WorldWideScience

Sample records for subcellular localization electronic

  1. Subcellular localization of cadmium in hyperaccumulator Populus ...

    African Journals Online (AJOL)

    In this study, subcellular localization of cadmium in hyperaccumulator grey poplar (Populus × canescens) was investigated by the transmission electron microscopy (TEM) method. Young Populus × canescens were grown and hydroponic experiments were conducted under four Cd2+ concentrations (10, 30, 50, and 70 μM) ...

  2. Subcellular localization of pituitary enzymes

    Science.gov (United States)

    Smith, R. E.

    1970-01-01

    A cytochemical procedure is reported for identifying subcellular sites of enzymes hydrolyzing beta-naphthylamine substrates, and to study the sites of reaction product localization in cells of various tissues. Investigations using the substrate Leu 4-methoxy-8-naphthylamine, a capture with hexonium pararosaniline, and the final chelation of osmium have identified the hydrolyzing enzyme of rat liver cells; this enzyme localized on cell membranes with intense deposition in the areas of the parcanaliculi. The study of cells in the anterior pituitary of the rat showed the deposition of reaction product on cell membrane; and on the membranes of secretion granules contained within the cell. The deposition of reaction product on the cell membrane however showed no increase or decrease with changes in the physiological state of the gland and release of secretion granules from specific cells.

  3. Expression and subcellular localization of antiporter regulating ...

    African Journals Online (AJOL)

    We examined the expression and subcellular localization of antiporter regulating protein OsARP in a submergence tolerant rice (Oryza sativa L.) cultivar FR13A. In the public databases, this protein was designated as putative Os02g0465900 protein. The cDNA containing the full-length sequence of OsARP gene was ...

  4. Tau regulates the subcellular localization of calmodulin

    Energy Technology Data Exchange (ETDEWEB)

    Barreda, Elena Gomez de [Centro de Biologia Molecular ' Severo Ochoa' , CSIC/UAM, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Avila, Jesus, E-mail: javila@cbm.uam.es [Centro de Biologia Molecular ' Severo Ochoa' , CSIC/UAM, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); CIBER de Enfermedades Neurodegenerativas, 28031 Madrid (Spain)

    2011-05-13

    Highlights: {yields} In this work we have tried to explain how a cytoplasmic protein could regulate a cell nuclear function. We have tested the role of a cytoplasmic protein (tau) in regulating the expression of calbindin gene. We found that calmodulin, a tau-binding protein with nuclear and cytoplasmic localization, increases its nuclear localization in the absence of tau. Since nuclear calmodulin regulates calbindin expression, a decrease in nuclear calmodulin, due to the presence of tau that retains it at the cytoplasm, results in a change in calbindin expression. -- Abstract: Lack of tau expression in neuronal cells results in a change in the expression of few genes. However, little is known about how tau regulates gene expression. Here we show that the presence of tau could alter the subcellular localization of calmodulin, a protein that could be located at the cytoplasm or in the nucleus. Nuclear calmodulin binds to co-transcription factors, regulating the expression of genes like calbindin. In this work, we have found that in neurons containing tau, a higher proportion of calmodulin is present in the cytoplasm compared with neurons lacking tau and that an increase in cytoplasmic calmodulin correlates with a higher expression of calbindin.

  5. Tau regulates the subcellular localization of calmodulin

    International Nuclear Information System (INIS)

    Barreda, Elena Gomez de; Avila, Jesus

    2011-01-01

    Highlights: → In this work we have tried to explain how a cytoplasmic protein could regulate a cell nuclear function. We have tested the role of a cytoplasmic protein (tau) in regulating the expression of calbindin gene. We found that calmodulin, a tau-binding protein with nuclear and cytoplasmic localization, increases its nuclear localization in the absence of tau. Since nuclear calmodulin regulates calbindin expression, a decrease in nuclear calmodulin, due to the presence of tau that retains it at the cytoplasm, results in a change in calbindin expression. -- Abstract: Lack of tau expression in neuronal cells results in a change in the expression of few genes. However, little is known about how tau regulates gene expression. Here we show that the presence of tau could alter the subcellular localization of calmodulin, a protein that could be located at the cytoplasm or in the nucleus. Nuclear calmodulin binds to co-transcription factors, regulating the expression of genes like calbindin. In this work, we have found that in neurons containing tau, a higher proportion of calmodulin is present in the cytoplasm compared with neurons lacking tau and that an increase in cytoplasmic calmodulin correlates with a higher expression of calbindin.

  6. Nanodiamond Landmarks for Subcellular Multimodal Optical and Electron Imaging

    Science.gov (United States)

    Zurbuchen, Mark A.; Lake, Michael P.; Kohan, Sirus A.; Leung, Belinda; Bouchard, Louis-S.

    2013-01-01

    There is a growing need for biolabels that can be used in both optical and electron microscopies, are non-cytotoxic, and do not photobleach. Such biolabels could enable targeted nanoscale imaging of sub-cellular structures, and help to establish correlations between conjugation-delivered biomolecules and function. Here we demonstrate a sub-cellular multi-modal imaging methodology that enables localization of inert particulate probes, consisting of nanodiamonds having fluorescent nitrogen-vacancy centers. These are functionalized to target specific structures, and are observable by both optical and electron microscopies. Nanodiamonds targeted to the nuclear pore complex are rapidly localized in electron-microscopy diffraction mode to enable “zooming-in” to regions of interest for detailed structural investigations. Optical microscopies reveal nanodiamonds for in-vitro tracking or uptake-confirmation. The approach is general, works down to the single nanodiamond level, and can leverage the unique capabilities of nanodiamonds, such as biocompatibility, sensitive magnetometry, and gene and drug delivery. PMID:24036840

  7. Subcellular Iron Localization Mechanisms in Plants

    Directory of Open Access Journals (Sweden)

    Emre Aksoy

    2017-12-01

    Full Text Available The basic micro-nutrient element iron (Fe is present as a cofactor in the active sites of many metalloproteins with important roles in the plant. On the other hand, since it is excessively reactive, excess accumulation in the cell triggers the production of reactive oxygen species, leading to cell death. Therefore, iron homeostasis in the cell is very important for plant growth. Once uptake into the roots, iron is distributed to the subcellular compartments. Subcellular iron transport and hence cellular iron homeostasis is carried out through synchronous control of different membrane protein families. It has been discovered that expression levels of these membrane proteins increase under iron deficiency. Examination of the tasks and regulations of these carriers is very important in terms of understanding the iron intake and distribution mechanisms in plants. Therefore, in this review, the transporters responsible for the uptake of iron into the cell and its subcellular distribution between organelles will be discussed with an emphasis on the current developments about these transporters.

  8. Subcellular localization of hepatitis E virus (HEV) replicase

    International Nuclear Information System (INIS)

    Rehman, Shagufta; Kapur, Neeraj; Durgapal, Hemlata; Panda, Subrat Kumar

    2008-01-01

    Hepatitis E virus (HEV) is a hepatotropic virus with a single sense-strand RNA genome of ∼ 7.2 kb in length. Details of the intracellular site of HEV replication can pave further understanding of HEV biology. In-frame fusion construct of functionally active replicase-enhanced green fluorescent protein (EGFP) gene was made in eukaryotic expression vector. The functionality of replicase-EGFP fusion protein was established by its ability to synthesize negative-strand viral RNA in vivo, by strand-specific anchored RT-PCR and molecular beacon binding. Subcellular co-localization was carried out using organelle specific fluorophores and by immuno-electron microscopy. Fluorescence Resonance Energy Transfer (FRET) demonstrated the interaction of this protein with the 3' end of HEV genome. The results show localization of replicase on the endoplasmic reticulum membranes. The protein regions responsible for membrane localization was predicted and identified by use of deletion mutants. Endoplasmic reticulum was identified as the site of replicase localization and possible site of replication

  9. Protein subcellular localization assays using split fluorescent proteins

    Science.gov (United States)

    Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

    2009-09-08

    The invention provides protein subcellular localization assays using split fluorescent protein systems. The assays are conducted in living cells, do not require fixation and washing steps inherent in existing immunostaining and related techniques, and permit rapid, non-invasive, direct visualization of protein localization in living cells. The split fluorescent protein systems used in the practice of the invention generally comprise two or more self-complementing fragments of a fluorescent protein, such as GFP, wherein one or more of the fragments correspond to one or more beta-strand microdomains and are used to "tag" proteins of interest, and a complementary "assay" fragment of the fluorescent protein. Either or both of the fragments may be functionalized with a subcellular targeting sequence enabling it to be expressed in or directed to a particular subcellular compartment (i.e., the nucleus).

  10. Protein subcellular localization prediction using artificial intelligence technology.

    Science.gov (United States)

    Nair, Rajesh; Rost, Burkhard

    2008-01-01

    Proteins perform many important tasks in living organisms, such as catalysis of biochemical reactions, transport of nutrients, and recognition and transmission of signals. The plethora of aspects of the role of any particular protein is referred to as its "function." One aspect of protein function that has been the target of intensive research by computational biologists is its subcellular localization. Proteins must be localized in the same subcellular compartment to cooperate toward a common physiological function. Aberrant subcellular localization of proteins can result in several diseases, including kidney stones, cancer, and Alzheimer's disease. To date, sequence homology remains the most widely used method for inferring the function of a protein. However, the application of advanced artificial intelligence (AI)-based techniques in recent years has resulted in significant improvements in our ability to predict the subcellular localization of a protein. The prediction accuracy has risen steadily over the years, in large part due to the application of AI-based methods such as hidden Markov models (HMMs), neural networks (NNs), and support vector machines (SVMs), although the availability of larger experimental datasets has also played a role. Automatic methods that mine textual information from the biological literature and molecular biology databases have considerably sped up the process of annotation for proteins for which some information regarding function is available in the literature. State-of-the-art methods based on NNs and HMMs can predict the presence of N-terminal sorting signals extremely accurately. Ab initio methods that predict subcellular localization for any protein sequence using only the native amino acid sequence and features predicted from the native sequence have shown the most remarkable improvements. The prediction accuracy of these methods has increased by over 30% in the past decade. The accuracy of these methods is now on par with

  11. Evaluation and comparison of mammalian subcellular localization prediction methods

    Directory of Open Access Journals (Sweden)

    Fink J Lynn

    2006-12-01

    Full Text Available Abstract Background Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These data are difficult to obtain experimentally but have become especially important since many whole genome sequencing projects have been finished and many resulting protein sequences are still lacking detailed functional information. In order to address this paucity of data, many computational prediction methods have been developed. However, these methods have varying levels of accuracy and perform differently based on the sequences that are presented to the underlying algorithm. It is therefore useful to compare these methods and monitor their performance. Results In order to perform a comprehensive survey of prediction methods, we selected only methods that accepted large batches of protein sequences, were publicly available, and were able to predict localization to at least nine of the major subcellular locations (nucleus, cytosol, mitochondrion, extracellular region, plasma membrane, Golgi apparatus, endoplasmic reticulum (ER, peroxisome, and lysosome. The selected methods were CELLO, MultiLoc, Proteome Analyst, pTarget and WoLF PSORT. These methods were evaluated using 3763 mouse proteins from SwissProt that represent the source of the training sets used in development of the individual methods. In addition, an independent evaluation set of 2145 mouse proteins from LOCATE with a bias towards the subcellular localization underrepresented in SwissProt was used. The sensitivity and specificity were calculated for each method and compared to a theoretical value based on what might be observed by random chance. Conclusion No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins. All methods showed lower performance on the LOCATE

  12. Determination of elemental distribution in green micro-algae using synchrotron radiation nano X-ray fluorescence (SR-nXRF) and electron microscopy techniques--subcellular localization and quantitative imaging of silver and cobalt uptake by Coccomyxa actinabiotis.

    Science.gov (United States)

    Leonardo, T; Farhi, E; Boisson, A-M; Vial, J; Cloetens, P; Bohic, S; Rivasseau, C

    2014-02-01

    The newly discovered unicellular micro-alga Coccomyxa actinabiotis proves to be highly radio-tolerant and strongly concentrates radionuclides, as well as large amounts of toxic metals. This study helps in the understanding of the mechanisms involved in the accumulation and detoxification of silver and cobalt. Elemental distribution inside Coccomyxa actinabiotis cells was determined using synchrotron nano X-ray fluorescence spectroscopy at the ID22 nano fluorescence imaging beamline of the European Synchrotron Radiation Facility. The high resolution and high sensitivity of this technique enabled the assessment of elemental associations and exclusions in subcellular micro-algae compartments. A quantitative treatment of the scans was implemented to yield absolute concentrations of each endogenous and exogenous element with a spatial resolution of 100 nm and compared to the macroscopic content in cobalt and silver determined using inductively coupled plasma-mass spectrometry. The nano X-ray fluorescence imaging was complemented by transmission electron microscopy coupled to X-ray microanalysis (TEM-EDS), yielding differential silver distribution in the cell wall, cytosol, nucleus, chloroplast and mitochondria with unique resolution. The analysis of endogenous elements in control cells revealed that iron had a unique distribution; zinc, potassium, manganese, molybdenum, and phosphate had their maxima co-localized in the same area; and sulfur, copper and chlorine were almost homogeneously distributed among the whole cell. The subcellular distribution and quantification of cobalt and silver in micro-alga, assessed after controlled exposure to various concentrations, revealed that exogenous metals were mainly sequestered inside the cell rather than on mucilage or the cell wall, with preferential compartmentalization. Cobalt was homogeneously distributed outside of the chloroplast. Silver was localized in the cytosol at low concentration and in the whole cell excluding the

  13. Subcellular localization of ammonium transporters in Dictyostelium discoideum

    Directory of Open Access Journals (Sweden)

    Davis Carter T

    2008-12-01

    Full Text Available Abstract Background With the exception of vertebrates, most organisms have plasma membrane associated ammonium transporters which primarily serve to import a source of nitrogen for nutritional purposes. Dictyostelium discoideum has three ammonium transporters, Amts A, B and C. Our present work used fluorescent fusion proteins to determine the cellular localization of the Amts and tested the hypothesis that the transporters mediate removal of ammonia generated endogenously from the elevated protein catabolism common to many protists. Results Using RFP and YFP fusion constructs driven by the actin 15 promoter, we found that the three ammonium transporters were localized on the plasma membrane and on the membranes of subcellular organelles. AmtA and AmtB were localized on the membranes of endolysosomes and phagosomes, with AmtB further localized on the membranes of contractile vacuoles. AmtC also was localized on subcellular organelles when it was stabilized by coexpression with either the AmtA or AmtB fusion transporter. The three ammonium transporters exported ammonia linearly with regard to time during the first 18 hours of the developmental program as revealed by reduced export in the null strains. The fluorescently tagged transporters rescued export when expressed in the null strains, and thus they were functional transporters. Conclusion Unlike ammonium transporters in most organisms, which import NH3/NH4+ as a nitrogen source, those of Dictyostelium export ammonia/ammonium as a waste product from extensive catabolism of exogenously derived and endogenous proteins. Localization on proteolytic organelles and on the neutral contractile vacuole suggests that Dictyostelium ammonium transporters may have unique subcellular functions and play a role in the maintenance of intracellular ammonium distribution. A lack of correlation between the null strain phenotypes and ammonia excretion properties of the ammonium transporters suggests that it is not

  14. Gene ontology based transfer learning for protein subcellular localization

    Directory of Open Access Journals (Sweden)

    Zhou Shuigeng

    2011-02-01

    Full Text Available Abstract Background Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting multi-aspect protein feature information. Gene ontology, hereinafter referred to as GO, uses a controlled vocabulary to depict biological molecules or gene products in terms of biological process, molecular function and cellular component. With the rapid expansion of annotated protein sequences, gene ontology has become a general protein feature that can be used to construct predictive models in computational biology. Existing models generally either concatenated the GO terms into a flat binary vector or applied majority-vote based ensemble learning for protein subcellular localization, both of which can not estimate the individual discriminative abilities of the three aspects of gene ontology. Results In this paper, we propose a Gene Ontology Based Transfer Learning Model (GO-TLM for large-scale protein subcellular localization. The model transfers the signature-based homologous GO terms to the target proteins, and further constructs a reliable learning system to reduce the adverse affect of the potential false GO terms that are resulted from evolutionary divergence. We derive three GO kernels from the three aspects of gene ontology to measure the GO similarity of two proteins, and derive two other spectrum kernels to measure the similarity of two protein sequences. We use simple non-parametric cross validation to explicitly weigh the discriminative abilities of the five kernels, such that the time & space computational complexities are greatly reduced when compared to the complicated semi-definite programming and semi-indefinite linear programming. The five kernels are then linearly merged into one single kernel for

  15. Subcellular localization of the antidepressant-sensitive norepinephrine transporter

    Directory of Open Access Journals (Sweden)

    Winder Danny G

    2009-06-01

    Full Text Available Abstract Background Reuptake of synaptic norepinephrine (NE via the antidepressant-sensitive NE transporter (NET supports efficient noradrenergic signaling and presynaptic NE homeostasis. Limited, and somewhat contradictory, information currently describes the axonal transport and localization of NET in neurons. Results We elucidate NET localization in brain and superior cervical ganglion (SCG neurons, aided by a new NET monoclonal antibody, subcellular immunoisolation techniques and quantitative immunofluorescence approaches. We present evidence that axonal NET extensively colocalizes with syntaxin 1A, and to a limited degree with SCAMP2 and synaptophysin. Intracellular NET in SCG axons and boutons also quantitatively segregates from the vesicular monoamine transporter 2 (VMAT2, findings corroborated by organelle isolation studies. At the surface of SCG boutons, NET resides in both lipid raft and non-lipid raft subdomains and colocalizes with syntaxin 1A. Conclusion Our findings support the hypothesis that SCG NET is segregated prior to transport from the cell body from proteins comprising large dense core vesicles. Once localized to presynaptic boutons, NET does not recycle via VMAT2-positive, small dense core vesicles. Finally, once NET reaches presynaptic plasma membranes, the transporter localizes to syntaxin 1A-rich plasma membrane domains, with a portion found in cholera toxin-demarcated lipid rafts. Our findings indicate that activity-dependent insertion of NET into the SCG plasma membrane derives from vesicles distinct from those that deliver NE. Moreover, NET is localized in presynaptic membranes in a manner that can take advantage of regulatory processes targeting lipid raft subdomains.

  16. Accumulation of fission fragment 147Pm in subcellular level studied by electron microscopic autoradiography

    International Nuclear Information System (INIS)

    Zhu Shoupeng; Wang Yuanchang

    1990-11-01

    The subcellular localization of fission fragment 147 Pm in tissue cells by electron microscopic autoradiography was investigated. The early harm of internal contaminated accumulation of 147 Pm appeared in blood cells and endothelium cells, obviously in erythrocytes. Then 147 Pm was selectively deposited in ultrastructure of liver cells. Autoradiographic study demonstrated that dense tracks appeared in mitochondria and lysosome of podal cells within renal corpuscle. In nucleus as well as in mitochondria and microbodies of epicyte of kidney near-convoluted tubule, there are numerous radioactive 149 Pm accumulated. With the prolongation of observing time, 149 Pm was selectively and steadily deposited in subcellular level of organic component bone. The radionuclides could be accumulated in nucleus of osteoclasts and osteoblasts. In organelles, the radionuclides was mainly accumulated in rough endoplasmic reticulum and mitochondria. Autoradiographic tracks of 149 Pm was obviously found to be localized in combined point between Golgi complex and transitive vesicle of rough endoplasmic reticulum

  17. Expression and subcellular localization of ORC1 in Leishmania major

    International Nuclear Information System (INIS)

    Kumar, Diwakar; Mukherji, Agnideep; Saha, Swati

    2008-01-01

    The mechanism of DNA replication is highly conserved in eukaryotes, with the process being preceded by the ordered assembly of pre-replication complexes (pre-RCs). Pre-RC formation is triggered by the association of the origin replication complex (ORC) with chromatin. Leishmania major appears to have only one ORC ortholog, ORC1. ORC1 in other eukaryotes is the largest of the ORC subunits and is believed to play a significant role in modulating replication initiation. Here we report for the first time, the cloning of ORC1 from L. major, and the analysis of its expression in L. major promastigotes. In human cells ORC1 levels have been found to be upregulated in G1 and subsequently degraded, thus playing a role in controlling replication initiation. We examine the subcellular localization of L. major ORC1 in relation to the different stages of the cell cycle. Our results show that, unlike what is widely believed to be the case with ORC1 in human cells, ORC1 in L. major is nuclear at all stages of the cell cycle

  18. Predicting the subcellular localization of viral proteins within a mammalian host cell

    Directory of Open Access Journals (Sweden)

    Thomas DY

    2006-04-01

    Full Text Available Abstract Background The bioinformatic prediction of protein subcellular localization has been extensively studied for prokaryotic and eukaryotic organisms. However, this is not the case for viruses whose proteins are often involved in extensive interactions at various subcellular localizations with host proteins. Results Here, we investigate the extent of utilization of human cellular localization mechanisms by viral proteins and we demonstrate that appropriate eukaryotic subcellular localization predictors can be used to predict viral protein localization within the host cell. Conclusion Such predictions provide a method to rapidly annotate viral proteomes with subcellular localization information. They are likely to have widespread applications both in the study of the functions of viral proteins in the host cell and in the design of antiviral drugs.

  19. Physiological aspects of the subcellular localization of glycogen in skeletal muscle

    DEFF Research Database (Denmark)

    Nielsen, Joachim; Ørtenblad, Niels

    2013-01-01

    Glucose is stored in skeletal muscle fibers as glycogen, a branched-chain polymer observed in electron microscopy images as roughly spherical particles (known as β-particles of 10-45 nm in diameter), which are distributed in distinct localizations within the myofibers and are physically associated...... investigated the role and regulation of these distinct deposits of glycogen. In this report, we review the available literature regarding the subcellular localization of glycogen in skeletal muscle as investigated by electron microscopy studies and put this into perspective in terms of the architectural......, topological, and dynamic organization of skeletal muscle fibers. In summary, the distribution of glycogen within skeletal muscle fibers has been shown to depend on the fiber phenotype, individual training status, short-term immobilization, and exercise and to influence both muscle contractility...

  20. ALG-2 oscillates in subcellular localization, unitemporally with calcium oscillations

    DEFF Research Database (Denmark)

    la Cour, Jonas Marstrand; Mollerup, Jens; Berchtold, Martin Werner

    2007-01-01

    discovered that the subcellular distribution of a tagged version of ALG-2 could be directed by physiological external stimuli (including ATP, EGF, prostaglandin, histamine), which provoke intracellular Ca2+ oscillations. Cellular stimulation led to a redistribution of ALG-2 from the cytosol to a punctate...

  1. Predicting Subcellular Localization of Proteins by Bioinformatic Algorithms

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2015-01-01

    was used. Various statistical and machine learning algorithms are used with all three approaches, and various measures and standards are employed when reporting the performances of the developed methods. This chapter presents a number of available methods for prediction of sorting signals and subcellular...

  2. Subcellular localization for Gram positive and Gram negative bacterial proteins using linear interpolation smoothing model.

    Science.gov (United States)

    Saini, Harsh; Raicar, Gaurav; Dehzangi, Abdollah; Lal, Sunil; Sharma, Alok

    2015-12-07

    Protein subcellular localization is an important topic in proteomics since it is related to a protein׳s overall function, helps in the understanding of metabolic pathways, and in drug design and discovery. In this paper, a basic approximation technique from natural language processing called the linear interpolation smoothing model is applied for predicting protein subcellular localizations. The proposed approach extracts features from syntactical information in protein sequences to build probabilistic profiles using dependency models, which are used in linear interpolation to determine how likely is a sequence to belong to a particular subcellular location. This technique builds a statistical model based on maximum likelihood. It is able to deal effectively with high dimensionality that hinders other traditional classifiers such as Support Vector Machines or k-Nearest Neighbours without sacrificing performance. This approach has been evaluated by predicting subcellular localizations of Gram positive and Gram negative bacterial proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Cellular and Subcellular Immunohistochemical Localization and Quantification of Cadmium Ions in Wheat (Triticum aestivum.

    Directory of Open Access Journals (Sweden)

    Wei Gao

    Full Text Available The distribution of metallic ions in plant tissues is associated with their toxicity and is important for understanding mechanisms of toxicity tolerance. A quantitative histochemical method can help advance knowledge of cellular and subcellular localization and distribution of heavy metals in plant tissues. An immunohistochemical (IHC imaging method for cadmium ions (Cd2+ was developed for the first time for the wheat Triticum aestivum grown in Cd2+-fortified soils. Also, 1-(4-Isothiocyanobenzyl-ethylenediamine-N,N,N,N-tetraacetic acid (ITCB-EDTA was used to chelate the mobile Cd2+. The ITCB-EDTA/Cd2+ complex was fixed with proteins in situ via the isothiocyano group. A new Cd2+-EDTA specific monoclonal antibody, 4F3B6D9A1, was used to locate the Cd2+-EDTA protein complex. After staining, the fluorescence intensities of sections of Cd2+-positive roots were compared with those of Cd2+-negative roots under a laser confocal scanning microscope, and the location of colloidal gold particles was determined with a transmission electron microscope. The results enable quantification of the Cd2+ content in plant tissues and illustrate Cd2+ translocation and cellular and subcellular responses of T. aestivum to Cd2+ stress. Compared to the conventional metal-S coprecipitation histochemical method, this new IHC method is quantitative, more specific and has less background interference. The subcellular location of Cd2+ was also confirmed with energy-dispersive X-ray microanalysis. The IHC method is suitable for locating and quantifying Cd2+ in plant tissues and can be extended to other heavy metallic ions.

  4. Cellular and Subcellular Immunohistochemical Localization and Quantification of Cadmium Ions in Wheat (Triticum aestivum).

    Science.gov (United States)

    Gao, Wei; Nan, Tiegui; Tan, Guiyu; Zhao, Hongwei; Tan, Weiming; Meng, Fanyun; Li, Zhaohu; Li, Qing X; Wang, Baomin

    2015-01-01

    The distribution of metallic ions in plant tissues is associated with their toxicity and is important for understanding mechanisms of toxicity tolerance. A quantitative histochemical method can help advance knowledge of cellular and subcellular localization and distribution of heavy metals in plant tissues. An immunohistochemical (IHC) imaging method for cadmium ions (Cd2+) was developed for the first time for the wheat Triticum aestivum grown in Cd2+-fortified soils. Also, 1-(4-Isothiocyanobenzyl)-ethylenediamine-N,N,N,N-tetraacetic acid (ITCB-EDTA) was used to chelate the mobile Cd2+. The ITCB-EDTA/Cd2+ complex was fixed with proteins in situ via the isothiocyano group. A new Cd2+-EDTA specific monoclonal antibody, 4F3B6D9A1, was used to locate the Cd2+-EDTA protein complex. After staining, the fluorescence intensities of sections of Cd2+-positive roots were compared with those of Cd2+-negative roots under a laser confocal scanning microscope, and the location of colloidal gold particles was determined with a transmission electron microscope. The results enable quantification of the Cd2+ content in plant tissues and illustrate Cd2+ translocation and cellular and subcellular responses of T. aestivum to Cd2+ stress. Compared to the conventional metal-S coprecipitation histochemical method, this new IHC method is quantitative, more specific and has less background interference. The subcellular location of Cd2+ was also confirmed with energy-dispersive X-ray microanalysis. The IHC method is suitable for locating and quantifying Cd2+ in plant tissues and can be extended to other heavy metallic ions.

  5. Human skeletal muscle glycogen utilization in exhaustive exercise: role of subcellular localization and fibre type

    Science.gov (United States)

    Nielsen, Joachim; Holmberg, Hans-Christer; Schrøder, Henrik D; Saltin, Bengt; Ørtenblad, Niels

    2011-01-01

    Abstract Although glycogen is known to be heterogeneously distributed within skeletal muscle cells, there is presently little information available about the role of fibre types, utilization and resynthesis during and after exercise with respect to glycogen localization. Here, we tested the hypothesis that utilization of glycogen with different subcellular localizations during exhaustive arm and leg exercise differs and examined the influence of fibre type and carbohydrate availability on its subsequent resynthesis. When 10 elite endurance athletes (22 ± 1 years, = 68 ± 5 ml kg−1 min−1, mean ± SD) performed one hour of exhaustive arm and leg exercise, transmission electron microscopy revealed more pronounced depletion of intramyofibrillar than of intermyofibrillar and subsarcolemmal glycogen. This phenomenon was the same for type I and II fibres, although at rest prior to exercise, the former contained more intramyofibrillar and subsarcolemmal glycogen than the latter. In highly glycogen-depleted fibres, the remaining small intermyofibrillar and subsarcolemmal glycogen particles were often found to cluster in groupings. In the recovery period, when the athletes received either a carbohydrate-rich meal or only water the impaired resynthesis of glycogen with water alone was associated primarily with intramyofibrillar glycogen. In conclusion, after prolonged high-intensity exercise the depletion of glycogen is dependent on subcellular localization. In addition, the localization of glycogen appears to be influenced by fibre type prior to exercise, as well as carbohydrate availability during the subsequent period of recovery. These findings provide insight into the significance of fibre type-specific compartmentalization of glycogen metabolism in skeletal muscle during exercise and subsequent recovery. PMID:21486810

  6. Prediction of protein subcellular localization using support vector machine with the choice of proper kernel

    Directory of Open Access Journals (Sweden)

    Al Mehedi Hasan

    2017-07-01

    Full Text Available The prediction of subcellular locations of proteins can provide useful hints for revealing their functions as well as for understanding the mechanisms of some diseases and, finally, for developing novel drugs. As the number of newly discovered proteins has been growing exponentially, laboratory-based experiments to determine the location of an uncharacterized protein in a living cell have become both expensive and time-consuming. Consequently, to tackle these challenges, computational methods are being developed as an alternative to help biologists in selecting target proteins and designing related experiments. However, the success of protein subcellular localization prediction is still a complicated and challenging problem, particularly when query proteins may have multi-label characteristics, i.e. their simultaneous existence in more than one subcellular location, or if they move between two or more different subcellular locations as well. At this point, to get rid of this problem, several types of subcellular localization prediction methods with different levels of accuracy have been proposed. The support vector machine (SVM has been employed to provide potential solutions for problems connected with the prediction of protein subcellular localization. However, the practicability of SVM is affected by difficulties in selecting its appropriate kernel as well as in selecting the parameters of that selected kernel. The literature survey has shown that most researchers apply the radial basis function (RBF kernel to build a SVM based subcellular localization prediction system. Surprisingly, there are still many other kernel functions which have not yet been applied in the prediction of protein subcellular localization. However, the nature of this classification problem requires the application of different kernels for SVM to ensure an optimal result. From this viewpoint, this paper presents the work to apply different kernels for SVM in protein

  7. MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction

    Directory of Open Access Journals (Sweden)

    Kohlbacher Oliver

    2009-09-01

    Full Text Available Abstract Background Knowledge of subcellular localization of proteins is crucial to proteomics, drug target discovery and systems biology since localization and biological function are highly correlated. In recent years, numerous computational prediction methods have been developed. Nevertheless, there is still a need for prediction methods that show more robustness and higher accuracy. Results We extended our previous MultiLoc predictor by incorporating phylogenetic profiles and Gene Ontology terms. Two different datasets were used for training the system, resulting in two versions of this high-accuracy prediction method. One version is specialized for globular proteins and predicts up to five localizations, whereas a second version covers all eleven main eukaryotic subcellular localizations. In a benchmark study with five localizations, MultiLoc2 performs considerably better than other methods for animal and plant proteins and comparably for fungal proteins. Furthermore, MultiLoc2 performs clearly better when using a second dataset that extends the benchmark study to all eleven main eukaryotic subcellular localizations. Conclusion MultiLoc2 is an extensive high-performance subcellular protein localization prediction system. By incorporating phylogenetic profiles and Gene Ontology terms MultiLoc2 yields higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. MultiLoc2 is available as user-friendly and free web-service, available at: http://www-bs.informatik.uni-tuebingen.de/Services/MultiLoc2.

  8. Determining the sub-cellular localization of proteins within Caenorhabditis elegans body wall muscle.

    Science.gov (United States)

    Meissner, Barbara; Rogalski, Teresa; Viveiros, Ryan; Warner, Adam; Plastino, Lorena; Lorch, Adam; Granger, Laure; Segalat, Laurent; Moerman, Donald G

    2011-01-01

    Determining the sub-cellular localization of a protein within a cell is often an essential step towards understanding its function. In Caenorhabditis elegans, the relatively large size of the body wall muscle cells and the exquisite organization of their sarcomeres offer an opportunity to identify the precise position of proteins within cell substructures. Our goal in this study is to generate a comprehensive "localizome" for C. elegans body wall muscle by GFP-tagging proteins expressed in muscle and determining their location within the cell. For this project, we focused on proteins that we know are expressed in muscle and are orthologs or at least homologs of human proteins. To date we have analyzed the expression of about 227 GFP-tagged proteins that show localized expression in the body wall muscle of this nematode (e.g. dense bodies, M-lines, myofilaments, mitochondria, cell membrane, nucleus or nucleolus). For most proteins analyzed in this study no prior data on sub-cellular localization was available. In addition to discrete sub-cellular localization we observe overlapping patterns of localization including the presence of a protein in the dense body and the nucleus, or the dense body and the M-lines. In total we discern more than 14 sub-cellular localization patterns within nematode body wall muscle. The localization of this large set of proteins within a muscle cell will serve as an invaluable resource in our investigation of muscle sarcomere assembly and function.

  9. Detrended cross-correlation coefficient: Application to predict apoptosis protein subcellular localization.

    Science.gov (United States)

    Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

    2016-12-01

    Apoptosis, or programed cell death, plays a central role in the development and homeostasis of an organism. Obtaining information on subcellular location of apoptosis proteins is very helpful for understanding the apoptosis mechanism. The prediction of subcellular localization of an apoptosis protein is still a challenging task, and existing methods mainly based on protein primary sequences. In this paper, we introduce a new position-specific scoring matrix (PSSM)-based method by using detrended cross-correlation (DCCA) coefficient of non-overlapping windows. Then a 190-dimensional (190D) feature vector is constructed on two widely used datasets: CL317 and ZD98, and support vector machine is adopted as classifier. To evaluate the proposed method, objective and rigorous jackknife cross-validation tests are performed on the two datasets. The results show that our approach offers a novel and reliable PSSM-based tool for prediction of apoptosis protein subcellular localization. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. The cellular and subcellular localization of zinc transporter 7 in the mouse spinal cord

    Science.gov (United States)

    The present work addresses the cellular and subcellular localization of the zinc transporter 7 (ZNT7, SLC30a7) protein and the distribution of zinc ions (Zn2+) in the mouse spinal cord. Our results indicated that the ZNT7 immunoreactive neurons were widely distributed in the Rexed’s laminae of the g...

  11. A novel representation for apoptosis protein subcellular localization prediction using support vector machine.

    Science.gov (United States)

    Zhang, Li; Liao, Bo; Li, Dachao; Zhu, Wen

    2009-07-21

    Apoptosis, or programmed cell death, plays an important role in development of an organism. Obtaining information on subcellular location of apoptosis proteins is very helpful to understand the apoptosis mechanism. In this paper, based on the concept that the position distribution information of amino acids is closely related with the structure and function of proteins, we introduce the concept of distance frequency [Matsuda, S., Vert, J.P., Ueda, N., Toh, H., Akutsu, T., 2005. A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci. 14, 2804-2813] and propose a novel way to calculate distance frequencies. In order to calculate the local features, each protein sequence is separated into p parts with the same length in our paper. Then we use the novel representation of protein sequences and adopt support vector machine to predict subcellular location. The overall prediction accuracy is significantly improved by jackknife test.

  12. Fast subcellular localization by cascaded fusion of signal-based and homology-based methods

    Directory of Open Access Journals (Sweden)

    Wang Wei

    2011-10-01

    Full Text Available Abstract Background The functions of proteins are closely related to their subcellular locations. In the post-genomics era, the amount of gene and protein data grows exponentially, which necessitates the prediction of subcellular localization by computational means. Results This paper proposes mitigating the computation burden of alignment-based approaches to subcellular localization prediction by a cascaded fusion of cleavage site prediction and profile alignment. Specifically, the informative segments of protein sequences are identified by a cleavage site predictor using the information in their N-terminal shorting signals. Then, the sequences are truncated at the cleavage site positions, and the shortened sequences are passed to PSI-BLAST for computing their profiles. Subcellular localization are subsequently predicted by a profile-to-profile alignment support-vector-machine (SVM classifier. To further reduce the training and recognition time of the classifier, the SVM classifier is replaced by a new kernel method based on the perturbational discriminant analysis (PDA. Conclusions Experimental results on a new dataset based on Swiss-Prot Release 57.5 show that the method can make use of the best property of signal- and homology-based approaches and can attain an accuracy comparable to that achieved by using full-length sequences. Analysis of profile-alignment score matrices suggest that both profile creation time and profile alignment time can be reduced without significant reduction in subcellular localization accuracy. It was found that PDA enjoys a short training time as compared to the conventional SVM. We advocate that the method will be important for biologists to conduct large-scale protein annotation or for bioinformaticians to perform preliminary investigations on new algorithms that involve pairwise alignments.

  13. Altered subcellular localization of ornithine decarboxylase in Alzheimer's disease brain

    DEFF Research Database (Denmark)

    Nilsson, Tatjana; Bogdanovic, Nenad; Volkman, Inga

    2006-01-01

    The amyloid precursor protein can through ligand-mimicking induce expression of ornithine decarboxylase (ODC), the initial and rate-limiting enzyme in polyamine biosynthesis. We report here the regional distribution and cellular localization of ODC immunoreactivity in Alzheimer's disease (AD...

  14. Analysis of the subcellular localization of the human histone methyltransferase SETDB1

    Energy Technology Data Exchange (ETDEWEB)

    Tachibana, Keisuke, E-mail: nya@phs.osaka-u.ac.jp [Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 (Japan); Gotoh, Eiko; Kawamata, Natsuko [Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 (Japan); Ishimoto, Kenji [Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 (Japan); Laboratory for System Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Uchihara, Yoshie [Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 (Japan); Iwanari, Hiroko [Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Sugiyama, Akira; Kawamura, Takeshi [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032 (Japan); Mochizuki, Yasuhiro [Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Tanaka, Toshiya [Laboratory for System Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Sakai, Juro [Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Hamakubo, Takao [Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Kodama, Tatsuhiko [Laboratory for System Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); and others

    2015-10-02

    SET domain, bifurcated 1 (SETDB1) is a histone methyltransferase that methylates lysine 9 on histone H3. Although it is important to know the localization of proteins to elucidate their physiological function, little is known of the subcellular localization of human SETDB1. In the present study, to investigate the subcellular localization of hSETDB1, we established a human cell line constitutively expressing enhanced green fluorescent protein fused to hSETDB1. We then generated a monoclonal antibody against the hSETDB1 protein. Expression of both exogenous and endogenous hSETDB1 was observed mainly in the cytoplasm of various human cell lines. Combined treatment with the nuclear export inhibitor leptomycin B and the proteasome inhibitor MG132 led to the accumulation of hSETDB1 in the nucleus. These findings suggest that hSETDB1, localized in the nucleus, might undergo degradation by the proteasome and be exported to the cytosol, resulting in its detection mainly in the cytosol. - Highlights: • Endogenous human SETDB1 was localized mainly in the cytoplasm. • Combined treatment with LMB and MG132 led to accumulation of human SETDB1 in the nucleus. • HeLa cells expressing EFGP-hSETDB1 are useful for subcellular localization analyses.

  15. Analysis of the subcellular localization of the human histone methyltransferase SETDB1

    International Nuclear Information System (INIS)

    Tachibana, Keisuke; Gotoh, Eiko; Kawamata, Natsuko; Ishimoto, Kenji; Uchihara, Yoshie; Iwanari, Hiroko; Sugiyama, Akira; Kawamura, Takeshi; Mochizuki, Yasuhiro; Tanaka, Toshiya; Sakai, Juro; Hamakubo, Takao; Kodama, Tatsuhiko

    2015-01-01

    SET domain, bifurcated 1 (SETDB1) is a histone methyltransferase that methylates lysine 9 on histone H3. Although it is important to know the localization of proteins to elucidate their physiological function, little is known of the subcellular localization of human SETDB1. In the present study, to investigate the subcellular localization of hSETDB1, we established a human cell line constitutively expressing enhanced green fluorescent protein fused to hSETDB1. We then generated a monoclonal antibody against the hSETDB1 protein. Expression of both exogenous and endogenous hSETDB1 was observed mainly in the cytoplasm of various human cell lines. Combined treatment with the nuclear export inhibitor leptomycin B and the proteasome inhibitor MG132 led to the accumulation of hSETDB1 in the nucleus. These findings suggest that hSETDB1, localized in the nucleus, might undergo degradation by the proteasome and be exported to the cytosol, resulting in its detection mainly in the cytosol. - Highlights: • Endogenous human SETDB1 was localized mainly in the cytoplasm. • Combined treatment with LMB and MG132 led to accumulation of human SETDB1 in the nucleus. • HeLa cells expressing EFGP-hSETDB1 are useful for subcellular localization analyses.

  16. Altered subcellular localization of ornithine decarboxylase in Alzheimer's disease brain

    International Nuclear Information System (INIS)

    Nilsson, Tatjana; Bogdanovic, Nenad; Volkman, Inga; Winblad, Bengt; Folkesson, Ronnie; Benedikz, Eirikur

    2006-01-01

    The amyloid precursor protein can through ligand-mimicking induce expression of ornithine decarboxylase (ODC), the initial and rate-limiting enzyme in polyamine biosynthesis. We report here the regional distribution and cellular localization of ODC immunoreactivity in Alzheimer's disease (AD) brains. In frontal cortex and hippocampus of control cases, the most pronounced ODC immunoreactivity was found in the nucleus. In possible and definite AD the immunoreactivity had shifted to the cytoplasm. In cerebellum of control cases, ODC staining was found in a small portion of Purkinje cells, mostly in the nucleus. In AD, both possible and definite, the number of stained Purkinje cells increased significantly and immunoreactivity was shifted to the cytoplasm, even though it was still prominent in the nucleus. In conclusion, our study reveals an early shift of the ODC immunoreactivity in AD from the nuclear compartment towards the cytoplasm

  17. Studies on the turnover and subcellular localization of membrane gangliosides in cultured neuroblastoma cells

    International Nuclear Information System (INIS)

    Clarke, J.T.; Cook, H.W.; Spence, M.W.

    1985-01-01

    To compare the subcellular distribution of endogenously synthesized and exogenous gangliosides, cultured murine neuroblastoma cells (N1E-115) were incubated in suspension for 22 h in the presence of D-[1- 3 H]galactose or [ 3 H]GM1 ganglioside, transferred to culture medium containing no radioisotope for periods of up to 72 hr, and then subjected to subcellular fractionation and analysis of lipid-sialic acid and radiolabeled ganglioside levels. The results indicated that GM2 and GM3 were the principal gangliosides in the cells with only traces of GM1 and small amounts of disialogangliosides present. About 50% of the endogenously synthesized radiolabelled ganglioside in the four major subcellular membrane fractions studied was recovered from plasma membrane and only 10-15% from the crude mitochondrial membrane fraction. In contrast, 45% of the exogenous [ 3 H]GM1 taken up into the same subcellular membrane fractions was recovered from the crude mitochondrial fraction; less than 15% was localized in the plasma membrane fraction. The results are similar to those obtained from previously reported studies on membrane phospholipid turnover. They suggest that exogenous GM1 ganglioside, like exogenous phosphatidylcholine, does not intermix freely with any quantitatively major pool of endogenous membrane lipid

  18. Skeletal muscle glycogen content and particle size of distinct subcellular localizations in the recovery period after a high-level soccer match

    DEFF Research Database (Denmark)

    Nielsen, Joachim; Krustrup, Peter; Nybo, Lars

    2012-01-01

    Whole muscle glycogen levels remain low for a prolonged period following a soccer match. The present study was conducted to investigate how this relates to glycogen content and particle size in distinct subcellular localizations. Seven high-level male soccer players had a vastus lateralis muscle...... biopsy collected immediately after and 24, 48, 72 and 120 h after a competitive soccer match. Transmission electron microscopy was used to estimate the subcellular distribution of glycogen and individual particle size. During the first day of recovery, glycogen content increased by ~60% in all...

  19. Iron in seeds – loading pathways and subcellular localization

    Directory of Open Access Journals (Sweden)

    Louis eGrillet

    2014-01-01

    Full Text Available Iron (Fe is one of the most abundant elements on earth, but its limited bioavailability poses a major constraint for agriculture and constitutes a serious problem in human health. Due to an improved understanding of the mechanisms that control Fe homeostasis in plants, major advances towards engineering biofortified crops have been made during the past decade. Examples of successful biofortification strategies are, however, still scarce and the process of Fe loading into seeds is far from being well understood in most crop species. In particular in grains where the embryo represents the main storage compartment such as legumes, increasing the seed Fe content remains a challenging task. This review aims at placing the recently identified actors in Fe transport into the unsolved puzzle of grain filling, taking the differences of Fe distribution between various species into consideration. We summarize the current knowledge on Fe transport between symplasmic and apoplasmic compartments, and provide models for Fe trafficking and localization in different seed types that may help to develop high seed Fe germplasms.

  20. DeepLoc: prediction of protein subcellular localization using deep learning

    DEFF Research Database (Denmark)

    Almagro Armenteros, Jose Juan; Sønderby, Casper Kaae; Sønderby, Søren Kaae

    2017-01-01

    The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from...... knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only. Here, we present a prediction algorithm using deep neural networks to predict...... current state-of-the-art algorithms, including those relying on homology information. The method is available as a web server at http://www.cbs.dtu.dk/services/DeepLoc . Example code is available at https://github.com/JJAlmagro/subcellular_localization . The dataset is available at http...

  1. ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes

    Directory of Open Access Journals (Sweden)

    King Brian R

    2012-07-01

    Full Text Available Abstract Background Understanding protein subcellular localization is a necessary component toward understanding the overall function of a protein. Numerous computational methods have been published over the past decade, with varying degrees of success. Despite the large number of published methods in this area, only a small fraction of them are available for researchers to use in their own studies. Of those that are available, many are limited by predicting only a small number of organelles in the cell. Additionally, the majority of methods predict only a single location for a sequence, even though it is known that a large fraction of the proteins in eukaryotic species shuttle between locations to carry out their function. Findings We present a software package and a web server for predicting the subcellular localization of protein sequences based on the ngLOC method. ngLOC is an n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The overall prediction accuracy varies from 89.8% to 91.4% across species. This program can predict 11 distinct locations each in plant and animal species. ngLOC also predicts 4 and 5 distinct locations on gram-positive and gram-negative bacterial datasets, respectively. Conclusions ngLOC is a generic method that can be trained by data from a variety of species or classes for predicting protein subcellular localization. The standalone software is freely available for academic use under GNU GPL, and the ngLOC web server is also accessible at http://ngloc.unmc.edu.

  2. Identifying essential proteins based on sub-network partition and prioritization by integrating subcellular localization information.

    Science.gov (United States)

    Li, Min; Li, Wenkai; Wu, Fang-Xiang; Pan, Yi; Wang, Jianxin

    2018-06-14

    Essential proteins are important participants in various life activities and play a vital role in the survival and reproduction of living organisms. Identification of essential proteins from protein-protein interaction (PPI) networks has great significance to facilitate the study of human complex diseases, the design of drugs and the development of bioinformatics and computational science. Studies have shown that highly connected proteins in a PPI network tend to be essential. A series of computational methods have been proposed to identify essential proteins by analyzing topological structures of PPI networks. However, the high noise in the PPI data can degrade the accuracy of essential protein prediction. Moreover, proteins must be located in the appropriate subcellular localization to perform their functions, and only when the proteins are located in the same subcellular localization, it is possible that they can interact with each other. In this paper, we propose a new network-based essential protein discovery method based on sub-network partition and prioritization by integrating subcellular localization information, named SPP. The proposed method SPP was tested on two different yeast PPI networks obtained from DIP database and BioGRID database. The experimental results show that SPP can effectively reduce the effect of false positives in PPI networks and predict essential proteins more accurately compared with other existing computational methods DC, BC, CC, SC, EC, IC, NC. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. Subcellular localization of class I histone deacetylases in the developing Xenopus tectum

    Directory of Open Access Journals (Sweden)

    Xia eGuo

    2016-01-01

    Full Text Available Histone deacetylases (HDACs are thought to localize in the nucleus to regulate gene transcription and play pivotal roles in neurogenesis, apoptosis and plasticity. However, the subcellular distribution of class I HDACs in the developing brain remains unclear. Here, we show that HDAC1 and HDAC2 are located in both the mitochondria and the nucleus in the Xenopus laevis stage 34 tectum and are mainly restricted to the nucleus following further brain development. HDAC3 is widely present in the mitochondria, nucleus and cytoplasm during early tectal development and is mainly distributed in the nucleus in stage 45 tectum. In contrast, HDAC8 is broadly located in the mitochondria, nucleus and cytoplasm during tectal development. These data demonstrate that HDAC1, HDAC2 and HDAC3 are transiently localized in the mitochondria and that the subcellular distribution of class I HDACs in the Xenopus tectum is heterogeneous. Furthermore, we observed that spherical mitochondria accumulate in the cytoplasm at earlier stages, whereas elongated mitochondria are evenly distributed in the tectum at later stages. The activity of histone acetylation (H4K12 remains low in mitochondria during tectal development. Pharmacological blockades of HDACs using a broad spectrum HDAC inhibitor of Trichostatin A (TSA or specific class I HDAC inhibitors of MS-275 and MGCD0103 decrease the number of mitochondria in the tectum at stage 34. These findings highlight a link between the subcellular distribution of class I HDACs and mitochondrial dynamics in the developing optic tectum of Xenopus laevis.

  4. ClubSub-P: Cluster-based subcellular localization prediction for Gram-negative bacteria and Archaea.

    Directory of Open Access Journals (Sweden)

    Nagarajan eParamasivam

    2011-11-01

    Full Text Available The subcellular localization of proteins provides important clues to their function in a cell. In our efforts to predict useful vaccine targets against Gram-negative bacteria, we noticed that misannotated start codons frequently lead to wrongly assigned subcellular localizations. This and other problems in subcellular localization prediction, such as the relatively high false positive and false negative rates of some tools, can be avoided by applying multiple prediction tools to groups of homologous proteins. Here we present ClubSub-P, an online database that combines existing subcellular localization prediction tools into a consensus pipeline from more than 600 proteomes of fully sequenced microorganisms. On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false positive and false negative predictions. ClubSub-P can assign the subcellular localization of proteins from Gram-negative bacteria and Archaea with high precision. The database is searchable, and can easily be expanded using either new bacterial genomes or new prediction tools as they become available. This will further improve the performance of the subcellular localization prediction, as well as the detection of misannotated start codons and other annotation errors. ClubSub-P is available online at http://toolkit.tuebingen.mpg.de/clubsubp/

  5. The subcellular localization of IGFBP5 affects its cell growth and migration functions in breast cancer

    International Nuclear Information System (INIS)

    Akkiprik, Mustafa; Hu, Limei; Sahin, Aysegul; Hao, Xishan; Zhang, Wei

    2009-01-01

    Insulin-like growth factor binding protein 5 (IGFBP5) has been shown to be associated with breast cancer metastasis in clinical marker studies. However, a major difficulty in understanding how IGFBP5 functions in this capacity is the paradoxical observation that ectopic overexpression of IGFBP5 in breast cancer cell lines results in suppressed cellular proliferation. In cancer tissues, IGFBP5 resides mainly in the cytoplasm; however, in transfected cells, IGFBP5 is mainly located in the nucleus. We hypothesized that subcellular localization of IGFBP5 affects its functions in host cells. To test this hypothesis, we generated wild-type and mutant IGFBP5 expression constructs. The mutation occurs within the nuclear localization sequence (NLS) of the protein and is generated by site-directed mutagenesis using the wild-type IGFBP5 expression construct as a template. Next, we transfected each expression construct into MDA-MB-435 breast cancer cells to establish stable clones overexpressing either wild-type or mutant IGFBP5. Functional analysis revealed that cells overexpressing wild-type IGFBP5 had significantly lower cell growth rate and motility than the vector-transfected cells, whereas cells overexpressing mutant IGFBP5 demonstrated a significantly higher ability to proliferate and migrate. To illustrate the subcellular localization of the proteins, we generated wild-type and mutant IGFBP5-pDsRed fluorescence fusion constructs. Fluorescence microscopy imaging revealed that mutation of the NLS in IGFBP5 switched the accumulation of IGFBP5 from the nucleus to the cytoplasm of the protein. Together, these findings imply that the mutant form of IGFBP5 increases proliferation and motility of breast cancer cells and that mutation of the NLS in IGFBP5 results in localization of IGFBP5 in the cytoplasm, suggesting that subcellular localization of IGFBP5 affects its cell growth and migration functions in the breast cancer cells

  6. Subcellular localization of an intracellular serine protease of 68 kDa in Leishmania (Leishmania amazonensis promastigotes

    Directory of Open Access Journals (Sweden)

    José Andrés Morgado-Díaz

    2005-07-01

    Full Text Available Here we report the subcellular localization of an intracellular serine protease of 68 kDa in axenic promastigotes of Leishmania (Leishmania amazonensis, using subcellular fractionation, enzymatic assays, immunoblotting, and immunocytochemistry. All fractions were evaluated by transmission electron microscopy and the serine protease activity was measured during the cell fractionation procedure using a-N-r-tosyl-L-arginine methyl ester (L-TAME as substrate, phenylmethylsulphone fluoride (PMSF and L-1-tosylamino-2-phenylethylchloromethylketone (TPCK as specific inhibitors. The enzymatic activity was detected mainly in a membranous vesicular fraction (6.5-fold enrichment relative to the whole homogenate, but also in a crude plasma membrane fraction (2.0-fold. Analysis by SDS-PAGE gelatin under reducing conditions demonstrated that the major proteolytic activity was found in a 68 kDa protein in all fractions studied. A protein with identical molecular weight was also recognized in immunoblots by a polyclonal antibody against serine protease (anti-SP, with higher immunoreactivity in the vesicular fraction. Electron microscopic immunolocalization using the same polyclonal antibody showed the enzyme present at the cell surface, as well as in cytoplasmic membranous compartments of the parasite. Our findings indicate that the internal location of this serine protease in L. amazonensis is mainly restricted to the membranes of intracellular compartments resembling endocytic/exocytic elements.

  7. Subcellular localization-dependent decrements in skeletal muscle glycogen and mitochondria content following short-term disuse in young and old men

    DEFF Research Database (Denmark)

    Nielsen, Joachim; Suetta, Charlotte; Hvid, Lars G

    2010-01-01

    of disuse and aging on human skeletal muscle glycogen and mitochondria content in subsarcolemmal (SS), intermyofibrillar (IMF), and intramyofibrillar (intra) localizations. Five young (∼23 yr) and five old (∼66 yr) recreationally active men had their quadriceps muscle immobilized for 2 wk by whole leg...... unchanged. A localization-dependent decrease (P = 0.03) in mitochondria content following immobilization was found in both age groups, where SS mitochondria decreased by 33% (P = 0.02), superficial IMF mitochondria decreased by 20% (P = 0.05), and central IMF mitochondria remained unchanged. In conclusion......Previous studies have shown that skeletal muscle glycogen and mitochondria are distributed in distinct subcellular localizations, but the role and regulation of these subcellular localizations are unclear. In the present study, we used transmission electron microscopy to investigate the effect...

  8. Differential subcellular localization of insulin receptor substrates depends on C-terminal regions and importin β

    International Nuclear Information System (INIS)

    Kabuta, Tomohiro; Take, Kazumi; Kabuta, Chihana; Hakuno, Fumihiko; Takahashi, Shin-Ichiro

    2008-01-01

    Insulin receptor substrates (IRSs) play essential roles in signal transduction of insulin and insulin-like growth factors. Previously, we showed that IRS-3 is localized to the nucleus as well as the cytosol, while IRS-1 and 2 are mainly localized to the cytoplasm. In the present study, we found that importin β directly interacts with IRS-3 and is able to mediate nuclear transport of IRS-3. Importin β interacted with the pleckstrin homology domain, the phosphotyrosine binding domain and the C-terminal region of IRS-3; indeed all of these fragments exhibited predominant nuclear localization. By contrast, almost no interaction of importin β with IRS-1 and -2 was observed, and their C-terminal regions displayed discrete spotty images in the cytosol. In addition, using chimeric proteins between IRS-1 and IRS-3, we revealed that the C-terminal regions are the main determinants of the differing subcellular localizations of IRS-1 and IRS-3.

  9. Subcellular localization and mechanism of secretion of vascular endothelial growth factor in human skeletal muscle

    DEFF Research Database (Denmark)

    Høier, Birgitte; Prats Gavalda, Clara; Qvortrup, Klaus

    2013-01-01

    The subcellular distribution and secretion of vascular endothelial growth factor (VEGF) was examined in skeletal muscle of healthy humans. Skeletal muscle biopsies were obtained from m.v. lateralis before and after a 2 h bout of cycling exercise. VEGF localization was conducted on preparations...... regions and between the contractile elements within the muscle fibers; and in pericytes situated on the skeletal muscle capillaries. Quantitation of the subsarcolemmal density of VEGF vesicles, calculated on top of myonuclei, in the muscle fibers revealed a ∼50% increase (P...

  10. Subcellular localization of YKL-40 in normal and malignant epithelial cells of the breast

    DEFF Research Database (Denmark)

    Roslind, A.; Balslev, E.; Kruse, H.

    2008-01-01

    . YKL-40 protein expression was redistributed in carcinoma versus normal glandular tissue of the breast. A reduced expression of YKL-40 in relation to intermediate filaments and desmosomes was found in tumor cells. Changes in YKL-40 expression suggest that the function of YKL-40 in cells of epithelial......YKL-40 is a new prognostic biomarker in cancer. The biological function is only poorly understood. This study aimed at determining the subcellular localization of YKL-40, using immunogold labeling, in normal epithelial cells and in malignant tumor cells of the breast by immunoelectron microscopy...

  11. Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning

    Directory of Open Access Journals (Sweden)

    Tanel Pärnamaa

    2017-05-01

    Full Text Available High-throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently-tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held-out images. We confirm that low-level network features correspond to basic image characteristics, while deeper layers separate localization classes. Using this network as a feature calculator, we train standard classifiers that assign proteins to previously unseen compartments after observing only a small number of training examples. Our results are the most accurate subcellular localization classifications to date, and demonstrate the usefulness of deep learning for high-throughput microscopy.

  12. Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning.

    Science.gov (United States)

    Pärnamaa, Tanel; Parts, Leopold

    2017-05-05

    High-throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently-tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held-out images. We confirm that low-level network features correspond to basic image characteristics, while deeper layers separate localization classes. Using this network as a feature calculator, we train standard classifiers that assign proteins to previously unseen compartments after observing only a small number of training examples. Our results are the most accurate subcellular localization classifications to date, and demonstrate the usefulness of deep learning for high-throughput microscopy. Copyright © 2017 Parnamaa and Parts.

  13. Osmotic stress changes the expression and subcellular localization of the Batten disease protein CLN3.

    Directory of Open Access Journals (Sweden)

    Amanda Getty

    Full Text Available Juvenile CLN3 disease (formerly known as juvenile neuronal ceroid lipofuscinosis is a fatal childhood neurodegenerative disorder caused by mutations in the CLN3 gene. CLN3 encodes a putative lysosomal transmembrane protein with unknown function. Previous cell culture studies using CLN3-overexpressing vectors and/or anti-CLN3 antibodies with questionable specificity have also localized CLN3 in cellular structures other than lysosomes. Osmoregulation of the mouse Cln3 mRNA level in kidney cells was recently reported. To clarify the subcellular localization of the CLN3 protein and to investigate if human CLN3 expression and localization is affected by osmotic changes we generated a stably transfected BHK (baby hamster kidney cell line that expresses a moderate level of myc-tagged human CLN3 under the control of the human ubiquitin C promoter. Hyperosmolarity (800 mOsm, achieved by either NaCl/urea or sucrose, dramatically increased the mRNA and protein levels of CLN3 as determined by quantitative real-time PCR and Western blotting. Under isotonic conditions (300 mOsm, human CLN3 was found in a punctate vesicular pattern surrounding the nucleus with prominent Golgi and lysosomal localizations. CLN3-positive early endosomes, late endosomes and cholesterol/sphingolipid-enriched plasma membrane microdomain caveolae were also observed. Increasing the osmolarity of the culture medium to 800 mOsm extended CLN3 distribution away from the perinuclear region and enhanced the lysosomal localization of CLN3. Our results reveal that CLN3 has multiple subcellular localizations within the cell, which, together with its expression, prominently change following osmotic stress. These data suggest that CLN3 is involved in the response and adaptation to cellular stress.

  14. Protein Subcellular Localization with Gaussian Kernel Discriminant Analysis and Its Kernel Parameter Selection.

    Science.gov (United States)

    Wang, Shunfang; Nie, Bing; Yue, Kun; Fei, Yu; Li, Wenjia; Xu, Dongshu

    2017-12-15

    Kernel discriminant analysis (KDA) is a dimension reduction and classification algorithm based on nonlinear kernel trick, which can be novelly used to treat high-dimensional and complex biological data before undergoing classification processes such as protein subcellular localization. Kernel parameters make a great impact on the performance of the KDA model. Specifically, for KDA with the popular Gaussian kernel, to select the scale parameter is still a challenging problem. Thus, this paper introduces the KDA method and proposes a new method for Gaussian kernel parameter selection depending on the fact that the differences between reconstruction errors of edge normal samples and those of interior normal samples should be maximized for certain suitable kernel parameters. Experiments with various standard data sets of protein subcellular localization show that the overall accuracy of protein classification prediction with KDA is much higher than that without KDA. Meanwhile, the kernel parameter of KDA has a great impact on the efficiency, and the proposed method can produce an optimum parameter, which makes the new algorithm not only perform as effectively as the traditional ones, but also reduce the computational time and thus improve efficiency.

  15. Synthesis, characterization, and subcellular localization studies of amino acid-substituted porphyrinic pigments

    Science.gov (United States)

    van Diggelen, Lisa; Khin, Hnin; Conner, Kip; Shao, Jenny; Sweezy, Margaretta; Jung, Anna H.; Isaac, Meden; Simonis, Ursula

    2009-06-01

    Stopping cancer in its path occurs when photosensitizers (PSs) induce apoptotic cell death after their exposure to light and the subsequent formation of reactive oxygen species. In pursuit of our hypothesis that mitochondrial localizing PSs will enhance the efficacy of the photosensitizing process in photodynamic therapy, since they provoke cell death by inducing apoptosis, we synthesized and characterized tetraphenylporphyrins (TPPs) that are substituted at the paraphenyl positions by two amino acids and two fluoro or hydroxyl groups, respectively. They were prepared according to the Lindsey-modified Adler-Longo methodology using trifluoromethanesulfonylchloride (CF3SO2Cl) as a catalyst instead of trifluoroacetic acid. The use of CF3SO2Cl yielded cleaner products in significantly higher yields. During the synthesis, not only the yields and work-up procedure of the TPPs were improved by using CF3SO2Cl as a catalyst, but also a better means of synthesizing the precursor dipyrromethanes was tested by using indium(III) chloride. Column chromatography, HPLC, and NMR spectroscopy were used to separate and characterize the di-amino acid-dihydroxy, or difluoro-substituted porphyrins and to ascertain their purity before subcellular localization studies were carried out. Studies using androgen-sensitive human prostate adenocarcinoma cells LNCaP revealed that certain amino acid substituted porphyrins that are positively charged in the slightly acidic medium of cancer cells are very useful in shedding light on the targets of TPPs in subcellular organelles of cancer cells. Although some of these compounds have properties of promising photosensitizers by revealing increased water solubility, acidic properties, and innate ability to provoke cell death by apoptosis, the cell killing efficacy of these TPPs is low. This correlates with their subcellular localization. The di-amino acid, di-hydroxy substituted TPPs localize mainly to the lysosomes, whereas the di

  16. CellMap visualizes protein-protein interactions and subcellular localization

    Science.gov (United States)

    Dallago, Christian; Goldberg, Tatyana; Andrade-Navarro, Miguel Angel; Alanis-Lobato, Gregorio; Rost, Burkhard

    2018-01-01

    Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers. PMID:29497493

  17. ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins

    Directory of Open Access Journals (Sweden)

    Raghava Gajendra PS

    2008-11-01

    Full Text Available Abstract Background The expansion of raw protein sequence databases in the post genomic era and availability of fresh annotated sequences for major localizations particularly motivated us to introduce a new improved version of our previously forged eukaryotic subcellular localizations prediction method namely "ESLpred". Since, subcellular localization of a protein offers essential clues about its functioning, hence, availability of localization predictor would definitely aid and expedite the protein deciphering studies. However, robustness of a predictor is highly dependent on the superiority of dataset and extracted protein attributes; hence, it becomes imperative to improve the performance of presently available method using latest dataset and crucial input features. Results Here, we describe augmentation in the prediction performance obtained for our most popular ESLpred method using new crucial features as an input to Support Vector Machine (SVM. In addition, recently available, highly non-redundant dataset encompassing three kingdoms specific protein sequence sets; 1198 fungi sequences, 2597 from animal and 491 plant sequences were also included in the present study. First, using the evolutionary information in the form of profile composition along with whole and N-terminal sequence composition as an input feature vector of 440 dimensions, overall accuracies of 72.7, 75.8 and 74.5% were achieved respectively after five-fold cross-validation. Further, enhancement in performance was observed when similarity search based results were coupled with whole and N-terminal sequence composition along with profile composition by yielding overall accuracies of 75.9, 80.8, 76.6% respectively; best accuracies reported till date on the same datasets. Conclusion These results provide confidence about the reliability and accurate prediction of SVM modules generated in the present study using sequence and profile compositions along with similarity search

  18. SMYD3 interacts with HTLV-1 Tax and regulates subcellular localization of Tax.

    Science.gov (United States)

    Yamamoto, Keiyu; Ishida, Takaomi; Nakano, Kazumi; Yamagishi, Makoto; Yamochi, Tadanori; Tanaka, Yuetsu; Furukawa, Yoichi; Nakamura, Yusuke; Watanabe, Toshiki

    2011-01-01

    HTLV-1 Tax deregulates signal transduction pathways, transcription of genes, and cell cycle regulation of host cells, which is mainly mediated by its protein-protein interactions with host cellular factors. We previously reported an interaction of Tax with a histone methyltransferase (HMTase), SUV39H1. As the interaction was mediated by the SUV39H1 SET domain that is shared among HMTases, we examined the possibility of Tax interaction with another HMTase, SMYD3, which methylates histone H3 lysine 4 and activates transcription of genes, and studied the functional effects. Expression of endogenous SMYD3 in T cell lines and primary T cells was confirmed by immunoblotting analysis. Co-immuno-precipitaion assays and in vitro pull-down assay indicated interaction between Tax and SMYD3. The interaction was largely dependent on the C-terminal 180 amino acids of SMYD3, whereas the interacting domain of Tax was not clearly defined, although the N-terminal 108 amino acids were dispensable for the interaction. In the cotransfected cells, colocalization of Tax and SMYD3 was indicated in the cytoplasm or nuclei. Studies using mutants of Tax and SMYD3 suggested that SMYD3 dominates the subcellular localization of Tax. Reporter gene assays showed that nuclear factor-κB activation promoted by cytoplasmic Tax was enhanced by the presence of SMYD3, and attenuated by shRNA-mediated knockdown of SMYD3, suggesting an increased level of Tax localization in the cytoplasm by SMYD3. Our study revealed for the first time Tax-SMYD3 direct interaction, as well as apparent tethering of Tax by SMYD3, influencing the subcellular localization of Tax. Results suggested that SMYD3-mediated nucleocytoplasmic shuttling of Tax provides one base for the pleiotropic effects of Tax, which are mediated by the interaction of cellular proteins localized in the cytoplasm or nucleus. © 2010 Japanese Cancer Association.

  19. Prediction of essential proteins based on subcellular localization and gene expression correlation.

    Science.gov (United States)

    Fan, Yetian; Tang, Xiwei; Hu, Xiaohua; Wu, Wei; Ping, Qing

    2017-12-01

    Essential proteins are indispensable to the survival and development process of living organisms. To understand the functional mechanisms of essential proteins, which can be applied to the analysis of disease and design of drugs, it is important to identify essential proteins from a set of proteins first. As traditional experimental methods designed to test out essential proteins are usually expensive and laborious, computational methods, which utilize biological and topological features of proteins, have attracted more attention in recent years. Protein-protein interaction networks, together with other biological data, have been explored to improve the performance of essential protein prediction. The proposed method SCP is evaluated on Saccharomyces cerevisiae datasets and compared with five other methods. The results show that our method SCP outperforms the other five methods in terms of accuracy of essential protein prediction. In this paper, we propose a novel algorithm named SCP, which combines the ranking by a modified PageRank algorithm based on subcellular compartments information, with the ranking by Pearson correlation coefficient (PCC) calculated from gene expression data. Experiments show that subcellular localization information is promising in boosting essential protein prediction.

  20. Tissue and subcellular localizations of 3H-cyclosporine A in mice

    International Nuclear Information System (INIS)

    Baeckman, L.; Brandt, I.; Appelkvist, E.-L.; Dallner, G.

    1988-01-01

    The tissue and subcellular localizations of 3 H-cyclosporine A after administration to mice were determined with whole-body autoradiography and scintillation counting of lipid extracts of tissues and subcellular fractions. The radioactivity was widely distributed in the body and the pattern of distribution after oral or parenteral administration was the same, except that tissue levels were generatlly lower after oral administration. Pretreatment of the animals with a diet containing cyclosporine A for 30 days before the injection of radioactive cyclosporine A did not change the pattern of distribution substantially. No significant radioactivity was found in the central nervous system, except for the choroidal plexus and the area postrema region of the brain. In pregnant mice no passage of radioactivity from the placentas to fetuses was observed after a single injection. 3 H-cyclosporine A and/or its metabolites showed a high affinity for the lympho-myeloid tissues, with a marked long-term retention in bone marrow and lymph nodes. There was massive excretion in the intestinal tract after parenteral administration, and the liver, bile, pancreas and salivary glands contained high levels of radioactivity. In the kidney radioactivity was confined to the outer zone of the outer kidney medulla. In liver homogenates no quantitatively significant binding of 3 H-cyclosporine A and/or its metabolites to cellular molecules such as proteins, DNA, phospho- or neutral lipids was found. After lipid extraction with organic solvents, almost all radioactivity was recovered in the organic phase. (author)

  1. The subcellular localization of natural 210Po in the hepatopancreas of the rock lobster (Jasus lalandii)

    International Nuclear Information System (INIS)

    Heyraud, M.; Dowdle, E.B.; Cherry, R.D.

    1987-01-01

    The subcellular localization of the naturally occurring nuclide 210 Po in the hepatopancreas of the South African rock lobster, Jasus lalandii, has been studied using centrifugation, ultrafiltration and chromatography. Just over half of the 210 Po was found to be associated with a component in the microsomal pellet. Most of the 210 Po was tightly bound to a component of high molecular mass. Dissociation of the 210 Po from this component required incubation with sulphydryl-reducing reagents, after which the 210 Po appeared to associate with a fraction having a molecular mass of 1500 daltons or less. A search for negatively-charged, hydrophobic, sulphur-containing membrane proteins which bind 210 Po is suggested. (author)

  2. Subcellular localization of natural /sup 210/Po in the hepatopancreas of the rock lobster (Jasus lalandii)

    Energy Technology Data Exchange (ETDEWEB)

    Heyraud, M; Dowdle, E B; Cherry, R D

    1987-01-01

    The subcellular localization of the naturally occurring nuclide /sup 210/Po in the hepatopancreas of the South African rock lobster, Jasus lalandii, has been studied using centrifugation, ultrafiltration and chromatography. Just over half of the /sup 210/Po was found to be associated with a component in the microsomal pellet. Most of the /sup 210/Po was tightly bound to a component of high molecular mass. Dissociation of the /sup 210/Po from this component required incubation with sulphydryl-reducing reagents, after which the /sup 210/Po appeared to associate with a fraction having a molecular mass of 1500 daltons or less. A search for negatively-charged, hydrophobic, sulphur-containing membrane proteins which bind /sup 210/Po is suggested.

  3. Dynamic Subcellular Localization of Iron during Embryo Development in Brassicaceae Seeds

    Directory of Open Access Journals (Sweden)

    Miguel A. Ibeas

    2017-12-01

    Full Text Available Iron is an essential micronutrient for plants. Little is know about how iron is loaded in embryo during seed development. In this article we used Perls/DAB staining in order to reveal iron localization at the cellular and subcellular levels in different Brassicaceae seed species. In dry seeds of Brassica napus, Nasturtium officinale, Lepidium sativum, Camelina sativa, and Brassica oleracea iron localizes in vacuoles of cells surrounding provasculature in cotyledons and hypocotyl. Using B. napus and N. officinale as model plants we determined where iron localizes during seed development. Our results indicate that iron is not detectable by Perls/DAB staining in heart stage embryo cells. Interestingly, at torpedo development stage iron localizes in nuclei of different cells type, including integument, free cell endosperm and almost all embryo cells. Later, iron is detected in cytoplasmic structures in different embryo cell types. Our results indicate that iron accumulates in nuclei in specific stages of embryo maturation before to be localized in vacuoles of cells surrounding provasculature in mature seeds.

  4. Characterization of intact subcellular bodies in whole bacteria by cryo-electron tomography and spectroscopic imaging.

    Science.gov (United States)

    Comolli, L R; Kundmann, M; Downing, K H

    2006-07-01

    We illustrate the combined use of cryo-electron tomography and spectroscopic difference imaging in the study of subcellular structure and subcellular bodies in whole bacteria. We limited our goal and focus to bodies with a distinct elemental composition that was in a sufficiently high concentration to provide the necessary signal-to-noise level at the relatively large sample thicknesses of the intact cell. This combination proved very powerful, as demonstrated by the identification of a phosphorus-rich body in Caulobacter crescentus. We also confirmed the presence of a body rich in carbon, demonstrated that these two types of bodies are readily recognized and distinguished from each other, and provided, for the first time to our knowledge, structural information about them in their intact state. In addition, we also showed the presence of a similar type of phosphorus-rich body in Deinococcus grandis, a member of a completely unrelated bacteria genus. Cryo-electron microscopy and tomography allowed the study of the biogenesis and morphology of these bodies at resolutions better than 10 nm, whereas spectroscopic difference imaging provided a direct identification of their chemical composition.

  5. CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

    Directory of Open Access Journals (Sweden)

    Lucchetti-Miganeh Céline

    2010-03-01

    Full Text Available Abstract Background The functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes but the experimental determination of the sub-cellular localization of proteomes is laborious and expensive. A fast and low-cost alternative approach is in silico prediction, based on features of the protein primary sequences. However, biologists are confronted with a very large number of computational tools that use different methods that address various localization features with diverse specificities and sensitivities. As a result, exploiting these computer resources to predict protein localization accurately involves querying all tools and comparing every prediction output; this is a painstaking task. Therefore, we developed a comprehensive database, called CoBaltDB, that gathers all prediction outputs concerning complete prokaryotic proteomes. Description The current version of CoBaltDB integrates the results of 43 localization predictors for 784 complete bacterial and archaeal proteomes (2.548.292 proteins in total. CoBaltDB supplies a simple user-friendly interface for retrieving and exploring relevant information about predicted features (such as signal peptide cleavage sites and transmembrane segments. Data are organized into three work-sets ("specialized tools", "meta-tools" and "additional tools". The database can be queried using the organism name, a locus tag or a list of locus tags and may be browsed using numerous graphical and text displays. Conclusions With its new functionalities, CoBaltDB is a novel powerful platform that provides easy access to the results of multiple localization tools and support for predicting prokaryotic protein localizations with higher confidence than previously possible. CoBaltDB is available at http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten.

  6. Subcellular fractionation and localization studies reveal a direct interaction of the Fragile X Mental Retardation Protein (FMRP) with nucleolin

    NARCIS (Netherlands)

    Taha, M.S.; Nouri, K.; Milroy, L.G.; Moll, J.M.; Herrmann, C.; Brunsveld, L.; Piekorz, R.P.; Ahmadian, M.R.

    2014-01-01

    Fragile X mental Retardation Protein (FMRP) is a well-known regulator of local translation of its mRNA targets in neurons. However, despite its ubiquitous expression, the role of FMRP remains ill-defined in other cell types. In this study we investigated the subcellular distribution of FMRP and its

  7. Subcellular localization of the delayed rectifier K(+) channels KCNQ1 and ERG1 in the rat heart

    DEFF Research Database (Denmark)

    Rasmussen, Hanne Borger; Møller, Morten; Knaus, Hans-Günther

    2003-01-01

    In the heart, several K(+) channels are responsible for the repolarization of the cardiac action potential, including transient outward and delayed rectifier K(+) currents. In the present study, the cellular and subcellular localization of the two delayed rectifier K(+) channels, KCNQ1 and ether...

  8. Subcellular localization and regulation of type-1C and type-5 phosphodiesterases

    International Nuclear Information System (INIS)

    Dolci, Susanna; Belmonte, Alessia; Santone, Rocco; Giorgi, Mauro; Pellegrini, Manuela; Carosa, Eleonora; Piccione, Emilio; Lenzi, Andrea; Jannini, Emmanuele A.

    2006-01-01

    We investigated the subcellular localization of PDE5 in in vitro human myometrial cells. We demonstrated for First time that PDE5 is localized in discrete cytoplasmic foci and vesicular compartments corresponding to centrosomes. We also found that PDE5 intracellular localization is not cell- or species-specific, as it is conserved in different animal and human cells. PDE5 protein levels are strongly regulated by the mitotic activity of the smooth muscle cells (SMCs), as they were increased in quiescent, contractile myometrial cultures, and conditions in which proliferation was inhibited. In contrast, PDE1C levels decreased in all conditions that inhibited proliferation. This mirrored the enzymatic activity of both PDE5 and PDE1C. Increasing cGMP intracellular levels by dbcGMP or sildenafil treatments did not block proliferation, while dbcAMP inhibited myometrial cell proliferation. Together, these results suggest that PDE5 regulation of cGMP intracellular levels is not involved in the control of SMC cycle progression, but may represent one of the markers of the contractile phenotype

  9. Astrocyte-neuron crosstalk regulates the expression and subcellular localization of carbohydrate metabolism enzymes.

    Science.gov (United States)

    Mamczur, Piotr; Borsuk, Borys; Paszko, Jadwiga; Sas, Zuzanna; Mozrzymas, Jerzy; Wiśniewski, Jacek R; Gizak, Agnieszka; Rakus, Dariusz

    2015-02-01

    Astrocytes releasing glucose- and/or glycogen-derived lactate and glutamine play a crucial role in shaping neuronal function and plasticity. Little is known, however, how metabolic functions of astrocytes, e.g., their ability to degrade glucosyl units, are affected by the presence of neurons. To address this issue we carried out experiments which demonstrated that co-culturing of rat hippocampal astrocytes with neurons significantly elevates the level of mRNA and protein for crucial enzymes of glycolysis (phosphofructokinase, aldolase, and pyruvate kinase), glycogen metabolism (glycogen synthase and glycogen phosphorylase), and glutamine synthetase in astrocytes. Simultaneously, the decrease of the capability of neurons to metabolize glucose and glutamine is observed. We provide evidence that neurons alter the expression of astrocytic enzymes by secretion of as yet unknown molecule(s) into the extracellular fluid. Moreover, our data demonstrate that almost all studied enzymes may localize in astrocytic nuclei and this localization is affected by the co-culturing with neurons which also reduces proliferative activity of astrocytes. Our results provide the first experimental evidence that the astrocyte-neuron crosstalk substantially affects the expression of basal metabolic enzymes in the both types of cells and influences their subcellular localization in astrocytes. © 2014 Wiley Periodicals, Inc.

  10. Subcellular localisation of radionuclides by transmission electronic microscopy in aquatic and terrestrial organisms

    Energy Technology Data Exchange (ETDEWEB)

    Floriani, M.; Grasset, G.; Simon, O.; Morlon, H.; Laroche, L. [CEA Cadarache (DEI/SECRE/LRE), Laboratory of Radioecology and Ecotoxicology, Institute for Radioprotection and Nuclear Safety, 13 - Saint-Paul-lez-Durance (France)

    2004-07-01

    The global framework of this study is to go further in the understanding of the involved mechanisms of uranium and selenium internalisation at the subcellular level and of their toxicity towards several aquatic and terrestrial organisms. In this context, the applications and performances of a Scanning Transmission Electron Microscope (TEM/STEM) equipped with CCD camera and Energy-Dispersive- X-Ray (EDAX) analysis are reported. The principal merit of this equipment is the clear expression of element distribution with nanometer resolution. The sample for TEM analysis were prepared in ultrathin sections of 70-140 nm (thickness) and those for EDAX in sections of 200-500 nm. This method offers the possibility of a direct correlation between histological image and distribution map of trace elements. For each sample, following TEM analysis, EDAX spectra or EDAX mapping were also recorded to confirm the identity of the electron dense material in the scanned sections. Demonstration of the usefulness of this method to understand the bioaccumulation mechanisms and to study the effect of the pollutant uptake at the subcellular level was performed for target organs of a metal (U) and a metalloid (Se) in various biological models: a higher rooted plant (Phaseolus vulgaris)) and a freshwater invertebrate (Orconectes Limosus) and a unicellular green alga (Chlamydomonas reinhardtii)). TEM-EDAX analysis revealed the presence of U-deposits in gills and digestive gland in crayfish, and in vacuoles or in the cytoplasm of different rooted cells bean. In the alga, the accumulation of Se was found in electron-dense granules within cytoplasm associated with ultrastructural changes and starch accumulation. (author)

  11. Subcellular localisation of radionuclides by transmission electronic microscopy in aquatic and terrestrial organisms

    International Nuclear Information System (INIS)

    Floriani, M.; Grasset, G.; Simon, O.; Morlon, H.; Laroche, L.

    2004-01-01

    The global framework of this study is to go further in the understanding of the involved mechanisms of uranium and selenium internalisation at the subcellular level and of their toxicity towards several aquatic and terrestrial organisms. In this context, the applications and performances of a Scanning Transmission Electron Microscope (TEM/STEM) equipped with CCD camera and Energy-Dispersive- X-Ray (EDAX) analysis are reported. The principal merit of this equipment is the clear expression of element distribution with nanometer resolution. The sample for TEM analysis were prepared in ultrathin sections of 70-140 nm (thickness) and those for EDAX in sections of 200-500 nm. This method offers the possibility of a direct correlation between histological image and distribution map of trace elements. For each sample, following TEM analysis, EDAX spectra or EDAX mapping were also recorded to confirm the identity of the electron dense material in the scanned sections. Demonstration of the usefulness of this method to understand the bioaccumulation mechanisms and to study the effect of the pollutant uptake at the subcellular level was performed for target organs of a metal (U) and a metalloid (Se) in various biological models: a higher rooted plant (Phaseolus vulgaris)) and a freshwater invertebrate (Orconectes Limosus) and a unicellular green alga (Chlamydomonas reinhardtii)). TEM-EDAX analysis revealed the presence of U-deposits in gills and digestive gland in crayfish, and in vacuoles or in the cytoplasm of different rooted cells bean. In the alga, the accumulation of Se was found in electron-dense granules within cytoplasm associated with ultrastructural changes and starch accumulation. (author)

  12. [Cloning, subcellular localization, and heterologous expression of ApNAC1 gene from Andrographis paniculata].

    Science.gov (United States)

    Wang, Jian; Qi, Meng-Die; Guo, Juan; Shen, Ye; Lin, Hui-Xin; Huang, Lu-Qi

    2017-03-01

    Andrographis paniculata is widely used as medicinal herb in China for a long time and andrographolide is its main medicinal constituent. To investigate the underlying andrographolide biosynthesis mechanisms, RNA-seq for A. paniculata leaves with MeJA treatment was performed. In A. paniculata transcriptomic data, the expression pattern of one member of NAC transcription factor family (ApNAC1) matched with andrographolide accumulation. The coding sequence of ApNAC1 was cloned by RT-PCR, and GenBank accession number was KY196416. The analysis of bioinformatics showed that the gene encodes a peptide of 323 amino acids, with a predicted relative molecular weight of 35.9 kDa and isoelectric point of 6.14. To confirm the subcellular localization, ApNAC1-GFP was transiently expressed in A. paniculata protoplast. The results indicated that ApNAC1 is a nucleus-localized protein. The analysis of real-time quantitative PCR revealed that ApNAC1 gene predominantly expresses in leaves. Compared with control sample, its expression abundance sharply increased with methyl jasmonate treatment. Based on its expression pattern, ApNAC1 gene might involve in andrographolide biosynthesis. ApNAC1 was heterologously expressed in Escherichia coli and recombinant protein was purified by Ni-NTA agarose. Further study will help us to understand the function of ApNAC1 in andrographolide biosynthesis. Copyright© by the Chinese Pharmaceutical Association.

  13. Requirements of cyclin a for mitosis are independent of its subcellular localization.

    Science.gov (United States)

    Dienemann, Axel; Sprenger, Frank

    2004-06-22

    Cyclin A (CycA), the only essential mitotic cyclin in Drosophila, is cytoplasmic during interphase and accumulates in the nucleus during prophase. We show that interphase localization is mediated by Leptomycin B (LMB)-sensitive nuclear export. This is a feature shared with human CyclinB1, and it is assumed that nuclear accumulation is necessary for mitotic entry. Here, we tested if the unique mitotic function of CycA requires nuclear accumulation. We fused subcellular localization signals to CycA and tested their mitotic capability. Surprisingly, nuclear accumulation was not required, and even a membrane-tethered form of CycA was able to induce mitosis. We noted that Cyclin B (CycB) protein disappears prematurely in CycA mutants, reminiscent of rca1 mutants. Rca1 is an inhibitor of Fizzy-related-APC/C activity, and in rca1 mutants, mitotic cyclins are degraded in G2 of the 16(th) embryonic cell cycle. Overexpression of Rca1 can restore mitosis in CycA mutants, indicating that the mitotic failure of CycA mutants is caused by premature activation of the APC/C. The essential mitotic function of CycA is therefore not the activation of numerous mitotic substrates by Cdk1-dependent phosphorylation. Rather, CycA-dependent kinase activity is required to inhibit one inhibitor of mitosis, the Fzr protein.

  14. Cell-Selective Biological Activity of Rhodium Metalloinsertors Correlates with Subcellular Localization

    Science.gov (United States)

    Komor, Alexis C.; Schneider, Curtis J.; Weidmann, Alyson G.; Barton, Jacqueline K.

    2013-01-01

    Deficiencies in the mismatch repair (MMR) pathway are associated with several types of cancers, as well as resistance to commonly used chemotherapeutics. Rhodium metalloinsertors have been found to bind DNA mismatches with high affinity and specificity in vitro, and also exhibit cell-selective cytotoxicity, targeting MMR-deficient cells over MMR-proficient cells. Ten distinct metalloinsertors with varying lipophilicities have been synthesized and their mismatch binding affinities and biological activities determined. Although DNA photocleavage experiments demonstrate that their binding affinities are quite similar, their cell-selective antiproliferative and cytotoxic activities vary significantly. Inductively coupled plasma mass spectrometry (ICP-MS) experiments have uncovered a relationship between the subcellular distribution of these metalloinsertors and their biological activities. Specifically, we find that all of our metalloinsertors localize in the nucleus at sufficient concentrations for binding to DNA mismatches. However, the metalloinsertors with high rhodium localization in the mitochondria show toxicity that is not selective for MMR-deficient cells, whereas metalloinsertors with less mitochondrial rhodium show activity that is highly selective for MMR-deficient versus proficient cells. This work supports the notion that specific targeting of the metalloinsertors to nuclear DNA gives rise to their cell-selective cytotoxic and antiproliferative activities. The selectivity in cellular targeting depends upon binding to mismatches in genomic DNA. PMID:23137296

  15. Correlation of N-myc downstream-regulated gene 1 subcellular localization and lymph node metastases of colorectal neoplasms

    Energy Technology Data Exchange (ETDEWEB)

    Song, Yan [Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014 (China); Lv, Liyang [Department of Health, Jinan Military Area Command, Jinan 250022 (China); Du, Juan; Yue, Longtao [Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014 (China); Cao, Lili, E-mail: cllly22@163.com [Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014 (China)

    2013-09-20

    Highlights: •We clarified NDRG1 subcellular location in colorectal cancer. •We found the changes of NDRG1 distribution during colorectal cancer progression. •We clarified the correlation between NDRG1 distribution and lymph node metastasis. •It is possible that NDRG1 subcellular localization may determine its function. •Maybe NDRG1 is valuable early diagnostic markers for metastasis. -- Abstract: In colorectal neoplasms, N-myc downstream-regulated gene 1 (NDRG1) is a primarily cytoplasmic protein, but it is also expressed on the cell membrane and in the nucleus. NDRG1 is involved in various stages of tumor development in colorectal cancer, and it is possible that the different subcellular localizations may determine the function of NDRG1 protein. Here, we attempt to clarify the characteristics of NDRG1 protein subcellular localization during the progression of colorectal cancer. We examined NDRG1 expression in 49 colorectal cancer patients in cancerous, non-cancerous, and corresponding lymph node tissues. Cytoplasmic and membrane NDRG1 expression was higher in the lymph nodes with metastases than in those without metastases (P < 0.01). Nuclear NDRG1 expression in colorectal neoplasms was significantly higher than in the normal colorectal mucosa, and yet the normal colorectal mucosa showed no nuclear expression. Furthermore, our results showed higher cytoplasmic NDRG1 expression was better for differentiation, and higher membrane NDRG1 expression resulted in a greater possibility of lymph node metastasis. These data indicate that a certain relationship between the cytoplasmic and membrane expression of NDRG1 in lymph nodes exists with lymph node metastasis. NDRG1 expression may translocate from the membrane of the colorectal cancer cells to the nucleus, where it is involved in lymph node metastasis. Combination analysis of NDRG1 subcellular expression and clinical variables will help predict the incidence of lymph node metastasis.

  16. Correlation of N-myc downstream-regulated gene 1 subcellular localization and lymph node metastases of colorectal neoplasms

    International Nuclear Information System (INIS)

    Song, Yan; Lv, Liyang; Du, Juan; Yue, Longtao; Cao, Lili

    2013-01-01

    Highlights: •We clarified NDRG1 subcellular location in colorectal cancer. •We found the changes of NDRG1 distribution during colorectal cancer progression. •We clarified the correlation between NDRG1 distribution and lymph node metastasis. •It is possible that NDRG1 subcellular localization may determine its function. •Maybe NDRG1 is valuable early diagnostic markers for metastasis. -- Abstract: In colorectal neoplasms, N-myc downstream-regulated gene 1 (NDRG1) is a primarily cytoplasmic protein, but it is also expressed on the cell membrane and in the nucleus. NDRG1 is involved in various stages of tumor development in colorectal cancer, and it is possible that the different subcellular localizations may determine the function of NDRG1 protein. Here, we attempt to clarify the characteristics of NDRG1 protein subcellular localization during the progression of colorectal cancer. We examined NDRG1 expression in 49 colorectal cancer patients in cancerous, non-cancerous, and corresponding lymph node tissues. Cytoplasmic and membrane NDRG1 expression was higher in the lymph nodes with metastases than in those without metastases (P < 0.01). Nuclear NDRG1 expression in colorectal neoplasms was significantly higher than in the normal colorectal mucosa, and yet the normal colorectal mucosa showed no nuclear expression. Furthermore, our results showed higher cytoplasmic NDRG1 expression was better for differentiation, and higher membrane NDRG1 expression resulted in a greater possibility of lymph node metastasis. These data indicate that a certain relationship between the cytoplasmic and membrane expression of NDRG1 in lymph nodes exists with lymph node metastasis. NDRG1 expression may translocate from the membrane of the colorectal cancer cells to the nucleus, where it is involved in lymph node metastasis. Combination analysis of NDRG1 subcellular expression and clinical variables will help predict the incidence of lymph node metastasis

  17. Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks.

    Directory of Open Access Journals (Sweden)

    Xiaoqing Peng

    Full Text Available Essential proteins are indispensable for living organisms to maintain life activities and play important roles in the studies of pathology, synthetic biology, and drug design. Therefore, besides experiment methods, many computational methods are proposed to identify essential proteins. Based on the centrality-lethality rule, various centrality methods are employed to predict essential proteins in a Protein-protein Interaction Network (PIN. However, neglecting the temporal and spatial features of protein-protein interactions, the centrality scores calculated by centrality methods are not effective enough for measuring the essentiality of proteins in a PIN. Moreover, many methods, which overfit with the features of essential proteins for one species, may perform poor for other species. In this paper, we demonstrate that the centrality-lethality rule also exists in Protein Subcellular Localization Interaction Networks (PSLINs. To do this, a method based on Localization Specificity for Essential protein Detection (LSED, was proposed, which can be combined with any centrality method for calculating the improved centrality scores by taking into consideration PSLINs in which proteins play their roles. In this study, LSED was combined with eight centrality methods separately to calculate Localization-specific Centrality Scores (LCSs for proteins based on the PSLINs of four species (Saccharomyces cerevisiae, Homo sapiens, Mus musculus and Drosophila melanogaster. Compared to the proteins with high centrality scores measured from the global PINs, more proteins with high LCSs measured from PSLINs are essential. It indicates that proteins with high LCSs measured from PSLINs are more likely to be essential and the performance of centrality methods can be improved by LSED. Furthermore, LSED provides a wide applicable prediction model to identify essential proteins for different species.

  18. Subcellular localization of anthracyclines in cultured rat cardiomyoblasts as possible predictors of cardiotoxicity.

    Science.gov (United States)

    Studzian, Kazimierz; Kik, Krzysztof; Lukawska, Malgorzata; Oszczapowicz, Irena; Strek, Malgorzata; Szmigiero, Leszek

    2015-10-01

    In this study, we compared the cellular uptake, intracellular localization and cytotoxicity of two groups of anthracycline derivatives in cultured H9c2(2-1) rat cardiomyoblasts. The first group consisted of doxorubicin (DOX) and two of its derivatives containing a formamidino group (-N = CH-N<) at the C-3' position with a morpholine (DOXM) or a hexamethyleneimine (DOXH) ring. The second group consisted of daunorubicin (DRB) and its derivatives containing a morpholine (DRBM) or a hexamethyleneimine (DRBH) ring. DOXH and DRBH were taken up by cardiomyoblasts more efficiently than estimated for other tested anthracyclines. The cellular uptakes of DOXM and DRBM were reduced compared to those of the parent compounds. Applied structural modifications of DOX and DRB influenced the subcellular localization of the tested derivatives. DOX and DOXH were localized primarily in nuclei, whereas the other anthracyclines were found in the nuclei and cytoplasm. The percentages of the compounds that accumulated in the nuclei were 80.2 and 54.2 % for DOX and DOXH, respectively. The lowest nuclear accumulation values were observed for DRBM (19.9 %), DRBH (21.9 %) and DOXM (23.7 %). The ability of anthracyclines to accumulate in the nuclei correlated with their DNA binding constants (r = 0.858, P = 0.029). A correlation was found between the accumulation of the tested anthracyclines in the nuclei of cardiomyoblasts and their cardiotoxicity in vivo, which was observed in our previous study. We suggest that cytotoxicity and the anthracycline accumulation level in the nuclei of cultured cardiomyoblasts could be used for early prediction of their cardiotoxicity.

  19. Using distant supervised learning to identify protein subcellular localizations from full-text scientific articles.

    Science.gov (United States)

    Zheng, Wu; Blake, Catherine

    2015-10-01

    Databases of curated biomedical knowledge, such as the protein-locations reflected in the UniProtKB database, provide an accurate and useful resource to researchers and decision makers. Our goal is to augment the manual efforts currently used to curate knowledge bases with automated approaches that leverage the increased availability of full-text scientific articles. This paper describes experiments that use distant supervised learning to identify protein subcellular localizations, which are important to understand protein function and to identify candidate drug targets. Experiments consider Swiss-Prot, the manually annotated subset of the UniProtKB protein knowledge base, and 43,000 full-text articles from the Journal of Biological Chemistry that contain just under 11.5 million sentences. The system achieves 0.81 precision and 0.49 recall at sentence level and an accuracy of 57% on held-out instances in a test set. Moreover, the approach identifies 8210 instances that are not in the UniProtKB knowledge base. Manual inspection of the 50 most likely relations showed that 41 (82%) were valid. These results have immediate benefit to researchers interested in protein function, and suggest that distant supervision should be explored to complement other manual data curation efforts. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Molecular basis of the specific subcellular localization of the C2-like domain of 5-lipoxygenase.

    Science.gov (United States)

    Kulkarni, Shilpa; Das, Sudipto; Funk, Colin D; Murray, Diana; Cho, Wonhwa

    2002-04-12

    The activation of 5-lipoxygenase (5-LO) involves its calcium-dependent translocation to the nuclear envelope, where it catalyzes the two-step transformation of arachidonic acid into leukotriene A(4), leading to the synthesis of various leukotrienes. To understand the mechanism by which 5-LO is specifically targeted to the nuclear envelope, we studied the membrane binding properties of the amino-terminal domain of 5-LO, which has been proposed to have a C2 domain-like structure. The model building, electrostatic potential calculation, and in vitro membrane binding studies of the isolated C2-like domain of 5-LO and selected mutants show that this Ca(2+)-dependent domain selectively binds zwitterionic phosphatidylcholine, which is conferred by tryptophan residues (Trp(13), Trp(75), and Trp(102)) located in the putative Ca(2+)-binding loops. The spatiotemporal dynamics of the enhanced green fluorescence protein-tagged C2-like domain of 5-LO and mutants in living cells also show that the phosphatidylcholine selectivity of the C2-like domain accounts for the specific targeting of 5-LO to the nuclear envelope. Together, these results show that the C2-like domain of 5-LO is a genuine Ca(2+)-dependent membrane-targeting domain and that the subcellular localization of the domain is governed in large part by its membrane binding properties.

  1. Detection and subcellular localization of dehydrin-like proteins in quinoa (Chenopodium quinoa Willd.) embryos.

    Science.gov (United States)

    Carjuzaa, P; Castellión, M; Distéfano, A J; del Vas, M; Maldonado, S

    2008-01-01

    The aim of this study was to characterize the dehydrin content in mature embryos of two quinoa cultivars, Sajama and Baer La Unión. Cultivar Sajama grows at 3600-4000 m altitude and is adapted to the very arid conditions characteristic of the salty soils of the Bolivian Altiplano, with less than 250 mm of annual rain and a minimum temperature of -1 degrees C. Cultivar Baer La Unión grows at sea-level regions of central Chile and is adapted to more humid conditions (800 to 1500 mm of annual rain), fertile soils, and temperatures above 5 degrees C. Western blot analysis of embryo tissues from plants growing under controlled greenhouse conditions clearly revealed the presence of several dehydrin bands (at molecular masses of approximately 30, 32, 50, and 55 kDa), which were common to both cultivars, although the amount of the 30 and 32 kDa bands differed. Nevertheless, when grains originated from their respective natural environments, three extra bands (at molecular masses of approximately 34, 38, and 40 kDa), which were hardly visible in Sajama, and another weak band (at a molecular mass of approximately 28 kDa) were evident in Baer La Unión. In situ immunolocalization microscopy detected dehydrin-like proteins in all axis and cotyledon tissues. At the subcellular level, dehydrins were detected in the plasma membrane, cytoplasm and nucleus. In the cytoplasm, dehydrins were found associated with mitochondria, rough endoplasmic reticulum cisternae, and proplastid membranes. The presence of dehydrins was also recognized in the matrix of protein bodies. In the nucleus, dehydrins were associated with the euchromatin. Upon examining dehydrin composition and subcellular localization in two quinoa cultivars belonging to highly contrasting environments, we conclude that most dehydrins detected here were constitutive components of the quinoa seed developmental program, but some of them (specially the 34, 38, and 40 kDa bands) may reflect quantitative molecular differences

  2. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.

    Science.gov (United States)

    Yu, Nancy Y; Wagner, James R; Laird, Matthew R; Melli, Gabor; Rey, Sébastien; Lo, Raymond; Dao, Phuong; Sahinalp, S Cenk; Ester, Martin; Foster, Leonard J; Brinkman, Fiona S L

    2010-07-01

    PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003. However, the recall needs to be improved and no accurate SCL predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program. We developed PSORTb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies. It features an improved standalone program, with a new batch results delivery system complementing its web interface. We evaluated the most accurate SCL predictors using 5-fold cross validation plus we performed an independent proteomics analysis, showing that PSORTb 3.0 is the most accurate but can benefit from being complemented by Proteome Analyst predictions. http://www.psort.org/psortb (download open source software or use the web interface). psort-mail@sfu.ca Supplementary data are available at Bioinformatics online.

  3. Tissue distribution, subcellular localization and endocrine disruption patterns induced by Cr and Mn in the crab Ucides cordatus

    International Nuclear Information System (INIS)

    Correa, Jose Dias; Ramos da Silva, Miguel; Bastos da Silva, Antonio Carlos; Araujo de Lima, Silene Maria; Malm, Olaf; Allodi, Silvana

    2005-01-01

    The essential trace elements Cr and Mn are toxic at high concentrations and information about low concentration is insufficient in the literature. In polluted mangroves, the crab Ucides cordatus can represent a useful tool to assess information on the potential impact of trace elements like Cr and Mn on the environment, since this species is comestible and thus, commercially negotiated. Therefore, U. cordatus crabs were exposed in vivo to different concentrations of Cr and Mn solved in seawater and had their tissue distribution and subcellular deposits evaluated. The gill, hepatopancreas and muscle concentrations were determined by atomic absorption spectroscopy and the results showed that Cr and Mn presented the highest values in the gills rather than in the hepatopancreas and muscular tissue. Electron microscopy and analytical X-ray microanalysis revealed Cr precipitates on the gill surface, co-localized with epiphyte bacteria. In addition, since Cr and Mn did not equally accumulate in most of the tissues studied, glycemic rate of animals, which received injections of extracts of eyestalks of the contaminated crabs, were measured in order to evaluate whether the studied concentrations of Cr and Mn could produce any metabolic alteration. The results indicated that extracts of the eyestalks of crabs submitted to Cr and Mn salts and injected into normal crabs markedly influenced crustacean hyperglycemic hormone synthesis and/or release. The results are discussed with respect to sensitivity of the employed methods and the possible significance of the concentrations of Cr and Mn in the organisms

  4. Role of the EHD2 unstructured loop in dimerization, protein binding and subcellular localization.

    Directory of Open Access Journals (Sweden)

    Kriti Bahl

    Full Text Available The C-terminal Eps 15 Homology Domain proteins (EHD1-4 play important roles in regulating endocytic trafficking. EHD2 is the only family member whose crystal structure has been solved, and it contains an unstructured loop consisting of two proline-phenylalanine (PF motifs: KPFRKLNPF. In contrast, despite EHD2 having nearly 70% amino acid identity with its paralogs, EHD1, EHD3 and EHD4, the latter proteins contain a single KPF or RPF motif, but no NPF motif. In this study, we sought to define the precise role of each PF motif in EHD2's homo-dimerization, binding with the protein partners, and subcellular localization. To test the role of the NPF motif, we generated an EHD2 NPF-to-NAF mutant to mimic the homologous sequences of EHD1 and EHD3. We demonstrated that this mutant lost both its ability to dimerize and bind to Syndapin2. However, it continued to localize primarily to the cytosolic face of the plasma membrane. On the other hand, EHD2 NPF-to-APA mutants displayed normal dimerization and Syndapin2 binding, but exhibited markedly increased nuclear localization and reduced association with the plasma membrane. We then hypothesized that the single PF motif of EHD1 (that aligns with the KPF of EHD2 might be responsible for both binding and localization functions of EHD1. Indeed, the EHD1 RPF motif was required for dimerization, interaction with MICAL-L1 and Syndapin2, as well as localization to tubular recycling endosomes. Moreover, recycling assays demonstrated that EHD1 RPF-to-APA was incapable of supporting normal receptor recycling. Overall, our data suggest that the EHD2 NPF phenylalanine residue is crucial for EHD2 localization to the plasma membrane, whereas the proline residue is essential for EHD2 dimerization and binding. These studies support the recently proposed model in which the EHD2 N-terminal region may regulate the availability of the unstructured loop for interactions with neighboring EHD2 dimers, thus promoting

  5. Protein kinase C ϵ stabilizes β-catenin and regulates its subcellular localization in podocytes.

    Science.gov (United States)

    Duong, Michelle; Yu, Xuejiao; Teng, Beina; Schroder, Patricia; Haller, Hermann; Eschenburg, Susanne; Schiffer, Mario

    2017-07-21

    Kidney disease has been linked to dysregulated signaling via PKC in kidney cells such as podocytes. PKCα is a conventional isoform of PKC and a well-known binding partner of β-catenin, which promotes its degradation. β-Catenin is the main effector of the canonical Wnt pathway and is critical in cell adhesion. However, whether other PKC isoforms interact with β-catenin has not been studied systematically. Here we demonstrate that PKCϵ-deficient mice, which develop proteinuria and glomerulosclerosis, display lower β-catenin expression compared with PKC wild-type mice, consistent with an altered phenotype of podocytes in culture. Remarkably, β-catenin showed a reversed subcellular localization pattern: Although β-catenin exhibited a perinuclear pattern in undifferentiated wild-type cells, it predominantly localized to the nucleus in PKCϵ knockout cells. Phorbol 12-myristate 13-acetate stimulation of both cell types revealed that PKCϵ positively regulates β-catenin expression and stabilization in a glycogen synthase kinase 3β-independent manner. Further, β-catenin overexpression in PKCϵ-deficient podocytes could restore the wild-type phenotype, similar to rescue with a PKCϵ construct. This effect was mediated by up-regulation of P-cadherin and the β-catenin downstream target fascin1. Zebrafish studies indicated three PKCϵ-specific phosphorylation sites in β-catenin that are required for full β-catenin function. Co-immunoprecipitation and pulldown assays confirmed PKCϵ and β-catenin as binding partners and revealed that ablation of the three PKCϵ phosphorylation sites weakens their interaction. In summary, we identified a novel pathway for regulation of β-catenin levels and define PKCϵ as an important β-catenin interaction partner and signaling opponent of other PKC isoforms in podocytes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Polycaprolactone/maltodextrin nanocarrier for intracellular drug delivery: formulation, uptake mechanism, internalization kinetics, and subcellular localization.

    Science.gov (United States)

    Korang-Yeboah, Maxwell; Gorantla, Yamini; Paulos, Simon A; Sharma, Pankaj; Chaudhary, Jaideep; Palaniappan, Ravi

    2015-01-01

    Prostate cancer (PCa) disease progression is associated with significant changes in intracellular and extracellular proteins, intracellular signaling mechanism, and cancer cell phenotype. These changes may have direct impact on the cellular interactions with nanocarriers; hence, there is the need for a much-detailed understanding, as nanocarrier cellular internalization and intracellular sorting mechanism correlate directly with bioavailability and clinical efficacy. In this study, we report the differences in the rate and mechanism of cellular internalization of a biocompatible polycaprolactone (PCL)/maltodextrin (MD) nanocarrier system for intracellular drug delivery in LNCaP, PC3, and DU145 PCa cell lines. PCL/MD nanocarriers were designed and characterized. PCL/MD nanocarriers significantly increased the intracellular concentration of coumarin-6 and fluorescein isothiocyanate-labeled bovine serum albumin, a model hydrophobic and large molecule, respectively. Fluorescence microscopy and flow cytometry analysis revealed rapid internalization of the nanocarrier. The extent of nanocarrier cellular internalization correlated directly with cell line aggressiveness. PCL/MD internalization was highest in PC3 followed by DU145 and LNCaP, respectively. Uptake in all PCa cell lines was metabolically dependent. Extraction of endogenous cholesterol by methyl-β-cyclodextrin reduced uptake by 75%±4.53% in PC3, 64%±6.01% in LNCaP, and 50%±4.50% in DU145, indicating the involvement of endogenous cholesterol in cellular internalization. Internalization of the nanocarrier in LNCaP was mediated mainly by macropinocytosis and clathrin-independent pathways, while internalization in PC3 and DU145 involved clathrin-mediated endocytosis, clathrin-independent pathways, and macropinocytosis. Fluorescence microscopy showed a very diffused and non-compartmentalized subcellular localization of the PCL/MD nanocarriers with possible intranuclear localization and minor colocalization in

  7. Expression, purification, characterization and subcellular localization of the goose parvovirus rep1 protein.

    Science.gov (United States)

    Chen, Zongyan; Li, Chuanfeng; Peng, Gaojing; Liu, Guangqing

    2013-07-01

    The goose parvovirus (GPV) Rep1 protein is both essential for viral replication and a potential target for GPV diagnosis, but its protein characterization and intracellular localization is not clear. We constructed a recombinant plasmid, pET28a/GPV-Rep1, and expressed the Rep1 gene in BL21 (DE3) Escherichia coli. A protein approximately 75 kDa in size was obtained from lysates of E. coli cells expressing the recombinant plasmid. SDS-PAGE analysis showed that after induction with 0.6 mM isopropyl β-D-thiogalactosidase (IPTG) at 30°C for 5 h, the Rep1 protein was highly overexpressed. Two methods used to purify proteins, a salinity-gradient elution and Ni-NTA affinity chromatography, were performed. The amount of Rep1 protein obtained by Ni-NTA affinity chromatography was 41.23 mg, while 119.9 mg of Rep1 protein was obtained by a salinity-gradient elution from a 1 L E. coli BL21 (DE3) culture. An immunogenicity analysis showed that the protein could significantly elicit a specific antibody response in immunized goslings compared to control groups. Antibody titers peaked to 1:5120 (optical density (OD) 450 = 3.9) on day 28 after immunization but had mean titers of 1:10,240 (OD450 = 4.2) in gosling groups immunized with a commercially available GPV-attenuated vaccine strain. Experiments examining subcellular localization showed that the Rep1 protein appeared to associate predominantly with the nuclear membrane, especially during later times of infection. This work provides a basis for biochemical and structural studies on the GPV Rep1 protein.

  8. Mutations in the C-terminal region affect subcellular localization of crucian carp herpesvirus (CaHV) GPCR.

    Science.gov (United States)

    Wang, Jun; Gui, Lang; Chen, Zong-Yan; Zhang, Qi-Ya

    2016-08-01

    G protein-coupled receptors (GPCRs) are known as seven transmembrane domain receptors and consequently can mediate diverse biological functions via regulation of their subcellular localization. Crucian carp herpesvirus (CaHV) was recently isolated from infected fish with acute gill hemorrhage. CaHV GPCR of 349 amino acids (aa) was identified based on amino acid identity. A series of variants with truncation/deletion/substitution mutation in the C-terminal (aa 315-349) were constructed and expressed in fathead minnow (FHM) cells. The roles of three key C-terminal regions in subcellular localization of CaHV GPCR were determined. Lysine-315 (K-315) directed the aggregation of the protein preferentially at the nuclear side. Predicted N-myristoylation site (GGGWTR, aa 335-340) was responsible for punctate distribution in periplasm or throughout the cytoplasm. Predicted phosphorylation site (SSR, aa 327-329) and GGGWTR together determined the punctate distribution in cytoplasm. Detection of organelles localization by specific markers showed that the protein retaining K-315 colocalized with the Golgi apparatus. These experiments provided first evidence that different mutations of CaHV GPCR C-terminals have different affects on the subcellular localization of fish herpesvirus-encoded GPCRs. The study provided valuable information and new insights into the precise interactions between herpesvirus and fish cells, and could also provide useful targets for antiviral agents in aquaculture.

  9. Specific primary sequence requirements for Aurora B kinase-mediated phosphorylation and subcellular localization of TMAP during mitosis.

    Science.gov (United States)

    Kim, Hyun-Jun; Kwon, Hye-Rim; Bae, Chang-Dae; Park, Joobae; Hong, Kyung U

    2010-05-15

    During mitosis, regulation of protein structures and functions by phosphorylation plays critical roles in orchestrating a series of complex events essential for the cell division process. Tumor-associated microtubule-associated protein (TMAP), also known as cytoskeleton-associated protein 2 (CKAP2), is a novel player in spindle assembly and chromosome segregation. We have previously reported that TMAP is phosphorylated at multiple residues specifically during mitosis. However, the mechanisms and functional importance of phosphorylation at most of the sites identified are currently unknown. Here, we report that TMAP is a novel substrate of the Aurora B kinase. Ser627 of TMAP was specifically phosphorylated by Aurora B both in vitro and in vivo. Ser627 and neighboring conserved residues were strictly required for efficient phosphorylation of TMAP by Aurora B, as even minor amino acid substitutions of the phosphorylation motif significantly diminished the efficiency of the substrate phosphorylation. Nearly all mutations at the phosphorylation motif had dramatic effects on the subcellular localization of TMAP. Instead of being localized to the chromosome region during late mitosis, the mutants remained associated with microtubules and centrosomes throughout mitosis. However, the changes in the subcellular localization of these mutants could not be completely explained by the phosphorylation status on Ser627. Our findings suggest that the motif surrounding Ser627 ((625) RRSRRL (630)) is a critical part of a functionally important sequence motif which not only governs the kinase-substrate recognition, but also regulates the subcellular localization of TMAP during mitosis.

  10. Subcellular localization of H(+)-ATPase from pumpkin hypocotyls (Cucurbita maxima L.) by membrane fractionation.

    Science.gov (United States)

    Scherer, G F

    1984-03-01

    A new method of preparing sealed vesicles from membrane fractions of pumpkin hypocotyls in ethanolamine-containing buffers was used to investigate the subcellular localization of H(+)-ATPase measured as nigericin-stimulated ATPase. In a fluorescence-quench assay, the H(+) pump was directly demonstrated. The H(+) pump was substrate-specific for Mg·ATP and 0.1 mM diethylstilbestrol completely prevented the development of a Δ pH. The presence of unsupecific phosphatase hampered the detection of nigericin-stimulated ATPase. Unspecific phosphatases could be demonstrated by comparing the broad substrate specificity of the hydrolytic activities of the fractions with the clear preference for Mg·ATP as the substrate for the proton pump. Inhibitor studies showed that neither orthovanadate nor molybdate are absolutely specific for ATPase or acid phosphatase, respectively. Diethylstilbestrol seemed to be a specific inhibitor of ATPase activity in fractions containing nigericin-stimulated ATPase, but it stimulated acid phosphatase which tended to obscure its effect on ATPase activity. Nigericin-stimulated ATPase had its optimum at pH 6.0 and the nigericin effect was K(+)-dependent. The combination of valinomycin and carbonylcyanide m-chlorophenylhydrazone had a similar effect to nigericin, but singly these ionophores were much less stimulatory. After prolonged centrifugation on linear sucrose gradients, nigericin-stimulated ATPase correlated in dense fractions with plasma membrane markers but a part of it remained at the interphase. This lessdense part of the nigericin-stimulated ATPase could be derived from tonoplast vesicles because α-mannosidase, an enzyme of the vacuolar sap, remained in the upper part of the gradient. Nigericinstimulated ATPase did not correlate with the mitochondrial marker, cytochrome c oxidase, whereas azide inhibition of ATPase activity did.

  11. Subcellular localization, mobility, and kinetic activity of glucokinase in glucose-responsive insulin-secreting cells.

    Science.gov (United States)

    Stubbs, M; Aiston, S; Agius, L

    2000-12-01

    We investigated the subcellular localization, mobility, and activity of glucokinase in MIN6 cells, a glucose-responsive insulin-secreting beta-cell line. Glucokinase is present in the cytoplasm and a vesicular/granule compartment that is partially colocalized with insulin granules. The granular staining of glucokinase is preserved after permeabilization of the cells with digitonin. There was no evidence for changes in distribution of glucokinase between the cytoplasm and the granule compartment during incubation of the cells with glucose. The rate of release of glucokinase and of phosphoglucoisomerase from digitonin-permeabilized cells was slower when cells were incubated at an elevated glucose concentration (S0.5 approximately 15 mmol/l). This effect of glucose was counteracted by competitive inhibitors of glucokinase (5-thioglucose and mannoheptulose) but was unaffected by fructose analogs and may be due to changes in cell shape or conformation of the cytoskeleton that are secondary to glucose metabolism. Based on the similar release of glucokinase and phosphoglucoisomerase, we found no evidence for specific binding of cytoplasmic digitonin-extractable glucokinase. The affinity of beta-cells for glucose is slightly lower than that in cell extracts and, unlike that in hepatocytes, is unaffected by fructose, tagatose, or a high-K+ medium, which is consistent with the lack of change in glucokinase distribution or release. We conclude that glucokinase is present in two locations, cytoplasm and the granular compartment, and that it does not translocate between them. This conclusion is consistent with the lack of adaptive changes in the glucose phosphorylation affinity. The glucokinase activity associated with the insulin granules may have a role in either direct or indirect coupling between glucose phosphorylation and insulin secretion.

  12. Subcellular Localization of Cadmium in Chlorella vulgaris Beijerinck Strain Bt-09

    Directory of Open Access Journals (Sweden)

    P.B. Lintongan

    2004-06-01

    Full Text Available Growth response curves of Chlorella vulgaris Beijerinck strain Bt-09 to sublethal concentrations of cadmium were evaluated. The growth responses of this microalgal isolate was determined through analysis of chlorophyll a levels. Cadmium was effectively taken up by the cells as determined by Flame Atomic Absorption Spectrophotometry (F-AAS. Subcellular fractionation was undertaken to locate sites that accumulate cadmium.

  13. Subcellular distribution of [3H]-dexamethasone mesylate binding sites in Leydig cells using electron microscope radioautography

    International Nuclear Information System (INIS)

    Stalker, A.; Hermo, L.; Antakly, T.

    1991-01-01

    The present view is that glucocorticoid hormones bind to their cytoplasmic receptors before reaching their nuclear target sites, which include specific DNA sequences. Although it is believed that cytoplasmic sequestration of steroid receptors and other transcription factors (such as NFKB) may regulate the overall activity of these factors, there is little information on the exact subcellular sites of steroid receptors or even of any other transcription factors. Tritiated (3H)-dexamethasone 21-mesylate (DM) is an affinity label that binds covalently to the glucocorticoid receptor (GR), thereby allowing morphological localization of the receptor at the light and electron microscope levels as well as for quantitative radioautographic (RAG) analysis. After injection of 3H-DM into the testis, a specific radioautographic signal was observed in Leydig cells, which correlated with a high level of immunocytochemically demonstrable GR in these cells at the light-microscope level. To localize the 3H-DM binding sites at the electron microscope (EM) level, the testes of 5 experimental and 3 control adrenalectomized rats were injected directly with 20 microCi 3H-DM; control rats received simultaneously a 25-fold excess of unlabeled dexamethasone; 15 min later, rats were fixed with glutaraldehyde and the tissue was processed for EM RAG analysis combined with quantitative morphometry. The radioautographs showed that the cytosol, nucleus, smooth endoplasmic reticulum (sER), and mitochondria were labeled. Since the cytosol was always adjacent to tubules of the sER, the term sER-rich cytosol was used to represent label over sER networks, which may also represent cytosol labeling due to the limited resolution of the radioautographic technique. Labeling was highest in sER-rich cytosol and mitochondria, at 53% and 31% of the total, respectively

  14. Electron localization in water clusters

    International Nuclear Information System (INIS)

    Landman, U.; Barnett, R.N.; Cleveland, C.L.; Jortner, J.

    1987-01-01

    Electron attachment to water clusters was explored by the quantum path integral molecular dynamics method, demonstrating that the energetically favored localization mode involves a surface state of the excess electron, rather than the precursor of the hydrated electron. The cluster size dependence, the energetics and the charge distribution of these novel electron-cluster surface states are explored. 20 refs., 2 figs., 1 tab

  15. Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.

    Directory of Open Access Journals (Sweden)

    Kuo-Chen Chou

    Full Text Available One of the fundamental goals in proteomics and cell biology is to identify the functions of proteins in various cellular organelles and pathways. Information of subcellular locations of proteins can provide useful insights for revealing their functions and understanding how they interact with each other in cellular network systems. Most of the existing methods in predicting plant protein subcellular localization can only cover three or four location sites, and none of them can be used to deal with multiplex plant proteins that can simultaneously exist at two, or move between, two or more different location sits. Actually, such multiplex proteins might have special biological functions worthy of particular notice. The present study was devoted to improve the existing plant protein subcellular location predictors from the aforementioned two aspects. A new predictor called "Plant-mPLoc" is developed by integrating the gene ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo amino acid composition. It can be used to identify plant proteins among the following 12 location sites: (1 cell membrane, (2 cell wall, (3 chloroplast, (4 cytoplasm, (5 endoplasmic reticulum, (6 extracellular, (7 Golgi apparatus, (8 mitochondrion, (9 nucleus, (10 peroxisome, (11 plastid, and (12 vacuole. Compared with the existing methods for predicting plant protein subcellular localization, the new predictor is much more powerful and flexible. Particularly, it also has the capacity to deal with multiple-location proteins, which is beyond the reach of any existing predictors specialized for identifying plant protein subcellular localization. As a user-friendly web-server, Plant-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to

  16. Dynamic changes to survivin subcellular localization are initiated by DNA damage

    Directory of Open Access Journals (Sweden)

    Maritess Gay Asumen

    2010-07-01

    Full Text Available Maritess Gay Asumen1, Tochukwu V Ifeacho2, Luke Cockerham3, Christina Pfandl4, Nathan R Wall31Touro University’s College of Osteopathic Medicine, Vallejo, CA, USA; 2University of Southern California, Los Angeles, CA, USA; 3Center for Health Disparities Research and Molecular Medicine, Loma Linda University, CA, USA; 4Green Mountain Antibodies, Burlington, VT, USAAbstract: Subcellular distribution of the apoptosis inhibitor survivin and its ability to relocalize as a result of cell cycle phase or therapeutic insult has led to the hypothesis that these subcellular pools may coincide with different survivin functions. The PIK kinases (ATM, ATR and DNA-PK phosphorylate a variety of effector substrates that propagate DNA damage signals, resulting in various biological outputs. Here we demonstrate that subcellular repartitioning of survivin in MCF-7 cells as a result of UV light-mediated DNA damage is dependent upon DNA damage-sensing proteins as treatment with the pan PIK kinase inhibitor wortmannin repartitioned survivin in the mitochondria and diminished it from the cytosol and nucleus. Mitochondrial redistribution of survivin, such as was recorded after wortmannin treatment, occurred in cells lacking any one of the three DNA damage sensing protein kinases: DNA-PK, ATM or ATR. However, failed survivin redistribution from the mitochondria in response to low-dose UV occurred only in the cells lacking ATM, implying that ATM may be the primary kinase involved in this process. Taken together, this data implicates survivian’s subcellular distribution is a dynamic physiological process that appears responsive to UV light- initiated DNA damage and that its distribution may be responsible for its multifunctionality.Keywords: survivin, PIK kinases, ATM, ATR, DNA-PK

  17. The in vitro sub-cellular localization and in vivo efficacy of novel chitosan/GMO nanostructures containing paclitaxel.

    Science.gov (United States)

    Trickler, W J; Nagvekar, A A; Dash, A K

    2009-08-01

    To determine the in vitro sub-cellular localization and in vivo efficacy of chitosan/GMO nanostructures containing paclitaxel (PTX) compared to a conventional PTX treatment (Taxol). The sub-cellular localization of coumarin-6 labeled chitosan/GMO nanostructures was determined by confocal microscopy in MDA-MB-231 cells. The antitumor efficacy was evaluated in two separate studies using FOX-Chase (CB17) SCID Female-Mice MDA-MB-231 xenograph model. Treatments consisted of intravenous Taxol or chitosan/GMO nanostructures with or without PTX, local intra-tumor bolus of Taxol or chitosan/GMO nanostructures with or without PTX. The tumor diameter and animal weight was monitored at various intervals. Histopathological changes were evaluated in end-point tumors. The tumor diameter increased at a constant rate for all the groups between days 7-14. After a single intratumoral bolus dose of chitosan/GMO containing PTX showed significant reduction in tumor diameter on day 15 when compared to control, placebo and intravenous PTX administration. The tumor diameter reached a maximal decrease (4-fold) by day 18, and the difference was reduced to approximately 2-fold by day 21. Qualitatively similar results were observed in a separate study containing PTX when administered intravenously. Chitosan/GMO nanostructures containing PTX are safe and effective administered locally or intravenously. Partially supported by DOD Award BC045664.

  18. HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins.

    Science.gov (United States)

    Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

    2014-01-01

    Protein subcellular localization prediction, as an essential step to elucidate the functions in vivo of proteins and identify drugs targets, has been extensively studied in previous decades. Instead of only determining subcellular localization of single-label proteins, recent studies have focused on predicting both single- and multi-location proteins. Computational methods based on Gene Ontology (GO) have been demonstrated to be superior to methods based on other features. However, existing GO-based methods focus on the occurrences of GO terms and disregard their relationships. This paper proposes a multi-label subcellular-localization predictor, namely HybridGO-Loc, that leverages not only the GO term occurrences but also the inter-term relationships. This is achieved by hybridizing the GO frequencies of occurrences and the semantic similarity between GO terms. Given a protein, a set of GO terms are retrieved by searching against the gene ontology database, using the accession numbers of homologous proteins obtained via BLAST search as the keys. The frequency of GO occurrences and semantic similarity (SS) between GO terms are used to formulate frequency vectors and semantic similarity vectors, respectively, which are subsequently hybridized to construct fusion vectors. An adaptive-decision based multi-label support vector machine (SVM) classifier is proposed to classify the fusion vectors. Experimental results based on recent benchmark datasets and a new dataset containing novel proteins show that the proposed hybrid-feature predictor significantly outperforms predictors based on individual GO features as well as other state-of-the-art predictors. For readers' convenience, the HybridGO-Loc server, which is for predicting virus or plant proteins, is available online at http://bioinfo.eie.polyu.edu.hk/HybridGoServer/.

  19. The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

    Science.gov (United States)

    Salvatore, M; Shu, N; Elofsson, A

    2018-01-01

    SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts. This makes SubCons ideal for proteome wide analyses allowing the user to scan a whole proteome in few days. From the web page, it is also possible to download precalculated predictions for several eukaryotic organisms. To evaluate the performance of SubCons we present a benchmark of LocTree3 and SubCons using two recent mass-spectrometry based datasets of mouse and drosophila proteins. The server is available at http://subcons.bioinfo.se/. © 2017 The Protein Society.

  20. Prequels to Synthetic Biology: From Candidate Gene Identification and Validation to Enzyme Subcellular Localization in Plant and Yeast Cells.

    Science.gov (United States)

    Foureau, E; Carqueijeiro, I; Dugé de Bernonville, T; Melin, C; Lafontaine, F; Besseau, S; Lanoue, A; Papon, N; Oudin, A; Glévarec, G; Clastre, M; St-Pierre, B; Giglioli-Guivarc'h, N; Courdavault, V

    2016-01-01

    Natural compounds extracted from microorganisms or plants constitute an inexhaustible source of valuable molecules whose supply can be potentially challenged by limitations in biological sourcing. The recent progress in synthetic biology combined to the increasing access to extensive transcriptomics and genomics data now provide new alternatives to produce these molecules by transferring their whole biosynthetic pathway in heterologous production platforms such as yeasts or bacteria. While the generation of high titer producing strains remains per se an arduous field of investigation, elucidation of the biosynthetic pathways as well as characterization of their complex subcellular organization are essential prequels to the efficient development of such bioengineering approaches. Using examples from plants and yeasts as a framework, we describe potent methods to rationalize the study of partially characterized pathways, including the basics of computational applications to identify candidate genes in transcriptomics data and the validation of their function by an improved procedure of virus-induced gene silencing mediated by direct DNA transfer to get around possible resistance to Agrobacterium-delivery of viral vectors. To identify potential alterations of biosynthetic fluxes resulting from enzyme mislocalizations in reconstituted pathways, we also detail protocols aiming at characterizing subcellular localizations of protein in plant cells by expression of fluorescent protein fusions through biolistic-mediated transient transformation, and localization of transferred enzymes in yeast using similar fluorescence procedures. Albeit initially developed for the Madagascar periwinkle, these methods may be applied to other plant species or organisms in order to establish synthetic biology platform. © 2016 Elsevier Inc. All rights reserved.

  1. Systemic distribution, subcellular localization and differential expression of sphingosine-1-phosphate receptors in benign and malignant human tissues.

    Science.gov (United States)

    Wang, Chunyi; Mao, Jinghe; Redfield, Samantha; Mo, Yinyuan; Lage, Janice M; Zhou, Xinchun

    2014-10-01

    Five sphingosine-1-phosphate receptors (S1PR): S1PR1, S1PR2, S1PR3, S1PR4 and S1PR5 (S1PR1-5) have been shown to be involved in the proliferation and progression of various cancers. However, none of the S1PRs have been systemically investigated. In this study, we performed immunohistochemistry (IHC) for S1PR1-S1PR5 on different tissues, in order to simultaneously determine the systemic distribution, subcellular localization and expression level of all five S1PRs. We constructed tissue microarrays (TMAs) from 384 formalin-fixed paraffin-embedded (FFPE) blocks containing 183 benign and 201 malignant tissues from 34 human organs/systems. Then we performed IHC for all five S1PRs simultaneously on these TMA slides. The distribution, subcellular localization and expression of each S1PR were determined for each tissue. The data in benign and malignant tissues from the same organ/tissue were then compared using the Student's t-test. In order to reconfirm the subcellular localization of each S1PR as determined by IHC, immunocytochemistry (ICC) was performed on several malignant cell lines. We found that all five S1PRs are widely distributed in multiple human organs/systems. All S1PRs are expressed in both the cytoplasm and nucleus, except S1PR3, whose IHC signals are only seen in the nucleus. Interestingly, the S1PRs are rarely expressed on cellular membranes. Each S1PR is unique in its organ distribution, subcellular localization and expression level in benign and malignant tissues. Among the five S1PRs, S1PR5 has the highest expression level (in either the nucleus or cytoplasm), with S1PR1, 3, 2 and 4 following in descending order. Strong nuclear expression was seen for S1PR1, S1PR3 and S1PR5, whereas S1PR2 and S1PR4 show only weak staining. Four organs/tissues (adrenal gland, liver, brain and colon) show significant differences in IHC scores for the multiple S1PRs (nuclear and/or cytoplasmic), nine (stomach, lymphoid tissues, lung, ovary, cervix, pancreas, skin, soft

  2. CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization.

    Science.gov (United States)

    Frias, Silvia; Bryan, Kenneth; Brinkman, Fiona S L; Lynn, David J

    2015-01-01

    CerebralWeb is a light-weight JavaScript plug-in that extends Cytoscape.js to enable fast and interactive visualization of molecular interaction networks stratified based on subcellular localization or other user-supplied annotation. The application is designed to be easily integrated into any website and is configurable to support customized network visualization. CerebralWeb also supports the automatic retrieval of Cerebral-compatible localizations for human, mouse and bovine genes via a web service and enables the automated parsing of Cytoscape compatible XGMML network files. CerebralWeb currently supports embedded network visualization on the InnateDB (www.innatedb.com) and Allergy and Asthma Portal (allergen.innatedb.com) database and analysis resources. Database tool URL: http://www.innatedb.com/CerebralWeb © The Author(s) 2015. Published by Oxford University Press.

  3. A comparative antibody analysis of Pannexin1 expression in four rat brain regions reveals varying subcellular localizations

    Directory of Open Access Journals (Sweden)

    Angela C Cone

    2013-02-01

    Full Text Available Pannexin1 (Panx1 channels release cytosolic ATP in response to signaling pathways. Panx1 is highly expressed in the central nervous system. We used four antibodies with different Panx1 anti-peptide epitopes to analyze four regions of rat brain. These antibodies labeled the same bands in Western blots and had highly similar patterns of immunofluorescence in tissue culture cells expressing Panx1, but Western blots of brain lysates from Panx1 knockout and control mice showed different banding patterns. Localizations of Panx1 in brain slices were generated using automated wide-field mosaic confocal microscopy for imaging large regions of interest while retaining maximum resolution for examining cell populations and compartments. We compared Panx1 expression over the cerebellum, hippocampus with adjacent cortex, thalamus and olfactory bulb. While Panx1 localizes to the same neuronal cell types, subcellular localizations differ. Two antibodies with epitopes against the intracellular loop and one against the carboxy terminus preferentially labeled cell bodies, while an antibody raised against an N-terminal peptide highlighted neuronal processes more than cell bodies. These labeling patterns may be a reflection of different cellular and subcellular localizations of full-length and/or modified Panx1 channels where each antibody is highlighting unique or differentially accessible Panx1 populations. However, we cannot rule out that one or more of these antibodies have specificity issues. All data associated with experiments from these four antibodies are presented in a manner that allows them to be compared and our claims thoroughly evaluated, rather than eliminating results that were questionable. Each antibody is given a unique identifier through the NIF Antibody Registry that can be used to track usage of individual antibodies across papers and all image and metadata are made available in the public repository, the Cell Centered Database, for on

  4. Subcellular localization of alkaline phosphatase in Bacillus licheniformis 749/C by immunoelectron microscopy with colloidal gold

    International Nuclear Information System (INIS)

    Tinglu, G.; Ghosh, A.; Ghosh, B.K.

    1984-01-01

    Subcellular distribution of the alkaline phosphatase of Bacillus licheniformis 749/C was determined by an immunoelectron microscopy method. Anti-alkaline phosphatase antibody labeled with 15- to 18-nm colloidal gold particles (gold-immunoglobulin G [IgG] complex) were used for the study. Both the plasma membrane and cytoplasmic material were labeled with the gold-IgG particles. These particles formed clusters in association with the plasma membrane; in contrast, in the cytoplasm the particles were largely dispersed, and only a few clusters were found. The gold-IgG binding was quantitatively estimated by stereological analysis of labeled, frozen thin sections. This estimation of a variety of control samples showed that the labeling was specific for the alkaline phosphatase. Cluster formation of the gold -IgG particles in association with the plasma membrane suggests that existence of specific alkaline phosphatase binding sites (receptors) in the plasma membrane of B. licheniformis 749/C. 27 references, 6 figures, 1 table

  5. Subcellular localization of glycolytic enzymes and characterization of intermediary metabolism of Trypanosoma rangeli.

    Science.gov (United States)

    Rondón-Mercado, Rocío; Acosta, Héctor; Cáceres, Ana J; Quiñones, Wilfredo; Concepción, Juan Luis

    2017-09-01

    Trypanosoma rangeli is a hemoflagellate protist that infects wild and domestic mammals as well as humans in Central and South America. Although this parasite is not pathogenic for human, it is being studied because it shares with Trypanosoma cruzi, the etiological agent of Chagas' disease, biological characteristics, geographic distribution, vectors and vertebrate hosts. Several metabolic studies have been performed with T. cruzi epimastigotes, however little is known about the metabolism of T. rangeli. In this work we present the subcellular distribution of the T. rangeli enzymes responsible for the conversion of glucose to pyruvate, as determined by epifluorescense immunomicroscopy and subcellular fractionation involving either selective membrane permeabilization with digitonin or differential and isopycnic centrifugation. We found that in T. rangeli epimastigotes the first six enzymes of the glycolytic pathway, involved in the conversion of glucose to 1,3-bisphosphoglycerate are located within glycosomes, while the last four steps occur in the cytosol. In contrast with T. cruzi, where three isoenzymes (one cytosolic and two glycosomal) of phosphoglycerate kinase are expressed simultaneously, only one enzyme with this activity is detected in T. rangeli epimastigotes, in the cytosol. Consistent with this latter result, we found enzymes involved in auxiliary pathways to glycolysis needed to maintain adenine nucleotide and redox balances within glycosomes such as phosphoenolpyruvate carboxykinase, malate dehydrogenase, fumarate reductase, pyruvate phosphate dikinase and glycerol-3-phosphate dehydrogenase. Glucokinase, galactokinase and the first enzyme of the pentose-phosphate pathway, glucose-6-phosphate dehydrogenase, were also located inside glycosomes. Furthermore, we demonstrate that T. rangeli epimastigotes growing in LIT medium only consume glucose and do not excrete ammonium; moreover, they are unable to survive in partially-depleted glucose medium. The

  6. Sub-cellular mRNA localization modulates the regulation of gene expression by small RNAs in bacteria

    Science.gov (United States)

    Teimouri, Hamid; Korkmazhan, Elgin; Stavans, Joel; Levine, Erel

    2017-10-01

    Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that demonstrate that families of mRNAs show non-trivial sub-cellular distributions raise the question of how localization may affect the regulatory activity of sRNAs. Here we address this question within a simple mathematical model. We show that the non-uniform spatial distributions of mRNA can alter the threshold-linear response that characterizes sRNAs that act stoichiometrically, and modulate the hierarchy among targets co-regulated by the same sRNA. We also identify conditions where the sub-cellular organization of cofactors in the sRNA pathway can induce spatial heterogeneity on sRNA targets. Our results suggest that under certain conditions, interpretation and modeling of natural and synthetic gene regulatory circuits need to take into account the spatial organization of the transcripts of participating genes.

  7. Comparison of expressed human and mouse sodium/iodide sym-porters reveals differences in transport properties and subcellular localization

    Energy Technology Data Exchange (ETDEWEB)

    Dayem, M.; Basquin, C.; Navarro, V.; Carrier, P.; Marsault, R.; Lindenthal, S.; Pourcher, T. [Univ Nice Sophia Antipolis, Sch Med, CEA, DSV, iBEB, SBTN, TIRO, F-06107 Nice (France); Chang, P. [CNRS, UPMC Biol Dev, UMR 7009, F-06230 Villefranche Sur Mer (France); Huc, S.; Darrouzet, E. [CEA Valrho, DSV, iBEB, SBTN, F-30207 Bagnols Sur Ceze (France)

    2008-07-01

    The active transport of iodide from the blood stream into thyroid follicular cells is mediated by the Na{sup +}/I{sup -} sym-porter (NIS). We studied mouse NIS (mNIS) and found that it catalyzes iodide transport into transfected cells more efficiently than human NIS (hNIS). To further characterize this difference,we compared {sup 125}I, uptake in the transiently transfected human embryonic kidney (HEK) 293 cells. We found that the Vmax for mNIS was four times higher than that for hNIS, and that the iodide transport constant (Km) was 2-5-fold lower for hNIS than mNIS. We also performed immuno-cyto-localization studies and observed that the subcellular distribution of the two ortho-logs differed. While the mouse protein was predominantly found at the plasma membrane, its human ortho-log was intracellular in {approx} 40% of the expressing cells. Using cell surface protein-labeling assays, we found that the plasma membrane localization frequency of the mouse protein was only 2-5-fold higher than that of the human protein, and therefore cannot alone account for,x values. We reasoned that the difference in the obtained Vmax the observed difference could also be caused by a higher turnover number for iodide transport in the mouse protein. We then expressed and analyzed chimeric proteins. The data obtained with these constructs suggest that the iodide recognition site could be located in the region extending from the N-terminus to transmembrane domain 8, and that the region between transmembrane domain 5 and the C-terminus could play a role in the subcellular localization of the protein. (authors)

  8. Comparison of expressed human and mouse sodium/iodide sym-porters reveals differences in transport properties and subcellular localization

    International Nuclear Information System (INIS)

    Dayem, M.; Basquin, C.; Navarro, V.; Carrier, P.; Marsault, R.; Lindenthal, S.; Pourcher, T.; Chang, P.; Huc, S.; Darrouzet, E.

    2008-01-01

    The active transport of iodide from the blood stream into thyroid follicular cells is mediated by the Na + /I - sym-porter (NIS). We studied mouse NIS (mNIS) and found that it catalyzes iodide transport into transfected cells more efficiently than human NIS (hNIS). To further characterize this difference,we compared 125 I, uptake in the transiently transfected human embryonic kidney (HEK) 293 cells. We found that the Vmax for mNIS was four times higher than that for hNIS, and that the iodide transport constant (Km) was 2-5-fold lower for hNIS than mNIS. We also performed immuno-cyto-localization studies and observed that the subcellular distribution of the two ortho-logs differed. While the mouse protein was predominantly found at the plasma membrane, its human ortho-log was intracellular in ∼ 40% of the expressing cells. Using cell surface protein-labeling assays, we found that the plasma membrane localization frequency of the mouse protein was only 2-5-fold higher than that of the human protein, and therefore cannot alone account for,x values. We reasoned that the difference in the obtained Vmax the observed difference could also be caused by a higher turnover number for iodide transport in the mouse protein. We then expressed and analyzed chimeric proteins. The data obtained with these constructs suggest that the iodide recognition site could be located in the region extending from the N-terminus to transmembrane domain 8, and that the region between transmembrane domain 5 and the C-terminus could play a role in the subcellular localization of the protein. (authors)

  9. Analysis of the influence of subcellular localization of the HIV Rev protein on Rev-dependent gene expression by multi-fluorescence live-cell imaging

    International Nuclear Information System (INIS)

    Wolff, Horst; Hadian, Kamyar; Ziegler, Manja; Weierich, Claudia; Kramer-Hammerle, Susanne; Kleinschmidt, Andrea; Erfle, Volker; Brack-Werner, Ruth

    2006-01-01

    The human immunodeficiency virus Rev protein is a post-transcriptional activator of HIV gene expression. Rev is a nucleocytoplasmic shuttle protein that displays characteristic nuclear/nucleolar subcellular localization in various cell lines. Cytoplasmic localization of Rev occurs under various conditions disrupting Rev function. The goal of this study was to investigate the relationship between localization of Rev and its functional activity in living cells. A triple-fluorescent imaging assay, called AQ-FIND, was established for automatic quantitative evaluation of nucleocytoplasmic distribution of fluorescently tagged proteins. This assay was used to screen 500 rev genes generated by error-prone PCR for Rev mutants with different localization phenotypes. Activities of the Rev mutants were determined with a second quantitative, dual-fluorescent reporter assay. In HeLa cells, the majority of nuclear Rev mutants had activities similar to wild-type Rev. The activities of Rev mutants with abnormal cytoplasmic localization ranged from moderately impaired to nonfunctional. There was no linear correlation between subcellular distribution and levels of Rev activity. In astrocytes, nuclear Rev mutants showed similar impaired activities as the cytoplasmic wild-type Rev. Our data suggest that steady-state subcellular localization is not a primary regulator of Rev activity but may change as a secondary consequence of altered Rev function. The methodologies described here have potential for studying the significance of subcellular localization for functions of other regulatory factors

  10. Subcellular localization and logistics of integral membrane protein biogenesis in Escherichia coli.

    Science.gov (United States)

    Bogdanov, Mikhail; Aboulwafa, Mohammad; Saier, Milton H

    2013-01-01

    Transporters catalyze entry and exit of molecules into and out of cells and organelles, and protein-lipid interactions influence their activities. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) catalyzes transport-coupled sugar phosphorylation as well as nonvectorial sugar phosphorylation in the cytoplasm. The vectorial process is much more sensitive to the lipid environment than the nonvectorial process. Moreover, cytoplasmic micellar forms of these enzyme-porters have been identified, and non-PTS permeases have similarly been shown to exist in 'soluble' forms. The latter porters exhibit lipid-dependent activities and can adopt altered topologies by simply changing the lipid composition. Finally, intracellular membranes and vesicles exist in Escherichia coli leading to the following unanswered questions: (1) what determines whether a PTS permease catalyzes vectorial or nonvectorial sugar phosphorylation? (2) How do phospholipids influence relative amounts of the plasma membrane, intracellular membrane, inner membrane-derived vesicles and cytoplasmic micelles? (3) What regulates the route(s) of permease insertion and transfer into and between the different subcellular sites? (4) Do these various membranous forms have distinct physiological functions? (5) What methods should be utilized to study the biogenesis and interconversion of these membranous structures? While research concerning these questions is still in its infancy, answers will greatly enhance our understanding of protein-lipid interactions and how they control the activities, conformations, cellular locations and biogenesis of integral membrane proteins. Copyright © 2013 S. Karger AG, Basel.

  11. Expression and subcellular localization of the Qa-SNARE syntaxin17 in human eosinophils.

    Science.gov (United States)

    Carmo, Lívia A S; Dias, Felipe F; Malta, Kássia K; Amaral, Kátia B; Shamri, Revital; Weller, Peter F; Melo, Rossana C N

    2015-10-01

    SNARE members mediate membrane fusion during intracellular trafficking underlying innate and adaptive immune responses by different cells. However, little is known about the expression and function of these proteins in human eosinophils, cells involved in allergic, inflammatory and immunoregulatory responses. Here, we investigate the expression and distribution of the Qa-SNARE syntaxin17 (STX17) within human eosinophils isolated from the peripheral blood. Flow cytometry and a pre-embedding immunonanogold electron microscopy (EM) technique that combines optimal epitope preservation and secondary Fab-fragments of antibodies linked to 1.4 nm gold particles for optimal access to microdomains, were used to investigate STX17. STX17 was detected within unstimulated eosinophils. Immunogold EM revealed STX17 on secretory granules and on granule-derived vesiculotubular transport carriers (Eosinophil Sombrero Vesicles-EoSVs). Quantitative EM analyses showed that 77.7% of the granules were positive for STX17 with a mean±SEM of 3.9±0.2 gold particles/granule. Labeling was present on both granule outer membranes and matrices while EoSVs showed clear membrane-associated labeling. STX17 was also present in secretory granules in eosinophils stimulated with the cytokine tumor necrosis factor alpha (TNF-α) or the CC-chemokine ligand 11 CCL11 (eotaxin-1), stimuli that induce eosinophil degranulation. The number of secretory granules labeled for STX17 was significantly higher in CCL11 compared with the unstimulated group. The level of cell labeling did not change when unstimulated cells were compared with TNF-α-stimulated eosinophils. The present study clearly shows by immunanonogold EM that STX17 is localized in eosinophil secretory granules and transport vesicles and might be involved in the transport of granule-derived cargos. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Subcellular localization of class II HDAs in Arabidopsis thaliana: nucleocytoplasmic shuttling of HDA15 is driven by light.

    Directory of Open Access Journals (Sweden)

    Malona V Alinsug

    Full Text Available Class II histone deacetylases in humans and other model organisms undergo nucleocytoplasmic shuttling. This unique functional regulatory mechanism has been well elucidated in eukaryotic organisms except in plant systems. In this study, we have paved the baseline evidence for the cytoplasmic and nuclear localization of Class II HDAs as well as their mRNA expression patterns. RT-PCR analysis on the different vegetative parts and developmental stages reveal that Class II HDAs are ubiquitously expressed in all tissues with minimal developmental specificity. Moreover, stable and transient expression assays using HDA-YFP/GFP fusion constructs indicate cytoplasmic localization of HDA5, HDA8, and HDA14 further suggesting their potential for nuclear transport and deacetylating organellar and cytoplasmic proteins. Organelle markers and stains confirm HDA14 to abound in the mitochondria and chloroplasts while HDA5 localizes in the ER. HDA15, on the other hand, shuttles in and out of the nucleus upon light exposure. In the absence of light, it is exported out of the nucleus where further re-exposition to light treatments signals its nuclear import. Unlike HDA5 which binds with 14-3-3 proteins, HDA15 fails to interact with these chaperones. Instead, HDA15 relies on its own nuclear localization and export signals to navigate its subcellular compartmentalization classifying it as a Class IIb HDA. Our study indicates that nucleocytoplasmic shuttling is indeed a hallmark for all eukaryotic Class II histone deacetylases.

  13. Subcellular localization of acyl-CoA binding protein in Aspergillus oryzae is regulated by autophagy machinery.

    Science.gov (United States)

    Kawaguchi, Kouhei; Kikuma, Takashi; Higuchi, Yujiro; Takegawa, Kaoru; Kitamoto, Katsuhiko

    2016-11-04

    In eukaryotic cells, acyl-CoA binding protein (ACBP) is important for cellular activities, such as in lipid metabolism. In the industrially important fungus Aspergillus oryzae, the ACBP, known as AoACBP, has been biochemically characterized, but its physiological function is not known. In the present study, although we could not find any phenotype of AoACBP disruptants in the normal growth conditions, we examined the subcellular localization of AoACBP to understand its physiological function. Using an enhanced green fluorescent protein (EGFP)-tagged AoACBP construct we showed that AoACBP localized to punctate structures in the cytoplasm, some of which moved inside the cells in a microtubule-dependent manner. Further microscopic analyses showed that AoACBP-EGFP co-localized with the autophagy marker protein AoAtg8 tagged with red fluorescent protein (mDsRed). Expression of AoACBP-EGFP in disruptants of autophagy-related genes revealed aggregation of AoACBP-EGFP fluorescence in the cytoplasm of Aoatg1, Aoatg4 and Aoatg8 disruptant cells. However, in cells harboring disruption of Aoatg15, which encodes a lipase for autophagic body, puncta of AoACBP-EGFP fluorescence accumulated in vacuoles, indicating that AoACBP is transported to vacuoles via the autophagy machinery. Collectively, these results suggest the existence of a regulatory mechanism between AoACBP localization and autophagy. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites.

    Science.gov (United States)

    Cheng, Xiang; Zhao, Shu-Guang; Lin, Wei-Zhong; Xiao, Xuan; Chou, Kuo-Chen

    2017-11-15

    Cells are deemed the basic unit of life. However, many important functions of cells as well as their growth and reproduction are performed via the protein molecules located at their different organelles or locations. Facing explosive growth of protein sequences, we are challenged to develop fast and effective method to annotate their subcellular localization. However, this is by no means an easy task. Particularly, mounting evidences have indicated proteins have multi-label feature meaning that they may simultaneously exist at, or move between, two or more different subcellular location sites. Unfortunately, most of the existing computational methods can only be used to deal with the single-label proteins. Although the 'iLoc-Animal' predictor developed recently is quite powerful that can be used to deal with the animal proteins with multiple locations as well, its prediction quality needs to be improved, particularly in enhancing the absolute true rate and reducing the absolute false rate. Here we propose a new predictor called 'pLoc-mAnimal', which is superior to iLoc-Animal as shown by the compelling facts. When tested by the most rigorous cross-validation on the same high-quality benchmark dataset, the absolute true success rate achieved by the new predictor is 37% higher and the absolute false rate is four times lower in comparison with the state-of-the-art predictor. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mAnimal/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. xxiao@gordonlifescience.org or kcchou@gordonlifescience.org. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  15. iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins.

    Science.gov (United States)

    Lin, Wei-Zhong; Fang, Jian-An; Xiao, Xuan; Chou, Kuo-Chen

    2013-04-05

    Predicting protein subcellular localization is a challenging problem, particularly when query proteins have multi-label features meaning that they may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing methods can only be used to deal with the single-label proteins. Actually, multi-label proteins should not be ignored because they usually bear some special function worthy of in-depth studies. By introducing the "multi-label learning" approach, a new predictor, called iLoc-Animal, has been developed that can be used to deal with the systems containing both single- and multi-label animal (metazoan except human) proteins. Meanwhile, to measure the prediction quality of a multi-label system in a rigorous way, five indices were introduced; they are "Absolute-True", "Absolute-False" (or Hamming-Loss"), "Accuracy", "Precision", and "Recall". As a demonstration, the jackknife cross-validation was performed with iLoc-Animal on a benchmark dataset of animal proteins classified into the following 20 location sites: (1) acrosome, (2) cell membrane, (3) centriole, (4) centrosome, (5) cell cortex, (6) cytoplasm, (7) cytoskeleton, (8) endoplasmic reticulum, (9) endosome, (10) extracellular, (11) Golgi apparatus, (12) lysosome, (13) mitochondrion, (14) melanosome, (15) microsome, (16) nucleus, (17) peroxisome, (18) plasma membrane, (19) spindle, and (20) synapse, where many proteins belong to two or more locations. For such a complicated system, the outcomes achieved by iLoc-Animal for all the aforementioned five indices were quite encouraging, indicating that the predictor may become a useful tool in this area. It has not escaped our notice that the multi-label approach and the rigorous measurement metrics can also be used to investigate many other multi-label problems in molecular biology. As a user-friendly web-server, iLoc-Animal is freely accessible to the public at the web-site .

  16. Substrate specificity and subcellular localization of the aldehyde-alcohol redox-coupling reaction in carp cones.

    Science.gov (United States)

    Sato, Shinya; Fukagawa, Takashi; Tachibanaki, Shuji; Yamano, Yumiko; Wada, Akimori; Kawamura, Satoru

    2013-12-20

    Our previous study suggested the presence of a novel cone-specific redox reaction that generates 11-cis-retinal from 11-cis-retinol in the carp retina. This reaction is unique in that 1) both 11-cis-retinol and all-trans-retinal were required to produce 11-cis-retinal; 2) together with 11-cis-retinal, all-trans-retinol was produced at a 1:1 ratio; and 3) the addition of enzyme cofactors such as NADP(H) was not necessary. This reaction is probably part of the reactions in a cone-specific retinoid cycle required for cone visual pigment regeneration with the use of 11-cis-retinol supplied from Müller cells. In this study, using purified carp cone membrane preparations, we first confirmed that the reaction is a redox-coupling reaction between retinals and retinols. We further examined the substrate specificity, reaction mechanism, and subcellular localization of this reaction. Oxidation was specific for 11-cis-retinol and 9-cis-retinol. In contrast, reduction showed low specificity: many aldehydes, including all-trans-, 9-cis-, 11-cis-, and 13-cis-retinals and even benzaldehyde, supported the reaction. On the basis of kinetic studies of this reaction (aldehyde-alcohol redox-coupling reaction), we found that formation of a ternary complex of a retinol, an aldehyde, and a postulated enzyme seemed to be necessary, which suggested the presence of both the retinol- and aldehyde-binding sites in this enzyme. A subcellular fractionation study showed that the activity is present almost exclusively in the cone inner segment. These results suggest the presence of an effective production mechanism of 11-cis-retinal in the cone inner segment to regenerate visual pigment.

  17. Distinct domains within the NITROGEN LIMITATION ADAPTATION protein mediate its subcellular localization and function in the nitrate-dependent phosphate homeostasis pathway

    Science.gov (United States)

    The NITROGEN LIMITATION ADAPTATION (NLA) protein is a RING-type E3 ubiquitin ligase that plays an essential role in the regulation of nitrogen and phosphate homeostasis. NLA is localized to two distinct subcellular sites, the plasma membrane and nucleus, and contains four distinct domains: i) a RING...

  18. Expression and subcellular localization of the Qa-SNARE syntaxin17 in human eosinophils

    Energy Technology Data Exchange (ETDEWEB)

    Carmo, Lívia A.S.; Dias, Felipe F.; Malta, Kássia K.; Amaral, Kátia B. [Laboratory of Cellular Biology, Department of Biology, Federal University of Juiz de Fora, UFJF, Juiz de Fora, MG (Brazil); Shamri, Revital; Weller, Peter F. [Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA (United States); Melo, Rossana C.N., E-mail: rossana.melo@ufjf.edu.br [Laboratory of Cellular Biology, Department of Biology, Federal University of Juiz de Fora, UFJF, Juiz de Fora, MG (Brazil); Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA (United States)

    2015-10-01

    Background: SNARE members mediate membrane fusion during intracellular trafficking underlying innate and adaptive immune responses by different cells. However, little is known about the expression and function of these proteins in human eosinophils, cells involved in allergic, inflammatory and immunoregulatory responses. Here, we investigate the expression and distribution of the Qa-SNARE syntaxin17 (STX17) within human eosinophils isolated from the peripheral blood. Methods: Flow cytometry and a pre-embedding immunonanogold electron microscopy (EM) technique that combines optimal epitope preservation and secondary Fab-fragments of antibodies linked to 1.4 nm gold particles for optimal access to microdomains, were used to investigate STX17. Results: STX17 was detected within unstimulated eosinophils. Immunogold EM revealed STX17 on secretory granules and on granule-derived vesiculotubular transport carriers (Eosinophil Sombrero Vesicles-EoSVs). Quantitative EM analyses showed that 77.7% of the granules were positive for STX17 with a mean±SEM of 3.9±0.2 gold particles/granule. Labeling was present on both granule outer membranes and matrices while EoSVs showed clear membrane-associated labeling. STX17 was also present in secretory granules in eosinophils stimulated with the cytokine tumor necrosis factor alpha (TNF-α) or the CC-chemokine ligand 11 CCL11 (eotaxin-1), stimuli that induce eosinophil degranulation. The number of secretory granules labeled for STX17 was significantly higher in CCL11 compared with the unstimulated group. The level of cell labeling did not change when unstimulated cells were compared with TNF-α-stimulated eosinophils. Conclusions: The present study clearly shows by immunanonogold EM that STX17 is localized in eosinophil secretory granules and transport vesicles and might be involved in the transport of granule-derived cargos. - Highlights: • First demonstration of the Qa-SNARE syntaxin-17 (STX17) in human eosinophils. • High

  19. Expression and subcellular localization of the Qa-SNARE syntaxin17 in human eosinophils

    International Nuclear Information System (INIS)

    Carmo, Lívia A.S.; Dias, Felipe F.; Malta, Kássia K.; Amaral, Kátia B.; Shamri, Revital; Weller, Peter F.; Melo, Rossana C.N.

    2015-01-01

    Background: SNARE members mediate membrane fusion during intracellular trafficking underlying innate and adaptive immune responses by different cells. However, little is known about the expression and function of these proteins in human eosinophils, cells involved in allergic, inflammatory and immunoregulatory responses. Here, we investigate the expression and distribution of the Qa-SNARE syntaxin17 (STX17) within human eosinophils isolated from the peripheral blood. Methods: Flow cytometry and a pre-embedding immunonanogold electron microscopy (EM) technique that combines optimal epitope preservation and secondary Fab-fragments of antibodies linked to 1.4 nm gold particles for optimal access to microdomains, were used to investigate STX17. Results: STX17 was detected within unstimulated eosinophils. Immunogold EM revealed STX17 on secretory granules and on granule-derived vesiculotubular transport carriers (Eosinophil Sombrero Vesicles-EoSVs). Quantitative EM analyses showed that 77.7% of the granules were positive for STX17 with a mean±SEM of 3.9±0.2 gold particles/granule. Labeling was present on both granule outer membranes and matrices while EoSVs showed clear membrane-associated labeling. STX17 was also present in secretory granules in eosinophils stimulated with the cytokine tumor necrosis factor alpha (TNF-α) or the CC-chemokine ligand 11 CCL11 (eotaxin-1), stimuli that induce eosinophil degranulation. The number of secretory granules labeled for STX17 was significantly higher in CCL11 compared with the unstimulated group. The level of cell labeling did not change when unstimulated cells were compared with TNF-α-stimulated eosinophils. Conclusions: The present study clearly shows by immunanonogold EM that STX17 is localized in eosinophil secretory granules and transport vesicles and might be involved in the transport of granule-derived cargos. - Highlights: • First demonstration of the Qa-SNARE syntaxin-17 (STX17) in human eosinophils. • High

  20. Modeling curvature-dependent subcellular localization of a small sporulation protein in Bacillus subtilis

    Science.gov (United States)

    Wasnik, Vaibhav; Wingreen, Ned; Mukhopadhyay, Ranjan

    2012-02-01

    Recent experiments suggest that in the bacterium, B. subtilis, the cue for the localization of small sporulation protein, SpoVM, that plays a central role in spore coat formation, is curvature of the bacterial plasma membrane. This curvature-dependent localization is puzzling given the orders of magnitude difference in lengthscale of an individual protein and radius of curvature of the membrane. Here we develop a minimal model to study the relationship between curvature-dependent membrane absorption of SpoVM and clustering of membrane-associated SpoVM and compare our results with experiments.

  1. Subcellular localization of Cd in the root cells of Allium sativum by ...

    Indian Academy of Sciences (India)

    The ultrastructural investigation of the root cells of Allium sativum L. exposed to three different concentrations of Cd (100 M, 1 mM and 10 mM) for 9 days was carried out. The results showed that Cd induced several significant ultrastructural changes – high vacuolization in cytoplasm, deposition of electron-dense material in ...

  2. Backscattered electron SEM imaging of resin sections from plant specimens: observation of histological to subcellular structure and CLEM.

    Science.gov (United States)

    Rizzo, N W; Duncan, K E; Bourett, T M; Howard, R J

    2016-08-01

    We have refined methods for biological specimen preparation and low-voltage backscattered electron imaging in the scanning electron microscope that allow for observation at continuous magnifications of ca. 130-70 000 X, and documentation of tissue and subcellular ultrastructure detail. The technique, based upon early work by Ogura & Hasegawa (1980), affords use of significantly larger sections from fixed and resin-embedded specimens than is possible with transmission electron microscopy while providing similar data. After microtomy, the sections, typically ca. 750 nm thick, were dried onto the surface of glass or silicon wafer and stained with heavy metals-the use of grids avoided. The glass/wafer support was then mounted onto standard scanning electron microscopy sample stubs, carbon-coated and imaged directly at an accelerating voltage of 5 kV, using either a yttrium aluminum garnet or ExB backscattered electron detector. Alternatively, the sections could be viewed first by light microscopy, for example to document signal from a fluorescent protein, and then by scanning electron microscopy to provide correlative light/electron microscope (CLEM) data. These methods provide unobstructed access to ultrastructure in the spatial context of a section ca. 7 × 10 mm in size, significantly larger than the typical 0.2 × 0.3 mm section used for conventional transmission electron microscopy imaging. Application of this approach was especially useful when the biology of interest was rare or difficult to find, e.g. a particular cell type, developmental stage, large organ, the interface between cells of interacting organisms, when contextual information within a large tissue was obligatory, or combinations of these factors. In addition, the methods were easily adapted for immunolocalizations. © 2015 The Author. Journal of Microscopy published by John Wiley & Sons, Ltd on behalf of the Royal Microscopical Society.

  3. Subcellular localization of estradiol receptor in MCF7 cells studied with nanogold-labelled antibody fragments.

    Science.gov (United States)

    Kessels, M M; Qualmann, B; Thole, H H; Sierralta, W D

    1998-01-01

    Ultrastructural localization studies of estradiol receptor in hormone-deprived and hormone-stimulated MCF7 cells were done using F(ab') fragments of three different antibodies (#402, 13H2, HT277) covalently linked to nanogold. These ultra-small, non-charged immunoreagents, combined with a size-enlargement by silver enhancement, localized estradiol receptor in both nuclear and cytoplasmic areas of non-stimulated target cells; stimulation with the steroid induced a predominantly nuclear labelling. In the cytoplasm of resting cells, tagging was often observed at or in the proximity of stress fibers. In the nucleus a large proportion of receptor was found inside the nucleolus, specially with the reagent derived from antibody 13H2. We postulate that different accessibilities of receptor epitopes account for the different labelling densities observed at cytoskeletal elements and the nucleoli.

  4. Subcellular localization of Bombyx mori ribosomal protein S3a and ...

    African Journals Online (AJOL)

    USER

    2010-04-05

    Apr 5, 2010 ... In the present study, using a BV/PH-Bms3a-EGFP, we found that Bombyx mori ribosomal protein S3a. (BmS3a) with EGFP fused to its C-terminal, was predominantly localized in the cytoplasm of B. mori cells. Subsequently, to investigate the effect of BmS3a over-expression on BmNPV infection both at the.

  5. Subcellular Localization of Patched and Smoothened, the Receptors for Sonic Hedgehog Signaling, in the Hippocampal Neuron

    OpenAIRE

    Petralia, Ronald S.; Schwartz, Catherine M.; Wang, Ya-Xian; Mattson, Mark P.; Yao, Pamela J.

    2011-01-01

    Cumulative evidence suggests that, aside from patterning the embryonic neural tube, Sonic hedgehog (Shh) signaling plays important roles in the mature nervous system. In this study, we investigate the expression and localization of the Shh signaling receptors, Patched (Ptch) and Smoothened (Smo), in the hippocampal neurons of young and mature rats. Reverse transcriptase-polymerase chain reaction and immunoblotting analyses show that the expression of Ptch and Smo remains at a moderate level i...

  6. The subcellular localization of yeast glycogen synthase is dependent upon glycogen content

    OpenAIRE

    Wilson, Wayne A.; Boyer, Michael P.; Davis, Keri D.; Burke, Michael; Roach, Peter J.

    2010-01-01

    The budding yeast, Saccharomyces cerevisiae, accumulates the storage polysaccharide glycogen in response to nutrient limitation. Glycogen synthase, the major form of which is encoded by the GSY2 gene, catalyzes the key regulated step in glycogen storage. Here, we utilize Gsy2p fusions to green fluorescent protein (GFP) to determine where glycogen synthase is located within cells. We demonstrate that the localization pattern of Gsy2-GFP depends upon the glycogen content of the cell. When glyco...

  7. Identification and subcellular localization of porcine deltacoronavirus accessory protein NS6

    International Nuclear Information System (INIS)

    Fang, Puxian; Fang, Liurong; Liu, Xiaorong; Hong, Yingying; Wang, Yongle; Dong, Nan; Ma, Panpan; Bi, Jing; Wang, Dang; Xiao, Shaobo

    2016-01-01

    Porcine deltacoronavirus (PDCoV) is an emerging swine enteric coronavirus. Accessory proteins are genus-specific for coronavirus, and two putative accessory proteins, NS6 and NS7, are predicted to be encoded by PDCoV; however, this remains to be confirmed experimentally. Here, we identified the leader-body junction sites of NS6 subgenomic RNA (sgRNA) and found that the actual transcription regulatory sequence (TRS) utilized by NS6 is non-canonical and is located upstream of the predicted TRS. Using the purified NS6 from an Escherichia coli expression system, we obtained two anti-NS6 monoclonal antibodies that could detect the predicted NS6 in cells infected with PDCoV or transfected with NS6-expressing plasmids. Further studies revealed that NS6 is always localized in the cytoplasm of PDCoV-infected cells, mainly co-localizing with the endoplasmic reticulum (ER) and ER-Golgi intermediate compartments, as well as partially with the Golgi apparatus. Together, our results identify the NS6 sgRNA and demonstrate its expression in PDCoV-infected cells. -- Highlights: •The leader-body fusion site of NS6 sgRNA is identified. •NS6 sgRNA uses a non-canonical transcription regulatory sequence (TRS). •NS6 can be expressed in PDCoV-infected cell. •NS6 predominantly localize to the ER complex and ER-Golgi intermediate compartment.

  8. Identification and subcellular localization of porcine deltacoronavirus accessory protein NS6

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Puxian; Fang, Liurong; Liu, Xiaorong; Hong, Yingying; Wang, Yongle; Dong, Nan; Ma, Panpan [State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070 (China); The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070 (China); Bi, Jing [State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070 (China); Department of Immunology and Aetology, College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan 430065 (China); Wang, Dang [State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070 (China); The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070 (China); Xiao, Shaobo, E-mail: vet@mail.hzau.edu.cn [State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070 (China); The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070 (China)

    2016-12-15

    Porcine deltacoronavirus (PDCoV) is an emerging swine enteric coronavirus. Accessory proteins are genus-specific for coronavirus, and two putative accessory proteins, NS6 and NS7, are predicted to be encoded by PDCoV; however, this remains to be confirmed experimentally. Here, we identified the leader-body junction sites of NS6 subgenomic RNA (sgRNA) and found that the actual transcription regulatory sequence (TRS) utilized by NS6 is non-canonical and is located upstream of the predicted TRS. Using the purified NS6 from an Escherichia coli expression system, we obtained two anti-NS6 monoclonal antibodies that could detect the predicted NS6 in cells infected with PDCoV or transfected with NS6-expressing plasmids. Further studies revealed that NS6 is always localized in the cytoplasm of PDCoV-infected cells, mainly co-localizing with the endoplasmic reticulum (ER) and ER-Golgi intermediate compartments, as well as partially with the Golgi apparatus. Together, our results identify the NS6 sgRNA and demonstrate its expression in PDCoV-infected cells. -- Highlights: •The leader-body fusion site of NS6 sgRNA is identified. •NS6 sgRNA uses a non-canonical transcription regulatory sequence (TRS). •NS6 can be expressed in PDCoV-infected cell. •NS6 predominantly localize to the ER complex and ER-Golgi intermediate compartment.

  9. Subcellular localization and vacuolar targeting of sorbitol dehydrogenase in apple seed.

    Science.gov (United States)

    Wang, Xiu-Ling; Hu, Zi-Ying; You, Chun-Xiang; Kong, Xiu-Zhen; Shi, Xiao-Pu

    2013-09-01

    Sorbitol is the primary photosynthate and translocated carbohydrate in fruit trees of the Rosaceae family. NAD(+)-dependent sorbitol dehydrogenase (NAD-SDH, EC 1.1.1.14), which mainly catalyzes the oxidation of sorbitol to fructose, plays a key role in regulating sink strength in apple. In this study, we found that apple NAD-SDH was ubiquitously distributed in epidermis, parenchyma, and vascular bundle in developing cotyledon. NAD-SDH was localized in the cytosol, the membranes of endoplasmic reticulum and vesicles, and the vacuolar lumen in the cotyledon at the middle stage of seed development. In contrast, NAD-SDH was mainly distributed in the protein storage vacuoles in cotyledon at the late stage of seed development. Sequence analysis revealed there is a putative signal peptide (SP), also being predicated to be a transmembrane domain, in the middle of proteins of apple NAD-SDH isoforms. To investigate whether the putative internal SP functions in the vacuolar targeting of NAD-SDH, we analyzed the localization of the SP-deletion mutants of MdSDH5 and MdSDH6 (two NAD-SDH isoforms in apple) by the transient expression system in Arabidopsis protoplasts. MdSDH5 and MdSDH6 were not localized in the vacuoles after their SPs were deleted, suggesting the internal SP functions in the vacuolar targeting of apple NAD-SDH. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  10. Effect of cadmium on the physiological parameters and the subcellular cadmium localization in the potato (Solanum tuberosum L.).

    Science.gov (United States)

    Xu, Dongyu; Chen, Zhifan; Sun, Ke; Yan, Dong; Kang, Mingjie; Zhao, Ye

    2013-11-01

    The pollution of agricultural soils with cadmium (Cd) has become a serious problem worldwide. The potato (Solanum tuberosum L.) was used to investigate how different concentrations of Cd (1, 5, and 25mgkg(-1)) affected the physiological parameters and the subcellular distribution of Cd in the potato. The analyses were conducted using scanning electron microscopy coupled with energy dispersive X-ray (SEM-EDX). The results suggest that the leaf is the organ with the highest accumulation of Cd. The malondialdehyde (MDA) content increased and the chlorophyll content decreased in response to high level of Cd. The SEM-EDX microanalysis revealed that Cd was primarily deposited in the spongy and palisade tissues of the leaf. Furthermore, Cd was also detected in the cortex and the adjacent phloem and was observed inside the intercellular space, the interior surface of the plasma membrane, and on the surface of the elliptical starch granules in the tubers of the potato. Although low concentrations of Cd migrated from the root to the tuber, the accumulation of Cd in the tuber exceeded the standard for food security. Therefore, the planting of potato plants in farmland containing Cd should be seriously evaluated because Cd-containing potatoes might present high health risk to humans. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Different subcellular localization of neurotensin-receptor and neurotensin-acceptor sites in the rat brain dopaminergic system.

    Science.gov (United States)

    Schotte, A; Rostène, W; Laduron, P M

    1988-04-01

    The subcellular localization of neurotensin-receptor sites (NT2 sites) and neurotensin-acceptor sites (NT1 sites) was studied in rat caudate-putamen by isopycnic centrifugation in sucrose density gradients. [3H]Neurotensin binding to NT2 sites occurred as a major peak at higher sucrose densities, colocalized with [3H]dopamine uptake, and as a small peak at a lower density; whereas binding to NT1 sites occurred as a single large peak at an intermediate density. 6-Hydroxydopamine lesions of the median forebrain bundle resulted in a total loss of NT2 sites in the caudate-putamen but did not affect NT2 sites in the nucleus accumbens and the olfactory tubercle. NT1 sites were not affected. Kainic acid injections into the rat caudate-putamen led to a partial decrease of NT1 sites in this region 5 days later. After a few weeks they returned to normal. Therefore NT2 sites are probably associated with presynaptic nigrostriatal dopaminergic terminals in the caudate-putamen but not in the nucleus accumbens and the olfactory tubercle. A possible association of NT1 sites with glial cells is suggested.

  12. Influence of conversion of penicillin G into a basic derivative on its accumulation and subcellular localization in cultured macrophages

    International Nuclear Information System (INIS)

    Renard, C.; Vanderhaeghe, H.J.; Claes, P.J.; Zenebergh, A.; Tulkens, P.M.

    1987-01-01

    beta-Lactam antibiotics do not accumulate in phagocytes, probably because of their acidic character. We therefore synthesized a basic derivative of penicillin G, namely, 14 C-labeled N-(3-dimethylamino-propyl)benzylpenicillinamide (ABP), and studied its uptake and subcellular localization in J774 macrophages compared with that of 14 C-labeled penicillin G. Whereas the intracellular concentration (Ci) of penicillin G remained lower than its extracellular concentration (Ce), ABP reached a Ci/Ce ratio of 4 to 5. Moreover, approximately 50% of intracellular ABP was found associated with lysosomes after isopycnic centrifugation of cell homogenates in isoosmotic Percoll or hyperosmotic sucrose gradients. The behavior of ABP was thus partly consistent with the model of de Duve et al., in which they described the intralysosomal accumulation of weak organic bases in lysosomes. Although ABP is microbiologically inactive, our results show that beta-lactam antibiotics can be driven into cells by appropriate modification. Further efforts therefore may be warranted in the design of active compounds or prodrugs that may prove useful in the chemotherapy of intracellular infections

  13. ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea

    Science.gov (United States)

    Paramasivam, Nagarajan; Linke, Dirk

    2011-01-01

    The subcellular localization (SCL) of proteins provides important clues to their function in a cell. In our efforts to predict useful vaccine targets against Gram-negative bacteria, we noticed that misannotated start codons frequently lead to wrongly assigned SCLs. This and other problems in SCL prediction, such as the relatively high false-positive and false-negative rates of some tools, can be avoided by applying multiple prediction tools to groups of homologous proteins. Here we present ClubSub-P, an online database that combines existing SCL prediction tools into a consensus pipeline from more than 600 proteomes of fully sequenced microorganisms. On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false-positive and false-negative predictions. ClubSub-P can assign the SCL of proteins from Gram-negative bacteria and Archaea with high precision. The database is searchable, and can easily be expanded using either new bacterial genomes or new prediction tools as they become available. This will further improve the performance of the SCL prediction, as well as the detection of misannotated start codons and other annotation errors. ClubSub-P is available online at http://toolkit.tuebingen.mpg.de/clubsubp/ PMID:22073040

  14. Subcellular localization of low-abundance human immunodeficiency virus nucleic acid sequences visualized by fluorescence in situ hybridization

    International Nuclear Information System (INIS)

    Lawrence, J.B.; Marselle, L.M.; Byron, K.S.; Johnson, C.V.; Sullivan, J.L.; Singer, R.H.

    1990-01-01

    Detection and subcellular localization of human immunodeficiency virus (HIV) were investigated using sensitive high-resolution in situ hybridization methodology. Lymphocytes infected with HIV in vitro or in vivo were detected by fluorescence after hybridization with either biotin or digoxigenin-labeled probes. At 12 hr after infection in vitro, a single intense signal appeared in the nuclei of individual cells. Later in infection, when cytoplasmic fluorescence became intense, multiple nuclear foci frequently appeared. The nuclear focus consisted of newly synthesized HIV RNA as shown by hybridization in the absence of denaturation and by susceptibility to RNase and actinomycin D. Virus was detected in patient lymphocytes and it was shown that a singular nuclear focus also characterizes cells infected in vivo. The cell line 8E5/LAV containing one defective integrated provirus revealed a similar focus of nuclear RNA, and the single integrated HIV genome was unequivocally visualized on a D-group chromosome. This demonstrates an extremely sensitive single-cell assay for the presence of a single site of HIV transcription in vitro and in vivo and suggests that it derives from one (or very few) viral genomes per cell. In contrast, productive Epstein-Barr virus infection exhibited many foci of nuclear RNA per cell

  15. Endogenous spar tin, mutated in hereditary spastic paraplegia, has a complex subcellular localization suggesting diverse roles in neurons

    International Nuclear Information System (INIS)

    Robay, Dimitri; Patel, Heema; Simpson, Michael A.; Brown, Nigel A.; Crosby, Andrew H.

    2006-01-01

    Mutation of spartin (SPG20) underlies a complicated form of hereditary spastic paraplegia, a disorder principally defined by the degeneration of upper motor neurons. Using a polyclonal antibody against spartin to gain insight into the function of the endogenous molecule, we show that the endogenous molecule is present in two main isoforms of 85 kDa and 100 kDa, and 75 kDa and 85 kDa in human and murine, respectively, with restricted subcellular localization. Immunohistochemical studies on human and mouse embryo sections and in vitro cell studies indicate that spartin is likely to possess both nuclear and cytoplasmic functions. The nuclear expression of spartin closely mirrors that of the snRNP (small nuclear ribonucleoprotein) marker α-Sm, a component of the spliceosome. Spartin is also enriched at the centrosome within mitotic structures. Notably we show that spartin protein undergoes dynamic positional changes in differentiating human SH-SY5Y cells. In undifferentiated non-neuronal cells, spartin displays a nuclear and diffuse cytosolic profile, whereas spartin transiently accumulates in the trans-Golgi network and subsequently decorates discrete puncta along neurites in terminally differentiated neuroblastic cells. Investigation of these spartin-positive vesicles reveals that a large proportion colocalizes with the synaptic vesicle marker synaptotagmin. Spartin is also enriched in synaptic-like structures and in synaptic vesicle-enriched fraction

  16. Heat shock modulates the subcellular localization, stability, and activity of HIPK2

    International Nuclear Information System (INIS)

    Upadhyay, Mamta; Bhadauriya, Pratibha; Ganesh, Subramaniam

    2016-01-01

    The homeodomain-interacting protein kinase-2 (HIPK2) is a highly conserved serine/threonine kinase and is involved in transcriptional regulation. HIPK2 is a highly unstable protein, and is kept at a low level under normal physiological conditions. However, exposure of cells to physiological stress – such as hypoxia, oxidative stress, or UV damage – is known to stabilize HIPK2, leading to the HIPK2-dependent activation of p53 and the cell death pathway. Therefore HIPK2 is also known as a stress kinase and as a stress-activated pro-apoptotic factor. We demonstrate here that exposure of cells to heat shock results in the stabilization of HIPK2 and the stabilization is mediated via K63-linked ubiquitination. Intriguingly, a sub-lethal heat shock (42 °C, 1 h) results in the cytoplasmic localization of HIPK2, while a lethal heat shock (45 °C, 1 h) results in its nuclear localization. Cells exposed to the lethal heat shock showed significantly higher levels of the p53 activity than those exposed to the sub-lethal thermal stress, suggesting that both the level and the nuclear localization are essential for the pro-apoptotic activity of HIPK2 and that the lethal heat shock could retain the HIPK2 in the nucleus to promote the cell death. Taken together our study underscores the importance of HIPK2 in stress mediated cell death, and that the HIPK2 is a generic stress kinase that gets activated by diverse set of physiological stressors.

  17. Subcellular localization of human neutral ceramidase expressed in HEK293 cells

    International Nuclear Information System (INIS)

    Hwang, Young-ha; Tani, Motohiro; Nakagawa, Tetsuto; Okino, Nozomu; Ito, Makoto

    2005-01-01

    We previously reported that rat and mouse neutral ceramidases were mainly localized to plasma membranes as a type II integral membrane protein and partly detached from the cells via processing of the N-terminal/anchor sequence when expressed in HEK293 cells [M. Tani, H. Iida, M. Ito, O-glycosylation of mucin-like domain retains the neutral ceramidase on the plasma membranes as a type II integral membrane protein, J. Biol. Chem. 278 (2003) 10523-10530]. In contrast, the human homologue was exclusively detected in mitochondria when expressed in HEK293 and MCF7 cells as a fusion protein with green fluorescent protein at the N-terminal of the enzyme [S.E. Bawab, P. Roddy, T. Quian, A. Bielawska, J.J. Lemasters, Y.A. Hannun, Molecular cloning and characterization of a human mitochondrial ceramidase, J. Biol. Chem. 275 (2000) 21508-21513]. Given this discrepancy, we decided to clone the neutral ceramidase from human kidney cDNA and re-examine the intracellular localization of the enzyme when expressed in HEK293 cells. The putative amino acid sequence of the newly cloned enzyme was identical to that reported for human neutral ceramidase except at the N-terminal; the new protein was 19 amino acids longer at the N-terminal. We found that the putative full-length human neutral ceramidase was transported to plasma membranes, but not to mitochondria, possibly via a classical ER/Golgi pathway and localized mainly in plasma membranes when expressed in HEK293 cells. The N-terminal-truncated mutant, previously reported as a human mitochondrial ceramidase, was also weakly expressed in HEK293 cells but mainly released into the medium possibly due to the insufficient signal/anchor sequence

  18. Heat shock modulates the subcellular localization, stability, and activity of HIPK2

    Energy Technology Data Exchange (ETDEWEB)

    Upadhyay, Mamta; Bhadauriya, Pratibha; Ganesh, Subramaniam, E-mail: sganesh@iitk.ac.in

    2016-04-15

    The homeodomain-interacting protein kinase-2 (HIPK2) is a highly conserved serine/threonine kinase and is involved in transcriptional regulation. HIPK2 is a highly unstable protein, and is kept at a low level under normal physiological conditions. However, exposure of cells to physiological stress – such as hypoxia, oxidative stress, or UV damage – is known to stabilize HIPK2, leading to the HIPK2-dependent activation of p53 and the cell death pathway. Therefore HIPK2 is also known as a stress kinase and as a stress-activated pro-apoptotic factor. We demonstrate here that exposure of cells to heat shock results in the stabilization of HIPK2 and the stabilization is mediated via K63-linked ubiquitination. Intriguingly, a sub-lethal heat shock (42 °C, 1 h) results in the cytoplasmic localization of HIPK2, while a lethal heat shock (45 °C, 1 h) results in its nuclear localization. Cells exposed to the lethal heat shock showed significantly higher levels of the p53 activity than those exposed to the sub-lethal thermal stress, suggesting that both the level and the nuclear localization are essential for the pro-apoptotic activity of HIPK2 and that the lethal heat shock could retain the HIPK2 in the nucleus to promote the cell death. Taken together our study underscores the importance of HIPK2 in stress mediated cell death, and that the HIPK2 is a generic stress kinase that gets activated by diverse set of physiological stressors.

  19. The Subcellular Localization and Functional Analysis of Fibrillarin2, a Nucleolar Protein in Nicotiana benthamiana

    Directory of Open Access Journals (Sweden)

    Luping Zheng

    2016-01-01

    Full Text Available Nucleolar proteins play important roles in plant cytology, growth, and development. Fibrillarin2 is a nucleolar protein of Nicotiana benthamiana (N. benthamiana. Its cDNA was amplified by RT-PCR and inserted into expression vector pEarley101 labeled with yellow fluorescent protein (YFP. The fusion protein was localized in the nucleolus and Cajal body of leaf epidermal cells of N. benthamiana. The N. benthamiana fibrillarin2 (NbFib2 protein has three functional domains (i.e., glycine and arginine rich domain, RNA-binding domain, and α-helical domain and a nuclear localization signal (NLS in C-terminal. The protein 3D structure analysis predicted that NbFib2 is an α/β protein. In addition, the virus induced gene silencing (VIGS approach was used to determine the function of NbFib2. Our results showed that symptoms including growth retardation, organ deformation, chlorosis, and necrosis appeared in NbFib2-silenced N. benthamiana.

  20. Palmitic acid mediates hypothalamic insulin resistance by altering PKC-θ subcellular localization in rodents

    Science.gov (United States)

    Benoit, Stephen C.; Kemp, Christopher J.; Elias, Carol F.; Abplanalp, William; Herman, James P.; Migrenne, Stephanie; Lefevre, Anne-Laure; Cruciani-Guglielmacci, Céline; Magnan, Christophe; Yu, Fang; Niswender, Kevin; Irani, Boman G.; Holland, William L.; Clegg, Deborah J.

    2009-01-01

    Insulin signaling can be modulated by several isoforms of PKC in peripheral tissues. Here, we assessed whether one specific isoform, PKC-θ, was expressed in critical CNS regions that regulate energy balance and whether it mediated the deleterious effects of diets high in fat, specifically palmitic acid, on hypothalamic insulin activity in rats and mice. Using a combination of in situ hybridization and immunohistochemistry, we found that PKC-θ was expressed in discrete neuronal populations of the arcuate nucleus, specifically the neuropeptide Y/agouti-related protein neurons and the dorsal medial nucleus in the hypothalamus. CNS exposure to palmitic acid via direct infusion or by oral gavage increased the localization of PKC-θ to cell membranes in the hypothalamus, which was associated with impaired hypothalamic insulin and leptin signaling. This finding was specific for palmitic acid, as the monounsaturated fatty acid, oleic acid, neither increased membrane localization of PKC-θ nor induced insulin resistance. Finally, arcuate-specific knockdown of PKC-θ attenuated diet-induced obesity and improved insulin signaling. These results suggest that many of the deleterious effects of high-fat diets, specifically those enriched with palmitic acid, are CNS mediated via PKC-θ activation, resulting in reduced insulin activity. PMID:19726875

  1. Palmitic acid mediates hypothalamic insulin resistance by altering PKC-theta subcellular localization in rodents.

    Science.gov (United States)

    Benoit, Stephen C; Kemp, Christopher J; Elias, Carol F; Abplanalp, William; Herman, James P; Migrenne, Stephanie; Lefevre, Anne-Laure; Cruciani-Guglielmacci, Céline; Magnan, Christophe; Yu, Fang; Niswender, Kevin; Irani, Boman G; Holland, William L; Clegg, Deborah J

    2009-09-01

    Insulin signaling can be modulated by several isoforms of PKC in peripheral tissues. Here, we assessed whether one specific isoform, PKC-theta, was expressed in critical CNS regions that regulate energy balance and whether it mediated the deleterious effects of diets high in fat, specifically palmitic acid, on hypothalamic insulin activity in rats and mice. Using a combination of in situ hybridization and immunohistochemistry, we found that PKC-theta was expressed in discrete neuronal populations of the arcuate nucleus, specifically the neuropeptide Y/agouti-related protein neurons and the dorsal medial nucleus in the hypothalamus. CNS exposure to palmitic acid via direct infusion or by oral gavage increased the localization of PKC-theta to cell membranes in the hypothalamus, which was associated with impaired hypothalamic insulin and leptin signaling. This finding was specific for palmitic acid, as the monounsaturated fatty acid, oleic acid, neither increased membrane localization of PKC-theta nor induced insulin resistance. Finally, arcuate-specific knockdown of PKC-theta attenuated diet-induced obesity and improved insulin signaling. These results suggest that many of the deleterious effects of high-fat diets, specifically those enriched with palmitic acid, are CNS mediated via PKC-theta activation, resulting in reduced insulin activity.

  2. Anks3 alters the sub-cellular localization of the Nek7 kinase

    Energy Technology Data Exchange (ETDEWEB)

    Ramachandran, Haribaskar; Engel, Christina; Müller, Barbara [Renal Division, Department of Medicine, University Freiburg Medical Center, Hugstetter Str. 55, 79106 Freiburg (Germany); Dengjel, Jörn [Department of Dermatology, University Freiburg Medical Center and Center of Biological Systems Analysis, Habsburgerstr. 49, 79104 Freiburg (Germany); Walz, Gerd [Renal Division, Department of Medicine, University Freiburg Medical Center, Hugstetter Str. 55, 79106 Freiburg (Germany); Center for Biological Signaling Studies (BIOSS), Albertstr. 19, 79104 Freiburg (Germany); Yakulov, Toma A., E-mail: toma.antonov.yakulov@uniklinik-freiburg.de [Renal Division, Department of Medicine, University Freiburg Medical Center, Hugstetter Str. 55, 79106 Freiburg (Germany)

    2015-08-28

    Nephronophthisis (NPH) is an autosomal recessive cystic kidney disease, and a frequent cause of end-stage renal failure in children. To date, 17 NPH-associated gene products (NPHPs) have been identified. Most NPHPs participate in large multi-protein complexes that localize to the cilium and/or basal body; however, the precise composition of these complexes and their biological function remain largely unknown. We recently observed that the ankyrin repeat protein Anks3 interacts with the NPH family member Anks6. Both Anks3 and Anks6 form complexes with multiple other NPHPs, suggesting that both proteins function in similar or overlapping signaling pathways. Here, we show that Anks3, but not Anks6 interacted with the NIMA-related kinase Nek7, and was heavily modified in the presence of Nek7, resulting in an approximately 20 kD increase in molecular weight. Although mass spectrometry revealed increased serine and threonine phosphorylation of Anks3 primarily within the N-terminal ankyrin repeats also required for Nek7 interaction, the molecular weight increase occurred even in the presence of a kinase-dead Nek7 mutant, indicating that this modification was not caused by Nek7-dependent Anks3 phosphorylation. Furthermore, the Anks3 modification was specific for Nek7, and did not occur in the presence of Nek8. Importantly, Anks3 retained Nek7 in the cytoplasm, suggesting that, Nek7 triggers the modification of Anks3, which in turn prevents the nuclear localization of Nek7. - Highlights: • Anks3 interacted with Nek7 kinase, and was heavily modified in the presence of Nek7. • Anks3 N-terminal ankyrin repeats, but not SAM domain required for Nek7 interaction. • Nek7 increased Ser/Thr phosphorylation of Anks3 primarily within ankyrin domain. • Interaction with Anks3 led to cytoplasmic retention and nuclear exclusion of Nek7.

  3. Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa.

    Science.gov (United States)

    Ohara, Kazuaki; Sasaki, Kanako; Yazaki, Kazufumi

    2010-06-01

    Long chain prenyl diphosphates are crucial biosynthetic precursors of ubiquinone (UQ) in many organisms, ranging from bacteria to humans, as well as precursors of plastoquinone in photosynthetic organisms. The cloning and characterization of two solanesyl diphosphate synthase genes, OsSPS1 and OsSPS2, in Oryza sativa is reported here. OsSPS1 was highly expressed in root tissue whereas OsSPS2 was found to be high in both leaves and roots. Enzymatic characterization using recombinant proteins showed that both OsSPS1 and OsSPS2 could produce solanesyl diphosphates as their final product, while OsSPS1 showed stronger activity than OsSPS2. However, an important biological difference was observed between the two genes: OsSPS1 complemented the yeast coq1 disruptant, which does not form UQ, whereas OsSPS2 only very weakly complemented the growth defect of the coq1 mutant. HPLC analyses showed that both OsSPS1 and OsSPS2 yeast transformants produced UQ9 instead of UQ6, which is the native yeast UQ. According to the complementation study, the UQ9 levels in OsSPS2 transformants were much lower than that of OsSPS1. Green fluorescent protein fusion analyses showed that OsSPS1 localized to mitochondria, while OsSPS2 localized to plastids. This suggests that OsSPS1 is involved in the supply of solanesyl diphosphate for ubiquinone-9 biosynthesis in mitochondria, whereas OsSPS2 is involved in providing solanesyl diphosphate for plastoquinone-9 formation. These findings indicate that O. sativa has a different mechanism for the supply of isoprenoid precursors in UQ biosynthesis from Arabidopsis thaliana, in which SPS1 provides a prenyl moiety for UQ9 at the endoplasmic reticulum.

  4. Localization and subcellular association of Grapevine Pinot Gris Virus in grapevine leaf tissues.

    Science.gov (United States)

    Tarquini, Giulia; Ermacora, Paolo; Bianchi, Gian Luca; De Amicis, Francesca; Pagliari, Laura; Martini, Marta; Loschi, Alberto; Saldarelli, Pasquale; Loi, Nazia; Musetti, Rita

    2018-05-01

    Despite the increasing impact of Grapevine Pinot gris disease (GPG-disease) worldwide, etiology about this disorder is still uncertain. The presence of the putative causal agent, the Grapevine Pinot Gris Virus (GPGV), has been reported in symptomatic grapevines (presenting stunting, chlorotic mottling, and leaf deformation) as well as in symptom-free plants. Moreover, information on virus localization in grapevine tissues and virus-plant interactions at the cytological level is missing at all. Ultrastructural and cytochemical investigations were undertaken to detect virus particles and the associated cytopathic effects in field-grown grapevine showing different symptom severity. Asymptomatic greenhouse-grown grapevines, which tested negative for GPGV by real time RT-PCR, were sampled as controls. Multiplex real-time RT-PCR and ELISA tests excluded the presence of viruses included in the Italian certification program both in field-grown and greenhouse-grown grapevines. Conversely, evidence was found for ubiquitous presence of Grapevine Rupestris Stem Pitting-associated Virus (GRSPaV), Hop Stunt Viroid (HSVd), and Grapevine Yellow Speckle Viroid 1 (GYSVd-1) in both plant groups. Moreover, in every field-grown grapevine, GPGV was detected by real-time RT-PCR. Ultrastructural observations and immunogold labelling assays showed filamentous flexuous viruses in the bundle sheath cells, often located inside membrane-bound organelles. No cytological differences were observed among field-grown grapevine samples showing different symptom severity. GPGV localization and associated ultrastructural modifications are reported and discussed, in the perspective of assisting management and control of the disease.

  5. Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

    International Nuclear Information System (INIS)

    Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank

    2013-01-01

    Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

  6. Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank, E-mail: fkempken@bot.uni-kiel.de

    2013-08-30

    Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

  7. MNK1 expression increases during cellular senescence and modulates the subcellular localization of hnRNP A1

    International Nuclear Information System (INIS)

    Ziaei, Samira; Shimada, Naoko; Kucharavy, Herman; Hubbard, Karen

    2012-01-01

    Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is an RNA-binding protein that modulates splice site usage, polyadenylation, and cleavage efficiency. This protein has also been implicated in mRNA stability and transport from the nucleus. We have previously demonstrated that hnRNP A1 had diminished protein levels and showed cytoplasmic accumulation in senescent human diploid fibroblasts. Furthermore, we have shown that inhibition of p38 MAPK, a key regulator of cellular senescence, elevated hnRNP A1 protein levels and inhibited hnRNP A1 cytoplasmic localization. In this study, we have explored the possible involvement of MNK1, one of the downstream effector of p38 MAPK, in the regulation of hnRNP A1. We have demonstrated that pharmacological inhibition of MNK1 by CGP 57380 decreased the phosphorylation levels of hnRNP A1 in young and senescent fibroblast cells and blocked the cytoplasmic accumulation of hnRNP A1 in senescent cells. In addition, MNK1 formed a complex with hnRNP A1 in vivo. The expression levels of MNK1, phospho-MNK1, and phospho-eIF4E proteins were found to be elevated in senescent cells. These data suggest that MNK1 regulates the phosphorylation and the subcellular distribution of hnRNP A1 and that MNK1 may play a role in the induction of senescence. -- Highlights: ► MNK1 and not MAPKAPK2 phosphorylates hnRNP A1. ► MNK1 has elevated levels in senescent cells, this has not been reported previously. ► MNK1 activity induces cytoplasmic accumulation of hnRNP A1 in senescent cells. ► Altered cytoplasmic localization of hnRNP A1 may alter gene expression patterns. ► Our studies may increase our understanding of RNA metabolism during cellular aging.

  8. Characterization of two geraniol synthases from Valeriana officinalis and Lippia dulcis: similar activity but difference in subcellular localization.

    Science.gov (United States)

    Dong, Lemeng; Miettinen, Karel; Goedbloed, Miriam; Verstappen, Francel W A; Voster, Alessandra; Jongsma, Maarten A; Memelink, Johan; van der Krol, Sander; Bouwmeester, Harro J

    2013-11-01

    Two geraniol synthases (GES), from Valeriana officinalis (VoGES) and Lippia dulcis (LdGES), were isolated and were shown to have geraniol biosynthetic activity with Km values of 32 µM and 51 µM for GPP, respectively, upon expression in Escherichia coli. The in planta enzymatic activity and sub-cellular localization of VoGES and LdGES were characterized in stable transformed tobacco and using transient expression in Nicotiana benthamiana. Transgenic tobacco expressing VoGES or LdGES accumulate geraniol, oxidized geraniol compounds like geranial, geranic acid and hexose conjugates of these compounds to similar levels. Geraniol emission of leaves was lower than that of flowers, which could be related to higher levels of competing geraniol-conjugating activities in leaves. GFP-fusions of the two GES proteins show that VoGES resides (as expected) predominantly in the plastids, while LdGES import into to the plastid is clearly impaired compared to that of VoGES, resulting in both cytosolic and plastidic localization. Geraniol production by VoGES and LdGES in N. benthamiana was nonetheless very similar. Expression of a truncated version of VoGES or LdGES (cytosolic targeting) resulted in the accumulation of 30% less geraniol glycosides than with the plastid targeted VoGES and LdGES, suggesting that the substrate geranyl diphosphate is readily available, both in the plastids as well as in the cytosol. The potential role of GES in the engineering of the TIA pathway in heterologous hosts is discussed. © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  9. In Planta Functional Analysis and Subcellular Localization of the Oomycete Pathogen Plasmopara viticola Candidate RXLR Effector Repertoire

    Directory of Open Access Journals (Sweden)

    Yunxiao Liu

    2018-04-01

    Full Text Available Downy mildew is one of the most destructive diseases of grapevine, causing tremendous economic loss in the grape and wine industry. The disease agent Plasmopara viticola is an obligate biotrophic oomycete, from which over 100 candidate RXLR effectors have been identified. In this study, 83 candidate RXLR effector genes (PvRXLRs were cloned from the P. viticola isolate “JL-7-2” genome. The results of the yeast signal sequence trap assay indicated that most of the candidate effectors are secretory proteins. The biological activities and subcellular localizations of all the 83 effectors were analyzed via a heterologous Agrobacterium-mediated Nicotiana benthamiana expression system. Results showed that 52 effectors could completely suppress cell death triggered by elicitin, 10 effectors could partially suppress cell death, 11 effectors were unable to suppress cell death, and 10 effectors themselves triggered cell death. Live-cell imaging showed that the majority of the effectors (76 of 83 could be observed with informative fluorescence signals in plant cells, among which 34 effectors were found to be targeted to both the nucleus and cytosol, 29 effectors were specifically localized in the nucleus, and 9 effectors were targeted to plant membrane system. Interestingly, three effectors PvRXLR61, 86 and 161 were targeted to chloroplasts, and one effector PvRXLR54 was dually targeted to chloroplasts and mitochondria. However, western blot analysis suggested that only PvRXLR86 carried a cleavable N-terminal transit peptide and underwent processing in planta. Many effectors have previously been predicted to target organelles, however, to the best of our knowledge, this is the first study to provide experimental evidence of oomycete effectors targeted to chloroplasts and mitochondria.

  10. Expression and subcellular localization of p70S6 kinase under heart failure

    Directory of Open Access Journals (Sweden)

    Usenko V. S.

    2010-11-01

    Full Text Available The PI3K/PDK/Akt/mTOR/p70S6K signaling pathway is primary associated with the activation of insulin receptors and is important for cardiomyocytes survival. p70S6K is a key regulator of the speed and efficiency of protein biosynthesis within the cell. Recently the pro-apoptotic protein BAD has been identified as a new target for р70S6K1. BAD is inactivated in normal cardiomyocytes by р70S6K1 phosphorylation which prevents the cardiomyocytes apoptosis. Aim. To study possible changes in р70S6K1 expression and/or cellular localization at heart failure progression – in DCM- affected human myocardia and murine hearts with experimental DCM-like pathology. Methods. Western-blot analysis and immunohystochemistry. Results. The substantial decrease in р70S6K1 level was observed at the final stage of pathology progression and in the dynamics of DCM pathogenesis as well. For the first time relocalization of the protein to the connective tissue was shown according to the Western-blot results. Conclusions. The data obtained allow us to understand a possible role of р70S6K1 in the regulation of stress-induced apoptotic signaling in cardiomyocytes.

  11. Subcellular localization of Patched and Smoothened, the receptors for Sonic hedgehog signaling, in the hippocampal neuron.

    Science.gov (United States)

    Petralia, Ronald S; Schwartz, Catherine M; Wang, Ya-Xian; Mattson, Mark P; Yao, Pamela J

    2011-12-15

    Cumulative evidence suggests that, aside from patterning the embryonic neural tube, Sonic hedgehog (Shh) signaling plays important roles in the mature nervous system. In this study, we investigate the expression and localization of the Shh signaling receptors, Patched (Ptch) and Smoothened (Smo), in the hippocampal neurons of young and mature rats. Reverse transcriptase-polymerase chain reaction and immunoblotting analyses show that the expression of Ptch and Smo remains at a moderate level in young postnatal and adult brains. By using immunofluorescence light microscopy and immunoelectron microscopy, we examine the spatial distribution of Ptch and Smo within the hippocampal neurons. In young developing neurons, Ptch and Smo are present in the processes and are clustered at their growth cones. In mature neurons, Ptch and Smo are concentrated in dendrites, spines, and postsynaptic sites. Synaptic Ptch and Smo often co-exist with unusual structures-synaptic spinules and autophagosomes. Our results reveal the anatomical organization of the Shh receptors within both the young and the mature hippocampal neurons. Copyright © 2011 Wiley-Liss, Inc.

  12. Subcellular Localization of Large Yellow Croaker ( Larimichthys crocea) TLR21 and Expression Profiling of Its Gene in Immune Response

    Science.gov (United States)

    Sun, Qingxue; Fan, Zejun; Yao, Cuiluan

    2018-04-01

    Toll-like receptor 21 (TLR21) is a non-mammalian type TLR, and plays an important role in innate immune response in fish. In this paper, the full-length cDNA sequence of TLR21 gene was identified and characterized from large yellow croaker, Larimichthys crocea and was termed as LcTLR21. It consists of 3365 bp, including a 5'-terminal untranslated region (UTR) of 97 bp, a 3'-terminal UTR of 331 bp, and an open reading frame (ORF) of 2937 bp encoding a polypeptide of 978 amino acid residues. The deduced LcTLR21 contains a signal peptide domain at N-terminal, 12 leucine-rich repeats (LRRs) at the extracellular region, a transmembrane domain and a cytoplasmic toll-interleukin-1 receptor (TIR) domain at the C-terminal. Subcellular localization analysis revealed that the LcTLR21-GFP was constitutively expressed in cytoplasm. Tissue expression analysis indicated that LcTLR21 gene broadly expressed in most of the examined tissues, with the most predominant abundance in spleen, followed by head-kidney and liver, while the weakest expression was detected in brain. The expression level of LcTLR21 after LPS, poly I:C and Vibrio parahaemolyticus challenges was investigated in spleen, head-kidney and liver. LcTLR21 gene transcripts increased significantly in all examined tissues after the challenges, and the highest expression level was detected in liver at 24 h after poly I:C stimulation ( P < 0.05), suggesting that LcTLR21 might play a crucial role in fish resistance to viral and bacterial infections.

  13. The influence of differential processing of procathepsin H on its aminopeptidase activity, secretion and subcellular localization in human cell lines.

    Science.gov (United States)

    Rojnik, Matija; Jevnikar, Zala R; Doljak, Bojan; Turk, Samo; Zidar, Nace; Kos, Janko

    2012-10-01

    Cathepsin H is a unique member of the cysteine cathepsins that acts primarily as an aminopeptidase. Like other cysteine cathepsins, it is synthesized as an inactive precursor and activated by proteolytic removal of its propeptide. Here we demonstrate that, in human cells, the processing of the propeptide is an autocatalytic, multistep process proceeding from an inactive 41kDa pro-form, through a 30kDa intermediate form, to the 28kDa mature form. Tyr87P and Gly90P were identified as the two major endopeptidase cleavage sites, converting the 30kDa form into the mature 28kDa form. The level of processing differs significantly in different human cell lines. In monocyte-derived macrophages U937 and prostate cancer cells PC-3, the 28kDa form is predominant, whereas in osteoblasts HOS the processing from the 30kDa form to the 28kDa form is significantly lower. The aminopeptidase activity of the enzyme and its subcellular localization are independent of the product, however the 30kDa form was not secreted in HOS cells. The activity of the resulting cathepsin H in U937 cells was significantly lower than that in HOS cells, presumably due to the high levels of endogenous cysteine protease inhibitor cystatin F present specifically in this cell line. These results provide an insight into the dependence of human cathepsin H processing and regulation on cell type. Copyright © 2012 Elsevier GmbH. All rights reserved.

  14. Cloning, characterization and sub-cellular localization of gamma subunit of T-complex protein-1 (chaperonin) from Leishmania donovani

    Energy Technology Data Exchange (ETDEWEB)

    Bhaskar,; Kumari, Neeti [Division of Biochemistry, CSIR-Central Drug Research Institute, Chattar Manzil Palace, PO Box 173, Lucknow (India); Goyal, Neena, E-mail: neenacdri@yahoo.com [Division of Biochemistry, CSIR-Central Drug Research Institute, Chattar Manzil Palace, PO Box 173, Lucknow (India)

    2012-12-07

    Highlights: Black-Right-Pointing-Pointer The study presents cloning and characterization of TCP1{gamma} gene from L. donovani. Black-Right-Pointing-Pointer TCP1{gamma} is a subunit of T-complex protein-1 (TCP1), a chaperonin class of protein. Black-Right-Pointing-Pointer LdTCP{gamma} exhibited differential expression in different stages of promastigotes. Black-Right-Pointing-Pointer LdTCP{gamma} co-localized with actin, a cytoskeleton protein. Black-Right-Pointing-Pointer The data suggests that this gene may have a role in differentiation/biogenesis. Black-Right-Pointing-Pointer First report on this chapronin in Leishmania. -- Abstract: T-complex protein-1 (TCP1) complex, a chaperonin class of protein, ubiquitous in all genera of life, is involved in intracellular assembly and folding of various proteins. The gamma subunit of TCP1 complex (TCP1{gamma}), plays a pivotal role in the folding and assembly of cytoskeleton protein(s) as an individual or complexed with other subunits. Here, we report for the first time cloning, characterization and expression of the TCP1{gamma} of Leishmania donovani (LdTCP1{gamma}), the causative agent of Indian Kala-azar. Primary sequence analysis of LdTCP1{gamma} revealed the presence of all the characteristic features of TCP1{gamma}. However, leishmanial TCP1{gamma} represents a distinct kinetoplastid group, clustered in a separate branch of the phylogenic tree. LdTCP1{gamma} exhibited differential expression in different stages of promastigotes. The non-dividing stationary phase promastigotes exhibited 2.5-fold less expression of LdTCP1{gamma} as compared to rapidly dividing log phase parasites. The sub-cellular distribution of LdTCP1{gamma} was studied in log phase promastigotes by employing indirect immunofluorescence microscopy. The protein was present not only in cytoplasm but it was also localized in nucleus, peri-nuclear region, flagella, flagellar pocket and apical region. Co-localization of LdTCP1{gamma} with actin suggests

  15. Role of aldo-keto reductases and other doxorubicin pharmacokinetic genes in doxorubicin resistance, DNA binding, and subcellular localization

    International Nuclear Information System (INIS)

    Heibein, Allan D; Guo, Baoqing; Sprowl, Jason A; MacLean, David A; Parissenti, Amadeo M

    2012-01-01

    highly relevant genes associated with doxorubicin resistance. The induction of one or more of these genes was found to be correlated with changes in the drug’s properties, while inhibiting one specific class of these genes (the AKRs) increased cellular doxorubicin content and restored drug DNA binding, cytotoxicity, and subcellular localization

  16. Cloning, characterization and sub-cellular localization of gamma subunit of T-complex protein-1 (chaperonin) from Leishmania donovani

    International Nuclear Information System (INIS)

    Bhaskar,; Kumari, Neeti; Goyal, Neena

    2012-01-01

    Highlights: ► The study presents cloning and characterization of TCP1γ gene from L. donovani. ► TCP1γ is a subunit of T-complex protein-1 (TCP1), a chaperonin class of protein. ► LdTCPγ exhibited differential expression in different stages of promastigotes. ► LdTCPγ co-localized with actin, a cytoskeleton protein. ► The data suggests that this gene may have a role in differentiation/biogenesis. ► First report on this chapronin in Leishmania. -- Abstract: T-complex protein-1 (TCP1) complex, a chaperonin class of protein, ubiquitous in all genera of life, is involved in intracellular assembly and folding of various proteins. The gamma subunit of TCP1 complex (TCP1γ), plays a pivotal role in the folding and assembly of cytoskeleton protein(s) as an individual or complexed with other subunits. Here, we report for the first time cloning, characterization and expression of the TCP1γ of Leishmania donovani (LdTCP1γ), the causative agent of Indian Kala-azar. Primary sequence analysis of LdTCP1γ revealed the presence of all the characteristic features of TCP1γ. However, leishmanial TCP1γ represents a distinct kinetoplastid group, clustered in a separate branch of the phylogenic tree. LdTCP1γ exhibited differential expression in different stages of promastigotes. The non-dividing stationary phase promastigotes exhibited 2.5-fold less expression of LdTCP1γ as compared to rapidly dividing log phase parasites. The sub-cellular distribution of LdTCP1γ was studied in log phase promastigotes by employing indirect immunofluorescence microscopy. The protein was present not only in cytoplasm but it was also localized in nucleus, peri-nuclear region, flagella, flagellar pocket and apical region. Co-localization of LdTCP1γ with actin suggests that, this gene may have a role in maintaining the structural dynamics of cytoskeleton of parasite.

  17. Structure, kinetic characterization and subcellular localization of the two ribulose 5-phosphate epimerase isoenzymes from Trypanosoma cruzi.

    Directory of Open Access Journals (Sweden)

    Soledad Natalia Gonzalez

    Full Text Available The enzyme of the pentose phosphate pathway (PPP ribulose-5-phosphate-epimerase (RPE is encoded by two genes present in the genome of Trypanosoma cruzi CL Brener clone: TcRPE1 and TcRPE2. Despite high sequence similarity at the amino acid residue level, the recombinant isoenzymes show a strikingly different kinetics. Whereas TcRPE2 follows a typical michaelian behavior, TcRPE1 shows a complex kinetic pattern, displaying a biphasic curve, suggesting the coexistence of -at least- two kinetically different molecular forms. Regarding the subcellular localization in epimastigotes, whereas TcRPE1 is a cytosolic enzyme, TcRPE2 is localized in glycosomes. To our knowledge, TcRPE2 is the first PPP isoenzyme that is exclusively localized in glycosomes. Over-expression of TcRPE1, but not of TcRPE2, significantly reduces the parasite doubling time in vitro, as compared with wild type epimastigotes. Both TcRPEs represent single domain proteins exhibiting the classical α/β TIM-barrel fold, as expected for enzymes with this activity. With regard to the architecture of the active site, all the important amino acid residues for catalysis -with the exception of M58- are also present in both TcRPEs models. The superimposition of the binding pocket of both isoenzyme models shows that they adopt essentially identical positions in the active site with a residue specific RMSD < 2Å, with the sole exception of S12, which displays a large deviation (residue specific RMSD: 11.07 Å. Studies on the quaternary arrangement of these isoenzymes reveal that both are present in a mixture of various oligomeric species made up of an even number of molecules, probably pointing to the dimer as their minimal functional unit. This multiplicity of oligomeric species has not been reported for any of the other RPEs studied so far and it might bear implications for the regulation of TcRPEs activity, although further investigation will be necessary to unravel the physiological

  18. pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information.

    Science.gov (United States)

    Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen

    2018-05-01

    For in-depth understanding the functions of proteins in a cell, the knowledge of their subcellular localization is indispensable. The current study is focused on human protein subcellular location prediction based on the sequence information alone. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions that are particularly important for both basic research and drug design. Using the multi-label theory, we present a new predictor called 'pLoc-mHum' by extracting the crucial GO (Gene Ontology) information into the general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validations on a same stringent benchmark dataset have indicated that the proposed pLoc-mHum predictor is remarkably superior to iLoc-Hum, the state-of-the-art method in predicting the human protein subcellular localization. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mHum/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. xcheng@gordonlifescience.org. Supplementary data are available at Bioinformatics online.

  19. Subcellular localization analysis of the closely related Fps/Fes and Fer protein-tyrosine kinases suggests a distinct role for Fps/Fes in vesicular trafficking.

    Science.gov (United States)

    Zirngibl, R; Schulze, D; Mirski, S E; Cole, S P; Greer, P A

    2001-05-15

    The subcellular localizations of the Fps/Fes and closely related Fer cytoplasmic tyrosine kinases were studied using green fluorescent protein (GFP) fusions and confocal fluorescence microscopy. In contrast to previous reports, neither kinase localized to the nucleus. Fer was diffusely cytoplasmic throughout the cell cycle. Fps/Fes also displayed a diffuse cytoplasmic localization, but in addition it showed distinct accumulations in cytoplasmic vesicles as well as in a perinuclear region consistent with the Golgi. This localization was very similar to that of TGN38, a known marker of the trans Golgi. The localization of Fps/Fes and TGN38 were both perturbed by brefeldin A, a fungal metabolite that disrupts the Golgi apparatus. Fps/Fes was also found to colocalize to various extents with several Rab proteins, which are members of the monomeric G-protein superfamily involved in vesicular transport between specific subcellular compartments. Using Rabs that are involved in endocytosis (Rab5B and Rab7) or exocytosis (Rab1A and Rab3A), we showed that Fps/Fes is localized in both pathways. These results suggest that Fps/Fes may play a general role in the regulation of vesicular trafficking. Copyright 2001 Academic Press.

  20. Transcriptional Analysis and Subcellular Protein Localization Reveal Specific Features of the Essential WalKR System in Staphylococcus aureus.

    Directory of Open Access Journals (Sweden)

    Olivier Poupel

    Full Text Available The WalKR two-component system, controlling cell wall metabolism, is highly conserved among Bacilli and essential for cell viability. In Staphylococcus aureus, walR and walK are followed by three genes of unknown function: walH, walI and walJ. Sequence analysis and transcript mapping revealed a unique genetic structure for this locus in S. aureus: the last gene of the locus, walJ, is transcribed independently, whereas transcription of the tetra-cistronic walRKHI operon occurred from two independent promoters located upstream from walR. Protein topology analysis and protein-protein interactions in E. coli as well as subcellular localization in S. aureus allowed us to show that WalH and WalI are membrane-bound proteins, which associate with WalK to form a complex at the cell division septum. While these interactions suggest that WalH and WalI play a role in activity of the WalKR regulatory pathway, deletion of walH and/or walI did not have a major effect on genes whose expression is strongly dependent on WalKR or on associated phenotypes. No effect of WalH or WalI was seen on tightly controlled WalKR regulon genes such as sle1 or saouhsc_00773, which encodes a CHAP-domain amidase. Of the genes encoding the two major S. aureus autolysins, AtlA and Sle1, only transcription of atlA was increased in the ΔwalH or ΔwalI mutants. Likewise, bacterial autolysis was not increased in the absence of WalH and/or WalI and biofilm formation was lowered rather than increased. Our results suggest that contrary to their major role as WalK inhibitors in B. subtilis, the WalH and WalI proteins have evolved a different function in S. aureus, where they are more accessory. A phylogenomic analysis shows a striking conservation of the 5 gene wal cluster along the evolutionary history of Bacilli, supporting the key importance of this signal transduction system, and indicating that the walH and walI genes were lost in the ancestor of Streptococcaceae, leading to their

  1. Transcriptional Analysis and Subcellular Protein Localization Reveal Specific Features of the Essential WalKR System in Staphylococcus aureus.

    Science.gov (United States)

    Poupel, Olivier; Moyat, Mati; Groizeleau, Julie; Antunes, Luísa C S; Gribaldo, Simonetta; Msadek, Tarek; Dubrac, Sarah

    2016-01-01

    The WalKR two-component system, controlling cell wall metabolism, is highly conserved among Bacilli and essential for cell viability. In Staphylococcus aureus, walR and walK are followed by three genes of unknown function: walH, walI and walJ. Sequence analysis and transcript mapping revealed a unique genetic structure for this locus in S. aureus: the last gene of the locus, walJ, is transcribed independently, whereas transcription of the tetra-cistronic walRKHI operon occurred from two independent promoters located upstream from walR. Protein topology analysis and protein-protein interactions in E. coli as well as subcellular localization in S. aureus allowed us to show that WalH and WalI are membrane-bound proteins, which associate with WalK to form a complex at the cell division septum. While these interactions suggest that WalH and WalI play a role in activity of the WalKR regulatory pathway, deletion of walH and/or walI did not have a major effect on genes whose expression is strongly dependent on WalKR or on associated phenotypes. No effect of WalH or WalI was seen on tightly controlled WalKR regulon genes such as sle1 or saouhsc_00773, which encodes a CHAP-domain amidase. Of the genes encoding the two major S. aureus autolysins, AtlA and Sle1, only transcription of atlA was increased in the ΔwalH or ΔwalI mutants. Likewise, bacterial autolysis was not increased in the absence of WalH and/or WalI and biofilm formation was lowered rather than increased. Our results suggest that contrary to their major role as WalK inhibitors in B. subtilis, the WalH and WalI proteins have evolved a different function in S. aureus, where they are more accessory. A phylogenomic analysis shows a striking conservation of the 5 gene wal cluster along the evolutionary history of Bacilli, supporting the key importance of this signal transduction system, and indicating that the walH and walI genes were lost in the ancestor of Streptococcaceae, leading to their atypical 3 wal gene

  2. Immunohistochemical analysis based Ep-ICD subcellular localization index (ESLI) is a novel marker for metastatic papillary thyroid microcarcinoma

    International Nuclear Information System (INIS)

    Kunavisarut, Tada; Kak, Ipshita; MacMillan, Christina; Ralhan, Ranju; Walfish, Paul G

    2012-01-01

    Thyroid cancer is among the fastest growing malignancies; almost fifty-percent of these rapidly increasing incidence tumors are less than or equal to 1cm in size, termed papillary thyroid microcarcinoma (PTMC). The management of PTMC remains a controversy due to differing natural history of these patients. Epithelial cell adhesion molecule (EpCAM) is comprised of an extracellular domain (EpEx), a single transmembrane domain and an intracellular domain (Ep-ICD). Our group reported nuclear Ep-ICD correlated with poor prognosis in thyroid cancer (Ralhan et al., BMC Cancer 2010,10:331). Here in, we hypothesized nuclear and cytoplasmic accumulation of Ep-ICD and loss of membranous EpEx may aid in distinguishing metastatic from non-metastatic PTMC, which is an important current clinical challenge. To test our hypothesis, Ep-ICD and EpEx expression levels were analyzed in PTMC and the staining was correlated with metastatic potential of these carcinomas. Thirty-six PTMC patients (tumor size 0.5 - 1cm; metastatic 8 cases and non-metastatic 28 cases) who underwent total thyroidectomy were selected. The metastatic group consisted of patients who developed lymph node or distant metastasis at diagnosis or during follow up. The patients’ tissues were stained for Ep-ICD and EpEx using domain specific antibodies by immunohistochemistry and evaluated. PTMC patients with metastasis had higher scores for nuclear and cytoplasmic Ep-ICD immunostaining than the patients without metastasis (1.96 ± 0.86 vs. 1.22 ± 0.45; p = 0.007 and 5.37 ± 0.33 vs. 4.72 ± 1.07; p = 0.016, respectively). Concomitantly, the former had lower scores for membrane EpEx than the non-metastatic group (4.64 ± 1.08 vs. 5.64 ± 1.51; p = 0.026). An index of aggressiveness, Ep-ICD subcellular localization index (ESLI), was defined as sum of the IHC scores for accumulation of nuclear and cytoplasmic Ep-ICD and loss of membranous EpEx; ESLI = [Ep − ICD nuc + Ep − ICD cyt + loss of membranous EpEx]. Notably

  3. pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC.

    Science.gov (United States)

    Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen

    2017-09-10

    Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions. This kind of multiplex proteins is particularly important for both basic research and drug design. Using the multi-label theory, we present a new predictor called "pLoc-mVirus" by extracting the optimal GO (Gene Ontology) information into the general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validation on a same stringent benchmark dataset indicated that the proposed pLoc-mVirus predictor is remarkably superior to iLoc-Virus, the state-of-the-art method in predicting virus protein subcellular localization. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mVirus/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. pLoc-mPlant: predict subcellular localization of multi-location plant proteins by incorporating the optimal GO information into general PseAAC.

    Science.gov (United States)

    Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen

    2017-08-22

    One of the fundamental goals in cellular biochemistry is to identify the functions of proteins in the context of compartments that organize them in the cellular environment. To realize this, it is indispensable to develop an automated method for fast and accurate identification of the subcellular locations of uncharacterized proteins. The current study is focused on plant protein subcellular location prediction based on the sequence information alone. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most of the existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions. This kind of multiplex protein is particularly important for both basic research and drug design. Using the multi-label theory, we present a new predictor called "pLoc-mPlant" by extracting the optimal GO (Gene Ontology) information into the Chou's general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validation on the same stringent benchmark dataset indicated that the proposed pLoc-mPlant predictor is remarkably superior to iLoc-Plant, the state-of-the-art method for predicting plant protein subcellular localization. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at , by which users can easily get their desired results without the need to go through the complicated mathematics involved.

  5. Interferon-inducible p200-family protein IFI16, an innate immune sensor for cytosolic and nuclear double-stranded DNA: regulation of subcellular localization.

    Science.gov (United States)

    Veeranki, Sudhakar; Choubey, Divaker

    2012-01-01

    The interferon (IFN)-inducible p200-protein family includes structurally related murine (for example, p202a, p202b, p204, and Aim2) and human (for example, AIM2 and IFI16) proteins. All proteins in the family share a partially conserved repeat of 200-amino acid residues (also called HIN-200 domain) in the C-terminus. Additionally, most proteins (except the p202a and p202b proteins) also share a protein-protein interaction pyrin domain (PYD) in the N-terminus. The HIN-200 domain contains two consecutive oligosaccharide/oligonucleotide binding folds (OB-folds) to bind double stranded DNA (dsDNA). The PYD domain in proteins allows interactions with the family members and an adaptor protein ASC. Upon sensing cytosolic dsDNA, Aim2, p204, and AIM2 proteins recruit ASC protein to form an inflammasome, resulting in increased production of proinflammatory cytokines. However, IFI16 protein can sense cytosolic as well as nuclear dsDNA. Interestingly, the IFI16 protein contains a nuclear localization signal (NLS). Accordingly, the initial studies had indicated that the endogenous IFI16 protein is detected in the nucleus and within the nucleus in the nucleolus. However, several recent reports suggest that subcellular localization of IFI16 protein in nuclear versus cytoplasmic (or both) compartment depends on cell type. Given that the IFI16 protein can sense cytosolic as well as nuclear dsDNA and can initiate different innate immune responses (production of IFN-β versus proinflammatory cytokines), here we evaluate the experimental evidence for the regulation of subcellular localization of IFI16 protein in various cell types. We conclude that further studies are needed to understand the molecular mechanisms that regulate the subcellular localization of IFI16 protein. Published by Elsevier Ltd.

  6. Electron localization in one-dimensional systems

    International Nuclear Information System (INIS)

    Chao, K.A.

    1984-01-01

    The pure regional localization and the global localization have been investigated via the inverse participation ratio and te moment analysis. If the envelop function of a localized state is more complicated than the simple exponential function e sup(-r/xi), the inverse participation ratio is inadequate to describe the localization properties of an electron. This is the case discovered recently in a stereo-irregular chain fo atoms including the electron-electron interaction and the structure disorder. The localization properties in this system are analysed in terms of the moments. (Author) [pt

  7. Role of NH2-terminal hydrophobic motif in the subcellular localization of ATP-binding cassette protein subfamily D: Common features in eukaryotic organisms

    International Nuclear Information System (INIS)

    Lee, Asaka; Asahina, Kota; Okamoto, Takumi; Kawaguchi, Kosuke; Kostsin, Dzmitry G.; Kashiwayama, Yoshinori; Takanashi, Kojiro; Yazaki, Kazufumi; Imanaka, Tsuneo; Morita, Masashi

    2014-01-01

    Highlights: • ABCD proteins classifies based on with or without NH 2 -terminal hydrophobic segment. • The ABCD proteins with the segment are targeted peroxisomes. • The ABCD proteins without the segment are targeted to the endoplasmic reticulum. • The role of the segment in organelle targeting is conserved in eukaryotic organisms. - Abstract: In mammals, four ATP-binding cassette (ABC) proteins belonging to subfamily D have been identified. ABCD1–3 possesses the NH 2 -terminal hydrophobic region and are targeted to peroxisomes, while ABCD4 lacking the region is targeted to the endoplasmic reticulum (ER). Based on hydropathy plot analysis, we found that several eukaryotes have ABCD protein homologs lacking the NH 2 -terminal hydrophobic segment (H0 motif). To investigate whether the role of the NH 2 -terminal H0 motif in subcellular localization is conserved across species, we expressed ABCD proteins from several species (metazoan, plant and fungi) in fusion with GFP in CHO cells and examined their subcellular localization. ABCD proteins possessing the NH 2 -terminal H0 motif were localized to peroxisomes, while ABCD proteins lacking this region lost this capacity. In addition, the deletion of the NH 2 -terminal H0 motif of ABCD protein resulted in their localization to the ER. These results suggest that the role of the NH 2 -terminal H0 motif in organelle targeting is widely conserved in living organisms

  8. Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features.

    Science.gov (United States)

    Zhou, Hang; Yang, Yang; Shen, Hong-Bin

    2017-03-15

    Protein subcellular localization prediction has been an important research topic in computational biology over the last decade. Various automatic methods have been proposed to predict locations for large scale protein datasets, where statistical machine learning algorithms are widely used for model construction. A key step in these predictors is encoding the amino acid sequences into feature vectors. Many studies have shown that features extracted from biological domains, such as gene ontology and functional domains, can be very useful for improving the prediction accuracy. However, domain knowledge usually results in redundant features and high-dimensional feature spaces, which may degenerate the performance of machine learning models. In this paper, we propose a new amino acid sequence-based human protein subcellular location prediction approach Hum-mPLoc 3.0, which covers 12 human subcellular localizations. The sequences are represented by multi-view complementary features, i.e. context vocabulary annotation-based gene ontology (GO) terms, peptide-based functional domains, and residue-based statistical features. To systematically reflect the structural hierarchy of the domain knowledge bases, we propose a novel feature representation protocol denoted as HCM (Hidden Correlation Modeling), which will create more compact and discriminative feature vectors by modeling the hidden correlations between annotation terms. Experimental results on four benchmark datasets show that HCM improves prediction accuracy by 5-11% and F 1 by 8-19% compared with conventional GO-based methods. A large-scale application of Hum-mPLoc 3.0 on the whole human proteome reveals proteins co-localization preferences in the cell. www.csbio.sjtu.edu.cn/bioinf/Hum-mPLoc3/. hbshen@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  9. Multi-location gram-positive and gram-negative bacterial protein subcellular localization using gene ontology and multi-label classifier ensemble.

    Science.gov (United States)

    Wang, Xiao; Zhang, Jun; Li, Guo-Zheng

    2015-01-01

    It has become a very important and full of challenge task to predict bacterial protein subcellular locations using computational methods. Although there exist a lot of prediction methods for bacterial proteins, the majority of these methods can only deal with single-location proteins. But unfortunately many multi-location proteins are located in the bacterial cells. Moreover, multi-location proteins have special biological functions capable of helping the development of new drugs. So it is necessary to develop new computational methods for accurately predicting subcellular locations of multi-location bacterial proteins. In this article, two efficient multi-label predictors, Gpos-ECC-mPLoc and Gneg-ECC-mPLoc, are developed to predict the subcellular locations of multi-label gram-positive and gram-negative bacterial proteins respectively. The two multi-label predictors construct the GO vectors by using the GO terms of homologous proteins of query proteins and then adopt a powerful multi-label ensemble classifier to make the final multi-label prediction. The two multi-label predictors have the following advantages: (1) they improve the prediction performance of multi-label proteins by taking the correlations among different labels into account; (2) they ensemble multiple CC classifiers and further generate better prediction results by ensemble learning; and (3) they construct the GO vectors by using the frequency of occurrences of GO terms in the typical homologous set instead of using 0/1 values. Experimental results show that Gpos-ECC-mPLoc and Gneg-ECC-mPLoc can efficiently predict the subcellular locations of multi-label gram-positive and gram-negative bacterial proteins respectively. Gpos-ECC-mPLoc and Gneg-ECC-mPLoc can efficiently improve prediction accuracy of subcellular localization of multi-location gram-positive and gram-negative bacterial proteins respectively. The online web servers for Gpos-ECC-mPLoc and Gneg-ECC-mPLoc predictors are freely accessible

  10. mPLR-Loc: an adaptive decision multi-label classifier based on penalized logistic regression for protein subcellular localization prediction.

    Science.gov (United States)

    Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

    2015-03-15

    Proteins located in appropriate cellular compartments are of paramount importance to exert their biological functions. Prediction of protein subcellular localization by computational methods is required in the post-genomic era. Recent studies have been focusing on predicting not only single-location proteins but also multi-location proteins. However, most of the existing predictors are far from effective for tackling the challenges of multi-label proteins. This article proposes an efficient multi-label predictor, namely mPLR-Loc, based on penalized logistic regression and adaptive decisions for predicting both single- and multi-location proteins. Specifically, for each query protein, mPLR-Loc exploits the information from the Gene Ontology (GO) database by using its accession number (AC) or the ACs of its homologs obtained via BLAST. The frequencies of GO occurrences are used to construct feature vectors, which are then classified by an adaptive decision-based multi-label penalized logistic regression classifier. Experimental results based on two recent stringent benchmark datasets (virus and plant) show that mPLR-Loc remarkably outperforms existing state-of-the-art multi-label predictors. In addition to being able to rapidly and accurately predict subcellular localization of single- and multi-label proteins, mPLR-Loc can also provide probabilistic confidence scores for the prediction decisions. For readers' convenience, the mPLR-Loc server is available online (http://bioinfo.eie.polyu.edu.hk/mPLRLocServer). Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Imaging of Caenorhabditis elegans samples and sub-cellular localization of new generation photosensitizers for photodynamic therapy, using non-linear microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Filippidis, G [Institute of Electronic Structure and Laser, Foundation of Research and Technology-Hellas, PO Box 1527, 71110 Heraklion (Greece); Kouloumentas, C [Institute of Electronic Structure and Laser, Foundation of Research and Technology-Hellas, PO Box 1527, 71110 Heraklion (Greece); Kapsokalyvas, D [Institute of Electronic Structure and Laser, Foundation of Research and Technology-Hellas, PO Box 1527, 71110 Heraklion (Greece); Voglis, G [Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, Heraklion 71110, Crete (Greece); Tavernarakis, N [Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, Heraklion 71110, Crete (Greece); Papazoglou, T G [Institute of Electronic Structure and Laser, Foundation of Research and Technology-Hellas, PO Box 1527, 71110 Heraklion (Greece)

    2005-08-07

    Two-photon excitation fluorescence (TPEF) and second-harmonic generation (SHG) are relatively new promising tools for the imaging and mapping of biological structures and processes at the microscopic level. The combination of the two image-contrast modes in a single instrument can provide unique and complementary information concerning the structure and the function of tissues and individual cells. The extended application of this novel, innovative technique by the biological community is limited due to the high price of commercial multiphoton microscopes. In this study, a compact, inexpensive and reliable setup utilizing femtosecond pulses for excitation was developed for the TPEF and SHG imaging of biological samples. Specific cell types of the nematode Caenorhabditis elegans were imaged. Detection of the endogenous structural proteins of the worm, which are responsible for observation of SHG signals, was achieved. Additionally, the binding of different photosensitizers in the HL-60 cell line was investigated, using non-linear microscopy. The sub-cellular localization of photosensitizers of a new generation, very promising for photodynamic therapy (PDT) (Hypericum perforatum L. extracts) was achieved. The sub-cellular localization of these novel photosensitizers was linked with their photodynamic action during PDT, and the possible mechanisms for cell killing have been elucidated.

  12. How do electron localization functions describe π-electron delocalization?

    Science.gov (United States)

    Steinmann, Stephan N; Mo, Yirong; Corminboeuf, Clemence

    2011-12-14

    Scalar fields provide an intuitive picture of chemical bonding. In particular, the electron localization function (ELF) has proven to be highly valuable in interpreting a broad range of bonding patterns. The discrimination between enhanced or reduced electron (de)localization within cyclic π-conjugated systems remains, however, challenging for ELF. In order to clearly distinguish between the local properties of ten highly and weakly π-(de)localized prototype systems, we compare the ELFs of both the canonical wave functions and electron-localized states (diabatic) with those of two closely related scalar fields: the electron localizability indicator (ELI-D) and the localized orbital locator (LOL). The simplest LOL function distinguishes enhanced from weak π-(de)localization in an insightful and reliable manner. LOL offers the finest contrast between annulenes with 4n/4n + 2 π electrons and their inorganic analogues as well as between hyperconjugated cyclopentadiene derivatives. LOL(π) also gives an appealing and intuitive picture of the π-bond. In contrast, the most popular ELF fails to capture subtle contrasting local electronic properties and suffers from the arbitrariness of the σ/π dissection. The orbital separation of the most recent ELI-D is clear-cut but the interpretations sometime less straightforward in the present context.

  13. Analytical local electron-electron interaction model potentials for atoms

    International Nuclear Information System (INIS)

    Neugebauer, Johannes; Reiher, Markus; Hinze, Juergen

    2002-01-01

    Analytical local potentials for modeling the electron-electron interaction in an atom reduce significantly the computational effort in electronic structure calculations. The development of such potentials has a long history, but some promising ideas have not yet been taken into account for further improvements. We determine a local electron-electron interaction potential akin to those suggested by Green et al. [Phys. Rev. 184, 1 (1969)], which are widely used in atom-ion scattering calculations, electron-capture processes, and electronic structure calculations. Generalized Yukawa-type model potentials are introduced. This leads, however, to shell-dependent local potentials, because the origin behavior of such potentials is different for different shells as has been explicated analytically [J. Neugebauer, M. Reiher, and J. Hinze, Phys. Rev. A 65, 032518 (2002)]. It is found that the parameters that characterize these local potentials can be interpolated and extrapolated reliably for different nuclear charges and different numbers of electrons. The analytical behavior of the corresponding localized Hartree-Fock potentials at the origin and at long distances is utilized in order to reduce the number of fit parameters. It turns out that the shell-dependent form of Green's potential, which we also derive, yields results of comparable accuracy using only one shell-dependent parameter

  14. Primary structure and subcellular localization of two fimbrial subunit-like proteins involved in the biosynthesis of K99 fibrillae.

    Science.gov (United States)

    Roosendaal, E; Jacobs, A A; Rathman, P; Sondermeyer, C; Stegehuis, F; Oudega, B; de Graaf, F K

    1987-09-01

    Analysis of the nucleotide sequence of the distal part of the fan gene cluster encoding the proteins involved in the biosynthesis of the fibrillar adhesin, K99, revealed the presence of two structural genes, fanG and fanH. The amino acid sequence of the gene products (FanG and FanH) showed significant homology to the amino acid sequence of the fibrillar subunit protein (FanC). Introduction of a site-specific frameshift mutation in fanG or fanH resulted in a simultaneous decrease in fibrillae production and adhesive capacity. Analysis of subcellular fractions showed that, in contrast to the K99 fibrillar subunit (FanC), both the FanH and the FanG protein were loosely associated with the outer membrane, possibly on the periplasmic side, but were not components of the fimbriae themselves.

  15. Quantitative and subcellular localization analysis of the nuclear isoform dUTP pyrophosphatase in alkylating agent-induced cell responses

    International Nuclear Information System (INIS)

    Hu, Xiaolan; Yu, Yingnian; Li, Qian; Wu, Danxiao; Tan, Zhengning; Wang, Cheng; Wang, Jvping; Wu, Meiping

    2011-01-01

    Highlights: → MNNG-induced appearance of DUT-N in the extracellular fluid has cellular specificity. → MNNG alters the subcellular distribution of DUT-N in human cells in different ways. → DUT-N may be a potential biomarker to assess the risk of alkylating agents exposure. -- Abstract: Our previous proteome analysis showed that the nuclear isoform of dUTP pyrophosphatase (DUT-N) was identified in the culture medium of human amnion FL cells after exposure to the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). These results suggest that DUT-N may be a potential early biomarker to assess the risk of alkylating agents exposure. DUT-N is one of the two isoforms of deoxyuridine triphosphate nucleotidohydrolase (dUTPase). Our current knowledge of DUT-N expression in human cells is very limited. In the current study, we first investigated the appearance of DUT-N in the culture medium of different human cell lines in response to a low concentration of MNNG exposure. We verified that the MNNG-induced appearance of DUT-N in the extracellular environment is cell-specific. Western blot analysis confirmed that the intracellular DUT-N changes responded to MNNG in a concentration-dependent and cell-specific manner. Furthermore, subcellular fraction experiments showed that 0.25 μM MNNG treatment dramatically increased the DUT-N expression levels in the cytoplasmic extracts prepared from both FL and HepG2 cells, increased DUT-N levels in nuclear extracts prepared from HepG2 cells, and decreased DUT-N levels in nuclear extracts from FL cells. Morphological studies using immunofluorescence showed that a low concentration of MNNG could alter the distribution of DUT-N in FL and HepG2 cells in different ways. Taken together, these studies indicate a role of DUT-N in alkylating agent-induced cell responses.

  16. Interaction of HSP20 with a viral RdRp changes its sub-cellular localization and distribution pattern in plants.

    Science.gov (United States)

    Li, Jing; Xiang, Cong-Ying; Yang, Jian; Chen, Jian-Ping; Zhang, Heng-Mu

    2015-09-11

    Small heat shock proteins (sHSPs) perform a fundamental role in protecting cells against a wide array of stresses but their biological function during viral infection remains unknown. Rice stripe virus (RSV) causes a severe disease of rice in Eastern Asia. OsHSP20 and its homologue (NbHSP20) were used as baits in yeast two-hybrid (YTH) assays to screen an RSV cDNA library and were found to interact with the viral RNA-dependent RNA polymerase (RdRp) of RSV. Interactions were confirmed by pull-down and BiFC assays. Further analysis showed that the N-terminus (residues 1-296) of the RdRp was crucial for the interaction between the HSP20s and viral RdRp and responsible for the alteration of the sub-cellular localization and distribution pattern of HSP20s in protoplasts of rice and epidermal cells of Nicotiana benthamiana. This is the first report that a plant virus or a viral protein alters the expression pattern or sub-cellular distribution of sHSPs.

  17. Imbalanced multi-modal multi-label learning for subcellular localization prediction of human proteins with both single and multiple sites.

    Directory of Open Access Journals (Sweden)

    Jianjun He

    Full Text Available It is well known that an important step toward understanding the functions of a protein is to determine its subcellular location. Although numerous prediction algorithms have been developed, most of them typically focused on the proteins with only one location. In recent years, researchers have begun to pay attention to the subcellular localization prediction of the proteins with multiple sites. However, almost all the existing approaches have failed to take into account the correlations among the locations caused by the proteins with multiple sites, which may be the important information for improving the prediction accuracy of the proteins with multiple sites. In this paper, a new algorithm which can effectively exploit the correlations among the locations is proposed by using gaussian process model. Besides, the algorithm also can realize optimal linear combination of various feature extraction technologies and could be robust to the imbalanced data set. Experimental results on a human protein data set show that the proposed algorithm is valid and can achieve better performance than the existing approaches.

  18. Monoterpene biosynthesis potential of plant subcellular compartments

    NARCIS (Netherlands)

    Dong, L.; Jongedijk, E.J.; Bouwmeester, H.J.; Krol, van der A.R.

    2016-01-01

    Subcellular monoterpene biosynthesis capacity based on local geranyl diphosphate (GDP) availability or locally boosted GDP production was determined for plastids, cytosol and mitochondria. A geraniol synthase (GES) was targeted to plastids, cytosol, or mitochondria. Transient expression in Nicotiana

  19. Establishing the subcellular localization of photodynamically-induced ROS using 3,3′-diaminobenzidine: A methodological proposal, with a proof-of-concept demonstration

    DEFF Research Database (Denmark)

    Stockert, Juan Carlos; Blazquez-Castro, Alfonso

    2016-01-01

    The critical involvement of reactive oxygen species (ROS) in both physiological and pathological processes in cell biology makes their detection and assessment a fundamental topic in biomedical research. Established methodologies to study ROS in cell biology take advantage of oxidation reactions...... is proved in a photodynamic model of ROS generation, the principle is applicable to many different scenarios of intracellular ROS production. As a consequence this proposed methodology should greatly complement other techniques aiming at establishing a precise subcellular localization of ROS generation....... between the ROS and a reduced probe. After reacting the probe reveals the presence of ROS either by the appearance of colour (chromogenic reaction) or fluorescence (fluorogenic reaction). However current methodologies rarely allow for a site-specific detection of ROS production. Here we propose...

  20. Cell- and virus-mediated regulation of the barrier-to-autointegration factor's phosphorylation state controls its DNA binding, dimerization, subcellular localization, and antipoxviral activity.

    Science.gov (United States)

    Jamin, Augusta; Wicklund, April; Wiebe, Matthew S

    2014-05-01

    Barrier-to-autointegration factor (BAF) is a DNA binding protein with multiple cellular functions, including the ability to act as a potent defense against vaccinia virus infection. This antiviral function involves BAF's ability to condense double-stranded DNA and subsequently prevent viral DNA replication. In recent years, it has become increasingly evident that dynamic phosphorylation involving the vaccinia virus B1 kinase and cellular enzymes is likely a key regulator of multiple BAF functions; however, the precise mechanisms are poorly understood. Here we analyzed how phosphorylation impacts BAF's DNA binding, subcellular localization, dimerization, and antipoxviral activity through the characterization of BAF phosphomimetic and unphosphorylatable mutants. Our studies demonstrate that increased phosphorylation enhances BAF's mobilization from the nucleus to the cytosol, while dephosphorylation restricts BAF to the nucleus. Phosphorylation also impairs both BAF's dimerization and its DNA binding activity. Furthermore, our studies of BAF's antiviral activity revealed that hyperphosphorylated BAF is unable to suppress viral DNA replication or virus production. Interestingly, the unphosphorylatable BAF mutant, which is capable of binding DNA but localizes predominantly to the nucleus, was also incapable of suppressing viral replication. Thus, both DNA binding and localization are important determinants of BAF's antiviral function. Finally, our examination of how phosphatases are involved in regulating BAF revealed that PP2A dephosphorylates BAF during vaccinia infection, thus counterbalancing the activity of the B1 kinase. Altogether, these data demonstrate that phosphoregulation of BAF by viral and cellular enzymes modulates this protein at multiple molecular levels, thus determining its effectiveness as an antiviral factor and likely other functions as well. The barrier-to-autointegration factor (BAF) contributes to cellular genomic integrity in multiple ways

  1. Efficient Subcellular Targeting to the Cell Nucleus of Quantum Dots Densely Decorated with a Nuclear Localization Sequence Peptide.

    Science.gov (United States)

    Maity, Amit Ranjan; Stepensky, David

    2016-01-27

    development of subcellularly targeted DDSs that will deliver specific drugs to the nuclei of the target cells and will enhance efficacy and reduce toxicity of these drugs.

  2. In vivo subcellular localization of Mal de Rio Cuarto virus (MRCV) non-structural proteins in insect cells reveals their putative functions

    Energy Technology Data Exchange (ETDEWEB)

    Maroniche, Guillermo A.; Mongelli, Vanesa C.; Llauger, Gabriela; Alfonso, Victoria; Taboga, Oscar [Instituto de Biotecnologia, CICVyA, Instituto Nacional de Tecnologia Agropecuaria (IB-INTA), Las cabanas y Los Reseros s/n. Hurlingham Cp 1686, Buenos Aires (Argentina); Vas, Mariana del, E-mail: mdelvas@cnia.inta.gov.ar [Instituto de Biotecnologia, CICVyA, Instituto Nacional de Tecnologia Agropecuaria (IB-INTA), Las cabanas y Los Reseros s/n. Hurlingham Cp 1686, Buenos Aires (Argentina)

    2012-09-01

    The in vivo subcellular localization of Mal de Rio Cuarto virus (MRCV, Fijivirus, Reoviridae) non-structural proteins fused to GFP was analyzed by confocal microscopy. P5-1 showed a cytoplasmic vesicular-like distribution that was lost upon deleting its PDZ binding TKF motif, suggesting that P5-1 interacts with cellular PDZ proteins. P5-2 located at the nucleus and its nuclear import was affected by the deletion of its basic C-termini. P7-1 and P7-2 also entered the nucleus and therefore, along with P5-2, could function as regulators of host gene expression. P6 located in the cytoplasm and in perinuclear cloud-like inclusions, was driven to P9-1 viroplasm-like structures and co-localized with P7-2, P10 and {alpha}-tubulin, suggesting its involvement in viroplasm formation and viral intracellular movement. Finally, P9-2 was N-glycosylated and located at the plasma membrane in association with filopodia-like protrusions containing actin, suggesting a possible role in virus cell-to-cell movement and spread.

  3. Subcellular localization and photodynamic activity of Photodithazine (glucosamine salt of chlorin e6) in murine melanoma B16-F10: an in vitro and in vivo study

    Science.gov (United States)

    Ono, Bruno Andrade; Pires, Layla; Nogueira, Marcelo Saito; Kurachi, Cristina; Pratavieira, Sebastião.

    2018-02-01

    Photodynamic therapy (PDT) is already a good option for the clinical treatment of several lesions, including mainly nonmelanoma skin cancers. However, cutaneous melanoma treatment remains a challenge when using PDT. One of the reasons for its reduced efficacy is the high pigmentation of melanoma cells. The object of our study is to evaluate the feasibility of the Photodithazine as a photosensitizer for melanoma. Photodithazine is already used in some malignant tumors with satisfactory results and has significant absorption band around 660 nm where the absorption of melanin is low. In this study, we measured the subcellular localization and photodynamic activity of Photodithazine (PDZ) in murine melanoma B16-F10 cell culture. Additionally, a PDT procedure was applied in an animal melanoma model. This first result demonstrates that Photodithazine is more localized at mitochondria in B16F10 cell culture and the cell viability is reduced to less than 90% using 1 µg/mL (PDZ) and 2 J/cm2. We also noticed a rapid PDZ (less than one hour) accumulation in a murine melanoma model. The treatment of melanoma resulted in 20 % more animal survival after one session of PDT compared with the control group. More studies are required to evaluate the cytotoxic effects of Photodithazine at human melanoma.

  4. CRM1-dependent nuclear export and dimerization with hMSH5 contribute to the regulation of hMSH4 subcellular localization

    International Nuclear Information System (INIS)

    Neyton, Sophie; Lespinasse, Francoise; Lahaye, Francois; Staccini, Pascal; Paquis-Flucklinger, Veronique; Santucci-Darmanin, Sabine

    2007-01-01

    MSH4 and MSH5 are members of the MutS homolog family, a conserved group of proteins involved in DNA mismatch correction and homologous recombination. Although several studies have provided compelling evidences suggesting that MSH4 and MSH5 could act together in early and late stages of meiotic recombination, their precise roles are poorly understood and recent findings suggest that the human MSH4 protein may also exert a cytoplasmic function. Here we show that MSH4 is present in the cytoplasm and the nucleus of both testicular cells and transfected somatic cells. Confocal studies on transfected cells provide the first evidence that the subcellular localization of MSH4 is regulated, at least in part, by an active nuclear export pathway dependent on the exportin CRM1. We used deletion mapping and mutagenesis to define two functional nuclear export sequences within the C-terminal part of hMSH4 that mediate nuclear export through the CRM1 pathway. Our results suggest that CRM1 is also involved in MSH5 nuclear export. In addition, we demonstrate that dimerization of MSH4 and MSH5 facilitates their nuclear localization suggesting that dimerization may regulate the intracellular trafficking of these proteins. Our findings suggest that nucleocytoplasmic traffic may constitute a regulatory mechanism for MSH4 and MSH5 functions

  5. Tissue distribution and subcellular localizations determine in vivo functional relationship among prostasin, matriptase, HAI-1, and HAI-2 in human skin.

    Science.gov (United States)

    Lee, Shiao-Pieng; Kao, Chen-Yu; Chang, Shun-Cheng; Chiu, Yi-Lin; Chen, Yen-Ju; Chen, Ming-Hsing G; Chang, Chun-Chia; Lin, Yu-Wen; Chiang, Chien-Ping; Wang, Jehng-Kang; Lin, Chen-Yong; Johnson, Michael D

    2018-01-01

    The membrane-bound serine proteases prostasin and matriptase and the Kunitz-type protease inhibitors HAI-1 and HAI-2 are all expressed in human skin and may form a tightly regulated proteolysis network, contributing to skin pathophysiology. Evidence from other systems, however, suggests that the relationship between matriptase and prostasin and between the proteases and the inhibitors can be context-dependent. In this study the in vivo zymogen activation and protease inhibition status of matriptase and prostasin were investigated in the human skin. Immunohistochemistry detected high levels of activated prostasin in the granular layer, but only low levels of activated matriptase restricted to the basal layer. Immunoblot analysis of foreskin lysates confirmed this in vivo zymogen activation status and further revealed that HAI-1 but not HAI-2 is the prominent inhibitor for prostasin and matriptase in skin. The zymogen activation status and location of the proteases does not support a close functional relation between matriptase and prostasin in the human skin. The limited role for HAI-2 in the inhibition of matriptase and prostasin is the result of its primarily intracellular localization in basal and spinous layer keratinocytes, which probably prevents the Kunitz inhibitor from interacting with active prostasin or matriptase. In contrast, the cell surface expression of HAI-1 in all viable epidermal layers renders it an effective regulator for matriptase and prostasin. Collectively, our study suggests the importance of tissue distribution and subcellular localization in the functional relationship between proteases and protease inhibitors.

  6. Electronically controllable spoof localized surface plasmons

    Science.gov (United States)

    Zhou, Yong Jin; Zhang, Chao; Yang, Liu; Xun Xiao, Qian

    2017-10-01

    Electronically controllable multipolar spoof localized surface plasmons (LSPs) are experimentally demonstrated in the microwave frequencies. It has been shown that half integer order LSPs modes exist on the corrugated ring loaded with a slit, which actually arise from the Fabry-Perot-like resonances. By mounting active components across the slit in the corrugated rings, electronic switchability and tunability of spoof LSPs modes have been accomplished. Both simulated and measured results demonstrate efficient dynamic control of the spoof LSPs. These elements may form the basis of highly integrated programmable plasmonic circuits in microwave and terahertz regimes.

  7. Analysis of the subcellular localization of the proteins Rep, Rep' and Cap of porcine circovirus type 1

    International Nuclear Information System (INIS)

    Finsterbusch, T.; Steinfeldt, T.; Caliskan, R.; Mankertz, A.

    2005-01-01

    Porcine circovirus type 1 (PCV1) encodes two major ORFs. The cap gene comprises the major structural protein of PCV, the rep gene specifies Rep and Rep', which are both essential for initiating the replication of the viral DNA. Rep corresponds to the full-length protein, whereas Rep' is a truncated splice product that is frame-shifted in its C-terminal sequence. In this study, the cellular localization of PCV1-encoded proteins was investigated by immune fluorescence techniques using antibodies against Rep, Rep' and Cap and by expression of viral proteins fused to green and red fluorescence proteins. Rep and Rep' protein co-localized in the nucleus of infected cells as well as in cells transfected with plasmids expressing Rep and Rep' fused to fluorescence proteins, but no signal was seen in the nucleoli. Rep and Rep' carry three potential nuclear localization signals in their identical N-termini, and the contribution of these motifs to nuclear import was experimentally dissected. In contrast to the rep gene products, the localization of the Cap protein varied. While the Cap protein was restricted to the nucleoli in plasmid-transfected cells and was also localized in the nucleoli at an early stage of PCV1 infection, it was seen in the nucleoplasm and the cytoplasm later in infection, suggesting that a shuttling between distinct cellular compartments occurs

  8. Subcellular localization of Aleutian mink disease parvovirus proteins and DNA during permissive infection of Crandell feline kidney cells

    DEFF Research Database (Denmark)

    Oleksiewicz, M.B.; Costello, F.; Huhtanen, M.

    1996-01-01

    Confocal microscopy allowed us to localize viral nonstructural (NS) and capsid (VP) proteins and DNA simultaneously in cells permissively infected with Aleutian mink disease parvovirus (ADV). Early after infection, NS proteins colocalized with viral DNA to form intranuclear inclusions, whereas VP...

  9. hnRNPs H, H' and F behave differently with respect to posttranslational cleavage and subcellular localization

    DEFF Research Database (Denmark)

    Honoré, B; Vorum, H; Baandrup, U

    1999-01-01

    cytoplasmic localization in other cells. The different fates may reflect differences in functional roles that so far only have included nuclear functions. The presence of significant quantities of hnRNP F in the cytoplasm of many cells indicates that it also may have a functional role here. Udgivelsesdato...

  10. Attractive electron-electron interactions within robust local fitting approximations.

    Science.gov (United States)

    Merlot, Patrick; Kjærgaard, Thomas; Helgaker, Trygve; Lindh, Roland; Aquilante, Francesco; Reine, Simen; Pedersen, Thomas Bondo

    2013-06-30

    An analysis of Dunlap's robust fitting approach reveals that the resulting two-electron integral matrix is not manifestly positive semidefinite when local fitting domains or non-Coulomb fitting metrics are used. We present a highly local approximate method for evaluating four-center two-electron integrals based on the resolution-of-the-identity (RI) approximation and apply it to the construction of the Coulomb and exchange contributions to the Fock matrix. In this pair-atomic resolution-of-the-identity (PARI) approach, atomic-orbital (AO) products are expanded in auxiliary functions centered on the two atoms associated with each product. Numerical tests indicate that in 1% or less of all Hartree-Fock and Kohn-Sham calculations, the indefinite integral matrix causes nonconvergence in the self-consistent-field iterations. In these cases, the two-electron contribution to the total energy becomes negative, meaning that the electronic interaction is effectively attractive, and the total energy is dramatically lower than that obtained with exact integrals. In the vast majority of our test cases, however, the indefiniteness does not interfere with convergence. The total energy accuracy is comparable to that of the standard Coulomb-metric RI method. The speed-up compared with conventional algorithms is similar to the RI method for Coulomb contributions; exchange contributions are accelerated by a factor of up to eight with a triple-zeta quality basis set. A positive semidefinite integral matrix is recovered within PARI by introducing local auxiliary basis functions spanning the full AO product space, as may be achieved by using Cholesky-decomposition techniques. Local completion, however, slows down the algorithm to a level comparable with or below conventional calculations. Copyright © 2013 Wiley Periodicals, Inc.

  11. Nucleolin modulates the subcellular localization of GDNF-inducible zinc finger protein 1 and its roles in transcription and cell proliferation

    International Nuclear Information System (INIS)

    Dambara, Atsushi; Morinaga, Takatoshi; Fukuda, Naoyuki; Yamakawa, Yoshinori; Kato, Takuya; Enomoto, Atsushi; Asai, Naoya; Murakumo, Yoshiki; Matsuo, Seiichi; Takahashi, Masahide

    2007-01-01

    GZF1 is a zinc finger protein induced by glial cell-line-derived neurotrophic factor (GDNF). It is a sequence-specific transcriptional repressor with a BTB/POZ (Broad complex, Tramtrack, Bric a brac/Poxvirus and zinc finger) domain and ten zinc finger motifs. In the present study, we used immunoprecipitation and mass spectrometry to identify nucleolin as a GZF1-binding protein. Deletion analysis revealed that zinc finger motifs 1-4 of GZF1 mediate its association with nucleolin. When zinc fingers 1-4 were deleted from GZF1 or nucleolin expression was knocked down by short interference RNA (siRNA), nuclear localization of GZF1 was impaired. These results suggest that nucleolin is involved in the proper subcellular distribution of GZF1. In addition, overexpression of nucleolin moderately inhibited the transcriptional repressive activity of GZF1 whereas knockdown of nucleolin expression by siRNA enhanced its activity. Thus, the repressive activity of GZF1 is modulated by the level at which nucleolin is expressed. Finally, we found that knockdown of GZF1 and nucleolin expression markedly impaired cell proliferation. These findings suggest that the physiological functions of GZF1 may be regulated by the protein's association with nucleolin

  12. Comparative studies of a new subfamily of human Ste20-like kinases: homodimerization, subcellular localization, and selective activation of MKK3 and p38.

    Science.gov (United States)

    Yustein, Jason T; Xia, Liang; Kahlenburg, J Michelle; Robinson, Dan; Templeton, Dennis; Kung, Hsing-Jien

    2003-09-18

    The Sterile-20 or Ste20 family of serine/threonine kinases is a group of signaling molecules whose physiological roles within mammalian cells are just starting to be elucidated. Here, in this report we present the characterization of three human Ste20-like kinases with greater than 90% similarity within their catalytic domains that define a novel subfamily of Ste20s. Members of this kinase family include rat thousand and one (TAO1) and chicken KFC (kinase from chicken). For the lack of a consensus nomenclature in the literature, in this report, we shall call this family hKFC (for their homology to chicken KFC) and the three members hKFC-A, hKFC-B, and hKFC-C, respectively. These kinases have many similarities including an aminoterminal kinase domain, a serine-rich region, and a coiled-coil configuration within the C-terminus. All three kinases are able to activate the p38 MAP kinase pathway through the specific activation of the upstream MKK3 kinase. We also offer evidence, both theoretical and biochemical, showing that these kinases can undergo self-association. Despite these similarities, these kinases differ in tissue distribution, apparent subcellular localization, and feature structural differences largely within the carboxyl-terminal sequence.

  13. Up-regulation and subcellular localization of hnRNP A2/B1 in the development of hepatocellular carcinoma

    International Nuclear Information System (INIS)

    Cui, Huaqing; Wu, Feng; Sun, Yanling; Fan, Guocai; Wang, Qingming

    2010-01-01

    Hepatocellular carcinoma (HCC) is one of the world's leading causes of death among cancer patients. It is important to find a new biomarker that diagnoses HCC and monitors its treatment. In our previous work, we screened a single-chain antibody (scFv) N14, which could specifically recognize human HepG2 HCC cells but not human non-cancerous liver LO2 cells. However, the antigen it recognized in the cells remained unknown. Recombinant scFv N14 antibody was expressed as an active antibody. Using this antibody with a combination of immunological and proteomic approaches, we identified the antigen of scFv N14 antibody as the heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1). The expression of hnRNP A2/B1 in HCC cells was then investigated by semi-quantitative RT-PCR and immunohistochemistry. We found that the up-regulation of hnRNP A2/B1 was measured at both transcriptional and translational levels in rat HCC cells but not in rat hepatic cells. We also found that in various human hepatic tissues, hnRNP A2/B1 was highly expressed in both human hepatitis virus positive liver tissues and human HCC tissues but not in normal liver tissues. Interestingly, we observed that the localization of hnRNP A2/B1 in HCC cells was altered during the development of HCC. In human hepatitis virus infected tissues hnRNP A2/B1 resides exclusively in the nuclei of hepatocytes. However, when the HCC progressed from a well differentiated to a poorly differentiated stage, hnRNP A2/B1 was increasingly localized in the cytoplasm. In contrast, the HCC tissues with hnRNP A2/B1 highly expressed in the nucleus decreased. This work is the first to show that hnRNP A2/B1 is the antigen specifically recognized by the scFv N14 antibody in HCC cells. The over-expression of hnRNP A2/B1 was confirmed in cultured human and rat HCC cell lines, human virus related hepatitis liver tissues and human HCC tissues. The increased localization of hnRNP A2/B1 in the cytoplasm of HCC cells was revealed

  14. Phosphorylation and subcellular localization of p27Kip1 regulated by hydrogen peroxide modulation in cancer cells.

    Directory of Open Access Journals (Sweden)

    Irene L Ibañez

    Full Text Available The Cyclin-dependent kinase inhibitor 1B (p27Kip1 is a key protein in the decision between proliferation and cell cycle exit. Quiescent cells show nuclear p27Kip1, but this protein is exported to the cytoplasm in response to proliferating signals. We recently reported that catalase treatment increases the levels of p27Kip1 in vitro and in vivo in a murine model. In order to characterize and broaden these findings, we evaluated the regulation of p27Kip1 by hydrogen peroxide (H(2O(2 in human melanoma cells and melanocytes. We observed a high percentage of p27Kip1 positive nuclei in melanoma cells overexpressing or treated with exogenous catalase, while non-treated controls showed a cytoplasmic localization of p27Kip1. Then we studied the levels of p27Kip1 phosphorylated (p27p at serine 10 (S10 and at threonine 198 (T198 because phosphorylation at these sites enables nuclear exportation of this protein, leading to accumulation and stabilization of p27pT198 in the cytoplasm. We demonstrated by western blot a decrease in p27pS10 and p27pT198 levels in response to H(2O(2 removal in melanoma cells, associated with nuclear p27Kip1. Melanocytes also exhibited nuclear p27Kip1 and lower levels of p27pS10 and p27pT198 than melanoma cells, which showed cytoplasmic p27Kip1. We also showed that the addition of H(2O(2 (0.1 µM to melanoma cells arrested in G1 by serum starvation induces proliferation and increases the levels of p27pS10 and p27pT198 leading to cytoplasmic localization of p27Kip1. Nuclear localization and post-translational modifications of p27Kip1 were also demonstrated by catalase treatment of colorectal carcinoma and neuroblastoma cells, extending our findings to these other human cancer types. In conclusion, we showed in the present work that H(2O(2 scavenging prevents nuclear exportation of p27Kip1, allowing cell cycle arrest, suggesting that cancer cells take advantage of their intrinsic pro-oxidant state to favor cytoplasmic localization

  15. Dynamic subcellular localization of isoforms of the folate pathway enzyme serine hydroxymethyltransferase (SHMT through the erythrocytic cycle of Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Mitchell Sarah L

    2010-12-01

    Full Text Available Abstract Background The folate pathway enzyme serine hydroxymethyltransferase (SHMT converts serine to glycine and 5,10-methylenetetrahydrofolate and is essential for the acquisition of one-carbon units for subsequent transfer reactions. 5,10-methylenetetrahydrofolate is used by thymidylate synthase to convert dUMP to dTMP for DNA synthesis. In Plasmodium falciparum an enzymatically functional SHMT (PfSHMTc and a related, apparently inactive isoform (PfSHMTm are found, encoded by different genes. Here, patterns of localization of the two isoforms during the parasite erythrocytic cycle are investigated. Methods Polyclonal antibodies were raised to PfSHMTc and PfSHMTm, and, together with specific markers for the mitochondrion and apicoplast, were employed in quantitative confocal fluorescence microscopy of blood-stage parasites. Results As well as the expected cytoplasmic occupancy of PfSHMTc during all stages, localization into the mitochondrion and apicoplast occurred in a stage-specific manner. Although early trophozoites lacked visible organellar PfSHMTc, a significant percentage of parasites showed such fluorescence during the mid-to-late trophozoite and schizont stages. In the case of the mitochondrion, the majority of parasites in these stages at any given time showed no marked PfSHMTc fluorescence, suggesting that its occupancy of this organelle is of limited duration. PfSHMTm showed a distinctly more pronounced mitochondrial location through most of the erythrocytic cycle and GFP-tagging of its N-terminal region confirmed the predicted presence of a mitochondrial signal sequence. Within the apicoplast, a majority of mitotic schizonts showed a marked concentration of PfSHMTc, whose localization in this organelle was less restricted than for the mitochondrion and persisted from the late trophozoite to the post-mitotic stages. PfSHMTm showed a broadly similar distribution across the cycle, but with a distinctive punctate accumulation towards

  16. Fe-S cluster coordination of the chromokinesin KIF4A alters its sub-cellular localization during mitosis.

    Science.gov (United States)

    Ben-Shimon, Lilach; Paul, Viktoria D; David-Kadoch, Galit; Volpe, Marina; Stümpfig, Martin; Bill, Eckhard; Mühlenhoff, Ulrich; Lill, Roland; Ben-Aroya, Shay

    2018-05-30

    Fe-S clusters act as co-factors of proteins with diverse functions, e.g. in DNA repair. Down-regulation of the cytosolic iron-sulfur protein assembly (CIA) machinery promotes genomic instability by the inactivation of multiple DNA repair pathways. Furthermore, CIA deficiencies are associated with so far unexplained mitotic defects. Here, we show that CIA2B and MMS19, constituents of the CIA targeting complex involved in facilitating Fe-S cluster insertion into cytosolic and nuclear target proteins, co-localize with components of the mitotic machinery. Down-regulation of CIA2B and MMS19 impairs the mitotic cycle. We identify the chromokinesin KIF4A as a mitotic component involved in these effects. KIF4A binds a Fe-S cluster in vitro through its conserved cysteine-rich domain. We demonstrate in vivo that this domain is required for the mitosis-related KIF4A localization and for the mitotic defects associated with KIF4A knockout. KIF4A is the first identified mitotic component carrying such a post-translational modification. These findings suggest that the lack of Fe-S clusters in KIF4A upon down-regulation of the CIA targeting complex contributes to the mitotic defects. © 2018. Published by The Company of Biologists Ltd.

  17. Subcellular localization of proteins in the anaerobic sulfate reducer Desulfovibrio vulgaris via SNAP-tag labeling and photoconversion

    Energy Technology Data Exchange (ETDEWEB)

    Gorur, A.; Leung, C. M.; Jorgens, D.; Tauscher, A.; Remis, J. P.; Ball, D. A.; Chhabra, S.; Fok, V.; Geller, J. T.; Singer, M.; Hazen, T. C.; Juba, T.; Elias, D.; Wall, J.; Biggin, M.; Downing, K. H.; Auer, M.

    2010-06-01

    Systems Biology studies the temporal and spatial 3D distribution of macromolecular complexes with the aim that such knowledge will allow more accurate modeling of biological function and will allow mathematical prediction of cellular behavior. However, in order to accomplish accurate modeling precise knowledge of spatial 3D organization and distribution inside cells is necessary. And while a number of macromolecular complexes may be identified by its 3D structure and molecular characteristics alone, the overwhelming number of proteins will need to be localized using a reporter tag. GFP and its derivatives (XFPs) have been traditionally employed for subcelllar localization using photoconversion approaches, but this approach cannot be taken for obligate anaerobic bacteria, where the intolerance towards oxygen prevents XFP approaches. As part of the GTL-funded PCAP project (now ENIGMA) genetic tools have been developed for the anaerobe sulfate reducer Desulfovibrio vulgaris that allow the high-throughput generation of tagged-protein mutant strains, with a focus on the commercially available SNAP-tag cell system (New England Biolabs, Ipswich, MA), which is based on a modified O6-alkylguanine-DNA alkyltransferase (AGT) tag, that has a dead-end reaction with a modified O6-benzylguanine (BG) derivative and has been shown to function under anaerobic conditions. After initial challenges with respect to variability, robustness and specificity of the labeling signal we have optimized the labeling. Over the last year, as a result of the optimized labeling protocol, we now obtain robust labeling of 20 out of 31 SNAP strains. Labeling for 13 strains were confirmed at least five times. We have also successfully performed photoconversion on 5 of these 13 strains, with distinct labeling patterns for different strains. For example, DsrC robustly localizes to the periplasmic portion of the inner membrane, where as a DNA-binding protein localizes to the center of the cell, where the

  18. Identification and subcellular localization of a 21-kilodalton molecule using affinity-purified antibodies against α-transforming growth factor

    International Nuclear Information System (INIS)

    Hazarika, P.; Pardue, R.L.; Earls, R.; Dedman, J.R.

    1987-01-01

    Monospecific antibodies were generated against each of six different peptide sequences derived from rat and human α-transforming growth factor (α-TGF). The affinity-purified antibody to the 17 amino acid carboxyl-terminal portion of the molecule proved most useful in detecting α-TGF. When used in a peptide-based radioimmunoassay, it was possible to measure nanogram quantities of native α-TGF in conditioned cell culture media. When used to analyze cell lysate, these antibodies specifically recognized a 21-kilodalton protein species. Indirect immunofluorescence localization procedures revealed a high concentration of α-TCF in a perinuclear ring with a diffuse cytoplasmic distribution. These results suggest that a precursor form of α-TGF has a cellular role beyond that of an autocrine growth factor

  19. Identification and subcellular localization of a 21-kilodalton molecule using affinity-purified antibodies against. cap alpha. -transforming growth factor

    Energy Technology Data Exchange (ETDEWEB)

    Hazarika, P.; Pardue, R.L.; Earls, R.; Dedman, J.R.

    1987-04-07

    Monospecific antibodies were generated against each of six different peptide sequences derived from rat and human ..cap alpha..-transforming growth factor (..cap alpha..-TGF). The affinity-purified antibody to the 17 amino acid carboxyl-terminal portion of the molecule proved most useful in detecting ..cap alpha..-TGF. When used in a peptide-based radioimmunoassay, it was possible to measure nanogram quantities of native ..cap alpha..-TGF in conditioned cell culture media. When used to analyze cell lysate, these antibodies specifically recognized a 21-kilodalton protein species. Indirect immunofluorescence localization procedures revealed a high concentration of ..cap alpha..-TCF in a perinuclear ring with a diffuse cytoplasmic distribution. These results suggest that a precursor form of ..cap alpha..-TGF has a cellular role beyond that of an autocrine growth factor.

  20. Variation in the Subcellular Localization and Protein Folding Activity among Arabidopsis thaliana Homologs of Protein Disulfide Isomerase

    Directory of Open Access Journals (Sweden)

    Christen Y. L. Yuen

    2013-10-01

    Full Text Available Protein disulfide isomerases (PDIs catalyze the formation, breakage, and rearrangement of disulfide bonds to properly fold nascent polypeptides within the endoplasmic reticulum (ER. Classical animal and yeast PDIs possess two catalytic thioredoxin-like domains (a, a′ and two non-catalytic domains (b, b′, in the order a-b-b′-a′. The model plant, Arabidopsis thaliana, encodes 12 PDI-like proteins, six of which possess the classical PDI domain arrangement (AtPDI1 through AtPDI6. Three additional AtPDIs (AtPDI9, AtPDI10, AtPDI11 possess two thioredoxin domains, but without intervening b-b′ domains. C-terminal green fluorescent protein (GFP fusions to each of the nine dual-thioredoxin PDI homologs localized predominantly to the ER lumen when transiently expressed in protoplasts. Additionally, expression of AtPDI9:GFP-KDEL and AtPDI10: GFP-KDDL was associated with the formation of ER bodies. AtPDI9, AtPDI10, and AtPDI11 mediated the oxidative folding of alkaline phosphatase when heterologously expressed in the Escherichia coli protein folding mutant, dsbA−. However, only three classical AtPDIs (AtPDI2, AtPDI5, AtPDI6 functionally complemented dsbA−. Interestingly, chemical inducers of the ER unfolded protein response were previously shown to upregulate most of the AtPDIs that complemented dsbA−. The results indicate that Arabidopsis PDIs differ in their localization and protein folding activities to fulfill distinct molecular functions in the ER.

  1. Genome-wide identification, subcellular localization and gene expression analysis of the members of CESA gene family in common tobacco (Nicotiana tabacum L.).

    Science.gov (United States)

    Xu, Zong-Chang; Kong, Yingzhen

    2017-06-20

    Cellulose-synthase proteins (CESAs) are membrane localized proteins and they form protein complexes to produce cellulose in the plasma membrane. CESA proteins play very important roles in cell wall construction during plant growth and development. In this study, a total of 21 NtCESA gene sequences were identified by using PF03552 conserved protein sequence and 10 AtCESA protein sequences of Arabidopsis thaliana to blast against the common tobacco (Nicotiana tabacum L.) genome database with TBLASTN protocol. We analyzed the physical and chemical properties of protein sequences based on some software or on-line analysis tools. The results showed that there were no significant variances in terms of the physical and chemical properties of the 21 NtCESA proteins. First, phylogenetic tree analysis showed that 21 NtCESA genes and 10 AtCESA genes were clustered into five groups, and the gene structures were similar among the genes that are clustered into the same group. Second, in all of the 21 NtCESA proteins the conserved zinc finger domain was identified in the N-terminus, transmembrane domains were identified in the C-terminus and the DDD-QXXRW conserved domains were also identified. Third, gene expression analysis results indicated that most NtCESA genes were expressed in roots and leaves of seedling or mature tissues of tobacco, seeds and callus tissues. The genes that clustered into the same group share similar expression patterns. Importantly, NtCESA proteins that are involved in secondary cell wall cellulose synthesis have two extra transmembrane domains compared with that involved in primary cell wall cellulose biosynthesis. In addition, subcellular localization results showed that NtCESA9 and NtCESA14 were two plasma membrane anchored proteins. This study will lay a foundation for further functional characterization of these NtCESA genes.

  2. Subcellular localization, interactions and dynamics of the phage-shock protein-like Lia response in Bacillus subtilis.

    Science.gov (United States)

    Domínguez-Escobar, Julia; Wolf, Diana; Fritz, Georg; Höfler, Carolin; Wedlich-Söldner, Roland; Mascher, Thorsten

    2014-05-01

    The liaIH operon of Bacillus subtilis is the main target of the envelope stress-inducible two-component system LiaRS. Here, we studied the localization, interaction and cellular dynamics of Lia proteins to gain insights into the physiological role of the Lia response. We demonstrate that LiaI serves as the membrane anchor for the phage-shock protein A homologue LiaH. Under non-inducing conditions, LiaI locates in highly motile membrane-associated foci, while LiaH is dispersed throughout the cytoplasm. Under stress conditions, both proteins are strongly induced and colocalize in numerous distinct static spots at the cytoplasmic membrane. This behaviour is independent of MreB and does also not correlate with the stalling of the cell wall biosynthesis machinery upon antibiotic inhibition. It can be induced by antibiotics that interfere with the membrane-anchored steps of cell wall biosynthesis, while compounds that inhibit the cytoplasmic or extracytoplasmic steps do not trigger this response. Taken together, our data are consistent with a model in which the Lia system scans the cytoplasmic membrane for envelope perturbations. Upon their detection, LiaS activates the cognate response regulator LiaR, which in turn strongly induces the liaIH operon. Simultaneously, LiaI recruits LiaH to the membrane, presumably to protect the envelope and counteract the antibiotic-induced damage. © 2014 John Wiley & Sons Ltd.

  3. Spastin subcellular localization is regulated through usage of different translation start sites and active export from the nucleus

    International Nuclear Information System (INIS)

    Claudiani, Pamela; Riano, Elena; Errico, Alessia; Andolfi, Gennaro; Rugarli, Elena I.

    2005-01-01

    Most cases of autosomal-dominant hereditary spastic paraplegia are linked to mutations in SPG4 encoding spastin, a protein involved in microtubule dynamics and membrane trafficking. In pyramidal neurons of the motor cortex and in immortalized motor neurons, spastin is localized to the synaptic terminals and growth cones. However, in other neurons and in proliferating cells spastin is prevalently nuclear. The mechanisms that determine targeting of spastin to the nucleus or the cytoplasm are unknown. We show here that the SPG4 mRNA is able to direct synthesis of two spastin isoforms, 68 and 60 kDa, respectively, through usage of two different translational start sites. Both isoforms are imported into the nucleus, but the 68-kDa isoform contains two nuclear export signals that efficiently drive export to the cytoplasm. Nuclear export is leptomycin-B sensitive. The cytoplasmic 68-kDa spastin isoform is more abundant in the brain and the spinal cord than in other tissues. Our data indicate that spastin function is modulated through usage of alternative translational start sites and active nuclear import and export, and open new perspectives for the pathogenesis of hereditary spastic paraplegia

  4. Optogenetic Tools for Subcellular Applications in Neuroscience.

    Science.gov (United States)

    Rost, Benjamin R; Schneider-Warme, Franziska; Schmitz, Dietmar; Hegemann, Peter

    2017-11-01

    The ability to study cellular physiology using photosensitive, genetically encoded molecules has profoundly transformed neuroscience. The modern optogenetic toolbox includes fluorescent sensors to visualize signaling events in living cells and optogenetic actuators enabling manipulation of numerous cellular activities. Most optogenetic tools are not targeted to specific subcellular compartments but are localized with limited discrimination throughout the cell. Therefore, optogenetic activation often does not reflect context-dependent effects of highly localized intracellular signaling events. Subcellular targeting is required to achieve more specific optogenetic readouts and photomanipulation. Here we first provide a detailed overview of the available optogenetic tools with a focus on optogenetic actuators. Second, we review established strategies for targeting these tools to specific subcellular compartments. Finally, we discuss useful tools and targeting strategies that are currently missing from the optogenetics repertoire and provide suggestions for novel subcellular optogenetic applications. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Establishment of a human cell line stably overexpressing mouse Nip45 and characterization of Nip45 subcellular localization

    Energy Technology Data Exchange (ETDEWEB)

    Hashiguchi, Kohtaro; Ozaki, Masumi [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto (Japan); Kuraoka, Isao [Biological Chemistry Group, Division of Chemistry, Graduate School of Engineering Science, Osaka University, Osaka (Japan); Saitoh, Hisato, E-mail: hisa@kumamoto-u.ac.jp [Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto (Japan); Department of New Frontier Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto (Japan); Global COE (Centers of Excellence) Program, Global Initiative Center for Pulsed Power Engineering, Kumamoto University, Kumamoto (Japan)

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer A human cell line expressing a mouse Nip45 has facilitated Nip45 analysis. Black-Right-Pointing-Pointer Nip45 does not effectively inhibit polySUMOylation in vivo. Black-Right-Pointing-Pointer Nip45 interacts directly with SUMO and SUMO chains. Black-Right-Pointing-Pointer Nip45 accumulates at PML bodies in response to proteasome inhibition. -- Abstract: The nuclear factor of activated T cells, cytoplasmic, calcineurin dependent 2 interacting protein, Nfatc2ip (Nip45), has been implicated as a crucial coordinator of the immune response and of cellular differentiation in humans and mice, and contains SUMO-like domains in its C-terminal region. However, the significance of its N-terminal region and its correlation to the SUMO modification pathway remain largely uncharacterized. In this study, a human cultured cell line was established, in which FLAG-tagged mouse Nip45 (FLAG-mNip45) was stably overexpressed. Under standard, non-stressful conditions, we detected FLAG-mNip45 diffusely distributed in the nucleus. Intriguingly, proteasome inhibition by MG132 caused FLAG-mNip45, together with SUMOylated proteins, to localize in nuclear domains associated with promyelocytic leukemia protein. Finally, using an in vitro binding assay, we showed interaction of the N-terminal region of mNip45 with both free SUMO-3 and SUMO-3 chains, indicating that Nip45 may, in part, exert its function via interaction with SUMO/SUMOylated proteins. Taken together, our study provides novel information on a poorly characterized mammalian protein and suggests that our newly established cell line will be useful for elucidating the physiological role of Nip45.

  6. The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization

    Directory of Open Access Journals (Sweden)

    Tam Michael WC

    2010-03-01

    Full Text Available Abstract Background Puf proteins have important roles in controlling gene expression at the post-transcriptional level by promoting RNA decay and repressing translation. The Pumilio homology domain (PUM-HD is a conserved region within Puf proteins that binds to RNA with sequence specificity. Although Puf proteins have been well characterized in animal and fungal systems, little is known about the structural and functional characteristics of Puf-like proteins in plants. Results The Arabidopsis and rice genomes code for 26 and 19 Puf-like proteins, respectively, each possessing eight or fewer Puf repeats in their PUM-HD. Key amino acids in the PUM-HD of several of these proteins are conserved with those of animal and fungal homologs, whereas other plant Puf proteins demonstrate extensive variability in these amino acids. Three-dimensional modeling revealed that the predicted structure of this domain in plant Puf proteins provides a suitable surface for binding RNA. Electrophoretic gel mobility shift experiments showed that the Arabidopsis AtPum2 PUM-HD binds with high affinity to BoxB of the Drosophila Nanos Response Element I (NRE1 RNA, whereas a point mutation in the core of the NRE1 resulted in a significant reduction in binding affinity. Transient expression of several of the Arabidopsis Puf proteins as fluorescent protein fusions revealed a dynamic, punctate cytoplasmic pattern of localization for most of these proteins. The presence of predicted nuclear export signals and accumulation of AtPuf proteins in the nucleus after treatment of cells with leptomycin B demonstrated that shuttling of these proteins between the cytosol and nucleus is common among these proteins. In addition to the cytoplasmically enriched AtPum proteins, two AtPum proteins showed nuclear targeting with enrichment in the nucleolus. Conclusions The Puf family of RNA-binding proteins in plants consists of a greater number of members than any other model species studied to

  7. On the Localisation of d-Tubocurarine in Rat Liver Lysosomes in vivo by Electron Microscopy and Subcellular Fractionation

    NARCIS (Netherlands)

    Weitering, Jeanette G.; Mulder, Gerard J.; Meijer, Dirk K.F.; Lammers, Wim; Veenhuis, Maarten; Wendelaar Bonga, Sjoerd E.

    1975-01-01

    After i.v. injection in the rat, d-tubocurarine is taken up and concentrated by the liver. A method is developed for the visualisation of d-tubocurarine inside the liver cell by electron microscopy. Glutaraldehyde fixed liver blocks were immersed in an ammonium molybdate solution; d-tubocurarine was

  8. Plutonium Elastic Moduli, Electron Localization, and Temperature

    International Nuclear Information System (INIS)

    Migliori, Albert; Mihut-Stroe, Izabella; Betts, Jon B.

    2008-01-01

    In almost all materials, compression is accompanied naturally by stiffening. Even in materials with zero or negative thermal expansion, where warming is accompanied by volume contraction it is the volume change that primarily controls elastic stiffness. Not so in the metal plutonium. In plutonium, alloying with gallium can change the sign of thermal expansion, but for the positive thermal- expansion monoclinic phase as well as the face-centered-cubic phase with either sign of thermal expansion, and the orthorhombic phase, recent measurements of elastic moduli show soften on warming by an order of magnitude more than expected, the shear and compressional moduli track, and volume seems irrelevant. These effects point toward a novel mechanism for electron localization, and have important implication for the pressure dependence of the bulk compressibility. (authors)

  9. Local moment formation in Dirac electrons

    International Nuclear Information System (INIS)

    Mashkoori, M; Mahyaeh, I; Jafari, S A

    2015-01-01

    Elemental bismuth and its compounds host strong spin-orbit interaction which is at the heart of topologically non-trivial alloys based on bismuth. These class of materials are described in terms of 4x4 matrices at each v point where spin and orbital labels of the underlying electrons are mixed. In this work we investigate the single impurity Anderson model (SIAM) within a mean field approximation to address the nature of local magnetic moment formation in a generic Dirac Hamiltonian. Despite the spin-mixing in the Hamiltonian, within the Hartree approximation it turns out that the impuritys Green function is diagonal in spin label. In the three dimensional Dirac materials defined over a bandwidth D and spin-orbit parameter γ, that hybridizes with impurity through V, a natural dimensionless parameter V 2 D/2πγ 3 emerges. So neither the hybridization strength, V, nor the spin-orbit coupling γ, but a combination thereof governs the phase diagram. By tuning chemical potential and the impurity level, we present phase diagram for various values of Hubbard U. Numerical results suggest that strong spin-orbit coupling enhances the local moment formation both in terms of its strength and the area of the local moment region. In the case that we tune the chemical potential in a similar way as normal metal we find that magnetic region is confined to μ ≥ ε 0 , in sharp contrast to 2D Dirac fermions. If one fixes the chemical potential and tunes the impurity level, phase diagram has two magnetic regions which corresponds to hybridization of impurity level with lower and upper bands. (paper)

  10. Two-Photon Irradiation of an Intracellular Singlet Oxygen Photosensitizer: Achieving Localized Sub-Cellular Excitation in Spatially-Resolved Experiments

    DEFF Research Database (Denmark)

    Pedersen, Brian Wett; Breitenbach, Thomas; Redmond, Robert W.

    2010-01-01

    The response of a given cell to spatially-resolved sub-cellular irradiation of a singlet oxygen photosensitizer (protoporphyrin IX, PpIX) using a focused laser was assessed. In these experiments, incident light was scattered over a volume greater than that defi ned by the dimensions of the laser...

  11. Molecular cloning, transcriptional profiling, and subcellular localization of signal transducer and activator of transcription 2 (STAT2) ortholog from rock bream, Oplegnathus fasciatus.

    Science.gov (United States)

    Bathige, S D N K; Umasuthan, Navaneethaiyer; Priyathilaka, Thanthrige Thiunuwan; Thulasitha, William Shanthakumar; Jayasinghe, J D H E; Wan, Qiang; Nam, Bo-Hye; Lee, Jehee

    2017-08-30

    Signal transducer and activator of transcription 2 (STAT2) is a key element that transduces signals from the cell membrane to the nucleus via the type I interferon-signaling pathway. Although the structural and functional aspects of STAT proteins are well studied in mammals, information on teleostean STATs is very limited. In this study, a STAT paralog, which is highly homologous to the STAT2 members, was identified from a commercially important fish species called rock bream and designated as RbSTAT2. The RbSTAT2 gene was characterized at complementary DNA (cDNA) and genomic sequence levels, and was found to possess structural features common with its mammalian counterparts. The complete cDNA sequence was distributed into 24 exons in the genomic sequence. The promoter proximal region was analyzed and found to contain potential transcription factor binding sites to regulate the transcription of RbSTAT2. Phylogenetic studies and comparative genomic structure organization revealed the distinguishable evolution for fish and other vertebrate STAT2 orthologs. Transcriptional quantification was performed by SYBR Green quantitative real-time PCR (qPCR) and the ubiquitous expression of RbSTAT2 transcripts was observed in all tissues analyzed from healthy fish, with a remarkably high expression in blood cells. Significantly (Prock bream irido virus; RBIV), bacterial (Edwardsiella tarda and Streptococcus iniae), and immune stimulants (poly I:C and LPS). Antiviral potential was further confirmed by WST-1 assay, by measuring the viability of rock bream heart cells treated with RBIV. In addition, results of an in vitro challenge experiment signified the influence of rock bream interleukin-10 (RbIL-10) on transcription of RbSTAT2. Subcellular localization studies by transfection of pEGFP-N1/RbSTAT2 into rock bream heart cells revealed that the RbSTAT2 was usually located in the cytoplasm and translocated near to the nucleus upon poly I:C administration. Altogether, these

  12. Unraveling 14-3-3 proteins in C4 panicoids with emphasis on model plant Setaria italica reveals phosphorylation-dependent subcellular localization of RS splicing factor.

    Directory of Open Access Journals (Sweden)

    Karunesh Kumar

    Full Text Available 14-3-3 proteins are a large multigenic family of regulatory proteins ubiquitously found in eukaryotes. In plants, 14-3-3 proteins are reported to play significant role in both development and response to stress stimuli. Therefore, considering their importance, genome-wide analyses have been performed in many plants including Arabidopsis, rice and soybean. But, till date, no comprehensive investigation has been conducted in any C4 panicoid crops. In view of this, the present study was performed to identify 8, 5 and 26 potential 14-3-3 gene family members in foxtail millet (Si14-3-3, sorghum (Sb14-3-3 and maize (Zm14-3-3, respectively. In silico characterization revealed large variations in their gene structures; segmental and tandem duplications have played a major role in expansion of these genes in foxtail millet and maize. Gene ontology annotation showed the participation of 14-3-3 proteins in diverse biological processes and molecular functions, and in silico expression profiling indicated their higher expression in all the investigated tissues. Comparative mapping was performed to derive the orthologous relationships between 14-3-3 genes of foxtail millet and other Poaceae members, which showed a higher, as well as similar percentage of orthology among these crops. Expression profiling of Si14-3-3 genes during different time-points of abiotic stress and hormonal treatments showed a differential expression pattern of these genes, and sub-cellular localization studies revealed the site of action of Si14-3-3 proteins within the cells. Further downstream characterization indicated the interaction of Si14-3-3 with a nucleocytoplasmic shuttling phosphoprotein (SiRSZ21A in a phosphorylation-dependent manner, and this demonstrates that Si14-3-3 might regulate the splicing events by binding with phosphorylated SiRSZ21A. Taken together, the present study is a comprehensive analysis of 14-3-3 gene family members in foxtail millet, sorghum and maize

  13. Unraveling 14-3-3 proteins in C4 panicoids with emphasis on model plant Setaria italica reveals phosphorylation-dependent subcellular localization of RS splicing factor.

    Science.gov (United States)

    Kumar, Karunesh; Muthamilarasan, Mehanathan; Bonthala, Venkata Suresh; Roy, Riti; Prasad, Manoj

    2015-01-01

    14-3-3 proteins are a large multigenic family of regulatory proteins ubiquitously found in eukaryotes. In plants, 14-3-3 proteins are reported to play significant role in both development and response to stress stimuli. Therefore, considering their importance, genome-wide analyses have been performed in many plants including Arabidopsis, rice and soybean. But, till date, no comprehensive investigation has been conducted in any C4 panicoid crops. In view of this, the present study was performed to identify 8, 5 and 26 potential 14-3-3 gene family members in foxtail millet (Si14-3-3), sorghum (Sb14-3-3) and maize (Zm14-3-3), respectively. In silico characterization revealed large variations in their gene structures; segmental and tandem duplications have played a major role in expansion of these genes in foxtail millet and maize. Gene ontology annotation showed the participation of 14-3-3 proteins in diverse biological processes and molecular functions, and in silico expression profiling indicated their higher expression in all the investigated tissues. Comparative mapping was performed to derive the orthologous relationships between 14-3-3 genes of foxtail millet and other Poaceae members, which showed a higher, as well as similar percentage of orthology among these crops. Expression profiling of Si14-3-3 genes during different time-points of abiotic stress and hormonal treatments showed a differential expression pattern of these genes, and sub-cellular localization studies revealed the site of action of Si14-3-3 proteins within the cells. Further downstream characterization indicated the interaction of Si14-3-3 with a nucleocytoplasmic shuttling phosphoprotein (SiRSZ21A) in a phosphorylation-dependent manner, and this demonstrates that Si14-3-3 might regulate the splicing events by binding with phosphorylated SiRSZ21A. Taken together, the present study is a comprehensive analysis of 14-3-3 gene family members in foxtail millet, sorghum and maize, which provides

  14. On the electron density localization in elemental cubic ceramic and FCC transition metals by means of a localized electrons detector.

    Science.gov (United States)

    Aray, Yosslen; Paredes, Ricardo; Álvarez, Luis Javier; Martiz, Alejandro

    2017-06-14

    The electron density localization in insulator and semiconductor elemental cubic materials with diamond structure, carbon, silicon, germanium, and tin, and good metallic conductors with face centered cubic structure such as α-Co, Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au, was studied using a localized electrons detector defined in the local moment representation. Our results clearly show an opposite pattern of the electron density localization for the cubic ceramic and transition metal materials. It was found that, for the elemental ceramic materials, the zone of low electron localization is very small and is mainly localized on the atomic basin edges. On the contrary, for the transition metals, there are low-valued localized electrons detector isocontours defining a zone of highly delocalized electrons that extends throughout the material. We have found that the best conductors are those in which the electron density at this low-value zone is the lowest.

  15. High-resolution sub-cellular imaging by correlative NanoSIMS and electron microscopy of amiodarone internalisation by lung macrophages as evidence for drug-induced phospholipidosis.

    Science.gov (United States)

    Jiang, Haibo; Passarelli, Melissa K; Munro, Peter M G; Kilburn, Matt R; West, Andrew; Dollery, Colin T; Gilmore, Ian S; Rakowska, Paulina D

    2017-01-26

    Correlative NanoSIMS and EM imaging of amiodarone-treated macrophages shows the internalisation of the drug at a sub-cellular level and reveals its accumulation within the lysosomes, providing direct evidence for amiodarone-induced phospholipidosis. Chemical fixation using tannic acid effectively seals cellular membranes aiding intracellular retention of diffusible drugs.

  16. Electron localization functions and local measures of the covariance ∑

    Indian Academy of Sciences (India)

    Unknown

    rectly from the correlated electron density, without recourse to the Kohn-Sham orbitals,33–35 and in §2.5 we discuss this approach and offer a small refine- ment. Throughout these sections, we shall use the neon atom as a representative example. In §2.6, we extend our analysis to the argon, krypton, and xenon atoms.

  17. Proposed ripplon induced weak localization of electrons over liquid helium

    International Nuclear Information System (INIS)

    Dahm, A.J.

    1997-01-01

    Ripplon induced weak localization is proposed for electrons on a liquid helium surface. Ripplon scattering is quasi-elastic, the ripplon are quasi-static relative to the electron velocity, and the relative change in occupation number of the ripplon state in a scattering event is small. Conditions for the observation of ripplon induced weak localization are calculated

  18. ELECTRONIC ACCOUNTING INFORMATION IN LOCAL PUBLIC ADMINISTRATION

    Directory of Open Access Journals (Sweden)

    Rodica Gabriela Blidişel

    2012-01-01

    Full Text Available Major changes in information technologies characterize the current period through which humanity creates the conditions shift from information society to the knowledge. In this context of the changing of the public administration through the implementation of ITC and the reform that lead to the new public management, our paper wants to see the development of E-governance in Romanian local public administration and the influence of the main financial indicators on e-governance elements. Countries adopt e-governance in ways that reinforce traditional bureaucratic structures, cultures and links from administration to citizens and politics, in some cases making these traditional forms more responsive. The paper studies the accounting information disclosed on the internet sites of public sector entities. The research use an empirical approach to test impact of the quality of accounting information on e-financial reporting in public sector. The research use a quantitative methodology, based on surveys and author's observations. The methods chosen in this paper are reliable for this empirical study that tries to identify at a national level the problems that could improve the financial information disclosed by the public sector. The paper aims to measure the financial performance in local public administration and the main indicators of e-governance. The main objective of the paper is to make a model that demonstrates the impact of the local public administration financial performance on the e-governance. Due to the fact that the main problem of the Romanian local public administration is the lack of performance tools that could improve the e-governance, the research wants use an empirical approach to test the impact of the financial performance on the local public administration on e-governance. The research use a quantitative methodology, based on surveys and author's observations.

  19. Wigner-like crystallization of Anderson-localized electron systems with low electron densities

    CERN Document Server

    Slutskin, A A; Pepper, M

    2002-01-01

    We consider an electron system under conditions of strong Anderson localization, taking into account interelectron long-range Coulomb repulsion. We establish that at sufficiently low electron densities and sufficiently low temperatures the Coulomb electron interaction brings about ordering of the Anderson-localized electrons into a structure that is close to an ideal (Wigner) crystal lattice, provided the dimension of the system is > 1. This Anderson-Wigner glass (AWG) is a new macroscopic electron state that, on the one hand, is beyond the conventional Fermi glass concept, and on the other hand, qualitatively differs from the known 'plain' Wigner glass (inherent in self-localized electron systems) in that the random slight electron displacements from the ideal crystal sites essentially depend on the electron density. With increasing electron density the AWG is found to turn into the plain Wigner glass or Fermi glass, depending on the width of the random spread of the electron levels. It is shown that the res...

  20. WE-AB-204-12: Dosimetry at the Sub-Cellular Scale of Auger-Electron Emitter 99m-Tc in a Mouse Single Thyroid Follicle Model

    Energy Technology Data Exchange (ETDEWEB)

    Taborda, A; Benabdallah, N; Desbree, A [Institut de Radioprotection et de Surete Nucleaire, Fontenay-aux-roses (France)

    2015-06-15

    Purpose: To perform a dosimetry study at the sub-cellular scale of Auger-electron emitter 99m-Tc using a mouse single thyroid cellular model to investigate the contribution of the 99m-Tc Auger-electrons to the absorbed dose and possible link to the thyroid stunning in in vivo experiments in mice, recently reported in literature. Methods: The simulation of S-values for Auger-electron emitting radionuclides was performed using both the recent MCNP6 software and the Geant4-DNA extension of the Geant4 toolkit. The dosimetric calculations were validated through comparison with results from literature, using a simple model of a single cell consisting of two concentric spheres of unit density water and for six Auger-electron emitting radionuclides. Furthermore, the S-values were calculated using a single thyroid follicle model for uniformly distributed 123-I and 125-I radionuclides and compared with published S-values. After validation, the simulation of the S-values was performed for the 99m-Tc radionuclide within the several mouse thyroid follicle cellular compartments, considering the radiative and non-radiative transitions of the 99m-Tc radiation spectrum. Results: The calculated S-values using MCNP6 are in good agreement with the results from literature, validating its use for the 99m-Tc S-values calculations. The most significant absorbed dose corresponds to the case where the radionuclide is uniformly distributed in the follicular cell’s nucleus, with a S-value of 7.8 mGy/disintegration, due mainly to the absorbed Auger-electrons. The results show that, at a sub-cellular scale, the emitted X-rays and gamma particles do not contribute significantly to the absorbed dose. Conclusion: In this work, MCNP6 was validated for dosimetric studies at the sub-cellular scale. It was shown that the contribution of the Auger-electrons to the absorbed dose is important at this scale compared to the emitted photons’ contribution and can’t be neglected. The obtained S

  1. Fluctuations and localization in mesoscopic electron

    CERN Document Server

    Janssen, Martin

    2001-01-01

    The quantum phenomena of tunneling and interference show up not only in the microscopic world of atoms and molecules, but also in cold materials of the real world, such as metals and semiconductors. Though not fully macroscopic, such mesoscopic systems contain a huge number of particles, and the holistic nature of quantum mechanics becomes evident already in simple electronic measurements. The measured quantity fluctuates as a function of applied fields in an unpredictable, yet reproducible way. Despite this fingerprint character of fluctuations, their statistical properties are universal, i.e

  2. Local charge measurement using off-axis electron holography

    DEFF Research Database (Denmark)

    Beleggia, Marco; Gontard, L.C.; Dunin-Borkowski, R.0E.

    2016-01-01

    A model-independent approach based on Gauss’ theorem for measuring the local charge in a specimen from an electron-optical phase image recorded using off-axis electron holography was recently proposed. Here, we show that such a charge measurement is reliable when it is applied to determine the to...

  3. Cellular and subcellular distribution of BSH in human glioblastoma multiforme

    International Nuclear Information System (INIS)

    Neumann, M.; Gabel, D.

    2000-01-01

    The cellular and subcellular distribution of mercaptoundecahydrododecaborate (BSH) in seven glioblastoma multiforme tissue sections of six patients having received BSH prior to surgery was investigated by light, fluorescence and electron microscopy. With use of specific antibodies against BSH its localization could be found in tissue sections predominantly (approx. 90%) in the cytoplasm of GFAP-positive cells of all but one patient. The latter was significantly younger (33 years in contrast of 46-71 (mean 60) years). In none of the tissue sections BSH could be found to a significant amount in the cell nuclei. In contrast, electron microscopy studies show BSH as well associated with the cell membrane as with the chromatin in the nucleus. (author)

  4. Subcellular localization of skeletal muscle lipid droplets and PLIN family proteins OXPAT and ADRP at rest and following contraction in rat soleus muscle.

    Science.gov (United States)

    MacPherson, Rebecca E K; Herbst, Eric A F; Reynolds, Erica J; Vandenboom, Rene; Roy, Brian D; Peters, Sandra J

    2012-01-01

    Skeletal muscle lipid droplet-associated proteins (PLINs) are thought to regulate lipolysis through protein-protein interactions on the lipid droplet surface. In adipocytes, PLIN2 [adipocyte differentiation-related protein (ADRP)] is found only on lipid droplets, while PLIN5 (OXPAT, expressed only in oxidative tissues) is found both on and off the lipid droplet and may be recruited to lipid droplet membranes when needed. Our purpose was to determine whether PLIN5 is recruited to lipid droplets with contraction and to investigate the myocellular location and colocalization of lipid droplets, PLIN2, and PLIN5. Rat solei were isolated, and following a 30-min equilibration period, they were assigned to one of two groups: 1) 30 min of resting incubation and 2) 30 min of stimulation (n = 10 each). Immunofluorescence microscopy was used to determine subcellular content, distribution, and colocalization of lipid droplets, PLIN2, and PLIN5. There was a main effect for lower lipid and PLIN2 content in stimulated compared with rested muscles (P muscles (P = 0.001, r(2) = 0.99) and linearly in stimulated muscles (slope = -0.0023 ± 0.0006, P muscles (P contraction in isolated skeletal muscle.

  5. 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.

  6. Applicability of the local field concept for the electron gas

    International Nuclear Information System (INIS)

    Neilson, D.; Sjoelander, A.; Swierkowski, L.

    1990-01-01

    The static exchange-correlation hole surrounding an electron in an electron gas at metallic densities has been a highly successful and useful concept. The properties of the static exchange-correlation hole can be accurately reflected by the construction of a static local field. This field surrounds each electron and modifies it interaction with the other electrons in the system. An important limitation of the local field concept is that it does not handle the time-dependent relaxation of the surrounding electron cloud in a particularly transparent way. At metallic densities this is if no consequence since relaxation effects are only small corrections anyway, but at lower densities and in two-dimensional systems they become increasingly important. Approaches which attempt to address these problems are discussed. (author). 12 refs, 4 figs

  7. Sub-cellular Electrical Heterogeneity Revealed by Loose Patch Recording Reflects Differential Localization of Sarcolemmal Ion Channels in Intact Rat Hearts

    Directory of Open Access Journals (Sweden)

    Igor V. Kubasov

    2018-02-01

    Full Text Available The cardiac action potential (AP is commonly recoded as an integral signal from isolated myocytes or ensembles of myocytes (with intracellular microelectrodes and extracellular macroelectrodes, respectively. These signals, however, do not provide a direct measure of activity of ion channels and transporters located in two major compartments of a cardiac myocyte: surface sarcolemma and the T-tubule system, which differentially contribute to impulse propagation and excitation-contraction (EC coupling. In the present study we investigated electrical properties of myocytes within perfused intact rat heart employing loose patch recording with narrow-tip (2 μm diameter extracellular electrodes. Using this approach, we demonstrated two distinct types of electric signals with distinct waveforms (single peak and multi-peak AP; AP1 and AP2, respectively during intrinsic pacemaker activity. These two types of waveforms depend on the position of the electrode tip on the myocyte surface. Such heterogeneity of electrical signals was lost when electrodes of larger pipette diameter were used (5 or 10 μm, which indicates that the electric signal was assessed from a region of <5 μm. Importantly, both pharmacological and mathematical simulation based on transverse (T-tubular distribution suggested that while the AP1 and the initial peak of AP2 are predominantly attributable to the fast, inward Na+ current in myocyte's surface sarcolemma, the late components of AP2 are likely representative of currents associated with L-type Ca2+ channel and Na+/Ca2+ exchanger (NCX currents which are predominantly located in T-tubules. Thus, loose patch recording with narrow-tip pipette provides a valuable tool for studying cardiac electric activity on the subcellular level in the intact heart.

  8. Local vs. Non-local core potentials in electron scattering from sodium atoms

    International Nuclear Information System (INIS)

    Bartschat, K.; Bray, I.

    1996-02-01

    We have tested the use of a local potential instead of the non-local Hartree-Fock potential to represent exchange effects between the valence or the projectile electron and the core in electron scattering from sodium atoms For some of the most detailed observables in this collision system/ the results of the two approaches are nearly identical, even though the effect of the exchange part is shown to be particularly large. (authors). 16 refs., 4 figs

  9. Local versus non-local core potentials in electron scattering from sodium atoms

    International Nuclear Information System (INIS)

    Bartschat, K.; Bray, I.

    1996-01-01

    We have tested the use of a local potential instead of the non-local Hartree-Fock potential to represent exchange effects between the valence or the projectile electron and the core in electron scattering from sodium atoms. For some of the most detailed observables in this collision system, the results of the two approaches are nearly identical, even though the effect of the exchange part is shown to be particularly large. (Author)

  10. Interplay of hot electrons from localized and propagating plasmons.

    Science.gov (United States)

    Hoang, Chung V; Hayashi, Koki; Ito, Yasuo; Gorai, Naoki; Allison, Giles; Shi, Xu; Sun, Quan; Cheng, Zhenzhou; Ueno, Kosei; Goda, Keisuke; Misawa, Hiroaki

    2017-10-03

    Plasmon-induced hot-electron generation has recently received considerable interest and has been studied to develop novel applications in optoelectronics, photovoltaics and green chemistry. Such hot electrons are typically generated from either localized plasmons in metal nanoparticles or propagating plasmons in patterned metal nanostructures. Here we simultaneously generate these heterogeneous plasmon-induced hot electrons and exploit their cooperative interplay in a single metal-semiconductor device to demonstrate, as an example, wavelength-controlled polarity-switchable photoconductivity. Specifically, the dual-plasmon device produces a net photocurrent whose polarity is determined by the balance in population and directionality between the hot electrons from localized and propagating plasmons. The current responsivity and polarity-switching wavelength of the device can be varied over the entire visible spectrum by tailoring the hot-electron interplay in various ways. This phenomenon may provide flexibility to manipulate the electrical output from light-matter interaction and offer opportunities for biosensors, long-distance communications, and photoconversion applications.Plasmon-induced hot electrons have potential applications spanning photodetection and photocatalysis. Here, Hoang et al. study the interplay between hot electrons generated by localized and propagating plasmons, and demonstrate wavelength-controlled polarity-switchable photoconductivity.

  11. Localization of calcium in the cyanobiont and gonidial zone of Cycas revoluta Thunb. by microelectrodes, chlorotetracycline, electron spectroscopic imaging and electron energy loss spectroscopy

    International Nuclear Information System (INIS)

    Caiola, M.G.; Canini, A.; Brandizzi, F.

    1994-01-01

    Ionic calcium concentration was measured in the gonidial zone of fresh coralloid roots by means of calcium microelectrodes. It was 10 -6 M in the apical segments of coralloid roots and increased to 10 -5 M in the gonidial zones of median and basal segments. Loosely membrane-bound calcium was evidenced by using chloro-tetracycline (CTC) or ethylene glycol-bis-(β-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA) and CTC, in cell walls of columnar cells of Cycas and in the cytoplasm of cyanobiont. Sub-cellular localization of calcium was obtained by electron spectroscopic imaging (ESI) and electron energy loss spectroscopy (EELS) analyses applied at transmission electron microscopy on thin, unstained sections of gonidial zone of coralloid roots. By means of these techniques, bound-calcium was detected inside the mucilage of apical and median segments whereas, in the basal segments, it was completely absent. In the heterocysts of apical segments of coralloid, calcium was localized on the envelope, cell walls, thylakoids and cyanophycin granules. In the gonidial zone of the basal segments, dead or degenerating heterocysts completely lacked calcium. Therefore, the high ionic calcium amounts detected in the gonidial zone of median and basal segments could represent a minor calcium uptake by the cells or release by lysed ones. The decreases in nitrogenase activity recorded in the median and basal segments of the coralloid roots paralleled the decrease in calcium amount in heterocyst envelope. (authors)

  12. Electron localization and optical absorption of polygonal quantum rings

    Science.gov (United States)

    Sitek, Anna; Serra, Llorenç; Gudmundsson, Vidar; Manolescu, Andrei

    2015-06-01

    We investigate theoretically polygonal quantum rings and focus mostly on the triangular geometry where the corner effects are maximal. Such rings can be seen as short core-shell nanowires, a generation of semiconductor heterostructures with multiple applications. We show how the geometry of the sample determines the electronic energy spectrum, and also the localization of electrons, with effects on the optical absorption. In particular, we show that irrespective of the ring shape low-energy electrons are always attracted by corners and are localized in their vicinity. The absorption spectrum in the presence of a magnetic field shows only two peaks within the corner-localized state domain, each associated with different circular polarization. This picture may be changed by an external electric field which allows previously forbidden transitions, and thus enables the number of corners to be determined. We show that polygonal quantum rings allow absorption of waves from distant ranges of the electromagnetic spectrum within one sample.

  13. Program For Local-Area-Network Electronic Mail

    Science.gov (United States)

    Weiner, Michael J.

    1989-01-01

    MailRoom is computer program for local-area network (LAN) electronic mail. Enables users of LAN to exchange electronically notes, letters, reminders, or any sort of communication via their computers. Links all users of LAN into communication circle in which messages created, sent, copied, printed, downloaded, uploaded, and deleted through series of menu-driven screens. Includes feature that enables users to determine whether messages sent have been read by receivers. Written in Microsoft QuickBasic.

  14. Localized electronic states: the small radius potential approximation

    International Nuclear Information System (INIS)

    Steslicka, M.; Jurczyszyn, L.

    1984-09-01

    Using a quasi three-dimensional crystal model we investigate the localized electronic states, generated by the crystal surface covered by foreign atoms. Two such states are found in the first forbidden energy gap and, because of their localization properties, called the Tamm-like and adsorption-like states. Using the small radius potential approximation, the properties of both types of states were discussed in detail. (author)

  15. Liver X receptor ligand cytotoxicity in colon cancer cells and not in normal colon epithelial cells depends on LXRβ subcellular localization.

    Science.gov (United States)

    Courtaut, Flavie; Derangère, Valentin; Chevriaux, Angélique; Ladoire, Sylvain; Cotte, Alexia K; Arnould, Laurent; Boidot, Romain; Rialland, Mickaël; Ghiringhelli, François; Rébé, Cédric

    2015-09-29

    Increasing evidence indicates that Liver X Receptors (LXRs) have some anticancer properties. We recently demonstrated that LXR ligands induce colon cancer cell pyroptosis through an LXRβ-dependent pathway. In the present study, we showed that human colon cancer cell lines presented differential cytoplasmic localizations of LXRβ. This localization correlated with caspase-1 activation and cell death induction under treatment with LXR ligand. The association of LXRβ with the truncated form of RXRα (t-RXRα) was responsible for the sequestration of LXRβ in the cytoplasm in colon cancer cells. Moreover t-RXRα was not expressed in normal colon epithelial cells. These cells presented a predominantly nuclear localization of LXRβ and were resistant to LXR ligand cytotoxicity. Our results showed that predominant cytoplasmic localization of LXRβ, which occurs in colon cancer cells but not in normal colon epithelial cells, allowed LXR ligand-induced pyroptosis. This study strengthens the hypothesis that LXRβ could be a promising target in cancer therapy.

  16. Localized Electron Heating by Strong Guide-Field Magnetic Reconnection

    Science.gov (United States)

    Guo, Xuehan; Sugawara, Takumichi; Inomoto, Michiaki; Yamasaki, Kotaro; Ono, Yasushi; UTST Team

    2015-11-01

    Localized electron heating of magnetic reconnection was studied under strong guide-field (typically Bt 15Bp) using two merging spherical tokamak plasmas in Univ. Tokyo Spherical Tokamak (UTST) experiment. Our new slide-type two-dimensional Thomson scattering system documented for the first time the electron heating localized around the X-point. The region of high electron temperature, which is perpendicular to the magnetic field, was found to have a round shape with radius of 2 [cm]. Also, it was localized around the X-point and does not agree with that of energy dissipation term Et .jt . When we include a guide-field effect term Bt / (Bp + αBt) for Et .jt where α =√{ (vin2 +vout2) /v∥2 } , the energy dissipation area becomes localized around the X-point, suggesting that the electrons are accelerated by the reconnection electric field parallel to the magnetic field and thermalized around the X-point. This work was supported by JSPS A3 Foresight Program ``Innovative Tokamak Plasma Startup and Current Drive in Spherical Torus,'' a Grant-in-Aid from the Japan Society for the Promotion of Science (JSPS) Fellows 15J03758.

  17. Wigner-like crystallization of Anderson-localized electron systems with low electron densities

    International Nuclear Information System (INIS)

    Slutskin, A.A.; Kovtun, H.A.; Pepper, M.

    2002-01-01

    We consider an electron system under conditions of strong Anderson localization, taking into account interelectron long-range Coulomb repulsion. We establish that at sufficiently low electron densities and sufficiently low temperatures the Coulomb electron interaction brings about ordering of the Anderson-localized electrons into a structure that is close to an ideal (Wigner) crystal lattice, provided the dimension of the system is > 1. This Anderson-Wigner glass (AWG) is a new macroscopic electron state that, on the one hand, is beyond the conventional Fermi glass concept, and on the other hand, qualitatively differs from the known 'plain' Wigner glass (inherent in self-localized electron systems) in that the random slight electron displacements from the ideal crystal sites essentially depend on the electron density. With increasing electron density the AWG is found to turn into the plain Wigner glass or Fermi glass, depending on the width of the random spread of the electron levels. It is shown that the residual disorder of the AWG is characterized by a multi-valley ground-state degeneracy akin to that in a spin glass. Some general features of the AWG are discussed, and a new conduction mechanism of a creep type is predicted

  18. Non-Local Diffusion of Energetic Electrons during Solar Flares

    Science.gov (United States)

    Bian, N. H.; Emslie, G.; Kontar, E.

    2017-12-01

    The transport of the energy contained in suprathermal electrons in solar flares plays a key role in our understanding of many aspects of flare physics, from the spatial distributions of hard X-ray emission and energy deposition in the ambient atmosphere to global energetics. Historically the transport of these particles has been largely treated through a deterministic approach, in which first-order secular energy loss to electrons in the ambient target is treated as the dominant effect, with second-order diffusive terms (in both energy and angle) generally being either treated as a small correction or even neglected. Here, we critically analyze this approach, and we show that spatial diffusion through pitch-angle scattering necessarily plays a very significant role in the transport of electrons. We further show that a satisfactory treatment of the diffusion process requires consideration of non-local effects, so that the electron flux depends not just on the local gradient of the electron distribution function but on the value of this gradient within an extended region encompassing a significant fraction of a mean free path. Our analysis applies generally to pitch-angle scattering by a variety of mechanisms, from Coulomb collisions to turbulent scattering. We further show that the spatial transport of electrons along the magnetic field of a flaring loop can be modeled as a Continuous Time Random Walk with velocity-dependent probability distribution functions of jump sizes and occurrences, both of which can be expressed in terms of the scattering mean free path.

  19. Determination of localized visibility in off-axis electron holography

    International Nuclear Information System (INIS)

    McLeod, Robert A.; Kupsta, Martin; Malac, Marek

    2014-01-01

    Off-axis electron holography is a wavefront-split interference method for the transmission electron microscope that allows the phase shift and amplitude of the electron wavefront to be separated and quantitatively measured. An additional, third component of the holographic signal is the coherence of the electron wavefront. Historically, wavefront coherence has been evaluated by measurement of the holographic fringe visibility (or contrast) based on the minimum and maximum intensity values. We present a method based on statistical moments is presented that allows allow the visibility to be measured in a deterministic and reproducible fashion suitable for quantitative analysis. We also present an algorithm, based on the Fourier-ratio method, which allows the visibility to be resolved in two-dimensions, which we term the local visibility. The local visibility may be used to evaluate the loss of coherence due to electron scattering within a specimen, or as an aid in image analysis and segmentation. The relationship between amplitude and visibility may be used to evaluate the composition and mass thickness of a specimen by means of a 2-D histogram. Results for a selection of elements (C, Al, Si, Ti, Cr, Cu, Ge, and Au) are provided. All presented visibility metrics are biased at low-dose conditions by the presence of shot-noise, for which we provide methods for empirical normalization to achieve linear response. - Highlights: • Report on a new statistical metric to determine holographic fringe visibility. • Adds new signal to electron holography: measure of electron coherence loss in 2-D. • Provide algorithm to calculate 2-D local visibility map. • Show that amplitude and visibility may be used for compositional analysis and segmentation. • Corrected for data bias such as shot noise

  20. The Subcellular Dynamics of the Gs-Linked Receptor GPR3 Contribute to the Local Activation of PKA in Cerebellar Granular Neurons.

    Science.gov (United States)

    Miyagi, Tatsuhiro; Tanaka, Shigeru; Hide, Izumi; Shirafuji, Toshihiko; Sakai, Norio

    2016-01-01

    G-protein-coupled receptor (GPR) 3 is a member of the GPR family that constitutively activates adenylate cyclase. We have reported that the expression of GPR3 in cerebellar granular neurons (CGNs) contributes to neurite outgrowth and modulates neuronal proliferation and survival. To further identify its role, we have analyzed the precise distribution and local functions of GPR3 in neurons. The fluorescently tagged GPR3 protein was distributed in the plasma membrane, the Golgi body, and the endosomes. In addition, we have revealed that the plasma membrane expression of GPR3 functionally up-regulated the levels of PKA, as measured by a PKA FRET indicator. Next, we asked if the PKA activity was modulated by the expression of GPR3 in CGNs. PKA activity was highly modulated at the neurite tips compared to the soma. In addition, the PKA activity at the neurite tips was up-regulated when GPR3 was transfected into the cells. However, local PKA activity was decreased when endogenous GPR3 was suppressed by a GPR3 siRNA. Finally, we determined the local dynamics of GPR3 in CGNs using time-lapse analysis. Surprisingly, the fluorescent GPR3 puncta were transported along the neurite in both directions over time. In addition, the anterograde movements of the GPR3 puncta in the neurite were significantly inhibited by actin or microtubule polymerization inhibitors and were also disturbed by the Myosin II inhibitor blebbistatin. Moreover, the PKA activity at the tips of the neurites was decreased when blebbistatin was administered. These results suggested that GPR3 was transported along the neurite and contributed to the local activation of PKA in CGN development. The local dynamics of GPR3 in CGNs may affect local neuronal functions, including neuronal differentiation and maturation.

  1. DNA Electronic Fingerprints by Local Spectroscopy on Graphene

    Science.gov (United States)

    Balatsky, Alexander

    2013-03-01

    Working and scalable alternatives to the conventional chemical methods of DNA sequencing that are based on electronic/ionic signatures would revolutionize the field of sequencing. The approach of a single molecule imaging and spectroscopy with unprecedented resolution, achieved by Scanning Tunneling Spectroscopy (STS) and nanopore electronics could enable this revolution. We use the data from our group and others in applying this local scanning tunneling microscopy and illustrate possibilities of electronic sequencing of freeze dried deposits on graphene. We will present two types of calculated fingerprints: first in Local Density of States (LDOS) of DNA nucleotide bases (A,C,G,T) deposited on graphene. Significant base-dependent features in the LDOS in an energy range within few eV of the Fermi level were found in our calculations. These features can serve as electronic fingerprints for the identification of individual bases in STS. In the second approach we present calculated base dependent electronic transverse conductance as DNA translocates through the graphene nanopore. Thus we argue that the fingerprints of DNA-graphene hybrid structures may provide an alternative route to DNA sequencing using STS. Work supported by US DOE, NORDITA.

  2. Radially localized measurements of superthermal electrons using oblique electron cyclotron emission

    International Nuclear Information System (INIS)

    Preische, S.; Efthimion, P.C.; Kaye, S.M.

    1996-05-01

    It is shown that radial localization of optically tin Electron Cyclotron Emission from superthermal electrons can be imposed by observation of emission upshifted from the thermal cyclotron resonance in the horizontal midplane of a tokamak. A new and unique diagnostic has been proposed and operated to make radially localized measurements of superthermal electrons during Lower Hybrid Current Drive on the PBX-M tokamak. The superthermal electron density profile as well as moments of the electron energy distribution as a function of radius are measured during Lower Hybrid Current Drive. The time evolution of these measurements after the Lower Hybrid power is turned off are given and the observed behavior reflects the collisional isotropization of the energy distribution and radial diffusion of the spatial profile

  3. Localization of lead in rat peripheral nerve by electron microscopy

    International Nuclear Information System (INIS)

    Windebank, A.J.; Dyck, P.J.

    1985-01-01

    Lead intoxication in rats reliably produces segmental demyelination. Following a single intravenous injection of radioactive lead, localization of tracer was observed sequentially by quantitative electron microscopical autoradiography. The animals injected had been on a lead-containing diet for 70 days; as a result, the blood-nerve barrier was broken down and demyelination was proceeding. Six hours after a single dose, the lead was localized to the endoneurial space of the peroneal nerve, and 72 hours later, to the myelin membrane. Lead may exert a direct effect on the membrane and alter its stability both by altering the lipid content of the membrane and by directly interfering with the lamellar structure

  4. Crossover in tunneling hops in systems of strongly localized electrons

    International Nuclear Information System (INIS)

    Lien Nguyen, V.; Gamietea, A.D.

    1995-11-01

    Accurate Monte-Carlo simulation data show a consistent crossover in different characters of tunneling hops in two-dimensional systems of strongly localized electrons in the presence of scattering and quantum interference of hopping paths. The results also suggest a negative answer to the question whether there is a two-dimensional sign phase transition. The fractal behaviour observed in the direction perpendicular to the hopping direction is found to be similar to that for eigenstates in one-dimensional localized systems. (author). 16 refs, 6 figs

  5. Plant subcellular proteomics: Application for exploring optimal cell function in soybean.

    Science.gov (United States)

    Wang, Xin; Komatsu, Setsuko

    2016-06-30

    Plants have evolved complicated responses to developmental changes and stressful environmental conditions. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular compartments during plant development and in response to biotic and abiotic stresses. Soybean, which is a valuable legume crop rich in protein and vegetable oil, can grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. To date, numerous proteomic studies have been performed in soybean to examine the specific protein profiles of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum. In this review, methods for the purification and purity assessment of subcellular organelles from soybean are summarized. In addition, the findings from subcellular proteomic analyses of soybean during development and under stresses, particularly flooding stress, are presented and the proteins regulated among subcellular compartments are discussed. Continued advances in subcellular proteomics are expected to greatly contribute to the understanding of the responses and interactions that occur within and among subcellular compartments during development and under stressful environmental conditions. Subcellular proteomics has the potential to investigate the cellular events and interactions among subcellular compartments in response to development and stresses in plants. Soybean could grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. Numerous proteomics of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum was carried out to investigate the respecting proteins and their functions in soybean during development or under stresses. In this review, methods of subcellular-organelle enrichment and purity assessment are summarized. In addition, previous findings of

  6. Sub-chronic inhalation of lead oxide nanoparticles revealed their broad distribution and tissue-specific subcellular localization in target organs

    Czech Academy of Sciences Publication Activity Database

    Dumková, J.; Smutná, Tereza; Vrlíková, Lucie; Le Coustumer, P.; Večeřa, Zbyněk; Dočekal, Bohumil; Mikuška, Pavel; Čapka, Lukáš; Fictum, P.; Hampl, A.; Buchtová, Marcela

    2017-01-01

    Roč. 14, č. 1 (2017), č. článku 55. ISSN 1743-8977 R&D Projects: GA ČR(CZ) GAP503/11/2315; GA ČR(CZ) GBP503/12/G147 Institutional support: RVO:67985904 ; RVO:68081715 Keywords : nanoparticles * lead oxide * electron microscopy * toxicity * inhalation Subject RIV: FP - Other Medical Disciplines; CB - Analytical Chemistry, Separation (UIACH-O) OBOR OECD: Toxicology; Analytical chemistry (UIACH-O) Impact factor: 8.577, year: 2016

  7. Subcellular localization of SV2 and other secretory vesicle components in PC12 cells by an efficient method of preembedding EM immunocytochemistry for cell cultures

    DEFF Research Database (Denmark)

    Tanner, V A; Ploug, Thorkil; Tao-Cheng, J H

    1996-01-01

    substantially improved the efficiency of the preembedding EM ICC procedures for cell cultures. The advantages and related caveats of this method are discussed. SV2 was distinctly localized on dusters of synaptic vesicles and large dense-cored vesicles (LDCV). The distribution of SV2 on these two types...... of secretory vesicles was compared quantitatively to that of another secretory vesicle-associated transmembrane protein, synaptophysin. In cultures under similar experimental conditions, the ratio of SV2 vs synaptophysin ICC staining on synaptic vesicle dusters was about 1:1, whereas it was about 9:1 on LDCV...

  8. Local electronic and electrical properties of functionalized graphene nano flakes

    International Nuclear Information System (INIS)

    Chutia, Arunabhiram; Sahnoun, Riadh; Deka, Ramesh C.; Zhu, Zhigang; Tsuboi, Hideyuki; Takaba, Hiromitsu; Miyamoto, Akira

    2011-01-01

    Based on experimental findings models of amorphous graphene related carbon materials were generated using graphene nano flakes. On the optimized structures detailed local electronic properties were investigated using density functional theory. The electrical conductivities of all these models were also estimated using an in-house program based on tight-binding method. The calculated electrical conductivity values of all the models agreed well with the trend of calculated energy gap and graphitic character.

  9. Interference of HTLV-1 Tax Protein with Cell Polarity Regulators: Defining the Subcellular Localization of the Tax-DLG1 Interaction.

    Science.gov (United States)

    Marziali, Federico; Bugnon Valdano, Marina; Brunet Avalos, Clarisse; Moriena, Lucía; Cavatorta, Ana Laura; Gardiol, Daniela

    2017-11-23

    Human T cell leukemia virus (HTLV)-1 Tax (Tax) protein is very important in viral replication and cell transformation. Tax localizes in the nucleus and cytoplasm in association with organelles. Some activities of Tax depend on interactions with PDZ (PSD-95/Discs Large/Z0-1) domain-containing proteins such as Discs large protein 1 (DLG1) which is involved in cell polarity and proliferation. The DLG1 interaction results in a cytoplasmic co-localization pattern resembling vesicular aggregates, the nature of which is still unknown. To further explore the role of PDZ proteins in HTLV-1 cell transformation, we deeply investigated the Tax-DLG1 association. By fluorescence resonance energy transfer (FRET), we detected, for the first time, the direct binding of Tax to DLG1 within the cell. We showed that the interaction specifically affects the cellular distribution of not only DLG1, but also Tax. After studying different cell structures, we demonstrated that the aggregates distribute into the Golgi apparatus in spatial association with the microtubule-organizing center (MTOC). This study contributes to understand the biological significance of Tax-PDZ interactions.

  10. Interference of HTLV-1 Tax Protein with Cell Polarity Regulators: Defining the Subcellular Localization of the Tax-DLG1 Interaction

    Directory of Open Access Journals (Sweden)

    Federico Marziali

    2017-11-01

    Full Text Available Human T cell leukemia virus (HTLV-1 Tax (Tax protein is very important in viral replication and cell transformation. Tax localizes in the nucleus and cytoplasm in association with organelles. Some activities of Tax depend on interactions with PDZ (PSD-95/Discs Large/Z0-1 domain–containing proteins such as Discs large protein 1 (DLG1 which is involved in cell polarity and proliferation. The DLG1 interaction results in a cytoplasmic co-localization pattern resembling vesicular aggregates, the nature of which is still unknown. To further explore the role of PDZ proteins in HTLV-1 cell transformation, we deeply investigated the Tax-DLG1 association. By fluorescence resonance energy transfer (FRET, we detected, for the first time, the direct binding of Tax to DLG1 within the cell. We showed that the interaction specifically affects the cellular distribution of not only DLG1, but also Tax. After studying different cell structures, we demonstrated that the aggregates distribute into the Golgi apparatus in spatial association with the microtubule-organizing center (MTOC. This study contributes to understand the biological significance of Tax-PDZ interactions.

  11. Application of local vacuum slide sealing electron beam welding procedure

    International Nuclear Information System (INIS)

    Sato, Shozo; Takano, Genta; Minami, Masaharu; Enami, Koji; Uchikawa, Takashi; Kuri, Shuhei

    1982-01-01

    Electron beam welding process is efficient and is superior in workmanship and its application to the welding of large plate structures is eagerly awaited. However, since electron beam welding is generally performed with the object of welding entirely put in a vacuum chamber, high welding cost becomes a problem. In response to this demand, two kinds of local vacuum slide sealing type electron beam welding machines have been developed. These welding machines are designed to perform welding with only the neighborhood of the weld line put in vacuum, one of which is for longitudinal joints and the other for circumferential joints. The welding machine for circumferential joints has been put to practical use for the welding of nucear fusion reactor vacuum vessels (outside diameter 3.5 m, inside diameter 1.7 m), showing that it is applicable to the welding of large structures. (author)

  12. Local texture measurements with the scanning electron microscope

    International Nuclear Information System (INIS)

    Gottstein, G.; Engler, O.

    1993-01-01

    Techniques for convenient measurement of the crystallographic orientation of small volumes in bulk samples by electron diffraction in the SEM are discussed. They make use of Selected Area Electron Channelling Patterns (SAECP) and Electron Back Scattering Patterns (EBSP). The principle of pattern formation as well as measuring and evaluation procedure are introduced. The methods offer a viable procedure for obtaining information on the spatial arrangement of orientations, i.e. on orientation topography. Thus, they provide a new level of information on crystallographic texture. An application of the techniques for local texture measurements is demonstrated by an example, namely for investigation of considering the recrystallization behaviour of binary Al-1.3% Mn with large precipitates. Finally, further developments of the EBSP technique are addressed. (orig.)

  13. Localization and regulation of mouse pantothenate kinase 2 [The PanK2 Genes of Mouse and Human Specify Proteins with Distinct Subcellular Locations

    Energy Technology Data Exchange (ETDEWEB)

    Leonardi, Roberta [St. Jude Children' s Research Hospital, Memphis, TN (United States); Zhang, Yong-Mei [St. Jude Children' s Research Hospital, Memphis, TN (United States); Lykidis, Athanasios [DOE Joint Genome Inst., Walnut Creek, CA (United States); Rock, Charles O. [St. Jude Children' s Research Hospital, Memphis, TN (United States); Jackowski, Suzanne [St. Jude Children' s Research Hospital, Memphis, TN (United States)

    2007-09-07

    Coenzyme A (CoA) biosynthesis is initiated by pantothenatekinase (PanK) and CoA levels are controlled through differentialexpression and feedback regulation of PanK isoforms. PanK2 is amitochondrial protein in humans, but comparative genomics revealed thatacquisition of a mitochondrial targeting signal was limited to primates.Human and mouse PanK2 possessed similar biochemical properties, withinhibition by acetylCoA and activation by palmitoylcarnitine. Mouse PanK2localized in the cytosol, and the expression of PanK2 was higher in humanbrain compared to mouse brain. Differences in expression and subcellularlocalization should be considered in developing a mouse model for humanPanK2 deficiency.

  14. Yersinia pestis insecticidal-like toxin complex (Tc family proteins: characterization of expression, subcellular localization, and potential role in infection of the flea vector

    Directory of Open Access Journals (Sweden)

    Spinner Justin L

    2012-12-01

    Full Text Available Abstract Background Toxin complex (Tc family proteins were first identified as insecticidal toxins in Photorhabdus luminescens and have since been found in a wide range of bacteria. The genome of Yersinia pestis, the causative agent of bubonic plague, contains a locus that encodes the Tc protein homologues YitA, YitB, YitC, and YipA and YipB. Previous microarray data indicate that the Tc genes are highly upregulated by Y. pestis while in the flea vector; however, their role in the infection of fleas and pathogenesis in the mammalian host is unclear. Results We show that the Tc proteins YitA and YipA are highly produced by Y. pestis while in the flea but not during growth in brain heart infusion (BHI broth at the same temperature. Over-production of the LysR-type regulator YitR from an exogenous plasmid increased YitA and YipA synthesis in broth culture. The increase in production of YitA and YipA correlated with the yitR copy number and was temperature-dependent. Although highly synthesized in fleas, deletion of the Tc proteins did not alter survival of Y. pestis in the flea or prevent blockage of the proventriculus. Furthermore, YipA was found to undergo post-translational processing and YipA and YitA are localized to the outer membrane of Y. pestis. YitA was also detected by immunofluorescence microscopy on the surface of Y. pestis. Both YitA and YipA are produced maximally at low temperature but persist for several hours after transfer to 37°C. Conclusions Y. pestis Tc proteins are highly expressed in the flea but are not essential for Y. pestis to stably infect or produce a transmissible infection in the flea. However, YitA and YipA localize to the outer membrane and YitA is exposed on the surface, indicating that at least YitA is present on the surface when Y. pestis is transmitted into the mammalian host from the flea.

  15. Identification of a multifunctional protein, PhaM, that determines number, surface to volume ratio, subcellular localization and distribution to daughter cells of poly(3-hydroxybutyrate), PHB, granules in Ralstonia eutropha H16.

    Science.gov (United States)

    Pfeiffer, Daniel; Wahl, Andreas; Jendrossek, Dieter

    2011-11-01

    A two-hybrid approach was applied to screen for proteins with the ability to interact with PHB synthase (PhaC1) of Ralstonia eutropha. The H16_A0141 gene (phaM) was identified in the majority of positive clones. PhaM (26.6 kDa) strongly interacted with PhaC1 and with phasin PhaP5 but not with PhaP1 or other PHB granule-associated proteins. A ΔphaM mutant accumulated only one or two large PHB granules instead of three to six medium-sized PHB granules of the wild type, and distribution of granules to daughter cells was disordered. All three phenotypes (number, size and distribution of PHB granules) were reversed by reintroduction of phaM. Purified PhaM revealed DNA-binding properties in gel mobility shift experiments. Expression of a fusion of the yellow fluorescent protein (eYfp) with PhaM resulted in formation of many small fluorescent granules that were bound to the nucleoid region. Remarkably, an eYfp-PhaP5 fusion localized at the cell poles in a PHB-negative background and overexpression of eYfp-PhaP5 in the wild type conferred binding of PHB granules to the cell poles. In conclusion, subcellular localization of PHB granules in R. eutropha depends on a concerted expression of at least three PHB granule-associated proteins, namely PhaM, PhaP5 and PHB synthase PhaC1. © 2011 Blackwell Publishing Ltd.

  16. Molecular cloning, functional expression and subcellular localization of two putative vacuolar voltage-gated chloride channels in rice (Oryza sativa L.).

    Science.gov (United States)

    Nakamura, Atsuko; Fukuda, Atsunori; Sakai, Shingo; Tanaka, Yoshiyuki

    2006-01-01

    We isolated two cDNA clones (OsCLC-1 and OsCLC-2) homologous to tobacco CLC-Nt1, which encodes a voltage-gated chloride channel, from rice (Oryza sativa L. ssp. japonica, cv. Nipponbare). The deduced amino acid sequences were highly conserved (87.9% identity with each other). Southern blot analysis of the rice genomic DNA revealed that OsCLC-1 and OsCLC-2 were single-copy genes on chromosomes 4 and 2, respectively. OsCLC-1 was expressed in most tissues, whereas OsCLC-2 was expressed only in the roots, nodes, internodes and leaf sheaths. The level of expression of OsCLC-1, but not of OsCLC-2, was increased by treatment with NaCl. Both genes could partly substitute for GEF1, which encodes the sole chloride channel in yeast, by restoring growth under ionic stress. These results indicate that both genes are chloride channel genes. The proteins from both genes were immunochemically detected in the tonoplast fraction. Tagged synthetic green fluorescent protein which was fused to OsCLC-1 or OsCLC-2 localized in the vacuolar membranes. These results indicate that the proteins may play a role in the transport of chloride ions across the vacuolar membrane. We isolated loss-of-function mutants of both genes from a panel of rice mutants produced by the insertion of a retrotransposon, Tos17, in the exon region, and found inhibition of growth at all life stages.

  17. Delta opioid receptor on equine sperm cells: subcellular localization and involvement in sperm motility analyzed by computer assisted sperm analyzer (CASA

    Directory of Open Access Journals (Sweden)

    Lacalandra Giovanni M

    2010-06-01

    Full Text Available Abstract Background Opioid receptors and endogenous opioid peptides act not only in the control of nociceptive pathways, indeed several reports demonstrate the effects of opiates on sperm cell motility and morphology suggesting the importance of these receptors in the modulation of reproduction in mammals. In this study we investigated the expression of delta opioid receptors on equine spermatozoa by western blot/indirect immunofluorescence and its relationship with sperm cell physiology. Methods We analyzed viability, motility, capacitation, acrosome reaction and mitochondrial activity in the presence of naltrindole and DPDPE by means of a computer assisted sperm analyzer and a fluorescent confocal microscope. The evaluation of viability, capacitation and acrosome reaction was carried out by the double CTC/Hoechst staining, whereas mitochondrial activity was assessed by means of MitoTracker Orange dye. Results We showed that in equine sperm cells, delta opioid receptor is expressed as a doublet of 65 and 50 kDa molecular mass and is localized in the mid piece of tail; we also demonstrated that naltrindole, a delta opioid receptor antagonist, could be utilized in modulating several physiological parameters of the equine spermatozoon in a dose-dependent way. We also found that low concentrations of the antagonist increase sperm motility whereas high concentrations show the opposite effect. Moreover low concentrations hamper capacitation, acrosome reaction and viability even if the percentage of cells with active mitochondria seems to be increased; the opposite effect is exerted at high concentrations. We have also observed that the delta opioid receptor agonist DPDPE is scarcely involved in affecting the same parameters at the employed concentrations. Conclusions The results described in this paper add new important details in the comprehension of the mammalian sperm physiology and suggest new insights for improving reproduction and for

  18. Local Trigger Electronics for the CMS Drift Tubes Muon detector

    CERN Document Server

    Travaglini, R

    2003-01-01

    In the CMS detector in preparation for the CERN LHC collider, the Drift Tubes Muon Chambers are equipped with mini-crates hosting custom electronics for fast data processing and local trigger generation. In particular the Trigger Server of a DTC consists of Track Sorter Slave ASICs and a Track Sorter Master system. The trigger electronics boards are in production, to be ready for the muon detector installation in the CMS barrel starting at the end of 2003.In this work, the performance of the Trigger Server will be discussed, on the basis both of high-statistics tests with predefined patterns and of test beam data collected at CERN, where a DTC was exposed to a muon beam having an LHC-like bunch structure. Finally, some system performance expectations, concerning radiation tolerance and signal transmission issues during LHC running, will be also discussed.

  19. Electronic properties of polycrystalline graphene under large local strain

    International Nuclear Information System (INIS)

    He, Xin; Tang, Ning; Duan, Junxi; Mei, Fuhong; Meng, Hu; Lu, Fangchao; Xu, Fujun; Yang, Xuelin; Gao, Li; Wang, Xinqiang; Shen, Bo; Ge, Weikun

    2014-01-01

    To explore the transport properties of polycrystalline graphene under large tensile strain, a strain device has been fabricated using piezocrystal to load local strain onto graphene, up to 22.5%. Ionic liquid gate whose capability of tuning carrier density being much higher than that of a solid gate is used to survey the transfer characteristics of the deformed graphene. The conductance of the Dirac point and field effect mobility of electrons and holes is found to decrease with increasing strain, which is attributed to the scattering of the graphene grain boundaries, the strain induced change of band structure, and defects. However, the transport gap is still not opened. Our study is helpful to evaluate the application of graphene in stretchable electronics.

  20. Localization of electrons by electron-electron interaction in an Anderson model

    International Nuclear Information System (INIS)

    Ritala, R.K.; Kurkijaervi, J.

    1981-01-01

    We study the effect of attractive Hubbard interaction on disordered electron system. We map the interacting system back to noninteracting one and determine self-consistently the disorder change due to interaction in the system. (author)

  1. Local energy equation for two-electron atoms and relation between kinetic energy and electron densities

    International Nuclear Information System (INIS)

    March, N.H.

    2002-08-01

    In early work, Dawson and March [J. Chem. Phys. 81, 5850 (1984)] proposed a local energy method for treating both Hartree-Fock and correlated electron theory. Here, an exactly solvable model two-electron atom with pure harmonic interactions is treated in its ground state in the above context. A functional relation between the kinetic energy density t(r) at the origin r=0 and the electron density p(r) at the same point then emerges. The same approach is applied to the Hookean atom; in which the two electrons repel with Coulombic energy e 2 /r 12 , with r 12 the interelectronic separation, but are still harmonically confined. Again the kinetic energy density t(r) is the focal point, but now generalization away from r=0 is also effected. Finally, brief comments are added about He-like atomic ions in the limit of large atomic number. (author)

  2. Expression and subcellular localization of antiporter regulating ...

    African Journals Online (AJOL)

    Md. Imtiaz Uddin

    2012-02-14

    Feb 14, 2012 ... important factors, the limitation of gas diffusion under water and reduced irradiance, which impair photo- synthesis ... functions as cell expansion, universal stress protein, and putative ..... They catalyze the exchange of Na+.

  3. Subcellular localization of casein kinase I

    DEFF Research Database (Denmark)

    Grankowski, N; Issinger, O G

    1990-01-01

    An anti-yeast CKI antiserum was shown to cross-react with CKI isolated from Krebs II mouse ascites tumour cells. The mammalian CKI showed virtually the same molecular mass (app. 45 kDa) as the yeast enzyme. By immunofluorescence it could be shown that CKI is preferably located in the nucleolus....

  4. Local Electronic And Dielectric Properties at Nanosized Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Bonnell, Dawn A. [Univ. of Pennsylvania, Philadelphia, PA (United States)

    2015-02-23

    Final Report to the Department of Energy for period 6/1/2000 to 11/30/2014 for Grant # DE-FG02-00ER45813-A000 to the University of Pennsylvania Local Electronic And Dielectric Properties at Nanosized Interfaces PI: Dawn Bonnell The behavior of grain boundaries and interfaces has been a focus of fundamental research for decades because variations of structure and composition at interfaces dictate mechanical, electrical, optical and dielectric properties in solids. Similarly, the consequence of atomic and electronic structures of surfaces to chemical and physical interactions are critical due to their implications to catalysis and device fabrication. Increasing fundamental understanding of surfaces and interfaces has materially advanced technologies that directly bear on energy considerations. Currently, exciting developments in materials processing are enabling creative new electrical, optical and chemical device configurations. Controlled synthesis of nanoparticles, semiconducting nanowires and nanorods, optical quantum dots, etc. along with a range of strategies for assembling and patterning nanostructures portend the viability of new devices that have the potential to significantly impact the energy landscape. As devices become smaller the impact of interfaces and surfaces grows geometrically. As with other nanoscale phenomena, small interfaces do not exhibit the same properties as do large interfaces. The size dependence of interface properties had not been explored and understanding at the most fundamental level is necessary to the advancement of nanostructured devices. An equally important factor in the behavior of interfaces in devices is the ability to examine the interfaces under realistic conditions. For example, interfaces and boundaries dictate the behavior of oxide fuel cells which operate at extremely high temperatures in dynamic high pressure chemical environments. These conditions preclude the characterization of local properties during fuel cell

  5. Electron localization in liquid hydrocarbons: The Anderson model

    International Nuclear Information System (INIS)

    Hug, Gordon L.; Mozumder, A.

    2008-01-01

    Anderson's model is applied for initial localization in liquid hydrocarbons (particularly n-alkanes) in conjunction with certain results of scaling theory. Medium connectivity is calculated using experimental X-ray data on liquid structure, from which critical disorder (W/V) c is computed, where W is diagonal disorder and V is the transfer energy. Actual W prevailing in the liquid is computed from anisotropic molecular polarizability. V is estimated by a heuristic procedure originating in scaling theory. These values are used to compute the percentage of initially delocalized states available for low-energy electrons in alkane liquids. This percentage decreases monotonically from methane (100%) to n-pentane and beyond (0%). In ethane and propane, the initial states are highly delocalized (97.6% and 83.9%, respectively). Subsequent trapping changes the situation as evidenced in mobility studies. Butane presents a partially, intermediate delocalized case (53.2%)

  6. Fundamental length, bubble electrons and non-local quantum electrodynamics

    International Nuclear Information System (INIS)

    Hsu, J.P.; Mac, E.

    1977-06-01

    Based on the concept of a bubble electron and the approach of Pais and Uhlenbeck, one constructs a finite quantum electrodynamics which is relativistically invariant, macro-causal and unitary. In this model, fields and their interaction are local, but the action function of free fields is nonlocal. The propagators are modified so that a fundamental length L is naturally introduced to physics. The modified static potential is given by V(r) = e/r for r greater than L and V(r) = 0 for r less than L, which is produced by the bubble source r -1 ddelta(r-L)/dr rather than a point source. It is found that L less than 4 x 10 -15 cm. Experimental consequences and modifications of strict causality at short distances, vertical bars 2 vertical bar approximately L 2 , are discussed

  7. Electron localization, polarons and clustered states in manganites

    International Nuclear Information System (INIS)

    Mannella, N.

    2004-01-01

    Full text: A recent multi-spectroscopic study of prototypical colossal magnetoresistance (CMR) compounds La 1-x Sr x MnO 3 (LSMO, x = 0.3, 0.4) using photoemission (PE), x-ray absorption (XAS), x-ray emission (XES) and extended x-ray absorption e structure (EXAFS) has exposed a dramatic change in the electronic structure on crossing the ferromagnetic-to-paramagnetic transition temperature (T C ). In particular, this investigation revealed an increase of the Mn magnetic moment by ca. 1 Bohr magneton and charge transfer to the Mn atom on crossing T C concomitant with the presence of Jahn-Teller distortions, thus providing direct evidence of lattice polaron formation. These results thus challenge the belief of some authors that the LSMO compounds are canonical double-exchange (DE) systems in which polaron formation is unimportant, and thus help to unify the theoretical description of the CMR oxides. The relationship of these data to other recent work suggesting electron localization, polarons and phase separation, along with additional measurements of magnetic susceptibility indicating the formation of ferromagnetic clusters in the metallic paramagnetic state above T C will be discussed

  8. MAILROOM- A LOCAL AREA NETWORK ELECTRONIC MAIL PROGRAM

    Science.gov (United States)

    Weiner, M. J.

    1994-01-01

    The Mailroom program is a Local Area Network (LAN) electronic mail program. It allows LAN users to electronically exchange notes, letters, reminders, or any sort of communication via their computer. The Mailroom program links all LAN users into a communication circle where messages can be created, sent, copied, printed, downloaded, uploaded, and deleted through a series of menu-driven screens. Mailroom includes a feature which allows users to determine if a message they have sent has been read by the receiver. Each user must be separately installed and removed from Mailroom as they join or leave the network. Mailroom comes with a program that accomplishes this with minimum of effort on the part of the Network Administrator/Manager. There is also a program that allows the Network Administrator/Manager to install Mailroom on each user's workstation so that on execution of Mailroom the user's station may be identified and the configurations settings activated. It will create its own configuration and data/supporting files during the setup and installation process. The Mailroom program is written in Microsoft QuickBasic. It was developed to run on networked IBM XT/ATs or compatibles and requires that all participating workstations share a common drive. It has been implemented under DOS 3.2 and has a memory requirement of 71K. Mailroom was developed in 1988.

  9. Dynamical localization of two electrons in triple-quantum-dot shuttles

    International Nuclear Information System (INIS)

    Qu, Jinxian; Duan, Suqing; Yang, Ning

    2012-01-01

    The dynamical localization phenomena in two-electron quantum-dot shuttles driven by an ac field have been investigated and analyzed by the Floquet theory. The dynamical localization occurs near the anti-crossings in Floquet eigenenergy spectrum. The oscillation of the quantum-dot shuttles may increase the possibility of the dynamical localization. Especially, even if the two electrons are initialized in two neighbor dots, they can be localized there for appropriate intensity of the driven field. The studies may help the understanding of dynamical localization in electron shuttles and expand the application potential of nanoelectromechanical devices. -- Highlights: ► The dynamical localization in electron shuttle is studied by Floquet theory. ► There is a relation between quasi-energy anti-crossings and dynamical localization. ► The oscillation of quantum dot increases the dynamical localization. ► Even the electrons are initialized in different dots, the localization can occur.

  10. Very local interstellar spectra for galactic electrons, protons and helium

    Energy Technology Data Exchange (ETDEWEB)

    Potgieter, Marius S., E-mail: Marius.Potgieter@nwu.ac.za [Centre for Space Research, North-West University (South Africa)

    2014-07-01

    The local interstellar spectra (LIS) for cosmic rays at energies below ∼30 GeV/nuc are increasingly obscured from view at Earth by solar modulation, the lower the energy becomes. These charged particles encounter significant changes in the heliosphere, over an 11-year cycle, which include processes such as convection, diffusion, adiabatic energy losses and gradient, curvature and current sheet drifts. Particle drifts cause charge-sign-dependent modulation and a 22-year cycle, adding complexity to determining the respective very LIS from observations only at Earth. However, with measurements now made by the Voyager 1 spacecraft in the vicinity of the helio pause, it is possible to determine a very LIS for galactic electrons between ∼5 and ∼120 MeV. At these low energies, also galactic protons observed in the outer heliosphere had been completely obscured by the so-called anomalous component which is accelerated inside the helio sheath. Since August 2012, these anomalous cosmic rays are substantially depleted at Voyager 1 so that for cosmic ray ions, it is now possible to obtain a lower limit to their very LIS. Combining numerical modelling of solar modulation with the accurate measurements by the PAMELA mission and with Voyager observations, the lower limit of the very LIS for electrons, protons and helium and other ions can be determined from ∼5 MeV and above. These spectra are called helio pause spectra which is considered to be the lowest possible very LIS. Also, from an astrophysics point of view, the determination of what can be called a very LIS, not just an averaged galactic spectrum, is encouraging. The mentioned aspects are discussed, focusing on a comparison of recent heliospheric observations and corresponding solar modulation modelling. (author)

  11. Electronically Tuned Local Oscillators for the NOEMA Interferometer

    Science.gov (United States)

    Mattiocco, Francois; Garnier, Olivier; Maier, Doris; Navarrini, Alessandro; Serres, Patrice

    2016-03-01

    We present an overview of the electronically tuned local oscillator (LO) system developed at the Institut de RadioAstronomie millimetrique (IRAM) for the superconductor-insulator-superconductor (SIS) receivers of the NOrthern Extended Millimeter Array interferometer (NOEMA). We modified the frequency bands and extended the bandwidths of the LO designs developed by the National Radio Astronomy Observatory (NRAO) for the Atacama Large Millimeter Array (ALMA) project to cover the four NOEMA LO frequency ranges 82-108.3 GHz (Band 1), 138.6-171.3 GHz (Band 2), 207.7-264.4 GHz (Band 3), and 283-365 GHz (Band 4). The NOEMA LO system employs commercially available MMICs and GaAs millimeter MMICs from NRAO which are micro-assembled into active multiplied chain (AMC) and power amplifier (PA) modules. We discuss the problem of the LO spurious harmonics and of the LO signal directly multiplied by the SIS mixers that add extra noise and lead to detections of unwanted spectral lines from higher order sidebands. A waveguide filter in the LO path is used to reduce the higher order harmonics level of the LO at the output of the final frequency multiplier, thus mitigating the undesired effects and improving the system noise temperature.

  12. Plant sterol metabolism. Δ7-Sterol-C5-Desaturase (STE1/DWARF7), Δ5,7-Sterol-Δ7-Reductase (DWARF5) and Δ24-Sterol-Δ24-Reductase (DIMINUTO/DWARF1) show multiple subcellular localizations in Arabidopsis thaliana (Heynh) L

    DEFF Research Database (Denmark)

    Silvestro, Daniele; Andersen, Tonni Grube; Schaller, Hubert

    2013-01-01

    in the corresponding enzymes. All fusion proteins were found to localize in the endoplasmic reticulum in functionally complemented plants. The results show that both ¿(5,7)-sterol-¿(7)-reductase and ¿(24)-sterol-¿(24)-reductase are in addition localized to the plasma membrane, whereas ¿(7)-sterol-C(5)-desaturase......Sterols are crucial lipid components that regulate membrane permeability and fluidity and are the precursors of bioactive steroids. The plant sterols exist as three major forms, free sterols, steryl glycosides and steryl esters. The storage of steryl esters in lipid droplets has been shown...... to contribute to cellular sterol homeostasis. To further document cellular aspects of sterol biosynthesis in plants, we addressed the question of the subcellular localization of the enzymes implicated in the final steps of the post-squalene biosynthetic pathway. In order to create a clear localization map...

  13. Analysis of potato virus X replicase and TGBp3 subcellular locations

    International Nuclear Information System (INIS)

    Bamunusinghe, Devinka; Hemenway, Cynthia L.; Nelson, Richard S.; Sanderfoot, Anton A.; Ye, Chang M.; Silva, Muniwarage A.T.; Payton, M.; Verchot-Lubicz, Jeanmarie

    2009-01-01

    Potato virus X (PVX) infection leads to certain cytopathological modifications of the host endomembrane system. The subcellular location of the PVX replicase was previously unknown while the PVX TGBp3 protein was previously reported to reside in the ER. Using PVX infectious clones expressing the green fluorescent protein reporter, and antisera detecting the PVX replicase and host membrane markers, we examined the subcellular distribution of the PVX replicase in relation to the TGBp3. Confocal and electron microscopic observations revealed that the replicase localizes in membrane bound structures that derive from the ER. A subset of TGBp3 resides in the ER at the same location as the replicase. Sucrose gradient fractionation showed that the PVX replicase and TGBp3 proteins co-fractionate with ER marker proteins. This localization represents a region where both proteins may be synthesized and/or function. There is no evidence to indicate that either PVX protein moves into the Golgi apparatus. Cerulenin, a drug that inhibits de novo membrane synthesis, also inhibited PVX replication. These combined data indicate that PVX replication relies on ER-derived membrane recruitment and membrane proliferation.

  14. Targeted nanodiamonds for identification of subcellular protein assemblies in mammalian cells

    Science.gov (United States)

    Lake, Michael P.; Bouchard, Louis-S.

    2017-01-01

    Transmission electron microscopy (TEM) can be used to successfully determine the structures of proteins. However, such studies are typically done ex situ after extraction of the protein from the cellular environment. Here we describe an application for nanodiamonds as targeted intensity contrast labels in biological TEM, using the nuclear pore complex (NPC) as a model macroassembly. We demonstrate that delivery of antibody-conjugated nanodiamonds to live mammalian cells using maltotriose-conjugated polypropylenimine dendrimers results in efficient localization of nanodiamonds to the intended cellular target. We further identify signatures of nanodiamonds under TEM that allow for unambiguous identification of individual nanodiamonds from a resin-embedded, OsO4-stained environment. This is the first demonstration of nanodiamonds as labels for nanoscale TEM-based identification of subcellular protein assemblies. These results, combined with the unique fluorescence properties and biocompatibility of nanodiamonds, represent an important step toward the use of nanodiamonds as markers for correlated optical/electron bioimaging. PMID:28636640

  15. Targeted nanodiamonds for identification of subcellular protein assemblies in mammalian cells.

    Science.gov (United States)

    Lake, Michael P; Bouchard, Louis-S

    2017-01-01

    Transmission electron microscopy (TEM) can be used to successfully determine the structures of proteins. However, such studies are typically done ex situ after extraction of the protein from the cellular environment. Here we describe an application for nanodiamonds as targeted intensity contrast labels in biological TEM, using the nuclear pore complex (NPC) as a model macroassembly. We demonstrate that delivery of antibody-conjugated nanodiamonds to live mammalian cells using maltotriose-conjugated polypropylenimine dendrimers results in efficient localization of nanodiamonds to the intended cellular target. We further identify signatures of nanodiamonds under TEM that allow for unambiguous identification of individual nanodiamonds from a resin-embedded, OsO4-stained environment. This is the first demonstration of nanodiamonds as labels for nanoscale TEM-based identification of subcellular protein assemblies. These results, combined with the unique fluorescence properties and biocompatibility of nanodiamonds, represent an important step toward the use of nanodiamonds as markers for correlated optical/electron bioimaging.

  16. Observation of electron weak localization and correlation effects in disordered graphene

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    We have studied the electron transport properties of a disordered graphene sample, where the disorder was intentionally strengthened by Ga+ ion irradiation. The magneto-conductance of the sample exhibits a typical two-dimensional electron weak localization behavior, with electron-electron interaction as the dominant dephasing mechanism. The absence of electron anti-weak localization in the sample implies strong intersublattice and/or intervalley scattering caused by the disorders. The temperature and bias-voltage dependencies of conductance clearly reveal the suppression of conductance at low energies, indicating opening of a Coulomb gap due to electron-electron interaction in the disordered graphene sample.

  17. Plasma effects on subcellular structures

    International Nuclear Information System (INIS)

    Gweon, Bomi; Kim, Dan Bee; Jung, Heesoo; Choe, Wonho; Kim, Daeyeon; Shin, Jennifer H.

    2010-01-01

    Atmospheric pressure helium plasma treated human hepatocytes exhibit distinctive zones of necrotic and live cells separated by a void. We propose that plasma induced necrosis is attributed to plasma species such as oxygen radicals, charged particles, metastables and/or severe disruption of charged cytoskeletal proteins. Interestingly, uncharged cytoskeletal intermediate filaments are only minimally disturbed by plasma, elucidating the possibility of plasma induced electrostatic effects selectively destroying charged proteins. These bona fide plasma effects, which inflict alterations in specific subcellular structures leading to necrosis and cellular detachment, were not observed by application of helium flow or electric field alone.

  18. Monoterpene biosynthesis potential of plant subcellular compartments.

    Science.gov (United States)

    Dong, Lemeng; Jongedijk, Esmer; Bouwmeester, Harro; Van Der Krol, Alexander

    2016-01-01

    Subcellular monoterpene biosynthesis capacity based on local geranyl diphosphate (GDP) availability or locally boosted GDP production was determined for plastids, cytosol and mitochondria. A geraniol synthase (GES) was targeted to plastids, cytosol, or mitochondria. Transient expression in Nicotiana benthamiana indicated local GDP availability for each compartment but resulted in different product levels. A GDP synthase from Picea abies (PaGDPS1) was shown to boost GDP production. PaGDPS1 was also targeted to plastids, cytosol or mitochondria and PaGDPS1 and GES were coexpressed in all possible combinations. Geraniol and geraniol-derived products were analyzed by GC-MS and LC-MS, respectively. GES product levels were highest for plastid-targeted GES, followed by mitochondrial- and then cytosolic-targeted GES. For each compartment local boosting of GDP biosynthesis increased GES product levels. GDP exchange between compartments is not equal: while no GDP is exchanged from the cytosol to the plastids, 100% of GDP in mitochondria can be exchanged to plastids, while only 7% of GDP from plastids is available for mitochondria. This suggests a direct exchange mechanism for GDP between plastids and mitochondria. Cytosolic PaGDPS1 competes with plastidial GES activity, suggesting an effective drain of isopentenyl diphosphate from the plastids to the cytosol. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  19. Electronic Document Imaging and Optical Storage Systems for Local Governments: An Introduction. Local Government Records Technical Information Series. Number 21.

    Science.gov (United States)

    Schwartz, Stanley F.

    This publication introduces electronic document imaging systems and provides guidance for local governments in New York in deciding whether such systems should be adopted for their own records and information management purposes. It advises local governments on how to develop plans for using such technology by discussing its advantages and…

  20. High-sensitivity visualization of localized electric fields using low-energy electron beam deflection

    Science.gov (United States)

    Jeong, Samuel; Ito, Yoshikazu; Edwards, Gary; Fujita, Jun-ichi

    2018-06-01

    The visualization of localized electronic charges on nanocatalysts is expected to yield fundamental information about catalytic reaction mechanisms. We have developed a high-sensitivity detection technique for the visualization of localized charges on a catalyst and their corresponding electric field distribution, using a low-energy beam of 1 to 5 keV electrons and a high-sensitivity scanning transmission electron microscope (STEM) detector. The highest sensitivity for visualizing a localized electric field was ∼0.08 V/µm at a distance of ∼17 µm from a localized charge at 1 keV of the primary electron energy, and a weak local electric field produced by 200 electrons accumulated on the carbon nanotube (CNT) apex can be visualized. We also observed that Au nanoparticles distributed on a CNT forest tended to accumulate a certain amount of charges, about 150 electrons, at a ‑2 V bias.

  1. Exact solution of a coupled spin–electron linear chain composed of localized Ising spins and mobile electrons

    International Nuclear Information System (INIS)

    Čisárová, Jana; Strečka, Jozef

    2014-01-01

    Exact solution of a coupled spin–electron linear chain composed of localized Ising spins and mobile electrons is found. The investigated spin–electron model is exactly solvable by the use of a transfer-matrix method after tracing out the degrees of freedom of mobile electrons delocalized over a couple of interstitial (decorating) sites. The exact ground-state phase diagram reveals an existence of five phases with different number of mobile electrons per unit cell, two of which are ferromagnetic, two are paramagnetic and one is antiferromagnetic. We have studied in particular the dependencies of compressibility and specific heat on temperature and electron density. - Highlights: • A coupled spin–electron chain composed of Ising spins and mobile electrons is exactly solved. • Quantum paramagnetic, ferromagnetic and antiferromagnetic ground states are found. • A compressibility shows a non-monotonous dependence on temperature and electron density. • Thermal dependences of specific heat display two distinct peaks

  2. Challenges of biological sample preparation for SIMS imaging of elements and molecules at subcellular resolution

    Science.gov (United States)

    Chandra, Subhash

    2008-12-01

    Secondary ion mass spectrometry (SIMS) based imaging techniques capable of subcellular resolution characterization of elements and molecules are becoming valuable tools in many areas of biology and medicine. Due to high vacuum requirements of SIMS, the live cells cannot be analyzed directly in the instrument. The sample preparation, therefore, plays a critical role in preserving the native chemical composition for SIMS analysis. This work focuses on the evaluation of frozen-hydrated and frozen freeze-dried sample preparations for SIMS studies of cultured cells with a CAMECA IMS-3f dynamic SIMS ion microscope instrument capable of producing SIMS images with a spatial resolution of 500 nm. The sandwich freeze-fracture method was used for fracturing the cells. The complimentary fracture planes in the plasma membrane were characterized by field-emission secondary electron microscopy (FESEM) in the frozen-hydrated state. The cells fractured at the dorsal surface were used for SIMS analysis. The frozen-hydrated SIMS analysis of individual cells under dynamic primary ion beam (O 2+) revealed local secondary ion signal enhancements correlated with the water image signals of 19(H 3O) +. A preferential removal of water from the frozen cell matrix in the Z-axis was also observed. These complications render the frozen-hydrated sample type less desirable for subcellular dynamic SIMS studies. The freeze-drying of frozen-hydrated cells, either inside the instrument or externally in a freeze-drier, allowed SIMS imaging of subcellular chemical composition. Morphological evaluations of fractured freeze-dried cells with SEM and confocal laser scanning microscopy (CLSM) revealed well-preserved mitochondria, Golgi apparatus, and stress fibers. SIMS analysis of fractured freeze-dried cells revealed well-preserved chemical composition of even the most highly diffusible ions like K + and Na + in physiologically relevant concentrations. The high K-low Na signature in individual cells

  3. Challenges of biological sample preparation for SIMS imaging of elements and molecules at subcellular resolution

    International Nuclear Information System (INIS)

    Chandra, Subhash

    2008-01-01

    Secondary ion mass spectrometry (SIMS) based imaging techniques capable of subcellular resolution characterization of elements and molecules are becoming valuable tools in many areas of biology and medicine. Due to high vacuum requirements of SIMS, the live cells cannot be analyzed directly in the instrument. The sample preparation, therefore, plays a critical role in preserving the native chemical composition for SIMS analysis. This work focuses on the evaluation of frozen-hydrated and frozen freeze-dried sample preparations for SIMS studies of cultured cells with a CAMECA IMS-3f dynamic SIMS ion microscope instrument capable of producing SIMS images with a spatial resolution of 500 nm. The sandwich freeze-fracture method was used for fracturing the cells. The complimentary fracture planes in the plasma membrane were characterized by field-emission secondary electron microscopy (FESEM) in the frozen-hydrated state. The cells fractured at the dorsal surface were used for SIMS analysis. The frozen-hydrated SIMS analysis of individual cells under dynamic primary ion beam (O 2 + ) revealed local secondary ion signal enhancements correlated with the water image signals of 19 (H 3 O) + . A preferential removal of water from the frozen cell matrix in the Z-axis was also observed. These complications render the frozen-hydrated sample type less desirable for subcellular dynamic SIMS studies. The freeze-drying of frozen-hydrated cells, either inside the instrument or externally in a freeze-drier, allowed SIMS imaging of subcellular chemical composition. Morphological evaluations of fractured freeze-dried cells with SEM and confocal laser scanning microscopy (CLSM) revealed well-preserved mitochondria, Golgi apparatus, and stress fibers. SIMS analysis of fractured freeze-dried cells revealed well-preserved chemical composition of even the most highly diffusible ions like K + and Na + in physiologically relevant concentrations. The high K-low Na signature in individual cells

  4. Platinum replica electron microscopy: Imaging the cytoskeleton globally and locally.

    Science.gov (United States)

    Svitkina, Tatyana M

    2017-05-01

    Structural studies reveal how smaller components of a system work together as a whole. However, combining high resolution of details with full coverage of the whole is challenging. In cell biology, light microscopy can image many cells in their entirety, but at a lower resolution, whereas electron microscopy affords very high resolution, but usually at the expense of the sample size and coverage. Structural analyses of the cytoskeleton are especially demanding, because cytoskeletal networks are unresolvable by light microscopy due to their density and intricacy, whereas their proper preservation is a challenge for electron microscopy. Platinum replica electron microscopy can uniquely bridge the gap between the "comfort zones" of light and electron microscopy by allowing high resolution imaging of the cytoskeleton throughout the entire cell and in many cells in the population. This review describes the principles and applications of platinum replica electron microscopy for studies of the cytoskeleton. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Extreme localization of electrons in space and time.

    Science.gov (United States)

    Hommelhoff, Peter; Kealhofer, Catherine; Aghajani-Talesh, Anoush; Sortais, Yvan R P; Foreman, Seth M; Kasevich, Mark A

    2009-04-01

    Electron emission from sharp metal tips can take place on sub-femtosecond time scales if the emission is driven by few cycle femtosecond laser pulses. Here we outline the experimental prerequisites in detail, discuss emission regimes and relate them to recent experiments in the gas phase (attosecond physics). We present a process that leads to single atom tip emitters that are stable under laser illumination and conclude with a discussion of how to achieve short electron pulses at a target.

  6. Theoretical study of the localization of excess electrons at the surface of ice

    International Nuclear Information System (INIS)

    Hermann, A; Schwerdtfeger, P; Schmidt, W G

    2008-01-01

    The localization of excess electrons at the basal plane surface of hexagonal ice Ih is investigated theoretically, combining density functional theory (DFT) with a partial self-interaction correction (SIC) scheme, to account for spurious self-interaction effects that artificially delocalize the excess electrons. Starting from energetically favored surface geometries, we find strong localization of excess electrons at surface dangling bonds, in particular for surface adsorbed water monomers and dimers

  7. Determination of local absolute detection efficiency of a ceratron with 55Fe Auger electrons

    International Nuclear Information System (INIS)

    Mori, C.; Sugiyama, T.; Watanabe, T.

    1983-01-01

    The local absolute detection efficiency of a Ceratron (channel electron multiplier made of ceramics) was determined with collimated Mn K Auger electrons ( 5 keV) emitted from 55 Fe as a function of electron incident position and applied voltage. The local efficiency at the channel inlet did not depend so much on the applied voltage. The efficiency at the funnel increased with the applied voltage, while it was always lower than that at the channel inlet. (orig.)

  8. Exploring the electron density localization in single MoS2 monolayers by means of a localize-electrons detector and the quantum theory of atoms in molecules

    Directory of Open Access Journals (Sweden)

    Yosslen Aray

    2017-11-01

    Full Text Available The nature of the electron density localization in a MoS2 monolayer under 0 % to 11% tensile strain has been systematically studied by means of a localized electron detector function and the Quantum Theory of atoms in molecules. At 10% tensile strain, this monolayer become metallic. It was found that for less than 6.5% of applied stress, the same atomic structure of the equilibrium geometry (0% strain is maintained; while over 6.5% strain induces a transformation to a structure where the sulfur atoms placed on the top and bottom layer form S2 groups. The localized electron detector function shows the presence of zones of highly electron delocalization extending throughout the Mo central layer. For less than 10% tensile strain, these zones comprise the BCPs and the remainder CPs in separates regions of the space; while for the structures beyond 10% strain, all the critical points are involved in a region of highly delocalized electrons that extends throughout the material. This dissimilar electron localization pattern is like to that previously reported for semiconductors such as Ge bulk and metallic systems such as transition metals bulk.

  9. Quantum algebraic representation of localization and motion of a Dirac electron

    International Nuclear Information System (INIS)

    Jaekel, Marc-Thierry; Reynaud, Serge

    2001-01-01

    Quantum algebraic observables representing localization in space-time of a Dirac electron are defined. Inertial motion of the electron is represented in the quantum algebra with electron mass acting as the generator of motion. Since transformations to uniformly accelerated frames are naturally included in this conformally invariant description, the quantum algebra is also able to deal with uniformly accelerated motion

  10. The electron localization as the information content of the conditional pair density

    Energy Technology Data Exchange (ETDEWEB)

    Urbina, Andres S.; Torres, F. Javier [Universidad San Francisco de Quito (USFQ), Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Química e Ingeniería Química, Diego de Robles y Via Interoceanica, Quito 17-1200-841 (Ecuador); Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y Via Interoceanica, Quito 17-1200-841 (Ecuador); Rincon, Luis, E-mail: lrincon@usfq.edu.ec, E-mail: lrincon@ula.ve [Universidad San Francisco de Quito (USFQ), Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Química e Ingeniería Química, Diego de Robles y Via Interoceanica, Quito 17-1200-841 (Ecuador); Universidad San Francisco de Quito (USFQ), Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y Via Interoceanica, Quito 17-1200-841 (Ecuador); Departamento de Química, Facultad de Ciencias, Universidad de Los Andes (ULA), La Hechicera, Mérida-5101 (Venezuela, Bolivarian Republic of)

    2016-06-28

    In the present work, the information gained by an electron for “knowing” about the position of another electron with the same spin is calculated using the Kullback-Leibler divergence (D{sub KL}) between the same-spin conditional pair probability density and the marginal probability. D{sub KL} is proposed as an electron localization measurement, based on the observation that regions of the space with high information gain can be associated with strong correlated localized electrons. Taking into consideration the scaling of D{sub KL} with the number of σ-spin electrons of a system (N{sup σ}), the quantity χ = (N{sup σ} − 1) D{sub KL}f{sub cut} is introduced as a general descriptor that allows the quantification of the electron localization in the space. f{sub cut} is defined such that it goes smoothly to zero for negligible densities. χ is computed for a selection of atomic and molecular systems in order to test its capability to determine the region in space where electrons are localized. As a general conclusion, χ is able to explain the electron structure of molecules on the basis of chemical grounds with a high degree of success and to produce a clear differentiation of the localization of electrons that can be traced to the fluctuation in the average number of electrons in these regions.

  11. Pathways and Subcellular Compartmentation of NAD Biosynthesis in Human Cells

    Science.gov (United States)

    Nikiforov, Andrey; Dölle, Christian; Niere, Marc; Ziegler, Mathias

    2011-01-01

    NAD is a vital redox carrier, and its degradation is a key element of important regulatory pathways. NAD-mediated functions are compartmentalized and have to be fueled by specific biosynthetic routes. However, little is known about the different pathways, their subcellular distribution, and regulation in human cells. In particular, the route(s) to generate mitochondrial NAD, the largest subcellular pool, is still unknown. To visualize organellar NAD changes in cells, we targeted poly(ADP-ribose) polymerase activity into the mitochondrial matrix. This activity synthesized immunodetectable poly(ADP-ribose) depending on mitochondrial NAD availability. Based on this novel detector system, detailed subcellular enzyme localizations, and pharmacological inhibitors, we identified extracellular NAD precursors, their cytosolic conversions, and the pathway of mitochondrial NAD generation. Our results demonstrate that, besides nicotinamide and nicotinic acid, only the corresponding nucleosides readily enter the cells. Nucleotides (e.g. NAD and NMN) undergo extracellular degradation resulting in the formation of permeable precursors. These precursors can all be converted to cytosolic and mitochondrial NAD. For mitochondrial NAD synthesis, precursors are converted to NMN in the cytosol. When taken up into the organelles, NMN (together with ATP) serves as substrate of NMNAT3 to form NAD. NMNAT3 was conclusively localized to the mitochondrial matrix and is the only known enzyme of NAD synthesis residing within these organelles. We thus present a comprehensive dissection of mammalian NAD biosynthesis, the groundwork to understand regulation of NAD-mediated processes, and the organismal homeostasis of this fundamental molecule. PMID:21504897

  12. Immunogold electron microscopic localization of timothy grass (Phleum pratense) pollen major allergens Phl p I and Phl p V after anhydrous fixation in acrolein vapor

    NARCIS (Netherlands)

    Grote, M.; Dolecek, C.; van Ree, R.; Valenta, R.

    1994-01-01

    We used the vapor phase of acrolein as an anhydrous fixative for timothy grass pollen in an immunogold double-labeling localization study of two different major allergens, Phl p I and Phl p V. More than 48 hr of fixation were needed for the subcellular pollen structures to be satisfactorily

  13. Electron paramagnetic resonance parameters and local structure for ...

    Indian Academy of Sciences (India)

    HUA-MING ZHANG. 1. , GUANG-DUO LU. 1 ... the above ZFSs, the local structure information for the impurity Gd. 3+ is obtained, i.e., .... parameters, extended X-ray absorption fine-structure (EXAFS) measurements and crystal-field spectrum ...

  14. Local electron flow to the anode in a magnetically insulated diode

    International Nuclear Information System (INIS)

    Maron, Y.

    1984-01-01

    Local electron flux to the anode of a magnetically insulated diode is monitored. Intense electron burst to the anode and slow variations in the electron flux are observed. Unlike the slow signals the bursts are accompanied by sharp increases in microwave emission and by increases in the ion current density. The electron bursts are not affected by the presence of the anode plasma. Indications suggest that the bursts are initiated by processes in the cathode plasma

  15. Using the electron localization function to correct for confinement physics in semi-local density functional theory

    International Nuclear Information System (INIS)

    Hao, Feng; Mattsson, Ann E.; Armiento, Rickard

    2014-01-01

    We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu–O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry

  16. Multi-Label Learning via Random Label Selection for Protein Subcellular Multi-Locations Prediction.

    Science.gov (United States)

    Wang, Xiao; Li, Guo-Zheng

    2013-03-12

    Prediction of protein subcellular localization is an important but challenging problem, particularly when proteins may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular localization methods are only used to deal with the single-location proteins. In the past few years, only a few methods have been proposed to tackle proteins with multiple locations. However, they only adopt a simple strategy, that is, transforming the multi-location proteins to multiple proteins with single location, which doesn't take correlations among different subcellular locations into account. In this paper, a novel method named RALS (multi-label learning via RAndom Label Selection), is proposed to learn from multi-location proteins in an effective and efficient way. Through five-fold cross validation test on a benchmark dataset, we demonstrate our proposed method with consideration of label correlations obviously outperforms the baseline BR method without consideration of label correlations, indicating correlations among different subcellular locations really exist and contribute to improvement of prediction performance. Experimental results on two benchmark datasets also show that our proposed methods achieve significantly higher performance than some other state-of-the-art methods in predicting subcellular multi-locations of proteins. The prediction web server is available at http://levis.tongji.edu.cn:8080/bioinfo/MLPred-Euk/ for the public usage.

  17. Electron localization in a mixed-valence diniobium benzene complex.

    Science.gov (United States)

    Gianetti, Thomas L; Nocton, Grégory; Minasian, Stefan G; Kaltsoyannis, Nikolas; Kilcoyne, A L David; Kozimor, Stosh A; Shuh, David K; Tyliszczak, Tolek; Bergman, Robert G; Arnold, John

    2015-02-01

    Reaction of the neutral diniobium benzene complex {[Nb(BDI)N t Bu] 2 (μ-C 6 H 6 )} (BDI = N , N '-diisopropylbenzene-β-diketiminate) with Ag[B(C 6 F 5 ) 4 ] results in a single electron oxidation to produce a cationic diniobium arene complex, {[Nb(BDI)N t Bu] 2 (μ-C 6 H 6 )}{B(C 6 F 5 ) 4 }. Investigation of the solid state and solution phase structure using single-crystal X-ray diffraction, cyclic voltammetry, magnetic susceptibility, and multinuclear NMR spectroscopy indicates that the oxidation results in an asymmetric molecule with two chemically inequivalent Nb atoms. Further characterization using density functional theory (DFT) calculations, UV-visible, Nb L 3,2 -edge X-ray absorption near-edge structure (XANES), and EPR spectroscopies supports assignment of a diniobium complex, in which one Nb atom carries a single unpaired electron that is not largely delocalized on the second Nb atom. During the oxidative transformation, one electron is removed from the δ-bonding HOMO, which causes a destabilization of the molecule and formation of an asymmetric product. Subsequent reactivity studies indicate that the oxidized product allows access to metal-based chemistry with substrates that did not exhibit reactivity with the starting neutral complex.

  18. A scaling analysis of electronic localization in two-dimensional random media

    International Nuclear Information System (INIS)

    Ye Zhen

    2003-01-01

    By an improved scaling analysis, we suggest that there may appear two possibilities concerning the electronic localization in two-dimensional random media. The first is that all electronic states are localized in two dimensions, as conjectured previously. The second possibility is that electronic behaviors in two- and three-dimensional random systems are similar, in agreement with a recent calculation based on a direct calculation of the conductance with the use of the Kubo formula. In this case, non-localized states are possible in two dimensions, and have some peculiar properties. A few predictions are proposed. Moreover, the present analysis accommodates results from the previous scaling analysis

  19. Observation of electron weak localization and correlation effects in disordered graphene

    Institute of Scientific and Technical Information of China (English)

    TAN ChangLing; TAN ZhenBing; MA Li; QU FanMing; YANG Fan; CHEN Jun; LIU GuangTong; YANG HaiFang; YANG ChangLi; LU Li

    2009-01-01

    We have studied the electron transport properties of a disordered graphene sample,where the disorder was intentionally strengthened by Ga+ ion irradiation.The magneto-conductance of the sample exhibits a typical two-dimensional electron weak localization behavior,with electron-electron interaction as the dominant dephasing mechanism.The absence of electron anti-weak localization in the sample implies strong intersublattice and/or intervalley scattering caused by the disorders.The temperature and bias-voltage dependencies of conductance clearly reveal the suppression of conductance at low ener-gies,indicating opening of a Coulomb gap due to electron-electron interaction in the disordered gra-phene sample.

  20. Local food in European supply chains: reconnection and electronic networks

    Directory of Open Access Journals (Sweden)

    Georgina Holt

    2007-04-01

    Full Text Available Après une présentation du marché des produits locaux/localisés en Grande Bretagne, ainsi qu’une définition du concept en fonction des circuits de distribution courts, de l’agriculture biologique et du commerce équitable, cet article se fonde sur des études de cas, issus de projets de recherche européens, pour identifier des différents types de réseaux concernés par les concept de produit locaux durables. Les habitudes historiques concernant l’achat des produits alimentaires jouent ici un rôle central et l’article observe l’équilibre entre les composants historiques, sociaux et environnementaux des produits locaux/localisés. A partir de ces terrains de recherche et de ces expériences il s’est avéré possible de déterminer différentes compréhensions de « produits locaux » en relation avec le concept de « distance alimentaire/ food miles ». En se référant à six cas donnés, cet article souligne l’importance des systèmes localisés en matière de durabilité alimentaire, et met en valeur le poids des qualités humaines et sociales dans la balance commerciale.After giving an overview of the market for local food in the UK, as well as a definition of the concept in relation to short supply chains, organic agriculture and fair trade, the article draws on cases encountered through EC-funded research and networking to identify different types of network concerned with the concept of sustaining local food. Historical uses of shopping habits play here a central role and the article observes the balance between historical, social and environmental components of local food. From these researches and experiences, it has been possible to demonstrate a range of understandings in relation to the concept of ‘food miles’. With reference to six cases, the article underlines the importance of local food systems within food sustainability, and highlights the weight of human and social qualities in the market balance.

  1. Local electronic environment of protons in VHsub(x) alloys

    International Nuclear Information System (INIS)

    Kazama, Shigeo; Fukai, Yuh

    1977-01-01

    The Knight shift (Ksub(H)) and the spin-lattice relaxation time T 1 of protons have been measured in vanadium-hydrogen alloys (VHsub(x)) with hydrogen concentration x=0.042 -- 0.736, at temperatures between 100 0 and 200 0 C. The resolution of +-1 ppm in the shift was attained by using a high-resolution spectrometer, and the effect of demagnetizing field was isolated by using a single sheet of foil as a specimen. This allowed the simultaneous determination of Ksub(H) and the bulk magnetic susceptibility. Ksub(H) measured relative to bare protons was found to be negative and change little with hydrogen concentration. No temperature dependence of the shift was observed, even across the phase transition. These results are interpreted in terms of a contact interaction with the uniform spin-polarization in the interstitial region and some additional contributions from H-induced states. An evidence for the electron-electron interaction in VHsub(x) is derived from comparison of Ksub(H) and T 1 . (auth.)

  2. Weak localization and electron-electron interaction in modulation doped GaAs/AlGaAs heterostructures

    International Nuclear Information System (INIS)

    Taboryski, R.; Lindelof, P.E.

    1990-01-01

    The first heterostructure wafer only had one electronic subband at the GaAs/AlGaAs interface populated. Weak localization magnetoresistance was interpreted by a theory valid to relatively high magnetic fields and also valid for electrons with a long mean free path. The adjustable parameter in fitting the magnetoresistance was in each case the phasebreaking relaxation time, which could then subsequently be plotted as a function of temperature. The temperature dependence of the phasebreaking rate could be interpreted on the basic of existing theories, but the residual relaxation rate at the lowest temperature remains so far unexplained. Already at low magnetic fields the weak localization magnetoresistance saturates, indicating a complete quench of weak localization. We find that the value of saturation (i.e. the total weak localization at the appropriate temperature) was smaller than predicted by the existing theories. At magnetic fields of the order of the inverse electron mobility, a quadratic magnetoresistance show up in our experiments. This quadratic magnetoresistance corresponds to corrections to the conductivity of the order of e 2 /h. Whereas we find that the temperature dependence of this conductivity correction is well in agreement with predicted effects of electron-electron interaction, the dependence on mobility, which we can measure via our ion implantation, is larger than any existing theory predicts, yet still in the ballpark of the conductance quantum. (orig./BHO)

  3. Local Electronic Structure of a Single-Layer Porphyrin-Containing Covalent Organic Framework

    KAUST Repository

    Chen, Chen; Joshi, Trinity; Li, Huifang; Chavez, Anton D.; Pedramrazi, Zahra; Liu, Pei-Nian; Li, Hong; Dichtel, William R.; Bredas, Jean-Luc; Crommie, Michael F.

    2017-01-01

    We have characterized the local electronic structure of a porphyrin-containing single-layer covalent organic framework (COF) exhibiting a square lattice. The COF monolayer was obtained by the deposition of 2,5-dimethoxybenzene-1,4-dicarboxaldehyde

  4. Observing electron localization in a dissociating H2+ molecule in real time.

    Science.gov (United States)

    Xu, H; Li, Zhichao; He, Feng; Wang, X; Atia-Tul-Noor, A; Kielpinski, D; Sang, R T; Litvinyuk, I V

    2017-06-16

    Dissociation of diatomic molecules with odd number of electrons always causes the unpaired electron to localize on one of the two resulting atomic fragments. In the simplest diatomic molecule H 2 + dissociation yields a hydrogen atom and a proton with the sole electron ending up on one of the two nuclei. That is equivalent to breaking of a chemical bond-the most fundamental chemical process. Here we observe such electron localization in real time by performing a pump-probe experiment. We demonstrate that in H 2 + electron localization is complete in just 15 fs when the molecule's internuclear distance reaches 8 atomic units. The measurement is supported by a theoretical simulation based on numerical solution of the time-dependent Schrödinger equation. This observation advances our understanding of detailed dynamics of molecular dissociation.

  5. Reversed shear Alfven eigenmode stabilization by localized electron cyclotron heating

    Energy Technology Data Exchange (ETDEWEB)

    Van Zeeland, M A; Hyatt, A W; Lohr, J; Petty, C C [General Atomics, PO Box 85608 San Diego, CA 92186-5608 (United States); Heidbrink, W W [University of California-Irvine, Irvine, CA 92697 (United States); Nazikian, R; Solomon, W M; Gorelenkov, N N; Kramer, G J [Princeton Plasma Physics Laboratory, Princeton, NJ 08543-0451 (United States); Austin, M E [University of Texas-Austin, Austin, TX 78712 (United States); Berk, H L [Institute for Fusion Studies, University of Texas at Austin, Austin, TX 78712 (United States); Holcomb, C T; Makowski, M A [Lawrence Livermore National Laboratory, Livermore, CA (United States); McKee, G R [University of Wisconsin-Madison, Madison, WI 53726 (United States); Sharapov, S E [Euratom/UKAEA Fusion Association, Culham, Abingdon, Oxfordshire, OX14 3DB (United Kingdom); Rhodes, T L [University of California-Los Angeles, Los Angeles, California, 90095 (United States)], E-mail: vanzeeland@fusion.gat.com

    2008-03-15

    Reversed shear Alfven eigenmode (RSAE) activity in DIII-D is stabilized by electron cyclotron heating (ECH) applied near the minimum of the magnetic safety factor (q{sub min}) in neutral beam heated discharges with reversed-magnetic shear. The degree of RSAE stabilization, fast ion density and the volume averaged neutron production (S{sub n}) are highly dependent on ECH deposition location relative to q{sub min}. While discharges with ECH stabilization of RSAEs have higher S{sub n} and more peaked fast ion profiles than discharges with significant RSAE activity, neutron production remains strongly reduced (up to 60% relative to TRANSP predictions assuming classical fast ion transport) even when RSAEs are stabilized.

  6. Quantum transport through disordered 1D wires: Conductance via localized and delocalized electrons

    International Nuclear Information System (INIS)

    Gopar, Víctor A.

    2014-01-01

    Coherent electronic transport through disordered systems, like quantum wires, is a topic of fundamental and practical interest. In particular, the exponential localization of electron wave functions-Anderson localization-due to the presence of disorder has been widely studied. In fact, Anderson localization, is not an phenomenon exclusive to electrons but it has been observed in microwave and acoustic experiments, photonic materials, cold atoms, etc. Nowadays, many properties of electronic transport of quantum wires have been successfully described within a scaling approach to Anderson localization. On the other hand, anomalous localization or delocalization is, in relation to the Anderson problem, a less studied phenomenon. Although one can find signatures of anomalous localization in very different systems in nature. In the problem of electronic transport, a source of delocalization may come from symmetries present in the system and particular disorder configurations, like the so-called Lévy-type disorder. We have developed a theoretical model to describe the statistical properties of transport when electron wave functions are delocalized. In particular, we show that only two physical parameters determine the complete conductance distribution

  7. Enhanced Glycogen Storage of a Subcellular Hot Spot in Human Skeletal Muscle during Early Recovery from Eccentric Contractions

    Science.gov (United States)

    Nielsen, Joachim; Farup, Jean; Rahbek, Stine Klejs; de Paoli, Frank Vincenzo; Vissing, Kristian

    2015-01-01

    Unaccustomed eccentric exercise is accompanied by muscle damage and impaired glucose uptake and glycogen synthesis during subsequent recovery. Recently, it was shown that the role and regulation of glycogen in skeletal muscle are dependent on its subcellular localization, and that glycogen synthesis, as described by the product of glycogen particle size and number, is dependent on the time course of recovery after exercise and carbohydrate availability. In the present study, we investigated the subcellular distribution of glycogen in fibers with high (type I) and low (type II) mitochondrial content during post-exercise recovery from eccentric contractions. Analysis was completed on five male subjects performing an exercise bout consisting of 15 x 10 maximal eccentric contractions. Carbohydrate-rich drinks were subsequently ingested throughout a 48 h recovery period and muscle biopsies for analysis included time points 3, 24 and 48 h post exercise from the exercising leg, whereas biopsies corresponding to prior to and at 48 h after the exercise bout were collected from the non-exercising, control leg. Quantitative imaging by transmission electron microscopy revealed an early (post 3 and 24 h) enhanced storage of intramyofibrillar glycogen (defined as glycogen particles located within the myofibrils) of type I fibers, which was associated with an increase in the number of particles. In contrast, late in recovery (post 48 h), intermyofibrillar, intramyofibrillar and subsarcolemmal glycogen in both type I and II fibers were lower in the exercise leg compared with the control leg, and this was associated with a smaller size of the glycogen particles. We conclude that in the carbohydrate-supplemented state, the effect of eccentric contractions on glycogen metabolism depends on the subcellular localization, muscle fiber’s oxidative capacity, and the time course of recovery. The early enhanced storage of intramyofibrillar glycogen after the eccentric contractions may

  8. Magnetic response of localized spins coupled to itinerant electrons in an inhomogeneous crystal field

    International Nuclear Information System (INIS)

    Iannarella, L.; Guimaraes, A.P.; Silva, X.A. da.

    1990-01-01

    The magnetic behavior at T = O K of a system consisting of conduction electrons coupled to localized electrons, the latter submitted to an inhomogeneous crystal field distribution, is studied. The study implies that the inhomogeneity of the crystal field attenuates the quenching effects. The model is interesting to the study of disordered rare-earth intermetallic compounds. (A.C.A.S.) [pt

  9. To what extent can charge localization influence electron injection efficiency at graphene-porphyrin interfaces?

    KAUST Repository

    Parida, Manas R.

    2015-04-28

    Controlling the electron transfer process at donor- acceptor interfaces is a research direction that has not yet seen much progress. Here, with careful control of the charge localization on the porphyrin macrocycle using β -Cyclodextrin as an external cage, we are able to improve the electron injection efficiency from cationic porphyrin to graphene carboxylate by 120% . The detailed reaction mechanism is also discussed.

  10. Experimental evidence for electron localization on Au upon photo-activation of Au/anatase catalysts

    NARCIS (Netherlands)

    Carneiro, J.T.; Carneiro, Joana T.; Savenije, Tom J.; Mul, Guido

    2009-01-01

    Time resolved microwave conductivity (TRMC) measurements show that the presence of Au on anatase Hombikat UV100 significantly reduces the lifetime of mobile electrons formed by photo-excitation of this photocatalyst at 300 nm, providing evidence for the widely acclaimed electron localization effect

  11. Localization of fluorescently labeled structures in frozen-hydrated samples using integrated light electron microscopy

    NARCIS (Netherlands)

    Faas, F.G.A.; Bárcena, M.A.; Agronskaia, A.V.; Gerritsen, H.C.; Moscicka, K.B.; Diebolder, C.A.; Driel, L.F.; Limpens, R.W.A.L.; Bos, E.; Ravelli, R.B.G.; Koning, R.I.; Koster, A.J.

    2013-01-01

    Correlative light and electron microscopy is an increasingly popular technique to study complex biological systems at various levels of resolution. Fluorescence microscopy can be employed to scan large areas to localize regions of interest which are then analyzed by electron microscopy to obtain

  12. Local re-acceleration and a modified thick target model of solar flare electrons

    Science.gov (United States)

    Brown, J. C.; Turkmani, R.; Kontar, E. P.; MacKinnon, A. L.; Vlahos, L.

    2009-12-01

    Context: The collisional thick target model (CTTM) of solar hard X-ray (HXR) bursts has become an almost “standard model” of flare impulsive phase energy transport and radiation. However, it faces various problems in the light of recent data, particularly the high electron beam density and anisotropy it involves. Aims: We consider how photon yield per electron can be increased, and hence fast electron beam intensity requirements reduced, by local re-acceleration of fast electrons throughout the HXR source itself, after injection. Methods: We show parametrically that, if net re-acceleration rates due to e.g. waves or local current sheet electric (E) fields are a significant fraction of collisional loss rates, electron lifetimes, and hence the net radiative HXR output per electron can be substantially increased over the CTTM values. In this local re-acceleration thick target model (LRTTM) fast electron number requirements and anisotropy are thus reduced. One specific possible scenario involving such re-acceleration is discussed, viz, a current sheet cascade (CSC) in a randomly stressed magnetic loop. Results: Combined MHD and test particle simulations show that local E fields in CSCs can efficiently accelerate electrons in the corona and and re-accelerate them after injection into the chromosphere. In this HXR source scenario, rapid synchronisation and variability of impulsive footpoint emissions can still occur since primary electron acceleration is in the high Alfvén speed corona with fast re-acceleration in chromospheric CSCs. It is also consistent with the energy-dependent time-of-flight delays in HXR features. Conclusions: Including electron re-acceleration in the HXR source allows an LRTTM modification of the CTTM in which beam density and anisotropy are much reduced, and alleviates theoretical problems with the CTTM, while making it more compatible with radio and interplanetary electron numbers. The LRTTM is, however, different in some respects such as

  13. Fully local orbital-free calculation of electronic structure using pseudopotentials

    NARCIS (Netherlands)

    Pino, R.; Markvoort, Albert. J.; Santen, van R.A.; Hilbers, P.A.J.

    2003-01-01

    An exactly solvable orbital-free technique is applied to the calculation of the electronic structure of polyatomic systems. The Thomas–Fermi kinetic energy, local exchange, local electrostatic energy functionals, and pseudopotentials are used. Given the potential, the cost of the calculation of the

  14. Localized structures of electromagnetic waves in hot electron-positron plasma

    International Nuclear Information System (INIS)

    Kartal, S.; Tsintsadze, L.N.; Berezhiani, V.I.

    1995-08-01

    The dynamics of relatively strong electromagnetic (EM) wave propagation in hot electron-positron plasma is investigated. The possibility of finding localized stationary structures of EM waves is explored. It it shown that under certain conditions the EM wave forms a stable localized soliton-like structures where plasma is completely expelled from the region of EM field location. (author). 9 refs, 2 figs

  15. Local spin torque induced by electron electric dipole moment in the YbF molecule

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Masahiro; Senami, Masato; Ogiso, Yoji; Tachibana, Akitomo [Department of Micro Engineering, Kyoto University, Kyoto 615-8540 (Japan)

    2014-10-06

    In this study, we show the modification of the equation of motion of the electronic spin, which is derived by the quantum electron spin vorticity principle, by the effect of the electron electric dipole moment (EDM). To investigate the new contribution to spin torque by EDM, using first principle calculations, we visualize distributions of the local spin angular momentum density and local spin torque density of the YbF molecule on which the static electric field and magnetic field are applied at t = 0.

  16. Quantitative Analysis of Subcellular Distribution of the SUMO Conjugation System by Confocal Microscopy Imaging.

    Science.gov (United States)

    Mas, Abraham; Amenós, Montse; Lois, L Maria

    2016-01-01

    Different studies point to an enrichment in SUMO conjugation in the cell nucleus, although non-nuclear SUMO targets also exist. In general, the study of subcellular localization of proteins is essential for understanding their function within a cell. Fluorescence microscopy is a powerful tool for studying subcellular protein partitioning in living cells, since fluorescent proteins can be fused to proteins of interest to determine their localization. Subcellular distribution of proteins can be influenced by binding to other biomolecules and by posttranslational modifications. Sometimes these changes affect only a portion of the protein pool or have a partial effect, and a quantitative evaluation of fluorescence images is required to identify protein redistribution among subcellular compartments. In order to obtain accurate data about the relative subcellular distribution of SUMO conjugation machinery members, and to identify the molecular determinants involved in their localization, we have applied quantitative confocal microscopy imaging. In this chapter, we will describe the fluorescent protein fusions used in these experiments, and how to measure, evaluate, and compare average fluorescence intensities in cellular compartments by image-based analysis. We show the distribution of some components of the Arabidopsis SUMOylation machinery in epidermal onion cells and how they change their distribution in the presence of interacting partners or even when its activity is affected.

  17. A theory of local and global processes which affect solar wind electrons. 2. Experimental support

    International Nuclear Information System (INIS)

    Scudder, J.D.; Olbert, S.

    1979-05-01

    The microscopic characteristics of the Coulomb cross section show that there are three natural subpopulations for plasma electrons: the subthermals; the transthermals; and the extrathermals. Data from three experimental groups on three different spacecraft in the interplanetary medium over a radial range are presented to support the five interrelations projected between solar wind electron properties and changes in the interplanetary medium: (1) subthermals respond primarily to local changes (compression and rarefactions) in stream dynamics; (2) the extrathermal fraction of the ambient electron density should be anti-correlated with the asymptotic bulk speed; (3) the extrathermal 'temperature' should be anti-correlated with the local wind speed at 1 AU; (4) the heat flux carried by electrons should be anti-correlated with the local bulk speed; and (5) the extrathermal differential 'temperature' should be nearly independent of radius within 1 AU

  18. Localized conductive patterning via focused electron beam reduction of graphene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Songkil; Henry, Mathias [George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Kulkarni, Dhaval D.; Zackowski, Paul; Jang, Seung Soon; Tsukruk, Vladimir V. [School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Fedorov, Andrei G., E-mail: agf@gatech.edu [George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States)

    2015-03-30

    We report on a method for “direct-write” conductive patterning via reduction of graphene oxide (GO) sheets using focused electron beam induced deposition (FEBID) of carbon. FEBID treatment of the intrinsically dielectric graphene oxide between two metal terminals opens up the conduction channel, thus enabling a unique capability for nanoscale conductive domain patterning in GO. An increase in FEBID electron dose results in a significant increase of the domain electrical conductivity with improving linearity of drain-source current vs. voltage dependence, indicative of a change of graphene oxide electronic properties from insulating to semiconducting. Density functional theory calculations suggest a possible mechanism underlying this experimentally observed phenomenon, as localized reduction of graphene oxide layers via interactions with highly reactive intermediates of electron-beam-assisted dissociation of surface-adsorbed hydrocarbon molecules. These findings establish an unusual route for using FEBID as nanoscale lithography and patterning technique for engineering carbon-based nanomaterials and devices with locally tailored electronic properties.

  19. Communication: Near-locality of exchange and correlation density functionals for 1- and 2-electron systems

    Science.gov (United States)

    Sun, Jianwei; Perdew, John P.; Yang, Zenghui; Peng, Haowei

    2016-05-01

    The uniform electron gas and the hydrogen atom play fundamental roles in condensed matter physics and quantum chemistry. The former has an infinite number of electrons uniformly distributed over the neutralizing positively charged background, and the latter only one electron bound to the proton. The uniform electron gas was used to derive the local spin density approximation to the exchange-correlation functional that undergirds the development of the Kohn-Sham density functional theory. We show here that the ground-state exchange-correlation energies of the hydrogen atom and many other 1- and 2-electron systems are modeled surprisingly well by a different local spin density approximation (LSDA0). LSDA0 is constructed to satisfy exact constraints but agrees surprisingly well with the exact results for a uniform two-electron density in a finite, curved three-dimensional space. We also apply LSDA0 to excited or noded 1-electron densities, where it works less well. Furthermore, we show that the localization of the exact exchange hole for a 1- or 2-electron ground state can be measured by the ratio of the exact exchange energy to its optimal lower bound.

  20. Communication: Near-locality of exchange and correlation density functionals for 1- and 2-electron systems

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jianwei; Yang, Zenghui; Peng, Haowei [Department of Physics, Temple University, Philadelphia, Pennsylvania 19122 (United States); Perdew, John P. [Department of Physics, Temple University, Philadelphia, Pennsylvania 19122 (United States); Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122 (United States)

    2016-05-21

    The uniform electron gas and the hydrogen atom play fundamental roles in condensed matter physics and quantum chemistry. The former has an infinite number of electrons uniformly distributed over the neutralizing positively charged background, and the latter only one electron bound to the proton. The uniform electron gas was used to derive the local spin density approximation to the exchange-correlation functional that undergirds the development of the Kohn-Sham density functional theory. We show here that the ground-state exchange-correlation energies of the hydrogen atom and many other 1- and 2-electron systems are modeled surprisingly well by a different local spin density approximation (LSDA0). LSDA0 is constructed to satisfy exact constraints but agrees surprisingly well with the exact results for a uniform two-electron density in a finite, curved three-dimensional space. We also apply LSDA0 to excited or noded 1-electron densities, where it works less well. Furthermore, we show that the localization of the exact exchange hole for a 1- or 2-electron ground state can be measured by the ratio of the exact exchange energy to its optimal lower bound.

  1. Communication: Near-locality of exchange and correlation density functionals for 1- and 2-electron systems

    International Nuclear Information System (INIS)

    Sun, Jianwei; Yang, Zenghui; Peng, Haowei; Perdew, John P.

    2016-01-01

    The uniform electron gas and the hydrogen atom play fundamental roles in condensed matter physics and quantum chemistry. The former has an infinite number of electrons uniformly distributed over the neutralizing positively charged background, and the latter only one electron bound to the proton. The uniform electron gas was used to derive the local spin density approximation to the exchange-correlation functional that undergirds the development of the Kohn-Sham density functional theory. We show here that the ground-state exchange-correlation energies of the hydrogen atom and many other 1- and 2-electron systems are modeled surprisingly well by a different local spin density approximation (LSDA0). LSDA0 is constructed to satisfy exact constraints but agrees surprisingly well with the exact results for a uniform two-electron density in a finite, curved three-dimensional space. We also apply LSDA0 to excited or noded 1-electron densities, where it works less well. Furthermore, we show that the localization of the exact exchange hole for a 1- or 2-electron ground state can be measured by the ratio of the exact exchange energy to its optimal lower bound.

  2. Presolvated Electron Reaction with Methylacetoacetate: Electron Localization, Proton-Deuteron Exchange, and H-atom Abstraction

    Science.gov (United States)

    Petrovici, Alex; Adhikary, Amitava; Kumar, Anil; Sevilla, Michael D.

    2015-01-01

    Radiation-produced electrons initiate various reaction processes that are important to radiation damage to biomolecules. In this work, the site of attachment of the prehydrated electrons with methylacetoacetate (MAA, CH3-CO-CH2-CO-OCH3) at 77 K and subsequent reactions of the anion radical (CH3-CO•−-CH2-CO-OCH3) in the temperature range (77 to ca. 170 K) have been investigated in homogeneous H2O and D2O aqueous glasses by electron spin resonance (ESR) spectroscopy. At 77 K, the prehydrated electron attaches to MAA forming the anion radical in which the electron is delocalized over the two carbonyl groups. This species readily protonates to produce the protonated electron adduct radical CH3-C(•)OH-CH2-CO-OCH3. The ESR spectrum of CH3-C(•)OH-CH2-CO-OCH3 in H2O shows line components due to proton hyperfine couplings of the methyl and methylene groups. Whereas, the ESR spectrum of CH3-C(•)OH-CH2-CO-OCH3 in D2O glass shows only the line components due to proton hyperfine couplings of CH3 group. This is expected since the methylen protons in MAA are readily exchangeable in D2O. On stepwise annealing to higher temperatures (ca. 150 to 170 K), CH3-C(•)OH-CH2-CO-OCH3 undergoes bimolecular H-atom abstraction from MAA to form the more stable radical, CH3-CO-CH•-CO-OCH3. Theoretical calculations using density functional theory (DFT) support the radical assignments. PMID:25255751

  3. Proton-coupled electron transfer versus hydrogen atom transfer: generation of charge-localized diabatic states.

    Science.gov (United States)

    Sirjoosingh, Andrew; Hammes-Schiffer, Sharon

    2011-03-24

    The distinction between proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms is important for the characterization of many chemical and biological processes. PCET and HAT mechanisms can be differentiated in terms of electronically nonadiabatic and adiabatic proton transfer, respectively. In this paper, quantitative diagnostics to evaluate the degree of electron-proton nonadiabaticity are presented. Moreover, the connection between the degree of electron-proton nonadiabaticity and the physical characteristics distinguishing PCET from HAT, namely, the extent of electronic charge redistribution, is clarified. In addition, a rigorous diabatization scheme for transforming the adiabatic electronic states into charge-localized diabatic states for PCET reactions is presented. These diabatic states are constructed to ensure that the first-order nonadiabatic couplings with respect to the one-dimensional transferring hydrogen coordinate vanish exactly. Application of these approaches to the phenoxyl-phenol and benzyl-toluene systems characterizes the former as PCET and the latter as HAT. The diabatic states generated for the phenoxyl-phenol system possess physically meaningful, localized electronic charge distributions that are relatively invariant along the hydrogen coordinate. These diabatic electronic states can be combined with the associated proton vibrational states to generate the reactant and product electron-proton vibronic states that form the basis of nonadiabatic PCET theories. Furthermore, these vibronic states and the corresponding vibronic couplings may be used to calculate rate constants and kinetic isotope effects of PCET reactions.

  4. Excess-electron energy levels, localization and transport in disordered media

    International Nuclear Information System (INIS)

    Hamill, W.H.

    1980-01-01

    In disordered dielectrics, the fundamental parameters which control the physics and chemistry of excess electrons are time, temperature and energy or mean scattering distance. Viscosity and hardness do not directly affect the electron affinity of media, the optical spectra, or the chemical reactivity of dry or delocalized electrons or of relaxed localized or trapped electrons. Since the mean scattering distance and the transport mechanism, including barrier height, are fundamental, both liquids and glasses (including polymers) are considered in order to cover the range of relevant information. Based on the above described background, transport, localization, dry electron scavenging, trapped electron scavenging and recombination are explained. There are no available data for the energy of excess dry electrons in the media relative to vacuum in glasses, unfortunately, because of the very small yield of separated charge pairs at cryogenic temperature. Thermoplastic glassy solids provide attractive possibility above 250 K, and deserve consideration as the substitutes for cryogenic glasses. The same consideration applies to the measurements of electron drift mobility, which are essential for the adequate description of electron scavenging. (Wakatsuki, Y.)

  5. The Role of Localized Compressional Ultra-low Frequency Waves in Energetic Electron Precipitation

    Science.gov (United States)

    Rae, I. Jonathan; Murphy, Kyle R.; Watt, Clare E. J.; Halford, Alexa J.; Mann, Ian R.; Ozeke, Louis G.; Sibeck, David G.; Clilverd, Mark A.; Rodger, Craig J.; Degeling, Alex W.; Forsyth, Colin; Singer, Howard J.

    2018-03-01

    Typically, ultra-low frequency (ULF) waves have historically been invoked for radial diffusive transport leading to acceleration and loss of outer radiation belt electrons. At higher frequencies, very low frequency waves are generally thought to provide a mechanism for localized acceleration and loss through precipitation into the ionosphere of radiation belt electrons. In this study we present a new mechanism for electron loss through precipitation into the ionosphere due to a direct modulation of the loss cone via localized compressional ULF waves. We present a case study of compressional wave activity in tandem with riometer and balloon-borne electron precipitation across keV-MeV energies to demonstrate that the experimental measurements can be explained by our new enhanced loss cone mechanism. Observational evidence is presented demonstrating that modulation of the equatorial loss cone can occur via localized compressional wave activity, which greatly exceeds the change in pitch angle through conservation of the first and second adiabatic invariants. The precipitation response can be a complex interplay between electron energy, the localization of the waves, the shape of the phase space density profile at low pitch angles, ionospheric decay time scales, and the time dependence of the electron source; we show that two pivotal components not usually considered are localized ULF wave fields and ionospheric decay time scales. We conclude that enhanced precipitation driven by compressional ULF wave modulation of the loss cone is a viable candidate for direct precipitation of radiation belt electrons without any additional requirement for gyroresonant wave-particle interaction. Additional mechanisms would be complementary and additive in providing means to precipitate electrons from the radiation belts during storm times.

  6. Electron Transfer and Solvent-Mediated Electronic Localization in Molecular Photocatalysis

    DEFF Research Database (Denmark)

    Dohn, Asmus Ougaard; Kjær, Kasper Skov; Harlang, Tobias B.

    2016-01-01

    This work provides a detailed mechanism for electron transfer in a heterodinuclear complex designed as a model system in which to study homogeneous molecular photocatalysis. With efficient Born–Oppenheimer molecular dynamics simulations, we show how intermediate, charge-separated states can mediate...

  7. Unconventional scaling of the anomalous Hall effect accompanying electron localization correction in the dirty regime

    KAUST Repository

    Lu, Y. M.

    2013-03-05

    Scaling of the anomalous Hall conductivity to longitudinal conductivity σAH∝σ2xx has been observed in the dirty regime of two-dimensional weak and strong localization regions in ultrathin, polycrystalline, chemically disordered, ferromagnetic FePt films. The relationship between electron transport and temperature reveals a quantitatively insignificant Coulomb interaction in these films, while the temperature dependent anomalous Hall conductivity experiences quantum correction from electron localization. At the onset of this correction, the low-temperature anomalous Hall resistivity begins to be saturated when the thickness of the FePt film is reduced, and the corresponding Hall conductivity scaling exponent becomes 2, which is above the recent unified theory of 1.6 (σAH∝σ1.6xx). Our results strongly suggest that the correction of the electron localization modulates the scaling exponent of the anomalous Hall effect.

  8. Electronic structure and local distortions in epitaxial ScGaN films

    International Nuclear Information System (INIS)

    Knoll, S M; Zhang, S; Rovezzi, M; Joyce, T B; Moram, M A

    2014-01-01

    High energy resolution fluorescence-detected x-ray absorption spectroscopy and density functional theory calculations were used to investigate the local bonding and electronic structure of Sc in epitaxial wurtzite-structure Sc x Ga 1−x N films with x ≤ 0.059. Sc atoms are found to substitute for Ga atoms, accompanied by a local distortion involving an increase in the internal lattice parameter u around the Sc atoms. The local bonding and electronic structure at Sc are not affected strongly by the strain state or the defect microstructure of the films. These data are consistent with theoretical predictions regarding the electronic structure of dilute Sc x Ga 1−x N alloys. (paper)

  9. Grouping annotations on the subcellular layered interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line.

    Directory of Open Access Journals (Sweden)

    Xiuzhi Jia

    Full Text Available Human uveitis is a type of T cell-mediated autoimmune disease that often shows relapse-remitting courses affecting multiple biological processes. As a cytoplasmic process, autophagy has been seen as an adaptive response to cell death and survival, yet the link between autophagy and T cell-mediated autoimmunity is not certain. In this study, based on the differentially expressed genes (GSE19652 between the recurrent versus monophasic T cell lines, whose adoptive transfer to susceptible animals may result in respective recurrent or monophasic uveitis, we proposed grouping annotations on a subcellular layered interactome framework to analyze the specific bioprocesses that are linked to the recurrence of T cell autoimmunity. That is, the subcellular layered interactome was established by the Cytoscape and Cerebral plugin based on differential expression, global interactome, and subcellular localization information. Then, the layered interactomes were grouping annotated by the ClueGO plugin based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. The analysis showed that significant bioprocesses with autophagy were orchestrated in the cytoplasmic layered interactome and that mTOR may have a regulatory role in it. Furthermore, by setting up recurrent and monophasic uveitis in Lewis rats, we confirmed by transmission electron microscopy that, in comparison to the monophasic disease, recurrent uveitis in vivo showed significantly increased autophagy activity and extended lymphocyte infiltration to the affected retina. In summary, our framework methodology is a useful tool to disclose specific bioprocesses and molecular targets that can be attributed to a certain disease. Our results indicated that targeted inhibition of autophagy pathways may perturb the recurrence of uveitis.

  10. Local intelligent electronic device (IED) rendering templates over limited bandwidth communication link to manage remote IED

    Science.gov (United States)

    Bradetich, Ryan; Dearien, Jason A; Grussling, Barry Jakob; Remaley, Gavin

    2013-11-05

    The present disclosure provides systems and methods for remote device management. According to various embodiments, a local intelligent electronic device (IED) may be in communication with a remote IED via a limited bandwidth communication link, such as a serial link. The limited bandwidth communication link may not support traditional remote management interfaces. According to one embodiment, a local IED may present an operator with a management interface for a remote IED by rendering locally stored templates. The local IED may render the locally stored templates using sparse data obtained from the remote IED. According to various embodiments, the management interface may be a web client interface and/or an HTML interface. The bandwidth required to present a remote management interface may be significantly reduced by rendering locally stored templates rather than requesting an entire management interface from the remote IED. According to various embodiments, an IED may comprise an encryption transceiver.

  11. Effects of weak localization in quasi-one-dimensional electronic system over liquid helium

    CERN Document Server

    Kovdrya, Y Z; Gladchenko, S P

    2001-01-01

    One measured rho sub x sub x magnetoresistance of a quasi-one-dimensional electronic system over liquid helium within gas scattering range (1.3-2.0 K temperature range). It is shown that with increase of magnetic field the magnetoresistance is reduced at first and them upon passing over minimum it begins to increase from rho sub x sub x approx B sup 2 law. One anticipated that the negative magnetoresistance detected in the course of experiments resulted from the effects of weak localization. The experiment results are in qualitative conformity with the theoretical model describing processes of weak localization in single-dimensional nondegenerate electronic systems

  12. Electron and Nucleon Localization Functions of Oganesson: Approaching the Thomas-Fermi Limit

    Science.gov (United States)

    Jerabek, Paul; Schuetrumpf, Bastian; Schwerdtfeger, Peter; Nazarewicz, Witold

    2018-02-01

    Fermion localization functions are used to discuss electronic and nucleonic shell structure effects in the superheavy element oganesson, the heaviest element discovered to date. Spin-orbit splitting in the 7 p electronic shell becomes so large (˜10 eV ) that Og is expected to show uniform-gas-like behavior in the valence region with a rather large dipole polarizability compared to the lighter rare gas elements. The nucleon localization in Og is also predicted to undergo a transition to the Thomas-Fermi gas behavior in the valence region. This effect, particularly strong for neutrons, is due to the high density of single-particle orbitals.

  13. Local radiolytic effectiveness of Auger electrons of iodine-125 in benzene-iodine solutions

    International Nuclear Information System (INIS)

    Uenak, P.; Uenak, T.

    1987-01-01

    High radiotoxicity of iodine-125 has been mainly attributed to the local radiolytic effects of Auger electrons on biological systems. In the present study, experimental and theoretical results are compared. The agreement between the experimental and theoretical results explains that the energy absorption of iodine aggregates has an important role in the radiolytic effectiveness of Auger electrons and iodine-125 in benzene-iodine solutions. (author) 18 refs.; 3 figs

  14. Optimum launching of electron-cyclotron power for localized current drive in a hot tokamak

    International Nuclear Information System (INIS)

    Smith, G.R.

    1989-05-01

    Optimum launch parameters are determined for localized electron-cyclotron current drive near the magnetic axis and the q=2 surface by solving several minimization problems. For central current drive, equatorial and bottom launch are compared. Localized current drive near q=2 is studied for equatorial launch and for an alternative outside launch geometry that may be better for suppressing tearing modes and controlling disruptions. 6 refs., 2 figs

  15. Method for local temperature measurement in a nanoreactor for in situ high-resolution electron microscopy.

    Science.gov (United States)

    Vendelbo, S B; Kooyman, P J; Creemer, J F; Morana, B; Mele, L; Dona, P; Nelissen, B J; Helveg, S

    2013-10-01

    In situ high-resolution transmission electron microscopy (TEM) of solids under reactive gas conditions can be facilitated by microelectromechanical system devices called nanoreactors. These nanoreactors are windowed cells containing nanoliter volumes of gas at ambient pressures and elevated temperatures. However, due to the high spatial confinement of the reaction environment, traditional methods for measuring process parameters, such as the local temperature, are difficult to apply. To address this issue, we devise an electron energy loss spectroscopy (EELS) method that probes the local temperature of the reaction volume under inspection by the electron beam. The local gas density, as measured using quantitative EELS, is combined with the inherent relation between gas density and temperature, as described by the ideal gas law, to obtain the local temperature. Using this method we determined the temperature gradient in a nanoreactor in situ, while the average, global temperature was monitored by a traditional measurement of the electrical resistivity of the heater. The local gas temperatures had a maximum of 56 °C deviation from the global heater values under the applied conditions. The local temperatures, obtained with the proposed method, are in good agreement with predictions from an analytical model. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Concentration of 17 Elements in Subcellular Fractions of Beef Heart Tissue Determined by Neutron Activation Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wester, P O

    1964-12-15

    Subcellular fractions of beef heart tissue are investigated, by means of neutron activation analysis, with respect to their concentration of 17 different elements. A recently developed ion-exchange technique combined with gamma spectrometry is used. The homogeneity of the subcellular fractions is examined electron microscopically. The following elements are determined: As, Ba, Br, Cas Co, Cs, Cu, Fe, Hg, La, Mo, P, Rb, Se, Sm, W and Zn. The determination of Ag, Au, Cd, Ce, Cr, Sb and Sc is omitted, in view of contamination. Reproducible and characteristic patterns of distribution are obtained for all elements studied.

  17. Concentration of 17 Elements in Subcellular Fractions of Beef Heart Tissue Determined by Neutron Activation Analysis

    International Nuclear Information System (INIS)

    Wester, P.O.

    1964-12-01

    Subcellular fractions of beef heart tissue are investigated, by means of neutron activation analysis, with respect to their concentration of 17 different elements. A recently developed ion-exchange technique combined with gamma spectrometry is used. The homogeneity of the subcellular fractions is examined electron microscopically. The following elements are determined: As, Ba, Br, Cas Co, Cs, Cu, Fe, Hg, La, Mo, P, Rb, Se, Sm, W and Zn. The determination of Ag, Au, Cd, Ce, Cr, Sb and Sc is omitted, in view of contamination. Reproducible and characteristic patterns of distribution are obtained for all elements studied

  18. Subcellular sites for bacterial protein export

    NARCIS (Netherlands)

    Campo, Nathalie; Tjalsma, Harold; Buist, Girbe; Stepniak, Dariusz; Meijer, Michel; Veenhuis, Marten; Westermann, Martin; Müller, Jörg P.; Bron, Sierd; Kok, Jan; Kuipers, Oscar P.; Jongbloed, Jan D.H.

    2004-01-01

    Most bacterial proteins destined to leave the cytoplasm are exported to extracellular compartments or imported into the cytoplasmic membrane via the highly conserved SecA-YEG pathway. In the present studies, the subcellular distributions of core components of this pathway, SecA and SecY, and of the

  19. Subcellular sites for bacterial protein export.

    NARCIS (Netherlands)

    Campo, N.; Tjalsma, H.; Buist, G.; Stepniak, D.; Meijer, M.; Veenhuis, M.; Westermann, M.; Muller, J.P.; Bron, S.; Kok, J.; Kuipers, O.P.; Jongbloed, J.D.

    2004-01-01

    Most bacterial proteins destined to leave the cytoplasm are exported to extracellular compartments or imported into the cytoplasmic membrane via the highly conserved SecA-YEG pathway. In the present studies, the subcellular distributions of core components of this pathway, SecA and SecY, and of the

  20. Importance of non-local electron-positron correlations for positron annihilation characteristics in solids

    International Nuclear Information System (INIS)

    Rubaszek, A.

    2001-01-01

    Several methods to describe the electron-positron (e-p) correlation effects are used in calculations of positron annihilation characteristics in solids. The weighted density approximation (WDA), giving rise to the non-local, state-selective e-p correlation functions, is applied to calculate positron annihilation rates and e-p momentum densities in a variety of metals and silicon. The WDA results are compared to the results of other methods such as the independent particle model, local density approximation, generalised gradient approximation, and also to experiments. The importance of non-locality and state-dependence of the e-p correlation functions is discussed. (orig.)

  1. Electron transport in radiotherapy using local-to-global Monte Carlo

    International Nuclear Information System (INIS)

    Svatos, M.M.; Chandler, W.P.; Siantar, C.L.H.; Rathkopf, J.A.; Ballinger, C.T.

    1994-09-01

    Local-to-Global (L-G) Monte Carlo methods are a way to make three-dimensional electron transport both fast and accurate relative to other Monte Carlo methods. This is achieved by breaking the simulation into two stages: a local calculation done over small geometries having the size and shape of the ''steps'' to be taken through the mesh; and a global calculation which relies on a stepping code that samples the stored results of the local calculation. The increase in speed results from taking fewer steps in the global calculation than required by ordinary Monte Carlo codes and by speeding up the calculation per step. The potential for accuracy comes from the ability to use long runs of detailed codes to compile probability distribution functions (PDFs) in the local calculation. Specific examples of successful Local-to-Global algorithms are given

  2. Copper plasmonics and catalysis: role of electron-phonon interactions in dephasing localized surface plasmons

    Science.gov (United States)

    Sun, Qi-C.; Ding, Yuchen; Goodman, Samuel M.; H. Funke, Hans; Nagpal, Prashant

    2014-10-01

    Copper metal can provide an important alternative for the development of efficient, low-cost and low-loss plasmonic nanoparticles, and selective nanocatalysts. However, poor chemical stability and lack of insight into photophysics and plasmon decay mechanisms has impeded study. Here, we use smooth conformal ALD coating on copper nanoparticles to prevent surface oxidation, and study dephasing time for localized surface plasmons on different sized copper nanoparticles. Using dephasing time as a figure of merit, we elucidate the role of electron-electron, electron-phonon, impurity, surface and grain boundary scattering on the decay of localized surface plasmon waves. Using our quantitative analysis and different temperature dependent measurements, we show that electron-phonon interactions dominate over other scattering mechanisms in dephasing plasmon waves. While interband transitions in copper metal contributes substantially to plasmon losses, tuning surface plasmon modes to infrared frequencies leads to a five-fold enhancement in the quality factor. These findings demonstrate that conformal ALD coatings can improve the chemical stability for copper nanoparticles, even at high temperatures (>300 °C) in ambient atmosphere, and nanoscaled copper is a good alternative material for many potential applications in nanophotonics, plasmonics, catalysis and nanoscale electronics.Copper metal can provide an important alternative for the development of efficient, low-cost and low-loss plasmonic nanoparticles, and selective nanocatalysts. However, poor chemical stability and lack of insight into photophysics and plasmon decay mechanisms has impeded study. Here, we use smooth conformal ALD coating on copper nanoparticles to prevent surface oxidation, and study dephasing time for localized surface plasmons on different sized copper nanoparticles. Using dephasing time as a figure of merit, we elucidate the role of electron-electron, electron-phonon, impurity, surface and grain

  3. Probing the local, electronic and magnetic structure of matter under extreme conditions of temperature and pressure

    DEFF Research Database (Denmark)

    Torchio, R.; Boccato, S.; Cerantola, V.

    2016-01-01

    In this paper we present recent achievements in the field of investigation of the local, electronic and magnetic structure of the matter under extreme conditions of pressure and temperature. These results were obtained thanks to the coupling of a compact laser heating system to the energy-dispersive...

  4. Sustainable Development and African Local Government: Can Electronic Training Help Build Capacities?

    Science.gov (United States)

    Johnson, Hazel; Thomas, Alan

    2007-01-01

    A recent study carried out by European and African organizations into the potential for electronic distance training (EDT) on sustainability in African local governments concluded that EDT was both "useful and feasible". This article reflects on some of the theoretical and practical implications of that study. It focuses on the…

  5. Nuclear magnetic resonance and the question of 5F electron localization in the actinides

    International Nuclear Information System (INIS)

    Fradin, F.Y.

    1976-01-01

    Nuclear magnetic resonance results are presented for a number of NaCl-type compounds and cubic Laves-phase type compounds of uranium, neptunium, and plutonium. Special emphasis is placed on the Knight shift and spin-lattice relaxation time measurements and their interpretation in terms of localized or itinerant pictures of the 5Line integral electrons

  6. Strain localization band width evolution by electronic speckle pattern interferometry strain rate measurement

    Energy Technology Data Exchange (ETDEWEB)

    Guelorget, Bruno [Institut Charles Delaunay-LASMIS, Universite de technologie de Troyes, FRE CNRS 2848, 12 rue Marie Curie, B.P. 2060, 10010 Troyes Cedex (France)], E-mail: bruno.guelorget@utt.fr; Francois, Manuel; Montay, Guillaume [Institut Charles Delaunay-LASMIS, Universite de technologie de Troyes, FRE CNRS 2848, 12 rue Marie Curie, B.P. 2060, 10010 Troyes Cedex (France)

    2009-04-15

    In this paper, electronic speckle pattern interferometry strain rate measurements are used to quantify the width of the strain localization band, which occurs when a sheet specimen is submitted to tension. It is shown that the width of this band decreases with increasing strain. Just before fracture, this measured width is about five times wider than the shear band and the initial sheet thickness.

  7. Localized electronic states at grain boundaries on the surface of graphene and graphite

    DEFF Research Database (Denmark)

    Luican-Mayer, Adina; Barrios-Vargas, Jose E.; Falkenberg, Jesper Toft

    2016-01-01

    ecent advances in large-scale synthesis of graphene and other 2D materials have underscored the importance of local defects such as dislocations and grain boundaries (GBs), and especially their tendency to alter the electronic properties of the material. Understanding how the polycrystalline morp...

  8. The effect of electron localization on the electronic structure and migration barrier of oxygen vacancies in rutile.

    Science.gov (United States)

    Zhu, Linggang; Hu, Qing-Miao; Yang, Rui

    2014-02-05

    By applying the on-site Coulomb interaction (Hubbard term U) to the Ti d orbital, the influence of electron localization on the electronic structure as well as the transport of oxygen vacancies (VO) in rutile was investigated. With U = 4.5 eV, the positions of defect states in the bandgap were correctly reproduced. The unbonded electrons generated by taking out one neutral oxygen atom are spin parallel and mainly localized on the Ti atoms near VO, giving rise to a magnetic moment of 2 μB, in agreement with the experimental finding. With regard to the migration barrier of VO, surprisingly, we found that U = 4.5 eV only changed the value of the energy barrier by ±0.15 eV, depending on the diffusion path. The most probable diffusion path (along [110]) is the same as that calculated by using the traditional GGA functional. To validate the GGA + U method itself, a hybrid functional with a smaller supercell was used, and the trend of the more probable diffusion path was not changed. In this regard, the traditional GGA functional might still be reliable in the study of intrinsic-defect transportation in rutile. Analyzing the atomic distortion and density of states of the transition states for different diffusion paths, we found that the anisotropy of the diffusion could be rationalized according to the various atomic relaxations and the different positions of the valence bands relative to the Fermi level of the transition states.

  9. Localized second-order optical potential for electron scattering in terms of imaginary-frequency susceptibilities

    International Nuclear Information System (INIS)

    Valone, S.M.; Truhlar, D.G.; Thirumialai, D.

    1982-01-01

    A local approximation to the second-order optical potential for elastic scattering of low-energy electrons from ground-state atoms is expressed in terms of the imaginary-frequency susceptibilities of the atom due to a point charge and to modified perturbing potentials. This provides a basis for the physically appealing concept of regarding the perturbation due to the projectile as having a position-dependent effective frequency associated with it. The result is extended to higher energies with the use of the concept of a local kinetic energy. With a semiclassical approximation the result reduces to a simple general form that should be useful for model potential studies of electron-atom and electron-molecule scattering. Alternatively, variational functionals for the susceptibilities can be used to calculate the approximate optical potential most rigorously without making effective-frequency, average-kinetic-energy, or semiclassical approximations. Intermediate levels of rigor are also possible

  10. Theory of local and global processes which affect solar wind electrons. 2. Experimental support

    International Nuclear Information System (INIS)

    Scudder, J.D.; Olbert, S.

    1979-01-01

    We have extended the theoretical considerations of Scudder and Olbert (1979) (hereafter called paper 1) to show from the microscopic characteristics of the Coulomb cross section that there are three natural subpopulations for plasma electrons: the subthermals with local kinetic energy E 7kT/sub c/. We present experimental support from three experimental groups on three different spacecraft over a radial range in the interplanetary medium for the five interrelations projected in paper 1 between solar wind electron properties and changes in the interplanetary medium: (1) subthermals respond primarily to local changes (compressions and rarefactions) in stream dynamics: (2) the extrathermal fraction of the ambient electron density should be anticorrelated with the asymptotic bulk speed; (3) the extrathermal 'temperature' should be anticorrelated with the local wind speed at 1 AU; (4) the heat flux carried by electrons should be anticorrelated with the local bulk speed; and (5) the extrathermal differential 'temperature' should be nearly independent of radius within 1 Au. From first principles and the spatial inhomogeneity of the plasma we show that the velocity dependence of Coulomb collisions in the solar wind plasmaproduces a bifurcation in the solar wind electron distribution function at a transition energy E*. This energy is theoretically shown to scale with the local thermal temperature as E*(r) approx. =GAMMAkT/sub c/(r). This scaling is observationally supported over the radial range from 0.45 to 0.9 AU and at 1 AU. The extrathermals, defined on the basis of Coulomb collisions, are synonymous with the subpopulation previously labeled in the literature as the 'halo' or 'hot' component

  11. Topological analysis of the electron density and of the electron localization function of pyrene and its radicals

    International Nuclear Information System (INIS)

    Hernandez-Trujillo, Jesus; Garcia-Cruz, Isidoro; Martinez-Magadan, Jose Manuel

    2005-01-01

    The topological properties of the charge distribution of pyrene and the three derived monoradicals in their ground state and of didehydrogenated pyrenes in the lowest singlet and triplet electronic states are discussed in detail by means of the quantum theory of atoms in molecules (TAIM) and by the electron localization function (ELF). The non-equivalence of the fused aromatic rings of pyrene prevents one from anticipating the stability and reactivity of these species from the chemistry of didehydrogenated species derived from benzene only. Whereas some of these didehydrogenated molecules were found to display a diradical character in the singlet ground state, the topological analysis reveals that others correspond to normal closed shells. Using these theoretical tools, the energetic and geometric details of o-, m- and p-benzyne-like pyrene derivatives are explained

  12. Targeted nanodiamonds for identification of subcellular protein assemblies in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Michael P Lake

    Full Text Available Transmission electron microscopy (TEM can be used to successfully determine the structures of proteins. However, such studies are typically done ex situ after extraction of the protein from the cellular environment. Here we describe an application for nanodiamonds as targeted intensity contrast labels in biological TEM, using the nuclear pore complex (NPC as a model macroassembly. We demonstrate that delivery of antibody-conjugated nanodiamonds to live mammalian cells using maltotriose-conjugated polypropylenimine dendrimers results in efficient localization of nanodiamonds to the intended cellular target. We further identify signatures of nanodiamonds under TEM that allow for unambiguous identification of individual nanodiamonds from a resin-embedded, OsO4-stained environment. This is the first demonstration of nanodiamonds as labels for nanoscale TEM-based identification of subcellular protein assemblies. These results, combined with the unique fluorescence properties and biocompatibility of nanodiamonds, represent an important step toward the use of nanodiamonds as markers for correlated optical/electron bioimaging.

  13. Effect of oxygen deficiency on electronic properties and local structure of amorphous tantalum oxide thin films

    Energy Technology Data Exchange (ETDEWEB)

    Denny, Yus Rama [Department of Physics Education, University of Sultan Ageng Tirtayasa, Banten 42435 (Indonesia); Firmansyah, Teguh [Department of Electrical Engineering, University of Sultan Ageng Tirtayasa, Banten 42435 (Indonesia); Oh, Suhk Kun [Department of Physics, Chungbuk National University, Cheongju 28644 (Korea, Republic of); Kang, Hee Jae, E-mail: hjkang@cbu.ac.kr [Department of Physics, Chungbuk National University, Cheongju 28644 (Korea, Republic of); Yang, Dong-Seok [Department of Physics Education, Chungbuk National University, Cheongju 28644 (Korea, Republic of); Heo, Sung; Chung, JaeGwan; Lee, Jae Cheol [Analytical Engineering Center, Samsung Advanced Institute of Technology, Suwon 16678 (Korea, Republic of)

    2016-10-15

    Highlights: • The effect of oxygen flow rate on electronic properties and local structure of tantalum oxide thin films was studied. • The oxygen deficiency induced the nonstoichiometric state a-TaOx. • A small peak at 1.97 eV above the valence band side appeared on nonstoichiometric Ta{sub 2}O{sub 5} thin films. • The oxygen flow rate can change the local electronic structure of tantalum oxide thin films. - Abstract: The dependence of electronic properties and local structure of tantalum oxide thin film on oxygen deficiency have been investigated by means of X-ray photoelectron spectroscopy (XPS), Reflection Electron Energy Loss Spectroscopy (REELS), and X-ray absorption spectroscopy (XAS). The XPS results showed that the oxygen flow rate change results in the appearance of features in the Ta 4f at the binding energies of 23.2 eV, 24.4 eV, 25.8, and 27.3 eV whose peaks are attributed to Ta{sup 1+}, Ta{sup 2+}, Ta{sup 3+}/Ta{sup 4+}, and Ta{sup 5+}, respectively. The presence of nonstoichiometric state from tantalum oxide (TaOx) thin films could be generated by the oxygen vacancies. In addition, XAS spectra manifested both the increase of coordination number of the first Ta-O shell and a considerable reduction of the Ta-O bond distance with the decrease of oxygen deficiency.

  14. Non-local electron transport validation using 2D DRACO simulations

    Science.gov (United States)

    Cao, Duc; Chenhall, Jeff; Moll, Eli; Prochaska, Alex; Moses, Gregory; Delettrez, Jacques; Collins, Tim

    2012-10-01

    Comparison of 2D DRACO simulations, using a modified versionfootnotetextprivate communications with M. Marinak and G. Zimmerman, LLNL. of the Schurtz, Nicolai and Busquet (SNB) algorithmfootnotetextSchurtz, Nicolai and Busquet, ``A nonlocal electron conduction model for multidimensional radiation hydrodynamics codes,'' Phys. Plasmas 7, 4238(2000). for non-local electron transport, with direct drive shock timing experimentsfootnotetextT. Boehly, et. al., ``Multiple spherically converging shock waves in liquid deuterium,'' Phys. Plasmas 18, 092706(2011). and with the Goncharov non-local modelfootnotetextV. Goncharov, et. al., ``Early stage of implosion in inertial confinement fusion: Shock timing and perturbation evolution,'' Phys. Plasmas 13, 012702(2006). in 1D LILAC will be presented. Addition of an improved SNB non-local electron transport algorithm in DRACO allows direct drive simulations with no need for an electron conduction flux limiter. Validation with shock timing experiments that mimic the laser pulse profile of direct drive ignition targets gives a higher confidence level in the predictive capability of the DRACO code. This research was supported by the University of Rochester Laboratory for Laser Energetics.

  15. Effect of local atomic and electronic structures on thermoelectric properties of chemically substituted CoSi

    Science.gov (United States)

    Hsu, C. C.; Pao, C. W.; Chen, J. L.; Chen, C. L.; Dong, C. L.; Liu, Y. S.; Lee, J. F.; Chan, T. S.; Chang, C. L.; Kuo, Y. K.; Lue, C. S.

    2014-05-01

    We report the effects of Ge partial substitution for Si on local atomic and electronic structures of thermoelectric materials in binary compound cobalt monosilicides (\\text{CoSi}_{1-x}\\text{Ge}_{x}\\text{:}\\ 0 \\le x \\le 0.15 ). Correlations between local atomic/electronic structure and thermoelectric properties are investigated by means of X-ray absorption spectroscopy. The spectroscopic results indicate that as Ge is partially substituted onto Si sites at x \\le 0.05 , Co in CoSi1-xGex gains a certain amount of charge in its 3d orbitals. Contrarily, upon further replacing Si with Ge at x \\ge 0.05 , the Co 3d orbitals start to lose some of their charge. Notably, thermopower is strongly correlated with charge redistribution in the Co 3d orbital, and the observed charge transfer between Ge and Co is responsible for the variation of Co 3d occupancy number. In addition to Seebeck coefficient, which can be modified by tailoring the Co 3d states, local lattice disorder may also be beneficial in enhancing the thermoelectric properties. Extended X-ray absorption fine structure spectrum results further demonstrate that the lattice phonons can be enhanced by Ge doping, which results in the formation of the disordered Co-Co pair. Improvements in the thermoelectric properties are interpreted based on the variation of local atomic and electronic structure induced by lattice distortion through chemical substitution.

  16. Study of localized corrosion in AA2024 aluminium alloy using electron tomography

    International Nuclear Information System (INIS)

    Zhou, X.; Luo, C.; Hashimoto, T.; Hughes, A.E.; Thompson, G.E.

    2012-01-01

    Highlights: ► SEM tomography of localized corrosion has been achieved. ► Nanotomography provides evidence that links microstructure and corrosion propagation path. ► IGC stemmed from localized corrosion associated with buried clusters of intermetallics. ► IGC started beneath the alloy surface and may emerge on the alloy surface. - Abstract: SEM based tomography of localized corrosion has been achieved using selective detection of backscattered electrons. The high resolution tomography provides direct evidence that links the surface appearance of corroded alloy, the alloy microstructure and the corrosion propagation path. Stable localized corrosion of AA2024-T351 aluminium alloy was initiated at locations where large clusters of S phase particles were buried beneath the surface. Propagating away from the initiation sites, corrosion developed preferentially along the grain boundary network. The grain boundary attack started beneath the alloy surface, proceeded along preferred grain boundaries and may emerge at the alloy surface.

  17. Anisotropic light emission of single CdSe/CdS tetrapods due to asymmetric electron localization

    Energy Technology Data Exchange (ETDEWEB)

    Limmer, Thomas; Mauser, Christian; Como, Enrico da; Rogach, Andrey; Feldmann, Jochen [Photonics and Optoelectronics Group, Physics Department and CeNS, Ludwig-Maximilians-Universitaet Muenchen, Munich (Germany); Talapin, Dmitri V. [Department of Chemistry, University of Chicago, Chicago, IL (United States)

    2008-07-01

    We have recently reported on highly luminescent CdSe/CdS tetrapod heterostructures, where wurtzite CdS arms were grown on CdSe zinc-blend nuclei. Due to the peculiar energy band alignment the holes remain trapped in the CdSe core, whereas electrons in ideal tetrapods are expected to delocalize symmetrically into the four CdS arms. However, polarization dependent photoluminescence experiments on single tetrapods show asymmetric localization effects for electrons. Whereas in optical excitation nearly no polarization anisotropy is observed, high polarization degrees are present in the emission process. Calculations based on the effective mass approximation show that the electron wavefunction confinement is very sensitive to changes in the shape of the tetrapods. Breaking the symmetry by increasing the thickness of one arm gives rise to a strongly asymmetric localization of the electron and leads to high polarization degrees in emission. The related decrease in electron-hole wavefunction overlap results in a correlation between emission intensity and polarization anisotropy in agreement with our experimental findings.

  18. Delocalized and localized states of eg electrons in half-doped manganites.

    Science.gov (United States)

    Winkler, E L; Tovar, M; Causa, M T

    2013-07-24

    We have studied the magnetic behaviour of half-doped manganite Y0.5Ca0.5MnO3 in an extended range of temperatures by means of magnetic susceptibility, χ(T), and electron spin resonance (ESR) experiments. At high temperature the system crystallizes in an orthorhombic structure. The resistivity value, ρ ≃ 0.05 Ω cm at 500 K, indicates a metallic behaviour, while the Curie-Weiss dependence of χ(T) and the thermal evolution of the ESR parameters are very well described by a model that considers a system conformed by localized Mn(4+) cores, [Formula: see text], and itinerant, eg, electrons. The strong coupling between t2g and eg electrons results in an enhanced Curie constant and an FM Curie-Weiss temperature that overcomes the AFM interactions between the [Formula: see text] cores. A transition to a more distorted phase is observed at T ≈ 500 K and signatures of localization of the eg electrons appear in the χ(T) behaviour below 300 K. A new Curie-Weiss regime is observed, where the Curie-constant value is consistent with dimer formation. Based on mean-field calculations, the dimer formation is predicted as a function of the interaction strength between the t2g and eg electrons.

  19. Subcellular Nanoparticle Distribution from Light Transmission Spectroscopy

    Science.gov (United States)

    Deatsch, Alison; Sun, Nan; Johnson, Jeffrey; Stack, Sharon; Tanner, Carol; Ruggiero, Steven

    We have measured the particle-size distribution (PSD) of subcellular structures in plant and animal cells. We have employed a new technique developed by our group, Light Transmission Spectroscopy-combined with cell fractionation-to accurately measure PSDs over a wide size range: from 10 nm to 3000nm, which includes objects from the size of individual proteins to organelles. To date our experiments have included cultured human oral cells and spinach cells. These results show a power-law dependence of particle density with particle diameter, implying a universality of the packing distribution. We discuss modeling the cell as a self-similar (fractal) body comprised of spheres on all size scales. This goal of this work is to obtain a better understanding of the fundamental nature of particle packing within cells in order to enrich our knowledge of the structure, function, and interactions of sub-cellular nanostructures across cell types.

  20. Second Line of Defense: Electronic Maintenance Reports, Local Maintenance Provider User Guide, Rev. 3

    Energy Technology Data Exchange (ETDEWEB)

    Leigh, Richard J.

    2012-09-01

    The Electronic Maintenance Report forms allow Local Maintenance Providers (LMP) and other program staff to enter maintenance information into a simple and secure system. This document describes the features and information required to complete the Maintenance Report forms. It is expected that all Corrective Maintenance Reports from LMPs will be submitted electronically into the SLD Portal. As an exception (e.g., when access to the SLD Portal is unavailable), Maintenance Reports can be submitted via a secure Adobe PDF form available through the Sustainability Manager assigned to each country.

  1. On the local theory of resonant inelastic collisions of slow electrons with carbon dioxide

    International Nuclear Information System (INIS)

    Kazansky, A.K.; Sergeeva, L.Yu.

    1994-01-01

    A method of calculating the cross sections of inelastic vibronic transitions in collisions of slow electrons with polyatomic molecules in the framework of the local theory (the 'boomerang' model) is proposed. The method is based on the study of the time evolution of the initial vibronic wavefunction; the evolution is governed by the (complex valued) Hamiltonian of the intermediate anion state. The method has been applied to the consideration of inelastic electron collisions with the CO 2 molecule in the two-mode approximation (symmetrical stretching and bending). The results obtained demonstrate the importance of the two-mode description for the system which can undergo the Renner transition. (Author)

  2. Electronic structure of the Fe2 molecule in the local-spin-density approximation

    International Nuclear Information System (INIS)

    Dhar, S.; Kestner, N.R.

    1988-01-01

    Ab initio self-consistent all-electron spin-polarized calculations have been performed for the ground-state properties of the Fe 2 molecule using the local-spin-density approximation. A Gaussian orbital basis is employed and all the two-electron integrals are evaluated analytically. The matrix elements of the exchange-correlation potential are computed numerically. The total energy, the binding energy, the equilibrium distance, vibrational frequency, and the ground-state configurations are reported and compared with other calculations and experimental results

  3. Observation of weak superconductivity in electrons localized on a film surface

    International Nuclear Information System (INIS)

    Fogel', N.Y.; Kolin'ko, A.E.

    1984-01-01

    We have observed anomalous abrupt resistance changes in thick vanadium films [d>>xi(T)]. We have also observed a number of anomalies in the H--T phase diagrams for these films; these anomalies are most clearly seen when the field is parallel to, or at low angles of incidence with respect to, the film surface. We explain our results by assuming that there are two different electron systems present in the film. One of them is composed of electrons localized near a natural planar defect, the film surface. This subsystem is characterized by extremely small values of the critical current

  4. Analysis of local dislocation densities in cold-rolled alloy 690 using transmission electron microscopy

    International Nuclear Information System (INIS)

    Ahn, Tae-Young; Kim, Sung Woo; Hwang, Seong Sik

    2016-01-01

    Service failure of alloy 690 in NPP has not been reported. However, some research groups reported that primary water stress corrosion cracking (PWSCC) occurred in severely cold-rolled alloy 690. Transgranular craking was also reported in coll-rolled alloy 690 with a banded structure. In order to understand the effect of cold rolling on the cracking of alloy 690, many research groups have focused on the local strain and the cracked carbide induced by cold-rolling, by using electron backscatter diffraction (EBSD). Transmission electron microscopy (TEM) has been widely used to characterize structural materials because this technique has superior spatial resolution and allows for the analysis of crystallographic and chemical information. The aim of the present study is to understand the mechanism of the abnormally high crack growth rate (CGR) in cold-rolled alloy 690 with a banded structure. The local dislocation density was measured by TEM to confirm the effects of local strain on the stress corrosion cracking (SCC) of alloy 690 with a banded structure. The effects of intragranular carbides on the SCC were also evaluated in this study. The local dislocation densities were directly measured using TEM to understand the effect of local strain on the SCC of Ni-based alloy 690 with a banded structure. The dislocation densities in the interior of the grains sharply increased in highly cold-rolled specimens due to intragranular carbide, which acted as a dislocation source

  5. Atomistic spectrometrics of local bond-electron-energy pertaining to Na and K clusters

    Energy Technology Data Exchange (ETDEWEB)

    Bo, Maolin [Key Laboratory of Low-Dimensional Materials and Application Technologies, Ministry of Education, Xiangtan University, Hunan 411105 (China); Wang, Yan, E-mail: YWang8@hnust.edu.cn [School of Information and Electronic Engineering, Hunan University of Science and Technology, Hunan 411201 (China); Huang, Yongli; Liu, Yonghui [Key Laboratory of Low-Dimensional Materials and Application Technologies, Ministry of Education, Xiangtan University, Hunan 411105 (China); Li, Can [Center for Coordination Bond Engineering, School of Materials Science and Engineering, China Jiliang University, Hangzhou 330018 (China); Sun, Chang Q., E-mail: ecqsun@ntu.edu.sg [NOVITAS, School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore)

    2015-01-15

    Graphical abstract: - Highlights: • Coordination environment resolves electron binding-energy shift of Na and K clusters. • Cohesive energy of the representative bond determines the core-level shift. • XPS derives the energy level of an isolated atom and its bulk shift. • XPS derives the local bond length, bond energy, binding energy density. - Abstract: Consistency between density functional theory calculations and photoelectron spectroscopy measurements confirmed our predications on the undercoordination-induced local bond relaxation and core level shift of Na and K clusters. It is clarified that the shorter and stronger bonds between under-coordinated atoms cause local densification and local potential well depression and shift the electron binding-energy accordingly. Numerical consistency turns out the energy levels for an isolated Na (E{sub 2p} = 31.167 eV) and K (E{sub 3p} = 18.034 eV) atoms and their respective bulk shifts of 2.401 eV and 2.754 eV, which is beyond the scope of conventional approaches. This strategy has also resulted in quantification of the local bond length, bond energy, binding energy density, and atomic cohesive energy associated with the undercoordinated atoms.

  6. Detecting aroma changes of local flavored green tea (Camellia sinensis) using electronic nose

    Science.gov (United States)

    Ralisnawati, D.; Sukartiko, A. C.; Suryandono, A.; Triyana, K.

    2018-03-01

    Indonesia is currently the sixth largest tea producer in the world. However, consumption of the product in the country was considered low. Besides tea, the country also has various local flavor ingredients that are potential to be developed. The addition of local flavored ingredients such as ginger, lemon grass, and lime leaves on green tea products is gaining acceptance from consumers and producers. The aroma of local flavored green tea was suspected to changes during storage, while its sensory testing has some limitations. Therefore, the study aimed to detect aroma changes of local flavors added in green tea using electronic nose (e-nose), an instrument developed to mimic the function of the human nose. The test was performed on a four-gram sample. The data was collected with 120 seconds of sensing time and 60 seconds of blowing time. Principal Component Analysis (PCA) was used to find out the aroma changes of local flavored green tea during storage. We observed that electronic nose could detect aroma changes of ginger flavored green tea from day 0 to day 6 with variance percentage 99.6%. Variance proportion of aroma changes of lemon grass flavored green tea from day 0 to day 6 was 99.3%. Variance proportion of aroma changes of lime leaves flavored green tea from day 0 to day 6 was 99.4%.

  7. Spin inelastic electron tunneling spectroscopy on local spin adsorbed on surface.

    Science.gov (United States)

    Fransson, J

    2009-06-01

    The recent experimental conductance measurements taken on magnetic impurities on metallic surfaces, using scanning tunneling microscopy technique and suggesting occurrence of inelastic scattering processes, are theoretically addressed. We argue that the observed conductance signatures are caused by transitions between the spin states that have opened due to, for example, exchange coupling between the local spins and the tunneling electrons, and are directly interpretable in terms of inelastic transitions energies. Feasible measurements using spin-polarized scanning tunneling microscopy that would enable new information about the excitation spectrum of the local spins are discussed.

  8. Study of the local structure of binary surfaces by electron diffraction (XPS, LEED)

    OpenAIRE

    Gereová, Katarína

    2006-01-01

    Study of local structure of binary surface with usage of ultra-thin film of cerium deposited on a Pd (111) single-crystal surface is presented. X-ray photoelectron spectroscopy and diffraction (XPS, XPD), angle resolved UV photoemission spectroscopy (ARUPS) and low energy electron diffraction (LEED) was used for our investigations. LEED and X-ray excited photoemission intensities results represent a surface-geometrical structure. As well, mapping of ultra-violet photoelectron intensities as a...

  9. Magnetic forces and localized resonances in electron transfer through quantum rings.

    Science.gov (United States)

    Poniedziałek, M R; Szafran, B

    2010-11-24

    We study the current flow through semiconductor quantum rings. In high magnetic fields the current is usually injected into the arm of the ring preferred by classical magnetic forces. However, for narrow magnetic field intervals that appear periodically on the magnetic field scale the current is injected into the other arm of the ring. We indicate that the appearance of the anomalous-non-classical-current circulation results from Fano interference involving localized resonant states. The identification of the Fano interference is based on the comparison of the solution of the scattering problem with the results of the stabilization method. The latter employs the bound-state type calculations and allows us to extract both the energy of metastable states localized within the ring and the width of resonances by analysis of the energy spectrum of a finite size system as a function of its length. The Fano resonances involving states of anomalous current circulation become extremely narrow on both the magnetic field and energy scales. This is consistent with the orientation of the Lorentz force that tends to keep the electron within the ring and thus increases the lifetime of the electron localization within the ring. Absence of periodic Fano resonances in electron transfer probability through a quantum ring containing an elastic scatterer is also explained.

  10. Localization of fluorescently labeled structures in frozen-hydrated samples using integrated light electron microscopy.

    Science.gov (United States)

    Faas, F G A; Bárcena, M; Agronskaia, A V; Gerritsen, H C; Moscicka, K B; Diebolder, C A; van Driel, L F; Limpens, R W A L; Bos, E; Ravelli, R B G; Koning, R I; Koster, A J

    2013-03-01

    Correlative light and electron microscopy is an increasingly popular technique to study complex biological systems at various levels of resolution. Fluorescence microscopy can be employed to scan large areas to localize regions of interest which are then analyzed by electron microscopy to obtain morphological and structural information from a selected field of view at nm-scale resolution. Previously, an integrated approach to room temperature correlative microscopy was described. Combined use of light and electron microscopy within one instrument greatly simplifies sample handling, avoids cumbersome experimental overheads, simplifies navigation between the two modalities, and improves the success rate of image correlation. Here, an integrated approach for correlative microscopy under cryogenic conditions is presented. Its advantages over the room temperature approach include safeguarding the native hydrated state of the biological specimen, preservation of the fluorescence signal without risk of quenching due to heavy atom stains, and reduced photo bleaching. The potential of cryo integrated light and electron microscopy is demonstrated for the detection of viable bacteria, the study of in vitro polymerized microtubules, the localization of mitochondria in mouse embryonic fibroblasts, and for a search into virus-induced intracellular membrane modifications within mammalian cells. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Local conditions for the Pauli potential in order to yield self-consistent electron densities exhibiting proper atomic shell structure

    Energy Technology Data Exchange (ETDEWEB)

    Finzel, Kati, E-mail: kati.finzel@liu.se [Linköpings University, IFM Department of Physics, 58183 Linköping (Sweden)

    2016-01-21

    The local conditions for the Pauli potential that are necessary in order to yield self-consistent electron densities from orbital-free calculations are investigated for approximations that are expressed with the help of a local position variable. It is shown that those local conditions also apply when the Pauli potential is given in terms of the electron density. An explicit formula for the Ne atom is given, preserving the local conditions during the iterative procedure. The resulting orbital-free electron density exhibits proper shell structure behavior and is in close agreement with the Kohn-Sham electron density. This study demonstrates that it is possible to obtain self-consistent orbital-free electron densities with proper atomic shell structure from simple one-point approximations for the Pauli potential at local density level.

  12. A measure of localization properties of one-dimensional single electron lattice systems

    International Nuclear Information System (INIS)

    Gong, Longyan; Li, Wenjia; Zhao, Shengmei; Cheng, Weiwen

    2016-01-01

    We propose a novel quantity to measure the degree of localization properties of various types of one-dimension single electron states. The quantity includes information about the spatial variation of probability density of quantum states. Numerical results show that it can distinguish localized states from delocalized ones, so it can be used as a fruitful index to monitor the localization–delocalization transition. Comparing with existing measures, such as geometric average density of states, inverse participation ratio, and quantum information entropies, our proposed quantity has some advantages over them. - Highlights: • A novel quantity is proposed to measure the degree of localization. • It includes information about the spatial variation of probability density. • It is a fruitful index to monitor the localization–delocalization transition.

  13. A geometric initial guess for localized electronic orbitals in modular biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Beckman, P. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of Chicago, IL (United States); Fattebert, J. L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lau, E. Y. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Osei-Kuffuor, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-09-11

    Recent first-principles molecular dynamics algorithms using localized electronic orbitals have achieved O(N) complexity and controlled accuracy in simulating systems with finite band gaps. However, accurately deter- mining the centers of these localized orbitals during simulation setup may require O(N3) operations, which is computationally infeasible for many biological systems. We present an O(N) approach for approximating orbital centers in proteins, DNA, and RNA which uses non-localized solutions for a set of fixed-size subproblems to create a set of geometric maps applicable to larger systems. This scalable approach, used as an initial guess in the O(N) first-principles molecular dynamics code MGmol, facilitates first-principles simulations in biological systems of sizes which were previously impossible.

  14. Anderson localization and its ramifications disorder, phase coherence and electron correlations

    CERN Document Server

    Kettemann, S

    2003-01-01

    The phenomenon of localization of the electronic wave function in a random medium can be regarded as the key manifestation of quantum coherence in a condensed matter system. As one of the most remarkable phenomena in condensed matter physics discovered in the 20th century, the localization problem is an indispensable part of the theory of the quantum Hall effects and rivals superconductivity in its significance as a manifestation of quantum coherence at a macroscopic scale. The present volume, written by some of the leading experts in the field, is intended to highlight some of the recent progress in the field of localization, with particular emphasis on the effect of interactions on quantum coherence. The chapters are written in textbook style and should serve as a reliable and thorough introduction for advanced students or researchers already working in the field of mesoscopic physics.

  15. The Magnetic Local Time Distribution of Energetic Electrons in the Radiation Belt Region

    Science.gov (United States)

    Allison, H. J.

    2017-12-01

    Using fourteen years of electron flux data from the National Oceanic and Atmospheric Administration Polar Operational Environmental Satellites (POES), a statistical study of the magnetic local time (MLT) distribution of the electron population is performed across a range of activity levels, defined by AE, AE*, Kp, solar wind velocity (Vsw), and VswBz. Three electron energies (>30, >100, and >300 keV) are considered. Dawn-dusk flux asymmetries larger than order of magnitude were observed for >30 and >100 keV electrons. For >300 keV electrons, dawn-dusk asymmetries were primarily due to a decrease in the average dusk-side flux beyond L* ˜ 4.5 that arose with increasing activity. For the >30 keV population, substorm injections enhance the dawn-side flux, which may not reach the dusk-side as the electrons can be on open drift paths and lost to the magnetopause. The asymmetries in the >300 keV population are attributed to the combination of magnetopause shadowing and >300 keV electron injections by large electric fields. We suggest that 3D radiation belt models could set the minimum energy boundary (Emin) to 30 keV or above at L* ˜6 during periods of low activity. However, for more moderate conditions, Emin should be larger than 100 keV and, for very extreme activities, ˜300 keV. Our observations show the extent that in-situ electron flux readings may vary during active periods due to the MLT of the satellite and highlight the importance of 4D radiation belt models to fully understand radiation belt processes.

  16. Direct Visualization of Local Electromagnetic Field Structures by Scanning Transmission Electron Microscopy.

    Science.gov (United States)

    Shibata, Naoya; Findlay, Scott D; Matsumoto, Takao; Kohno, Yuji; Seki, Takehito; Sánchez-Santolino, Gabriel; Ikuhara, Yuichi

    2017-07-18

    The functional properties of materials and devices are critically determined by the electromagnetic field structures formed inside them, especially at nanointerface and surface regions, because such structures are strongly associated with the dynamics of electrons, holes and ions. To understand the fundamental origin of many exotic properties in modern materials and devices, it is essential to directly characterize local electromagnetic field structures at such defect regions, even down to atomic dimensions. In recent years, rapid progress in the development of high-speed area detectors for aberration-corrected scanning transmission electron microscopy (STEM) with sub-angstrom spatial resolution has opened new possibilities to directly image such electromagnetic field structures at very high-resolution. In this Account, we give an overview of our recent development of differential phase contrast (DPC) microscopy for aberration-corrected STEM and its application to many materials problems. In recent years, we have developed segmented-type STEM detectors which divide the detector plane into 16 segments and enable simultaneous imaging of 16 STEM images which are sensitive to the positions and angles of transmitted/scattered electrons on the detector plane. These detectors also have atomic-resolution imaging capability. Using these segmented-type STEM detectors, we show DPC STEM imaging to be a very powerful tool for directly imaging local electromagnetic field structures in materials and devices in real space. For example, DPC STEM can clearly visualize the local electric field variation due to the abrupt potential change across a p-n junction in a GaAs semiconductor, which cannot be observed by normal in-focus bright-field or annular type dark-field STEM imaging modes. DPC STEM is also very effective for imaging magnetic field structures in magnetic materials, such as magnetic domains and skyrmions. Moreover, real-time imaging of electromagnetic field structures can

  17. The effects of local correlations on the electronic structure of FeSe

    Science.gov (United States)

    Watson, Matthew; Kim, Timur; Haghighirad, Amir; Coldea, Amalia

    FeSe is structurally the simplest of Fe-based superconductors, but its complex and unique properties pose important theoretical questions. One important aspect of the physics of FeSe is the understanding of the strength and effects of electronic correlations. In order to explore this, we have performed angle-resolved photo-emission spectroscopy (ARPES) measurements on high quality bulk single crystals of FeSe over a wide range of binding energies, in different scattering geometries and with varying incident photon energies, analysing the quasiparticle renormalisations, scattering rates and degree of coherence. We find that FeSe exhibits moderately strong, orbital-dependent correlation effects which are understood to arise primarily due to local electron-electron interactions on the Fe sites. We conclude that electronic correlations constitute a key ingredient in understanding the electronic structure of FeSe. Part of this work was supported by EPSRC, UK (EP/I004475/1, EP/I017836/1). We thank Diamond Light Source for access to Beamline I05.

  18. Self-Attractive Hartree Decomposition: Partitioning Electron Density into Smooth Localized Fragments.

    Science.gov (United States)

    Zhu, Tianyu; de Silva, Piotr; Van Voorhis, Troy

    2018-01-09

    Chemical bonding plays a central role in the description and understanding of chemistry. Many methods have been proposed to extract information about bonding from quantum chemical calculations, the majority of them resorting to molecular orbitals as basic descriptors. Here, we present a method called self-attractive Hartree (SAH) decomposition to unravel pairs of electrons directly from the electron density, which unlike molecular orbitals is a well-defined observable that can be accessed experimentally. The key idea is to partition the density into a sum of one-electron fragments that simultaneously maximize the self-repulsion and maintain regular shapes. This leads to a set of rather unusual equations in which every electron experiences self-attractive Hartree potential in addition to an external potential common for all the electrons. The resulting symmetry breaking and localization are surprisingly consistent with chemical intuition. SAH decomposition is also shown to be effective in visualization of single/multiple bonds, lone pairs, and unusual bonds due to the smooth nature of fragment densities. Furthermore, we demonstrate that it can be used to identify specific chemical bonds in molecular complexes and provides a simple and accurate electrostatic model of hydrogen bonding.

  19. LocTree3 prediction of localization

    DEFF Research Database (Denmark)

    Goldberg, T.; Hecht, M.; Hamp, T.

    2014-01-01

    The prediction of protein sub-cellular localization is an important step toward elucidating protein function. For each query protein sequence, LocTree2 applies machine learning (profile kernel SVM) to predict the native sub-cellular localization in 18 classes for eukaryotes, in six for bacteria a...

  20. Localized versus collective behaviour of d-electrons in transition metal oxide systems of perovskite systems

    Energy Technology Data Exchange (ETDEWEB)

    Rao, C N.R. [Indian Inst. of Tech., Kanpur

    1974-12-01

    The behavior of d-electrons in perovskites of the type LnZO/sub 3/ (Z = trivalent transition metal ion and Ln = rare earth or yttrium) depends on the spin configuration of the transition metal ion. LaTiO/sub 3/ and LaNiO/sub 3/ with low-spin transition metal ions (S = 1/2) are metallic while LaCrO/sub 3/, LnMnO/sub 3/ and LnFeO/sub 3/ with high-spin ions are poor semiconductors exhibiting localized behavior of d-electrons. In rare earth cobaltites, the cobalt ions are present mainly in the diamagnetic low-spin Co /sup III/ state at low temperatures. The Co/sup III/ ions transform to high-spin Co/sup 3 +/ ions with increase in temperature. At higher temperatures, there is electron-transfer from Co/sup 3 +/ to Co/sup III/ions producing intermetallic states. Spin-state transitions are seen in these cobaltites in the range 150-870/sup 0/K. At high temperatures, the cobaltites show evidence for localized-itinerant electron transitions. In La/sub 1-x/ Sr/sub x/CoO/sub 3/ there is onset of ferromagnetism at x > 0.125, at which point there is a structural dicontinuity and electrons become itinerant. The composition with x = 0.5 is metallic and T/sub c/ = 230/sup 0/K. The ferromagnetic component in La/sub 1-x/Sr/sub x/ CoO/sub 3/ increases with x in the range 0.125-0.50. Catalytic properties of rare earth cobaltites appear to be related to the spin state equilibria. (auth)

  1. Subcellular distribution of curium in beagle liver

    International Nuclear Information System (INIS)

    Bruenger, F.W.; Grube, B.J.; Atherton, D.R.; Taylor, G.N.; Stevens, W.

    1976-01-01

    The subcellular distribution of curium ( 243 244 Cm) was studied in canine liver from 2 hr to 47 days after injection of 3 μCi 243 244 Cm/kg of body weight. The pattern of distribution for Cm was similar to other trivalent actinide elements studied previously (Am, Cf). Initially (2 hr), most of the nuclide was found in the cytosol and at least 90 percent was protein bound. About 70 percent of the Cm was bound to ferritin, approximately 5 percent was associated with a protein of MW approximately 200,000, and approximately 25 percent was found in the low-molecular-weight region (approximately 5000). The decrease in the Cm content of cytosol, nuclei, and microsomes coincided with an increase in the amount associated with mitochondria and lysosomes. The concentration of the Cm in the mitochondrial fraction was higher than it was in the lysosomal fraction at each time studied. In the mitochondrial fraction approximately 30 percent of the Cm was bound to membranous or granular material, and 70 percent was found in the soluble fraction. The Cm concentration initially associated with cell nuclei was high but had diminished to 20 percent of the 2 hr concentration by 20 days post injection (PI). The subcellular distribution of Cm in the liver of a dog which had received the same dose and was terminated because of severe liver damage was studied at 384 days PI. The liver weighed 130 g and contained approximately 30 percent of the injected Cm. In contrast, a normal liver weighs 280 g and at 2 hr PI contains approximately 40 percent of the injected dose. The subcellular distribution of Cm in this severely damaged liver differed from the pattern observed at earlier times after injection. The relative concentration of Cm in the cytosol was doubled; it was higher in the nuclei-debris fraction; and it was lower in the mitochondrial and lysosomal fractions when compared to earlier times

  2. Intranet and village community: optimization of public service based on electronic government at the local level

    Science.gov (United States)

    Pradana, G. W.; Fanida, E. H.; Niswah, F.

    2018-01-01

    The demand for good governance is directed towards the realization of efficiency, effectiveness, and clean government. The move is demonstrated through national and regional levels to develop and implement electronic government concepts. Through the development of electronic government is done structuring management systems and work processes in the government environment by optimizing the utilization of information technology. One of the real forms of electronic government (e-Gov) implementation at the local level is the Intranet Sub-District program in Sukodono Sub-District, Sidoarjo. Intranet Sub-District is an innovation whose purpose is to realize the availability of information on the utilization of management, distribution, and storage of official scripts, and also the optimal delivery of information and communication in the implementation of guidance and supervision of local administration. The type of this paper is descriptive with a qualitative approach and focus on the implementation of the Intranet District Program in Sukodono District, Sidoarjo. The findings of the study are the limited number of human resources who have mastered ICT, the uneven network, the adequacy of institutional needs and the existence of budget support from the authorized institution and the information system has not accommodated all the service needs.

  3. Local imaging of high mobility two-dimensional electron systems with virtual scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Pelliccione, M. [Department of Applied Physics, Stanford University, 348 Via Pueblo Mall, Stanford, California 94305 (United States); Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025 (United States); Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106 (United States); Bartel, J.; Goldhaber-Gordon, D. [Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025 (United States); Department of Physics, Stanford University, 382 Via Pueblo Mall, Stanford, California 94305 (United States); Sciambi, A. [Department of Applied Physics, Stanford University, 348 Via Pueblo Mall, Stanford, California 94305 (United States); Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025 (United States); Pfeiffer, L. N.; West, K. W. [Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544 (United States)

    2014-11-03

    Correlated electron states in high mobility two-dimensional electron systems (2DESs), including charge density waves and microemulsion phases intermediate between a Fermi liquid and Wigner crystal, are predicted to exhibit complex local charge order. Existing experimental studies, however, have mainly probed these systems at micron to millimeter scales rather than directly mapping spatial organization. Scanning probes should be well-suited to study the spatial structure of these states, but high mobility 2DESs are found at buried semiconductor interfaces, beyond the reach of conventional scanning tunneling microscopy. Scanning techniques based on electrostatic coupling to the 2DES deliver important insights, but generally with resolution limited by the depth of the 2DES. In this letter, we present our progress in developing a technique called “virtual scanning tunneling microscopy” that allows local tunneling into a high mobility 2DES. Using a specially designed bilayer GaAs/AlGaAs heterostructure where the tunnel coupling between two separate 2DESs is tunable via electrostatic gating, combined with a scanning gate, we show that the local tunneling can be controlled with sub-250 nm resolution.

  4. Local Electronic Structure of a Single-Layer Porphyrin-Containing Covalent Organic Framework

    KAUST Repository

    Chen, Chen

    2017-12-20

    We have characterized the local electronic structure of a porphyrin-containing single-layer covalent organic framework (COF) exhibiting a square lattice. The COF monolayer was obtained by the deposition of 2,5-dimethoxybenzene-1,4-dicarboxaldehyde (DMA) and 5,10,15,20-tetrakis(4-aminophenyl) porphyrin (TAPP) onto a Au(111) surface in ultrahigh vacuum followed by annealing to facilitate Schiff-base condensations between monomers. Scanning tunneling spectroscopy (STS) experiments conducted on isolated TAPP precursor molecules and the covalently linked COF networks yield similar transport (HOMO-LUMO) gaps of 1.85 ± 0.05 eV and 1.98 ± 0.04 eV, respectively. The COF orbital energy alignment, however, undergoes a significant downward shift compared to isolated TAPP molecules due to the electron-withdrawing nature of the imine bond formed during COF synthesis. Direct imaging of the COF local density of states (LDOS) via dI/dV mapping reveals that the COF HOMO and LUMO states are localized mainly on the porphyrin cores and that the HOMO displays reduced symmetry. DFT calculations reproduce the imine-induced negative shift in orbital energies and reveal that the origin of the reduced COF wave function symmetry is a saddle-like structure adopted by the porphyrin macrocycle due to its interactions with the Au(111) substrate.

  5. Accurate prediction of subcellular location of apoptosis proteins combining Chou’s PseAAC and PsePSSM based on wavelet denoising

    Science.gov (United States)

    Chen, Cheng; Chen, Rui-Xin; Wang, Lei; Wang, Ming-Hui; Zhang, Yan

    2017-01-01

    Apoptosis proteins subcellular localization information are very important for understanding the mechanism of programmed cell death and the development of drugs. The prediction of subcellular localization of an apoptosis protein is still a challenging task because the prediction of apoptosis proteins subcellular localization can help to understand their function and the role of metabolic processes. In this paper, we propose a novel method for protein subcellular localization prediction. Firstly, the features of the protein sequence are extracted by combining Chou's pseudo amino acid composition (PseAAC) and pseudo-position specific scoring matrix (PsePSSM), then the feature information of the extracted is denoised by two-dimensional (2-D) wavelet denoising. Finally, the optimal feature vectors are input to the SVM classifier to predict subcellular location of apoptosis proteins. Quite promising predictions are obtained using the jackknife test on three widely used datasets and compared with other state-of-the-art methods. The results indicate that the method proposed in this paper can remarkably improve the prediction accuracy of apoptosis protein subcellular localization, which will be a supplementary tool for future proteomics research. PMID:29296195

  6. Subcellular localization and expression analysis of the BmDSCLP ...

    African Journals Online (AJOL)

    In addition, real-time fluorescence quantification polymerase chain reaction studies were conducted to investigate BmDSCLP transcription at different developmental stages and in different tissues of the fifth instar larva. The results indicated that, BmDSCLP is widely transcribed in different stages and tissues of the silkworm.

  7. Convolutional LSTM Networks for Subcellular Localization of Proteins

    DEFF Research Database (Denmark)

    Sønderby, Søren Kaae; Sønderby, Casper Kaae; Nielsen, Henrik

    2015-01-01

    Machine learning is widely used to analyze biological sequence data. Non-sequential models such as SVMs or feed-forward neural networks are often used although they have no natural way of handling sequences of varying length. Recurrent neural networks such as the long short term memory (LSTM) model...

  8. Echinococcus granulosus fatty acid binding proteins subcellular localization.

    Science.gov (United States)

    Alvite, Gabriela; Esteves, Adriana

    2016-05-01

    Two fatty acid binding proteins, EgFABP1 and EgFABP2, were isolated from the parasitic platyhelminth Echinococcus granulosus. These proteins bind fatty acids and have particular relevance in flatworms since de novo fatty acids synthesis is absent. Therefore platyhelminthes depend on the capture and intracellular distribution of host's lipids and fatty acid binding proteins could participate in lipid distribution. To elucidate EgFABP's roles, we investigated their intracellular distribution in the larval stage by a proteomic approach. Our results demonstrated the presence of EgFABP1 isoforms in cytosolic, nuclear, mitochondrial and microsomal fractions, suggesting that these molecules could be involved in several cellular processes. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Subcellular localization and expression analysis of the BmDSCLP ...

    African Journals Online (AJOL)

    user

    2011-04-04

    Apr 4, 2011 ... The three-dimensional (3D) structure of the LRR present in a complex of ... expasy.org/) and viewed in the Swiss PDB viewer (Schwede et al.,. 2003). ... containing 0.1% trifluoroacetic acid/water) and injected into a. POROS 10 ...

  10. Electron-tunneling observation of local excited states in manganese-doped indium

    International Nuclear Information System (INIS)

    Tsang, J.; Ginsberg, D.M.

    1980-01-01

    We have measured the electron-tunneling characteristics of a dilute indium-manganese alloy. Well-defined structure was observed, corresponding to a band of local excited states within the energy gap. The measurements were made on two samples, and were quantitatively compared with the theory of Shiba and of Rusinov. We obtained good agreement of the tunneling data with the theory by taking into account only s-wave scattering of conduction electrons from the magnetic-impurity atoms. Even better agreement was obtained by including p- and d-wave scattering. Only by including these higher partial waves could we account for the magnitude of the observed depression of the transition temperature. The phase shifts used are in good agreement with band-theory values calculated recently

  11. Local recidivation of operated breast cancer after electron cineroentgenotherapy of the thorax wall

    International Nuclear Information System (INIS)

    Mutschler, J.

    1986-01-01

    Of 354 patients undergoing radiotherapy up to 31 Dec 1982, 268 comparable cases were examined with regard to local recurrences, metastases, and general health status. The incidence of local recurrences suggested a higher efficiency of this technique as compared with the formerly applied technique of 4-field high-voltage therapy. Medial or central tumours were found to have an almost significantly loss favourable prognosis, which suggests a first spread remote metastases via the parastermal lymphatic vessels. The other 86 patients were analyzed descriptively according to subgroups. Radiolesions of the skin and lungs were not significantly less or more frequent than with other radiotherapies. Electron cineroentgenotherapy is well tolerated even by pre-exposed skin: The Tuebingen experience so far proves the acceptability of the new technique. (orig./MG) [de

  12. Tip-induced local strain on Mo S2/graphite detected by inelastic electron tunneling spectroscopy

    Science.gov (United States)

    Ko, Wonhee; Hus, Saban M.; Li, Xufan; Berlijn, Tom; Nguyen, Giang D.; Xiao, Kai; Li, An-Ping

    2018-03-01

    We report the detection of tip-induced local strain applied to the monolayer Mo S2 grown on a graphite substrate by scanning tunneling microscope. Monolayer Mo S2 behaves as both mechanical and tunneling barriers that prevent the tip from contacting the graphite while maintaining the tunneling current. Inelastic tunneling electron spectroscopy (IETS) is utilized to probe the phonon modes in graphite. As the tip pushes the sample, IETS reveals a continuous phonon softening in graphite, corroborated by a downward shift of the phonon energy as calculated by density-functional theory. Our results demonstrate a way to apply local mechanical strain and simultaneously detect the induced change in phonon modes by unitizing IETS with two-dimensional materials as a tunneling barrier.

  13. Extending the random-phase approximation for electronic correlation energies: the renormalized adiabatic local density approximation

    DEFF Research Database (Denmark)

    Olsen, Thomas; Thygesen, Kristian S.

    2012-01-01

    The adiabatic connection fluctuation-dissipation theorem with the random phase approximation (RPA) has recently been applied with success to obtain correlation energies of a variety of chemical and solid state systems. The main merit of this approach is the improved description of dispersive forces...... while chemical bond strengths and absolute correlation energies are systematically underestimated. In this work we extend the RPA by including a parameter-free renormalized version of the adiabatic local-density (ALDA) exchange-correlation kernel. The renormalization consists of a (local) truncation...... of the ALDA kernel for wave vectors q > 2kF, which is found to yield excellent results for the homogeneous electron gas. In addition, the kernel significantly improves both the absolute correlation energies and atomization energies of small molecules over RPA and ALDA. The renormalization can...

  14. Variational and robust density fitting of four-center two-electron integrals in local metrics

    Science.gov (United States)

    Reine, Simen; Tellgren, Erik; Krapp, Andreas; Kjærgaard, Thomas; Helgaker, Trygve; Jansik, Branislav; Høst, Stinne; Salek, Paweł

    2008-09-01

    Density fitting is an important method for speeding up quantum-chemical calculations. Linear-scaling developments in Hartree-Fock and density-functional theories have highlighted the need for linear-scaling density-fitting schemes. In this paper, we present a robust variational density-fitting scheme that allows for solving the fitting equations in local metrics instead of the traditional Coulomb metric, as required for linear scaling. Results of fitting four-center two-electron integrals in the overlap and the attenuated Gaussian damped Coulomb metric are presented, and we conclude that density fitting can be performed in local metrics at little loss of chemical accuracy. We further propose to use this theory in linear-scaling density-fitting developments.

  15. Vascular damage after acute local irradiation: a light and electron microscope study

    International Nuclear Information System (INIS)

    Verola, O.; Brocheriou, C.

    1986-01-01

    A pig model was used to examine histological and ultrastructural changes after high-dose local irradiation. This model was chosen to simulate accidents which have occurred in man, enabling the determination of several post-irradiation phases. After an initial phase, with superficial lesions, ischaemic necrosis occurred 3 weeks after irradiation as the result of early vascular alterations. After 2 months, expanding necrosis became obvious in the deep muscle, preceded by an initial spread of vascular lesions: these alterations were obvious from the 30th day by light microscopy but could be detected by electron microscopy from the 9th day. (author)

  16. Subcellular distribution of glutathione and cysteine in cyanobacteria.

    Science.gov (United States)

    Zechmann, Bernd; Tomasić, Ana; Horvat, Lucija; Fulgosi, Hrvoje

    2010-10-01

    Glutathione plays numerous important functions in eukaryotic and prokaryotic cells. Whereas it can be found in virtually all eukaryotic cells, its production in prokaryotes is restricted to cyanobacteria and proteobacteria and a few strains of gram-positive bacteria. In bacteria, it is involved in the protection against reactive oxygen species (ROS), osmotic shock, acidic conditions, toxic chemicals, and heavy metals. Glutathione synthesis in bacteria takes place in two steps out of cysteine, glutamate, and glycine. Cysteine is the limiting factor for glutathione biosynthesis which can be especially crucial for cyanobacteria, which rely on both the sufficient sulfur supply from the growth media and on the protection of glutathione against ROS that are produced during photosynthesis. In this study, we report a method that allows detection and visualization of the subcellular distribution of glutathione in Synechocystis sp. This method is based on immunogold cytochemistry with glutathione and cysteine antisera and computer-supported transmission electron microscopy. Labeling of glutathione and cysteine was restricted to the cytosol and interthylakoidal spaces. Glutathione and cysteine could not be detected in carboxysomes, cyanophycin granules, cell walls, intrathylakoidal spaces, periplasm, and vacuoles. The accuracy of the glutathione and cysteine labeling is supported by two observations. First, preadsorption of the antiglutathione and anticysteine antisera with glutathione and cysteine, respectively, reduced the density of the gold particles to background levels. Second, labeling of glutathione and cysteine was strongly decreased by 98.5% and 100%, respectively, in Synechocystis sp. cells grown on media without sulfur. This study indicates a strong similarity of the subcellular distribution of glutathione and cysteine in cyanobacteria and plastids of plants and provides a deeper insight into glutathione metabolism in bacteria.

  17. Improved non-local electron thermal transport model for two-dimensional radiation hydrodynamics simulations

    International Nuclear Information System (INIS)

    Cao, Duc; Moses, Gregory; Delettrez, Jacques

    2015-01-01

    An implicit, non-local thermal conduction algorithm based on the algorithm developed by Schurtz, Nicolai, and Busquet (SNB) [Schurtz et al., Phys. Plasmas 7, 4238 (2000)] for non-local electron transport is presented and has been implemented in the radiation-hydrodynamics code DRACO. To study the model's effect on DRACO's predictive capability, simulations of shot 60 303 from OMEGA are completed using the iSNB model, and the computed shock speed vs. time is compared to experiment. Temperature outputs from the iSNB model are compared with the non-local transport model of Goncharov et al. [Phys. Plasmas 13, 012702 (2006)]. Effects on adiabat are also examined in a polar drive surrogate simulation. Results show that the iSNB model is not only capable of flux-limitation but also preheat prediction while remaining numerically robust and sacrificing little computational speed. Additionally, the results provide strong incentive to further modify key parameters within the SNB theory, namely, the newly introduced non-local mean free path. This research was supported by the Laboratory for Laser Energetics of the University of Rochester

  18. Improved non-local electron thermal transport model for two-dimensional radiation hydrodynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Duc; Moses, Gregory [University of Wisconsin—Madison, 1500 Engineering Drive, Madison, Wisconsin 53706 (United States); Delettrez, Jacques [Laboratory for Laser Energetics of the University of Rochester, 250 East River Road, Rochester, New York 14623 (United States)

    2015-08-15

    An implicit, non-local thermal conduction algorithm based on the algorithm developed by Schurtz, Nicolai, and Busquet (SNB) [Schurtz et al., Phys. Plasmas 7, 4238 (2000)] for non-local electron transport is presented and has been implemented in the radiation-hydrodynamics code DRACO. To study the model's effect on DRACO's predictive capability, simulations of shot 60 303 from OMEGA are completed using the iSNB model, and the computed shock speed vs. time is compared to experiment. Temperature outputs from the iSNB model are compared with the non-local transport model of Goncharov et al. [Phys. Plasmas 13, 012702 (2006)]. Effects on adiabat are also examined in a polar drive surrogate simulation. Results show that the iSNB model is not only capable of flux-limitation but also preheat prediction while remaining numerically robust and sacrificing little computational speed. Additionally, the results provide strong incentive to further modify key parameters within the SNB theory, namely, the newly introduced non-local mean free path. This research was supported by the Laboratory for Laser Energetics of the University of Rochester.

  19. Improved non-local electron thermal transport model for two-dimensional radiation hydrodynamics simulations

    Science.gov (United States)

    Cao, Duc; Moses, Gregory; Delettrez, Jacques

    2015-08-01

    An implicit, non-local thermal conduction algorithm based on the algorithm developed by Schurtz, Nicolai, and Busquet (SNB) [Schurtz et al., Phys. Plasmas 7, 4238 (2000)] for non-local electron transport is presented and has been implemented in the radiation-hydrodynamics code DRACO. To study the model's effect on DRACO's predictive capability, simulations of shot 60 303 from OMEGA are completed using the iSNB model, and the computed shock speed vs. time is compared to experiment. Temperature outputs from the iSNB model are compared with the non-local transport model of Goncharov et al. [Phys. Plasmas 13, 012702 (2006)]. Effects on adiabat are also examined in a polar drive surrogate simulation. Results show that the iSNB model is not only capable of flux-limitation but also preheat prediction while remaining numerically robust and sacrificing little computational speed. Additionally, the results provide strong incentive to further modify key parameters within the SNB theory, namely, the newly introduced non-local mean free path. This research was supported by the Laboratory for Laser Energetics of the University of Rochester.

  20. Treatment of local recurrent breast cancer by divided dose electron beam radiation twice a week

    International Nuclear Information System (INIS)

    Ito, Ichiro; Suzuki, Yoshihiko; Miyaishi, Kazuo; Mitsuhashi, Norio; Kimura, Makoto

    1978-01-01

    The objectives of this study were to investigate the effects of divided dose electron beam radiation twice a week (with a focal dose of 600 rads at a time) on local recurrent tumors of postoperative breast cancer and to compare it with the conventional photon radiation in the hope that it might be better tolerated by the patients, with less damage to normal skin and lung tissues. Out of 261 patients with breast cancer who came to the Department of Radiology, at Gunma Univ. Hospital, Maebashi, during the period Jan., 1970, through Jun., 1976, 41 patients who received electron beam radiation for local recurrence (in 81 sites) and 31 who received prophylactic radiation over the chest wall postoperatively. Tumors completely disappeared from 73 out of 81 sites irradiated for local recurrence (accounting 90% of the 81 sites). The local recurrent lesions were classified to the ''disseminated'' and the ''focal'' type to compare the effects of the radiation, and it was found that the radiation eliminated the tumors from all (100%) of the 63 sites of the former type, while the radiation was capable of eliminating the tumors from only 10 out of the 18 sites of the latter type (56%). When the focal type tumors were classified by histopathologic typing to compare the effects of the radiation, the radiation was assessed effective in papillotubular carcinoma, medullary tubular carcinoma and scirrhous carcinoma in the decreasing sequence of significance. Pulmonary disorders occurred in 12% of all the observed sites. However, it is possible to further reduce this incidence by the adequate use of the tissue compensating filter, Mix-R. A skin disorder (erosion) was observed in 59% of all the sites observed. However, it may be anticipated that the topical application of a suitable corticoid (Beta-methasone-17-valerate cream) preparation will by prophylactically effective. (auth.)

  1. Laserspritzer: a simple method for optogenetic investigation with subcellular resolutions.

    Directory of Open Access Journals (Sweden)

    Qian-Quan Sun

    Full Text Available To build a detailed circuit diagram in the brain, one needs to measure functional synaptic connections between specific types of neurons. A high-resolution circuit diagram should provide detailed information at subcellular levels such as soma, distal and basal dendrites. However, a limitation lies in the difficulty of studying long-range connections between brain areas separated by millimeters. Brain slice preparations have been widely used to help understand circuit wiring within specific brain regions. The challenge exists because long-range connections are likely to be cut in a brain slice. The optogenetic approach overcomes these limitations, as channelrhodopsin 2 (ChR2 is efficiently transported to axon terminals that can be stimulated in brain slices. Here, we developed a novel fiber optic based simple method of optogenetic stimulation: the laserspritzer approach. This method facilitates the study of both long-range and local circuits within brain slice preparations. This is a convenient and low cost approach that can be easily integrated with a slice electrophysiology setup, and repeatedly used upon initial validation. Our data with direct ChR2 mediated-current recordings demonstrates that the spatial resolution of the laserspritzer is correlated with the size of the laserspritzer, and the resolution lies within the 30 µm range for the 5 micrometer laserspritzer. Using olfactory cortical slices, we demonstrated that the laserspritzer approach can be applied to selectively activate monosynaptic perisomatic GABAergic basket synapses, or long-range intracortical glutamatergic inputs formed on different subcellular domains within the same cell (e.g. distal and proximal dendrites. We discuss significant advantages of the laserspritzer approach over the widely used collimated LED whole-field illumination method in brain slice electrophysiological research.

  2. The degree of 5f electron localization in URu2Si2: electron energy-loss spectroscopy and spin-orbit sum rule analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jeffries, J R; Moore, K T; Butch, N P; Maple, M B

    2010-05-19

    We examine the degree of 5f electron localization in URu{sub 2}Si{sub 2} using spin-orbit sum rule analysis of the U N{sub 4,5} (4d {yields} 5f) edge. When compared to {alpha}-U metal, US, USe, and UTe, which have increasing localization of the 5f states, we find that the 5f states of URu{sub 2}Si{sub 2} are more localized, although not entirely. Spin-orbit analysis shows that intermediate coupling is the correct angular momentum coupling mechanism for URu{sub 2}Si{sub 2} when the 5f electron count is between 2.6 and 2.8. These results have direct ramifications for theoretical assessment of the hidden order state of URu{sub 2}Si{sub 2}, where the degree of localization of the 5f electrons and their contribution to the Fermi surface are critical.

  3. Calculation of neutron radiation energy deposition distribution in subcellular parts of tissue using recombination chamber microdosimetry

    International Nuclear Information System (INIS)

    Golnik, N.; Zielczynski, M.

    1999-01-01

    Recombination chamber microdosimetry was used as an instrument for determination of local neutron radiation energy deposition distribution. The method allows to simulate of subcellular regions of tissue of the order of 70 nm in size. The results obtained qualitatively correspond to relationship between biological efficiency and neutron energy, and show regular differences of distributions achieved by the recombination method and distributions measured using tissue equivalent proportional counters (TEPC), which simulates greater tissue regions of 1 μm in size

  4. Optically-controlled platforms for transfection and single- and sub-cellular surgery

    DEFF Research Database (Denmark)

    Villangca, Mark Jayson; Casey, Duncan; Glückstad, Jesper

    2015-01-01

    and specificity of optical trapping in conjunction with other modalities to perform single and sub-cellular surgery. These tools form highly tuneable platforms for the delivery or removal of material from cells of interest, but can simultaneously excite fluorescent probes for imaging purposes or plasmonic...... structures for very local heating. We discuss both the history and recent applications of the field, highlighting the key findings and developments over the last 40 years of biophotonics research....

  5. Curvature-induced electron localization in developable Moebius-like nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Korte, A P; Van der Heijden, G H M, E-mail: a.korte@ucl.ac.u, E-mail: g.heijden@ucl.ac.u [Centre for Nonlinear Dynamics, University College London, Chadwick Building, Gower Street, London WC1E 6BT (United Kingdom)

    2009-12-02

    We study curvature effects and localization of non-interacting electrons confined to developable one-sided elastic sheets motivated by recent nanostructured origami techniques for creating and folding extremely thin membrane structures. The most famous one-sided sheet is the Moebius strip but the theory we develop allows for arbitrary linking number. Unlike previous work in the literature we do not assume a shape for the elastic structures. Rather, we find the shape by minimizing the elastic energy, i.e., solving the Euler-Lagrange equations for the bending energy functional. This shape varies with the aspect ratio of the sheet and affects the potential experienced by the particles. Depending on the link there is a number of singular points on the edge of the structure where the bending energy density goes to infinity, leading to deep potential wells. The inverse participation ratio is used to show that electrons are increasingly localized to the higher-curvature regions of the higher-width structures, where sharp creases radiating out from the singular points could form channels for particle transport. Our geometric formulation could be used to study transport properties of Moebius strips and other components in nanoscale devices.

  6. Curvature-induced electron localization in developable Moebius-like nanostructures

    International Nuclear Information System (INIS)

    Korte, A P; Van der Heijden, G H M

    2009-01-01

    We study curvature effects and localization of non-interacting electrons confined to developable one-sided elastic sheets motivated by recent nanostructured origami techniques for creating and folding extremely thin membrane structures. The most famous one-sided sheet is the Moebius strip but the theory we develop allows for arbitrary linking number. Unlike previous work in the literature we do not assume a shape for the elastic structures. Rather, we find the shape by minimizing the elastic energy, i.e., solving the Euler-Lagrange equations for the bending energy functional. This shape varies with the aspect ratio of the sheet and affects the potential experienced by the particles. Depending on the link there is a number of singular points on the edge of the structure where the bending energy density goes to infinity, leading to deep potential wells. The inverse participation ratio is used to show that electrons are increasingly localized to the higher-curvature regions of the higher-width structures, where sharp creases radiating out from the singular points could form channels for particle transport. Our geometric formulation could be used to study transport properties of Moebius strips and other components in nanoscale devices.

  7. Non-local electron transport through normal and topological ladder-like atomic systems

    Science.gov (United States)

    Kurzyna, Marcin; Kwapiński, Tomasz

    2018-05-01

    We propose a locally protected ladder-like atomic system (nanoconductor) on a substrate that is insensitive to external perturbations. The system corresponds to coupled atomic chains fabricated on different surfaces. Electron transport properties of such conductors are studied theoretically using the model tight-binding Su-Schriffer-Hegger (SSH) Hamiltonian and Green's function formalism. We have found that the conductance of the system is almost insensitive to single adatoms and oscillates as a function of the side chain length with very large periods. Non-local character of the electron transport was observed also for topological SSH chains where nontrivial end states survive in the presence of disturbances as well as for different substrates. We have found that the careful inspection of the density of states or charge waves can provide the information about the atom energy levels and hopping amplitudes. Moreover, the ladder-like geometry allows one to distinguish between normal and topological zero-energy states. It is important that topological chains do not reveal Friedel oscillations which are observed in non-topological chains.

  8. Localization of (/sup 3/H). gamma. -aminobutyric acid in the cochlea. Light and electron microscopic autoradiography

    Energy Technology Data Exchange (ETDEWEB)

    Richrath, W; Kraus, H; Fromme, H G [Muenster Univ. (F.R. Germany). Hals-, Nasen- und Ohrenklinik; Muenster Univ. (F.R. Germany). Inst. fuer Medizinische Physik)

    1974-01-01

    In guinea pigs, 1 h after intraarterial and local administration of /sup 3/H-GABA, autoradiographs of the cochlea and the brain were performed. As a parameter of distribution of this substance, silver grain density was examined by means of light and electron microscopy. Intraarterial injection was not followed by any activity neither in brain nor in the cochlea, an observation suggesting the existence of a blood-perilymph barrier additional to the blood-brain barrier. Perfusion of the cochlea produced a marked activity in the spiral ganglion. Different from other tritium labelled amino acids, /sup 3/H-GABA activity could be found only in glia cells but not in nerve cell bodies or axons. The significance of this finding is open to question. In the organ of Corti a selective labelling of efferent nerve fibres could be found by means of light microscopy, additionally, using electron microscopy, only efferent synapses proved to be labelled. Most of silver grains were attached to vesicles and mitochondria, some grains to the synaptie deft. Afferent synapses remained unlabelled. Comparing with publications concerning GABA localization and concentration in the brain, we conclude that the efferent system of the Organ of Corti contains a high concentration of GABA. As present electrophysiological results are contradictory the GABA distribution alone gives no convincing evidence that this substance may serve as a transmitter.

  9. Theoretical studies of π-electron delocalization and localization on intramolecular proton transfer in the ground state

    Science.gov (United States)

    Peng, Hongliang; Huang, Pengru; Yi, Pinggui; Xu, Fen; Sun, Lixian

    2018-02-01

    Proton transfer processes of 15 benzimidazole compounds are studied by density functional theory methods, and natural orbital energy index (NOEI) is introduced. Here, NOEI and nucleus independent chemical shift (NICS) are applied to estimate the π-electron localization and delocalization, respectively. Proton transfer potential energy surfaces are calculated to explore these processes, and the results show that the changes of the π-electron delocalization of the phenyl (pyridyl) is the main factors for the stability of keto form. There is high correlation between the π-electron delocalization and the proton transfer barrier. When the π-electron localization is considered, the regression increases the correlation coefficient, increasing from 0.9663 to 0.9864. NOEI index is sensitive to π-electron localization; it is a beneficial and useful complement to NICS.

  10. Studies on proinsulin and proglucagon biosynthesis and conversion at the subcellular level: I. Fractionation procedure and characterization of the subcellular fractions

    Science.gov (United States)

    Noe, BD; Baste, CA; Bauer, GE

    1977-01-01

    Anglerfish islets were homogenized in 0.25 M sucrose and separated into seven separate subcellular fractions by differential and discontinuous density gradient centrifugation. The objective was to isolate microsomes and secretory granules in a highly purified state. The fractions were characterized by electron microscopy and chemical analyses. Each fraction was assayed for its content of protein, RNA, DNA, immunoreactive insulin (IRI), and immunoreactive glucagon (IRG). Ultrastructural examination showed that two of the seven subcellular fractions contain primarily mitochondria, and that two others consist almost exclusively of secretory granules. A fifth fraction contains rough and smooth microsomal vesicles. The remaining two fractions are the cell supernate and the nuclei and cell debris. The content of DNA and RNA in all fractions is consistent with the observed ultrastructure. More than 82 percent of the total cellular IRI and 89(percent) of the total cellular IRG are found in the fractions of secretory granules. The combined fractions of secretory granules and microsomes consistently yield >93 percent of the total IRG. These results indicate that the fractionation procedure employed yields fractions of microsomes and secretory granules that contain nearly all the immunoassayable insulin and glucagons found in whole islet tissue. These fractions are thus considered suitable for study of proinsulin and proglucagon biosynthesis and their metabolic conversion at the subcellular level. PMID:328517

  11. Annihilation of positrons with localized electrons in oxides and YBa2Cu3O7-x ceramics

    International Nuclear Information System (INIS)

    Nishchenko, M.M.; Likhtorovich, S.P.

    1997-01-01

    The angular correlation of annihilation photons (ACAP) has been studied in CuO, Cu 2 O,BaO,Y 2 O 3 and YBa 2 Cu 3 O 7-x oxides. Localization radius of the electron wave function is found to be about 0,8 A. It is also shown that with the more localization of the electron its probability of annihilation with positrons is less

  12. Matrix-product-state method with local basis optimization for nonequilibrium electron-phonon systems

    Science.gov (United States)

    Heidrich-Meisner, Fabian; Brockt, Christoph; Dorfner, Florian; Vidmar, Lev; Jeckelmann, Eric

    We present a method for simulating the time evolution of quasi-one-dimensional correlated systems with strongly fluctuating bosonic degrees of freedom (e.g., phonons) using matrix product states. For this purpose we combine the time-evolving block decimation (TEBD) algorithm with a local basis optimization (LBO) approach. We discuss the performance of our approach in comparison to TEBD with a bare boson basis, exact diagonalization, and diagonalization in a limited functional space. TEBD with LBO can reduce the computational cost by orders of magnitude when boson fluctuations are large and thus it allows one to investigate problems that are out of reach of other approaches. First, we test our method on the non-equilibrium dynamics of a Holstein polaron and show that it allows us to study the regime of strong electron-phonon coupling. Second, the method is applied to the scattering of an electronic wave packet off a region with electron-phonon coupling. Our study reveals a rich physics including transient self-trapping and dissipation. Supported by Deutsche Forschungsgemeinschaft (DFG) via FOR 1807.

  13. Customization of a Severity of Illness Score Using Local Electronic Medical Record Data.

    Science.gov (United States)

    Lee, Joon; Maslove, David M

    2017-01-01

    Severity of illness (SOI) scores are traditionally based on archival data collected from a wide range of clinical settings. Mortality prediction using SOI scores tends to underperform when applied to contemporary cases or those that differ from the case-mix of the original derivation cohorts. We investigated the use of local clinical data captured from hospital electronic medical records (EMRs) to improve the predictive performance of traditional severity of illness scoring. We conducted a retrospective analysis using data from the Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database, which contains clinical data from the Beth Israel Deaconess Medical Center in Boston, Massachusetts. A total of 17 490 intensive care unit (ICU) admissions with complete data were included, from 4 different service types: medical ICU, surgical ICU, coronary care unit, and cardiac surgery recovery unit. We developed customized SOI scores trained on data from each service type, using the clinical variables employed in the Simplified Acute Physiology Score (SAPS). In-hospital, 30-day, and 2-year mortality predictions were compared with those obtained from using the original SAPS using the area under the receiver-operating characteristics curve (AUROC) as well as the area under the precision-recall curve (AUPRC). Test performance in different cohorts stratified by severity of organ injury was also evaluated. Most customized scores (30 of 39) significantly outperformed SAPS with respect to both AUROC and AUPRC. Enhancements over SAPS were greatest for patients undergoing cardiovascular surgery and for prediction of 2-year mortality. Custom models based on ICU-specific data provided better mortality prediction than traditional SAPS scoring using the same predictor variables. Our local data approach demonstrates the value of electronic data capture in the ICU, of secondary uses of EMR data, and of local customization of SOI scoring. © The Author(s) 2015.

  14. Patterns of Failure and Local Control After Intraoperative Electron Boost Radiotherapy to the Presacral Space in Combination with Total Mesorectal Excision in Patients with Locally Advanced Rectal Cancer

    International Nuclear Information System (INIS)

    Roeder, Falk; Treiber, Martina; Oertel, Susanne; Dinkel, Julien; Timke, Carmen; Funk, Angela; Garcia-Huttenlocher, Helena; Bischof, Marc; Weitz, Juergen; Harms, Wolfgang; Hensley, Frank W.; Buchler, Markus W.; Debus, Juergen; Krempien, Robert

    2007-01-01

    Purpose: To evaluate local control and patterns of failure in patients treated with intraoperative electron beam radiotherapy (IOERT) after total mesorectal excision (TME), to appraise the effectiveness of intraoperative target definition. Methods and Materials: We analyzed the outcome of 243 patients with rectal cancer treated with IOERT (median dose, 10 Gy) after TME. Eighty-eight patients received neoadjuvant and 122 patients adjuvant external beam radiotherapy (EBRT) (median dose, 41.4 Gy), and in 88% simultaneous chemotherapy was applied. Median follow-up was 59 months. Results: Local failure was observed in 17 patients (7%), resulting in a 5-year local control rate of 92%. Only complete resection and absence of nodal involvement correlated positively with local control. Considering IOERT fields, seven infield recurrences were seen in the presacral space, resulting in a 5-year local control rate of 97%. The remaining local relapses were located as follows: retrovesical/retroprostatic (5), anastomotic site (2), promontorium (1), ileocecal (1), and perineal (1). Conclusion: Intraoperative electron beam radiotherapy as part of a multimodal treatment approach including TME is a highly effective regimen to prevent local failure. The presacral space remains the site of highest risk for local failure, but IOERT can decrease the percentage of relapses in this area

  15. Local time, substorm, and seasonal dependence of electron precipitation at L≅4 inferred from riometer measurements

    International Nuclear Information System (INIS)

    Rosenberg, T.J.; Dudeney, J.R.

    1986-01-01

    We have examined the variations of electron precipitation at L≅4 as inferred from riometer measurements of cosmic radio noise absorption made during 1975 at Siple Station and Halley Bay, Antarctica. The results are presented in the form of annual and seasonal averages of 1/2-hourly values for two geomagnetic activity subsets, AE>140 nT (disturbed) and AE≤ 140 nT (quiet). Monthly quiet day curves were used to remove the diurnal and seasonal variations in the background noise levels. Generally, the local time characteristics of the absorption were the same at both stations; the highest absorption occurred in the 0400--1600 MLT sector during disturbed conditions and in the 1200--2000 MLT sector during quiet conditions. For high AE, the highest correlation was obtained at a lag equal to the magnetic local time difference (1.5 hours) between the two stations. On the other hand, for low AE, the highest correlation occurred for a lag of 3.0 hours, nearer the local solar time difference (3.8 hours). Consistently higher absorption was measured at Halley on the average during both levels of magnetic disturbance and in all seasons. At both locations, and for both geomagnetic activity subsets, more absorption was observed in summer and equinox than in winter. This is in contrast to earlier studies for L≥6, and suggests that a meridional reversal of seasonal behavior occurs between L = 4 and L = 6

  16. Mapping the Subcellular Proteome of Shewanella oneidensis MR-1 using Sarkosyl-based fractionation and LC-MS/MS protein identification

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Roslyn N.; Romine, Margaret F.; Schepmoes, Athena A.; Smith, Richard D.; Lipton, Mary S.

    2010-07-19

    A simple and effective subcellular proteomic method for fractionation and analysis of gram-negative bacterial cytoplasm, periplasm, inner, and outer membranes was applied to Shewanella oneidensis to gain insight into its subcellular architecture. A combination of differential centrifugation, Sarkosyl solubilization, and osmotic lysis was used to prepare subcellular fractions. Global differences in protein fractions were observed by SDS PAGE and heme staining, and tryptic peptides were analyzed using high-resolution LC-MS/MS. Compared to crude cell lysates, the fractionation method achieved a significant enrichment (average ~2-fold) in proteins predicted to be localized to each subcellular fraction. Compared to other detergent, organic solvent, and density-based methods previously reported, Sarkosyl most effectively facilitated separation of the inner and outer membranes and was amenable to mass spectrometry, making this procedure ideal for probing the subcellular proteome of gram-negative bacteria via LC-MS/MS. With 40% of the observable proteome represented, this study has provided extensive information on both subcellular architecture and relative abundance of proteins in S. oneidensis and provides a foundation for future work on subcellular organization and protein-membrane interactions in other gram-negative bacteria.

  17. Electronic hole localization in rutile and anatase TiO2 - Self-interaction correction in Delta-SCF DFT

    DEFF Research Database (Denmark)

    Zawadzki, Pawel; Jacobsen, Karsten Wedel; Rossmeisl, Jan

    2011-01-01

    We study electronic hole localization in rutile and anatase titanium dioxide by means of Δ-Self-Consistent Field Density Functional Theory. In order to compare stabilities of the localized and the delocalized hole states we introduce a simple correction to the wrong description of the localizatio...

  18. Enhanced Glycogen Storage of a Subcellular Hot Spot in Human Skeletal Muscle during Early Recovery from Eccentric Contractions

    DEFF Research Database (Denmark)

    Nielsen, Joachim; Farup, Jean; Rahbek, Stine Klejs

    2015-01-01

    Unaccustomed eccentric exercise is accompanied by muscle damage and impaired glucose uptake and glycogen synthesis during subsequent recovery. Recently, it was shown that the role and regulation of glycogen in skeletal muscle are dependent on its subcellular localization, and that glycogen synthe...

  19. Curly arrows meet electron density transfers in chemical reaction mechanisms: from electron localization function (ELF) analysis to valence-shell electron-pair repulsion (VSEPR) inspired interpretation.

    Science.gov (United States)

    Andrés, Juan; Berski, Sławomir; Silvi, Bernard

    2016-07-07

    Probing the electron density transfers during a chemical reaction can provide important insights, making possible to understand and control chemical reactions. This aim has required extensions of the relationships between the traditional chemical concepts and the quantum mechanical ones. The present work examines the detailed chemical insights that have been generated through 100 years of work worldwide on G. N. Lewis's ground breaking paper on The Atom and the Molecule (Lewis, G. N. The Atom and the Molecule, J. Am. Chem. Soc. 1916, 38, 762-785), with a focus on how the determination of reaction mechanisms can be reached applying the bonding evolution theory (BET), emphasizing how curly arrows meet electron density transfers in chemical reaction mechanisms and how the Lewis structure can be recovered. BET that combines the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT) provides a powerful tool providing insight into molecular mechanisms of chemical rearrangements. In agreement with physical laws and quantum theoretical insights, BET can be considered as an appropriate tool to tackle chemical reactivity with a wide range of possible applications. Likewise, the present approach retrieves the classical curly arrows used to describe the rearrangements of chemical bonds for a given reaction mechanism, providing detailed physical grounds for this type of representation. The ideas underlying the valence-shell-electron pair-repulsion (VSEPR) model applied to non-equilibrium geometries provide simple chemical explanations of density transfers. For a given geometry around a central atom, the arrangement of the electronic domain may comply or not with the VSEPR rules according with the valence shell population of the considered atom. A deformation yields arrangements which are either VSEPR defective (at least a domain is missing to match the VSEPR arrangement corresponding to the geometry of the ligands), VSEPR compliant

  20. Electronic Transport Properties of One Dimensional Zno Nanowires Studied Using Maximally-Localized Wannier Functions

    Science.gov (United States)

    Sun, Xu; Gu, Yousong; Wang, Xueqiang

    2012-08-01

    One dimensional ZnO NWs with different diameters and lengths have been investigated using density functional theory (DFT) and Maximally Localized Wannier Functions (MLWFs). It is found that ZnO NWs are direct band gap semiconductors and there exist a turn on voltage for observable current. ZnO nanowires with different diameters and lengths show distinctive turn-on voltage thresholds in I-V characteristics curves. The diameters of ZnO NWs are greatly influent the transport properties of ZnO NWs. For the ZnO NW with large diameter that has more states and higher transmission coefficients leads to narrow band gap and low turn on voltage. In the case of thinner diameters, the length of ZnO NW can effects the electron tunneling and longer supercell lead to higher turn on voltage.

  1. Local analysis of strains and rotations for macromolecular electron microscopy maps

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Ramos, A.; Prieto, F.; Melero, R.; Martin-Benito, J.; Jonic, S.; Navas-Calvente, J.; Vargas, J.; Oton, J.; Abrishami, V.; Rosa-Trevin, J.L. de la; Gomez-Blanco, J.; Vilas, J.L.; Marabini, R.; Carazo, R.; Sorzano, C.O.S.

    2016-07-01

    Macromolecular complexes can be considered as molecular nano-machines that must have mobile parts in order to perform their physiological functions. The reordering of their parts is essential to execute their task. These rearrangements induce local strains and rotations which, after analyzing them, may provide relevant information about how the proteins perform their function. In this project these deformations of the macromolecular complexes are characterized, translating into a “mathematical language” the conformational changes of the complexes when they perform their function. Electron Microscopy (EM) volumes are analyzed using a method that uses B-splines as its basis functions. It is shown that the results obtained are consistent with the conformational changes described in their corresponding reference publications. (Author)

  2. Local Magnetism in Strongly Correlated Electron Systems with Orbital Degrees of Freedom

    Science.gov (United States)

    Ducatman, Samuel Charles

    The central aim of my research is to explain the connection between the macroscopic behavior and the microscopic physics of strongly correlated electron systems with orbital degrees of freedom through the use of effective models. My dissertation focuses on the sub-class of these materials where electrons appear to be localized by interactions, and magnetic ions have well measured magnetic moments. This suggests that we can capture the low-energy physics of the material by employing a minimal model featuring localized spins which interact with each other through exchange couplings. I describe Fe1+y Te and beta-Li2IrO3 with effective models primarily focusing on the spins of the magnetic ions, in this case Fe and Ir, respectively. The goal with both materials is to gain insight and make predictions for experimentalists. In chapter 2, I focus on Fe1+yTe. I describe why we believe the magnetic ground state of this material, with an observed Bragg peak at Q +/- pi/2, pi/2), can be described by a Heisenberg model with 1st, 2nd, and 3rd neighbor interactions. I present two possible ground states of this model in the small J1 limit, the bicollinear and plaquette states. In order to predict which ground state the model prefers, I calculate the spin wave spectrum with 1/S corrections, and I find the model naturally selects the "plaquette state." I give a brief description of the ways this result could be tested using experimental techniques such as polarized neutron scattering. In chapter 3, I extend the model used in chapter 2. This is necessary because the Heisenberg model we employed cannot explain why Fe1+yTe undergoes a phase transition as y is increased. We add an additional elements to our calculation; we assume that electrons in some of the Fe 3D orbitals have selectively localized while others remain itinerant. We write a new Hamiltonian, where localized moments acquire a new long-range RKKY-like interaction from interactions with the itinerant electrons. We are

  3. Probing the local environment of a single OPE3 molecule using inelastic tunneling electron spectroscopy.

    Science.gov (United States)

    Frisenda, Riccardo; Perrin, Mickael L; van der Zant, Herre S J

    2015-01-01

    We study single-molecule oligo(phenylene ethynylene)dithiol junctions by means of inelastic electron tunneling spectroscopy (IETS). The molecule is contacted with gold nano-electrodes formed with the mechanically controllable break junction technique. We record the IETS spectrum of the molecule from direct current measurements, both as a function of time and electrode separation. We find that for fixed electrode separation the molecule switches between various configurations, which are characterized by different IETS spectra. Similar variations in the IETS signal are observed during atomic rearrangements upon stretching of the molecular junction. Using quantum chemistry calculations, we identity some of the vibrational modes which constitute a chemical fingerprint of the molecule. In addition, changes can be attributed to rearrangements of the local molecular environment, in particular at the molecule-electrode interface. This study shows the importance of taking into account the interaction with the electrodes when describing inelastic contributions to transport through single-molecule junctions.

  4. Localized and collectivized behaviour of d-electrons in complicated titanium, vanadium and niobium oxides

    International Nuclear Information System (INIS)

    Bazuev, G.V.; Shvejkin, G.P.

    1980-01-01

    On the basis of investigation of electric and magnetic properties of oxide compounds of transition metals made are the conclusions on the degree of localization and delocalization of d-electrons in them. Generalized are the investigation results of complicated titanium, vanadium, niobium oxide compounds in low degrees of oxidation with rare earth and alkaline earth elements belonging to the two structural types: perovskite and pyrochlore. Presented are the results of investigations of perovskite-like solid solutions and of variable-content phases containing cations of transition metals in two different oxidation degrees: oxide niobium bronzes of two-valent europium and titanium bronzes of rare-earth elements, as well as Lnsub(1-x)Msub(x)Vsub(1-x)sup(3+)Vsub(x)sup(4+)Osub(3), where M is an alkaline earth element

  5. Strain rate measurement by Electronic Speckle Pattern Interferometry: A new look at the strain localization onset

    International Nuclear Information System (INIS)

    Guelorget, Bruno; Francois, Manuel; Vial-Edwards, Cristian; Montay, Guillaume; Daniel, Laurent; Lu, Jian

    2006-01-01

    In-plane Electronic Speckle Pattern Interferometry has been successfully used during tensile testing of semi-hard copper sheets in order to measure the strain rate. On one hand, heterogeneity in strain rate field has been found before the maximum of the tensile force (ε t ≅ 19.4 and 25.4%, respectively). Thus, a localization phenomenon occurs before the classic Considere's criterion (dF = 0) for the diffuse neck initiation. On the other hand, strain rate measurement before fracture shows the moment where one of the two slip band systems becomes predominant, then strain concentrates in a small area, the shear band. Uncertainty evaluation has been carried out, which shows a very good accuracy of the total strain and the strain rate measurements

  6. Strain rate measurement by Electronic Speckle Pattern Interferometry: A new look at the strain localization onset

    Energy Technology Data Exchange (ETDEWEB)

    Guelorget, Bruno [Universite de Technologie de Troyes (UTT), Laboratoire des Systemes Mecaniques et d' ingenierie Simultanee (LASMIS, CNRS FRE 2719), 12 rue Marie Curie, B.P. 2060, 10010 Troyes Cedex (France)]. E-mail: bruno.guelorget@utt.fr; Francois, Manuel [Universite de Technologie de Troyes (UTT), Laboratoire des Systemes Mecaniques et d' ingenierie Simultanee (LASMIS, CNRS FRE 2719), 12 rue Marie Curie, B.P. 2060, 10010 Troyes Cedex (France); Vial-Edwards, Cristian [Departemento de Ingenieria Mecanica y Metalurgica, Pontificia Universidad Catolica de Chile, Vicuna Mackenna 4860, 6904411 Santiago (Chile); Montay, Guillaume [Universite de Technologie de Troyes (UTT), Laboratoire des Systemes Mecaniques et d' ingenierie Simultanee (LASMIS, CNRS FRE 2719), 12 rue Marie Curie, B.P. 2060, 10010 Troyes Cedex (France); Daniel, Laurent [Universite de Technologie de Troyes (UTT), Laboratoire des Systemes Mecaniques et d' ingenierie Simultanee (LASMIS, CNRS FRE 2719), 12 rue Marie Curie, B.P. 2060, 10010 Troyes Cedex (France); Lu, Jian [Universite de Technologie de Troyes (UTT), Laboratoire des Systemes Mecaniques et d' ingenierie Simultanee (LASMIS, CNRS FRE 2719), 12 rue Marie Curie, B.P. 2060, 10010 Troyes Cedex (France)

    2006-01-15

    In-plane Electronic Speckle Pattern Interferometry has been successfully used during tensile testing of semi-hard copper sheets in order to measure the strain rate. On one hand, heterogeneity in strain rate field has been found before the maximum of the tensile force ({epsilon} {sup t} {approx_equal} 19.4 and 25.4%, respectively). Thus, a localization phenomenon occurs before the classic Considere's criterion (dF = 0) for the diffuse neck initiation. On the other hand, strain rate measurement before fracture shows the moment where one of the two slip band systems becomes predominant, then strain concentrates in a small area, the shear band. Uncertainty evaluation has been carried out, which shows a very good accuracy of the total strain and the strain rate measurements.

  7. Charging dynamics and strong localization of a two-dimensional electron cloud

    International Nuclear Information System (INIS)

    Dianoux, R; Smilde, H J H; Marchi, F; Buffet, N; Mur, P; Comin, F; Chevrier, J

    2007-01-01

    The dynamics of charge injection in silicon nanocrystals embedded in a silicon dioxide matrix is studied using electrostatic force microscopy. We show that the presence of silicon nanocrystals with a density of 10 11 cm -2 is essential for strong localization of charges, and results in exceptional charge retention properties compared to nanocrystal-free SiO 2 samples. In both systems, a logarithmic dependence of the diameter of the charged area on the injection time is experimentally observed on a timescale between 0.1 and 10 s (voltage≤10 V). A field-emission injection, limited by Coulomb blockade and a lateral charge spreading due to a repulsive radial electric field are used to model the sample charging. Once the tip is retracted, the electron cloud is strongly confined in the nanocrystals and remains static

  8. Field-aligned plasma-potential structure formed by local electron cyclotron resonance

    International Nuclear Information System (INIS)

    Hatakeyama, Rikizo; Kaneko, Toshiro; Sato, Noriyoshi

    2001-01-01

    The significance of basic experiments on field-aligned plasma-potential structure formed by local electron cyclotron resonance (ECR) is claimed based on the historical development of the investigation on electric double layer and electrostatic potential confinement of open-ended fusion-oriented plasmas. In the presence of a single ECR point in simple mirror-type configurations of magnetic field, a potential dip (thermal barrier) appears around this point, being followed by a subsequent potential hump (plug potential) along a collisionless plasma flow. The observed phenomenon gives a clear-cut physics to the formation of field-aligned plug potential with thermal barrier, which is closely related to the double layer formation triggered by a negative dip. (author)

  9. Local probe studies on lattice distortions and electronic correlations in manganites

    CERN Document Server

    lopes, Armandina; Correia, João Guilherme

    This thesis presents an experimental study on lattice distortions and electronic correlations in colossal magnetoresistive magnetic oxides. The Perturbed Angular Correlation local probe technique is used to study selected manganite systems in order to obtain relevant insight into microscopic phenomena responsible for their macroscopic pr operties. Complementary structural, magnetic and electric characterization was performed. The work is focused on the following aspects: \\\\Lattice distortions and polaron clusters in LaMnO$_{3+ \\Delta}$ system. A study of the electric field gradi ent and magnetic hyperfine field was performed in representative samples of the LaMnO$_{3+ \\Delta}$ system, and correlated with macroscopic information obtained in the same samples. Particular attention was given to the LaMnO$_{3.12}$ sample since this compound is a prototype of a ferromagnetic-insulat or manganite, presenting a rhombohedric- orthorhombic structural phase transition near room temperature. We found that random distribu...

  10. The impact of pedestal turbulence and electron inertia on edge-localized-mode crashes

    Energy Technology Data Exchange (ETDEWEB)

    Xi, P. W. [FSC and State Key Lab of Nuclear Physics and Technology, Department of Physics, Peking University, Beijing 100871 (China); Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Xu, X. Q. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Diamond, P. H. [WCI Center for Fusion Theory, National Fusion Research Institute, Daejeon (Korea, Republic of); Center for Astrophysics and Space Sciences and Department of Physics, University of California San Diego, La Jolla, California 92093-0429 (United States)

    2014-05-15

    We demonstrate that the occurrence of Edge-Localized-Modes (ELM) crashes does not depend only on the linear peeling-ballooning threshold, but also relies on nonlinear processes. Wave-wave interaction constrains the growth time of a mode, thus inducing a shift in the criterion for triggering an ELM crash. An ELM crash requires the P-B growth rate to exceed a critical value γ>γ{sub c}, where γ{sub c} is set by 1/τ{sup ¯}{sub c}, and τ{sup ¯}{sub c} is the averaged mode phase coherence time. For 0<γ<γ{sub c}, P-B turbulence develops but drives enhanced turbulent transport. We also show that electron inertia dramatically changes the instability threshold when density is low. However, P-B turbulence alone cannot generate enough current transport to allow fast reconnection during an ELM crash.

  11. Magnetic field in laser plasmas: non-local electron transport and reconnection

    International Nuclear Information System (INIS)

    Riquier, Raphael

    2016-01-01

    In the framework of the inertial confinement fusion, a pellet filled with the deuterium-tritium fuel is imploded, either through laser irradiation (direct drive, laser - low atomic number target interaction) or by the black body radiation from a cavity converting the laser radiation (indirect drive, laser - high atomic number target interaction). In both cases, a correct modeling of the electron transport is of first importance in order to have predictive hydro-radiative simulations. Nonetheless, it has been shown early on that the hypothesis of the linear transport are not valid in the framework of a solid target irradiated by a high power laser (I≅10 14 W/cm 2 ). This is due in part to very steep temperature gradients (kinetic effects, so-called 'non-local') and because of a magnetic field self-generated through the thermo-electric effect. Finally, the heat flux and the magnetic field are strongly coupled through two mechanisms: the advection of the field with the heat flux (Nernst effect) and the rotation and inhibition of the heat flux by the plasma's magnetization (Righi-Leduc effect).In this manuscript, we will first present the various electron transport models, particularly the non-local with magnetic field model included in the hydro-radiative code FCI2. Following, in order to validate this model, we will compare it first against a kinetic code, and then with an experiment during which the magnetic field has been probed through proton radiography. Once the model validated, we will use FCI2 simulations to explain the source and transport of the field, as well as its effect on the interaction. Finally, the reconnection of the magnetic field, during the irradiation of a solid target by two laser beams, will be studied. (author) [fr

  12. Renormalization group-theoretic approach to electron localization in disordered systems

    International Nuclear Information System (INIS)

    Kumar, N.; Heinrichs, J.

    1977-06-01

    The localization problem for the Anderson tight-binding model with site-diagonal (gaussian) disorder is studied, using a previously established analogy between this problem and the statistical mechanics of a zero-component classical field. The equivalent free-energy functional turns out to have complex coefficients in the bilinear terms but involves a real repulsive quartic interaction. The averaged one-electron propagator corresponds to the two-point correlation function for the equivalent statistical problem and the critical point gives the mobility edge, which is identified with the (real) fixed point energy of the associated renormalization group. Since for convergence reasons the conventional perturbative treatment of Wilson's formula is invalid, it is resorted to a non-perturbative approach which leads to a physical fixed point corresponding to a repulsive quartic interaction. The results for the mobility edge in three dimensions and for the critical disorder for an Anderson transition in two dimensions agree well with previous detailed predictions. The critical indices describing the approach of the transition at the mobility edge of various physical quantities, within the epsilon-expansion are also discussed. The more general problem where both diagonal and off-diagonal disorder is present in the Anderson hamiltonian is considered. In this case it is shown that the Hamilton function for the equivalent zero-component classical field model involves an additional biquadratic exchange term. From a simple generalization of Wilson's recursion relation and its non-perturbative solution explicit expressions for the mobility edges for weak diagonal and off-diagonal disorder in two and three dimensions are obtained. Our treatment casts doubts on the validity of recent conclusions about electron localization based on the renormalization group study of the nm-component spin model

  13. A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Roslyn N.; Sanford, James A.; Park, Jea H.; Deatherage, Brooke L.; Champion, Boyd L.; Smith, Richard D.; Heffron, Fred; Adkins, Joshua N.

    2012-06-01

    Towards developing a systems-level pathobiological understanding of Salmonella enterica, we performed a subcellular proteomic analysis of this pathogen grown under standard laboratory and infection-mimicking conditions in vitro. Analysis of proteins from cytoplasmic, inner membrane, periplasmic, and outer membrane fractions yielded coverage of over 30% of the theoretical proteome. Confident subcellular location could be assigned to over 1000 proteins, with good agreement between experimentally observed location and predicted/known protein properties. Comparison of protein location under the different environmental conditions provided insight into dynamic protein localization and possible moonlighting (multiple function) activities. Notable examples of dynamic localization were the response regulators of two-component regulatory systems (e.g., ArcB, PhoQ). The DNA-binding protein Dps that is generally regarded as cytoplasmic was significantly enriched in the outer membrane for all growth conditions examined, suggestive of moonlighting activities. These observations imply the existence of unknown transport mechanisms and novel functions for a subset of Salmonella proteins. Overall, this work provides a catalog of experimentally verified subcellular protein location for Salmonella and a framework for further investigations using computational modeling.

  14. Differential subcellular distribution of ion channels and the diversity of neuronal function.

    Science.gov (United States)

    Nusser, Zoltan

    2012-06-01

    Following the astonishing molecular diversity of voltage-gated ion channels that was revealed in the past few decades, the ion channel repertoire expressed by neurons has been implicated as the major factor governing their functional heterogeneity. Although the molecular structure of ion channels is a key determinant of their biophysical properties, their subcellular distribution and densities on the surface of nerve cells are just as important for fulfilling functional requirements. Recent results obtained with high resolution quantitative localization techniques revealed complex, subcellular compartment-specific distribution patterns of distinct ion channels. Here I suggest that within a given neuron type every ion channel has a unique cell surface distribution pattern, with the functional consequence that this dramatically increases the computational power of nerve cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Strong Depletion in Hybrid Perovskite p-n Junctions Induced by Local Electronic Doping.

    Science.gov (United States)

    Ou, Qingdong; Zhang, Yupeng; Wang, Ziyu; Yuwono, Jodie A; Wang, Rongbin; Dai, Zhigao; Li, Wei; Zheng, Changxi; Xu, Zai-Quan; Qi, Xiang; Duhm, Steffen; Medhekar, Nikhil V; Zhang, Han; Bao, Qiaoliang

    2018-04-01

    A semiconductor p-n junction typically has a doping-induced carrier depletion region, where the doping level positively correlates with the built-in potential and negatively correlates with the depletion layer width. In conventional bulk and atomically thin junctions, this correlation challenges the synergy of the internal field and its spatial extent in carrier generation/transport. Organic-inorganic hybrid perovskites, a class of crystalline ionic semiconductors, are promising alternatives because of their direct badgap, long diffusion length, and large dielectric constant. Here, strong depletion in a lateral p-n junction induced by local electronic doping at the surface of individual CH 3 NH 3 PbI 3 perovskite nanosheets is reported. Unlike conventional surface doping with a weak van der Waals adsorption, covalent bonding and hydrogen bonding between a MoO 3 dopant and the perovskite are theoretically predicted and experimentally verified. The strong hybridization-induced electronic coupling leads to an enhanced built-in electric field. The large electric permittivity arising from the ionic polarizability further contributes to the formation of an unusually broad depletion region up to 10 µm in the junction. Under visible optical excitation without electrical bias, the lateral diode demonstrates unprecedented photovoltaic conversion with an external quantum efficiency of 3.93% and a photodetection responsivity of 1.42 A W -1 . © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. On the importance of local orbitals using second energy derivatives for d and f electrons

    Science.gov (United States)

    Karsai, Ferenc; Tran, Fabien; Blaha, Peter

    2017-11-01

    The all-electron linearized augmented plane wave (LAPW) methods are among the most accurate to solve the Kohn-Sham equations of density functional theory for periodic solids. In the LAPW methods, the unit cell is partitioned into spheres surrounding the atoms, inside which the wave functions are expanded into spherical harmonics, and the interstitial region, where the wave functions are expanded in Fourier series. Recently, Michalicek et al. (2013) reported an analysis of the so-called linearization error, which is inherent to the basis functions inside the spheres, and advocated the use of local orbital basis functions involving the second energy derivative of the radial part (HDLO). In the present work, we report the implementation of such basis functions into the WIEN2k code, and discuss in detail the improvement in terms of accuracy. From our tests, which involve atoms from the whole periodic table, it is concluded that for ground-state properties (e.g., equilibrium volume) the use of HDLO is necessary only for atoms with d or f electrons in the valence and large atomic spheres. For unoccupied states which are not too high above the Fermi energy, HDLO systematically improve the band structure, which may be of importance for the calculation of optical properties.

  17. Local instability driving extreme events in a pair of coupled chaotic electronic circuits

    Science.gov (United States)

    de Oliveira, Gilson F.; Di Lorenzo, Orlando; de Silans, Thierry Passerat; Chevrollier, Martine; Oriá, Marcos; Cavalcante, Hugo L. D. de Souza

    2016-06-01

    For a long time, extreme events happening in complex systems, such as financial markets, earthquakes, and neurological networks, were thought to follow power-law size distributions. More recently, evidence suggests that in many systems the largest and rarest events differ from the other ones. They are dragon kings, outliers that make the distribution deviate from a power law in the tail. Understanding the processes of formation of extreme events and what circumstances lead to dragon kings or to a power-law distribution is an open question and it is a very important one to assess whether extreme events will occur too often in a specific system. In the particular system studied in this paper, we show that the rate of occurrence of dragon kings is controlled by the value of a parameter. The system under study here is composed of two nearly identical chaotic oscillators which fail to remain in a permanently synchronized state when coupled. We analyze the statistics of the desynchronization events in this specific example of two coupled chaotic electronic circuits and find that modifying a parameter associated to the local instability responsible for the loss of synchronization reduces the occurrence of dragon kings, while preserving the power-law distribution of small- to intermediate-size events with the same scaling exponent. Our results support the hypothesis that the dragon kings are caused by local instabilities in the phase space.

  18. A comparison of non-local electron transport models relevant to inertial confinement fusion

    Science.gov (United States)

    Sherlock, Mark; Brodrick, Jonathan; Ridgers, Christopher

    2017-10-01

    We compare the reduced non-local electron transport model developed by Schurtz et al. to Vlasov-Fokker-Planck simulations. Two new test cases are considered: the propagation of a heat wave through a high density region into a lower density gas, and a 1-dimensional hohlraum ablation problem. We find the reduced model reproduces the peak heat flux well in the ablation region but significantly over-predicts the coronal preheat. The suitability of the reduced model for computing non-local transport effects other than thermal conductivity is considered by comparing the computed distribution function to the Vlasov-Fokker-Planck distribution function. It is shown that even when the reduced model reproduces the correct heat flux, the distribution function is significantly different to the Vlasov-Fokker-Planck prediction. Two simple modifications are considered which improve agreement between models in the coronal region. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  19. Accuracy of the Hartree-Fock and local density approximations for electron densities: a study for light atoms

    International Nuclear Information System (INIS)

    Almbladh, C.-O.; Ekenberg, U.; Pedroza, A.C.

    1983-01-01

    The authors compare the electron densities and Hartree potentials in the local density and the Hartree-Fock approximations to the corresponding quantities obtained from more accurate correlated wavefunctions. The comparison is made for a number of two-electron atoms, Li, and for Be. The Hartree-Fock approximation is more accurate than the local density approximation within the 1s shell and for the spin polarization in Li, while the local density approximation is slightly better than the Hartree-Fock approximation for charge densities in the 2s shell. The inaccuracy of the Hartree-Fock and local density approximations to the Hartree potential is substantially smaller than the inaccuracy of the local density approximation to the ground-state exchange-correlation potential. (Auth.)

  20. Subcellular site and nature of intracellular cadmium in plants

    International Nuclear Information System (INIS)

    Wagner, G.J.

    1979-01-01

    The mechanisms underlying heavy metal accumulation, toxicity, and tolerance in higher plants are poorly understood. Since subcellular processes are undoubtedly involved in all these phenomena, it is of interest to study the extent, subcellular site and nature of intracellularly accumulated cadmium in higher plants. Whole plants supplied 109 CdCl 2 or 112 CdSO 4 accumulated Cd into roots and aerial tissues. Preparation of protoplasts from aerial tissues followed by subcellular fractionation of the protoplasts to obtain intact vacuoles, chloroplasts and cytosol revealed the presence of Cd in the cytosol but not in vacuoles or chloroplasts. No evidence was obtained for the production of volatile Cd complexes in tobacco

  1. Experimental study of water absorption of electronic components and internal local temperature and humidity into electronic enclosure

    DEFF Research Database (Denmark)

    Conseil, Helene; Jellesen, Morten Stendahl; Ambat, Rajan

    2014-01-01

    Corrosion reliability of electronic products is a key factor for electronics industry, and today there is a large demand for performance reliability in large spans of temperature and humidity during day and night shifts. Corrosion failures are still seen due to the effects of temperature, humidity......, differential humidity, and temperature effects simulating day/night, and the use of desiccants....

  2. Diversity and subcellular distribution of archaeal secreted proteins.

    Science.gov (United States)

    Szabo, Zalan; Pohlschroder, Mechthild

    2012-01-01

    Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis, and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat) pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as phyla-specific pathways among the archaea. A more comprehensive understanding of the transport pathways used and post-translational modifications of secreted archaeal proteins will also facilitate the identification and heterologous expression of commercially valuable archaeal enzymes.

  3. local

    Directory of Open Access Journals (Sweden)

    Abílio Amiguinho

    2005-01-01

    Full Text Available The process of socio-educational territorialisation in rural contexts is the topic of this text. The theme corresponds to a challenge to address it having as main axis of discussion either the problem of social exclusion or that of local development. The reasons to locate the discussion in this last field of analysis are discussed in the first part of the text. Theoretical and political reasons are there articulated because the question is about projects whose intentions and practices call for the political both in the theoretical debate and in the choices that anticipate intervention. From research conducted for several years, I use contributions that aim at discuss and enlighten how school can be a potential locus of local development. Its identification and recognition as local institution (either because of those that work and live in it or because of those that act in the surrounding context are crucial steps to progressively constitute school as a partner for development. The promotion of the local values and roots, the reconstruction of socio-personal and local identities, the production of sociabilities and the equation and solution of shared problems were the dimensions of a socio-educative intervention, markedly globalising. This scenario, as it is argued, was also, intentionally, one of transformation and of deliberate change of school and of the administration of the educative territoires.

  4. Local Dynamic Stability Assessment of Motion Impaired Elderly Using Electronic Textile Pants.

    Science.gov (United States)

    Liu, Jian; Lockhart, Thurmon E; Jones, Mark; Martin, Tom

    2008-10-01

    A clear association has been demonstrated between gait stability and falls in the elderly. Integration of wearable computing and human dynamic stability measures into home automation systems may help differentiate fall-prone individuals in a residential environment. The objective of the current study was to evaluate the capability of a pair of electronic textile (e-textile) pants system to assess local dynamic stability and to differentiate motion-impaired elderly from their healthy counterparts. A pair of e-textile pants comprised of numerous e-TAGs at locations corresponding to lower extremity joints was developed to collect acceleration, angular velocity and piezoelectric data. Four motion-impaired elderly together with nine healthy individuals (both young and old) participated in treadmill walking with a motion capture system simultaneously collecting kinematic data. Local dynamic stability, characterized by maximum Lyapunov exponent, was computed based on vertical acceleration and angular velocity at lower extremity joints for the measurements from both e-textile and motion capture systems. Results indicated that the motion-impaired elderly had significantly higher maximum Lyapunov exponents (computed from vertical acceleration data) than healthy individuals at the right ankle and hip joints. In addition, maximum Lyapunov exponents assessed by the motion capture system were found to be significantly higher than those assessed by the e-textile system. Despite the difference between these measurement techniques, attaching accelerometers at the ankle and hip joints was shown to be an effective sensor configuration. It was concluded that the e-textile pants system, via dynamic stability assessment, has the potential to identify motion-impaired elderly.

  5. Local, atomic-level elastic strain measurements of metallic glass thin films by electron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Ebner, C. [Physics of Nanostructured Materials, Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna (Austria); Sarkar, R. [Department of Materials Science and Engineering, School for Engineering of Matter Transport and Energy, Arizona State University, Tempe 85287 (United States); Rajagopalan, J. [Department of Materials Science and Engineering, School for Engineering of Matter Transport and Energy, Arizona State University, Tempe 85287 (United States); Department of Mechanical and Aerospace Engineering, School for Engineering of Matter Transport and Energy, Arizona State University, Tempe 85287 (United States); Rentenberger, C., E-mail: christian.rentenberger@univie.ac.at [Physics of Nanostructured Materials, Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna (Austria)

    2016-06-15

    A novel technique is used to measure the atomic-level elastic strain tensor of amorphous materials by tracking geometric changes of the first diffuse ring of selected area electron diffraction patterns (SAD). An automatic procedure, which includes locating the centre and fitting an ellipse to the diffuse ring with sub-pixel precision is developed for extracting the 2-dimensional strain tensor from the SAD patterns. Using this technique, atomic-level principal strains from micrometre-sized regions of freestanding amorphous Ti{sub 0.45}Al{sub 0.55} thin films were measured during in-situ TEM tensile deformation. The thin films were deformed using MEMS based testing stages that allow simultaneous measurement of the macroscopic stress and strain. The calculated atomic-level principal strains show a linear dependence on the applied stress, and good correspondence with the measured macroscopic strains. The calculated Poisson’s ratio of 0.23 is reasonable for brittle metallic glasses. The technique yields a strain accuracy of about 1×10{sup −4} and shows the potential to obtain localized strain profiles/maps of amorphous thin film samples. - Highlights: • A TEM method to measure elastic strain in metallic glass films is proposed. • Method is based on tracking geometric changes in TEM diffraction patterns. • An automatic procedure is developed for extracting the local strain tensor. • Atomic-level strain in amorphous TiAl film was analysed during in-situ deformation. • Capability of the method to obtain micrometer scale strain profiles/maps is shown.

  6. Subcellular analysis by laser ablation electrospray ionization mass spectrometry

    Science.gov (United States)

    Vertes, Akos; Stolee, Jessica A; Shrestha, Bindesh

    2014-12-02

    In various embodiments, a method of laser ablation electrospray ionization mass spectrometry (LAESI-MS) may generally comprise micro-dissecting a cell comprising at least one of a cell wall and a cell membrane to expose at least one subcellular component therein, ablating the at least one subcellular component by an infrared laser pulse to form an ablation plume, intercepting the ablation plume by an electrospray plume to form ions, and detecting the ions by mass spectrometry.

  7. Temporal evolutions of electron temperature and density with edge localized mode in the JT-60U divertor plasma

    International Nuclear Information System (INIS)

    Nakano, T; Kubo, H; Asakura, N

    2010-01-01

    From the intensity ratios of the three He I lines measured at 20 kHz, the temporal evolutions of the electron temperature and density during and after the power and the particle flow into the divertor plasma caused by edge localized modes are determined. The electron temperature increases from 70 eV to 80 eV with increasing D α intensity. Then, at the peak of D α intensity, the electron temperature starts decreasing down to 60 eV. The electron density increases from 0.1 x 10 19 m -3 to 0.3 x 10 19 m -3 with increasing D α intensity, and then starts to decrease more gradually compared with the electron temperature after the peak of D α intensity. It is interpreted that the increase of the electron temperature is ascribed to the power and the particle flow into the divertor plasma, and that the decrease of the electron temperature and the increase of the electron density are ascribed to the ionization of the recycled neutrals, which consumes the electron energy and produces electrons.

  8. Magnetic susceptibility measurements of σ plutonium alloys. Contribution to the study of the 5f electrons localization in the plutonium

    International Nuclear Information System (INIS)

    Meot-Reymond, S.

    1996-01-01

    Physical properties of actinide metals are essentially ruled by the 5f electrons localization. From a theoretically point of view, this localization is more important in the δ-phase than in the α-one. To compare their magnetic behaviour, low temperature magnetic susceptibility measurements have been performed and previous-resistivity data have been analysed. Experimental results and theoretical data can be conciliate by the existence of a Kondo effect in the δ-Pu phase. (author)

  9. Subcellular controls of mercury trophic transfer to a marine fish

    International Nuclear Information System (INIS)

    Dang Fei; Wang Wenxiong

    2010-01-01

    Different behaviors of inorganic mercury [Hg(II)] and methylmercury (MeHg) during trophic transfer along the marine food chain have been widely reported, but the mechanisms are not fully understood. The bioavailability of ingested mercury, quantified by assimilation efficiency (AE), was investigated in a marine fish, the grunt Terapon jarbua, based on mercury subcellular partitioning in prey and purified subcellular fractions of prey tissues. The subcellular distribution of Hg(II) differed substantially among prey types, with cellular debris being a major (49-57% in bivalves) or secondary (14-19% in other prey) binding pool. However, MeHg distribution varied little among prey types, with most MeHg (43-79%) in heat-stable protein (HSP) fraction. The greater AEs measured for MeHg (90-94%) than for Hg(II) (23-43%) confirmed the findings of previous studies. Bioavailability of each purified subcellular fraction rather than the proposed trophically available metal (TAM) fraction could better elucidate mercury assimilation difference. Hg(II) associated with insoluble fraction (e.g. cellular debris) was less bioavailable than that in soluble fraction (e.g. HSP). However, subcellular distribution was shown to be less important for MeHg, with each fraction having comparable MeHg bioavailability. Subcellular distribution in prey should be an important consideration in mercury trophic transfer studies.

  10. Subcellular controls of mercury trophic transfer to a marine fish

    Energy Technology Data Exchange (ETDEWEB)

    Dang Fei [Department of Biology, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong); Wang Wenxiong, E-mail: wwang@ust.hk [Department of Biology, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong)

    2010-09-15

    Different behaviors of inorganic mercury [Hg(II)] and methylmercury (MeHg) during trophic transfer along the marine food chain have been widely reported, but the mechanisms are not fully understood. The bioavailability of ingested mercury, quantified by assimilation efficiency (AE), was investigated in a marine fish, the grunt Terapon jarbua, based on mercury subcellular partitioning in prey and purified subcellular fractions of prey tissues. The subcellular distribution of Hg(II) differed substantially among prey types, with cellular debris being a major (49-57% in bivalves) or secondary (14-19% in other prey) binding pool. However, MeHg distribution varied little among prey types, with most MeHg (43-79%) in heat-stable protein (HSP) fraction. The greater AEs measured for MeHg (90-94%) than for Hg(II) (23-43%) confirmed the findings of previous studies. Bioavailability of each purified subcellular fraction rather than the proposed trophically available metal (TAM) fraction could better elucidate mercury assimilation difference. Hg(II) associated with insoluble fraction (e.g. cellular debris) was less bioavailable than that in soluble fraction (e.g. HSP). However, subcellular distribution was shown to be less important for MeHg, with each fraction having comparable MeHg bioavailability. Subcellular distribution in prey should be an important consideration in mercury trophic transfer studies.

  11. Local electronic and geometric structures of silicon atoms implanted in graphite

    International Nuclear Information System (INIS)

    Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao

    2002-01-01

    Low-energy Si + ions were implanted in highly oriented pyrolitic graphite (HOPG) up to 1% of surface atomic concentration, and the local electronic and geometric structures around the silicon atoms were in situ investigated by means of the Si K-edge X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy using linearly polarized synchrotron radiation. The resonance peak appeared at 1839.5 eV in the Si K-edge XANES spectra for Si + -implanted HOPG. This energy is lower than those of the Si 1s→σ * resonance peaks in any other Si-containing materials. The intensity of the resonance peak showed strong polarization dependence, which suggests that the final state orbitals around the implanted Si atoms have π * -like character. It is concluded that the σ-type Si-C bonds produced by the Si + -ion implantation are nearly parallel to the graphite plane, and Si x C phase forms two-dimensionally spread graphite-like layer with sp 2 bonds

  12. Computation of quantum electron transport with local current conservation using quantum trajectories

    International Nuclear Information System (INIS)

    Alarcón, A; Oriols, X

    2009-01-01

    A recent proposal for modeling time-dependent quantum electron transport with Coulomb and exchange correlations using quantum (Bohm) trajectories (Oriols 2007 Phys. Rev. Lett. 98 066803) is extended towards the computation of the total (particle plus displacement) current in mesoscopic devices. In particular, two different methods for the practical computation of the total current are compared. The first method computes the particle and the displacement currents from the rate of Bohm particles crossing a particular surface and the time-dependent variations of the electric field there. The second method uses the Ramo–Shockley theorem to compute the total current on that surface from the knowledge of the Bohm particle dynamics in a 3D volume and the time-dependent variations of the electric field on the boundaries of that volume. From a computational point of view, it is shown that both methods achieve local current conservation, but the second is preferred because it is free from 'spurious' peaks. A numerical example, a Bohm trajectory crossing a double-barrier tunneling structure, is presented, supporting the conclusions

  13. The isotropic local Wigner-Seitz model: An accurate theoretical model for the quasi-free electron energy in fluids

    Science.gov (United States)

    Evans, Cherice; Findley, Gary L.

    The quasi-free electron energy V0 (ρ) is important in understanding electron transport through a fluid, as well as for modeling electron attachment reactions in fluids. Our group has developed an isotropic local Wigner-Seitz model that allows one to successfully calculate the quasi-free electron energy for a variety of atomic and molecular fluids from low density to the density of the triple point liquid with only a single adjustable parameter. This model, when coupled with the quasi-free electron energy data and the thermodynamic data for the fluids, also can yield optimized intermolecular potential parameters and the zero kinetic energy electron scattering length. In this poster, we give a review of the isotropic local Wigner-Seitz model in comparison to previous theoretical models for the quasi-free electron energy. All measurements were performed at the University of Wisconsin Synchrotron Radiation Center. This work was supported by a Grants from the National Science Foundation (NSF CHE-0956719), the Petroleum Research Fund (45728-B6 and 5-24880), the Louisiana Board of Regents Support Fund (LEQSF(2006-09)-RD-A33), and the Professional Staff Congress City University of New York.

  14. Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL).

    Science.gov (United States)

    Hooper, Cornelia M; Castleden, Ian R; Aryamanesh, Nader; Jacoby, Richard P; Millar, A Harvey

    2016-01-01

    Barley, wheat, rice and maize provide the bulk of human nutrition and have extensive industrial use as agricultural products. The genomes of these crops each contains >40,000 genes encoding proteins; however, the major genome databases for these species lack annotation information of protein subcellular location for >80% of these gene products. We address this gap, by constructing the compendium of crop protein subcellular locations called crop Proteins with Annotated Locations (cropPAL). Subcellular location is most commonly determined by fluorescent protein tagging of live cells or mass spectrometry detection in subcellular purifications, but can also be predicted from amino acid sequence or protein expression patterns. The cropPAL database collates 556 published studies, from >300 research institutes in >30 countries that have been previously published, as well as compiling eight pre-computed subcellular predictions for all Hordeum vulgare, Triticum aestivum, Oryza sativa and Zea mays protein sequences. The data collection including metadata for proteins and published studies can be accessed through a search portal http://crop-PAL.org. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  15. Presolvated Electron Reactions with Methyl Acetoacetate: Electron Localization, Proton-Deuteron Exchange, and H-Atom Abstraction

    Directory of Open Access Journals (Sweden)

    Alex Petrovici

    2014-09-01

    Full Text Available Radiation-produced electrons initiate various reaction processes that are important to radiation damage to biomolecules. In this work, the site of attachment of the prehydrated electrons with methyl acetoacetate (MAA, CH3-CO-CH2-COOCH3 at 77 K and subsequent reactions of the anion radical (CH3-CO•−-CH2-COOCH3 in the 77 to ca. 170 K temperature range have been investigated in homogeneous H2O and D2O aqueous glasses by electron spin resonance (ESR spectroscopy. At 77 K, the prehydrated electron attaches to MAA forming the anion radical in which the electron is delocalized over the two carbonyl groups. This species readily protonates to produce the protonated electron adduct radical CH3-C(•OH-CH2-COOCH3. The ESR spectrum of CH3-C(•OH-CH2-COOCH3 in H2O shows line components due to proton hyperfine couplings of the methyl and methylene groups. Whereas, the ESR spectrum of CH3-C(•OH-CH2-COOCH3 in D2O glass shows only the line components due to proton hyperfine couplings of CH3 group. This is expected since the methylene protons in MAA are readily exchangeable in D2O. On stepwise annealing to higher temperatures (ca. 150 to 170 K, CH3-C(•OH-CH2-COOCH3 undergoes bimolecular H-atom abstraction from MAA to form the more stable radical, CH3-CO-CH•-COOCH3. Theoretical calculations using density functional theory (DFT support the radical assignments.

  16. Presolvated electron reactions with methyl acetoacetate: electron localization, proton-deuteron exchange, and H-atom abstraction.

    Science.gov (United States)

    Petrovici, Alex; Adhikary, Amitava; Kumar, Anil; Sevilla, Michael D

    2014-09-01

    Radiation-produced electrons initiate various reaction processes that are important to radiation damage to biomolecules. In this work, the site of attachment of the prehydrated electrons with methyl acetoacetate (MAA, CH3-CO-CH2-COOCH3) at 77 K and subsequent reactions of the anion radical (CH3-CO•--CH2-COOCH3) in the 77 to ca. 170 K temperature range have been investigated in homogeneous H2O and D2O aqueous glasses by electron spin resonance (ESR) spectroscopy. At 77 K, the prehydrated electron attaches to MAA forming the anion radical in which the electron is delocalized over the two carbonyl groups. This species readily protonates to produce the protonated electron adduct radical CH3-C(•)OH-CH2-COOCH3. The ESR spectrum of CH3-C(•)OH-CH2-COOCH3 in H2O shows line components due to proton hyperfine couplings of the methyl and methylene groups. Whereas, the ESR spectrum of CH3-C(•)OH-CH2-COOCH3 in D2O glass shows only the line components due to proton hyperfine couplings of CH3 group. This is expected since the methylene protons in MAA are readily exchangeable in D2O. On stepwise annealing to higher temperatures (ca. 150 to 170 K), CH3-C(•)OH-CH2-COOCH3 undergoes bimolecular H-atom abstraction from MAA to form the more stable radical, CH3-CO-CH•-COOCH3. Theoretical calculations using density functional theory (DFT) support the radical assignments.

  17. Propagation of localized structures in relativistic magnetized electron-positron plasmas using particle-in-cell simulations

    Energy Technology Data Exchange (ETDEWEB)

    López, Rodrigo A. [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Concepción, Concepción 4070386 (Chile); Muñoz, Víctor [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago (Chile); Viñas, Adolfo F. [Geospace Physics Laboratory, Heliophysics Science Division, NASA Goddard Space Flight Center, Greenbelt, Maryland 20771 (United States); Valdivia, Juan A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Santiago 9170124 (Chile)

    2015-09-15

    We use a particle-in-cell simulation to study the propagation of localized structures in a magnetized electron-positron plasma with relativistic finite temperature. We use as initial condition for the simulation an envelope soliton solution of the nonlinear Schrödinger equation, derived from the relativistic two fluid equations in the strongly magnetized limit. This envelope soliton turns out not to be a stable solution for the simulation and splits in two localized structures propagating in opposite directions. However, these two localized structures exhibit a soliton-like behavior, as they keep their profile after they collide with each other due to the periodic boundary conditions. We also observe the formation of localized structures in the evolution of a spatially uniform circularly polarized Alfvén wave. In both cases, the localized structures propagate with an amplitude independent velocity.

  18. Propagation of localized structures in relativistic magnetized electron-positron plasmas using particle-in-cell simulations

    International Nuclear Information System (INIS)

    López, Rodrigo A.; Muñoz, Víctor; Viñas, Adolfo F.; Valdivia, Juan A.

    2015-01-01

    We use a particle-in-cell simulation to study the propagation of localized structures in a magnetized electron-positron plasma with relativistic finite temperature. We use as initial condition for the simulation an envelope soliton solution of the nonlinear Schrödinger equation, derived from the relativistic two fluid equations in the strongly magnetized limit. This envelope soliton turns out not to be a stable solution for the simulation and splits in two localized structures propagating in opposite directions. However, these two localized structures exhibit a soliton-like behavior, as they keep their profile after they collide with each other due to the periodic boundary conditions. We also observe the formation of localized structures in the evolution of a spatially uniform circularly polarized Alfvén wave. In both cases, the localized structures propagate with an amplitude independent velocity

  19. Light and electron microscopic localization of GABAA-receptors on cultured cerebellar granule cells and astrocytes using immunohistochemical techniques

    DEFF Research Database (Denmark)

    Hansen, Gert Helge; Hösli, E; Belhage, B

    1991-01-01

    . At the light microscope level specific staining of GABAA-receptors was localized in various types of neurones in explant cultures of rat cerebellum using the indirect peroxidase-antiperoxidase (PAP) technique, whereas no specific staining was found in astrocytes. At the electron microscope level labeling...

  20. Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Berendzen, Joel

    1999-01-01

    The correlation of local r.m.s. density is shown to be a good measure of the presence of distinct solvent and macromolecule regions in macromolecular electron-density maps. It has recently been shown that the standard deviation of local r.m.s. electron density is a good indicator of the presence of distinct regions of solvent and protein in macromolecular electron-density maps [Terwilliger & Berendzen (1999 ▶). Acta Cryst. D55, 501–505]. Here, it is demonstrated that a complementary measure, the correlation of local r.m.s. density in adjacent regions on the unit cell, is also a good measure of the presence of distinct solvent and protein regions. The correlation of local r.m.s. density is essentially a measure of how contiguous the solvent (and protein) regions are in the electron-density map. This statistic can be calculated in real space or in reciprocal space and has potential uses in evaluation of heavy-atom solutions in the MIR and MAD methods as well as for evaluation of trial phase sets in ab initio phasing procedures

  1. Femtosecond excitations in metallic nanostructures. From ultrafast light confinement to a local electron source

    Energy Technology Data Exchange (ETDEWEB)

    Ropers, C.

    2007-07-11

    This thesis contributes to the understanding of optical excitations in metallic nanostructures. In experiments on selected model structures, the dynamics of these excitations and their electromagnetic spatial modes are investigated with femtosecond temporal and nanometer spatial resolution, respectively. Angle- and time-resolved transmission experiments on metallic thin film gratings demonstrate the dominant role resonant surface plasmon polaritons (SPPs) play in the optical properties of such structures. The lifetimes of these excitations are determined, and it is shown that coherent couplings among SPP-resonances result in drastic lifetime modifications. Near the visible part of the spectrum, subradiant SPP lifetimes of up to 200 femtoseconds are observed, which is considerably longer than previously expected for these structures. The spatial SPP mode profiles are imaged using a custom-built near-field optical microscope. The experiments reveal a direct correlation between the spatial mode structure and the dynamics of different SPP resonances. Coupling-induced SPP band gaps are identified as splittings into symmetric and antisymmetric surface modes. These findings allow for an interpretation of the near-field optical image contrast in terms of the contributions of different vectorial components of the electromagnetic near-field. A selective imaging of different electric and magnetic field components is demonstrated for various types of near-field probes. Furthermore, the excitation of SPPs in periodic structures is employed in a novel type of near-field tip. The resonant excitation of SPPs in a nanofabricated grating on the shaft of a sharp metallic tip results in their concentration at the tip apex. The final part of the thesis highlights the importance of optical field enhancements for the local generation of nonlinear optical signals at the apex of sharp metallic tips. Specifically, the observation of intense multiphoton electron emission after femtosecond

  2. Unconventional scaling of the anomalous Hall effect accompanying electron localization correction in the dirty regime

    KAUST Repository

    Lu, Y. M.; Cai, J. W.; Guo, Zaibing; Zhang, Xixiang

    2013-01-01

    Pt films. The relationship between electron transport and temperature reveals a quantitatively insignificant Coulomb interaction in these films, while the temperature dependent anomalous Hall conductivity experiences quantum correction from electron

  3. Communication: Recovering the flat-plane condition in electronic structure theory at semi-local DFT cost

    Science.gov (United States)

    Bajaj, Akash; Janet, Jon Paul; Kulik, Heather J.

    2017-11-01

    The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addition and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local density functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i.e., Hartree-Fock exchange), it worsens FSE. To find an alternative strategy, we examine the shape of semi-local DFT deviations from the exact flat plane and we find this shape to be remarkably consistent across ions and molecules. We introduce the judiciously modified DFT (jmDFT) approach, wherein corrections are constructed from few-parameter, low-order functional forms that fit the shape of semi-local DFT errors. We select one such physically intuitive form and incorporate it self-consistently to correct semi-local DFT. We demonstrate on model systems that jmDFT represents the first easy-to-implement, no-overhead approach to recovering the flat plane from semi-local DFT.

  4. Effect of interior geometry on local climate inside an electronic device enclosure

    DEFF Research Database (Denmark)

    Joshy, Salil; Jellesen, Morten Stendahl; Ambat, Rajan

    2017-01-01

    Electronic enclosure design and the internal arrangement of PCBs and components influence microclimate inside the enclosure. This work features a general electronic unit with parallel PCBs. One of the PCB is considered to have heat generating components on it. The humidity and temperature profiles...... geometry of the device and related enclosure design parameters on the humidity and temperature profiles inside the electronic device enclosure....

  5. Local 3d Electronic Structures of Co-Based Complexes with Medicinal Molecules Probed by Soft X-ray Absorption

    Science.gov (United States)

    Yamagami, Kohei; Fujiwara, Hidenori; Imada, Shin; Kadono, Toshiharu; Yamanaka, Keisuke; Muro, Takayuki; Tanaka, Arata; Itai, Takuma; Yoshinari, Nobuto; Konno, Takumi; Sekiyama, Akira

    2017-07-01

    We have examined the local 3d electronic structures of Co-Au multinuclear complexes with the medicinal molecules d-penicillaminate (d-pen) [Co{Au(PPh3)(d-pen)}2]ClO4 and [Co3{Au3(tdme)(d-pen)3}2] by Co L2,3-edge soft X-ray absorption (XAS) spectroscopy, where PPh3 denotes triphenylphosphine and tdme stands for 1,1,1-tris[(diphenylphosphino)methyl]ethane. The Co L2,3-edge XAS spectra indicate the localized ionic 3d electronic states in both materials. The experimental spectra are well explained by spectral simulation for a localized Co ion under ligand fields with the full multiplet theory, which verifies that the ions are in the low-spin Co3+ state in the former compound and in the high-spin Co2+ state in the latter.

  6. Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.

    Science.gov (United States)

    Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

    2013-12-01

    Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au). © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  7. Distinct cellular and subcellular distributions of G protein-coupled receptor kinase and arrestin isoforms in the striatum.

    Directory of Open Access Journals (Sweden)

    Evgeny Bychkov

    Full Text Available G protein-coupled receptor kinases (GRKs and arrestins mediate desensitization of G protein-coupled receptors (GPCR. Arrestins also mediate G protein-independent signaling via GPCRs. Since GRK and arrestins demonstrate no strict receptor specificity, their functions in the brain may depend on their cellular complement, expression level, and subcellular targeting. However, cellular expression and subcellular distribution of GRKs and arrestins in the brain is largely unknown. We show that GRK isoforms GRK2 and GRK5 are similarly expressed in direct and indirect pathway neurons in the rat striatum. Arrestin-2 and arrestin-3 are also expressed in neurons of both pathways. Cholinergic interneurons are enriched in GRK2, arrestin-3, and GRK5. Parvalbumin-positive interneurons express more of GRK2 and less of arrestin-2 than medium spiny neurons. The GRK5 subcellular distribution in the human striatal neurons is altered by its phosphorylation: unphosphorylated enzyme preferentially localizes to synaptic membranes, whereas phosphorylated GRK5 is found in plasma membrane and cytosolic fractions. Both GRK isoforms are abundant in the nucleus of human striatal neurons, whereas the proportion of both arrestins in the nucleus was equally low. However, overall higher expression of arrestin-2 yields high enough concentration in the nucleus to mediate nuclear functions. These data suggest cell type- and subcellular compartment-dependent differences in GRK/arrestin-mediated desensitization and signaling.

  8. Nonadiabatic effects on surfaces: Kohn anomaly, electronic damping of adsorbate vibrations, and local heating of single molecules

    International Nuclear Information System (INIS)

    Kroeger, J

    2008-01-01

    Three aspects of electron-phonon coupling at metal surfaces are reviewed. One aspect is the Kohn effect, which describes an anomalous dispersion relation of surface phonons due to quasi-one-dimensional nesting of Fermi surface contours. The combination of electron energy loss spectroscopy and angle-resolved photoelectron spectroscopy allows us to unambiguously characterize Kohn anomaly systems. A second aspect is the nonadiabatic damping of adsorbate vibrations. Characteristic spectroscopic line shapes of vibrational modes allow us to estimate the amount of energy transfer between the vibrational mode and electron-hole pairs. Case studies of a Kohn anomaly and nonadiabatic damping are provided by the hydrogen- and deuterium-covered Mo(110) surface. As a third aspect of interaction between electrons and phonons, local heating of a C 60 molecule adsorbed on Cu(100) and in contact with the tip of a scanning tunnelling microscope is covered

  9. Reversal of local spins in transport of electrons through a one-dimensional chain

    International Nuclear Information System (INIS)

    Hu, D.-S.; Xiong, S.-J.

    2003-01-01

    We investigate the spin reversal of two coupled magnetic impurities in the transport processes of electrons in a one-dimensional chain. The impurities are side coupled to the chain and the electrons are injected and tunneling through it. The transmission coefficient of electrons and the polarization of impurities are calculated by the use of the equivalent single-particle network method for the correlated system. It is found that both the transmission coefficient and the polarization of impurities depend on the initial state of impurities and the impurity spins can be converted into the direction of electron spin if the injected electrons are polarized and the number of electrons is large enough. The evolution of the spin-reversal processes is studied in details

  10. Local structural and electronic properties of V2O3 and ZnV2O4

    International Nuclear Information System (INIS)

    Pfalzer, P.

    2004-01-01

    In this thesis the electronically correlated transition metal oxide compounds V 2 O 3 and ZnV 2 O 4 , which are of basic interest for solid state physics, are investigated using X-ray absorption techniques. Measurements of the fine structure at Vanadium and Oxygen K absorption edges together with a comparison to theoretically calculated spectra show that the local properties of these materials, which under certain conditions deviate drastically from the long-range properties known so far, crucially influence the characteristic behaviour. It is shown that the two insulating phases of V 2 O 3 (the paramagnetic insulating (PI) and the antiferromagnetic insulating (AFI) phase) exhibit very similar local properties which are well distinguished from those of the paramagnetic metallic (PM) phase. In particular, a disagreement is found between the local and the long-range spatial symmetry of the PI phase. It is further shown that at the metal-insulator transition from the PM to the AFI phase structural changes preceed changes of the electronic and magnetic properties. This suggests that the metal-insulator transition is structurally driven. In ZnV 2 O 4 characteristic differences are found between the local properties of single crystalline and powdered samples. These originate either from strain in the single crystals or from anisotropy of the electronic states

  11. Electron spin resonance in YbRh2Si2: local-moment, unlike-spin and quasiparticle descriptions.

    Science.gov (United States)

    Huber, D L

    2012-06-06

    Electron spin resonance (ESR) in the Kondo lattice compound YbRh(2)Si(2) has stimulated discussion as to whether the low-field resonance outside the Fermi liquid regime in this material is more appropriately characterized as a local-moment phenomenon or one that requires a Landau quasiparticle interpretation. In earlier work, we outlined a collective mode approach to the ESR that involves only the local 4f moments. In this paper, we extend the collective mode approach to a situation where there are two subsystems of unlike spins: the pseudospins of the ground multiplet of the Yb ions and the spins of the itinerant conduction electrons. We assume a weakly anisotropic exchange interaction between the two subsystems. With suitable approximations our expression for the g-factor also reproduces that found in recent unlike-spin quasiparticle calculations. It is pointed out that the success of the local-moment approach in describing the resonance is due to the fact that the susceptibility of the Yb subsystem dominates that of the conduction electrons with the consequence that the relative shift in the resonance frequency predicted by the unlike-spin models (and absent in the local-moment models) is ≪ 1. The connection with theoretical studies of a two-component model with like spins is also discussed.

  12. Diversity and subcellular distribution of archaeal secreted proteins

    Directory of Open Access Journals (Sweden)

    Mechthild ePohlschroder

    2012-07-01

    Full Text Available Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell-wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as archaeal kingdom-specific pathways. A more comprehensive understanding of the transport pathways and post-translational modifications of secreted archaeal proteins will also generate invaluable insights that will facilitate the identification of commercially valuable archaeal enzymes and the development of heterologous systems in which to efficiently express them.

  13. Organ accumulation and subcellular location of Cicer arietinum ST1 protein.

    Science.gov (United States)

    Albornos, Lucía; Cabrera, Javier; Hernández-Nistal, Josefina; Martín, Ignacio; Labrador, Emilia; Dopico, Berta

    2014-07-01

    The ST (ShooT Specific) proteins are a new family of proteins characterized by a signal peptide, tandem repeats of 25/26 amino acids, and a domain of unknown function (DUF2775), whose presence is limited to a few families of dicotyledonous plants, mainly Fabaceae and Asteraceae. Their function remains unknown, although involvement in plant growth, fruit morphogenesis or in biotic and abiotic interactions have been suggested. This work is focused on ST1, a Cicer arietinum ST protein. We established the protein accumulation in different tissues and organs of chickpea seedlings and plants and its subcellular localization, which could indicate the possible function of ST1. The raising of specific antibodies against ST1 protein revealed that its accumulation in epicotyls and radicles was related to their elongation rate. Its pattern of tissue location in cotyledons during seed formation and early seed germination, as well as its localization in the perivascular fibres of epicotyls and radicles, indicated a possible involvement in seed germination and seedling growth. ST1 protein appears both inside the cell and in the cell wall. This double subcellular localization was found in every organ in which the ST1 protein was detected: seeds, cotyledons and seedling epicotyls and radicles. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  14. Local electron mean energy profile of positive primary streamer discharge with pin-plate electrodes in oxygen—nitrogen mixtures

    International Nuclear Information System (INIS)

    Sima Wen-Xia; Peng Qing-Jun; Yang Qing; Yuan Tao; Shi Jian

    2013-01-01

    Local electron mean energy (LEME) has a direct effect on the rates of collisional ionization of molecules and atoms by electrons. Electron-impact ionization plays an important role and is the main process for the production of charged particles in a primary streamer discharge. Detailed research on the LEME profile in a primary streamer discharge is extremely important for a comprehensive understanding of the local physical mechanism of a streamer. In this study, the LEME profile of the primary streamer discharge in oxygen-nitrogen mixtures with a pin-plate gap of 0.5 cm under an impulse voltage is investigated using a fluid model. The fluid model includes the electron mean energy density equation, as well as continuity equations for electrons and ions and Poisson's electric field equation. The study finds that, except in the initial stage of the primary streamer, the LEME in the primary streamer tip tends to increase as the oxygen-nitrogen mole ratio increases and the pressure decreases. When the primary streamer bridges the gap, the LEME in the primary streamer channel is smaller than the first ionization energies of oxygen and nitrogen. The LEME in the primary streamer channel then decreases as the oxygen-nitrogen mole ratio increases and the pressure increases. The LEME in the primary streamer tip is primarily dependent on the reduced electric field with mole ratios of oxygen-nitrogen given in the oxygen-nitrogen mixtures. (physics of gases, plasmas, and electric discharges)

  15. Subcellular site and nature of intracellular cadmium in plants

    International Nuclear Information System (INIS)

    Wagner, G.J.

    1979-01-01

    The mechanisms underlying heavy metal accumulation, toxicity and tolerance in higher plants are poorly understood. Since subcellular processes are undoubtedly involved in all these phenomena, it is of interest to study the extent of, subcellular site of and nature of intracellularly accumulated cadmium in higher plants. Whole plants supplied 109 CdCl 2 or 112 CdSO 4 accumulated Cd into roots and aerial tissues. Preparation of protoplasts from aerial tissue followed by subcellular fractionation of the protoplasts to obtain intact vacuoles, chloroplasts and cytosol revealed the presence of Cd in the cytosol but not in vacuoles or chloroplasts. Particulate materials containing other cell components were also labeled. Of the 109 Cd supplied to plants, 2 to 10% was recovered in both cytosol preparations and in particulate materials. Cytosol contained proteinaceous--Cd complexes, free metal and low molecular weight Cd complexes. Labeling of protoplasts gave similar results. No evidence was obtained for the production of volatile Cd complexes in tobacco

  16. The impact of edge gradients in the pressure, density, ion temperature, and electron temperature on edge-localized modes

    International Nuclear Information System (INIS)

    Kleva, Robert G.; Guzdar, Parvez N.

    2011-01-01

    The magnitude of the energy and particle fluxes in simulations of edge-localized modes (ELMs) is determined by the edge gradients in the pressure, density, ion temperature, and electron temperature. The total edge pressure gradient is the dominant influence on ELMs by far. An increase (decrease) of merely 2% in the pressure gradient results in an increase (decrease) of more than a factor of ten in the size of the ELM bursts. At a fixed pressure gradient, the size of the ELM bursts decreases as the density gradient increases, while the size of the bursts increases as the electron temperature gradient or, especially, the ion temperature gradient increases.

  17. Electronic structure of the actinide-Rh3 systems and the 5f localization in UPd3

    DEFF Research Database (Denmark)

    Eriksson, Olle; Johansson, Börje; Brooks, M. S. S.

    1989-01-01

    We present electronic-structure calculations for the isostructural (AuCu3-structure) series of intermetallic compounds ARh3 (A=Ac, Th, Pa, U, Np, Pu, Am, and Cm). The calculations were performed using both the scalar relativistic and the fully relativistic linear muffin-tin orbital (LMTO) method........ The localization of the 5f electrons in UPd3 as opposed to the itinerant 5f behavior for the earlier compounds (UMo3, UTc3 , URu3, and URh3) is explained in terms of the variation of the hybridization between 5f and ligand 4d states through the series....

  18. The subcellular compartmentalization of arginine metabolizing enzymes and their role in endothelial dysfunction

    Directory of Open Access Journals (Sweden)

    Feng eChen

    2013-07-01

    Full Text Available The endothelial production of nitric oxide (NO mediates endothelium-dependent vasorelaxation and restrains vascular inflammation, smooth muscle proliferation and platelet aggregation. Impaired production of NO is a hallmark of endothelial dysfunction and promotes the development of cardiovascular disease. In endothelial cells, NO is generated by endothelial nitric oxide synthase (eNOS through the conversion of its substrate, L-arginine to L-citrulline. Reduced access to L-arginine has been proposed as a major mechanism underlying reduced eNOS activity and NO production in cardiovascular disease. The arginases (Arg1 and Arg2 metabolize L-arginine to generate L-ornithine and urea and increased expression of arginase has been proposed as a mechanism of reduced eNOS activity secondary to the depletion of L-arginine. Indeed, supplemental L-arginine and suppression of arginase activity has been shown to improve endothelium-dependent relaxation and ameliorate cardiovascular disease. However, L-arginine concentrations in endothelial cells remain sufficiently high to support NO synthesis suggesting additional mechanisms. The compartmentalization of intracellular L-arginine into poorly interchangeable pools has been proposed to allow for the local depletion of L-arginine. Indeed the subcellular location of L-arginine metabolizing enzymes plays important functional roles. In endothelial cells, eNOS is found in discrete intracellular locations and the capacity to generate NO is heavily influenced by its localtion. Arg1 and Arg2 also reside in different subcellular environments and are thought to differentially influence endothelial function. The plasma membrane solute transporter, CAT-1 and the arginine recycling enzyme, ASL, co-localize with eNOS and facilitate NO release. This review highlights the importance of the subcellular location of eNOS and arginine transporting and metabolizing enzymes to NO release and cardiovascular disease.

  19. Theory of inelastic electron tunneling from a localized spin in the impulsive approximation.

    Science.gov (United States)

    Persson, Mats

    2009-07-31

    A simple expression for the conductance steps in inelastic electron tunneling from spin excitations in a single magnetic atom adsorbed on a nonmagnetic metal surface is derived. The inelastic coupling between the tunneling electron and the spin is via the exchange coupling and is treated in an impulsive approximation using the Tersoff-Hamann approximation for the tunneling between the tip and the sample.

  20. Electron microscopy localization and characterization of functionalized composite organic-inorganic SERS nanoparticles on leukemia cells.

    Science.gov (United States)

    Koh, Ai Leen; Shachaf, Catherine M; Elchuri, Sailaja; Nolan, Garry P; Sinclair, Robert

    2008-12-01

    We demonstrate the use of electron microscopy as a powerful characterization tool to identify and locate antibody-conjugated composite organic-inorganic nanoparticle (COINs) surface enhanced Raman scattering (SERS) nanoparticles on cells. U937 leukemia cells labeled with antibody CD54-conjugated COINs were characterized in their native, hydrated state using wet scanning electron microscopy (SEM) and in their dehydrated state using high-resolution SEM. In both cases, the backscattered electron (BSE) detector was used to detect and identify the silver constituents in COINs due to its high sensitivity to atomic number variations within a specimen. The imaging and analytical capabilities in the SEM were further complemented by higher resolution transmission electron microscopy (TEM) images and scanning Auger electron spectroscopy (AES) data to give reliable and high-resolution information about nanoparticles and their binding to cell surface antigens.

  1. Electron microscopy localization and characterization of functionalized composite organic-inorganic SERS nanoparticles on leukemia cells

    International Nuclear Information System (INIS)

    Koh, Ai Leen; Shachaf, Catherine M.; Elchuri, Sailaja; Nolan, Garry P.; Sinclair, Robert

    2008-01-01

    We demonstrate the use of electron microscopy as a powerful characterization tool to identify and locate antibody-conjugated composite organic-inorganic nanoparticle (COINs) surface enhanced Raman scattering (SERS) nanoparticles on cells. U937 leukemia cells labeled with antibody CD54-conjugated COINs were characterized in their native, hydrated state using wet scanning electron microscopy (SEM) and in their dehydrated state using high-resolution SEM. In both cases, the backscattered electron (BSE) detector was used to detect and identify the silver constituents in COINs due to its high sensitivity to atomic number variations within a specimen. The imaging and analytical capabilities in the SEM were further complemented by higher resolution transmission electron microscopy (TEM) images and scanning Auger electron spectroscopy (AES) data to give reliable and high-resolution information about nanoparticles and their binding to cell surface antigens.

  2. Calculation of electrostatic multipoles of electron localized in narrow-band InSb spherical nanolayer

    International Nuclear Information System (INIS)

    Amirkhanyan, S.M.; Kazaryan, E.M.; Sarkisyan, H.A.

    2015-01-01

    Behavior of electron in narrow-gap spherical nanolayer of InSb is considered. Dispersion law of electron is described within the double-gap Kane model, when arises a necessity for considering of Klein-Gordon equation for description of behavior of electrons and light holes. Dipole and quadrupole momentums of electron in specified systems are defined on the base of the obtained expressions. It is shown, that average value of dipole momentum equals to zero and that for definition of average value of tensor of quadrupole momentum it is enough to calculate the average value of diagonal z-component of this tensor. Electrostatic potentials and tensions of fields created by electron located in different quantum states are defined

  3. Local electronic structure at organic–metal interface studied by UPS, MAES, and first-principles calculation

    Energy Technology Data Exchange (ETDEWEB)

    Aoki, M., E-mail: cmaoki@mail.ecc.u-tokyo.ac.jp; Masuda, S.

    2015-10-01

    Understanding and controlling local electronic structures at organic–metal interfaces are crucial for fabricating novel organic-based electronics, as in the case of heterojunctions in semiconductor devices. Here, we report recent studies of valence electronic states at organic–metal interfaces (especially those near the Fermi level of a metal substrate) by the combined analysis of ultraviolet photoemission spectroscopy (UPS), metastable atom electron spectroscopy (MAES), and first-principles calculations. New electronic states in the HOMO (highest occupied molecular orbital)–LUMO (lowest unoccupied molecular orbital) gap formed at an organic–metal interface are classified as a chemisorption-induced gap state (CIGS) and a complex-based gap state (CBGS). The CIGS is further characterized by an asymptotic feature of the metal wave function in the chemisorbed species. The CIGSs in alkanethiolates on Pt(1 1 1) and C{sub 60} on Pt(1 1 1) can be regarded as damping and propagating types, respectively. The CBGSs in K-doped dibenzopentacene (DBP) are composed of DBP-derived MOs and K sp states and distributed over the complex film. No metallic structures were found in the K{sub 1}DBP and K{sub 3}DBP phases, suggesting that they are Mott–Hubbard insulators due to strong electron correlation. The local electronic structures of a pentacene film bridged by Au electrodes under bias voltages were examined by an FET-like specimen. The pentacene-derived bands were steeply shifted at the positively biased electrode, reflecting the p-type character of the film.

  4. Biomechanics of subcellular structures by non-invasive Brillouin microscopy

    Science.gov (United States)

    Antonacci, Giuseppe; Braakman, Sietse

    2016-11-01

    Cellular biomechanics play a pivotal role in the pathophysiology of several diseases. Unfortunately, current methods to measure biomechanical properties are invasive and mostly limited to the surface of a cell. As a result, the mechanical behaviour of subcellular structures and organelles remains poorly characterised. Here, we show three-dimensional biomechanical images of single cells obtained with non-invasive, non-destructive Brillouin microscopy with an unprecedented spatial resolution. Our results quantify the longitudinal elastic modulus of subcellular structures. In particular, we found the nucleoli to be stiffer than both the nuclear envelope (p biomechanics and its role in pathophysiology.

  5. Neptunium 237 behaviour in subcellular fractions of rat kidneys

    International Nuclear Information System (INIS)

    Kreslov, V.V.; Maksutova, A.Ya.; Mushkacheva, G.S.

    1978-01-01

    Subcellular distribution of intravenously injected (1 and 0.5 μCi/rat) neptunium nitrate (5- and 6-valent) in kidneys of rat males and females has been investigated. It has been shown that the radionuclide was unevenly distributed within the cell. As early as 24 hours after administration, about 50 per cent of neptunium were concentrated in the mitochondrial fraction. The data are presented on variations in neptunium behaviour within subcellular fractions of rat kidneys depending on the sex of animals, valency and dose of the isotope

  6. Tests to evaluate public health disease reporting systems in local public health agencies (electronic resource)

    National Research Council Canada - National Science Library

    Ricci, Karen; Lurie, Nicole; Stoto, Michael A; Wasserman, Jeffrey; Dausey, David J; Meade, Barbara; Diamond, Alexis; Molander, Roger C

    2005-01-01

    ... to evaluate the ability to receive and respond to case reports 24 hours a day, 7 days a week. We refined these tests by beta-testing them at 20 metropolitan area local public health agencies across the country over the course of 10 months. The contents of this manual will be of interest to public health professionals at the state and local l...

  7. Local versus global electronic properties of chalcopyrite alloys: X-ray absorption spectroscopy and ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sarmiento-Pérez, Rafael; Botti, Silvana, E-mail: silvana.botti@univ-lyon1.fr [Institut Lumière Matière and ETSF, UMR5306 Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne Cedex (France); Schnohr, Claudia S., E-mail: c.schnohr@uni-jena.de [Institut für Festkörperphysik, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, 07743 Jena (Germany); Lauermann, Iver [Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner Platz 1, 14109 Berlin (Germany); Rubio, Angel [Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de Física de Materiales, Centro de Física de Materiales CSIC-MPC and DIPC, Universidad del País Vasco UPV/EHU, Avenida de Tolosa 72, E-20018 San Sebastián (Spain); Fritz Haber Institute, Max Planck Society, Faradayweg 4-6, 14195 Berlin (Germany); Johnson, Benjamin, E-mail: benjamin.johnson@alumni.tu-berlin.de [Fritz Haber Institute, Max Planck Society, Faradayweg 4-6, 14195 Berlin (Germany)

    2014-09-07

    Element-specific unoccupied electronic states of Cu(In, Ga)S{sub 2} were studied as a function of the In/Ga ratio by combining X-ray absorption spectroscopy with density functional theory calculations. The S absorption edge shifts with changing In/Ga ratio as expected from the variation of the band gap. In contrast, the cation edge positions are largely independent of composition despite the changing band gap. This unexpected behavior is well reproduced by our calculations and originates from the dependence of the electronic states on the local atomic environment. The changing band gap arises from a changing spatial average of these localized states with changing alloy composition.

  8. Real-space local polynomial basis for solid-state electronic-structure calculations: A finite-element approach

    International Nuclear Information System (INIS)

    Pask, J.E.; Klein, B.M.; Fong, C.Y.; Sterne, P.A.

    1999-01-01

    We present an approach to solid-state electronic-structure calculations based on the finite-element method. In this method, the basis functions are strictly local, piecewise polynomials. Because the basis is composed of polynomials, the method is completely gener