources in the presence of multi-photon processes. We conduct experiments in silicon and gallium indium phosphide photonic crystal waveguides which display inherently different nonlinear absorption processes, namely two-photon (TPA) and three-photon absorption (ThPA), respectively. We develop a novel model capturing these diverse effects which is in excellent quantitative agreement with measurements of brightness, coincidence-to-accidental ratio (CAR) and second-order correlation function g(2)(0), showing that TPA imposes an intrinsic limit on heralded single photon sources. We build on these observations to devise a new metric, the quantum utility (QMU), enabling further optimisation of single photon sources. PMID:24186400

Ellipsometric studies of ErMnO₃ single crystals

DEFF Research Database (Denmark)

Babonas, G.-J.; Grivel, Jean-Claude; Reza, A.

2007-01-01

Ellipsometric studies of ErMnO3 single crystals have been carried out in the spectral range of 1-5 eV by means of photometric ellipsometers. Experimental ellipsometric data were analysed in the uniaxial crystal model. For the first time, the components of dielectric function of ErMnO3 were...

Employment, Work Conditions, and the Home Environment in Single-Mother Families

Science.gov (United States)

Lleras, Christy

2008-01-01

This study investigates the impact of employment status and work conditions on the quality of the home environment provided by single mothers of preschool-age children. Multivariate analyses were conducted using data from the National Longitudinal Survey of Youth. The results indicate that employment status is not a significant predictor of the…

Meta-Analysis of Behavioral Self-Management Interventions in Single-Case Research

Science.gov (United States)

Briesch, Amy M.; Briesch, Jacquelyn M.

2016-01-01

The current study meta-analyzed 47 single-subject studies of behavioral self-management interventions that were published between 1971 and 2011. In addition to obtaining an overall measure of effect across all self-management studies (f = 0.93), analyses were conducted to assess whether treatment effectiveness was moderated by factors such as…

Analyses of Interactions Between Heparin and the Apical Surface Proteins of Plasmodium falciparum

Science.gov (United States)

Kobayashi, Kyousuke; Takano, Ryo; Takemae, Hitoshi; Sugi, Tatsuki; Ishiwa, Akiko; Gong, Haiyan; Recuenco, Frances C.; Iwanaga, Tatsuya; Horimoto, Taisuke; Akashi, Hiroomi; Kato, Kentaro

2013-11-01

Heparin, a sulfated glycoconjugate, reportedly inhibits the blood-stage growth of the malaria parasite Plasmodium falciparum. Elucidation of the inhibitory mechanism is valuable for developing novel invasion-blocking treatments based on heparin. Merozoite surface protein 1 has been reported as a candidate target of heparin; however, to better understand the molecular mechanisms involved, we characterized the molecules that bind to heparin during merozoite invasion. Here, we show that heparin binds only at the apical tip of the merozoite surface and that multiple heparin-binding proteins localize preferentially in the apical organelles. To identify heparin-binding proteins, parasite proteins were fractionated by means of heparin affinity chromatography and subjected to immunoblot analysis with ligand-specific antibodies. All tested members of the Duffy and reticulocyte binding-like families bound to heparin with diverse affinities. These findings suggest that heparin masks the apical surface of merozoites and blocks interaction with the erythrocyte membrane after initial attachment.

Residual Stress State in Single-Edge Notched Tension Specimen Caused by the Local Compression Technique

Directory of Open Access Journals (Sweden)

Huang Yifan

2016-12-01

Full Text Available Three-dimensional (3D finite element analyses (FEA are performed to simulate the local compression (LC technique on the clamped single-edge notched tension (SE(T specimens. The analysis includes three types of indenters, which are single pair of cylinder indenters (SPCI, double pairs of cylinder indenters (DPCI and single pair of ring indenters (SPRI. The distribution of the residual stress in the crack opening direction in the uncracked ligament of the specimen is evaluated. The outcome of this study can facilitate the use of LC technique on SE(T specimens.

Exploring the energy landscape of biopolymers using single molecule force spectroscopy and molecular simulations

OpenAIRE

Hyeon, Changbong

2010-01-01

In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule force experiments, quantitative analyses of measurements employing sound theoretical models and molecular simulations play central role more than any other field. With a brief description of basic theories for force mechanics and molecular simulation techniqu...

Waterbomb base: a symmetric single-vertex bistable origami mechanism

International Nuclear Information System (INIS)

Hanna, Brandon H; Lund, Jason M; Magleby, Spencer P; Howell, Larry L; Lang, Robert J

2014-01-01

The origami waterbomb base is a single-vertex bistable origami mechanism that has unique properties which may prove useful in a variety of applications. It also shows promise as a test bed for smart materials and actuation because of its straightforward geometry and multiple phases of motion, ranging from simple to more complex. This study develops a quantitative understanding of the symmetric waterbomb base's kinetic behavior. This is done by completing kinematic and potential energy analyses to understand and predict bistable behavior. A physical prototype is constructed and tested to validate the results of the analyses. Finite element and virtual work analyses based on the prototype are used to explore the locations of the stable equilibrium positions and the force–deflection response. The model results are verified through comparisons to measurements on a physical prototype. The resulting models describe waterbomb base behavior and provide an engineering tool for application development. (paper)

A new organellar complex in rat sympathetic neurons.

Directory of Open Access Journals (Sweden)

Matt S Ramer

Full Text Available Membranous compartments of neurons such as axons, dendrites and modified primary cilia are defining features of neuronal phenotype. This is unlike organelles deep to the plasma membrane, which are for the most part generic and not related directly to morphological, neurochemical or functional specializations. However, here we use multi-label immunohistochemistry combined with confocal and electron microscopy to identify a very large (approximately 6 microns in diameter, entirely intracellular neuronal organelle which occurs singly in a ubiquitous but neurochemically distinct and morphologically simple subset of sympathetic ganglion neurons. Although usually toroidal, it also occurs as twists or rods depending on its intracellular position: tori are most often perinuclear whereas rods are often found in axons. These 'loukoumasomes' (doughnut-like bodies bind a monoclonal antibody raised against beta-III-tubulin (SDL.3D10, although their inability to bind other beta-III-tubulin monoclonal antibodies indicate that the responsible antigen is not known. Position-morphology relationships within neurons and their expression of non-muscle heavy chain myosin suggest a dynamic structure. They associate with nematosomes, enigmatic nucleolus-like organelles present in many neural and non-neural tissues, which we now show to be composed of filamentous actin. Loukoumasomes also separately interact with mother centrioles forming the basal body of primary cilia. They express gamma tubulin, a microtubule nucleator which localizes to non-neuronal centrosomes, and cenexin, a mother centriole-associated protein required for ciliogenesis. These data reveal a hitherto undescribed organelle, and depict it as an intracellular transport machine, shuttling material between the primary cilium, the nematosome, and the axon.

Simultaneous ultrastructural analysis of fluorochrome-photoconverted diaminobenzidine and gold immunolabeling in cultured cells

Directory of Open Access Journals (Sweden)

M. Malatesta

2013-09-01

Full Text Available Diaminobenzidine photoconversion is a technique by which a fluorescent dye is transformed into a stably insoluble, brown, electrondense signal, thus enabling examination at both bright field light microscopy and transmission electron microscopy. In this work, a procedure is proposed for combining photoconversion and immunoelectron microscopy: in vitro cell cultures have been first submitted to photoconversion to analyse the intracellular fate of either fluorescent nanoparticles or photosensitizing molecules, then processed for transmission electron microscopy; different fixative solutions and embedding media have been used, and the ultrathin sections were finally submitted to post-embedding immunogold cytochemistry. Under all conditions the photoconversion reaction product and the target antigen were properly detected in the same section; Epon-embedded, osmicated samples required a pre-treatment with sodium metaperiodate to unmask the antigenic sites. This simple and reliable procedure exploits a single sample to simultaneously localise the photoconversion product and a variety of antigens allowing a specific identification of subcellular organelles at the ultrastructural level.

Phylogenetic tree based on complete genomes using fractal and correlation analyses without sequence alignment

Directory of Open Access Journals (Sweden)

Zu-Guo Yu

2006-06-01

Full Text Available The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped resolve the evolution of this organelle in photosynthetic eukaryotes. In this review, we describe two algorithms to construct phylogenetic trees based on the theories of fractals and dynamic language using complete genomes. These algorithms were developed by our research group in the past few years. Our distance-based phylogenetic tree of 109 prokaryotes and eukaryotes agrees with the biologists' "tree of life" based on the 16S-like rRNA genes in a majority of basic branchings and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated into two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution.

Microfluidic platform for multiplexed detection in single cells and methods thereof

Science.gov (United States)

Wu, Meiye; Singh, Anup K.

2018-05-01

The present invention relates to a microfluidic device and platform configured to conduct multiplexed analysis within the device. In particular, the device allows multiple targets to be detected on a single-cell level. Also provided are methods of performing multiplexed analyses to detect one or more target nucleic acids, proteins, and post-translational modifications.

Single Shell Tank Waste Characterization Project for Tank B-110, Core 9 - data package and PNL validation summary report

International Nuclear Information System (INIS)

Pool, K.N.; Jones, T.E.; McKinley, S.G.; Tingey, J.M.; Longaker, T.M.; Gibson, J.A.

1990-01-01

This Data Package contains results obtained by Pacific Northwest Laboratory (PNL) staff in the characterization and analyses of Core 9 segments taken from the Single-Shell Tank (SST) 110B. The characterization and analysis of Core 9 segments are outlined in the Waste Characterization Plan for Hanford Site Single-Shell Tanks and in the Pacific Northwest Laboratory (PNL) Single-Shell Tank Waste Characterization Support FY 89/90 Statement of Work (SOW), Rev. 1 dated March, 1990. Specific analyses for each sub-sample taken from a segment are delineated in Test Instructions prepared by the PNL Single-Shell Tank Waste Characterization Project Management Office (SST Project) in accordance with procedures contained in the SST Waste Characterization Procedure Compendium (PNL-MA-599). Analytical procedures used in the characterization activities are also included in PNL-MA-599. Core 9 included five segments although segment 1 did not have sufficient material for characterization. The five samplers were received from Westinghouse Hanford Company (WHC) on 11/21-22/89. Each segment was contained in a sampler and was enclosed in a shipping cask. The shipping cask was butted up to the 325-A hot cell and the sampler moved into the hot cell. The material in the sampler (i.e., the segment) was extruded from the sampler, limited physical characteristics assessed, and photographed. At this point samples were taken for particle size and volatile organic analyses. Each segment was then homogenized. Sub-samples were taken for required analyses as delineated in the appropriate Test Instruction. Table 1 includes sample numbers assigned to Core 9 segment materials being transferred from 325-A Hot Cell. Sample numbers 90-0298, 90-0299, 90-0302, and 90-0303 were included in Table 1 although no analyses were requested for these samples. Table 2 lists Core 9 sub-sample numbers per sample preparation method

A high sensitivity optically stimulated luminescence scanning system for measurement of single sand-sized grains

DEFF Research Database (Denmark)

Duller, G.A.T.; Bøtter-Jensen, L.; Kohsiek, P.

1999-01-01

An instrument has been designed for the routine analysis of the optically stimulated luminescence signal from single grains of sand. The system is capable of analysing over 3000 individual grains in a single measurement sequence, and the OSL signal from each grain can be read in less than 3 s....... The design principles are described, along with preliminary measurements that illustrate the operation of the system and its capabilities....

Optical measuring system with an interrogator and a polymer-based single-mode fibre optic sensor system

DEFF Research Database (Denmark)

2017-01-01

The present invention relates to an optical measuring system comprising a polymer-based single-mode fibre-optic sensor system (102), an optical interrogator (101), and an optical arrangement (103) interconnecting the optical interrogator (101) and the polymer-based single-mode fibre-optic sensor...... system (102). The invention further relates to an optical interrogator adapted to be connected to a polymer-based single-mode fibre-optic sensor system via an optical arrangement. The interrogator comprises a broadband light source arrangement (104) and a spectrum analysing arrangement which receives...

Interpretation of single grain De distributions and calculation of De

International Nuclear Information System (INIS)

Jacobs, Z.; Duller, G.A.T.; Wintle, A.G.

2006-01-01

Recent development of an instrument for measuring the optically stimulated luminescence signal from individual mineral grains has made it practicable to measure the equivalent dose (D e ) from many hundreds or thousands of single mineral grains from a sample. Such measurements can potentially be used to address issues such as sample integrity, and to make it possible to obtain ages from samples that consist of mixtures of grains, enlarging the range of materials to which luminescence dating can be applied. However, for reliable ages to be obtained, the characteristics of the equipment and the sample being analysed need to be understood. Using sensitised sedimentary quartz grains, the instrumental uncertainty in repeated optically stimulated luminescence measurements made using a single grain laser luminescence unit attached to a conventional luminescence reader was evaluated; a value of 1.2% was obtained. Grains from this sample were then used to investigate the uncertainty in a measured dose distribution obtained using the single aliquot measurement protocol on each grain that had previously received a known laboratory dose; after systematic rejection of grains that did not pass defined acceptance criteria, overdispersion of 7% was found. Additional spread in data was found when uniform aeolian sands were examined, resulting in overdispersion of ∼12%; this was attributed to a combination of factors relating to differences in field and laboratory conditions. A similar value was found for an archaeological horizon below this sand. For another sample from the same section, a significantly larger value was found, ∼29%; on this basis the finite mixture model was applied to obtain the likely dose components. The paper demonstrates the importance of correct assessment of error terms when analysing single grain D e distributions and a number of rejection criteria that are vital to avoid the inclusion of data that could lead to misinterpretation of the degree of

Single side damage simulations and detection in beam-like structures

International Nuclear Information System (INIS)

Zhou, Yun-Lai; Perera, R; Wahab, M Abdel; Maia, N; Sampaio, R; Figueiredo, E

2015-01-01

Beam-like structures are the most common components in real engineering, while single side damage is often encountered. In this study, a numerical analysis of single side damage in a free-free beam is analysed with three different finite element models; namely solid, shell and beam models for demonstrating their performance in simulating real structures. Similar to experiment, damage is introduced into one side of the beam, and natural frequencies are extracted from the simulations and compared with experimental and analytical results. Mode shapes are also analysed with modal assurance criterion. The results from simulations reveal a good performance of the three models in extracting natural frequencies, and solid model performs better than shell while shell model performs better than beam model under intact state. For damaged states, the natural frequencies captured from solid model show more sensitivity to damage severity than shell model and shell model performs similar to the beam model in distinguishing damage. The main contribution of this paper is to perform a comparison between three finite element models and experimental data as well as analytical solutions. The finite element results show a relatively well performance. (paper)

The induction of streptomycin resistance in tomato

International Nuclear Information System (INIS)

Jansen, D.E.; Snel, E.A.M.; Akerboom, M.; HiIle, J.

1990-01-01

Full text: The aim of the research is to investigate cytoplasmic genetics. For the analysis of organelle transfer and segregation in cybrids the presence of selectable and easily screenable genetic markers on organelles is indispensable. Streptomycin resistance is the best characterised cytoplasmic marker. The resistance is dominant and can be induced by a single basepair change in the chloroplast DNA. Protoplasts were treated with several MNU concentrations directly after isolation. Three months after the protoplast mutagenesis about 600 green colonies were isolated from 28x10 6 treated protoplasts. These colonies were retested several times on streptomycin containing media and approximately 150 colonies remained. We distinguished four classes of streptomycin resistance. Experiments were also done without the use of MNU. By somaclonal variation, only a small quantity of streptomycin resistant colonies was isolated at a 50 fold lower frequency. (author)

In-cell protease assay systems based on trans-localizing molecular beacon proteins using HCV protease as a model system.

Directory of Open Access Journals (Sweden)

Jeong Hee Kim

Full Text Available This study describes a sensitive in-cell protease detection system that enables direct fluorescence detection of a target protease and its inhibition inside living cells. This live-cell imaging system provides a fluorescent molecular beacon protein comprised of an intracellular translocation signal sequence, a protease-specific cleavage sequence, and a fluorescent tag sequence(s. The molecular beacon protein is designed to change its intracellular localization upon cleavage by a target protease, i.e., from the cytosol to a subcellular organelle or from a subcellular organelle to the cytosol. Protease activity can be monitored at the single cell level, and accordingly the entire cell population expressing the protease can be accurately enumerated. The clear cellular change in fluorescence pattern makes this system an ideal tool for various life science and drug discovery research, including high throughput and high content screening applications.

A qualitative single case study of parallel processes

DEFF Research Database (Denmark)

Jacobsen, Claus Haugaard

2007-01-01

Parallel process in psychotherapy and supervision is a phenomenon manifest in relationships and interactions, that originates in one setting and is reflected in another. This article presents an explorative single case study of parallel processes based on qualitative analyses of two successive...... randomly chosen psychotherapy sessions with a schizophrenic patient and the supervision session given in between. The author's analysis is verified by an independent examiner's analysis. Parallel processes are identified and described. Reflections on the dynamics of parallel processes and supervisory...

Anti-control of chaos of single time-scale brushless DC motor.

Science.gov (United States)

Ge, Zheng-Ming; Chang, Ching-Ming; Chen, Yen-Sheng

2006-09-15

Anti-control of chaos of single time-scale brushless DC motors is studied in this paper. In order to analyse a variety of periodic and chaotic phenomena, we employ several numerical techniques such as phase portraits, bifurcation diagrams and Lyapunov exponents. Anti-control of chaos can be achieved by adding an external constant term or an external periodic term.

Buckling of ZnS-filled single-walled carbon nanotubes – The influence of aspect ratio

KAUST Repository

Monteiro, André O.; Da Costa, Pedro M. F. J.; Cachim, Paulo B.; Holec, David

2014-01-01

The mechanical response of single-walled carbon nanotubes (SWCNT) filled with crystalline zinc sulphide (ZnS) nanowires under uniaxial compression is studied using classical molecular dynamics. These simulations were used to analyse the behaviour

Dissecting stem cell differentiation using single cell expression profiling

OpenAIRE

Moignard, Victoria Rachel; Göttgens, Berthold

2016-01-01

Many assumptions about the way cells behave are based on analyses of populations. However, it is now widely recognized that even apparently pure populations can display a remarkable level of heterogeneity. This is particularly true in stem cell biology where it hinders our understanding of normal development and the development of strategies for regenerative medicine. Over the past decade technologies facilitating gene expression analysis at the single cell level have become widespread, provi...

Review of accident analyses performed at Mochovce NPP

International Nuclear Information System (INIS)

Siko, D.

2000-01-01

In this paper the review of accident analysis performed in NPP Mochovce V-1 is presented. The scope of these safety measures was defined and development in the T SSM for NPP Mochovce Nuclear Safety Improvements Report' issued in July 1995. The main objectives of these safety measures were the followings: (a) to establish the criteria for selection and classification of accidental events, as well as defining the list of initiating events to be analysed. Accident classification to the individual groups must be performed in accordance with RG 1.70 and IAEA recommendations 'Guidelines for Accidental Analysis of WWER NPP' (IAEA-EBR-WWER-01) to select boundary cases to be calculated from the scope of initiating events; (b ) to elaborate the accident analysis methodology that also includes acceptance criteria for their result evaluation, initial and boundary conditions, assumption related with the application of the single failure criteria, requirements on the analysis quality, used computer codes, as well as NPP models and input data for the accident analysis; (c) to perform the accident analysis for the Pre-operational Safety Report (POSAR); (d) to provide a synthetic report addressing the validity range of codes models and correlations, the assessment against relevant tests results, the evidence of the user qualification, the modernisation and nodding scheme for the plant and the justification of used computer codes. Analyses results showed that all acceptance criteria were met with satisfactory margin and design of the NPP Mochovce is accurate. (author)

Living in single person households and the risk of isolation in later life

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Laura Banks

2009-10-01

Full Text Available Data from the International Social Survey Programme (2001 was used to analyse the social networks of older people and whether living in single person households increased the risk of isolation. When comparing respondents with one or more adult children, there was no significant difference in the likelihood of experiencing familial isolation between people living in single person households and those living in larger households. A majority of those living in single person households had at least regular contact with a sibling, adult child or close friend and participated in a social organisation. Friends compensate to some extent for a lack of support from the family, although in southern and eastern European countries, other relatives appeared to be more important in support networks. People living in single person households were more likely to experience isolation, but this was largely related to advanced age and childlessness. Whilst a very small minority in Japan were living in single person households, they were significantly more likely to be severely isolated than those living in single person households in other countries.

Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?

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Paweł Mackiewicz

2014-12-01

Full Text Available One of the key evolutionary events on the scale of the biosphere was an endosymbiosis between a heterotrophic eukaryote and a cyanobacterium, resulting in a primary plastid. Such an organelle is characteristic of three eukaryotic lineages, glaucophytes, red algae and green plants. The three groups are usually united under the common name Archaeplastida or Plantae in modern taxonomic classifications, which indicates they are considered monophyletic. The methods generally used to verify this monophyly are phylogenetic analyses. In this article we review up-to-date results of such analyses and discussed their inconsistencies. Although phylogenies of plastid genes suggest a single primary endosymbiosis, which is assumed to mean a common origin of the Archaeplastida, different phylogenetic trees based on nuclear markers show monophyly, paraphyly, polyphyly or unresolved topologies of Archaeplastida hosts. The difficulties in reconstructing host cell relationships could result from stochastic and systematic biases in data sets, including different substitution rates and patterns, gene paralogy and horizontal/endosymbiotic gene transfer into eukaryotic lineages, which attract Archaeplastida in phylogenetic trees. Based on results to date, it is neither possible to confirm nor refute alternative evolutionary scenarios to a single primary endosymbiosis. Nevertheless, if trees supporting monophyly are considered, relationships inferred among Archaeplastida lineages can be discussed. Phylogenetic analyses based on nuclear genes clearly show the earlier divergence of glaucophytes from red algae and green plants. Plastid genes suggest a more complicated history, but at least some studies are congruent with this concept. Additional research involving more representatives of glaucophytes and many understudied lineages of Eukaryota can improve inferring phylogenetic relationships related to the Archaeplastida. In addition, alternative approaches not directly

Proteomic analysis of mitochondria in respiratory epithelial cells infected with human respiratory syncytial virus and functional implications for virus and cell biology.

Science.gov (United States)

Munday, Diane C; Howell, Gareth; Barr, John N; Hiscox, Julian A

2015-03-01

The aim of this study was to quantitatively characterise the mitochondrial proteome of airway epithelial cells infected with human respiratory syncytial virus (HRSV), a major cause of paediatric illness. Quantitative proteomics, underpinned by stable isotope labelling with amino acids in cell culture, coupled to LC-MS/MS, was applied to mitochondrial fractions prepared from HRSV-infected and mock-infected cells 12 and 24 h post-infection. Datasets were analysed using ingenuity pathway analysis, and the results were validated and characterised using bioimaging, targeted inhibition and gene depletion. The data quantitatively indicated that antiviral signalling proteins converged on mitochondria during HRSV infection. The mitochondrial receptor protein Tom70 was found to act in an antiviral manner, while its chaperone, Hsp90, was confirmed to be a positive viral factor. Proteins associated with different organelles were also co-enriched in the mitochondrial fractions from HRSV-infected cells, suggesting that alterations in organelle dynamics and membrane associations occur during virus infection. Protein and pathway-specific alterations occur to the mitochondrial proteome in a spatial and temporal manner during HRSV infection, suggesting that this organelle may have altered functions. These could be targeted as part of potential therapeutic strategies to disrupt virus biology. © 2014 Royal Pharmaceutical Society.

An overexpression screen of Toxoplasma gondii Rab-GTPases reveals distinct transport routes to the micronemes.

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Katrin Kremer

2013-03-01

Full Text Available The basic organisation of the endomembrane system is conserved in all eukaryotes and comparative genome analyses provides compelling evidence that the endomembrane system of the last common eukaryotic ancestor (LCEA is complex with many genes required for regulated traffic being present. Although apicomplexan parasites, causative agents of severe human and animal diseases, appear to have only a basic set of trafficking factors such as Rab-GTPases, they evolved unique secretory organelles (micronemes, rhoptries and dense granules that are sequentially secreted during invasion of the host cell. In order to define the secretory pathway of apicomplexans, we performed an overexpression screen of Rabs in Toxoplasma gondii and identified Rab5A and Rab5C as important regulators of traffic to micronemes and rhoptries. Intriguingly, we found that not all microneme proteins traffic depends on functional Rab5A and Rab5C, indicating the existence of redundant microneme targeting pathways. Using two-colour super-resolution stimulated emission depletion (STED we verified distinct localisations of independent microneme proteins and demonstrate that micronemal organelles are organised in distinct subsets or subcompartments. Our results suggest that apicomplexan parasites modify classical regulators of the endocytic system to carryout essential parasite-specific roles in the biogenesis of their unique secretory organelles.

A single-atom quantum memory.

Science.gov (United States)

Specht, Holger P; Nölleke, Christian; Reiserer, Andreas; Uphoff, Manuel; Figueroa, Eden; Ritter, Stephan; Rempe, Gerhard

2011-05-12

The faithful storage of a quantum bit (qubit) of light is essential for long-distance quantum communication, quantum networking and distributed quantum computing. The required optical quantum memory must be able to receive and recreate the photonic qubit; additionally, it must store an unknown quantum state of light better than any classical device. So far, these two requirements have been met only by ensembles of material particles that store the information in collective excitations. Recent developments, however, have paved the way for an approach in which the information exchange occurs between single quanta of light and matter. This single-particle approach allows the material qubit to be addressed, which has fundamental advantages for realistic implementations. First, it enables a heralding mechanism that signals the successful storage of a photon by means of state detection; this can be used to combat inevitable losses and finite efficiencies. Second, it allows for individual qubit manipulations, opening up avenues for in situ processing of the stored quantum information. Here we demonstrate the most fundamental implementation of such a quantum memory, by mapping arbitrary polarization states of light into and out of a single atom trapped inside an optical cavity. The memory performance is tested with weak coherent pulses and analysed using full quantum process tomography. The average fidelity is measured to be 93%, and low decoherence rates result in qubit coherence times exceeding 180  microseconds. This makes our system a versatile quantum node with excellent prospects for applications in optical quantum gates and quantum repeaters.

Improving Climate Communication through Comprehensive Linguistic Analyses Using Computational Tools

Science.gov (United States)

Gann, T. M.; Matlock, T.

2014-12-01

An important lesson on climate communication research is that there is no single way to reach out and inform the public. Different groups conceptualize climate issues in different ways and different groups have different values and assumptions. This variability makes it extremely difficult to effectively and objectively communicate climate information. One of the main challenges is the following: How do we acquire a better understanding of how values and assumptions vary across groups, including political groups? A necessary starting point is to pay close attention to the linguistic content of messages used across current popular media sources. Careful analyses of that information—including how it is realized in language for conservative and progressive media—may ultimately help climate scientists, government agency officials, journalists and others develop more effective messages. Past research has looked at partisan media coverage of climate change, but little attention has been given to the fine-grained linguistic content of such media. And when researchers have done detailed linguistic analyses, they have relied primarily on hand-coding, an approach that is costly, labor intensive, and time-consuming. Our project, building on recent work on partisan news media (Gann & Matlock, 2014; under review) uses high dimensional semantic analyses and other methods of automated classification techniques from the field of natural language processing to quantify how climate issues are characterized in media sources that differ according to political orientation. In addition to discussing varied linguistic patterns, we share new methods for improving climate communication for varied stakeholders, and for developing better assessments of their effectiveness.

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.

Uncertainty and sensitivity analyses for gas and brine migration at the Waste Isolation Pilot Plant, May 1992

International Nuclear Information System (INIS)

Helton, J.C.; Bean, J.E.; Butcher, B.M.; Garner, J.W.; Vaughn, P.; Schreiber, J.D.; Swift, P.N.

1993-08-01

Uncertainty and sensitivity analysis techniques based on Latin hypercube sampling, partial correlation analysis, stepwise regression analysis and examination of scatterplots are used in conjunction with the BRAGFLO model to examine two phase flow (i.e., gas and brine) at the Waste Isolation Pilot Plant (WIPP), which is being developed by the US Department of Energy as a disposal facility for transuranic waste. The analyses consider either a single waste panel or the entire repository in conjunction with the following cases: (1) fully consolidated shaft, (2) system of shaft seals with panel seals, and (3) single shaft seal without panel seals. The purpose of this analysis is to develop insights on factors that are potentially important in showing compliance with applicable regulations of the US Environmental Protection Agency (i.e., 40 CFR 191, Subpart B; 40 CFR 268). The primary topics investigated are (1) gas production due to corrosion of steel, (2) gas production due to microbial degradation of cellulosics, (3) gas migration into anhydrite marker beds in the Salado Formation, (4) gas migration through a system of shaft seals to overlying strata, and (5) gas migration through a single shaft seal to overlying strata. Important variables identified in the analyses include initial brine saturation of the waste, stoichiometric terms for corrosion of steel and microbial degradation of cellulosics, gas barrier pressure in the anhydrite marker beds, shaft seal permeability, and panel seal permeability

Strengthening mechanisms of Fe nanoparticles for single crystal Cu–Fe alloy

International Nuclear Information System (INIS)

Shi, Guodong; Chen, Xiaohua; Jiang, Han; Wang, Zidong; Tang, Hao; Fan, Yongquan

2015-01-01

A single crystal Cu–Fe alloy with finely dispersed precipitate Fe nanoparticles was fabricated in this study. The interface relationship of iron nanoparticle and copper matrix was analyzed with a high-resolution transmission electron microscope (HRTEM), and the effect of Fe nanoparticles on mechanical properties of single crystal Cu–Fe alloy was discussed. Results show that, the finely dispersed Fe nanoparticles can be obtained under the directional solidification condition, with the size of 5–50 nm and the coherent interface between the iron nanoparticle and the copper matrix. Single crystal Cu–Fe alloy possesses improved tensile strength of 194.64 MPa, and total elongation of 44.72%, respectively, at room temperature, in contrast to pure Cu sample. Nanoparticles which have coherent interface with matrix can improve the dislocation motion state. Some dislocations can slip through the nanoparticle along the coherent interface and some dislocations can enter into the nanoparticles. Thus to improve the tensile strength of single crystal Cu–Fe alloy without sacrificing the ductility simultaneously. Based on the above analyses, strengthening mechanisms of Fe nanoparticles for single crystal Cu–Fe alloy was described

Systematic literature reviews and meta-analyses: part 6 of a series on evaluation of scientific publications.

Science.gov (United States)

Ressing, Meike; Blettner, Maria; Klug, Stefanie J

2009-07-01

Because of the rising number of scientific publications, it is important to have a means of jointly summarizing and assessing different studies on a single topic. Systematic literature reviews, meta-analyses of published data, and meta-analyses of individual data (pooled reanalyses) are now being published with increasing frequency. We here describe the essential features of these methods and discuss their strengths and weaknesses. This article is based on a selective literature search. The different types of review and meta-analysis are described, the methods used in each are outlined so that they can be evaluated, and a checklist is given for the assessment of reviews and meta-analyses of scientific articles. Systematic literature reviews provide an overview of the state of research on a given topic and enable an assessment of the quality of individual studies. They also allow the results of different studies to be evaluated together when these are inconsistent. Meta-analyses additionally allow calculation of pooled estimates of an effect. The different types of review and meta-analysis are discussed with examples from the literature on one particular topic. Systematic literature reviews and meta-analyses enable the research findings and treatment effects obtained in different individual studies to be summed up and evaluated.

Bioinformatics approaches to single-cell analysis in developmental biology.

Science.gov (United States)

Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

2016-03-01

Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. © The Author 2015. Published by Oxford University Press on behalf of the European

AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

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Mevik Bjørn-Helge

2009-10-01

Full Text Available Abstract Background Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites. Results Here we present a batch-oriented web-based program package, named AIR that allows 1 transformation of several single genes to one multigene alignment, 2 identification of evolutionary rates in multigene alignments and 3 removal of fast evolving sites. These three processes can be done with the programs AIR-Appender, AIR-Identifier, and AIR-Remover (AIR, which can be used independently or in a semi-automated pipeline. AIR produces user-friendly output files with filtered and non-filtered alignments where residues are colored according to their evolutionary rates. Other bioinformatics applications linked to the AIR package are available at the Bioportal http://www.bioportal.uio.no, University of Oslo; together these greatly improve the flexibility, efficiency and quality of phylogenomic analyses. Conclusion The AIR program package allows for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes.

Fire resistance of single pitched-roof steel portal frame

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J. J. Ferrán Gozálvez

2017-03-01

Full Text Available The standard procedure of structural fire design is based on the simplified analysis of single members. This method leads to conservative results in the case of structures able to redistribution of forces. The failure mechanism affecting both life safety and fire propagation is unknown. This work proposes a methodology for the advanced fire calculation of single pitched-roof portal frame for an agroindustrial building according to the Spanish Specifications with the structural software SAP2000. A non-linear dynamic and plastic, geometric (P-Delta and large-displacements calculation method has been developed. The different failure mechanisms and their influence are studied in terms of fire time resistance, human hazard and good safety. Also, parametric analyses were conducted: load level, rotational stiffness of the base and finally, support fire protection.

A single incision transaxillary thoracoscopic sympathectomy

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Marić Nebojša

2014-01-01

Full Text Available Background/Aim. Primary hyperhidrosis causes are unknown. The disorder begins in early childhood. It intensifies in puberty and maturity. It is equally present in both sexes. The symptoms exacerbate when the body temperature rises and due to emotional stimuli affecting the sympathetic nerve system. The aim of this study was to demonstrate that videoassisted thoracoscopic surgery (VATS sympathectomy is a method for primary focal hyperhidrosis permanent treatment. The single incision method in properly selected patients maximizes the intervention effectiveness and minimizes aesthetic side effects. Methods. This prospective study analysed the findings in patients who had been operated on due to primary focal hyperhidrosis (face, palms, and armpits using a single small transaxilarry incision in the third inter-rib space at the level of the anterior axillary line with two 5 mm flexible ports. All the patients, with T2-T5 thoracoscopic sympathectomy of the sympathetic chain using a single small incision in the third inter-rib space in the anterior axillary line, were analysed in the period from September 2009 to November 2010 regarding the postoperative morbidity and outcomes of the operation (clinical evaluation and visual analogue scale with a view to assessing the effectiveness of the surgery conducted in this manner. Results. A total of 47 patients (18 men, 29 women, 18 to 48 years old (29 on average had underwent 94 bilateral video-assisted thoracoscopic sympathectomies. The sympathectomy was indicated in cases of facial blushing and sweating (6.38%, palmary sweating (34.04%, axillary sweating (14.89% or both palmary and axillary sweating (44.68%. The largest percentage of patients (98.6% had left the hospital the following day. The postoperative 30 day’s mortality was 0 and the conversion into open surgery was not necessary. As for complications, there had been an occurrence of partial pneumothorax in two patients treated by means of

Single site laparoscopic right hemicolectomy: an oncological feasible option

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Lim Yon Kuei

2010-09-01

Full Text Available Abstract Introduction We present the first 7 cases of single site right hemicolectomy in Asia using the new Single Site Laparoscopy (SSL access system from Ethicon Endo-surgery. Methods Right hemicolectomy was performed using the new Single Site Laparoscopy (SSL access system. Patient demographics, operative time, histology and post operative recovery and complications were collected and analysed. Results The median operative time was 90 mins (range 60 - 150 mins and a median wound size of 2.5 cm (range 2 to 4.5 cm. The median number of lymph nodes harvested was 24 (range 20 to 34 lymph nodes. The median length of proximal margin was 70 mm (range 30 to 145 mm and that of distal margin was 50 mm (35 to 120 mm. All patients had a median hospital stay of 7 days (range 5 to 11 and there were no significant perioperative complications except for 1 patient who had a minor myocardial event. Conclusion Right hemicolectomy using SSL access system is feasible and safe for oncologic surgery.

Towards radiocarbon dating of single foraminifera with a gas ion source

Science.gov (United States)

Wacker, L.; Lippold, J.; Molnár, M.; Schulz, H.

2013-01-01

Carbonate shells from foraminifera are often analysed for radiocarbon to determine the age of deep-sea sediments or to assess radiocarbon reservoir ages. However, a single foraminiferal test typically contains only a few micrograms of carbon, while most laboratories require more than 100 μg for radiocarbon dating with an accelerator mass spectrometry (AMS) system. The collection of the required amount of foraminifera for a single analyses is therefore time consuming and not always possible. Here, we present a convenient method to measure the radiocarbon content of foraminifera using an AMS system fitted with a gas ion source. CO2 is liberated from 150 to 1150 μg of carbonate in septum sealed vials by acid decomposition of the carbonate. The CO2 is collected on a zeolite trap and subsequently transferred to a syringe from where it is delivered to the ion source. A sample of 400 μg (50 μg C) typically gives a 12C- ion source current of 10-15 μA over 20 min, yielding a measurement precision of less than 7 per mil for a modern sample. Using this method, we were able to date a single 560 μg Cibicides pseudoungerianus test at 14,030 ± 160 radiocarbon years. Only a minor modification to our existing gas handling system was required and the system is fully automatable to further reduce the effort involved for sample preparation.

Towards radiocarbon dating of single foraminifera with a gas ion source

International Nuclear Information System (INIS)

Wacker, L.; Lippold, J.; Molnár, M.; Schulz, H.

2013-01-01

Carbonate shells from foraminifera are often analysed for radiocarbon to determine the age of deep-sea sediments or to assess radiocarbon reservoir ages. However, a single foraminiferal test typically contains only a few micrograms of carbon, while most laboratories require more than 100 μg for radiocarbon dating with an accelerator mass spectrometry (AMS) system. The collection of the required amount of foraminifera for a single analyses is therefore time consuming and not always possible. Here, we present a convenient method to measure the radiocarbon content of foraminifera using an AMS system fitted with a gas ion source. CO 2 is liberated from 150 to 1150 μg of carbonate in septum sealed vials by acid decomposition of the carbonate. The CO 2 is collected on a zeolite trap and subsequently transferred to a syringe from where it is delivered to the ion source. A sample of 400 μg (50 μg C) typically gives a 12 C − ion source current of 10–15 μA over 20 min, yielding a measurement precision of less than 7 per mil for a modern sample. Using this method, we were able to date a single 560 μg Cibicides pseudoungerianus test at 14,030 ± 160 radiocarbon years. Only a minor modification to our existing gas handling system was required and the system is fully automatable to further reduce the effort involved for sample preparation.

Towards radiocarbon dating of single foraminifera with a gas ion source

Energy Technology Data Exchange (ETDEWEB)

Wacker, L., E-mail: wacker@phys.ethz.ch [Laboratory of Ion Beam Physics, ETH Zurich, 8093 Zurich (Switzerland); Lippold, J. [Heidelberg Academy of Sciences, 69120 Heidelberg (Germany); Molnar, M. [Laboratory of Ion Beam Physics, ETH Zurich, 8093 Zurich (Switzerland); Institute of Nuclear Research, Hungarian Academy of Sciences, 4026 Debrecen (Hungary); Schulz, H. [Institute for Geosciencies, University of Tuebingen, 72076 Tuebingen (Germany)

2013-01-15

Carbonate shells from foraminifera are often analysed for radiocarbon to determine the age of deep-sea sediments or to assess radiocarbon reservoir ages. However, a single foraminiferal test typically contains only a few micrograms of carbon, while most laboratories require more than 100 {mu}g for radiocarbon dating with an accelerator mass spectrometry (AMS) system. The collection of the required amount of foraminifera for a single analyses is therefore time consuming and not always possible. Here, we present a convenient method to measure the radiocarbon content of foraminifera using an AMS system fitted with a gas ion source. CO{sub 2} is liberated from 150 to 1150 {mu}g of carbonate in septum sealed vials by acid decomposition of the carbonate. The CO{sub 2} is collected on a zeolite trap and subsequently transferred to a syringe from where it is delivered to the ion source. A sample of 400 {mu}g (50 {mu}g C) typically gives a {sup 12}C{sup -} ion source current of 10-15 {mu}A over 20 min, yielding a measurement precision of less than 7 per mil for a modern sample. Using this method, we were able to date a single 560 {mu}g Cibicides pseudoungerianus test at 14,030 {+-} 160 radiocarbon years. Only a minor modification to our existing gas handling system was required and the system is fully automatable to further reduce the effort involved for sample preparation.

Analyses of integrated aircraft cabin contaminant monitoring network based on Kalman consensus filter.

Science.gov (United States)

Wang, Rui; Li, Yanxiao; Sun, Hui; Chen, Zengqiang

2017-11-01

The modern civil aircrafts use air ventilation pressurized cabins subject to the limited space. In order to monitor multiple contaminants and overcome the hypersensitivity of the single sensor, the paper constructs an output correction integrated sensor configuration using sensors with different measurement theories after comparing to other two different configurations. This proposed configuration works as a node in the contaminant distributed wireless sensor monitoring network. The corresponding measurement error models of integrated sensors are also proposed by using the Kalman consensus filter to estimate states and conduct data fusion in order to regulate the single sensor measurement results. The paper develops the sufficient proof of the Kalman consensus filter stability when considering the system and the observation noises and compares the mean estimation and the mean consensus errors between Kalman consensus filter and local Kalman filter. The numerical example analyses show the effectiveness of the algorithm. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Stable carbon isotope analyses of nanogram quantities of particulate organic carbon (pollen) with laser ablation nano combustion gas chromatography/isotope ratio mass spectrometry

Science.gov (United States)

Sluijs, Appy; Laks, Jelmer J.; Reichart, Gert‐Jan

2016-01-01

Rationale Analyses of stable carbon isotope ratios (δ 13C values) of organic and inorganic matter remains have been instrumental for much of our understanding of present and past environmental and biological processes. Until recently, the analytical window of such analyses has been limited to samples containing at least several μg of carbon. Methods Here we present a setup combining laser ablation, nano combustion gas chromatography and isotope ratio mass spectrometry (LA/nC/GC/IRMS). A deep UV (193 nm) laser is used for optimal fragmentation of organic matter with minimum fractionation effects and an exceptionally small ablation chamber and combustion oven are used to reduce the minimum sample mass requirement compared with previous studies. Results Analyses of the international IAEA CH‐7 polyethylene standard show optimal accuracy, and precision better than 0.5‰, when measuring at least 42 ng C. Application to untreated modern Eucalyptus globulus (C3 plant) and Zea mays (C4 plant) pollen grains shows a ~ 16‰ offset between these species. Within each single Z. mays pollen grain, replicate analyses show almost identical δ 13C values. Conclusions Isotopic offsets between individual pollen grains exceed analytical uncertainties, therefore probably reflecting interspecimen variability of ~0.5–0.9‰. These promising results set the stage for investigating both δ 13C values and natural carbon isotopic variability between single specimens of a single population of all kinds of organic particles yielding tens of nanograms of carbon. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd. PMID:27766694

Single-Parent Families: The Role of Parent's and Child's Gender on Academic Achievement

Science.gov (United States)

Lee, Sang Min; Kushner, Jason

2008-01-01

Using national survey data, the present study investigated whether adolescents living with parents of their same gender fare better on academic achievement than their peers living with opposite-gender parents. Multiple analyses of covariance (MANCOVA) procedures were employed to examine the effects of the children's gender in single-father and…

Single-photon sources based on single molecules in solids

International Nuclear Information System (INIS)

Moerner, W E

2004-01-01

Single molecules in suitable host crystals have been demonstrated to be useful single-photon emitters both at liquid-helium temperatures and at room temperature. The low-temperature source achieved controllable emission of single photons from a single terrylene molecule in p-terphenyl by an adiabatic rapid passage technique. In contrast with almost all other single-molecule systems, terrylene single molecules show extremely high photostability under continuous, high-intensity irradiation. A room-temperature source utilizing this material has been demonstrated, in which fast pumping into vibrational sidebands of the electronically excited state achieved efficient inversion of the emissive level. This source yielded a single-photon emission probability p(1) of 0.86 at a detected count rate near 300 000 photons s -1 , with very small probability of emission of more than one photon. Thus, single molecules in solids can be considered as contenders for applications of single-photon sources such as quantum key distribution

Single photon sources with single semiconductor quantum dots

Science.gov (United States)

Shan, Guang-Cun; Yin, Zhang-Qi; Shek, Chan Hung; Huang, Wei

2014-04-01

In this contribution, we briefly recall the basic concepts of quantum optics and properties of semiconductor quantum dot (QD) which are necessary to the understanding of the physics of single-photon generation with single QDs. Firstly, we address the theory of quantum emitter-cavity system, the fluorescence and optical properties of semiconductor QDs, and the photon statistics as well as optical properties of the QDs. We then review the localization of single semiconductor QDs in quantum confined optical microcavity systems to achieve their overall optical properties and performances in terms of strong coupling regime, efficiency, directionality, and polarization control. Furthermore, we will discuss the recent progress on the fabrication of single photon sources, and various approaches for embedding single QDs into microcavities or photonic crystal nanocavities and show how to extend the wavelength range. We focus in particular on new generations of electrically driven QD single photon source leading to high repetition rates, strong coupling regime, and high collection efficiencies at elevated temperature operation. Besides, new developments of room temperature single photon emission in the strong coupling regime are reviewed. The generation of indistinguishable photons and remaining challenges for practical single-photon sources are also discussed.

SM and BSM physics in single top quark at the LHC

CERN Document Server

Escobar, Carlos; The ATLAS collaboration

2017-01-01

A comprehensive review of the recent results on measurements of single top-quark production cross-sections at $\\sqrt{s}$ = 7, 8 and 13 TeV performed by the ATLAS and CMS Collaborations is presented. The cross-section measurements include inclusive, fiducial and differential results. In addition, the latest measurements, based on angular distributions in $t$-channel single-top-quark processes, of the top-quark polarisation and $W$ boson spin observables at $\\sqrt{s}$ = 8 TeV, and the analyses of the $Wtb$ vertex at $\\sqrt{s}$ = 7 and 8 TeV are also discussed. All measurements are in good agreement with predictions and no deviations from Standard Model expectations have been observed so far.

α-Tubulin Tyrosination and CLIP-170 Phosphorylation Regulate the Initiation of Dynein-Driven Transport in Neurons

Directory of Open Access Journals (Sweden)

Jeffrey J. Nirschl

2016-03-01

Full Text Available Motor-cargo recruitment to microtubules is often the rate-limiting step of intracellular transport, and defects in this recruitment can cause neurodegenerative disease. Here, we use in vitro reconstitution assays with single-molecule resolution, live-cell transport assays in primary neurons, computational image analysis, and computer simulations to investigate the factors regulating retrograde transport initiation in the distal axon. We find that phosphorylation of the cytoskeletal-organelle linker protein CLIP-170 and post-translational modifications of the microtubule track combine to precisely control the initiation of retrograde transport. Computer simulations of organelle dynamics in the distal axon indicate that while CLIP-170 primarily regulates the time to microtubule encounter, the tyrosination state of the microtubule lattice regulates the likelihood of binding. These mechanisms interact to control transport initiation in the axon in a manner sensitive to the specialized cytoskeletal architecture of the neuron.

Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Science.gov (United States)

Mitchell, Kieren J; Cooper, Alan; Phillips, Matthew J

2015-09-25

Jarvis et al. (Research Articles, 12 December 2014, p. 1320) presented molecular clock analyses that suggested that most modern bird orders diverged just after the mass extinction event at the Cretaceous-Paleogene boundary (about 66 million years ago). We demonstrate that this conclusion results from the use of a single inappropriate maximum bound, which effectively precludes the Cretaceous diversification overwhelmingly supported by previous molecular studies. Copyright © 2015, American Association for the Advancement of Science.

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

An optical channel modeling of a single mode fiber

Science.gov (United States)

Nabavi, Neda; Liu, Peng; Hall, Trevor James

2018-05-01

The evaluation of the optical channel model that accurately describes the single mode fibre as a coherent transmission medium is reviewed through analytical, numerical and experimental analysis. We used the numerical modelling of the optical transmission medium and experimental measurements to determine the polarization drift as a function of time for a fixed length of fibre. The probability distribution of the birefringence vector was derived, which is associated to the 'Poole' equation. The theory and experimental evidence that has been disclosed in the literature in the context of polarization mode dispersion - Stokes & Jones formulations and solutions for key statistics by integration of stochastic differential equations has been investigated. Besides in-depth definition of the single-mode fibre-optic channel, the modelling which concerns an ensemble of fibres each with a different instance of environmental perturbation has been analysed.

Analysis of single oil-bearing fluid inclusions in mid-Proterozoic sandstones (Roper Group, Australia)

Science.gov (United States)

Siljeström, Sandra; Volk, Herbert; George, Simon C.; Lausmaa, Jukka; Sjövall, Peter; Dutkiewicz, Adriana; Hode, Tomas

2013-12-01

Hydrocarbons and organic biomarkers extracted from black shales and other carbonaceous sedimentary rocks are valuable sources of information on the biodiversity and environment of early Earth. However, many Precambrian hydrocarbons including biomarkers are suspected of being younger contamination. An alternative approach is to study biomarkers trapped in oil-bearing fluid inclusions by bulk crushing samples and subsequently analysing the extracted hydrocarbons with gas chromatography-mass spectrometry. However, this method does not constrain the hydrocarbons to one particular oil inclusion, which means that if several different generations of oil inclusions are present in the sample, a mix of the content from these oil inclusions will be analysed. In addition, samples with few and/or small inclusions are often below the detection limit. Recently, we showed that it is possible to detect organic biomarkers in single oil-bearing fluid inclusions using time-of-flight secondary ion mass spectrometry (ToF-SIMS). In the present study, single fluid inclusion analysis has been performed on Proterozoic samples for the first time. Four individual oil-bearing fluid inclusions, found in 1430 Ma sandstone from the Roper Superbasin in Northern Australia, were analysed with ToF-SIMS. The ToF-SIMS spectra of the oil in the different inclusions are very similar to each other and are consistent with the presence of n-alkanes/branched alkanes, monocyclic alkanes, bicyclic alkanes, aromatic hydrocarbons, and tetracyclic and pentacyclic hydrocarbons. These results are in agreement with those obtained from bulk crushing of inclusions trapped in the same samples. The capability to analyse the hydrocarbon and biomarker composition of single oil-bearing fluid inclusions is a major breakthrough, as it opens up a way of obtaining molecular compositional data on ancient oils without the ambiguity of the origin of these hydrocarbons. Additionally, this finding suggests that it will be possible

Influence of solvents on the habit modification of alpha lactose monohydrate single crystals

Science.gov (United States)

Parimaladevi, P.; Srinivasan, K.

2013-02-01

Restricted evaporation of solvent method was adopted for the growth of alpha lactose monohydrate single crystals from different solvents. The crystal habits of grown crystals were analysed. The form of crystallization was confirmed by powder x-ray diffraction analysis. Thermal behaviour of the grown crystals was studied by using differential scanning calorimetry.

Biotechnologische Nutzung der Schwerelosigkeit für medizinische Forschung - Analyse humaner Zellen nach Schwerelosigkeit

DEFF Research Database (Denmark)

Grimm, Daniela Gabriele; Bauer, Johann; Hemmersbach, Ruth

2013-01-01

For periods of time ranging from 22 seconds in parabolic flights and up to two weeks on sattilites, human cells were exposed to real or simulated weightlessness on a Random Positioning Machine and a 2D clinostat and analysed afterwards. By this approach we can increase our knowledge regarding...... health problems of space travellers and in parallel we get new information concerning several diseases of humans on Earth. Surprisingly, we also observed that single cells exposed to simulated microgravity assemble to three-dimensional aggregates resembling the tissues from which these cells...

Pathological mechanisms underlying single large‐scale mitochondrial DNA deletions

Science.gov (United States)

Rocha, Mariana C.; Rosa, Hannah S.; Grady, John P.; Blakely, Emma L.; He, Langping; Romain, Nadine; Haller, Ronald G.; Newman, Jane; McFarland, Robert; Ng, Yi Shiau; Gorman, Grainne S.; Schaefer, Andrew M.; Tuppen, Helen A.; Taylor, Robert W.

2018-01-01

Objective Single, large‐scale deletions in mitochondrial DNA (mtDNA) are a common cause of mitochondrial disease. This study aimed to investigate the relationship between the genetic defect and molecular phenotype to improve understanding of pathogenic mechanisms associated with single, large‐scale mtDNA deletions in skeletal muscle. Methods We investigated 23 muscle biopsies taken from adult patients (6 males/17 females with a mean age of 43 years) with characterized single, large‐scale mtDNA deletions. Mitochondrial respiratory chain deficiency in skeletal muscle biopsies was quantified by immunoreactivity levels for complex I and complex IV proteins. Single muscle fibers with varying degrees of deficiency were selected from 6 patient biopsies for determination of mtDNA deletion level and copy number by quantitative polymerase chain reaction. Results We have defined 3 “classes” of single, large‐scale deletion with distinct patterns of mitochondrial deficiency, determined by the size and location of the deletion. Single fiber analyses showed that fibers with greater respiratory chain deficiency harbored higher levels of mtDNA deletion with an increase in total mtDNA copy number. For the first time, we have demonstrated that threshold levels for complex I and complex IV deficiency differ based on deletion class. Interpretation Combining genetic and immunofluorescent assays, we conclude that thresholds for complex I and complex IV deficiency are modulated by the deletion of complex‐specific protein‐encoding genes. Furthermore, removal of mt‐tRNA genes impacts specific complexes only at high deletion levels, when complex‐specific protein‐encoding genes remain. These novel findings provide valuable insight into the pathogenic mechanisms associated with these mutations. Ann Neurol 2018;83:115–130 PMID:29283441

Item response theory analysis of the life orientation test-revised: age and gender differential item functioning analyses.

Science.gov (United States)

Steca, Patrizia; Monzani, Dario; Greco, Andrea; Chiesi, Francesca; Primi, Caterina

2015-06-01

This study is aimed at testing the measurement properties of the Life Orientation Test-Revised (LOT-R) for the assessment of dispositional optimism by employing item response theory (IRT) analyses. The LOT-R was administered to a large sample of 2,862 Italian adults. First, confirmatory factor analyses demonstrated the theoretical conceptualization of the construct measured by the LOT-R as a single bipolar dimension. Subsequently, IRT analyses for polytomous, ordered response category data were applied to investigate the items' properties. The equivalence of the items across gender and age was assessed by analyzing differential item functioning. Discrimination and severity parameters indicated that all items were able to distinguish people with different levels of optimism and adequately covered the spectrum of the latent trait. Additionally, the LOT-R appears to be gender invariant and, with minor exceptions, age invariant. Results provided evidence that the LOT-R is a reliable and valid measure of dispositional optimism. © The Author(s) 2014.

Thermal Safety Analyses for the Production of Plutonium-238 at the High Flux Isotope Reactor

Energy Technology Data Exchange (ETDEWEB)

Hurt, Christopher J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Freels, James D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hobbs, Randy W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Jain, Prashant K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Maldonado, G. Ivan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2016-08-01

There has been a considerable effort over the previous few years to demonstrate and optimize the production of plutonium-238 (²³⁸Pu) at the High Flux Isotope Reactor (HFIR). This effort has involved resources from multiple divisions and facilities at the Oak Ridge National Laboratory (ORNL) to demonstrate the fabrication, irradiation, and chemical processing of targets containing neptunium-237 (²³⁷Np) dioxide (NpO₂)/aluminum (Al) cermet pellets. A critical preliminary step to irradiation at the HFIR is to demonstrate the safety of the target under irradiation via documented experiment safety analyses. The steady-state thermal safety analyses of the target are simulated in a finite element model with the COMSOL Multiphysics code that determines, among other crucial parameters, the limiting maximum temperature in the target. Safety analysis efforts for this model discussed in the present report include: (1) initial modeling of single and reduced-length pellet capsules in order to generate an experimental knowledge base that incorporate initial non-linear contact heat transfer and fission gas equations, (2) modeling efforts for prototypical designs of partially loaded and fully loaded targets using limited available knowledge of fabrication and irradiation characteristics, and (3) the most recent and comprehensive modeling effort of a fully coupled thermo-mechanical approach over the entire fully loaded target domain incorporating burn-up dependent irradiation behavior and measured target and pellet properties, hereafter referred to as the production model. These models are used to conservatively determine several important steady-state parameters including target stresses and temperatures, the limiting condition of which is the maximum temperature with respect to the melting point. The single pellet model results provide a basis for the safety of the irradiations, followed by parametric analyses in the initial prototypical designs

Wrinkle-Free Single-Crystal Graphene Wafer Grown on Strain-Engineered Substrates.

Science.gov (United States)

Deng, Bing; Pang, Zhenqian; Chen, Shulin; Li, Xin; Meng, Caixia; Li, Jiayu; Liu, Mengxi; Wu, Juanxia; Qi, Yue; Dang, Wenhui; Yang, Hao; Zhang, Yanfeng; Zhang, Jin; Kang, Ning; Xu, Hongqi; Fu, Qiang; Qiu, Xiaohui; Gao, Peng; Wei, Yujie; Liu, Zhongfan; Peng, Hailin

2017-12-26

Wrinkles are ubiquitous for graphene films grown on various substrates by chemical vapor deposition at high temperature due to the strain induced by thermal mismatch between the graphene and substrates, which greatly degrades the extraordinary properties of graphene. Here we show that the wrinkle formation of graphene grown on Cu substrates is strongly dependent on the crystallographic orientations. Wrinkle-free single-crystal graphene was grown on a wafer-scale twin-boundary-free single-crystal Cu(111) thin film fabricated on sapphire substrate through strain engineering. The wrinkle-free feature of graphene originated from the relatively small thermal expansion of the Cu(111) thin film substrate and the relatively strong interfacial coupling between Cu(111) and graphene, based on the strain analyses as well as molecular dynamics simulations. Moreover, we demonstrated the transfer of an ultraflat graphene film onto target substrates from the reusable single-crystal Cu(111)/sapphire growth substrate. The wrinkle-free graphene shows enhanced electrical mobility compared to graphene with wrinkles.

Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy.

Science.gov (United States)

Wang, Quanli; Niemi, Jarad; Tan, Chee-Meng; You, Lingchong; West, Mike

2010-01-01

An increasingly common component of studies in synthetic and systems biology is analysis of dynamics of gene expression at the single-cell level, a context that is heavily dependent on the use of time-lapse movies. Extracting quantitative data on the single-cell temporal dynamics from such movies remains a major challenge. Here, we describe novel methods for automating key steps in the analysis of single-cell, fluorescent images-segmentation and lineage reconstruction-to recognize and track individual cells over time. The automated analysis iteratively combines a set of extended morphological methods for segmentation, and uses a neighborhood-based scoring method for frame-to-frame lineage linking. Our studies with bacteria, budding yeast and human cells, demonstrate the portability and usability of these methods, whether using phase, bright field or fluorescent images. These examples also demonstrate the utility of our integrated approach in facilitating analyses of engineered and natural cellular networks in diverse settings. The automated methods are implemented in freely available, open-source software.

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

A d-statistic for single-case designs that is equivalent to the usual between-groups d-statistic.

Science.gov (United States)

Shadish, William R; Hedges, Larry V; Pustejovsky, James E; Boyajian, Jonathan G; Sullivan, Kristynn J; Andrade, Alma; Barrientos, Jeannette L

2014-01-01

We describe a standardised mean difference statistic (d) for single-case designs that is equivalent to the usual d in between-groups experiments. We show how it can be used to summarise treatment effects over cases within a study, to do power analyses in planning new studies and grant proposals, and to meta-analyse effects across studies of the same question. We discuss limitations of this d-statistic, and possible remedies to them. Even so, this d-statistic is better founded statistically than other effect size measures for single-case design, and unlike many general linear model approaches such as multilevel modelling or generalised additive models, it produces a standardised effect size that can be integrated over studies with different outcome measures. SPSS macros for both effect size computation and power analysis are available.

Protein fraction heterogeneity in donkey’s milk analysed by proteomic methods

Directory of Open Access Journals (Sweden)

G. D'Urso

2010-04-01

Full Text Available Donkey’s milk is often well tolerate by patients affected by cow’s milk protein allergy, probably thanks to its protein composition. This empiric evidence, confirmed by some clinical trials, needs to be better investigated. A preliminary survey on the protein fraction of donkey’s milk was carried out: fifty-six individual milk samples have been collected and analysed by IEF and SDS-PAGE. Five different IEF patterns have been identified, showing a marked heterogeneity both in casein and whey protein fractions. A single IEF pattern showed an apparent reduced amount of casein fraction highlighted by SDS. Three of the five IEF patterns have been further investigated by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS.

An integrated overview of spatiotemporal organization and regulation in mitosis in terms of the proteins in the functional supercomplexes

Directory of Open Access Journals (Sweden)

Yueyuan eZheng

2014-10-01

Full Text Available Eukaryotic cells may divide via the critical cellular process of cell division/mitosis, resulting in two daughter cells with the same genetic information. A large number of dedicated proteins are involved in this process and spatiotemporally assembled into three distinct super-complex structures/organelles, including the centrosome/spindle pole body, kinetochore/centromere and cleavage furrow/midbody/bud neck, so as to precisely modulate the cell division/mitosis events of chromosome alignment, chromosome segregation and cytokinesis in an orderly fashion. In recent years, many efforts have been made to identify the protein components and architecture of these subcellular organelles, aiming to uncover the organelle assembly pathways, determine the molecular mechanisms underlying the organelle functions, and thereby provide new therapeutic strategies for a variety of diseases. However, the organelles are highly dynamic structures, making it difficult to identify the entire components. Here, we review the current knowledge of the identified protein components governing the organization and functioning of organelles, especially in human and yeast cells, and discuss the multi-localized protein components mediating the communication between organelles during cell division.

Validating experimental and theoretical Langmuir probe analyses

Science.gov (United States)

Pilling, L. S.; Carnegie, D. A.

2007-08-01

Analysis of Langmuir probe characteristics contains a paradox in that it is unknown a priori which theory is applicable before it is applied. Often theories are assumed to be correct when certain criteria are met although they may not validate the approach used. We have analysed the Langmuir probe data from cylindrical double and single probes acquired from a dc discharge plasma over a wide variety of conditions. This discharge contains a dual-temperature distribution and hence fitting a theoretically generated curve is impractical. To determine the densities, an examination of the current theories was necessary. For the conditions where the probe radius is the same order of magnitude as the Debye length, the gradient expected for orbital-motion limited (OML) is approximately the same as the radial-motion gradients. An analysis of the 'gradients' from the radial-motion theory was able to resolve the differences from the OML gradient value of two. The method was also able to determine whether radial or OML theories applied without knowledge of the electron temperature, or separation of the ion and electron contributions. Only the value of the space potential is necessary to determine the applicable theory.

Preparation and characterization of single-crystal multiferroic nanofiber composites

Energy Technology Data Exchange (ETDEWEB)

Ren, Zhaohui; Xiao, Zhen; Yin, Simin; Mai, Jiangquan; Liu, Zhenya; Xu, Gang; Li, Xiang; Shen, Ge [State Key Lab of Silicon Materials, Department of Material Science and Engineering, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou 310027 (China); Han, Gaorong, E-mail: hgr@zju.edu.cn [State Key Lab of Silicon Materials, Department of Material Science and Engineering, Cyrus Tang Center for Sensor Materials and Applications, Zhejiang University, Hangzhou 310027 (China)

2013-03-05

Graphical abstract: One-dimensional single-crystal multiferroic composites composed of PbTiO{sub 3} nanofiber-CoFe{sub 2}O{sub 4} nanodot have been prepared for the first time by a facile in situ solid state sintering method. The composites demonstrate ferroelectricity and ferromagnetism as well as strong coupling between them. Highlights: ► 1D single-crystal multiferroic PTO-CFO was prepared via in situ solid state sintering method. ► A simple epitaxial growth relation has been found between the PTO–CFO composites. ► The composites reveal ferroelectricity and ferromagnetism as well as coupling between them. -- Abstract: One-dimensional single-crystal multiferroic composites consisting of PbTiO{sub 3} (PTO) nanofiber-CoFe{sub 2}O{sub 4} (CFO) nanodot were prepared using an in situ solid state sintering method, where pre-perovskite PTO nanofibers and CFO nanodots were used as precursors. Structural analyses by using transmission electron microscopy, scanning electron microscopy and X-ray diffraction determined a epitaxial growth relation between the PTO nanofiber and the CFO nanodot. Ferromagnetism and ferroelectricity of the nanofiber composites were investigated by using vibarting sample magnetometer (VSM) and piezoresponse force microscopy (PFM)

A neutral glyoxal gel electrophoresis method for the detection and semi-quantitation of DNA single-strand breaks.

Science.gov (United States)

Pachkowski, Brian; Nakamura, Jun

2013-01-01

Single-strand breaks are among the most prevalent lesions found in DNA. Traditional electrophoretic methods (e.g., the Comet assay) used for investigating these lesions rely on alkaline conditions to denature DNA prior to electrophoresis. However, the presence of alkali-labile sites in DNA can result in the introduction of additional single-strand breaks upon alkali treatment during DNA sample processing. Herein, we describe a neutral glyoxal gel electrophoresis assay which is based on alkali-free DNA denaturation and is suitable for qualitative and semi-quantitative analyses of single-strand breaks in DNA isolated from different organisms.

A new support measure to quantify the impact of local optima in phylogenetic analyses.

KAUST Repository

Brammer, Grant

2011-09-29

Phylogentic analyses are often incorrectly assumed to have stabilized to a single optimum. However, a set of trees from a phylogenetic analysis may contain multiple distinct local optima with each optimum providing different levels of support for each clade. For situations with multiple local optima, we propose p-support which is a clade support measure that shows the impact optima have on a final consensus tree. Our p-support measure is implemented in our PeakMapper software package. We study our approach on two published, large-scale biological tree collections. PeakMapper shows that each data set contains multiple local optima. p-support shows that both datasets contain clades in the majority consensus tree that are only supported by a subset of the local optima. Clades with low p-support are most likely to benefit from further investigation. These tools provide researchers with new information regarding phylogenetic analyses beyond what is provided by other support measures alone.

Subcellular distribution of uranium in the roots of Spirodela punctata and surface interactions

Energy Technology Data Exchange (ETDEWEB)

Nie, Xiaoqin, E-mail: xiaoqin_nie@163.com [Fundamental Science on Nuclear Wastes and Environmental Safety Laboratory, Mianyang 621010 (China); Key Laboratory of Radiation Physics and Technology (Sichuan University), Ministry of Education, Institute of Nuclear Science and Technology, Sichuan University, Chengdu 610064 (China); Dong, Faqin, E-mail: fqdong2004@163.com [Fundamental Science on Nuclear Wastes and Environmental Safety Laboratory, Mianyang 621010 (China); Liu, Ning [Key Laboratory of Radiation Physics and Technology (Sichuan University), Ministry of Education, Institute of Nuclear Science and Technology, Sichuan University, Chengdu 610064 (China); Liu, Mingxue [Fundamental Science on Nuclear Wastes and Environmental Safety Laboratory, Mianyang 621010 (China); Zhang, Dong; Kang, Wu [Institute of Nuclear Physics and Chemistry,China Academy of Engineering Physics, Mianyang 621900 (China); Sun, Shiyong; Zhang, Wei; Yang, Jie [Fundamental Science on Nuclear Wastes and Environmental Safety Laboratory, Mianyang 621010 (China)

2015-08-30

Graphical abstract: - Highlights: • The proportion of uranium concentration approximate as 8:2:1 in the cell wall organelle and cytosol fractions of roots of S. punctata. • The particles including 35% Fe (wt%) released from the cells after 100 mg/L U treatment 48 h. • Most of the uranium bound onto the root surface and contacted with phosphorus ligands and formed as nano-scales U-P lamellar crystal. • FTIR and XPS analyses result indicates the uranium changed the band position and shapes of phosphate group, and the region of characteristic peak belongs to U(VI) and U(IV) were also observed. - Abstract: The subcellular distribution of uranium in roots of Spirodela punctata (duckweed) and the process of surface interaction were studied upon exposure to U (0, 5–200 mg/L) at pH 5. The concentration of uranium in each subcelluar fraction increased significantly with increasing solution U level, after 200 mg/L uranium solution treatment 120 h, the proportion of uranium concentration approximate as 8:2:1 in the cell wall organelle and cytosol fractions of roots of S. punctata. OM SEM and EDS showed after 5–200 mg/L U treatment 4–24 h, some intracellular fluid released from the root cells, after 100 mg/L U treatment 48 h, the particles including 35% Fe (wt%) and other organic matters such as EPS released from the cells, most of the uranium bound onto the root surface and contacted with phosphorus ligands and formed as nano-scales U-P lamellar crystal, similar crystal has been found in the cell wall and organelle fractions after 50 mg/L U treatment 120 h. FTIR and XPS analyses result indicates the uranium changed the band position and shapes of phosphate group, and the region of characteristic peak belongs to U(VI) and U(IV) were also observed.

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......The quantitative and qualitative description of laser beam characteristics is important for process implementation and optimisation. In particular, a need for quantitative characterisation of beam diameter was identified when using fibre lasers for micro manufacturing. Here the beam diameter limits...... 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...

An FtsH protease is recruited to the mitochondrion of Plasmodium falciparum.

Directory of Open Access Journals (Sweden)

Aiman Tanveer

Full Text Available The two organelles, apicoplast and mitochondrion, of the malaria parasite Plasmodium falciparum have unique morphology in liver and blood stages; they undergo complex branching and looping prior to division and segregation into daughter merozoites. Little is known about the molecular processes and proteins involved in organelle biogenesis in the parasite. We report the identification of an AAA+/FtsH protease homolog (PfFtsH1 that exhibits ATP- and Zn(2+-dependent protease activity. PfFtsH1 undergoes processing, forms oligomeric assemblies, and is associated with the membrane fraction of the parasite cell. Generation of a transfectant parasite line with hemagglutinin-tagged PfFtsH1, and immunofluorescence assay with anti-PfFtsH1 Ab demonstrated that the protein localises to P. falciparum mitochondria. Phylogenetic analysis and the single transmembrane region identifiable in PfFtsH1 suggest that it is an i-AAA like inner mitochondrial membrane protein. Expression of PfFtsH1 in Escherichia coli converted a fraction of bacterial cells into division-defective filamentous forms implying a sequestering effect of the Plasmodium factor on the bacterial homolog, indicative of functional conservation with EcFtsH. These results identify a membrane-associated mitochondrial AAA+/FtsH protease as a candidate regulatory protein for organelle biogenesis in P. falciparum.

Systematics of intermediate-energy single-nucleon removal cross sections

Science.gov (United States)

Tostevin, J. A.; Gade, A.

2014-11-01

There is now a large and increasing body of experimental data and theoretical analyses for reactions that remove a single nucleon from an intermediate-energy beam of neutron- or proton-rich nuclei. In each such measurement, one obtains the inclusive cross section for the population of all bound final states of the mass A -1 reaction residue. These data, from different regions of the nuclear chart, and that involve weakly and strongly bound nucleons, are compared with theoretical expectations. These calculations include an approximate treatment of the reaction dynamics and shell-model descriptions of the projectile initial state, the bound final states of the residues, and the single-particle strengths computed from their overlap functions. The results are discussed in the light of recent data, more exclusive tests of the eikonal dynamical description, and calculations that take input from more microscopic nuclear structure models.

Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides.

Science.gov (United States)

Ducani, Cosimo; Kaul, Corinna; Moche, Martin; Shih, William M; Högberg, Björn

2013-07-01

Single-stranded oligonucleotides are important as research tools, as diagnostic probes, in gene therapy and in DNA nanotechnology. Oligonucleotides are typically produced via solid-phase synthesis, using polymer chemistries that are limited relative to what biological systems produce. The number of errors in synthetic DNA increases with oligonucleotide length, and the resulting diversity of sequences can be a problem. Here we present the 'monoclonal stoichiometric' (MOSIC) method for enzyme-mediated production of DNA oligonucleotides. We amplified oligonucleotides from clonal templates derived from single bacterial colonies and then digested cutter hairpins in the products, which released pools of oligonucleotides with precisely controlled relative stoichiometric ratios. We prepared 14-378-nucleotide MOSIC oligonucleotides either by in vitro rolling-circle amplification or by amplification of phagemid DNA in Escherichia coli. Analyses of the formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides.

Influence of gender, single-sex and co-educational schooling on students' enjoyment and achievement in mathematics

Science.gov (United States)

Prendergast, Mark; O'Donoghue, John

2014-11-01

This research investigates the influence that gender, single-sex and co-educational schooling can have on students' mathematics education in second-level Irish classrooms. Although gender differences in mathematics education have been the subject of research for many years, recent results from PISA (Programme for International Student Assessment) show that there are still marked differences between the achievement and attitude of male and female students in Irish mathematics classrooms. This paper examines the influence of gender in more detail and also investigates the impact of single-sex or co-educational schooling. This is a follow on study which further analyses data collected by the authors when they designed a pedagogical framework and used this to develop, implement and evaluate a teaching intervention in four second-level Irish schools. The aim of this pedagogical framework was to promote student interest in the topic of algebra through effective teaching of the domain. This paper further analyses the quantitative data collected and investigates whether there were differences in students' enjoyment and achievement scores based on their gender and whether they attended single-sex or co-educational schools.

Mapping and characterizing N6-methyladenine in eukaryotic genomes using single molecule real-time sequencing.

Science.gov (United States)

Zhu, Shijia; Beaulaurier, John; Deikus, Gintaras; Wu, Tao; Strahl, Maya; Hao, Ziyang; Luo, Guanzheng; Gregory, James A; Chess, Andrew; He, Chuan; Xiao, Andrew; Sebra, Robert; Schadt, Eric E; Fang, Gang

2018-05-15

N6-methyladenine (m6dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes, however, methods for high resolution mapping of m6dA events are still lacking. Single-molecule real-time (SMRT) sequencing has enabled the detection of m6dA events at single-nucleotide resolution in prokaryotic genomes, but its application to detecting m6dA in eukaryotic genomes has not been rigorously examined. Herein, we identified unique characteristics of eukaryotic m6dA methylomes that fundamentally differ from those of prokaryotes. Based on these differences, we describe the first approach for mapping m6dA events using SMRT sequencing specifically designed for the study of eukaryotic genomes, and provide appropriate strategies for designing experiments and carrying out sequencing in future studies. We apply the novel approach to study two eukaryotic genomes. For green algae, we construct the first complete genome-wide map of m6dA at single nucleotide and single molecule resolution. For human lymphoblastoid cells (hLCLs), joint analyses of SMRT sequencing and independent sequencing data suggest that putative m6dA events are enriched in the promoters of young, full length LINE-1 elements (L1s). These analyses demonstrate a general method for rigorous mapping and characterization of m6dA events in eukaryotic genomes. Published by Cold Spring Harbor Laboratory Press.

Grundlegende quantitative Analysen medizinischer Prüfungen [Basic quantitative analyses of medical examinations

Directory of Open Access Journals (Sweden)

Möltner, Andreas

2006-08-01

Full Text Available [english] The evaluation steps are described which are necessary for an elementary test-theoretic analysis of an exam and sufficient as a basis of item-revisions, improvements of the composition of tests and feedback to teaching coordinators and curriculum developers. These steps include the evaluation of the results, the analysis of item difficulty and discrimination and - where appropriate - the corresponding evaluation of single answers. To complete the procedure, the internal consistency is determined, which makes an estimate of the reliability and significance of the examination. [german] Es werden die Auswertungsschritte beschrieben, die für eine einfache testtheoretische Analyse einer Prüfung notwendig sowie als Grundlage von Aufgabenrevisionen, Verbesserungen von Prüfungszusammenstellungen und Rückmeldung an Lehrbeauftragte und Curriculumsentwickler ausreichend sind. Diese Schritte umfassen die Ergebnisauswertung, die Analyse der Aufgabenschwierigkeiten und der Trennschärfen, sowie - wo angebracht - die entsprechenden Auswertungen der Einzelantworten. Vervollständigt wird das Vorgehen durch die Bestimmung der internen Konsistenz, durch die die Zuverlässigkeit und Aussagekraft (Reliabilität der Prüfung abgeschätzt wird.

A simple route to the synthesis of single crystalline copper metagermanate nanowires

Energy Technology Data Exchange (ETDEWEB)

Pei, L.Z., E-mail: lzpei@ahut.edu.cn [School of Materials Science and Engineering, Institute of Molecular Engineering and Applied Chemistry, Key Lab of Materials Science and Processing of Anhui Province, Anhui University of Technology, Ma' anshan, Anhui 243002 (China); Zhao, H.S. [School of Materials Science and Engineering, Institute of Molecular Engineering and Applied Chemistry, Key Lab of Materials Science and Processing of Anhui Province, Anhui University of Technology, Ma' anshan, Anhui 243002 (China); Tan, W. [Henkel Huawei Electronics Co. Ltd., Lian' yungang, Jiangsu 222006 (China); Yu, H.Y. [School of Materials Science and Engineering, Institute of Molecular Engineering and Applied Chemistry, Key Lab of Materials Science and Processing of Anhui Province, Anhui University of Technology, Ma' anshan, Anhui 243002 (China); Chen, Y.W. [Department of Materials Science, Fudan University, Shanghai 200433 (China); Zhang Qianfeng; Fan, C.G. [School of Materials Science and Engineering, Institute of Molecular Engineering and Applied Chemistry, Key Lab of Materials Science and Processing of Anhui Province, Anhui University of Technology, Ma' anshan, Anhui 243002 (China)

2009-12-15

Single crystalline copper metagermanate (CuGeO{sub 3}) nanowires with the diameter of 30-300 nm and length of longer than 100 {mu}m have been prepared by a simple hydrothermal deposition route. X-ray diffraction (XRD), selected area electron diffraction (SAED), high-resolution transmission electron microscopy (HRTEM) and Raman analyses confirm that the nanowires are orthorhombic single crystals with a main growth direction along <101>. Room temperature photoluminescence (PL) measurement shows a strong blue emission peak at 442 nm with a broad emission band. The blue emission may be ascribed to radiative recombination of oxygen vacancies and oxygen-germanium vacancies. The formation process of CuGeO{sub 3} nanowires is also discussed.

Auto-ignition generated combustion. Pt. 2. Thermodynamic fundamentals; Verbrennungssteuerung durch Selbstzuendung. T. 2. Experimentelle Analyse

Energy Technology Data Exchange (ETDEWEB)

Guibert, P. [Paris-6 Univ. (France). Lab. de Mecanique Physique; Morin, C. [Paris-6 Univ. (France); Mokhtari, S.

2004-02-01

The combustion initiation by auto-ignition demonstrates benefits in NO{sub x} reduction and in process stability for both spark-ignited and compression ignited engines. Based on the better thermodynamic particularities of the auto-ignition, which have been presented in the first part, the characteristics of this process are demonstrated in the second part by experimental analysis. For comparison with similar studies, the analyses have been carried out in base of a two stroke loop scavenged spark-ignition single cylinder engine. (orig.) [German] Die Steuerung der Verbrennung durch Selbstzuendung zeigt Vorteile bezueglich Senkung der NO{sub x}-Emission und Prozessstabilitaet, sowohl bei Otto- als auch bei Dieselmotoren. Auf Grundlage der thermodynamischen Besonderheiten der Selbstzuendvorgaenge, die im ersten Teil praesentiert wurden, erfolgt im zweiten Teil eine experimentelle Betrachtung der Prozesscharakteristika. Zur Vergleichbarkeit mit aehnlichen Untersuchungen wird die experimentelle Analyse auf Basis eines Zweitakt-Einzylinder-Ottomotors mit Umkehrspuelung durchgefuehrt. (orig.)

Thermal analyses. Information on the expected baking process; Thermische analyses. Informatie over een te verwachten bakgedrag

Energy Technology Data Exchange (ETDEWEB)

Van Wijck, H. [Stichting Technisch Centrum voor de Keramische Industrie TCKI, Velp (Netherlands)

2009-09-01

The design process and the drying process for architectural ceramics and pottery partly determine the characteristics of the final product, but the largest changes occur during the baking process. An overview is provided of the different thermal analyses and how the information from these analyses can predict the process in practice. (mk) [Dutch] Het vormgevingsproces en het droogproces voor bouwkeramische producten en aardewerk bepalen voor een deel de eigenschappen van de eindproducten, maar de grootste veranderingen treden op bij het bakproces. Een overzicht wordt gegeven van de verschillende thermische analyses en hoe de informatie uit deze analyses het in de praktijk te verwachten gedrag kan voorspellen.

Chin Shan analyses show advantages of whole pool multi-rack approach

International Nuclear Information System (INIS)

Singh, K.P.; Soler, A.I.

1991-01-01

Nuclear fuel storage racks are essentially thin-walled, cellular structures of prismatic cross-section. Although the details of design vary from one supplier to another, certain key physical attributes are common to all designs. For example, all racks feature square cells of sufficient opening size and height to enable insertion and withdrawal of the fuel assembly. The array of cells is positioned in a vertical orientation and is supported off the pool slab surface by four or more support legs. The spent fuel pool is filled with the individual fuel racks. The plenum created by the support legs is essential for proper cooling of the fuel assemblies stored in the rack, which relies on natural convective cooling to extract the heat emitted by the spent fuel. However, it has the insalutary effect of making it kinematically less stable. Regulatory authorities require careful and comprehensive analysis of the response of the racks under the seismic motions postulated for the pool slab. Results from whole pool multi-rack (WPMR) analyses at the Chin Shan and Oyster Creek nuclear plants point up the potential inadequacies of single rack 3D analyses, and show just how important it is to carry out WPMR simulations, despite their abstruseness and high cost. (author)

Two-dimensional Kikuchi patterns of Si as measured using an electrostatic analyser

Energy Technology Data Exchange (ETDEWEB)

Vos, Maarten, E-mail: maarten.vos@anu.edu.au [Electronic Materials Engineering Department, Research School of Physics and Engineering, The Australian National University, Canberra 2601 (Australia); Winkelmann, Aimo [Bruker Nano GmbH, Am Studio 2D, Berlin 12489 (Germany)

2016-12-15

We present Kikuchi patterns of Si single crystals measured with an electrostatic analyser, where the kinetic energy of the diffracted electron is known with sub-eV precision. Two-dimensional patterns are acquired by rotating the crystal under computer control. This makes detailed comparison of calculated and measured distributions possible with precise knowledge of the energy of the scattered electrons. The case of Si is used to validate the method, and these experiments provide a detailed comparison of measured and calculated Kikuchi patterns. In this way, we can gain more insight on Kikuchi pattern formation in non-energy resolved measurements of conventional electron backscatter diffraction (EBSD) and electron channeling patterns (ECP). It was possible to identify the influence of channeling of the incoming beam on the measured Kikuchi pattern. The effect of energy loss on the Kikuchi pattern was established, and it is demonstrated that, under certain conditions, the channeling features have a different dependence on the energy loss compared to the Kikuchi lines. - Highlights: • Two-dimensional Kikuchi patterns measured for Silicon with electrostatic analyser. • Good agreement obtained with dynamical theory of diffraction. • Channeling effects of the incoming beam are identified.

Morphoelastic rods. Part I: A single growing elastic rod

KAUST Repository

Moulton, D.E.

2013-02-01

A theory for the dynamics and statics of growing elastic rods is presented. First, a single growing rod is considered and the formalism of three-dimensional multiplicative decomposition of morphoelasticity is used to describe the bulk growth of Kirchhoff elastic rods. Possible constitutive laws for growth are discussed and analysed. Second, a rod constrained or glued to a rigid substrate is considered, with the mismatch between the attachment site and the growing rod inducing stress. This stress can eventually lead to instability, bifurcation, and buckling. © 2012 Elsevier Ltd. All rights reserved.

Optofluidics for handling and analysis of single living cells

KAUST Repository

Perozziello, Gerardo

2017-12-07

Optofluidics is a field with important applications in areas such as biotechnology, chemical synthesis and analytical chemistry. Optofluidic devices combine optical elements into microfluidic devices in ways that increase portability and sensitivity of analysis for diagnostic or screening purposes .In fact in these devices fluids give fine adaptability, mobility and accessibility to nanoscale photonic devices which otherwise could not be realized using conventional devices. This review describes several cases inwhich optical or microfluidic approaches are used to trap single cells in proximity of integrated optical sensor for being analysed.

Optofluidics for handling and analysis of single living cells

KAUST Repository

Perozziello, Gerardo; Candeloro, Patrizio; Coluccio, Maria Laura; Di Fabrizio, Enzo M.

2017-01-01

Optofluidics is a field with important applications in areas such as biotechnology, chemical synthesis and analytical chemistry. Optofluidic devices combine optical elements into microfluidic devices in ways that increase portability and sensitivity of analysis for diagnostic or screening purposes .In fact in these devices fluids give fine adaptability, mobility and accessibility to nanoscale photonic devices which otherwise could not be realized using conventional devices. This review describes several cases inwhich optical or microfluidic approaches are used to trap single cells in proximity of integrated optical sensor for being analysed.

Morphoelastic rods. Part I: A single growing elastic rod

KAUST Repository

Moulton, D.E.; Lessinnes, T.; Goriely, A.

2013-01-01

A theory for the dynamics and statics of growing elastic rods is presented. First, a single growing rod is considered and the formalism of three-dimensional multiplicative decomposition of morphoelasticity is used to describe the bulk growth of Kirchhoff elastic rods. Possible constitutive laws for growth are discussed and analysed. Second, a rod constrained or glued to a rigid substrate is considered, with the mismatch between the attachment site and the growing rod inducing stress. This stress can eventually lead to instability, bifurcation, and buckling. © 2012 Elsevier Ltd. All rights reserved.

Overexpression of mtDNA-associated AtWhy2 compromises mitochondrial function

Directory of Open Access Journals (Sweden)

Abou-Rached Charbel

2008-04-01

Full Text Available Abstract Background StWhy1, a member of the plant-specific Whirly single-stranded DNA-binding protein family, was first characterized as a transcription factor involved in the activation of the nuclear PR-10a gene following defense-related stress in potato. In Arabidopsis thaliana, Whirlies have recently been shown to be primarily localized in organelles. Two representatives of the family, AtWhy1 and AtWhy3 are imported into plastids while AtWhy2 localizes to mitochondria. Their function in organelles is currently unknown. Results To understand the role of mitochondrial Whirlies in higher plants, we produced A. thaliana lines with altered expression of the atwhy2 gene. Organellar DNA immunoprecipitation experiments demonstrated that AtWhy2 binds to mitochondrial DNA. Overexpression of atwhy2 in plants perturbs mitochondrial function by causing a diminution in transcript levels and mtDNA content which translates into a low activity level of respiratory chain complexes containing mtDNA-encoded subunits. This lowered activity of mitochondria yielded plants that were reduced in size and had distorted leaves that exhibited accelerated senescence. Overexpression of atwhy2 also led to early accumulation of senescence marker transcripts in mature leaves. Inactivation of the atwhy2 gene did not affect plant development and had no detectable effect on mitochondrial morphology, activity of respiratory chain complexes, transcription or the amount of mtDNA present. This lack of phenotype upon abrogation of atwhy2 expression suggests the presence of functional homologues of the Whirlies or the activation of compensating mechanisms in mitochondria. Conclusion AtWhy2 is associated with mtDNA and its overexpression results in the production of dysfunctional mitochondria. This report constitutes the first evidence of a function for the Whirlies in organelles. We propose that they could play a role in the regulation of the gene expression machinery of organelles.

An Interactome-Centered Protein Discovery Approach Reveals Novel Components Involved in Mitosome Function and Homeostasis in Giardia lamblia.

Directory of Open Access Journals (Sweden)

Samuel Rout

2016-12-01

Full Text Available Protozoan parasites of the genus Giardia are highly prevalent globally, and infect a wide range of vertebrate hosts including humans, with proliferation and pathology restricted to the small intestine. This narrow ecological specialization entailed extensive structural and functional adaptations during host-parasite co-evolution. An example is the streamlined mitosomal proteome with iron-sulphur protein maturation as the only biochemical pathway clearly associated with this organelle. Here, we applied techniques in microscopy and protein biochemistry to investigate the mitosomal membrane proteome in association to mitosome homeostasis. Live cell imaging revealed a highly immobilized array of 30-40 physically distinct mitosome organelles in trophozoites. We provide direct evidence for the single giardial dynamin-related protein as a contributor to mitosomal morphogenesis and homeostasis. To overcome inherent limitations that have hitherto severely hampered the characterization of these unique organelles we applied a novel interaction-based proteome discovery strategy using forward and reverse protein co-immunoprecipitation. This allowed generation of organelle proteome data strictly in a protein-protein interaction context. We built an initial Tom40-centered outer membrane interactome by co-immunoprecipitation experiments, identifying small GTPases, factors with dual mitosome and endoplasmic reticulum (ER distribution, as well as novel matrix proteins. Through iterative expansion of this protein-protein interaction network, we were able to i significantly extend this interaction-based mitosomal proteome to include other membrane-associated proteins with possible roles in mitosome morphogenesis and connection to other subcellular compartments, and ii identify novel matrix proteins which may shed light on mitosome-associated metabolic functions other than Fe-S cluster biogenesis. Functional analysis also revealed conceptual conservation of protein

P-fimbriae in the presence of anti-PapA antibodies: new insight of antibodies action against pathogens

Science.gov (United States)

Mortezaei, Narges; Singh, Bhupender; Bullitt, Esther; Uhlin, Bernt Eric; Andersson, Magnus

2013-12-01

Uropathogenic strains of Escherichia coli establish urinary tract infections by attaching to host epithelial cells using adhesive organelles called fimbriae. Fimbriae are helix-like structures with a remarkable adaptability, offering safeguarding for bacteria exposed to changing fluid forces in the urinary tract. We challenged this property of P-fimbriae by cross-linking their subunits with shaft-specific antibodies and measuring the corresponding force response at a single organelle level. Our data show compromised extension and rewinding of P-fimbriae in the presence of antibodies and reduced fimbrial elasticity, which are important properties of fimbriae contributing to the ability of bacteria to cause urinary tract infections. The reduced elasticity found by cross-linking fimbrial subunits could thus be another assignment for antibodies; in addition to marking bacteria as foreign, antibodies physically compromise fimbrial function. We suggest that our assay and results will be a starting point for further investigations aimed at inhibiting sustained bacterial adhesion by antibodies.

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate

KAUST Repository

Gornik, Sebastian G.; Febrimarsa,; Cassin, Andrew M.; MacRae, James I.; Ramaprasad, Abhinay; Rchiad, ‍ Zineb; McConville, Malcolm J.; Bacic, Antony; McFadden, Geoffrey I.; Pain, Arnab; Waller, Ross F.

2015-01-01

Organelle gain through endosymbiosis has been integral to the origin and diversification of eukaryotes, and, once gained, plastids and mitochondria seem seldom lost. Indeed, discovery of nonphotosynthetic plastids in many eukaryotes - notably, the apicoplast in apicomplexan parasites such as the malaria pathogen Plasmodium - highlights the essential metabolic functions performed by plastids beyond photosynthesis. Once a cell becomes reliant on these ancillary functions, organelle dependence is apparently difficult to overcome. Previous examples of endosymbiotic organelle loss (either mitochondria or plastids), which have been invoked to explain the origin of eukaryotic diversity, have subsequently been recognized as organelle reduction to cryptic forms, such as mitosomes and apicoplasts. Integration of these ancient symbionts with their hosts has been too well developed to reverse. Here, we provide evidence that the dinoflagellate Hematodinium sp., a marine parasite of crustaceans, represents a rare case of endosymbiotic organelle loss by the elimination of the plastid. Extensive RNA and genomic sequencing data provide no evidence for a plastid organelle, but, rather, reveal a metabolic decoupling from known plastid functions that typically impede organelle loss. This independence has been achieved through retention of ancestral anabolic pathways, enzyme relocation from the plastid to the cytosol, and metabolic scavenging from the parasite's host. Hematodinium sp. thus represents a further dimension of endosymbiosis-life after the organelle. © 2015, National Academy of Sciences. All rights reserved.

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate

KAUST Repository

Gornik, Sebastian G.

2015-04-20

Organelle gain through endosymbiosis has been integral to the origin and diversification of eukaryotes, and, once gained, plastids and mitochondria seem seldom lost. Indeed, discovery of nonphotosynthetic plastids in many eukaryotes - notably, the apicoplast in apicomplexan parasites such as the malaria pathogen Plasmodium - highlights the essential metabolic functions performed by plastids beyond photosynthesis. Once a cell becomes reliant on these ancillary functions, organelle dependence is apparently difficult to overcome. Previous examples of endosymbiotic organelle loss (either mitochondria or plastids), which have been invoked to explain the origin of eukaryotic diversity, have subsequently been recognized as organelle reduction to cryptic forms, such as mitosomes and apicoplasts. Integration of these ancient symbionts with their hosts has been too well developed to reverse. Here, we provide evidence that the dinoflagellate Hematodinium sp., a marine parasite of crustaceans, represents a rare case of endosymbiotic organelle loss by the elimination of the plastid. Extensive RNA and genomic sequencing data provide no evidence for a plastid organelle, but, rather, reveal a metabolic decoupling from known plastid functions that typically impede organelle loss. This independence has been achieved through retention of ancestral anabolic pathways, enzyme relocation from the plastid to the cytosol, and metabolic scavenging from the parasite\\'s host. Hematodinium sp. thus represents a further dimension of endosymbiosis-life after the organelle. © 2015, National Academy of Sciences. All rights reserved.

Single-particle characterization of 'Asian Dust' certified reference materials using low-Z particle electron probe X-ray microanalysis

International Nuclear Information System (INIS)

Hwang, Hee Jin; Ro, Chul-Un

2006-01-01

In order to clearly elucidate whether Asian Dust particles experience chemical modification during long-range transport, it is necessary to characterize soil particles where Asian Dust particles originate. If chemical compositions of source soil particles are well characterized, then chemical compositions of Asian Dust particles collected outside source regions can be compared with those of source soil particles in order to find out the occurrence of chemical modification. Asian Dust particles are chemically and morphologically heterogeneous, and thus the average composition and the average aerodynamic diameter (obtainable by bulk analysis) are not much relevant if the chemical modifications of the particles must be followed. The major elemental composition and abundance of the particle types that are potential subjects of chemical modification can only be obtained using single-particle analysis. A single particle analytical technique, named low-Z particle electron probe X-ray microanalysis (low-Z particle EPMA), was applied to characterize two certified reference materials (CRMs) for Asian Dust particles, which were collected from a loess plateau area and a desert of China. The CRMs were defined by bulk analyses to provide certified concentrations for 13 chemical elements. Using the low-Z particle EPMA technique, the concentrations of major chemical species such as aluminosilicates, SiO 2 , CaCO 3 , and carbonaceous species were obtained. Elemental concentrations obtained by the low-Z particle EPMA are close to the certified values, with considering that the single particle and bulk analyses employ very different approaches. There are still some discrepancies between those concentration values, resulting from analyses of particles with different sizes, different sample amounts analyzed, and uncertainties involved in the single particle analysis

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...

Linkage and related analyses of Barrett's esophagus and its associated adenocarcinomas.

Science.gov (United States)

Sun, Xiangqing; Elston, Robert; Falk, Gary W; Grady, William M; Faulx, Ashley; Mittal, Sumeet K; Canto, Marcia I; Shaheen, Nicholas J; Wang, Jean S; Iyer, Prasad G; Abrams, Julian A; Willis, Joseph E; Guda, Kishore; Markowitz, Sanford; Barnholtz-Sloan, Jill S; Chandar, Apoorva; Brock, Wendy; Chak, Amitabh

2016-07-01

Familial aggregation and segregation analysis studies have provided evidence of a genetic basis for esophageal adenocarcinoma (EAC) and its premalignant precursor, Barrett's esophagus (BE). We aim to demonstrate the utility of linkage analysis to identify the genomic regions that might contain the genetic variants that predispose individuals to this complex trait (BE and EAC). We genotyped 144 individuals in 42 multiplex pedigrees chosen from 1000 singly ascertained BE/EAC pedigrees, and performed both model-based and model-free linkage analyses, using S.A.G.E. and other software. Segregation models were fitted, from the data on both the 42 pedigrees and the 1000 pedigrees, to determine parameters for performing model-based linkage analysis. Model-based and model-free linkage analyses were conducted in two sets of pedigrees: the 42 pedigrees and a subset of 18 pedigrees with female affected members that are expected to be more genetically homogeneous. Genome-wide associations were also tested in these families. Linkage analyses on the 42 pedigrees identified several regions consistently suggestive of linkage by different linkage analysis methods on chromosomes 2q31, 12q23, and 4p14. A linkage on 15q26 is the only consistent linkage region identified in the 18 female-affected pedigrees, in which the linkage signal is higher than in the 42 pedigrees. Other tentative linkage signals are also reported. Our linkage study of BE/EAC pedigrees identified linkage regions on chromosomes 2, 4, 12, and 15, with some reported associations located within our linkage peaks. Our linkage results can help prioritize association tests to delineate the genetic determinants underlying susceptibility to BE and EAC.

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

KAUST Repository

Serag, Maged F.

2014-10-06

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

KAUST Repository

Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

2014-01-01

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

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

Intracellular dynamics and fate of polystyrene nanoparticles in A549 Lung epithelial cells monitored by image (cross-) correlation spectroscopy and single particle tracking.

Science.gov (United States)

Deville, Sarah; Penjweini, Rozhin; Smisdom, Nick; Notelaers, Kristof; Nelissen, Inge; Hooyberghs, Jef; Ameloot, Marcel

2015-10-01

Novel insights in nanoparticle (NP) uptake routes of cells, their intracellular trafficking and subcellular targeting can be obtained through the investigation of their temporal and spatial behavior. In this work, we present the application of image (cross-) correlation spectroscopy (IC(C)S) and single particle tracking (SPT) to monitor the intracellular dynamics of polystyrene (PS) NPs in the human lung carcinoma A549 cell line. The ensemble kinetic behavior of NPs inside the cell was characterized by temporal and spatiotemporal image correlation spectroscopy (TICS and STICS). Moreover, a more direct interpretation of the diffusion and flow detected in the NP motion was obtained by SPT by monitoring individual NPs. Both techniques demonstrate that the PS NP transport in A549 cells is mainly dependent on microtubule-assisted transport. By applying spatiotemporal image cross-correlation spectroscopy (STICCS), the correlated motions of NPs with the early endosomes, late endosomes and lysosomes are identified. PS NPs were equally distributed among the endolysosomal compartment during the time interval of the experiments. The cotransport of the NPs with the lysosomes is significantly larger compared to the other cell organelles. In the present study we show that the complementarity of ICS-based techniques and SPT enables a consistent elaborate model of the complex behavior of NPs inside biological systems. Copyright © 2015 Elsevier B.V. All rights reserved.

Mode I crack analysis in single crystals with anisotropic discrete dislocation plasticity : I. Formulation and crack growth

NARCIS (Netherlands)

Shishvan, Siamak Soleymani; Van der Giessen, Erik

Analyses of monotonic loading of a plane-strain mode I crack in an fcc single crystal under small-scale yielding are carried out using discrete dislocation plasticity (DDP) incorporating anisotropic elasticity. Two crystallographically symmetric crack orientations are considered where plane-strain

Assessing the validity of single-item life satisfaction measures: results from three large samples.

Science.gov (United States)

Cheung, Felix; Lucas, Richard E

2014-12-01

The present paper assessed the validity of single-item life satisfaction measures by comparing single-item measures to the Satisfaction with Life Scale (SWLS)-a more psychometrically established measure. Two large samples from Washington (N = 13,064) and Oregon (N = 2,277) recruited by the Behavioral Risk Factor Surveillance System and a representative German sample (N = 1,312) recruited by the Germany Socio-Economic Panel were included in the present analyses. Single-item life satisfaction measures and the SWLS were correlated with theoretically relevant variables, such as demographics, subjective health, domain satisfaction, and affect. The correlations between the two life satisfaction measures and these variables were examined to assess the construct validity of single-item life satisfaction measures. Consistent across three samples, single-item life satisfaction measures demonstrated substantial degree of criterion validity with the SWLS (zero-order r = 0.62-0.64; disattenuated r = 0.78-0.80). Patterns of statistical significance for correlations with theoretically relevant variables were the same across single-item measures and the SWLS. Single-item measures did not produce systematically different correlations compared to the SWLS (average difference = 0.001-0.005). The average absolute difference in the magnitudes of the correlations produced by single-item measures and the SWLS was very small (average absolute difference = 0.015-0.042). Single-item life satisfaction measures performed very similarly compared to the multiple-item SWLS. Social scientists would get virtually identical answer to substantive questions regardless of which measure they use.

Single-layer ZnMN2 (M = Si, Ge, Sn) zinc nitrides as promising photocatalysts.

Science.gov (United States)

Bai, Yujie; Luo, Gaixia; Meng, Lijuan; Zhang, Qinfang; Xu, Ning; Zhang, Haiyang; Wu, Xiuqiang; Kong, Fanjie; Wang, Baolin

2018-05-30

Searching for two-dimensional semiconductor materials that are suitable for visible-light photocatalytic water splitting provides a sustainable solution to deal with the future energy crisis and environmental problems. Herein, based on first-principles calculations, single-layer ZnMN2 (M = Si, Ge, Sn) zinc nitrides are proposed as efficient photocatalysts for water splitting. Stability analyses show that the single-layer ZnMN2 zinc nitrides exhibit energetic and dynamical stability. The electronic properties reveal that all of the single-layer ZnMN2 zinc nitrides are semiconductors. Interestingly, single-layer ZnSnN2 is a direct band gap semiconductor with a desirable band gap (1.74 eV), and the optical adsorption spectrum confirms its optical absorption in the visible light region. The hydrogen evolution reaction (HER) calculations show that the catalytic activity for single-layer ZnMN2 (M = Ge, Sn) is better than that of single-layer ZnSiN2. Furthermore, the band gaps and band edge positions for the single-layer ZnMN2 zinc nitrides can be effectively tuned by biaxial strain. Especially, single-layer ZnGeN2 can be effectively tuned to match better with the redox potentials of water and enhance the light absorption in the visible light region at a tensile strain of 5%, which is confirmed by the corresponding optical absorption spectrum. Our results provide guidance for experimental synthesis efforts and future searches for single-layer materials suitable for photocatalytic water splitting.

Single-cell force spectroscopy of pili-mediated adhesion

Science.gov (United States)

Sullan, Ruby May A.; Beaussart, Audrey; Tripathi, Prachi; Derclaye, Sylvie; El-Kirat-Chatel, Sofiane; Li, James K.; Schneider, Yves-Jacques; Vanderleyden, Jos; Lebeer, Sarah; Dufrêne, Yves F.

2013-12-01

Although bacterial pili are known to mediate cell adhesion to a variety of substrates, the molecular interactions behind this process are poorly understood. We report the direct measurement of the forces guiding pili-mediated adhesion, focusing on the medically important probiotic bacterium Lactobacillus rhamnosus GG (LGG). Using non-invasive single-cell force spectroscopy (SCFS), we quantify the adhesion forces between individual bacteria and biotic (mucin, intestinal cells) or abiotic (hydrophobic monolayers) surfaces. On hydrophobic surfaces, bacterial pili strengthen adhesion through remarkable nanospring properties, which - presumably - enable the bacteria to resist high shear forces under physiological conditions. On mucin, nanosprings are more frequent and adhesion forces larger, reflecting the influence of specific pili-mucin bonds. Interestingly, these mechanical responses are no longer observed on human intestinal Caco-2 cells. Rather, force curves exhibit constant force plateaus with extended ruptures reflecting the extraction of membrane nanotethers. These single-cell analyses provide novel insights into the molecular mechanisms by which piliated bacteria colonize surfaces (nanosprings, nanotethers), and offer exciting avenues in nanomedicine for understanding and controlling the adhesion of microbial cells (probiotics, pathogens).

Single European currency and Monetary Union. Macroeconomic implications for pharmaceutical spending.

Science.gov (United States)

Kanavos, P

1998-01-01

This article examines the potential implications of introducing a single currency among the Member States of the European Union for national pharmaceutical prices and spending. In doing so, it provides a brief account of the direct effects of introducing a single currency on pharmaceutical business. These are static in nature and include the elimination of exchange rate volatility and transaction costs, increased price transparency and limited potential for parallel trade. It subsequently analyses the potential medium and long term macroeconomic policy choices facing the Member States and their impact on pharmaceutical spending following the introduction of a single currency. These include policy directions in order to meet the Maastricht convergence criteria in the run-up to forming an Economic and Monetary Union (EMU) and the implications of EMU on national macroeconomic policy thereafter. This article argues that the necessity for tight fiscal policies across the EU and, in particular, in those Member States facing high budget deficits and overall debt levels, will continue to exert considerable downward pressure on pharmaceutical spending.

Meta- and statistical analysis of single-case intervention research data: quantitative gifts and a wish list.

Science.gov (United States)

Kratochwill, Thomas R; Levin, Joel R

2014-04-01

In this commentary, we add to the spirit of the articles appearing in the special series devoted to meta- and statistical analysis of single-case intervention-design data. Following a brief discussion of historical factors leading to our initial involvement in statistical analysis of such data, we discuss: (a) the value added by including statistical-analysis recommendations in the What Works Clearinghouse Standards for single-case intervention designs; (b) the importance of visual analysis in single-case intervention research, along with the distinctive role that could be played by single-case effect-size measures; and (c) the elevated internal validity and statistical-conclusion validity afforded by the incorporation of various forms of randomization into basic single-case design structures. For the future, we envision more widespread application of quantitative analyses, as critical adjuncts to visual analysis, in both primary single-case intervention research studies and literature reviews in the behavioral, educational, and health sciences. Copyright © 2014 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

Membrane Lipid Replacement for chronic illnesses, aging and cancer using oral glycerolphospholipid formulations with fructooligosaccharides to restore phospholipid function in cellular membranes, organelles, cells and tissues.

Science.gov (United States)

Nicolson, Garth L; Ash, Michael E

2017-09-01

Membrane Lipid Replacement is the use of functional, oral supplements containing mixtures of cell membrane glycerolphospholipids, plus fructooligosaccharides (for protection against oxidative, bile acid and enzymatic damage) and antioxidants, in order to safely replace damaged, oxidized, membrane phospholipids and restore membrane, organelle, cellular and organ function. Defects in cellular and intracellular membranes are characteristic of all chronic medical conditions, including cancer, and normal processes, such as aging. Once the replacement glycerolphospholipids have been ingested, dispersed, complexed and transported, while being protected by fructooligosaccharides and several natural mechanisms, they can be inserted into cell membranes, lipoproteins, lipid globules, lipid droplets, liposomes and other carriers. They are conveyed by the lymphatics and blood circulation to cellular sites where they are endocytosed or incorporated into or transported by cell membranes. Inside cells the glycerolphospholipids can be transferred to various intracellular membranes by lipid globules, liposomes, membrane-membrane contact or by lipid carrier transfer. Eventually they arrive at their membrane destinations due to 'bulk flow' principles, and there they can stimulate the natural removal and replacement of damaged membrane lipids while undergoing further enzymatic alterations. Clinical trials have shown the benefits of Membrane Lipid Replacement in restoring mitochondrial function and reducing fatigue in aged subjects and chronically ill patients. Recently Membrane Lipid Replacement has been used to reduce pain and other symptoms as well as removing hydrophobic chemical contaminants, suggesting that there are additional new uses for this safe, natural medicine supplement. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights

A comparison of muscular activity during single and double mouse clicks.

Science.gov (United States)

Thorn, Stefan; Forsman, Mikael; Hallbeck, Susan

2005-05-01

Work-related musculoskeletal disorders (WMSDs) in the neck/shoulder region and the upper extremities are a common problem among computer workers. Occurrences of motor unit (MU) double discharges with very short inter-firing intervals (doublets) have been hypothesised as a potential additional risk for overuse of already exhausted fibres during long-term stereotyped activity. Doublets are reported to be present during double-click mouse work tasks. A few comparative studies have been carried out on overall muscle activities for short-term tasks with single types of actions, but none on occurrences of doublets during double versus single clicks. The main purpose of this study was to compare muscle activity levels of single and double mouse clicks during a long-term combined mouse/keyboard work task. Four muscles were studied: left and right upper trapezius, right extensor digitorum communis (EDC) and right flexor carpi ulnaris. Additionally, MU activity was analysed through intramuscular electromyography in the EDC muscle for a selection of subjects. The results indicate that double clicking produces neither higher median or 90th percentile levels in the trapezius and EDC muscles, nor a higher disposition for MU doublets, than does single clicking. Especially for the 90th percentile levels, the indications are rather the opposite (in the EDC significantly higher during single clicks in 8 of 11 subjects, P < 0.05). Although it cannot be concluded from the present study that double clicks are harmless, there were no signs that double clicks during computer work generally constitute a larger risk factor for WMSDs than do single clicks.

Lattice and Molecular Vibrations in Single Crystal I2 at 77 K by Inelastic Neutron Scattering

DEFF Research Database (Denmark)

Smith, H. G.; Nielsen, Mourits; Clark, C. B.

1975-01-01

Phonon dispersion curves of single crystal iodine at 77 K have been measured by one-phonon coherent inelastic neutron scattering techniques. The data are analysed in terms of two Buckingham-six intermolecular potentials; one to represent the shortest intermolecular interaction (3.5 Å) and the other...

Everyday life and occupational deprivation in single migrant mothers living in Denmark

DEFF Research Database (Denmark)

Kielsgaard, Kamilla; Kristensen, Hanne Kaae; Nielsen, Dorthe Susanne

2018-01-01

/objectives: To explore how single migrant mothers experience their living conditions and the significance of those conditions on their exclusion from everyday life occupations. Material and methods: In-depth interviews were used to find how occupational deprivation manifests in the everyday lives of three women. Based......ABSTRACT Background: Socio-economically disadvantaged single migrant mothers in Denmark risk poor health and social marginalisation, which affects participation in relevant occupations. Literature focusing on occupational deprivation in vulnerable groups such as migrants is sparse. Aim...... on Ricoeur’s theory of interpretation, data were analysed and the meaning structures, in the form of three themes, were identified. Results: The societal and individual conditions of women’s everyday lives interact in a complex interplay, where immigration, illness and divorce, in particular, deprive...

Fractal and Morphological Characteristics of Single Marble Particle Crushing in Uniaxial Compression Tests

Directory of Open Access Journals (Sweden)

Yidong Wang

2015-01-01

Full Text Available Crushing of rock particles is a phenomenon commonly encountered in geotechnical engineering practice. It is however difficult to study the crushing of rock particles using classical theory because the physical structure of the particles is complex and irregular. This paper aims at evaluating fractal and morphological characteristics of single rock particle. A large number of particle crushing tests are conducted on single rock particle. The force-displacement curves and the particle size distributions (PSD of crushed particles are analysed based on particle crushing tests. Particle shape plays an important role in both the micro- and macroscale responses of a granular assembly. The PSD of an assortment of rocks are analysed by fractal methods, and the fractal dimension is obtained. A theoretical formula for particle crushing strength is derived, utilising the fractal model, and a simple method is proposed for predicting the probability of particle survival based on the Weibull statistics. Based on a few physical assumptions, simple equations are derived for determining particle crushing energy. The results of applying these equations are tested against the actual experimental data and prove to be very consistent. Fractal theory is therefore applicable for analysis of particle crushing.