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Sample records for subcellular fractionation studies

  1. Distribution, isomerization and enantiomer selectivity of hexabromocyclododecane (HBCD) diastereoisomers in different tissue and subcellular fractions of earthworms.

    Science.gov (United States)

    Li, Bing; Chen, Hao; Sun, Hongwen; Lan, Zhonghui

    2017-05-01

    In this study, earthworms Eisenia fetida (E. fetida) were exposed to a soil artificially contaminated with individual hexabromocyclododecane (HBCD) diastereoisomers (α-, β- and γ-HBCDs) to investigate the distribution, isomerization and enantiomer selectivity of HBCDs at tissue and subcellular levels. At the tissue level, the concentrations of HBCDs all followed the order of gut>bodyfluid>body wall, which suggested that earthworms accumulated HBCDs mainly via ingesting soil particles. At the subcellular level, the concentrations of HBCDs in an extracellular fraction consisting of granules, tissue fragment, cell membrane and intact cells (fraction A) were higher than those in an intracellular fractions consisting of the microsomal and cytosol (fraction B+C). This confirmed the passive diffusion during the distribution of HBCDs into the intracellular compartment. The distribution proportions of HBCDs varied among different tissue and subcellular fractions, and all changed over time within 14 days. The variable distributions of HBCDs in different fractions were a result of the comprehensive effects of dynamics and thermodynamics processes. The β- and γ-HBCDs were isomerized to α-HBCD in all tissue and subcellular fractions except for fraction C, and the isomerization ratios varied a lot, which seemed to be related to HBCDs residence time. The selective enrichment of (-) α-, (-) β and (-) γ-HBCDs was found in all fractions and this is consistent with that in the whole earthworm. Besides, the extents of enantio-selectivity did not change significantly among different tissue and subcellular fractions. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Chagas' disease: humoral response to subcellular fraction of Trypanosoma cruzi in symptomatic and asymptomatic patients.

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    de Titto, E H; Moreno, M; Braun, M; Segura, E L

    1987-09-01

    The capacity of antibodies in serum from individuals with chronic Chagas' disease to react with antigens in different subcellular fractions of Trypanosoma cruzi varied according to the clinical status of the patients. Antibodies in serum of asymptomatic patients were directed mostly against antigens in the citosol of the parasite, whereas in overtly cardiopathic patients antibodies were directed mostly against antigens in the microsomal fractions.

  3. Metabolism of the environmental toxicant benzo(a)pyrene by subcellular fractions of human ovary

    Science.gov (United States)

    Rekhadevi, PV; Diggs, DL; Huderson, AC; Harris, KL; Archibong, AE; Ramesh, A

    2014-01-01

    Knowledge of the ability of the female reproductive system to metabolize environmental chemicals is critical not only from the standpoint of toxicity but also from infertility risk assessment. Benzo(a)pyrene (BaP) is a toxicant that is released into the environment from automobile exhausts, cigarette smoke, burning of refuse, industrial emissions, and hazardous waste sites. In exposed animals, BaP becomes activated to reactive meta-bolites that interfere with target organ function and as a consequence cause toxicity. Studies on animal models conducted in our laboratories and those of others have shown that BaP possess endocrine disrupting properties. Thus, this chemical has the potential to cause infertility and cancers in the female genital tract. An understanding of BaP metabolism in the female reproductive system will be of importance in the diagnosis and management of female fertility as well as cancers in the reproductive tissues. Therefore, the objective of our study was to examine the metabolism of BaP by human ovarian subcellular fractions. Human ovary samples (eight individuals) were obtained from postoperative tissue removed from subjects with uterine tumors. Sub-cellular fractions (nuclear, cytosolic, mitochondrial, and microsomal) were prepared by differential centrifugation. BaP (1 μM and 3 μM) was individually incubated with individual subcellular fractions for 15 min and the products were analyzed by high-performance liquid chromatography. Among the different fractions tested, microsomal BaP metabolism was higher than the rest of the fractions. The BaP metabolites identified were as follows: BaP-9,10-diol, BaP-4,5-diol, BaP-7,8-diol, 9(OH) BaP, 3(OH) BaP, BaP-1,6-dione, BaP-3,6-dione, and BaP-6,12-dione. Of interest was the presence of DNA-reactive metabolites such as BaP-3,6-dione, BaP-6,12-dione, and BaP 7,8-diol, which have been implicated in the causation of infertility and cancer. Our results indicate that women who are exposed to BaP via

  4. Absorption Kinetics and Subcellular Fractionation of Zinc in Winter Wheat in Response to Nitrogen Supply

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    Zhaojun Nie

    2017-08-01

    Full Text Available Nitrogen (N is critical for zinc (Zn absorption into plant roots; this in turn allows for Zn accumulation and biofortification of grain in winter wheat (Triticum aestivum L., an important food crop. However, little is known about root morphology and subcellular Zn distribution in response to N treatment at different levels of Zn supply. In this study, two nutrient solution culture experiments were conducted to examine Zn accumulation, Zn absorption kinetics, root morphology, and Zn subcellular distribution in wheat seedlings pre-cultured with different N concentrations. The results showed positive correlations between N and Zn concentrations, and N and Zn accumulation, respectively. The findings suggested that an increase in N supply enhanced root absorption and the root-to-shoot transport of Zn. Nitrogen combined with the high Zn (Zn10 treatment increased the Zn concentration and consequently its accumulation in both shoots and roots. The maximum influx rate (Vmax, root length, surface area, and volume of 14-d-old seedlings, and root growth from 7 to 14 d in the medium N (N7.5 treatment were higher, but the Michaelis constant (Km and minimum equilibrium concentrations (Cmin in this treatment were lower than those in the low (N0.05 and high (N15 N treatments, when Zn was supplied at a high level (Zn10. Meanwhile, there were no pronounced differences in the above root traits between the N0.05Zn0 and N7.5Zn10 treatments. An increase in N supply decreased Zn in cell walls and cell organelles, while it increased Zn in the root soluble fraction. In leaves, an increase in N supply significantly decreased Zn in cell walls and the soluble fraction, while it increased Zn in cell organelles under Zn deficiency, but increased Zn distribution in the soluble fraction under medium and high Zn treatments. Therefore, a combination of medium N and high Zn treatments enhanced Zn absorption, apparently by enhancing Zn membrane transport and stimulating root

  5. Subcellular fractionation associated to radionuclide analysis in various tissues: validation of the technique by using light and electron observations applied on gills bivalves and uranium

    Energy Technology Data Exchange (ETDEWEB)

    Camilleri, V.; Simon, O.; Grasset, G. [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 metal bioaccumulation levels in target-organs associated with micro-localization approaches at the subcellular level provide information for the understanding of the metabolic metal cycle. These findings could be used to select relevant bio-markers of exposure and to focus on specific contaminated organelles to study potential biological effects. Moreover, the metal accumulated in the cytosol fraction can be bound to macromolecules in order to be eliminated and/or to induce a potential cellular effect. Tissular distribution, transfer efficiency from water and subcellular fractionation were investigated on the freshwater bivalve, Corbicula fluminea after uranium aqueous exposure. The subcellular fractionation was performed while measuring associated uranium to each cellular different fraction as follows: cellular debris and nuclei, mitochondria and lysosomes, membranes, microsomes and cytosol. In our experimental conditions, the accumulation in the cytosol fraction was low and more than 80 % of the total uranium in gills and visceral mass was accumulated in the insoluble fraction. Main results presented in this poster come from light and electron microscope observations of subcellular fractions (nuclei/debris and lysosomes/mitochondria) in order to validate the efficiency of the fractionation technique. An adaptation of the fractionation technique is proposed. This set of data confirms high differences of fractionation efficiency as a function of fractionation technique and organs/biological model used (gills of bivalves, digestive gland of crayfish). (author)

  6. Glycoproteomics of Trypanosoma cruzi trypomastigotes using subcellular fractionation, lectin affinity, and stable isotope labeling.

    Science.gov (United States)

    Atwood, James A; Minning, Todd; Ludolf, Fernanda; Nuccio, Arthur; Weatherly, Daniel B; Alvarez-Manilla, Gerardo; Tarleton, Rick; Orlando, Ron

    2006-12-01

    Herein we detail the first glycoproteomic analysis of a human pathogen. We describe an approach that enables the identification of organelle and cell surface N-linked glycoproteins from Trypanosoma cruzi, the causative agent of Chagas' disease. This approach is based on a subcellular fractionation protocol to produce fractions enriched in either organelle or plasma membrane/cytoplasmic proteins. Through lectin affinity capture of the glycopeptides from each subcellular fraction and stable isotope labeling of the glycan attachment sites with H(2)18O, we unambiguously identified 36 glycosylation sites on 35 glycopeptides which mapped to 29 glycoproteins. We also present the first expression evidence for 11 T. cruzi specific glycoproteins and provide experimental data indicating that the mucin associated surface protein family (MASP) and dispersed gene family (DGF-1) are post-translationally modified by N-linked glycans.

  7. Phosphatidic acid phosphatase activity in subcellular fractions of normal and dystrophic human muscle.

    Science.gov (United States)

    Kunze, D; Rüstow, B; Olthoff, D; Jung, K

    1985-03-15

    Biopsy samples from normal and dystrophic human muscle (Duchenne type) were fractionated by differential centrifugation and microsomes, mitochondria and cytosol were assayed for phosphatidic acid phosphatase (EC 3.1.3.4) and marker enzymes of mitochondria and cytosol. The activity of phosphatidic acid phosphatase was significantly lower in microsomes and higher in cytosol and mitochondria of dystrophic muscle than in the corresponding subcellular fractions of normal muscle. The results support an explanation of earlier findings that there is reduced G3P incorporation into diglycerides and phosphatidylcholine and a qualitative and quantitative change in the amount of phosphatidylcholine in dystrophic microsomes. The possible reasons for the reduction in the activity of only microsomal PA-P-ase were discussed.

  8. Programmed subcellular release to study the dynamics of cell detachment

    Science.gov (United States)

    Wildt, Bridget

    Cell detachment is central to a broad range of physio-pathological changes however there are no quantitative methods to study this process. Here we report programmed subcellular release, a method for spatially and temporally controlled cellular detachment and present the first quantitative results of the detachment dynamics of 3T3 fibroblasts at the subcellular level. Programmed subcellular release is an in vitro technique designed to trigger the detachment of distinct parts of a single cell from a patterned substrate with both spatial and temporal control. Subcellular release is achieved by plating cells on an array of patterned gold electrodes created by standard microfabrication techniques. The electrodes are biochemically functionalized with an adhesion-promoting RGD peptide sequence that is attached to the gold electrode via a thiol linkage. Each electrode is electrically isolated so that a subcellular section of a single cell spanning multiple electrodes can be released independently. Upon application of a voltage pulse to a single electrode, RGD-thiol molecules on an individual electrode undergo rapid electrochemical desorption that leads to subsequent cell contraction. The dynamics of cell contraction are found to have characteristic induction and contraction times. This thesis presents the first molecular inhibition studies conducted using programmed subcellular release verifying that this technique can be used to study complex signaling pathways critical to cell motility. Molecular level dynamics of focal adhesion proteins and actin stress fibers provide some insight into the complexities associated with triggered cell detachment. In addition to subcellular release, the programmed release of alkanethiols provides a tool for to study the spatially and temporally controlled release of small molecules or particles from individually addressable gold electrodes. Here we report on experiments which determine the dynamics of programmed release using fluorophore

  9. Distribution and Characterization of Antigens Found in Subcellular Fractions of African Trypanosomes.

    Science.gov (United States)

    1979-08-01

    Islation of bodies % containing the cyanide insensitive glycerophosphate oxidase of Trypanosoma - equiperdum . Comp. Biochem. Physiol. 30 1049-1054. S...commenced on a project aimed at characterizing the subcellular distribution and nature of antigens found in the African trypanosome, Trypanosoma rhodesiense...current project concerning the subcellular distribution and characterization of antigens in the African trypanosome, Trypanosoma rhodesiense. During

  10. Experimental Leishmania (L.) amazonensis leishmaniasis: characterization and immunogenicity of subcellular fractions.

    Science.gov (United States)

    do Valle, T Zaverucha; Gaspar, E B; Souza-Lemos, C; Souza, C S F; Márquez, F B Zamora; Baetas-da-Cruz, W; d'Escofier, L N; Côrte-Real, S; Calabrese, K S; da Costa, S C Gonçalves

    2007-01-01

    A technique developed in Trypanosoma cruzi biochemical studies was successfully used to fractionate Leishmania (Leishmania) amazonensis promastigotes. Ultrastructural analyses revealed a membrane fraction (MF) associated to subpellicular microtubules, a ribosomal-rich microsomal fraction (MicF), and a flagellar fraction (FF) free of associated membrane. All fractions proved to be immunogenic through delayed type hypersensitivity reaction assays. Therefore, a protocol was designed to test whether these fractions could elicit a protective response in mice infected by L. (L), amazonensis. The protocol consisted of a BCG injection (as cellular immunity inducer), followed by cyclophosphamide (once its cytotoxic effect is over, this immunosuppressor can increase the number of circulating leukocytes), then an injection with one of the fractions followed by a challenge. When compared to infected control animals, mice injected with any of the fractions presented a smaller footpad swelling, especially those injected with MicF or FF. Macroscopically, immunized mice under modulation by BCG presented no swelling. Histopathological studies performed on day 120 revealed fewer amastigotes and more intense inflammation in lesions of MicF and FF injected mice. Animals injected with MF presented an intermediate pattern. Parasite quantification corroborated these results. The results show that all fractions are potent immunostimulators, but MicF and FF have the strongest protective ability.

  11. Distribution of the intracellular Ca(2+)-ATPase isoform 2b in pig brain subcellular fractions and cross-reaction with a monoclonal antibody raised against the enzyme isoform.

    Science.gov (United States)

    Salvador, J M; Berengena, M; Sepúlveda, M R; Mata, A M

    2001-04-01

    The presence and distribution of sarco-endoplasmic reticulum Ca(2+)-ATPase (SERCA) isoform 2b in microsomes and other subcellular fractions isolated from pig brain has been demonstrated by the combined use of a specific antibody raised against the SERCA2b isoform and ATP phosphorylation experiments. All subcellular fractions show an approximately 110 kDa phosphorylated protein, the band intensity being stronger in microsomes. Preliminary treatment of the samples with trypsin generates two phosphorylated fragments of about 57 and 33 kDa in the presence of Ca(2+). The observed fragments are typical trypsinized products of the SERCA2b isoform. The monoclonal antibody Y/1F4 raised against the sarcoplasmic reticulum Ca(2+)-ATPase (isoform 1) binds to the 110 kDa band in membranes isolated from brain. The binding was stronger in microsomes than in other fractions. Furthermore, this antibody also recognizes a clear band at around 115 kDa. This band is always stronger in plasma membrane than in synaptosomes or microsomes and is unaffected by trypsin. Phosphorylation studies in the absence of Ca(2+) suggest that the 115 kDa protein is not a Ca(2+)-ATPase.

  12. Studies on the subcellular localization of the porphycene CPO.

    Science.gov (United States)

    Kessel, David; Conley, Mary; Vicente, M Graça H; Reiners, John J

    2005-01-01

    This study was designed to provide more detailed information on the subcellular sites of binding of the porphycene, termed 9-capronyloxytetrakis (methoxyethyl) porphycene (CPO), with a fluorescence resonance energy transfer (FRET) technique. The proximity of CPO to two fluorescent probes was determined: nonyl acridine orange (NAO), a dye with specific affinity for the mitochondrial lipid cardiolipin, and dihexa-oxacarbocyanine iodide (DiOC6), an agent that labels the endoplasmic reticulum (ER). FRET spectra indicated energy transfer between DiOC6 and CPO but no significant transfer between NAO and CPO. These results confirm data obtained by fluorescence microscopy, suggesting a similar pattern of subcellular localization by CPO and DiOC6 but not by CPO and NAO. However, when cells containing CPO were irradiated and then loaded with NAO, FRET between the two fluorophores was observed. Hence, a relocalization of CPO can occur during irradiation. These data provide an explanation for recent studies on CPO-catalyzed photodamage to both ER and mitochondrial Bcl-2.

  13. Studies on the Subcellular Localization of the Porphycene CPO¶

    Science.gov (United States)

    Kessel, David; Conley, Mary; Vicente, M. Graça H.; Reiners, John J.

    2010-01-01

    This study was designed to provide more detailed information on the subcellular sites of binding of the porphycene, termed 9-capronyloxytetrakis (methoxyethyl) porphycene (CPO), with a fluorescence resonance energy transfer (FRET) technique. The proximity of CPO to two fluorescent probes was determined: nonyl acridine orange (NAO), a dye with specific affinity for the mitochondrial lipid cardiolipin, and dihexaoxacarbocyanine iodide (DiOC6), an agent that labels the endoplasmic reticulum (ER). FRET spectra indicated energy transfer between DiOC6 and CPO but no significant transfer between NAO and CPO. These results confirm data obtained by fluorescence microscopy, suggesting a similar pattern of subcellular localization by CPO and DiOC6 but not by CPO and NAO. However, when cells containing CPO were irradiated and then loaded with NAO, FRET between the two fluorophores was observed. Hence, a relocalization of CPO can occur during irradiation. These data provide an explanation for recent studies on CPO-catalyzed photodamage to both ER and mitochondrial Bcl-2. PMID:15745423

  14. Distribution and Characterization of Antigens Found in Subcellular Fractions of African Trypanosomes.

    Science.gov (United States)

    1981-08-01

    Recent studies have been reported for Trypanosoma cruzi (Gonzalez Cappa et al, 1980) but were mainly concerned with establishing the antigenicity of...fractions in the presence of 0.5% Triton X-100 10.1% Zwittergent. For both A and B anti Pb IgG was used. (A) Demonstration of acid phosphatase activity ...demonstration of cysosomal proteolytic activity . Nature 224:279-281. Bawden, M.P. 1975. Whence comes Trypanosoma lewisi antigen which induces ablastic antibody

  15. Nitric oxide measurements in hTERT-RPE cells and subcellular fractions exposed to low levels of red light

    Science.gov (United States)

    Wigle, Jeffrey C.; Castellanos, Cherry C.; Denton, Michael L.; Holwitt, Eric A.

    2014-02-01

    Cells in a tissue culture model for laser eye injury exhibit increased resistance to a lethal pulse of 2.0-μm laser radiation if the cells are first exposed to 2.88 J/cm2 of red light 24 hr prior to the lethal laser exposure. Changes in expression of various genes associated with apoptosis have been observed, but the biochemical link between light absorption and gene expression remains unknown. Cytochome c oxidase (CCOX), in the electron transport chain, is the currentlyhypothesized absorber. Absorption of the red light by CCOX is thought to facilitate displacement of nitric oxide (NO) by O2 in the active site, increasing cellular respiration and intracellular ATP. However, NO is also an important regulator and mediator of numerous physiological processes in a variety of cell and tissue types that is synthesized from l-arginine by NO synthases. In an effort to determine the relative NO contributions from these competing pathways, we measured NO levels in whole cells and subcellular fractions, with and without exposure to red light, using DAF-FM, a fluorescent dye that stoichiometrically reacts with NO. Red light induced a small, but consistently reproducible, increase in fluorescence intensity in whole cells and some subcellular fractions. Whole cells exhibited the highest overall fluorescence intensity followed by (in order) cytosolic proteins, microsomes, then nuclei and mitochondria.

  16. Nifurtimox biotransformation to reactive metabolites or nitrite in liver subcellular fractions and model systems.

    Science.gov (United States)

    Montalto de Mecca, M; Diaz, E G; Castro, J A

    2002-11-15

    Liver microsomal (mic); nuclei (N) and mitochondria (mit) anaerobically nitroreduce Nifurtimox (Nfx) in the presence of NADPH generating system. Simultaneous formation of small amounts of nitrite was observed in microsomes and nuclei but not in mitochondria. The microsomal nitroreductase activity was enhanced by the presence of flavine-adenine-dinucleotide disodium salt (FAD), was not inhibited by CO and was significantly inhibited by diphenyleneiodonium (DPI). In the microsomal NADPH-dependent fraction nitrite formation was null in the presence of FAD, DPI and under air and was partially inhibited by pure CO. Pure human cytochrome P450 reductase in the presence of NADPH significantly nitroreduced Nfx and produced small amounts of nitrite. The nitroreductive process was significantly enhanced by FAD but the nitrite formation became null. FAD itself was able to chemically nitroreduce Nfx without production of nitrite. NADPH generating system enhanced the FAD nitroreductive effect and led to small production of nitrite. Formation of reactive metabolites and nitric oxide during Nfx metabolism might contribute to its toxicity.

  17. Glycolytic pathway (GP), kreb's cycle (KC), and hexose monophosphate shunt (HMS) activity in myocardial subcellular fractions exposed to cannabinoids

    Energy Technology Data Exchange (ETDEWEB)

    Watson, A.T.; Manno, B.R.; King, J.W.; Fowler, M.R.; Dempsey, C.A.; Manno, J.E.

    1986-03-05

    Delta-9-tetrahydrocannabinol (..delta../sup 9/-THC), the primary psychoactive component of marihuana, and its active metabolite 11-hydroxy-..delta../sup 9/-tetrahydrocannabinol (11-OH-..delta../sup 9/-THC) have been reported to produce a direct cardiac depressant effect. Studies in isolated perfused rat hearts have indicated a decreased force of contraction (inotropic response) when ..delta../sup 9/-THC or 11-OH-..delta../sup 9/-THC was administered in microgram amounts. The mechanism and site of action have not been explained or correlated with associated metabolic pathways. The purpose of this study was to investigate the effects of cannabinoids on major myocardial energy producing pathways, GP and KC, and a non-energy producing pathway, HMS. Cardiac ventricular tissue from male Sprague-Dawley rats (250-300 g) was excised and homogenized for subcellular fractionation. KC, GP and HMS activity was assayed in the appropriate fractions by measuring /sup 14/CO/sub 2/ generation from /sup 14/C-2-pyruvate, /sup 14/C-6-glucose and /sup 14/C-1-glucose respectively. Duplicate assays (n=8) were performed on tissue exposed to saline (control), empty liposomes (vehicle) and four doses each of ..delta../sup 9/-THC and 11-OH-..delta../sup 9/-THC. Changes in metabolic activity and decreases in cardiac contractile performance may be associated.

  18. Nerolidol and Farnesol Inhibit Some Cytochrome P450 Activities but Did Not Affect Other Xenobiotic-Metabolizing Enzymes in Rat and Human Hepatic Subcellular Fractions

    Directory of Open Access Journals (Sweden)

    Alena Špičáková

    2017-03-01

    Full Text Available Sesquiterpenes, 15-carbon compounds formed from three isoprenoid units, are the main components of plant essential oils. Sesquiterpenes occur in human food, but they are principally taken as components of many folk medicines and dietary supplements. The aim of our study was to test and compare the potential inhibitory effect of acyclic sesquiterpenes, trans-nerolidol, cis-nerolidol and farnesol, on the activities of the main xenobiotic-metabolizing enzymes in rat and human liver in vitro. Rat and human subcellular fractions, relatively specific substrates, corresponding coenzymes and HPLC, spectrophotometric or spectrofluorometric analysis of product formation were used. The results showed significant inhibition of cytochromes P450 (namely CYP1A, CYP2B and CYP3A subfamilies activities by all tested sesquiterpenes in rat as well as in human hepatic microsomes. On the other hand, all tested sesquiterpenes did not significantly affect the activities of carbonyl-reducing enzymes and conjugation enzymes. The results indicate that acyclic sesquiterpenes might affect CYP1A, CYP2B and CYP3A mediated metabolism of concurrently administered drugs and other xenobiotics. The possible drug–sesquiterpene interactions should be verified in in vivo experiments.

  19. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications

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    Huang Yong

    2009-11-01

    Full Text Available Abstract Background Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families. Results The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64% consisted of both mitochondrial and cytosolic (non-mitochondrial proteins (mt-cy families while the remaining 33 (36% were composed of mitochondrial proteins (mt-mt families. Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1 relocalization from mitochondria to cytosol, 2 from cytosol to mitochondria and 3 multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on

  20. Differential uptake and oxidative stress response in zebrafish fed a single dose of the principal copper and zinc enriched sub-cellular fractions of Gammarus pulex

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    Khan, Farhan R., E-mail: f.khan@nhm.ac.uk [Nutritional Sciences Division, King' s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH (United Kingdom); Bury, Nicolas R.; Hogstrand, Christer [Nutritional Sciences Division, King' s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH (United Kingdom)

    2010-09-15

    The sub-cellular compartmentalisation of trace metals and its effect on trophic transfer and toxicity in the aquatic food chain has been a subject of growing interest. In the present study, the crustacean Gammarus pulex was exposed to either 11 {mu}g Cu l{sup -1}, added solely as the enriched stable isotope {sup 65}Cu, or 660 {mu}g Zn l{sup -1}, radiolabeled with 2MBq {sup 65}Zn, for 16 days. Post-exposure the heat stable cytosol containing metallothionein-like proteins (MTLP) and a combined granular and exoskeletal (MRG + exo) fractions were isolated by differential centrifugation, incorporated into gelatin and fed to zebrafish as a single meal. Assimilation efficiency (AE) and intestinal lipid peroxidation, as malondialdehyde (MDA) were measured. There was a significant difference (p < 0.05) between the retention of the MTLP-Zn (39.0 {+-} 6.4%) and MRG + exo-Zn (17.2 {+-} 3.7%) and of this zinc retained by the zebrafish a significantly greater proportion of the MTLP-Zn feed had been transported away from the site of uptake. For {sup 65}Cu, although the results pointed towards greater bioavailability of the MTLP fraction compared to MRG + exo during the slow elimination phase (24-72 h) these results were not significant (p = 0.155). Neither zinc feed provoked a lipid peroxidation response in the intestinal tissue of zebrafish compared to control fish (gelatin fed), but both {sup 65}Cu labeled feeds did. The greater effect was exerted by the MRG + exo (2.96 {+-} 0.29 nmol MDA mg protein{sup -1}) feed which three-fold greater than control (p < 0.01) and almost twice the MDA concentration of the MTLP feed (1.76 {+-} 0.21 nmol MDA mg protein{sup -1}, p < 0.05). The oxidative stress response produced by Zn and Cu is in keeping with their respective redox potentials; Zn being oxidatively inert and Cu being redox active. These results are similar, in terms of bioavailability and stress response of each feed, to those in our previous study in which {sup 109}Cd labeled G

  1. Processing of the insulin-like growth factor-II-mannose 6-phosphate receptor in isolated liver subcellular fractions

    National Research Council Canada - National Science Library

    Tahiri K; Cam L; Desbuquois B; Chauvet G

    2001-01-01

    .... The receptor in plasma membrane fractions differed from that in Golgi-endosomal fractions by: (i) a lower molecular size upon reducing polyacrylamide gel electrophoresis (245 vs. 255 kDa); (ii...

  2. Subcellular localization and function study of a secreted phospholipase C from Nocardia seriolae.

    Science.gov (United States)

    Xia, Liqun; Liang, Haiying; Xu, Liang; Chen, Jianlin; Bekaert, Michaël; Zhang, Honglian; Lu, Yishan

    2017-09-15

    Fish nocardiosis is a chronic systemic granulomatous disease, and Nocardia seriolae is the main pathogen that causes it. The pathogenesis and virulence factors of N. seriolae are not fully understood. A phospholipase C (PLC), which is likely to be a secreted protein targeting host cell mitochondria, was found by a bioinformatics analysis of the whole genome sequence of N. seriolae. In order to determine the subcellular localization and study the preliminary function of PLC from N. seriolae (NsPLC), in this study gene cloning, secreted protein identification, subcellular localization in host cells and apoptosis detection of NsPLC were carried out. Mass spectrometry analysis of extracellular products from N. seriolae showed that NsPLC was a secreted protein. Subcellular localization of NsPLC-GFP fusion protein in fathead minnow (FHM) cells revealed that the green fluorescence exhibited a punctate distribution near the nucleus and did not co-localize with mitochondria. In addition, an apoptosis assay suggested that apoptosis was induced in FHM cells by the overexpression of NsPLC. This study may lay the foundations for further studies on the function of NsPLC and promote the understanding of the virulence factors and pathogenic mechanism of N. seriolae. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Growth-associated protein, GAP-43, a polypeptide that is induced when neurons extend axons, is a component of growth cones and corresponds to pp46, a major polypeptide of a subcellular fraction enriched in growth cones.

    OpenAIRE

    Meiri, K F; Pfenninger, K H; Willard, M B

    1986-01-01

    Growth-associated protein, GAP-43, is a polypeptide that is induced in neurons when they grow axons. We show by means of subcellular fractionation and immunohistochemical localization that GAP-43 is a component of neuronal growth cones as well as growing neurites; it is similar to a major phosphoprotein, pp46, of a growth cone-enriched subcellular fraction. These conclusions are consistent with the possibility that the induction of GAP-43/pp46 is an important event in the establishment of a p...

  4. STUDY OF SUBCELLULAR DISTRIBUTION OF CRYSTALLINE MESO-TETRA(3-PYRIDYLBACTERIOCHLORIN NANOPARTICLES

    Directory of Open Access Journals (Sweden)

    Yu. S. Maklygina

    2016-01-01

    Full Text Available The results of the study of subcellular distribution of molecular meso-tetra(3-pyridylbacteriochlorin nanocrystals proposed as therapeutic agents for photodynamic therapy are represented in the article. Investigations and measurement of spectroscopic properties of molecular crystals of near-infrared photosensitizer were conducted using special device complex based on fiber-optic spectrometer. Investigation and analysis of the pattern of subcellular accumulation of meso-tetra(3-pyridylbacteriochlorin in molecular (dimethyl sulfoxide (DMSO as solvent and nanocrystalline forms on different cell lines: human monocytes (THP-1, human cervical cancer cells (HeLa and mouse malignant brain tumor cells (glioma C6. The dynamics of subcellylar accumulation of the agent at concentration of 5 and 10 mg/l was assessed with laser microscope-spectrum analyzer and by confocal microscopy. The study showed that in the course of interaction with cell lines molecular nanocrystals of the agent developed ability to fluorescence. Hence, in the cellular environment meso-tetra(3-pyridyl bacteriochlorin nanoparticles became phototoxic giving opportunities for their use for fluorescence diagnosis and photodynamic therapy. Specific role of meso-tetra(3-pyridylbacteriochlorin in the range of photosensitizers is determined by its spectral characteristics, i.e. absorption and fluorescence in near-infrared band, which allows measuring and affecting on deeper layers of biotissue. Thus, the use of meso-tetra(3-pyridylbacteriochlorin nanoparticles as nanophotosensitizers may improve the efficacy of diagnosis and treatment of deep-seated tumors.

  5. Analysis of Subcellular RNA Fractions Revealed a Transcription-Independent Effect of Tumor Necrosis Factor Alpha on Splicing, Mediated by Spt5.

    Science.gov (United States)

    Diamant, Gil; Eisenbaum, Tal; Leshkowitz, Dena; Dikstein, Rivka

    2016-05-01

    The proinflammatory cytokine tumor necrosis factor alpha (TNF-α) modulates the expression of many genes, primarily through activation of NF-κB. Here, we examined the global effects of the elongation factor Spt5 on nascent and mature mRNAs of TNF-α-induced cells using chromatin and cytosolic subcellular fractions. We identified several classes of TNF-α-induced genes controlled at the level of transcription, splicing, and chromatin retention. Spt5 was found to facilitate splicing and chromatin release in genes displaying high induction rates. Further analysis revealed striking effects of TNF-α on the splicing of 25% of expressed genes; the vast majority were not transcriptionally induced. Splicing enhancement of noninduced genes by TNF-α was transient and independent of NF-κB. Investigating the underlying basis, we found that Spt5 is required for the splicing facilitation of the noninduced genes. In line with this, Spt5 interacts with Sm core protein splicing factors. Furthermore, following TNF-α treatment, levels of RNA polymerase II (Pol II) but not Spt5 are reduced from the splicing-induced genes, suggesting that these genes become enriched with a Pol II-Spt5 form. Our findings revealed the Pol II-Spt5 complex as a highly competent coordinator of cotranscriptional splicing. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  6. Studying subcellular detail in fixed astrocytes: Dissociation of morphologically intact glial cells (DIMIGs

    Directory of Open Access Journals (Sweden)

    Julia eHaseleu

    2013-05-01

    Full Text Available Studying the distribution of astrocytic antigens is particularly hard when they are localized in their fine, peripheral astrocyte processes (PAPs, since these processes often have a diameter comparable to vesicles and small organelles. The most appropriate technique is immunoelectron microscopy, which is, however, a time-consuming procedure. Even in high resolution light microscopy, antigen localization is difficult to detect due to the small dimensions of these processes, and overlay from antigen in surrounding non-glial cells. Yet, PAPs frequently display antigens related to motility and glia-synaptic interaction. Here, we describe the dissociation of morphologically intact glial cells (DIMIGs, permitting unambiguous antigen localization using epifluorescence microscopy. Astrocytes are dissociated from juvenile (p13-15 mouse cortex by applying papain treatment and cytospin centrifugation to attach the cells to a slide. The cells and their complete processes including the PAPs is thus projected in 2D. The entire procedure takes 2½-3 hours. We show by morphometry that the diameter of DIMIGs, including the PAPs is similar to that of astrocytes in situ. In contrast to cell culture, results derived from this procedure allow for direct conclusions relating to (i the presence of an antigen in cortical astrocytes, (ii subcellular antigen distribution, in particular when localized in the PAPs. The detailed resolution is shown in an exemplary study of the organization of the astrocytic cytoskeleton components actin, ezrin, tubulin, and GFAP. The distribution of connexin 43 in relation to a single astrocyte’s process tree is also investigated.

  7. Studying subcellular detail in fixed astrocytes: dissociation of morphologically intact glial cells (DIMIGs).

    Science.gov (United States)

    Haseleu, Julia; Anlauf, Enrico; Blaess, Sandra; Endl, Elmar; Derouiche, Amin

    2013-01-01

    Studying the distribution of astrocytic antigens is particularly hard when they are localized in their fine, peripheral astrocyte processes (PAPs), since these processes often have a diameter comparable to vesicles and small organelles. The most appropriate technique is immunoelectron microscopy, which is, however, a time-consuming procedure. Even in high resolution light microscopy, antigen localization is difficult to detect due to the small dimensions of these processes, and overlay from antigen in surrounding non-glial cells. Yet, PAPs frequently display antigens related to motility and glia-synaptic interaction. Here, we describe the dissociation of morphologically intact glial cells (DIMIGs), permitting unambiguous antigen localization using epifluorescence microscopy. Astrocytes are dissociated from juvenile (p13-15) mouse cortex by applying papain treatment and cytospin centrifugation to attach the cells to a slide. The cells and their complete processes including the PAPs is thus projected in 2D. The entire procedure takes 2.5-3 h. We show by morphometry that the diameter of DIMIGs, including the PAPs is similar to that of astrocytes in situ. In contrast to cell culture, results derived from this procedure allow for direct conclusions relating to (1) the presence of an antigen in cortical astrocytes, (2) subcellular antigen distribution, in particular when localized in the PAPs. The detailed resolution is shown in an exemplary study of the organization of the astrocytic cytoskeleton components actin, ezrin, tubulin, and GFAP. The distribution of connexin 43 in relation to a single astrocyte's process tree is also investigated.

  8. Second Study of Hyper-Fractionated Radiotherapy

    Directory of Open Access Journals (Sweden)

    R. Jacob

    1999-01-01

    Full Text Available Purpose and Method. Hyper-fractionated radiotherapy for treatment of soft tissue sarcomas is designed to deliver a higher total dose of radiation without an increase in late normal tissue damage. In a previous study at the Royal Marsden Hospital, a total dose of 75 Gy using twice daily 1.25 Gy fractions resulted in a higher incidence of late damage than conventional radiotherapy using 2 Gy daily fractions treating to a total of 60 Gy. The current trial therefore used a lower dose per fraction of 1.2 Gy and lower total dose of 72 Gy, with 60 fractions given over a period of 6 weeks.

  9. Aggregatory behaviour of platelets incubated with subcellular fractions of normal and chagasic human syncytiotrophoblast Comportamento agregatório das plaquetas incubadas com frações subcelulares de sinciciotrofoblasto humano normal e chagásico

    Directory of Open Access Journals (Sweden)

    A.R. Eynard

    1993-06-01

    Full Text Available The surface of human syncytiotrophoblast does not induce maternal blood platelet aggregation even though it is not an endothelium. It can be surmised that as occurs in endothelial injury the subcellular components of the syncytiotrophoblast may have pro-or antiaggregatory activity. During congenital Chagas' disease which is associated to trophoblast lesions, platelets may play a role in the development of T. cruzi-induced placentitis. In the present work the aggregatory behaviour of normal human blood platelets was recorded after their challenging with subcellular fractions of syncytiotrophoblast isolated from normal and chagasic women. Nuclear, Mitochondrial, Microsomal and Supernatant fractions isolated from normal and chagasic syncytiotrophoblast failed to induce per se any aggregatory reaction on platelets. When samples of platelet-rich plasma (PRP were preincubated with normal and chagasic nuclear fractions and then stimulated with collagen at threshold level (CT-PRP an inhibition of the aggregatory response was observed. Treatment of CT-PRP with normal and chagasic mitochondrial fractions induced inhibition of platelet aggregation whereas only chagasic fraction reduced latency time. Microsornal fraction from normal placentas showed no significant effects on platelet aggregation. It is concluded that subcellular fractions of normal human syncytiotrophoblast do not exhibit any effect on platelet aggregation, whereas those subcellular fractions enriched in intracellular membrane components isolated from chagasic placentas inhibit platelet aggregation.A superficie do sinciciotrofoblasto humano não induz agregação das plaquetas maternas apesar de não ser um endotélio. Lesões endoteliais propiciam o aparecimento de agregados plaquetários, o que nos leva a questionar se os componentes subcelulares do sinciciotrofoblasto também poderiam propiciar eventos semelhantes. Na doença de Chagas congênita, que está associada a lesões a nivel de

  10. Subcellular localization of leptin and leptin receptor in breast cancer detected in an electron microscopic study.

    Science.gov (United States)

    Al-Shibli, Saad M; Amjad, Nasser M; Al-Kubaisi, Muna K; Mizan, Shaikh

    2017-01-22

    Leptin (LEP) and leptin receptor (LEPR) have long been found associated with breast cancer. So far no high-resolution method such as electron microscopy has been used to investigate the subcellular localization of leptin and leptin receptor in breast cancer. We collected cancer and non-cancer breast tissues from 51 women with invasive ductal breast cancer. Leptin and leptin receptor in the tissues were estimated using immunohistochemistry (IHC). LEP and LEPR were localized at subcellular level by immunocytochemistry (ICC) using ultra-fine gold particle conjugated antibody, and visualized with transmission electron microscopy (TEM). IHC showed high presence of LEP and LEPR in 65% and 67% respectively of the breast cancer samples, 100% and 0% respectively of the adipose tissue samples, and no high presence in the non-cancer breast tissue samples. On TEM views both LEP and LEPR were found highly concentrated within the nucleus of the cancer cells, indicating that nucleus is the principal seat of action. However, presence of high concentration of LEP does not necessarily prove its over-expression, as often concluded, because LEP could be internalized from outside by LEPR in the cells. In contrast, LEPR is definitely over-expressed in the ductal breast cancer cells. Therefore, we hypothesize that over-expression of LEPR, rather than that of LEP has a fundamental role in breast carcinogenesis in particular, and probably for LEP-LEPR associated tumors in general. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Application of green fluorescent protein-labeled assay for the study of subcellular localization of Newcastle disease virus matrix protein.

    Science.gov (United States)

    Duan, Zhiqiang; Li, Qunhui; He, Liang; Zhao, Guo; Chen, Jian; Hu, Shunlin; Liu, Xiufan

    2013-12-01

    Green fluorescent protein (GFP) used as a powerful marker of gene expression in vivo has so far been applied widely in studying the localizations and functions of protein in living cells. In this study, GFP-labeled assay was used to investigate the subcellular localization of matrix (M) protein of different virulence and genotype Newcastle disease virus (NDV) strains. The M protein of ten NDV strains fused with GFP (GFP-M) all showed nuclear-and-nucleolar localization throughout transfection, whereas that of the other two strains were observed in the nucleus and nucleolus early in transfection but in the cytoplasm late in transfection. In addition, mutations to the previously defined nuclear localization signal in the GFP-M fusion protein were studied as well. Single changes at positions 262 and 263 did not affect nuclear localization of M, while changing both of these arginine residues to asparagine caused re-localization of M mainly to the cytoplasm. The GFP-M was validated as a suitable system for studying the subcellular localization of M protein and could be used to assist us in further identifying the signal sequences responsible for the nucleolar localization and cytoplasmic localization of M protein. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles.

    Science.gov (United States)

    Colcombet, Jean; Lopez-Obando, Mauricio; Heurtevin, Laure; Bernard, Clément; Martin, Karine; Berthomé, Richard; Lurin, Claire

    2013-01-01

    Four hundred and fifty-eight genes coding for PentatricoPeptide Repeat (PPR) proteins are annotated in the Arabidopsis thaliana genome. Over the past 10 years, numerous reports have shown that many of these proteins function in organelles to target specific transcripts and are involved in post-transcriptional regulation. Therefore, they are thought to be important players in the coordination between nuclear and organelle genome expression. Only four of these proteins have been described to be addressed outside organelles, indicating that some PPRs could function in post-transcriptional regulations of nuclear genes. In this work, we updated and improved our current knowledge on the localization of PPR proteins of Arabidopsis within the plant cell. We particularly investigated the subcellular localization of 166 PPR proteins whose targeting predictions were ambiguous, using a combination of high-throughput cloning and microscopy. Through systematic localization experiments and data integration, we confirmed that PPR proteins are largely targeted to organelles and showed that dual targeting to both the mitochondria and plastid occurs more frequently than expected. These results allow us to speculate that dual-targeted PPR proteins could be important for the fine coordination of gene expressions in both organelles.

  13. Using fluorescence lifetime microscopy to study the subcellular localization of anthocyanins.

    Science.gov (United States)

    Chanoca, Alexandra; Burkel, Brian; Kovinich, Nik; Grotewold, Erich; Eliceiri, Kevin W; Otegui, Marisa S

    2016-12-01

    Anthocyanins are flavonoid pigments that accumulate in most seed plants. They are synthesized in the cytoplasm but accumulate inside the vacuoles. Anthocyanins are pigmented at the lower vacuolar pH, but in the cytoplasm they can be visualized based on their fluorescence properties. Thus, anthocyanins provide an ideal system for the development of new methods to investigate cytoplasmic pools and association with other molecular components. We have analyzed the fluorescence decay of anthocyanins by fluorescence lifetime imaging microscopy (FLIM), in both in vitro and in vivo conditions, using wild-type and mutant Arabidopsis thaliana seedlings. Within plant cells, the amplitude-weighted mean fluorescence lifetime (τm ) correlated with distinct subcellular localizations of anthocyanins. The vacuolar pool of anthocyanins exhibited shorter τm than the cytoplasmic pool. Consistently, lowering the pH of anthocyanins in solution shortened their fluorescence decay. We propose that FLIM is a useful tool for understanding the trafficking of anthocyanins and, potentially, for estimating vacuolar pH inside intact plant cells. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  14. Numerical study of fractional nonlinear Schrodinger equations

    KAUST Repository

    Klein, Christian

    2014-10-08

    Using a Fourier spectral method, we provide a detailed numerical investigation of dispersive Schrödinger-type equations involving a fractional Laplacian in an one-dimensional case. By an appropriate choice of the dispersive exponent, both mass and energy sub- and supercritical regimes can be identified. This allows us to study the possibility of finite time blow-up versus global existence, the nature of the blow-up, the stability and instability of nonlinear ground states and the long-time dynamics of solutions. The latter is also studied in a semiclassical setting. Moreover, we numerically construct ground state solutions of the fractional nonlinear Schrödinger equation.

  15. Study of acetowhitening mechanisms in live mammalian cells with label-free subcellular-level multimodal nonlinear optical microscopy

    Science.gov (United States)

    Lin, Jian; Teh, Sengkhoon; Zheng, Wei; Wang, Zi; Huang, Zhiwei

    2015-03-01

    The tissue acetowhitening effect in acetic acid instillation procedure is a simple and economic method for neoplasia detection and has been clinically utilized since 1925. It is suspected that the optical property (e.g. scattering) change in acetowhitening is due to coagulation of intracellular proteins, but no experimental proof has been reported yet. In this work, we use third-harmonic generation (THG) and two-photon excited fluorescence (TPEF) to investigate the acetowhitening phenomenon induced by acidic acid in live mammalian cells without labeling. We studied the acetowhitening effect with different acetic acid concentrations and the co-localized TPEF and THG imaging on tryptophan and NADH at subcellular-level reveals that the acetowhitening phenomenon is highly related with proteins involved in metabolic pathways in the nucleus and cytoplasm in live cells.

  16. Subcellular Fractionation of Human Neutrophils and Analysis of Subcellular Markers

    DEFF Research Database (Denmark)

    Clemmensen, Stine Novrup; Udby, Lene; Borregaard, Niels

    2014-01-01

    The neutrophil has long been recognized for its impressive number of cytoplasmic granules that harbor proteins indispensable for innate immunity. Analysis of isolated granules has provided important information on how the neutrophil grades its response to match the challenges it meets on its...

  17. Intracellular And Subcellular Partitioning Of Nickel In Aureococcus Anophagefferens

    Science.gov (United States)

    Wang, B.; Axe, L.; Wei, L.; Bagheri, S.; Michalopoulou, Z.

    2008-12-01

    Brown tides are caused by Aureococcus anophagefferens, a species of Pelagophyceae, and have been observed in NY/NJ waterways effecting ecosystems by attenuating light, changing water color, reducing eelgrass beds, decreasing shellfisheries, and further impacting the food web by reducing phytoplankton. Although the impact of macronutrients and iron on A. anophagefferens has been well studied, contaminants, and specifically trace metals have not. In long-term experiments designed to investigate the growth and toxicity, Cd, Cu, Ni, and Zn exposure was evaluated over 10-13 to 10-7 M for the free metal ion. While growth was inhibited or terminated from exposure to Cd and Cu, nickel addition ([Ni2+]: 10-11.23 to 10-10.23 M) promoted A. anophagefferens growth. Short-term experiments are being conducted to better understand mechanistically nickel speciation and distribution. Both total intracellular and subcellular metal concentrations are being assessed with radio-labeled 63Ni. Subcellular fractions are defined as metal-sensitive fractions (MSF) constituting organelles, cell debris, and heat-denatured protein [HDP] and biologically detoxified metal comprising heat-stabilized protein [HSP] and metal-rich granules [MRG]. Based on subcellular distribution, aqueous [Ni2+] concentrations, and A. anophagefferens growth rates, potential reaction pathways promoting A. anophagefferens growth can be addressed.

  18. Single fraction versus multiple fraction radiotherapy for palliation of painful vertebral bone metastases: A prospective study

    Directory of Open Access Journals (Sweden)

    Dipanjan Majumder

    2012-01-01

    Conclusions: Different fractionation of radiation has same response and toxicity in treatment of vertebral bone metastasis. Single fraction RT may be safely used to treat these cases as this is more cost effective and less time consuming. Studies may be conducted to find out particular subgroup of patients to be benefitted more by either fractionation schedule; however, our study cannot comment on that issue.

  19. Ischemia-related subcellular redistribution of sodium channels enhances the proarrhythmic effect of class I antiarrhythmic drugs: a simulation study.

    Directory of Open Access Journals (Sweden)

    Kunichika Tsumoto

    Full Text Available Cardiomyocytes located at the ischemic border zone of infarcted ventricle are accompanied by redistribution of gap junctions, which mediate electrical transmission between cardiomyocytes. This ischemic border zone provides an arrhythmogenic substrate. It was also shown that sodium (Na+ channels are redistributed within myocytes located in the ischemic border zone. However, the roles of the subcellular redistribution of Na+ channels in the arrhythmogenicity under ischemia remain unclear.Computer simulations of excitation conduction were performed in a myofiber model incorporating both subcellular Na+ channel redistribution and the electric field mechanism, taking into account the intercellular cleft potentials.We found in the myofiber model that the subcellular redistribution of the Na+ channels under myocardial ischemia, decreasing in Na+ channel expression of the lateral cell membrane of each myocyte, decreased the tissue excitability, resulting in conduction slowing even without any ischemia-related electrophysiological change. The conventional model (i.e., without the electric field mechanism did not reproduce the conduction slowing caused by the subcellular Na+ channel redistribution. Furthermore, Na+ channel blockade with the coexistence of a non-ischemic zone with an ischemic border zone expanded the vulnerable period for reentrant tachyarrhythmias compared to the model without the ischemic border zone. Na+ channel blockade tended to cause unidirectional conduction block at sites near the ischemic border zone. Thus, such a unidirectional conduction block induced by a premature stimulus at sites near the ischemic border zone is associated with the initiation of reentrant tachyarrhythmias.Proarrhythmia of Na+ channel blockade in patients with old myocardial infarction might be partly attributable to the ischemia-related subcellular Na+ channel redistribution.

  20. A set of GFP-based organelle marker lines combined with DsRed-based gateway vectors for subcellular localization study in rice (Oryza sativa L.).

    Science.gov (United States)

    Wu, Tsung-Meng; Lin, Ke-Chun; Liau, Wei-Shiang; Chao, Yun-Yang; Yang, Ling-Hung; Chen, Szu-Yun; Lu, Chung-An; Hong, Chwan-Yang

    2016-01-01

    In the post-genomic era, many useful tools have been developed to accelerate the investigation of gene functions. Fluorescent proteins have been widely used as protein tags for studying the subcellular localization of proteins in plants. Several fluorescent organelle marker lines have been generated in dicot plants; however, useful and reliable fluorescent organelle marker lines are lacking in the monocot model rice. Here, we developed eight different GFP-based organelle markers in transgenic rice and created a set of DsRed-based gateway vectors for combining with the marker lines. Two mitochondrial-localized rice ascorbate peroxidase genes fused to DsRed and successfully co-localized with mitochondrial-targeted marker lines verified the practical use of this system. The co-localization of GFP-fusion marker lines and DsRed-fusion proteins provide a convenient platform for in vivo or in vitro analysis of subcellular localization of rice proteins.

  1. Using Femtosecond Laser Subcellular Surgery as a Tool to Study Cell Biology

    Energy Technology Data Exchange (ETDEWEB)

    Shen, N; Colvin, M E; Huser, T

    2007-02-27

    Research on cellular function and regulation would be greatly advanced by new instrumentation using methods to alter cellular processes with spatial discrimination on the nanometer-scale. We present a novel technique for targeting submicrometer sized organelles or other biologically important regions in living cells using femtosecond laser pulses. By tightly focusing these pulses beneath the cell membrane, we can vaporize cellular material inside the cell through nonlinear optical processes. This technique enables non-invasive manipulation of the physical structure of a cell with sub-micrometer resolution. We propose to study the role mitochondria play in cell proliferation and apoptosis. Our technique provides a unique tool for the study of cell biology.

  2. Studying subcellular detail in fixed astrocytes: Dissociation of morphologically intact glial cells (DIMIGs)

    OpenAIRE

    Julia eHaseleu; Enrico eAnlauf; Enrico eAnlauf; Sandra eBlaess; Elmar eEndl; Amin eDerouiche; Amin eDerouiche; Amin eDerouiche

    2013-01-01

    Studying the distribution of astrocytic antigens is particularly hard when they are localized in their fine, peripheral astrocyte processes (PAPs), since these processes often have a diameter comparable to vesicles and small organelles. The most appropriate technique is immunoelectron microscopy, which is, however, a time-consuming procedure. Even in high resolution light microscopy, antigen localization is difficult to detect due to the small dimensions of these processes, and overlay from a...

  3. Studying subcellular detail in fixed astrocytes: dissociation of morphologically intact glial cells (DIMIGs)

    OpenAIRE

    Haseleu, Julia; Anlauf, Enrico; Blaess, Sandra; Endl, Elmar; Derouiche, Amin

    2013-01-01

    Studying the distribution of astrocytic antigens is particularly hard when they are localized in their fine, peripheral astrocyte processes (PAPs), since these processes often have a diameter comparable to vesicles and small organelles. The most appropriate technique is immunoelectron microscopy, which is, however, a time-consuming procedure. Even in high resolution light microscopy, antigen localization is difficult to detect due to the small dimensions of these processes, and overlay from a...

  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. Studying Coxiella burnetii Type IV Substrates in the Yeast Saccharomyces cerevisiae: Focus on Subcellular Localization and Protein Aggregation.

    Science.gov (United States)

    Rodríguez-Escudero, María; Cid, Víctor J; Molina, María; Schulze-Luehrmann, Jan; Lührmann, Anja; Rodríguez-Escudero, Isabel

    2016-01-01

    Coxiella burnetii is a Gram-negative obligate parasitic bacterium that causes the disease Q-fever in humans. To establish its intracellular niche, it utilizes the Icm/Dot type IVB secretion system (T4BSS) to inject protein effectors into the host cell cytoplasm. The host targets of most cognate and candidate T4BSS-translocated effectors remain obscure. We used the yeast Saccharomyces cerevisiae as a model to express and study six C. burnetii effectors, namely AnkA, AnkB, AnkF, CBU0077, CaeA and CaeB, in search for clues about their role in C. burnetii virulence. When ectopically expressed in HeLa cells, these effectors displayed distinct subcellular localizations. Accordingly, GFP fusions of these proteins produced in yeast also decorated distinct compartments, and most of them altered cell growth. CaeA was ubiquitinated both in yeast and mammalian cells and, in S. cerevisiae, accumulated at juxtanuclear quality-control compartments (JUNQs) and insoluble protein deposits (IPODs), characteristic of aggregative or misfolded proteins. AnkA, which was not ubiquitinated, accumulated exclusively at the IPOD. CaeA, but not AnkA or the other effectors, caused oxidative damage in yeast. We discuss that CaeA and AnkA behavior in yeast may rather reflect misfolding than recognition of conserved targets in the heterologous system. In contrast, CBU0077 accumulated at vacuolar membranes and abnormal ER extensions, suggesting that it interferes with vesicular traffic, whereas AnkB associated with the yeast nucleolus. Both effectors shared common localization features in HeLa and yeast cells. Our results support the idea that C. burnetii T4BSS effectors manipulate multiple host cell targets, which can be conserved in higher and lower eukaryotic cells. However, the behavior of CaeA and AnkA prompt us to conclude that heterologous protein aggregation and proteostatic stress can be a limitation to be considered when using the yeast model to assess the function of bacterial effectors.

  6. A study of fractional Schrödinger equation composed of Jumarie fractional derivative

    Science.gov (United States)

    Banerjee, Joydip; Ghosh, Uttam; Sarkar, Susmita; Das, Shantanu

    2017-04-01

    In this paper we have derived the fractional-order Schrödinger equation composed of Jumarie fractional derivative. The solution of this fractional-order Schrödinger equation is obtained in terms of Mittag-Leffler function with complex arguments, and fractional trigonometric functions. A few important properties of the fractional Schrödinger equation are then described for the case of particles in one-dimensional infinite potential well. One of the motivations for using fractional calculus in physical systems is that the space and time variables, which we often deal with, exhibit coarse-grained phenomena. This means infinitesimal quantities cannot be arbitrarily taken to zero - rather they are non-zero with a minimum spread. This type of non-zero spread arises in the microscopic to mesoscopic levels of system dynamics, which means that, if we denote x as the point in space and t as the point in time, then limit of the differentials d x (and d t) cannot be taken as zero. To take the concept of coarse graining into account, use the infinitesimal quantities as (Δ x) α (and (Δ t) α ) with 0 Δ x and (Δ t) α > Δ t. This way of defining the fractional differentials helps us to use fractional derivatives in the study of dynamic systems.

  7. Subcellular interactions of dietary cadmium, copper and zinc in rainbow trout (Oncorhynchus mykiss)

    Energy Technology Data Exchange (ETDEWEB)

    Kamunde, Collins, E-mail: ckamunde@upei.ca [Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE, C1A 4P3 (Canada); MacPhail, Ruth [Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE, C1A 4P3 (Canada)

    2011-10-15

    Highlights: Interactions of Cu, Cd and Zn were studied at the subcellular level in rainbow trout. Metals accumulated in the liver were predominantly metabolically active. Cd, Cu and Zn exhibited both competitive and cooperative interactions. The metal-metal interactions altered subcellular metals partitioning. - Abstract: Interactions of Cu, Cd and Zn were studied at the subcellular level in juvenile rainbow trout (Oncorhynchus mykiss) fed diets containing ({mu}g/g) 500 Cu, 1000 Zn and 500 Cd singly and as a ternary mixture for 28 days. Livers were harvested and submitted to differential centrifugation to isolate components of metabolically active metal pool (MAP: heat-denaturable proteins (HDP), organelles, nuclei) and metabolically detoxified metal pool (MDP: heat stable proteins (HSP), NaOH-resistant granules). Results indicated that Cd accumulation was enhanced in all the subcellular compartments, albeit at different time points, in fish exposed to the metals mixture relative to those exposed to Cd alone, whereas Cu alone exposure increased Cd partitioning. Exposure to the metals mixture reduced (HDP) and enhanced (HSP, nuclei and granules) Cu accumulation while exposure to Zn alone enhanced Cu concentration in all the fractions analyzed without altering proportional distribution in MAP and MDP. Although subcellular Zn accumulation was less pronounced than that of either Cu or Cd, concentrations of Zn were enhanced in HDP, nuclei and granules from fish exposed to the metals mixture relative to those exposed to Zn alone. Cadmium alone exposure mobilized Zn and Cu from the nuclei and increased Zn accumulation in organelles and Cu in granules, while Cu alone exposure stimulated Zn accumulation in HSP, HDP and organelles. Interestingly, Cd alone exposure increased the partitioning of the three metals in MDP indicative of enhanced detoxification. Generally the accumulated metals were predominantly metabolically active: Cd, 67-83%; Cu, 68-79% and Zn, 60-76%. Taken

  8. A Study of Fractional Schrodinger Equation-composed via Jumarie fractional derivative

    CERN Document Server

    Banerjee, Joydip; Sarkar, Susmita; Das, Shantanu

    2016-01-01

    One of the motivations for using fractional calculus in physical systems is due to fact that many times, in the space and time variables we are dealing which exhibit coarse-grained phenomena, meaning that infinitesimal quantities cannot be placed arbitrarily to zero-rather they are non-zero with a minimum length. Especially when we are dealing in microscopic to mesoscopic level of systems. Meaning if we denote x the point in space and t as point in time; then the differentials dx (and dt) cannot be taken to limit zero, rather it has spread. A way to take this into account is to use infinitesimal quantities as (\\Deltax)^\\alpha (and (\\Deltat)^\\alpha) with 0\\Deltax. This way defining the differentials-or rather fractional differentials makes us to use fractional derivatives in the study of dynamic systems. In fractional calculus the fractional order trigonometric functions play important role. The Mittag-Leffler function which plays important role in the field of fractional calculus; and the fractional order tri...

  9. Sub-cellular localisation studies may spuriously detect the Yes-associated protein, YAP, in nucleoli leading to potentially invalid conclusions of its function.

    Directory of Open Access Journals (Sweden)

    Megan L Finch

    Full Text Available The Yes-associated protein (YAP is a potent transcriptional co-activator that functions as a nuclear effector of the Hippo signaling pathway. YAP is oncogenic and its activity is linked to its cellular abundance and nuclear localisation. Activation of the Hippo pathway restricts YAP nuclear entry via its phosphorylation by Lats kinases and consequent cytoplasmic retention bound to 14-3-3 proteins. We examined YAP expression in liver progenitor cells (LPCs and surprisingly found that transformed LPCs did not show an increase in YAP abundance compared to the non-transformed LPCs from which they were derived. We then sought to ascertain whether nuclear YAP was more abundant in transformed LPCs. We used an antibody that we confirmed was specific for YAP by immunoblotting to determine YAP's sub-cellular localisation by immunofluorescence. This antibody showed diffuse staining for YAP within the cytosol and nuclei, but, noticeably, it showed intense staining of the nucleoli of LPCs. This staining was non-specific, as shRNA treatment of cells abolished YAP expression to undetectable levels by Western blot yet the nucleolar staining remained. Similar spurious YAP nucleolar staining was also seen in mouse embryonic fibroblasts and mouse liver tissue, indicating that this antibody is unsuitable for immunological applications to determine YAP sub-cellular localisation in mouse cells or tissues. Interestingly nucleolar staining was not evident in D645 cells suggesting the antibody may be suitable for use in human cells. Given the large body of published work on YAP in recent years, many of which utilise this antibody, this study raises concerns regarding its use for determining sub-cellular localisation. From a broader perspective, it serves as a timely reminder of the need to perform appropriate controls to ensure the validity of published data.

  10. Subcellular distribution and chemical forms of antimony in Ficus tikoua.

    Science.gov (United States)

    Wang, Yong; Chai, Liyuan; Yang, Zhihui; Mubarak, Hussani; Xiao, Ruiyang; Tang, Chongjian

    2017-02-01

    Ficus tikoua (F. tikoua) was a potential species for antimony (Sb) phytoremediation due to its wide growth in the mining area. However, little was known about its tolerance mechanisms toward Sb. The determination of the distribution and chemical speciation of Sb in F. tikoua is essential for understanding the mechanisms involved in Sb accumulation, transportation, and detoxification. The present study investigated the subcellular distribution and chemical forms of Sb in F. tikoua. The plant was exposed to different Sb concentrations (0, 30, 90, and 180 μmol/L) for 30 days. The results showed that F. tikoua possessed a marked ability to tolerate and accumulate Sb. The proportional Sb increased with increasing Sb concentration in the solution, and the highest Sb concentration occurred in roots (1274.5-1580.9 mg/kg), followed by stems (133.5-498.9 mg/kg) and leaves (4.1-15.7 mg/kg). In the subcellular sequestration of Sb in F. tikoua, the largest accumulation of Sb occurred in cell walls (72.4-87.5%) followed by cytoplasmic organelles (8.2-18.6%) and cytoplasmic supernatant. The results suggested that cell walls act as important protective barriers against Sb toxicity in F. tikoua. Although Sb in all plant tissues found primarily in the fractions extracted by ethanol and distilled water, the current study found that the Sb amounts in the HAc-extractable fraction, HCl-extractable fraction, and residue fraction increased at the highest Sb level (180 μmol/L) compared to that under lower Sb levels. These results indicate that excessive Sb accumulated in F. tikoua under Sb stress is bound to non-dissolved or low-bioavailable compounds, a biochemical mechanism that benefits F. tikoua because it helps alleviate Sb toxicity.

  11. Single Fraction versus Multiple Fraction Radiotherapy for Palliation of Painful Vertebral Bone Metastases: A Prospective Study

    Science.gov (United States)

    Majumder, Dipanjan; Chatterjee, Debashis; Bandyopadhyay, Anis; Mallick, Swapan Kumar; Sarkar, Shyamal Kumar; Majumdar, Anjali

    2012-01-01

    Context: Metastatic bone disease is a commonly encountered problem in oncology practice. The most useful and cost effective treatment is radiotherapy (RT). Different fractionation schedule of RT can be used to treat such condition. Aims: Assessment of pain response in patients with vertebral bone metastasis after treating them with various radiation fractionations and to compare the toxicity profile in the treatment arms. Settings and Design: A prospective randomized study was designed to include total 64 patients from July 2010 to May 2011. Patients with histopathologically proven primary malignancy having symptomatic secondary deposits to vertebra were selected for the study. Patients were randomized to two arms receiving multiple fraction of RT with 30 Gy in 10 fractions and 8 Gy in single fraction RT, respectively. Materials and Methods: Patients with age >75 years, Karnofsky Performance Status (KPS) <40, features of cord compression were excluded from study. Initial pain response was assessed using Visual Analogue Scale (VAS) and compared using the same scale at weekly interval up to 1 month after treatment completion. Results: Arm A comprised of 33 patients while 31 patients were enrolled in Arm B. Baseline patient characteristics were comparable. Eleven patients were lost to follow-up. Initial pain scores were 7.23 ± 0.765 and 7.51 ± 0.55 in arm A and arm B, respectively. Pain scores reduced significantly in both the arms after 1 month (4.39 ± 1.82 in arm A; 5.25 ± 2.39 in arm B). Time of initiation of pain response was earlier in arm A (P = 0.0281), statistically significant. Mild G-I toxicity was noted in both the arms but differences in two arms were not statistically significant (P = 0.49), no interruption of treatment was required because of side effects. Conclusions: Different fractionation of radiation has same response and toxicity in treatment of vertebral bone metastasis. Single fraction RT may be safely used to treat these cases as this is

  12. Domains involved in TAF15 subcellular localisation

    DEFF Research Database (Denmark)

    Marko, Marija; Vlassis, Arsenios; Guialis, Apostolia

    2012-01-01

    to play important roles in the onset of specific tumours, certain forms of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). In this study we identified the domains of TAF15 responsible for its subcellular localisation in human (HeLa) cells and experimentally confirmed...

  13. Subcellular localization of a PhoE-LacZ fusion protein in E. coli by protease accessibility experiments reveals an inner-membrane-spanning form of the protein

    NARCIS (Netherlands)

    Tommassen, J.P.M.; Kroon, T. de

    1987-01-01

    Protease accessibility experiments were employed to localize a PhoE-LacZ hybrid protein, encompassing a large N-terminal fragment of the outer membrane PhoE protein of E. coli, fused to β-galactosidase, at the subcellular level. In previous studies, this protein was shown to co-fractionate with the

  14. Subcellular distribution of molybdenum, ultrastructural and antioxidative responses in soybean seedlings under excess molybdenum stress.

    Science.gov (United States)

    Xu, Shoujun; Hu, Chengxiao; Tan, Qiling; Qin, Shiyu; Sun, Xuecheng

    2017-12-05

    Some studies have shown that excess molybdenum (Mo) could produce toxic effects on plants. However, little is known about the subcellular distribution of Mo and cell ultrastructure within plants under excess Mo stress. Here, we comprehensively analyzed the changes of Mo distribution in subcellular fractions, cell ultrastructure and antioxidant enzymes in leaves and roots of soybean seedlings in response to excess Mo stress. The results showed that roots exhibited higher Mo accumulation than leaves at the 100 mg L-1 Mo level, about 38.58-, 171.48- and 52.99-fold higher in cell walls, cell organelles and soluble fractions, respectively. Subcellular fractionations of Mo-containing tissues indicated that approximately 90% of Mo was accumulated in the soluble fractions and cell walls of the roots and leaves, and soluble fractions (accumulated 66.3-72.2% Mo) might serve as an effective storage site for excess Mo. Furthermore, excess Mo caused ultrastructural alterations in roots and leaves of soybean seedlings, leading to structural abnormality of chloroplast in leaf cells, plasmolysis, cellular deformity, vacuole enlargement and the swelling of cell wall and cytoplasm in root cells. Meanwhile, under excess Mo stress, the activity of POD, CAT and APX enzymes in roots was 1.43, 2.35 and 1.23 times that under standard Mo condition, while that of SOD and CAT enzymes in leaves was 1.23 and 1.94 times, respectively. This study provided novel insights into the mechanisms of excess Mo toxicity in soybean seedlings. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  15. Differential subcellular targeting and activity-dependent subcellular localization of diacylglycerol kinase isozymes in transfected cells.

    Science.gov (United States)

    Kobayashi, Naoki; Hozumi, Yasukazu; Ito, Tsukasa; Hosoya, Takaaki; Kondo, Hisatake; Goto, Kaoru

    2007-08-01

    Diacylglycerol kinase (DGK) plays a pivotal role in cellular signal transduction through regulating levels of the second messenger diacylglycerol (DG). Previous studies have revealed that DGK is composed of a family of isozymes that show remarkable heterogeneity in terms of molecular structure, functional domains, tissue and cellular gene expression. Recently, it has been shown that DG is produced in various subcellular compartments including the plasma membrane, internal membranes, cytoskeleton, and nucleus. However, it remains unclear how DG is regulated at distinct subcellular sites. To address this point, we have used an epitope-tag expression system in cultured cells and investigated the subcellular localization of DGK isozymes under the same experimental conditions. We show here that DGK isozymes are targeted differentially to unique subcellular sites in transfected COS7 cells, including the cytoplasm, actin stress fibers, Golgi complex, endoplasmic reticulum, and nucleus. It is also shown that among the isozymes overexpression of DGKbeta causes fragmentation of actin stress fibers while a kinase-dead mutant of DGKbeta abolishes its colocalization with actin stress fibers. These data strongly suggest that each isozyme may be responsible for the metabolism of DG that is produced upon stimulation at a different and specific subcellular site and that DGKbeta activity might have effects on the reorganization of actin stress fibers in transfected COS7 cells.

  16. Identification of proteins in the postsynaptic density fraction by mass spectrometry

    DEFF Research Database (Denmark)

    Walikonis, R S; Jensen, Ole Nørregaard; Mann, M

    2000-01-01

    Our understanding of the organization of postsynaptic signaling systems at excitatory synapses has been aided by the identification of proteins in the postsynaptic density (PSD) fraction, a subcellular fraction enriched in structures with the morphology of PSDs. In this study, we have completed...

  17. Correlation profiling of brain sub-cellular proteomes reveals co-assembly of synaptic proteins and subcellular distribution

    NARCIS (Netherlands)

    Pandya, N.J. (Nikhil J.); Koopmans, F. (Frank); J.A. Slotman (Johan A.); Paliukhovich, I. (Iryna); A.B. Houtsmuller (Adriaan); A.B. Smit (August); Li, K.W. (Ka Wan)

    2017-01-01

    textabstractProtein correlation profiling might assist in defining co-assembled proteins and subcellular distribution. Here, we quantified the proteomes of five biochemically isolated mouse brain cellular sub-fractions, with emphasis on synaptic compartments, from three brain regions, hippocampus,

  18. Effect of subcellular distribution on nC₆₀ uptake and transfer efficiency from Scenedesmus obliquus to Daphnia magna.

    Science.gov (United States)

    Chen, Qiqing; Hu, Xialin; Yin, Daqiang; Wang, Rui

    2016-06-01

    The potential uptake and trophic transfer ability of nanoparticles (NPs) in aquatic organisms have not been well understood yet. There has been an increasing awareness of the subcellular fate of NPs in organisms, but how the subcellular distribution of NPs subsequently affects the trophic transfer to predator remains to be answered. In the present study, the food chain from Scenedesmus obliquus to Daphnia magna was established to simulate the trophic transfer of fullerene aqueous suspension (nC60). The nC60 contaminated algae were separated into three fractions: cell wall (CW), cell organelle (CO), and cell membrane (CM) fractions, and we investigated the nC60 uptake amounts and trophic transfer efficiency to the predator through dietary exposure to algae or algal subcellular fractions. The nC60 distribution in CW fraction of S. obliquus was the highest, following by CO and CM fractions. nC60 uptake amounts in D. magna were found to be mainly relative to the NPs' distribution in CW fraction and daphnia uptake ability from CW fraction, whereas the nC60 trophic transfer efficiency (TE) were mainly in accordance with the transfer ability of NPs from the CO fraction. CW fed group possessed the highest uptake amount, followed by CO and CM fed groups, but the presence of humic acid (HA) significantly decreased the nC60 uptake from CW fed group. The CO fed groups acquired high TE values for nC60, while CM fed groups had low TE values. Moreover, even though CW fed group had a high TE value; it decreased significantly with the presence of HA. This study contributes to the understanding of fullerene NPs' dietary exposure to aquatic organisms, suggesting that NPs in different food forms are not necessarily equally trophically available to the predator. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. 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.

  20. 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.

  1. Subcellular partitioning profiles and metallothionein levels in indigenous clams Moerella iridescens from a metal-impacted coastal bay

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zaosheng, E-mail: zswang@iue.ac.cn [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Boulevard, Xiamen 361021 (China); State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Feng, Chenglian; Ye, Chun [State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Wang, Youshao [State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301 (China); Yan, Changzhou, E-mail: czyan@iue.ac.cn [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Boulevard, Xiamen 361021 (China); Li, Rui; Yan, Yijun; Chi, Qiaoqiao [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Boulevard, Xiamen 361021 (China)

    2016-07-15

    Highlights: • Subcellular partitioning profile of metals were investigated in biomonitor organism. • Cu, Zn and Cd levels in main fraction of HSP increase along accumulation gradients. • Despite MTs as the major binding pool, detoxification of Cd and Pb was incomplete. • Induced MTs were sequentially correlated with Cu, Zn and Cd levels in HSP fraction. • Intracellular metal fates highlighted the metabolic availability within organism. - Abstract: In this study, the effect of environmental metal exposure on the accumulation and subcellular distribution of metals in the digestive gland of clams with special emphasis on metallothioneins (MTs) was investigated. Specimens of indigenous Moerella iridescens were collected from different natural habitats in Maluan Bay (China), characterized by varying levels of metal contamination. The digestive glands were excised, homogenized and six subcellular fractions were separated by differential centrifugation procedures and analyzed for their Cu, Zn, Cd and Pb contents. MTs were quantified independently by spectrophotometric measurements of thiols. Site-specific differences were observed in total metal concentrations in the tissues, correlating well with variable environmental metal concentrations and reflecting the gradient trends in metal contamination. Concentrations of the non-essential Cd and Pb were more responsive to environmental exposure gradients than were tissue concentrations of the essential metals, Cu and Zn. Subcellular partitioning profiles for Cu, Zn and Cd were relatively similar, with the heat-stable protein (HSP) fraction as the dominant metal-binding compartment, whereas for Pb this fraction was much less important. The variations in proportions and concentrations of metals in this fraction along with the metal bioaccumulation gradients suggested that the induced MTs play an important role in metal homeostasis and detoxification for M. iridescens in the metal-contaminated bay. Nevertheless

  2. Subcellular partitioning of cadmium and zinc in mealworm beetle (Tenebrio molitor) larvae exposed to metal-contaminated flour.

    Science.gov (United States)

    Bednarska, Agnieszka J; Świątek, Zuzanna

    2016-11-01

    By studying the internal compartmentalization of metals in different subcellular fractions we are able to better understand the mechanisms of metal accumulation in organisms and the transfer of metals through trophic chains. We investigated the internal compartmentalization of cadmium (Cd) and zinc (Zn) in mealworm beetle (Tenebrio molitor) larvae by breeding them in flour contaminated with either Cd at 100, 300 and 600mgkg(-1), or Zn at 1000 and 2000mgkg(-1). We separated the cellular components of the larvae into 3 fractions: the S1 or cytosolic fraction containing organelles, heat-sensitive and heat-stable proteins, the S2 or cellular debris fraction and the G or metal-rich granule fraction. The concentration of Cd and Zn in each fraction was measured at 0, 7, 14 and 21 days of being fed the flour. The concentration of Cd in the flour affected the concentration of Cd measured in each larval subcellular fraction (p≤0.0001), while the concentration of Zn in the flour only affected the Zn concentration in the S2 and G fractions (p≤0.02). Both Cd and Zn concentrations in mealworms remained relatively constant during the exposure (days 7, 14 and 21) in all three fractions, but the Cd concentrations were much higher than those found in larvae before the exposure (day 0). The concentration of Cd in the flour, however, did not affect the percentage of Cd in the S1 fraction. The contribution of Cd in the G fraction to the total Cd amount was similar (30-40%) in all Cd treatments. The percentage of Zn in all three fractions was not affected by the concentration of Zn in the flour and the relative contributions of each subcellular fraction to the total burden of Zn remained generally constant for both control and treated larvae. In general, larvae sequestered approximately 30% of Cd and Zn in the S1 fraction, which is important for the transport of metals to higher trophic levels in a food web. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Multitask learning for protein subcellular location prediction.

    Science.gov (United States)

    Xu, Qian; Pan, Sinno Jialin; Xue, Hannah Hong; Yang, Qiang

    2011-01-01

    Protein subcellular localization is concerned with predicting the location of a protein within a cell using computational methods. The location information can indicate key functionalities of proteins. Thus, accurate prediction of subcellular localizations of proteins can help the prediction of protein functions and genome annotations, as well as the identification of drug targets. Machine learning methods such as Support Vector Machines (SVMs) have been used in the past for the problem of protein subcellular localization, but have been shown to suffer from a lack of annotated training data in each species under study. To overcome this data sparsity problem, we observe that because some of the organisms may be related to each other, there may be some commonalities across different organisms that can be discovered and used to help boost the data in each localization task. In this paper, we formulate protein subcellular localization problem as one of multitask learning across different organisms. We adapt and compare two specializations of the multitask learning algorithms on 20 different organisms. Our experimental results show that multitask learning performs much better than the traditional single-task methods. Among the different multitask learning methods, we found that the multitask kernels and supertype kernels under multitask learning that share parameters perform slightly better than multitask learning by sharing latent features. The most significant improvement in terms of localization accuracy is about 25 percent. We find that if the organisms are very different or are remotely related from a biological point of view, then jointly training the multiple models cannot lead to significant improvement. However, if they are closely related biologically, the multitask learning can do much better than individual learning.

  4. Differences in Mn uptake and subcellular distribution in different barley genotypes as a response to Cd toxicity.

    Science.gov (United States)

    Wu, Feibo; Dong, Jing; Cai, Yue; Chen, Fei; Zhang, Guoping

    2007-10-15

    A hydroponics experiment was carried out in greenhouse to study the genotypic differences in Mn uptake and subcellular distribution in response to Cd toxicity. Increased Cd level in medium caused a significant reduction in plant height and fresh weight, and ZAU3 and Wumaoliuling being the least and the most affected genotypes, respectively. There was a marked difference in proportion of Mn accumulation in different fractions relative to the total Mn amount in tissues among the 4 fractions, with the soluble fraction FIV showing the largest proportion in shoots, followed by organelle containing fraction (FIII), while cell wall (FI) and chloroplasts FII being the smallest. Meanwhile, Cd significantly increased FIII Mn accumulation proportion, but decreased FIV proportion, with significant genotypic difference of Wumaoliuling being the least increase in FIII and the greatest decrease in FIV among the 4 genotypes. In roots, the major pool of Mn content was FI, FIV, and FIII, and Cd induced no significant changes. Furthermore, Cd caused a significant reduction in subcellular Mn concentration of FI and FIV fractions in shoots and the 4 fractions in roots, with more pronounced in Cd-sensitive cultivar Wumaoliuling in root FII, FIII and FIV, and shoot FI, FII, and FIII, while little difference in both Mn concentrations of root FI, and shoot FIV.

  5. Isotope Fractionation Studies in Prestellar Cores: The Case of Nitrogen

    Science.gov (United States)

    Milam, Stefanie N.; Charnley, Steven B.

    2011-01-01

    Isotopically fractionated material is found in many solar system objects, including meteorites and comets. It is considered, in some cases, to trace interstellar material that was incorporated into the solar system without undergoing significant processing, thus preserving the fractionation. In interstellar molecular clouds, ion-molecule chemistry continually cycles nitrogen between the two main reservoirs - N and N2 - leading to only minor N-15 enrichments. Charnley and Rodgers showed that depletion of CO removes oxygen from the gas and weakens this cycle such that significant N-15 fractionation can occur for N2 and other N-bearing species in such cores. Observations are being conducted at millimeter and submillimeter wavelengths employing various facilities in order to both spatially and spectrally, resolve emission from these cores. A preliminary study to obtain the N-14/N-15 ratio in nitriles (HCN and HNC) was conducted at the Arizona Radio Observatory's 12m telescope on Kitt Peak, AZ. Spectra were obtained at high resolution (0.08 km/s) in order to resolve dynamic properties of each source as well as to resolve hyperfine structure present in certain isotopologues. This study included four dark cloud cores, observed to have varying levels of molecular depletion: L1521E, L1498, L1544, and L1521F. Previous studies of the N-14/N-15 ratio towards LI544 were obtained with N2H+ and NIH3, yielding ratios of 446 and >700, respectively. The discrepancy observed in these two measurements suggests a strong chemical dependence on the fractionation of nitrogen. Ratios (C,N, and D) obtained from isotopologues for a particular molecule are likely tracing the same chemical heritage and are directly comparable within a given source. Results and comparisons between the protostellar evolutionary state and isomer isotope fractionation as well as between other N-bearing species will be presented.

  6. Alternative splicing and differential subcellular localization of the rat FGF antisense gene product

    Directory of Open Access Journals (Sweden)

    Casson Alan G

    2008-01-01

    Full Text Available Abstract Background GFG/NUDT is a nudix hydrolase originally identified as the product of the fibroblast growth factor-2 antisense (FGF-AS gene. While the FGF-AS RNA has been implicated as an antisense regulator of FGF-2 expression, the expression and function of the encoded GFG protein is largely unknown. Alternative splicing of the primary FGF-AS mRNA transcript predicts multiple GFG isoforms in many species including rat. In the present study we focused on elucidating the expression and subcellular distribution of alternatively spliced rat GFG isoforms. Results RT-PCR and immunohistochemistry revealed tissue-specific GFG mRNA isoform expression and subcellular distribution of GFG immunoreactivity in cytoplasm and nuclei of a wide range of normal rat tissues. FGF-2 and GFG immunoreactivity were co-localized in some, but not all, tissues examined. Computational analysis identified a mitochondrial targeting sequence (MTS in the N-terminus of three previously described rGFG isoforms. Confocal laser scanning microscopy and subcellular fractionation analysis revealed that all rGFG isoforms bearing the MTS were specifically targeted to mitochondria whereas isoforms and deletion mutants lacking the MTS were localized in the cytoplasm and nucleus. Mutation and deletion analysis confirmed that the predicted MTS was necessary and sufficient for mitochondrial compartmentalization. Conclusion Previous findings strongly support a role for the FGF antisense RNA as a regulator of FGF2 expression. The present study demonstrates that the antisense RNA itself is translated, and that protein isoforms resulting form alternative RNA splicing are sorted to different subcellular compartments. FGF-2 and its antisense protein are co-expressed in many tissues and in some cases in the same cells. The strong conservation of sequence and genomic organization across animal species suggests important functional significance to the physical association of these transcript

  7. Subcellular location of the enzymes of purine breakdown in the yeast Candida famata grown on uric acid

    NARCIS (Netherlands)

    Large, Peter J.; Waterham, Hans R.; Veenhuis, Marten

    1990-01-01

    The subcellular location of the enzymes of purine breakdown in the yeast Candida famata, which grows on uric acid as sole carbon and nitrogen source, has been examined by subcellular fractionation methods. Uricase was confirmed as being peroxisomal, but the other three enzymes, allantoinase,

  8. Analysis of subcellular metabolite distributions within Arabidopsis thaliana leaf tissue: a primer for subcellular metabolomics.

    Science.gov (United States)

    Krueger, Stephan; Steinhauser, Dirk; Lisec, Jan; Giavalisco, Patrick

    2014-01-01

    Every biological organism relies for its proper function on interactions between a multitude of molecular entities like RNA, proteins, and metabolites. The comprehensive measurement and the analysis of all these entities would therefore provide the basis for our functional and mechanistic understanding of most biological processes. Next to their amount and identity, it is most crucial to also gain information about the subcellular distribution and the flux of the measured compounds between the cellular compartments. That is, we want to understand not only the individual functions of cellular components but also their functional implications within the whole organism. While the analysis of macromolecules like DNA, RNA, and proteins is quite established and robust, analytical techniques for small metabolites, which are prone to diffusion and degradation processes, provide a host of unsolved challenges. The major limitations here are the metabolite conversion and relocation processes. In this protocol we describe a methodological workflow which includes a nonaqueous fractionation method, a fractionated two-phase liquid/liquid extraction protocol, and a software package, which together allow extracting and analyzing starch, proteins, and especially polar and lipophilic metabolites from a single sample towards the estimation of their subcellular distributions.

  9. Numerical study of fractional nonlinear Schrödinger equations

    Science.gov (United States)

    Klein, Christian; Sparber, Christof; Markowich, Peter

    2014-01-01

    Using a Fourier spectral method, we provide a detailed numerical investigation of dispersive Schrödinger-type equations involving a fractional Laplacian in an one-dimensional case. By an appropriate choice of the dispersive exponent, both mass and energy sub- and supercritical regimes can be identified. This allows us to study the possibility of finite time blow-up versus global existence, the nature of the blow-up, the stability and instability of nonlinear ground states and the long-time dynamics of solutions. The latter is also studied in a semiclassical setting. Moreover, we numerically construct ground state solutions of the fractional nonlinear Schrödinger equation. PMID:25484604

  10. Measurement of endogenous subcellular concentration of steroids in tissue

    OpenAIRE

    Poortman, J.; Landeghem, A.A.J. van; Helmond-Agema, A.; Thussen, J.H.H.

    1984-01-01

    A reliable method for the extraction of steroid hormones from human uterine tissue and the subsequent measurement of these hormones in the subcellular compartments by radioimmunoassay is described. Extraction of radioactive steroid hormones from in vivo labelled human uterine tissue by different methods reveals that an almost quantitative extraction of steroid hormones from the nuclear fraction is obtained by sonication in ethanol-acetone. Extraction of steroid hormones with diethylether from...

  11. Pre-embedding staining of single muscle fibers for light and electron microscopy studies of subcellular organization

    DEFF Research Database (Denmark)

    Ralston, E; Ploug, Thorkil

    1996-01-01

    Skeletal muscle fibers are large, multinucleated cells which pose a challenge to the morphologist. In the course of studies of the distribution of the glucose transporter GLUT4, in muscle, we have compared different preparative procedures, for both light (LM) and electron microscopy (EM......) immunocytochemistry. Here we show that pre-embedding staining of single teased fibers, or of single enzymatically dissociated fibers, has several advantages over the use of sections for observing discrete patterns that extend over long distances in the cells. We report on an optimization study carried out...... to establish fixation and permeabilization conditions for EM immunogold labeling of the fibers. We find that a simple fixation with depolymerized paraformaldehyde alone, followed by permeabilization with 0.01% saponin, offers the best compromise between the conflicting demands of unhindered tissue penetration...

  12. Local progression and pseudo progression after single fraction or fractionated stereotactic radiotherapy for large brain metastases. A single centre study

    Energy Technology Data Exchange (ETDEWEB)

    Wiggenraad, R.; Verbeek-de Kanter, A.; Mast, M. [Radiotherapy Centre West, The Hague (Netherlands); Molenaar, R. [Diaconessenhuis, Leiden (Netherlands). Dept. of Neurology; Lycklama a Nijeholt, G. [Medical Centre Haagladen, The Hague (Netherlands). Dept. of Radiology; Vecht, C. [Medical Centre Haagladen, The Hague (Netherlands). Dept. of Neurology; Struikmans, H. [Radiotherapy Centre West, The Hague (Netherlands); Leiden Univ. Medical Centre (Netherlands). Dept. of Radiotherapy; Kal, H.B.

    2012-08-15

    Purpose: The 1-year local control rates after single-fraction stereotactic radiotherapy (SRT) for brain metastases > 3 cm diameter are less than 70%, but with fractionated SRT (FSRT) higher local control rates have been reported. The purpose of this study was to compare our treatment results with SRT and FSRT for large brain metastases. Materials and methods: In two consecutive periods, 41 patients with 46 brain metastases received SRT with 1 fraction of 15 Gy, while 51 patients with 65 brain metastases received FSRT with 3 fractions of 8 Gy. We included patients with brain metastases with a planning target volume of > 13 cm{sup 3} or metastases in the brainstem. Results: The minimum follow-up of patients still alive was 22 months. Comparing 1 fraction of 15 Gy with 3 fractions of 8 Gy, the 1-year rates of freedom from any local progression (54% and 61%, p = 0.93) and pseudo progression (85% and 75%, p = 0.25) were not significantly different. Overall survival rates were also not different. Conclusion: The 1-year local progression and pseudo progression rates after 1 fraction of 15 Gy or 3 fractions of 8 Gy for large brain metastases and metastases in the brainstem are similar. For better local control rates, FSRT schemes with a higher biological equivalent dose may be necessary. (orig.)

  13. Study of the localization of iron, ferritin, and hemosiderin in Alzheimer's disease hippocampus by analytical microscopy at the subcellular level.

    Science.gov (United States)

    Quintana, C; Bellefqih, S; Laval, J Y; Guerquin-Kern, J L; Wu, T D; Avila, J; Ferrer, I; Arranz, R; Patiño, C

    2006-01-01

    Previous studies of the structure of core nanocrystals of ferritin (Ft) in the brains of patients with Alzheimer's disease (AD) have shown differences in the mineral compound in comparison with physiological Ft. Both Ft cores have a polyphasic composition but whereas the major phase in physiological Ft is hexagonal ferric iron oxide (ferrihydrite), the major phases in brain AD Ft are two cubic mixed ferric-ferrous iron oxides (magnetite and wüstite). One of these (wüstite) is similar to what is detected in hemosiderin (Hm) cores in primary hemochromatosis (Quintana, C., Cowley, J.M, Marhic, C., 2004. Electron nanodiffraction and high resolution electron microscopy studies of the structure and composition of physiological and pathological ferritin. J. Struct. Biol. 147, 166-178). We have studied, herein, the distribution of iron, Ft, and Hm in sections of AD hippocampus using analytical microscopy. Iron present in Ft cores was directly mapped in a nanoSIMS microscope and the iron distribution has been correlated with the constituent elements N, P, and S. Ft and Hm cores were visualized at an ultrastructural level in an analytical transmission electron microscope. In senile plaques, Ft was observed in the coronal region associated with a non-beta-amyloid component and in the periphery of plaques, together with Hm, in sulfur-rich dense bodies of dystrophic neurites. Hm was also found in lysosomes and siderosomes of glial cells. Ft was observed in the cytoplasm and nucleus of oligodendrocytes. Ft was particularly abundant in myelinated axons in association with oligodendrocyte processes. These findings provide new arguments to support the hypothesis of a dysfunction of Ft (with eventual degradation to Hm) in AD resulting in an increase of toxic brain ferrous ions that may contribute to the production of free radicals that induce both cellular oxidative stress and aged-related myelin breakdown associated with cognitive decline and AD (Bartzokis, G., 2004. Age

  14. Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

    Science.gov (United States)

    Shah, Anup D; Inder, Kerry L; Shah, Alok K; Cristino, Alexandre S; McKie, Arthur B; Gabra, Hani; Davis, Melissa J; Hill, Michelle M

    2016-10-07

    Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and renal cell carcinoma. This analysis revealed that cancer development is associated with increased membrane raft-cytoskeleton interactions, with ∼40% of elevated lipid raft proteins being cytoskeletal components. Previous studies suggest a potential functional role for the raft-cytoskeleton in the action of the putative tumor suppressors PTRF/Cavin-1 and Merlin. To extend the observation, we examined lipid raft proteome modulation by an unrelated tumor suppressor opioid binding protein cell-adhesion molecule (OPCML) in ovarian cancer SKOV3 cells. In agreement with the other model systems, quantitative proteomics revealed that 39% of OPCML-depleted lipid raft proteins are cytoskeletal components, with microfilaments and intermediate filaments specifically down-regulated. Furthermore, protein-protein interaction network and simulation analysis showed significantly higher interactions among cancer raft proteins compared with general human raft proteins. Collectively, these results suggest increased cytoskeleton-mediated stabilization of lipid raft domains with greater molecular interactions as a common, functional, and reversible feature of cancer cells.

  15. Oxygen isotope fractionation between analcime and water - An experimental study

    Science.gov (United States)

    Karlsson, Haraldur R.; Clayton, Robert N.

    1990-01-01

    The oxygen isotope fractionation between analcime and water is studied to test the feasibility of using zeolites as low-temperature thermometers. The fractionation of oxygen isotopes between natural analcime and water is determined at 300, 350, and 400 C, and at fluid pressures ranging from 1.5 to 5.0 kbar. Also, isotope ratios for the analcime framework, the channel water, and bulk water are obtained. The results suggest that the channel water is depleted in O-18 relative to bulk water by a constant value of about 5 percent, nearly independent of temperature. The analcime-water fractionation curve is presented, showing that the exchange has little effect on grain morphology and does not involve recrystallization. The exchange is faster than any other observed for a silicate. The exchange rates suggest that zeolites in active high-temperature geothermal areas are in oxygen isotopic equilibrium with ambient fluids. It is concluded that calibrated zeolites may be excellent low-temperature oxygen isotope geothermometers.

  16. Subcellular compartmentation of glutathione in dicotyledonous plants

    Science.gov (United States)

    Müller, Maria

    2010-01-01

    This study describes the subcellular distribution of glutathione in roots and leaves of different plant species (Arabidopsis, Cucurbita, and Nicotiana). Glutathione is an important antioxidant and redox buffer which is involved in many metabolic processes including plant defense. Thus information on the subcellular distribution in these model plants especially during stress situations provides a deeper insight into compartment specific defense reactions and reflects the occurrence of compartment specific oxidative stress. With immunogold cytochemistry and computer-supported transmission electron microscopy glutathione could be localized in highest contents in mitochondria, followed by nuclei, peroxisomes, the cytosol, and plastids. Within chloroplasts and mitochondria, glutathione was restricted to the stroma and matrix, respectively, and did not occur in the lumen of cristae and thylakoids. Glutathione was also found at the membrane and in the lumen of the endoplasmic reticulum. It was also associated with the trans and cis side of dictyosomes. None or only very little glutathione was detected in vacuoles and the apoplast of mesophyll and root cells. Additionally, glutathione was found in all cell compartments of phloem vessels, vascular parenchyma cells (including vacuoles) but was absent in xylem vessels. The specificity of this method was supported by the reduction of glutathione labeling in all cell compartments (up to 98%) of the glutathione-deficient Arabidopsis thaliana rml1 mutant. Additionally, we found a similar distribution of glutathione in samples after conventional fixation and rapid microwave-supported fixation. Thus, indicating that a redistribution of glutathione does not occur during sample preparation. Summing up, this study gives a detailed insight into the subcellular distribution of glutathione in plants and presents solid evidence for the accuracy and specificity of the applied method. PMID:20186447

  17. Developing Children's Understanding of Fractions: An Intervention Study

    Science.gov (United States)

    Gabriel, Florence; Coche, Frederic; Szucs, Denes; Carette, Vincent; Rey, Bernard; Content, Alain

    2012-01-01

    Fractions constitute a stumbling block in mathematics education. To improve children's understanding of fractions, we designed an intervention based on learning-by-doing activities, which focused on the representation of the magnitude of fractions. Participants were 292 Grade 4 and 5 children. Half of the classes received experimental instruction,…

  18. Subcellular distribution and chemical forms of cadmium in Phytolacca americana L

    Energy Technology Data Exchange (ETDEWEB)

    Fu Xiaoping; Dou Changming [Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029 (China); Chen Yingxu, E-mail: yingxu_chen@hotmail.com [Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029 (China); Chen Xincai; Shi Jiyan; Yu Mingge; Xu Jie [Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029 (China)

    2011-02-15

    Phytolacca americana L. (pokeweed) is a promising species for Cd phytoextraction with large biomass and fast growth rate. To further understand the mechanisms involved in Cd tolerance and detoxification, the present study investigated subcellular distribution and chemical forms of Cd in pokeweed. Subcellular fractionation of Cd-containing tissues indicated that both in root and leaves, the majority of the element was located in soluble fraction and cell walls. Meanwhile, Cd taken up by pokeweed existed in different chemical forms. Results showed that the greatest amount of Cd was found in the extraction of 80% ethanol in roots, followed by 1 M NaCl, d-H{sub 2}O and 2% HAc, while in leaves and stems, most of the Cd was extracted by 1 M NaCl, and the subdominant amount of Cd was extracted by 80% ethanol. It could be suggested that Cd compartmentation with organo-ligands in vacuole or integrated with pectates and proteins in cell wall might be responsible for the adaptation of pokeweed to Cd stress.

  19. Subcellular proteomic characterization of the high-temperature stress response of the cyanobacterium Spirulina platensis

    Directory of Open Access Journals (Sweden)

    Cheevadhanarak Supapon

    2009-09-01

    Full Text Available Abstract The present study examined the changes in protein expression in Spirulina platensis upon exposure to high temperature, with the changes in expression analyzed at the subcellular level. In addition, the transcriptional expression level of some differentially expressed proteins, the expression pattern clustering, and the protein-protein interaction network were analyzed. The results obtained from differential expression analysis revealed up-regulation of proteins involved in two-component response systems, DNA damage and repair systems, molecular chaperones, known stress-related proteins, and proteins involved in other biological processes, such as capsule formation and unsaturated fatty acid biosynthesis. The clustering of all differentially expressed proteins in the three cellular compartments showed: (i the majority of the proteins in all fractions were sustained tolerance proteins, suggesting the roles of these proteins in the tolerance to high temperature stress, (ii the level of resistance proteins in the photosynthetic membrane was 2-fold higher than the level in two other fractions, correlating with the rapid inactivation of the photosynthetic system in response to high temperature. Subcellular communication among the three cellular compartments via protein-protein interactions was clearly shown by the PPI network analysis. Furthermore, this analysis also showed a connection between temperature stress and nitrogen and ammonia assimilation.

  20. Subcellular partitioning kinetics, metallothionein response and oxidative damage in the marine mussel Mytilus galloprovincialis exposed to cadmium-based quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, Thiago Lopes [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Gomes, Tânia [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo (Norway); Durigon, Emerson Giuliani [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Bebianno, Maria João, E-mail: mbebian@ualg.pt [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal)

    2016-06-01

    The environmental health impact of metal-based nanomaterials is of emerging concern, but their metabolism and detoxification pathways in marine bioindicator species remain unclear. This study investigated the role of subcellular partitioning kinetics, metallothioneins (MTs) response and oxidative damage (lipid peroxidation – LPO) in the marine mussel Mytilus galloprovincialis exposed to CdTe quantum dots (QDs) in comparison with its dissolved counterpart. Mussels were exposed to QDs and dissolved Cd for 21 days at 10 μg Cd L{sup −1} followed by a 50 days depuration. Higher Cd concentrations were detected in fractions containing mitochondria, nucleus and lysosomes, suggesting potential subcellular targets of QDs toxicity in mussel tissues. Tissue specific metabolism patterns were observed in mussels exposed to both Cd forms. Although MT levels were directly associated with Cd in both forms, QDs subcellular partitioning is linked to biologically active metal (BAM), but no increase in LPO occurred, while in the case of dissolved Cd levels are in the biologically detoxified metal (BDM) form, indicating nano-specific effects. Mussel gills showed lower detoxification capability of QDs, while the digestive gland is the major tissue for storage and detoxification of both Cd forms. Both mussel tissues were unable to completely eliminate the Cd accumulated in the QDs form (estimated half-life time > 50 days), highlighting the potential source of Cd and QDs toxicity for human and environmental health. Results indicate tissue specific metabolism patterns and nano-specific effects in marine mussel exposed to QDs. - Highlights: • Subcellular partitioning and MT response are Cd form, tissue and time dependent. • Tissue specific metabolism of Cd-based quantum dots (QDs) in marine mussels. • QDs are slower biologically detoxified when compared to dissolved Cd. • Subcellular partitioning and biomarker responses indicate nano-specific effects. • Subcellular

  1. Complexity metric based on fraction of penumbra dose - initial study

    Science.gov (United States)

    Bäck, A.; Nordström, F.; Gustafsson, M.; Götstedt, J.; Karlsson Hauer, A.

    2017-05-01

    Volumetric modulated arc therapy improve radiotherapy outcome for many patients compared to conventional three dimensional conformal radiotherapy but require a more extensive, most often measurement based, quality assurance. Multi leaf collimator (MLC) aperture-based complexity metrics have been suggested to be used to distinguish complex treatment plans unsuitable for treatment without time consuming measurements. This study introduce a spatially resolved complexity score that correlate to the fraction of penumbra dose and will give information on the spatial distribution and the clinical relevance of the calculated complexity. The complexity metric is described and an initial study on the correlation between the complexity score and the difference between measured and calculated dose for 30 MLC openings is presented. The result of an analysis of the complexity scores were found to correlate to differences between measurements and calculations with a Pearson’s r-value of 0.97.

  2. Subcellular partitioning of metals in Aporrectodea caliginosa along a gradient of metal exposure in 31 field-contaminated soils

    Energy Technology Data Exchange (ETDEWEB)

    Beaumelle, Léa [INRA, UR 251 PESSAC, 78026 Versailles Cedex (France); Gimbert, Frédéric [Laboratoire Chrono-Environnement, UMR 6249 University of Franche-Comté/CNRS Usc INRA, 16 route de Gray, 25030 Besançon Cedex (France); Hedde, Mickaël [INRA, UR 251 PESSAC, 78026 Versailles Cedex (France); Guérin, Annie [INRA, US 0010 LAS Laboratoire d' analyses des sols, 273 rue de Cambrai, 62000 Arras (France); Lamy, Isabelle, E-mail: lamy@versailles.inra.fr [INRA, UR 251 PESSAC, 78026 Versailles Cedex (France)

    2015-07-01

    Subcellular fractionation of metals in organisms was proposed as a better way to characterize metal bioaccumulation. Here we report the impact of a laboratory exposure to a wide range of field-metal contaminated soils on the subcellular partitioning of metals in the earthworm Aporrectodea caliginosa. Soils moderately contaminated were chosen to create a gradient of soil metal availability; covering ranges of both soil metal contents and of several soil parameters. Following exposure, Cd, Pb and Zn concentrations were determined both in total earthworm body and in three subcellular compartments: cytosolic, granular and debris fractions. Three distinct proxies of soil metal availability were investigated: CaCl{sub 2}-extractable content dissolved content predicted by a semi-mechanistic model and free ion concentration predicted by a geochemical speciation model. Subcellular partitionings of Cd and Pb were modified along the gradient of metal exposure, while stable Zn partitioning reflected regulation processes. Cd subcellular distribution responded more strongly to increasing soil Cd concentration than the total internal content, when Pb subcellular distribution and total internal content were similarly affected. Free ion concentrations were better descriptors of Cd and Pb subcellular distribution than CaCl{sub 2} extractable and dissolved metal concentrations. However, free ion concentrations and soil total metal contents were equivalent descriptors of the subcellular partitioning of Cd and Pb because they were highly correlated. Considering lowly contaminated soils, our results raise the question of the added value of three proxies of metal availability compared to soil total metal content in the assessment of metal bioavailability to earthworm. - Highlights: • Earthworms were exposed to a wide panel of historically contaminated soils • Subcellular partitioning of Cd, Pb and Zn was investigated in earthworms • Three proxies of soil metal availability were

  3. A study on rheological characteristics of roller milled fenugreek fractions.

    Science.gov (United States)

    Sakhare, Suresh D; Inamdar, Aashitosh A; Prabhasankar, P

    2016-01-01

    Fenugreek seeds were fractionated by roller milling to get various fractions. The roller milled fractions and whole fenugreek flour (WFF) were evaluated for the flow behavior and time-dependent flow properties using a rotational viscometer at the temperatures of 10-60 (0)C. The samples subjected to a programmed shear rate increase linearly from 0 to 300 s(-1) in 3 min and successive decrease linearly shear rate from 300 s(-1) to 0 in 3 min. The roller milled fractions and WFF paste exhibited non-Newtonian pseudoplastic behavior. Difference in hysteresis loop area was observed among the roller milled fractions and WFF, being more noticeable at lower temperatures. Power law and Casson models were used to predict flow properties of samples. The power law model described well the flow behavior of the roller milled fractions and WFF at temperatures tested. Except flour (FL) fraction, consistency coefficient, m, increased with the temperature both in the forward and backward measurements. The roller milled fractions and WFF exhibited rheopectic behavior that increased viscosity with increasing the shear speed and the temperature. For all the sample tested, initial shear stress increased with increase in shear rate and temperature.

  4. A preliminary study of cadmium mass fractionation in lunar soils

    Science.gov (United States)

    Sands, D. G.; Rosman, K. J. R.; de Laeter, J. R.

    2001-03-01

    This preliminary investigation reports evidence of linear mass fractionation in Cd in lunar soil samples. The isotopic and elemental abundance of cadmium in five lunar samples has been measured with high precision using thermal ionization mass spectrometry and the stable isotope dilution technique respectively. Although both positive and negative mass fractionation for Cd have been identified in meteorites, this is the first time that Cd isotope fractionation has been observed in lunar materials. Three of the four lunar soil samples analyzed gave positive (in the sense that the heavy isotopes of Cd are enriched with respect to a laboratory standard) mass fractionation, ranging in magnitude from 0.34 to 0.63% per mass unit. Cadmium is a volatile element and its elemental abundance in these fractionated lunar soil samples ranges from 57 to 112 ng/g as compared to the solar system abundance of 686 ng/g. There is a possible inverse correlation between the magnitude of the mass fractionation and the concentrations for the same samples. The fourth lunar soil sample, which has a Cd concentration approximately 11 times greater than the mean of the other soil samples, gave zero mass fractionation. The fifth sample is an orange-colored glass spherule which gave a small negative mass fractionation. Volatilization by micrometeorite impact and ion sputtering are both likely to have contributed to the mass fractionation observed in these lunar soils. It is also possible that redeposition of isotopically fractionated Cd may have been a factor in the magnitude of the observed effect.

  5. An ERP Study of the Processing of Common and Decimal Fractions: How Different They Are

    Science.gov (United States)

    Zhang, Li; Wang, Qi; Lin, Chongde; Ding, Cody; Zhou, Xinlin

    2013-01-01

    This study explored event-related potential (ERP) correlates of common fractions (1/5) and decimal fractions (0.2). Thirteen subjects performed a numerical magnitude matching task under two conditions. In the common fraction condition, a nonsymbolic fraction was asked to be judged whether its magnitude matched the magnitude of a common fraction; in the decimal fraction condition, a nonsymbolic fraction was asked to be matched with a decimal fraction. Behavioral results showed significant main effects of condition and numerical distance, but no significant interaction of condition and numerical distance. Electrophysiological data showed that when nonsymbolic fractions were compared to common fractions, they displayed larger N1 and P3 amplitudes than when they were compared to decimal fractions. This finding suggested that the visual identification for nonsymbolic fractions was different under the two conditions, which was not due to perceptual differences but to task demands. For symbolic fractions, the condition effect was observed in the N1 and P3 components, revealing stimulus-specific visual identification processing. The effect of numerical distance as an index of numerical magnitude representation was observed in the P2, N3 and P3 components under the two conditions. However, the topography of the distance effect was different under the two conditions, suggesting stimulus specific semantic processing of common fractions and decimal fractions. PMID:23894491

  6. An ERP study of the processing of common and decimal fractions: how different they are.

    Directory of Open Access Journals (Sweden)

    Li Zhang

    Full Text Available This study explored event-related potential (ERP correlates of common fractions (1/5 and decimal fractions (0.2. Thirteen subjects performed a numerical magnitude matching task under two conditions. In the common fraction condition, a nonsymbolic fraction was asked to be judged whether its magnitude matched the magnitude of a common fraction; in the decimal fraction condition, a nonsymbolic fraction was asked to be matched with a decimal fraction. Behavioral results showed significant main effects of condition and numerical distance, but no significant interaction of condition and numerical distance. Electrophysiological data showed that when nonsymbolic fractions were compared to common fractions, they displayed larger N1 and P3 amplitudes than when they were compared to decimal fractions. This finding suggested that the visual identification for nonsymbolic fractions was different under the two conditions, which was not due to perceptual differences but to task demands. For symbolic fractions, the condition effect was observed in the N1 and P3 components, revealing stimulus-specific visual identification processing. The effect of numerical distance as an index of numerical magnitude representation was observed in the P2, N3 and P3 components under the two conditions. However, the topography of the distance effect was different under the two conditions, suggesting stimulus specific semantic processing of common fractions and decimal fractions.

  7. Subcellular distribution of nitroblue tetrazolium reductase (NBT-R) in human polymorphonuclear leukocytes (PMN).

    Science.gov (United States)

    Baehner, R L

    1975-11-01

    Subcellular distribution study of cytoplasmic organelles was performed on human polymorphonuclear leukocytes after homogenization in 0.34 molar sucrose by differential centrifugation and sucrose density gradient centrifugation of the homogenate. The whole homogenate and each fraction was assayed for nitroblue tetrazolium (NBT)-reductase with and without 1 mM potassium cyanide, and the distribution of this enzyme was compared to the distribution of lysozyme, peroxidase, beta-glucuronidase, and acid and alkaline phosphatase. Enzyme recovery was 97 per cent and ranged between 74 and 124 per cent. Latent activity of all enzymes except NBT-reductase, acid, and alkaline phosphatase was demonstrated by observing a four- to sixfold increase in activity after the addition of Triton-X 100. Maximal relative specific activity using either DPNH or without cyanide for NBT-reductase was found in the 100,000 x g differential centrifugation fraction and was concentrated in the less dense top fraction of the sucrose density gradient. The distribution pattern was similar to acid and alkaline phosphatase. In contrast, the maximal concentration of beta-glucuronidase and peroxidase was found in the heavier 7,200 x g granule fraction and in the more dense bottom fractions of the sucrose density gradient. Maximal lysozyme activity was concentrated in the 30,000 x g granule fraction and in the fractions located between the heaviest and lightest fractions of the sucrose density gradient. The lack of latent activity and the similarity of subcellular distribution of NBT-reductase to acid and alkaline phosphatase, two enzymes associated with microsomes and plasmalemal membranes in human polymorphonuclear leukocytes (PMN), indicates that NBT-reductase is also a nonlysosomal enzyme located in microsomes or in plasmalemal membranes. These findings support the previously described histochemical observations that initial reduction of NBT to formazan occurs on the PMN plasmalemal surface membrane at

  8. Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria

    Directory of Open Access Journals (Sweden)

    Brinkman Fiona SL

    2005-11-01

    Full Text Available Abstract Background Identification of a bacterial protein's subcellular localization (SCL is important for genome annotation, function prediction and drug or vaccine target identification. Subcellular fractionation techniques combined with recent proteomics technology permits the identification of large numbers of proteins from distinct bacterial compartments. However, the fractionation of a complex structure like the cell into several subcellular compartments is not a trivial task. Contamination from other compartments may occur, and some proteins may reside in multiple localizations. New computational methods have been reported over the past few years that now permit much more accurate, genome-wide analysis of the SCL of protein sequences deduced from genomes. There is a need to compare such computational methods with laboratory proteomics approaches to identify the most effective current approach for genome-wide localization characterization and annotation. Results In this study, ten subcellular proteome analyses of bacterial compartments were reviewed. PSORTb version 2.0 was used to computationally predict the localization of proteins reported in these publications, and these computational predictions were then compared to the localizations determined by the proteomics study. By using a combined approach, we were able to identify a number of contaminants and proteins with dual localizations, and were able to more accurately identify membrane subproteomes. Our results allowed us to estimate the precision level of laboratory subproteome studies and we show here that, on average, recent high-precision computational methods such as PSORTb now have a lower error rate than laboratory methods. Conclusion We have performed the first focused comparison of genome-wide proteomic and computational methods for subcellular localization identification, and show that computational methods have now attained a level of precision that is exceeding that of high

  9. Subcellular Organization of GPCR Signaling.

    Science.gov (United States)

    Eichel, Kelsie; von Zastrow, Mark

    2018-02-01

    G protein-coupled receptors (GPCRs) comprise a large and diverse class of signal-transducing receptors that undergo dynamic and isoform-specific membrane trafficking. GPCRs thus have an inherent potential to initiate or regulate signaling reactions from multiple membrane locations. This review discusses emerging insights into the subcellular organization of GPCR function in mammalian cells, focusing on signaling transduced by heterotrimeric G proteins and β-arrestins. We summarize recent evidence indicating that GPCR-mediated activation of G proteins occurs not only from the plasma membrane (PM) but also from endosomes and Golgi membranes and that β-arrestin-dependent signaling can be transduced from the PM by β-arrestin trafficking to clathrin-coated pits (CCPs) after dissociation from a ligand-activated GPCR. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Protein Subcellular Relocalization of Duplicated Genes in Arabidopsis

    Science.gov (United States)

    Liu, Shao-Lun; Pan, An Qi; Adams, Keith L.

    2014-01-01

    Gene duplications during eukaroytic evolution, by successive rounds of polyploidy and by smaller scale duplications, have provided an enormous reservoir of new genes for the evolution of new functions. Preservation of many duplicated genes can be ascribed to changes in sequences, expression patterns, and functions. Protein subcellular relocalization (protein targeting to a new location within the cell) is another way that duplicated genes can diverge. We studied subcellular relocalization of gene pairs duplicated during the evolution of the Brassicaceae including gene pairs from the alpha whole genome duplication that occurred at the base of the family. We analyzed experimental localization data from green fluorescent protein experiments for 128 duplicate pairs in Arabidopsis thaliana, revealing 19 pairs with subcellular relocalization. Many more of the duplicate pairs with relocalization than with the same localization showed an accelerated rate of amino acid sequence evolution in one duplicate, and one gene showed evidence for positive selection. We studied six duplicate gene pairs in more detail. We used gene family analysis with several pairs to infer which gene shows relocalization. We identified potential sequence mutations through comparative analysis that likely result in relocalization of two duplicated gene products. We show that four cases of relocalization have new expression patterns, compared with orthologs in outgroup species, including two with novel expression in pollen. This study provides insights into subcellular relocalization of evolutionarily recent gene duplicates and features of genes whose products have been relocalized. PMID:25193306

  11. A study on nabla discrete fractional operator in mass - spring - damper system

    Directory of Open Access Journals (Sweden)

    Okkes Ozturk

    2016-10-01

    Full Text Available The fractional calculus that is one of the new trends in science and engineering is concept of derivative and integral with arbitrary order. And, discrete fractional calculus (DFC has an important place in fractional calculus which studied for the last 300 years. In present paper, we solved the equations of motion in mass-spring-damper system by using nabla (? discrete fractional operator. And, we also introduced some instructive examples.

  12. A Study of Impulsive Multiterm Fractional Differential Equations with Single and Multiple Base Points and Applications

    Directory of Open Access Journals (Sweden)

    Yuji Liu

    2014-01-01

    Full Text Available We discuss the existence and uniqueness of solutions for initial value problems of nonlinear singular multiterm impulsive Caputo type fractional differential equations on the half line. Our study includes the cases for a single base point fractional differential equation as well as multiple base points fractional differential equation. The asymptotic behavior of solutions for the problems is also investigated. We demonstrate the utility of our work by applying the main results to fractional-order logistic models.

  13. Comparative study of synchronization methods of fractional order chaotic systems

    Science.gov (United States)

    Singh, Ajit K.; Yadav, Vijay K.; Das, S.

    2016-09-01

    In this article, the active control method and the backstepping method are used during the synchronization of fractional order chaotic systems. The salient feature of the article is the analysis of time of synchronization between fractional order Chen and Qi systems using both the methods. Numerical simulation and graphical results clearly exhibit that backstepping approach is better than active control method for synchronization of the considered pair of systems, as it takes less time to synchronize while using the first one compare to second one.

  14. Malonyl-CoA decarboxylase (MCD) is differentially regulated in subcellular compartments by 5'AMP-activated protein kinase (AMPK). Studies using H9c2 cells overexpressing MCD and AMPK by adenoviral gene transfer technique.

    Science.gov (United States)

    Sambandam, Nandakumar; Steinmetz, Michael; Chu, Angel; Altarejos, Judith Y; Dyck, Jason R B; Lopaschuk, Gary D

    2004-07-01

    Malonyl-CoA, a potent inhibitor of carnitine pamitoyl transferase-I (CPT-I), plays a pivotal role in fuel selection in cardiac muscle. Malonyl-CoA decarboxylase (MCD) catalyzes the degradation of malonyl-CoA, removes a potent allosteric inhibition on CPT-I and thereby increases fatty acid oxidation in the heart. Although MCD has several Ser/Thr phosphorylation sites, whether it is regulated by AMP-activated protein kinase (AMPK) has been controversial. We therefore overexpressed MCD (Ad.MCD) and constitutively active AMPK (Ad.CA-AMPK) in H9c2 cells, using an adenoviral gene delivery approach in order to examine if MCD is regulated by AMPK. Cells infected with Ad.CA-AMPK demonstrated a fourfold increase in AMPK activity as compared with control cells expressing green fluorescent protein (Ad.GFP). MCD activity increased 40- to 50-fold in Ad.MCD + Ad.GFP cells when compared with Ad.GFP control. Co-expressing AMPK with MCD further augmented MCD expression and activity in Ad.MCD + Ad.CA-AMPK cells compared with the Ad.MCD + Ad.GFP control. Subcellular fractionation further revealed that 54.7 kDa isoform of MCD expression was significantly higher in cytosolic fractions of Ad.MCD + Ad.CA-AMPK cells than of the Ad.MCD +Ad.GFP control. However, the MCD activities in cytosolic fractions were not different between the two groups. Interestingly, in the mitochondrial fractions, MCD activity significantly increased in Ad.MCD + Ad.CA-AMPK cells when compared with Ad.MCD + Ad.GFP cells. Using phosphoserine and phosphothreonine antibodies, no phosphorylation of MCD by AMPK was observed. The increase in MCD activity in mitochondria-rich fractions of Ad.MCD + Ad.CA-AMPK cells was accompanied by an increase in the level of the 50.7 kDa isoform of MCD protein in the mitochondria. This differential regulation of MCD expression and activity in the mitochondria by AMPK may potentially regulate malonyl-CoA levels at sites nearby CPT-I on the mitochondria.

  15. 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.

  16. 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

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

    African Journals Online (AJOL)

    Expression and subcellular localization of antiporter regulating protein OsARP in rice induced by submergence, salt and drought stresses. Md Imtiaz Uddin, Maki Kihara, Lina Yin, Mst Farida Perveen, Kiyoshi Tanaka ...

  18. 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.

  19. A Monte Carlo study of energy deposition at the sub-cellular level for application to targeted radionuclide therapy with low-energy electron emitters

    Science.gov (United States)

    Emfietzoglou, D.; Bousis, C.; Hindorf, C.; Fotopoulos, A.; Pathak, A.; Kostarelos, K.

    2007-03-01

    Optimizing targeted radionuclide therapy for patients with circulating malignant cells (e.g. blood-related cancers) or a micrometastatic spread requires quantification of various dosimetric parameters at the single-cell level. We present results on the energy deposition of monoenergetic electrons of initial energy from 100 eV to 20 keV - relevant to Auger emitting radionuclides - distributed either uniformly or at the surface of spherical volumes of radii from 10 nm to 1 μm which correspond to critical sub-cellular targets. Calculations have been carried out by our detailed-history Monte Carlo (MC) code which simulates event-by-event the complete slowing down (to 1 Ry) of both the primary and all subsequent generations of electrons, as well as, by the continuous-slowing-down-approximation (CSDA) using analytic range-energy relationships. The latter method has been adopted by the MIRD committee of the Society of Nuclear Medicine for dosimetry at the cellular level (>1 μm). Differences between the MC and CSDA results are up to ∼50% and are expected to be even larger at higher energies and/or smaller volumes. They are attributed to the deficiencies of the CSDA method associated with the neglect of straggling and δ-ray transport. The results are particularly relevant to targeted radiotherapy at the genome level by Auger emitters.

  20. Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome.

    Science.gov (United States)

    Jadot, Michel; Boonen, Marielle; Thirion, Jaqueline; Wang, Nan; Xing, Jinchuan; Zhao, Caifeng; Tannous, Abla; Qian, Meiqian; Zheng, Haiyan; Everett, John K; Moore, Dirk F; Sleat, David E; Lobel, Peter

    2017-02-01

    Accurate knowledge of the intracellular location of proteins is important for numerous areas of biomedical research including assessing fidelity of putative protein-protein interactions, modeling cellular processes at a system-wide level and investigating metabolic and disease pathways. Many proteins have not been localized, or have been incompletely localized, partly because most studies do not account for entire subcellular distribution. Thus, proteins are frequently assigned to one organelle whereas a significant fraction may reside elsewhere. As a step toward a comprehensive cellular map, we used subcellular fractionation with classic balance sheet analysis and isobaric labeling/quantitative mass spectrometry to assign locations to >6000 rat liver proteins. We provide quantitative data and error estimates describing the distribution of each protein among the eight major cellular compartments: nucleus, mitochondria, lysosomes, peroxisomes, endoplasmic reticulum, Golgi, plasma membrane and cytosol. Accounting for total intracellular distribution improves quality of organelle assignments and assigns proteins with multiple locations. Protein assignments and supporting data are available online through the Prolocate website (http://prolocate.cabm.rutgers.edu). As an example of the utility of this data set, we have used organelle assignments to help analyze whole exome sequencing data from an infant dying at 6 months of age from a suspected neurodegenerative lysosomal storage disorder of unknown etiology. Sequencing data was prioritized using lists of lysosomal proteins comprising well-established residents of this organelle as well as novel candidates identified in this study. The latter included copper transporter 1, encoded by SLC31A1, which we localized to both the plasma membrane and lysosome. The patient harbors two predicted loss of function mutations in SLC31A1, suggesting that this may represent a heretofore undescribed recessive lysosomal storage disease

  1. An experimental study of radioprotective effect of ginseng alkaloid fraction on cellular damage

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Seong Yul; Cho, Chul Koo; Kim, Mi Sook; Yoo, Hyung Jun; Kim, Seong Ho; Kim, Tae Hwan [Korea Cancer Center Hospital, Seoul (Korea, Republic of)

    1997-09-01

    This paper is to assess the effect of Adaptagen as a radioprotector in which main component is alkaloid fraction of ginseng. Evaluation was made in vitro and in vivo study with NIGP(S) mouse by the measurement of regeneration of jejunal crypt cell and micronucleus assay to analyze radioprotective effect of ginseng alkaloid fraction in comparison with that of water fraction after whole body irradiation. The results were as follows, 1. The degree of radiation damage of mouse jejunal crypt cell was diminished in both of alkaloid and water fraction groups compared to control group but more in alkaloid fraction group than water fraction group. 2. Regeneration of mouse jejunal crypt cell was higher both in alkaloid and water fraction groups than control group. 3. In vitro study, frequency of micronucleus was diminished in tendency for the treated groups than control group but statistically insignificant. 4. In vitro study, frequency of micronucleus was diminished in both alkaloid and water fraction groups compared to control group but more in alkaloid fraction group than water fraction group.

  2. Thyroid states regulate subcellular glucose phosphorylation activity in male mice

    Directory of Open Access Journals (Sweden)

    Flavia Letícia Martins Peçanha

    2017-07-01

    Full Text Available The thyroid hormones (THs, triiodothyronine (T3 and thyroxine (T4, are very important in organism metabolism and regulate glucose utilization. Hexokinase (HK is responsible for the first step of glycolysis, catalyzing the conversion of glucose to glucose 6-phosphate. HK has been found in different cellular compartments, and new functions have been attributed to this enzyme. The effects of hyperthyroidism on subcellular glucose phosphorylation in mouse tissues were examined. Tissues were removed, subcellular fractions were isolated from eu- and hyperthyroid (T3, 0.25 μg/g, i.p. during 21 days mice and HK activity was assayed. Glucose phosphorylation was increased in the particulate fraction in soleus (312.4% ± 67.1, n = 10, gastrocnemius (369.2% ± 112.4, n = 10 and heart (142.2% ± 13.6, n = 10 muscle in the hyperthyroid group compared to the control group. Hexokinase activity was not affected in brain or liver. No relevant changes were observed in HK activity in the soluble fraction for all tissues investigated. Acute T3 administration (single dose of T3, 1.25 μg/g, i.p. did not modulate HK activity. Interestingly, HK mRNA levels remained unchanged and HK bound to mitochondria was increased by T3 treatment, suggesting a posttranscriptional mechanism. Analysis of the AKT pathway showed a 2.5-fold increase in AKT and GSK3B phosphorylation in the gastrocnemius muscle in the hyperthyroid group compared to the euthyroid group. Taken together, we show for the first time that THs modulate HK activity specifically in particulate fractions and that this action seems to be under the control of the AKT and GSK3B pathways.

  3. Subcellular partitioning of cadmium in the freshwater bivalve, Pyganodon grandis, after separate short-term exposures to waterborne or diet-borne metal

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, Sophie; Hare, Landis [INRS-Eau, Terre et Environnement, Universite du Quebec, 490 rue de la Couronne, Quebec, QC, G1K 9A9 (Canada); Campbell, Peter G.C., E-mail: peter.campbell@ete.inrs.ca [INRS-Eau, Terre et Environnement, Universite du Quebec, 490 rue de la Couronne, Quebec, QC, G1K 9A9 (Canada)

    2010-11-15

    The dynamics of cadmium uptake and subcellular partitioning were studied in laboratory experiments conducted on Pyganodon grandis, a freshwater unionid bivalve that shows promise as a biomonitor for metal pollution. Bivalves were collected from an uncontaminated lake, allowed to acclimate to laboratory conditions ({>=}25 days), and then either exposed to a low, environmentally relevant, concentration of dissolved Cd (5 nM; 6, 12 and 24 h), or fed Cd-contaminated algae ({approx}70 nmol Cd g{sup -1} dry weight; 4 x 4 h). In this latter case, the bivalves were allowed to depurate for up to 8 days after the end of the feeding phase. As anticipated, the gills were the main target organ during the aqueous Cd exposure whereas the intestine was the initial site of Cd accumulation during the dietary exposure; during the subsequent depuration period, the dietary Cd accumulated in both the digestive gland and in the gills. For the gills, the distribution of Cd among the subcellular fractions (i.e., granules > heat-denatured proteins (HDP) {approx} heat-stable proteins (HSP) > mitochondria {approx} lysosomes + microsomes) was insensitive to the exposure route; both waterborne and diet-borne Cd ended up largely bound to the granule fraction. The subcellular distribution of Cd in the digestive gland differed markedly from that in the gills (HDP > HSP {approx} granules {approx} mitochondria > lysosomes + microsomes), but as in the case of the gills, this distribution was relatively insensitive to the exposure route. For both the gills and the digestive gland, the subcellular distributions of Cd differed from those observed in native bivalves that are chronically exposed to Cd in the field - in the short-term experimental exposures of P. grandis, metal detoxification was less effective than in chronically exposed native bivalves.

  4. Cell fractionation of parasitic protozoa: a review

    Directory of Open Access Journals (Sweden)

    Souza Wanderley de

    2003-01-01

    Full Text Available Cell fractionation, a methodological strategy for obtaining purified organelle preparations, has been applied successfully to parasitic protozoa by a number of investigators. Here we present and discuss the work of several groups that have obtained highly purified subcellular fractions from trypanosomatids, Apicomplexa and trichomonads, and whose work have added substantially to our knowledge of the cell biology of these parasites.

  5. A Population-Based Study of the Fractionation of Postlumpectomy Breast Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Ashworth, Allison [Division of Cancer Care and Epidemiology, Queen' s University Cancer Research Institute, Kingston, Ontario (Canada); Cancer Center of Southeastern Ontario, Kingston, Ontario (Canada); Kong, Weidong [Division of Cancer Care and Epidemiology, Queen' s University Cancer Research Institute, Kingston, Ontario (Canada); Whelan, Timothy [Juravinski Cancer Center, Hamilton, Ontario (Canada); Mackillop, William J., E-mail: william.mackillop@krcc.on.ca [Division of Cancer Care and Epidemiology, Queen' s University Cancer Research Institute, Kingston, Ontario (Canada)

    2013-05-01

    Purpose: The optimal fractionation schedule of post lumpectomy radiation therapy remains controversial. The objective of this study was to describe the fractionation of post-lumpectomy radiation therapy (RT) in Ontario, before and after the seminal Ontario Clinical Oncology Group (OCOG) trial, which showed the equivalence of 16- and 25-fraction schedules. Methods and Materials: This was a retrospective cohort study conducted by linking electronic treatment records to a population-based cancer registry. The study population included all patients who underwent lumpectomy for invasive breast cancer in Ontario, Canada, between 1984 and 2008. Results: Over the study period, 41,747 breast cancer patients received post lumpectomy radiation therapy to the breast only. Both 16- and 25-fraction schedules were commonly used throughout the study period. In the early 1980s, shorter fractionation schedules were used in >80% of cases. Between 1985 and 1995, the proportion of patients treated with shorter fractionation decreased to 48%. After completion of the OCOG trial, shorter fractionation schemes were once again widely adopted across Ontario, and are currently used in about 71% of cases; however, large intercenter variations in fractionation persisted. Conclusions: The use of shorter schedules of post lumpectomy RT in Ontario increased after completion of the OCOG trial, but the trial had a less normative effect on practice than expected.

  6. 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.

  7. Imaging trace element distributions in single organelles and subcellular features

    Science.gov (United States)

    Kashiv, Yoav; Austin, Jotham R.; Lai, Barry; Rose, Volker; Vogt, Stefan; El-Muayed, Malek

    2016-02-01

    The distributions of chemical elements within cells are of prime importance in a wide range of basic and applied biochemical research. An example is the role of the subcellular Zn distribution in Zn homeostasis in insulin producing pancreatic beta cells and the development of type 2 diabetes mellitus. We combined transmission electron microscopy with micro- and nano-synchrotron X-ray fluorescence to image unequivocally for the first time, to the best of our knowledge, the natural elemental distributions, including those of trace elements, in single organelles and other subcellular features. Detected elements include Cl, K, Ca, Co, Ni, Cu, Zn and Cd (which some cells were supplemented with). Cell samples were prepared by a technique that minimally affects the natural elemental concentrations and distributions, and without using fluorescent indicators. It could likely be applied to all cell types and provide new biochemical insights at the single organelle level not available from organelle population level studies.

  8. A study of ∇-discrete fractional calculus operator on the radial ...

    African Journals Online (AJOL)

    The fractional calculus includes concepts of integrals and derivatives of any complex or real order. The fractional calculus is as old as the usual calculus. Recently, many scientists have been studying on this eld to provide the development and applicability to various areas of mathematics, physics, engineering and other ...

  9. Single-fraction vs. fractionated linac-based stereotactic radiosurgery for vestibular schwannoma: a single-institution study.

    NARCIS (Netherlands)

    Meijer, O.W.M.; Vandertop, W.P.; Baayen, J.C.; Slotman, B.J.

    2003-01-01

    PURPOSE: In this single-institution trial, we investigated whether fractionated stereotactic radiation therapy is superior to single-fraction linac-based radiosurgery with respect to treatment-related toxicity and local control in patients with vestibular schwannoma. METHODS AND MATERIALS: All 129

  10. Single-fraction vs. fractionated linac-based stereotactic radiosurgery for vestibular schwannoma: a single-institution study

    NARCIS (Netherlands)

    Meijer, O. W. M.; Vandertop, W. P.; Baayen, J. C.; Slotman, B. J.

    2003-01-01

    PURPOSE: In this single-institution trial, we investigated whether fractionated stereotactic radiation therapy is superior to single-fraction linac-based radiosurgery with respect to treatment-related toxicity and local control in patients with vestibular schwannoma. METHODS AND MATERIALS: All 129

  11. Combined fractional ablative and nonablative laser resurfacing treatment: a split-face comparative study.

    Science.gov (United States)

    Cohen, Joel L; Ross, E Victor

    2013-02-01

    Fractional ablative and nonablative lasers are useful tools for facial rejuvenation; however, ablative lasers require a period of downtime during reepthelialization. A procedure that combines both ablative and nonablative lasers may deliver good cosmetic results and reduce downtime or other side effects of treatment. The purpose of this study was to compare a combined fractional ablative and nonablative laser procedure to ablative-only procedures for facial rejuvenation. A total of 8 subjects in 2 study groups received a single, split-face, facial rejuvenation procedure in this study. In group A, we compared a combined procedure using a fractional nonablative 1,440-nm neodymium-doped yttrium aluminum garnet (YAG) laser and a fractional ablative 2,940-nm erbium (Er)-doped YAG laser on one side of the face, and a combined confluent/fractional ablative Er:YAG laser on the other. In group B, we compared the same 1,440/2,940 treatment as group A on one side of the face, and a fractional ablative CO2 laser on the other. Subjects were followed for 3 months to assess side effects and improvement in Fitzpatrick Wrinkle Score and pigmentation. Improvement in wrinkles and pigment were seen with all techniques in both groups, and results were equivalent. Areas treated with combined fractional nonablative and ablative technique demonstrated fewer immediate side effects. Facial rejuvenation using a combination treatment of fractional ablative 2,940 and nonablative 1,440 lasers provides improvement in wrinkles and pigment similar to conservative purely ablative approaches. These purely ablative approaches include the Er:YAG laser used in a sequential confluent fractional manner, or fractional CO2 laser alone. Reduced side effects make the combined procedure an attractive option for facial rejuvenation.

  12. The Subcellular Distribution of Small Molecules: from Pharmacokinetics to Synthetic Biology

    Science.gov (United States)

    Zheng, Nan; Tsai, Hobart Ng; Zhang, Xinyuan; Rosania, Gus R.

    2011-01-01

    The systemic pharmacokinetics and pharmacodynamics of small molecules are determined by subcellular transport phenomena. Although approaches used to study the subcellular distribution of small molecules have gradually evolved over the past several decades, experimental analysis and prediction of cellular pharmacokinetics remains a challenge. In this article, we surveyed the progress of subcellular distribution research since the 1960s, with a focus on the advantages, disadvantages and limitations of the various experimental techniques. Critical review of the existing body of knowledge pointed to many opportunities to advance the rational design of organelle-targeted chemical agents. These opportunities include: 1) development of quantitative, nonfluorescence-based, whole cell methods and techniques to measure the subcellular distribution of chemical agents in multiple compartments; 2) exploratory experimentation with nonspecific transport probes that have not been enriched with putative, organelle-targeting features; 3) elaboration of hypothesis-driven, mechanistic and modeling-based approaches to guide experiments aimed at elucidating subcellular distribution and transport; and 4) introduction of revolutionary conceptual approaches borrowed from the field of synthetic biology combined with cutting edge experimental strategies. In our laboratory, state-of-the-art subcellular transport studies are now being aimed at understanding the formation of new intracellular membrane structures in response to drug therapy, exploring the function of drug-membrane complexes as intracellular drug depots, and synthesizing new organelles with extraordinary physical and chemical properties. PMID:21805990

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

    African Journals Online (AJOL)

    Md. Imtiaz Uddin

    2012-02-14

    Feb 14, 2012 ... 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.

  14. Lipidomics in tissues, cells and subcellular compartments

    National Research Council Canada - National Science Library

    Horn, Patrick J; Chapman, Kent D

    2012-01-01

    ...‐infusion MS, localization of lipids in tissues and cells by laser desorption/ionization MS, and even profiling of lipids in individual subcellular compartments by direct‐organelle MS. Applications of these approaches to achieve improved understanding of plant lipid metabolism, compartmentation and function are discussed.

  15. SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations.

    Science.gov (United States)

    Hooper, Cornelia M; Castleden, Ian R; Tanz, Sandra K; Aryamanesh, Nader; Millar, A Harvey

    2017-01-04

    The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The experimental PPI data has been expanded to 26 327 PPI pairs including 856 PPI localizations from experimental fluorescent visualizations. The new SUBA4 user interface enables users to choose quickly from the filter categories: 'subcellular location', 'protein properties', 'protein-protein interaction' and 'affiliations' to build complex queries. This allows substantial expansion of search parameters into 80 annotation types comprising 1 150 204 new annotations to study metadata associated with subcellular localization. The 'BLAST' tab contains a sequence alignment tool to enable a sequence fragment from any species to find the closest match in Arabidopsis and retrieve data on subcellular location. Using the location consensus SUBAcon, the SUBA4 toolbox delivers three novel data services allowing interactive analysis of user data to provide relative compartmental protein abundances and proximity relationship analysis of PPI and coexpression partners from a submitted list of Arabidopsis gene identifiers. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Linking Subcellular Disturbance to Physiological Behavior and Toxicity Induced by Quantum Dots in Caenorhabditis elegans.

    Science.gov (United States)

    Wang, Qin; Zhou, Yanfeng; Song, Bin; Zhong, Yiling; Wu, Sicong; Cui, Rongrong; Cong, Haixia; Su, Yuanyuan; Zhang, Huimin; He, Yao

    2016-06-01

    The wide-ranging applications of fluorescent semiconductor quantum dots (QDs) have triggered increasing concerns about their biosafety. Most QD-related toxicity studies focus on the subcellular processes in cultured cells or global physiological effects on whole animals. However, it is unclear how QDs affect subcellular processes in living organisms, or how the subcellular disturbance contributes to the overall toxicity. Here the behavior and toxicity of QDs of three different sizes in Caenorhabditis elegans (C. elegans) are systematically investigated at both the systemic and the subcellular level. Specifically, clear size-dependent distribution and toxicity of the QDs in the digestive tract are observed. Short-term exposure of QDs leads to acute toxicity on C. elegans, yet incurring no lasting, irreversible damage. In contrast, chronic exposure of QDs severely inhibits development and shortens lifespan. Subcellular analysis reveals that endocytosis and nutrition storage are disrupted by QDs, which likely accounts for the severe deterioration in growth and longevity. This work reveals that QDs invasion disrupts key subcellular processes in living organisms, and may cause permanent damage to the tissues and organs over long-term retention. The findings provide invaluable information for safety evaluations of QD-based applications and offer new opportunities for design of novel nontoxic nanoprobes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. [Effects of pentacin on subcellular distribution of Pu-239 nitrate in the lungs of rats].

    Science.gov (United States)

    Kabirova, N R; Sokhranich, A L

    1991-01-01

    The method of differential centrifugation has shown that 26% of 239Pu-nitrate injected intratracheally, is detected in cells in 3 h (24.4% of Pu is bound with subcellular organellae). In 24 h the nuclear fraction acquires a paramount importance in Pu binding. In the hyaloplasm 239Pu is distributed equally between low molecular (32.9-42.9%) and high molecular (54.1-55.2%) proteins. Pentacine decreases the level of Pu in the lungs, in the sum of subcellular fractions and in the sum of organellae, but produces no noticeable action on the level of the radionuclide in hyaloplasmic proteins though promotes certain redistribution of the radionuclide between low- and high molecular proteins.

  18. Antidiabetic and antiplatelet aggregation study of various methanol fractions of Nymphaea stellata Willd. leaves

    Directory of Open Access Journals (Sweden)

    Raja Mohan Maruga

    2017-09-01

    Full Text Available Introduction: Nymphaea stellata Willd. (Nymphaeaceae is traditionally used for the treatment of diabetes. Alcohol extract of N. stellata leaves has been reported for hypoglycaemic activity. Objective: The aim of this study was to further investigate the different methanol fractions of N. stellata leaves for anti-diabetic activity and anti-platelet aggregation activity. Methods: Methanol extract was fractioned in to unsaponified petroleum ether fraction of methanol extract (UPFME, chloroform fraction of methanol extract (CFME and residual fraction of methanol extract (RFME. All fractions were evaluated for in vivo anti-diabetic activity (STZ-NAD-induced rat model, in vitro anti-diabetic activity (PTP1B inhibition study and anti-platelet aggregation activity. Results: UPFME showed significant changes in all studied parameters, compared to the diabetic control. UPFME also showed an IC50 value of 19.30±1.1 mg/ml and 13.11±0.7 μg/ml in PTP1B inhibition study and anti-platelet aggregation study, respectively. Conclusion: The study indicates that UPFME of N. stellata leaves exhibit anti-diabetic and anti-platelet aggregation activity.

  19. Numerical study of effect of oxygen fraction on local entropy ...

    Indian Academy of Sciences (India)

    This study considers numerical simulation of the combustion of methane with air, including oxygen and nitrogen, in a burner and the numerical solution of local entropy generation rate due to high temperature and velocity gradients in the combustion chamber. The effects of equivalence ratio () and oxygen percentage () ...

  20. Integration of Cadmium Accumulation, Subcellular Distribution, and Physiological Responses to Understand Cadmium Tolerance in Apple Rootstocks

    Directory of Open Access Journals (Sweden)

    Jiangtao Zhou

    2017-06-01

    Full Text Available Cadmium (Cd is a nonessential and highly toxic element causing agricultural problems. However, little information is available about the variation in Cd tolerance among apple rootstocks and its underlying physiological regulation mechanisms. This study investigated Cd accumulation, subcellular distribution, and chemical forms as well as physiological changes among four apple rootstocks exposed to either 0 or 300 μM CdCl2. The results showed that variations in Cd tolerance existed among these rootstocks. Cd exposure caused decline in photosynthesis, chlorophyll and biomass in four apple rootstocks, which was less pronounced in M. baccata, indicating its higher Cd tolerance. This finding was corroborated with higher Cd tolerance indexes (TIs of the whole plant in M. baccata than those in the other three apple rootstocks. Among the four apple rootstocks, M. baccata displayed the lowest Cd concentrations in roots, wood, and leaves, the smallest total Cd amounts as well as the lowest BCF. In apple rootstocks, it was found that to immobilize Cd in cell wall and soluble fraction (most likely in vacuole and to convert it into pectate- or protein- integrated forms and undissolved Cd phosphate forms may be the primary strategies to reduce Cd mobility and toxicity. The physiological changes including ROS, carbohydrates and antioxidants were in line with the variations of Cd tolerance among four apple rootstocks. In comparison with the other three apple rootstocks, M. baccata had lower concentrations of ROS in roots and bark, H2O2 in roots and leaves and MDA in roots, wood and bark, but higher concentrations of soluble sugars in bark and starch in roots and leaves, and enhanced antioxidants. These results indicate that M. baccata are more tolerant to Cd stress than the other three apple rootstocks under the current experiment conditions, which is probably related to Cd accumulation, subcellular partitioning and chemical forms of Cd and well

  1. Identification of an intrinsic determinant critical for maspin subcellular localization and function.

    Directory of Open Access Journals (Sweden)

    Sijana H Dzinic

    Full Text Available Maspin, a multifaceted tumor suppressor, belongs to the serine protease inhibitor superfamily, but only inhibits serine protease-like enzymes such as histone deacetylase 1 (HDAC1. Maspin is specifically expressed in epithelial cells and it is differentially regulated during tumor progression. A new emerging consensus suggests that a shift in maspin subcellular localization from the nucleus to the cytoplasm stratifies with poor cancer prognosis. In the current study, we employed a rational mutagenesis approach and showed that maspin reactive center loop (RCL and its neighboring sequence are critical for maspin stability. Further, when expressed in multiple tumor cell lines, single point mutation of Aspartate(346 (D(346 to Glutamate (E(346, maspin(D346E, was predominantly nuclear, whereas wild type maspin (maspin(WT was both cytoplasmic and nuclear. Evidence from cellular fractionation followed by immunological and proteomic protein identification, combined with the evidence from fluorescent imaging of endogenous proteins, fluorescent protein fusion constructs, as well as bimolecular fluorescence complementation (BiFC showed that the increased nuclear enrichment of maspin(D346E was, at least in part, due to its increased affinity to HDAC1. Maspin(D346E was also more potent than maspin(WT as an HDAC inhibitor. Taken together, our evidence demonstrates that D(346 is a critical cis-element in maspin sequence that determines the molecular context and subcellular localization of maspin. A mechanistic model derived from our evidence suggests a new window of opportunity for the development of maspin-based biologically competent HDAC inhibitors for cancer treatment.

  2. Experimental study of the kinetic inductance fraction of superconducting coplanar waveguide

    Energy Technology Data Exchange (ETDEWEB)

    Gao, J. [California Institute of Technology, Pasadena, CA 91125 (United States)]. E-mail: jgao@ist.caltech.edu; Zmuidzinas, J. [California Institute of Technology, Pasadena, CA 91125 (United States); Mazin, B.A. [Jet Propulsion Lab, Pasadena, CA 91107 (United States); Day, P.K. [Jet Propulsion Lab, Pasadena, CA 91107 (United States); Leduc, H.G. [Jet Propulsion Lab, Pasadena, CA 91107 (United States)

    2006-04-15

    We have studied the kinetic inductance fraction (ratio of kinetic inductance to total inductance) of superconducting coplanar waveguides (CPWs) by measuring the resonance frequency of CPW transmission line resonators. We describe a procedure for accurately determining the kinetic inductance of transmission line geometries with small kinetic inductance fractions. In this approach, we compare the temperature dependence of the resonance frequency with that of a resonator of the same film thickness but with a large kinetic inductance fraction. We present data for 200 nm-thick Al CPWs of several geometries and compare that with our own calculations and with calculations found in literature.

  3. Phytochemical screening and anticonvulsant studies of ethyl acetate fraction of Globimetula braunii on laboratory animals.

    Science.gov (United States)

    Aliyu, Musa Mumammad; Musa, Abdullahi Isma'il; Kamal, Muhammad Ja'afar; Mohammed, Magaji Garba

    2014-04-01

    To investigate the phytochemical properties and the anticonvulsant potential of the ethyl acetate soluble fraction of ethanol leaf extract of Globimetula braunii, a plant used in ethnomedicine for the treatment of epilepsy. The phytochemical screening was carried out using standard protocol while the anticonvulsant activity was studied using maximal electroshock test in chicks, pentylenetetrazole and 4-aminopyridine-induced seizures in mice. The preliminary phytochemical screening carried out on the crude ethanol extract revealed the presence of saponins, carbohydrates, flavonoids, tannins, anthraquinones and steroids. Similarly, tannins, flavonoids and steroids/terpenes were found to be present in the ethyl acetate fraction. In the pharmacological screening, 150 mg/kg of the fraction protected 83.33% of animals against pentylenetetrazole-induced seizure in mice whereas sodium valproate a standard anti-epileptic drug offered 100% protection. In the 4-aminopyridine-induced seizure model, the fraction produced a significant (P<0.05) increase in the mean onset of seizure in unprotected animals. The fraction did not exhibit a significant activity against maximal electroshock convulsion. The median lethal dose of the fraction was found to be 1 261.91 mg/kg. These results suggest that the ethyl acetate fraction of Globimetula braunii leaves extract possesses psychoactive compound that may be useful in the management of petit mal epilepsy and lend credence to the ethnomedical use of the plant in the management of epilepsy.

  4. Dose fractionation and single subject studies in PET

    Science.gov (United States)

    Balakrishnan, Karthikayan

    Conventional positron emission tomography (PET) for cognitive brain studies typically relies on information collected from the distribution of decays following an injection of 15O-labeled water. The number of injections that can be administered to the subject are constrained by radiation dose to the subject and total length of the PET scan. The standard protocol involves 8--10 injections of H152O separated by approximately 5--7 half-lives of 15O. The number of activation conditions that can be realistically studied in a standard PET session is between 8 and 10. This work investigates the physiological response of a simulated subject to H152O injections that are administered in small doses (1--5 mCi) with short inter-injection intervals (40--180 seconds). A larger number of activation conditions are presented to the subject with a wider variation in the activation paradigm. Repeat conditions are studies. Signal averaging methods are feasible with this method of dose administration. Sinograms from scans with similar activation conditions are summed together before reconstruction. The signal in the primary activation region of the brain is shown to increase while suppressing the contribution of secondary activation regions in the brain. The contrast of the final image is similarly increased which leads to easier identification of the primary activation region. An automated H152O -production unit controlled by a PC running LabView software was developed to produce the dose required for the injection sequence by controlling the flow of H152O -vapor that diffuses across a semi-permeable membrane into saline. The unit is capable of producing H152O rapidly for both the standard and the proposed dose administration methods. The system also detects the bolus arrival time at the subject's lungs using a small external plastic detector. Activation sequence commences with the rise in radioactivity observed by the detector. The simulations indicate that inter-injection intervals

  5. Screening studies of yeasts capable of utilizing petroleum fractions

    Energy Technology Data Exchange (ETDEWEB)

    El-Masry, H.G.; Foda, M.S.

    1979-01-01

    In these studies 23 yeasts cultures belonging to 10 genera of ascosporogenous, ballistosporogenous, and asporogenous yeasts, were screened with respect to their abilities of hydrocarbon utilization in synthetic media. Thus, kerosene, n-hexadecane, and wax distillate were compared as sole carbon sources in 2% final concentration. Kerosene exhibited marked inhibition on the growth of the majority of the strains, whereas active growth was observed with Debaryomyces vanrijii and many species of the genus Candida in media with n-hexadecane or wax distillate as sole source of carbon. In addition, some cultures belonging to the genera Sporobolomyces, Hansenula, Cryptococcus, and Trigonopsis could utilize some of these substrates, but to a lesser extent. Highest yield of cells and protein was obtained with Candida lipolytica NRRL 1094 in n-hexadecane medium, supplied with 0.03% yeast extract and trace element solutions. The results are discussed with respect to the possibilities of using new yeast genera, with special reference to the genus Debaryomyces, in microbial protein production.

  6. Temporal variations in metallothionein concentration and subcellular distribution of metals in gills and digestive glands of the oyster Crassostrea angulata

    Directory of Open Access Journals (Sweden)

    Chiara Trombini

    2010-11-01

    Full Text Available The metallothionein levels and metal concentrations in whole body, digestive gland and gills of Crassostrea angulata were analyzed in field samples collected from the River Guadalquivir estuary over several years following a mining waste spill upstream. The subcellular distribution of metals was analyzed to determine the mechanisms involved in the detoxification process. The highest metallothionein levels were reported in the digestive gland shortly after the mining contamination event. In this organ, metals are stored preferentially in the non-cytosolic fraction when increased bioaccumulation takes place. In the cytosol of the gills, metals are associated with metallothionein, whereas in the digestive gland, the distribution of metals between metallothioneins and high molecular weight proteins is similar. Metallothionein variation cannot be explained by metals alone; other abiotic factors must be taken into account. In order to use metallothionein as a metal exposure biomarker in field studies, natural variability needs to be taken into account for the correct interpretation of results.

  7. Capillary electrophoretic analysis reveals subcellular binding between individual mitochondria and cytoskeleton

    Science.gov (United States)

    Kostal, Vratislav; Arriaga, Edgar A.

    2011-01-01

    Interactions between the cytoskeleton and mitochondria are essential for normal cellular function. An assessment of such interactions is commonly based on bulk analysis of mitochondrial and cytoskeletal markers present in a given sample, which assumes complete binding between these two organelle types. Such measurements are biased because they rarely account for non-bound ‘free’ subcellular species. Here we report on the use of capillary electrophoresis with dual laser induced fluorescence detection (CE-LIF) to identify, classify, count and quantify properties of individual binding events of mitochondria and cytoskeleton. Mitochondria were fluorescently labeled with DsRed2 while F-actin, a major cytoskeletal component, was fluorescently labeled with Alexa488-phalloidin. In a typical subcellular fraction of L6 myoblasts, 79% of mitochondrial events did not have detectable levels of F-actin, while the rest had on average ~2 zeptomole F-actin, which theoretically represents a ~ 2.5-μm long network of actin filaments per event. Trypsin treatment of L6 subcellular fractions prior to analysis decreased the fraction of mitochondrial events with detectable levels of F-actin, which is expected from digestion of cytoskeletal proteins on the surface of mitochondria. The electrophoretic mobility distributions of the individual events were also used to further distinguish between cytoskeleton-bound from cytoskeleton-free mitochondrial events. The CE-LIF approach described here could be further developed to explore cytoskeleton interactions with other subcellular structures, the effects of cytoskeleton destabilizing drugs, and the progression of viral infections. PMID:21309532

  8. Exploitation of eukaryotic subcellular targeting mechanisms by bacterial effectors.

    Science.gov (United States)

    Hicks, Stuart W; Galán, Jorge E

    2013-05-01

    Several bacterial species have evolved specialized secretion systems to deliver bacterial effector proteins into eukaryotic cells. These effectors have the capacity to modulate host cell pathways in order to promote bacterial survival and replication. The spatial and temporal context in which the effectors exert their biochemical activities is crucial for their function. To fully understand effector function in the context of infection, we need to understand the mechanisms that lead to the precise subcellular localization of effectors following their delivery into host cells. Recent studies have shown that bacterial effectors exploit host cell machinery to accurately target their biochemical activities within the host cell.

  9. Subcellular Localization of Carotenoid Biosynthesis in Synechocystis sp. PCC 6803.

    Directory of Open Access Journals (Sweden)

    Lifang Zhang

    Full Text Available The biosynthesis pathway of carotenoids in cyanobacteria is partly described. However, the subcellular localization of individual steps is so far unknown. Carotenoid analysis of different membrane subfractions in Synechocystis sp. PCC6803 shows that "light" plasma membranes have a high carotenoid/protein ratio, when compared to "heavier" plasma membranes or thylakoids. The localization of CrtQ and CrtO, two well-defined carotenoid synthesis pathway enzymes in Synechocystis, was studied by epitope tagging and western blots. Both enzymes are locally more abundant in plasma membranes than in thylakoids, implying that the plasma membrane has higher synthesis rates of β-carotene precursor molecules and echinenone.

  10. Study of the reproducibility and selectivity of coal tar pitch fractionation by extrography on alumina

    Energy Technology Data Exchange (ETDEWEB)

    Cebolla, V.L.; Weber, J.V.; Swistek, M.; Krzton, A.; Wolszczak, J. (Instituto de Carboquimica, Zaragoza (Spain))

    1994-06-01

    The potential of extrography on alumina as a fractionation and characterization technique of coal tar pitches has been evaluated in terms of reproducibility and selectivity of separations. Parameters controlling extrography were carefully selected, and standard conditions were adopted by two different laboratories in a reproducibility study. Results relating to mass balances of extrography, selectivity of separation, thermal behaviour of the separated fractions and coke characteristics were comparable for interlaboratory runs. Selectivity of the separations was followed by chemical gas chromatography-mass spectrometry (g.c.-m.s.), nuclear magnetic resonance (n.m.r.). Fourier transform infrared (FT-i.r.) spectroscopy, thin layer chromatography-FID (t.l.c.-FID) and thermal thermogravimetric (TGA) and differential thermal analysis (DTA) characterizations of both fractions and subfractions collected. Their derived cokes were studied by optical microscopy to determine their respective degree of anisotropy to related chemical structure, thermal reactivity and coke quality. Concerning the mechanism of extrographic elution, analytical data suggest an extractive mechanism for the first eluted fraction, and dominant chromatographic processes for the more polar fractions. 24 refs., 4 figs., 5 tabs.

  11. Supranutritional vitamin E supplementation in pigs: Influence on subcellular deposition of α-tocopherol and on oxidative stability by conventional and derivative spectrophotometry.

    Science.gov (United States)

    Wen, J; Morrissey, P A; Buckley, D J; Sheehy, P J

    1997-11-01

    The influence of three levels of vitamin E (30, 200 and 1000mg kg(-1)) in the diet of pigs on the subcellular deposition of α-tocopherol in muscle and on the oxidative stability determined by conventional and first derivative Spectrophotometry was studied. The content of α-tocopherol in m. gluteo biceps and in mitochondrial and microsomal fractions of the muscle significantly increased (p vitamin E. Concentrations of α-tocopherol in muscle, mitochondria and microsomes of pigs fed diet supplemented with 1000 mg kg(-1) α-tocopheryl acetate were 3.2-, 6.1- and 5.6-fold greater, respectively, than those in their counterparts from the control animals. These differences in α-tocopherol concentration in the subcellular fractions and intact muscle resulted in enhanced stability of the membranes and the tissue when exposed to iron-ascorbate induced peroxidation. When lipid oxidation in the same samples was further measured by the first derivative method, the resultant MDA-TBA values were 59-69% lower in tissue samples, 16-19% lower in mitochondria and 6-9% lower in microsomes than the conventional TBARS values.

  12. Uranium isotope fractionation in Saanich Inlet: A modern analog study of a paleoredox tracer

    Science.gov (United States)

    Holmden, C.; Amini, M.; Francois, R.

    2015-03-01

    Uranium isotope fractionation was studied in the sediment and water of Saanich Inlet, a seasonally anoxic fjord on the east coast of Vancouver Island. The concentration of dissolved U is the same above and below the redoxcline at ˜120 m depth, with an average δ238U value of -0.45 ± 0.06‰ (2 s.e.), which is indistinguishable from seawater values reported in other studies. This finding is consistent with water renewal times for the inlet that are roughly seasonal in frequency, thus hiding the impact of the U losses to the anoxic sediment of the inlet. Complete digests of the anoxic sediment yielded higher δ238U values than seawater (-0.21 ± 0.11‰ (2 s.e.)). By contrast, complete digests of the sediment trap samples yielded lower δ238U values than seawater (-0.52 ± 0.10‰ (2 s.e.)), and marine plankton from the inlet yielded the lowest δ238U value of -1.24 ± 0.17‰ (2σ). Cross-plots of δ238U and δ234U vs. Th/U reveal strong correlations indicative of two-component mixing when the data from traps and anoxic inlet sediment are combined. One mixing end-member is fractionated uranium of seawater origin, with a δ238U value of 0.17 ± 0.14‰ (2σ). The other is detrital uranium with a δ238U value of -0.83 ± 0.12‰ (2σ). The detrital end-member is lower than the range of δ238U values reported in the literature for granitoid igneous rocks (-0.44‰ to -0.17‰, 2σ) (Telus et al., 2012), suggesting that continental weathering fractionates uranium isotopes, with preferential release of 238U. Development and application of U isotopes as a paleoredox proxy has its basis in the nuclear volume fractionation. The data from Saanich Inlet meets this expectation, with a positive fractionation factor (Δaq(VI)sed(IV)) of 0.62 ± 0.17‰ (2σ) calculated as the difference in δ238U between authigenic U in anoxic sediments and sediment traps (+0.17‰) and U dissolved in seawater (-0.45‰). However, it is widely believed that U(VI) reduction in the marine

  13. Experimental studies and model analysis of noble gas fractionation in low-permeability porous media

    Science.gov (United States)

    Ding, Xin; Mack Kennedy, B.; Molins, Sergi; Kneafsey, Timothy; Evans, William C.

    2017-05-01

    Gas flow through the vadose zone from sources at depth involves fractionation effects that can obscure the nature of transport and even the identity of the source. Transport processes are particularly complex in low permeability media but as shown in this study, can be elucidated by measuring the atmospheric noble gases. A series of laboratory column experiments was conducted to evaluate the movement of noble gas from the atmosphere into soil in the presence of a net efflux of CO2, a process that leads to fractionation of the noble gases from their atmospheric abundance ratios. The column packings were designed to simulate natural sedimentary deposition by interlayering low permeability ceramic plates and high permeability beach sand. Gas samples were collected at different depths at CO2 fluxes high enough to cause extreme fractionation of the noble gases (4He/36Ar > 20 times the air ratio). The experimental noble gas fractionation-depth profiles were in good agreement with those predicted by the dusty gas (DG) model, demonstrating the applicability of the DG model across a broad spectrum of environmental conditions. A governing equation based on the dusty gas model was developed to specifically describe noble gas fractionation at each depth that is controlled by the binary diffusion coefficient, Knudsen diffusion coefficient and the ratio of total advection flux to total flux. Finally, the governing equation was used to derive the noble gas fractionation pattern and illustrate how it is influenced by soil CO2 flux, sedimentary sequence, thickness of each sedimentary layer and each layer's physical parameters. Three potential applications of noble gas fractionation are provided: evaluating soil attributes in the path of gas flow from a source at depth to the atmosphere, testing leakage through low permeability barriers used to isolate buried waste, and tracking biological methanogenesis and methane oxidation associated with hydrocarbon degradation.

  14. Validating subcellular localization prediction tools with mycobacterial proteins

    Directory of Open Access Journals (Sweden)

    Niño Luis F

    2009-05-01

    Full Text Available Abstract Background The computational prediction of mycobacterial proteins' subcellular localization is of key importance for proteome annotation and for the identification of new drug targets and vaccine candidates. Several subcellular localization classifiers have been developed over the past few years, which have comprised both general localization and feature-based classifiers. Here, we have validated the ability of different bioinformatics approaches, through the use of SignalP 2.0, TatP 1.0, LipoP 1.0, Phobius, PA-SUB 2.5, PSORTb v.2.0.4 and Gpos-PLoc, to predict secreted bacterial proteins. These computational tools were compared in terms of sensitivity, specificity and Matthew's correlation coefficient (MCC using a set of mycobacterial proteins having less than 40% identity, none of which are included in the training data sets of the validated tools and whose subcellular localization have been experimentally confirmed. These proteins belong to the TBpred training data set, a computational tool specifically designed to predict mycobacterial proteins. Results A final validation set of 272 mycobacterial proteins was obtained from the initial set of 852 mycobacterial proteins. According to the results of the validation metrics, all tools presented specificity above 0.90, while dispersion sensitivity and MCC values were above 0.22. PA-SUB 2.5 presented the highest values; however, these results might be biased due to the methodology used by this tool. PSORTb v.2.0.4 left 56 proteins out of the classification, while Gpos-PLoc left just one protein out. Conclusion Both subcellular localization approaches had high predictive specificity and high recognition of true negatives for the tested data set. Among those tools whose predictions are not based on homology searches against SWISS-PROT, Gpos-PLoc was the general localization tool with the best predictive performance, while SignalP 2.0 was the best tool among the ones using a feature

  15. Validating subcellular localization prediction tools with mycobacterial proteins

    Science.gov (United States)

    Restrepo-Montoya, Daniel; Vizcaíno, Carolina; Niño, Luis F; Ocampo, Marisol; Patarroyo, Manuel E; Patarroyo, Manuel A

    2009-01-01

    Background The computational prediction of mycobacterial proteins' subcellular localization is of key importance for proteome annotation and for the identification of new drug targets and vaccine candidates. Several subcellular localization classifiers have been developed over the past few years, which have comprised both general localization and feature-based classifiers. Here, we have validated the ability of different bioinformatics approaches, through the use of SignalP 2.0, TatP 1.0, LipoP 1.0, Phobius, PA-SUB 2.5, PSORTb v.2.0.4 and Gpos-PLoc, to predict secreted bacterial proteins. These computational tools were compared in terms of sensitivity, specificity and Matthew's correlation coefficient (MCC) using a set of mycobacterial proteins having less than 40% identity, none of which are included in the training data sets of the validated tools and whose subcellular localization have been experimentally confirmed. These proteins belong to the TBpred training data set, a computational tool specifically designed to predict mycobacterial proteins. Results A final validation set of 272 mycobacterial proteins was obtained from the initial set of 852 mycobacterial proteins. According to the results of the validation metrics, all tools presented specificity above 0.90, while dispersion sensitivity and MCC values were above 0.22. PA-SUB 2.5 presented the highest values; however, these results might be biased due to the methodology used by this tool. PSORTb v.2.0.4 left 56 proteins out of the classification, while Gpos-PLoc left just one protein out. Conclusion Both subcellular localization approaches had high predictive specificity and high recognition of true negatives for the tested data set. Among those tools whose predictions are not based on homology searches against SWISS-PROT, Gpos-PLoc was the general localization tool with the best predictive performance, while SignalP 2.0 was the best tool among the ones using a feature-based approach. Even though PA-SUB 2

  16. Comparison of subcellular distribution and chemical forms of cadmium among four soybean cultivars at young seedlings.

    Science.gov (United States)

    Wang, Peng; Deng, Xiaojuan; Huang, Yian; Fang, Xiaolong; Zhang, Jie; Wan, Haibo; Yang, Cunyi

    2015-12-01

    The hydroponic experiment was carried out to investigate the Cd subcellular distribution and chemical forms in roots and shoots among four soybean seedling cultivars with two Cd treatments. HX3 and GC8, two tolerant and low-grain-Cd-accumulating cultivars, had the lowest Cd concentration in roots and high Cd concentration in shoots, while BX10 and ZH24, two sensitive and high-grain-Cd-accumulating cultivars, had the highest Cd concentration in roots and the lowest Cd concentration in shoots at young seedling stage. Furthermore, the sequence of Cd subcellular distribution in roots at two Cd levels was cell wall (53.4-75.5 %) > soluble fraction (15.8-40.4 %) > organelle fraction (2.0-14.7 %), but in shoots, was soluble fraction (39.3-74.8 %) > cell wall (16.0-52.0 %) > organelle (4.8-19.5 %). BX10 and ZH24 had higher Cd concentration in all subcellular fractions in roots, but HX3 and GC8 had higher Cd concentration of soluble fraction in shoots. The sequence of Cd chemical forms in roots was FNacl (64.1-79.5 %) > FHAC (3.4-21.5 %) > Fd-H2O (3.6-13.0 %) > Fethanol (1.4-21.8) > FHCl (0.3-1.6 %) > Fother (0.2-1.4 %) at two Cd levels but, in shoots, was FNacl (19.7-51.4 %) ≥ FHAC (10.2-31.4 %) ≥ Fd-H2O (8.8-28.2 %) ≥ Fethanol (8.9-38.6 %) > FHCl (0.2-9.6 %) > Fother (2.5-11.2 %). BX10 and ZH24 had higher Cd concentrations in each extracted solutions from roots, but from shoots for GC8 and HX3. Taken together, the results uncover that root cell walls and leaf vacuoles might play important roles in Cd detoxification and limiting the symplastic movement of Cd.

  17. Intracellular pH (pHin) and cytosolic calcium ([Ca2+]cyt) regulation via ATPases: studies in cell populations, single cells, and subcellular compartments

    Science.gov (United States)

    Rojas, Jose D.; Sanka, Shankar C.; Gyorke, Sandor; Wesson, Donald E.; Minta, Akwasi; Martinez-Zaguilan, Raul

    1999-07-01

    Changes in pHin and (Ca2+)cyt are important in the signal transduction mechanisms leading to many physiological responses including cell growth, motility, secretion/exocytosis, etc. The concentrations of these ions are regulated via primary and secondary ion transporting mechanisms. In diabetes, specific pH and Ca2+ regulatory mechanism might be altered. To study these ions, we employ fluorescence spectroscopy, and cell imagin spectroscopy/confocal microscopy. pH and Ca2+ indicators are loaded in the cytosol with acetoxymethyl ester forms of dyes, and in endosomal/lysosomal (E/L) compartments by overnight incubation of cells with dextran- conjugated ion fluorescent probes. We focus on specific pH and Ca2+ regulatory systems: plasmalemmal vacuolar- type H+-ATPases (pm V-ATPases) and sarcoplasmic/endoplasmic reticulum Ca2+-ATPases (SERCA). As experimental models, we employ vascular smooth muscle (VSM) and microvascular endothelial cells. We have chosen these cells because they are important in blood flow regulation and in angiogenesis. These processes are altered in diabetes. In many cell types, ion transport processes are dependent on metabolism of glucose for maximal activity. Our main findings are: (a) glycolysis coupling the activity of SERCA is required for cytosolic Ca2+ homeostasis in both VSM and microvascular endothelial cells; (b) E/L compartments are important for pH and Ca2+ regulation via H+-ATPases and SERCA, respectively; and (c) pm-V- ATPases are important for pHin regulation in microvascular endothelial cells.

  18. Sub-cellular force microscopy in single normal and cancer cells.

    Science.gov (United States)

    Babahosseini, H; Carmichael, B; Strobl, J S; Mahmoodi, S N; Agah, M

    2015-08-07

    This work investigates the biomechanical properties of sub-cellular structures of breast cells using atomic force microscopy (AFM). The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity, and the relaxation time of sub-cellular structures. The triple-layered modeling results allow for determination and comparison of the biomechanical properties of the three major sub-cellular structures between normal and cancerous cells: the up plasma membrane/actin cortex, the mid cytoplasm/nucleus, and the low nuclear/integrin sub-domains. The results reveal that the sub-domains become stiffer and significantly more viscous with depth, regardless of cell type. In addition, there is a decreasing trend in the average elastic modulus and apparent viscosity of the all corresponding sub-cellular structures from normal to cancerous cells, which becomes most remarkable in the deeper sub-domain. The presented modeling in this work constitutes a unique AFM-based experimental framework to study the biomechanics of sub-cellular structures. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. The study of polycyclic aromatic hydrocarbons in particulate fractions emitted by office printers and copiers

    Directory of Open Access Journals (Sweden)

    Małgorzata Szewczyńska

    2014-12-01

    Full Text Available Background: This article presents the study of polycyclic aromatic hydrocarbons (PAHs adsorbed on fine particles emitted during the simulated operation of office printers and copiers. Material and Methods: In the study three types of printers, and four types of office copiers were used. Measurements were carried out in a closed measuring chamber. Air samples (fractions of particulate matter, PM10 and PM2.5 were collected on Teflon filters. The analysis of PAHs was carried out according HPLC/FL. Results: The results of qualitative analysis of filters from PM2.5 and PM10 type samplers indicated the presence of the majority (10–14 of PAH congeners. The highest concentration of total PAHs was determined in the PM10 fraction in the air during the operation of a copier, and amounted to 36.52 μg×g–1. The total content of PAHs as determined in the fraction of fine particulates, size of < 2.5 μm, accounts for 48–84% of the PAH content in the < 10 μm fraction for printers and 63–89% for copiers. During the operation of both printers and copiers, benzo(apirene (BaP was identified in both fractions, PM2.5 and PM10. The maximum concentration of BaP in the fraction of < 10 μm particles emitted by a printer amounted to 3.29±0.2 μg×g–1. Conclusions: The studies showed that the composition of emitted substances and fine particles depends on the type of equipment and technology used. Fine particles emitted to the environment and organic compounds, including PAHs adsorbed on them may pose a threat to people working in such an environment. Med Pr 2014;65(6:733–741

  20. Biodynamics of copper oxide nanoparticles and copper ions in an oligochaete - Part II: Subcellular distribution following sediment exposure.

    Science.gov (United States)

    Thit, Amalie; Ramskov, Tina; Croteau, Marie-Noële; Selck, Henriette

    2016-11-01

    The use and likely incidental release of metal nanoparticles (NPs) is steadily increasing. Despite the increasing amount of published literature on metal NP toxicity in the aquatic environment, very little is known about the biological fate of NPs after sediment exposures. Here, we compare the bioavailability and subcellular distribution of copper oxide (CuO) NPs and aqueous Cu (Cu-Aq) in the sediment-dwelling worm Lumbriculus variegatus. Ten days (d) sediment exposure resulted in marginal Cu bioaccumulation in L. variegatus for both forms of Cu. Bioaccumulation was detected because isotopically enriched 65Cu was used as a tracer. Neither burrowing behavior or survival was affected by the exposure. Once incorporated into tissue, Cu loss was negligible over 10 d of elimination in clean sediment (Cu elimination rate constants were not different from zero). With the exception of day 10, differences in bioaccumulation and subcellular distribution between Cu forms were either not detectable or marginal. After 10 d of exposure to Cu-Aq, the accumulated Cu was primarily partitioned in the subcellular fraction containing metallothionein-like proteins (MTLP, ≈40%) and cellular debris (CD, ≈30%). Cu concentrations in these fractions were significantly higher than in controls. For worms exposed to CuO NPs for 10 d, most of the accumulated Cu was partitioned in the CD fraction (≈40%), which was the only subcellular fraction where the Cu concentration was significantly higher than for the control group. Our results indicate that L. variegatus handle the two Cu forms differently. However, longer-term exposures are suggested in order to clearly highlight differences in the subcellular distribution of these two Cu forms. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Biodynamics of copper oxide nanoparticles and copper ions in an oligochaete - Part II: Subcellular distribution following sediment exposure

    Science.gov (United States)

    Thit, Amalie; Ramskov, Tina; Croteau, Marie-Noele; Selck, Henriette

    2016-01-01

    The use and likely incidental release of metal nanoparticles (NPs) is steadily increasing. Despite the increasing amount of published literature on metal NP toxicity in the aquatic environment, very little is known about the biological fate of NPs after sediment exposures. Here, we compare the bioavailability and subcellular distribution of copper oxide (CuO) NPs and aqueous Cu (Cu-Aq) in the sediment-dwelling worm Lumbriculus variegatus. Ten days (d) sediment exposure resulted in marginal Cu bioaccumulation in L. variegatus for both forms of Cu. Bioaccumulation was detected because isotopically enriched 65Cu was used as a tracer. Neither burrowing behavior or survival was affected by the exposure. Once incorporated into tissue, Cu loss was negligible over 10 d of elimination in clean sediment (Cu elimination rate constants were not different from zero). With the exception of day 10, differences in bioaccumulation and subcellular distribution between Cu forms were either not detectable or marginal. After 10 d of exposure to Cu-Aq, the accumulated Cu was primarily partitioned in the subcellular fraction containing metallothionein-like proteins (MTLP, ≈40%) and cellular debris (CD, ≈30%). Cu concentrations in these fractions were significantly higher than in controls. For worms exposed to CuO NPs for 10 d, most of the accumulated Cu was partitioned in the CD fraction (≈40%), which was the only subcellular fraction where the Cu concentration was significantly higher than for the control group. Our results indicate that L. variegatus handle the two Cu forms differently. However, longer-term exposures are suggested in order to clearly highlight differences in the subcellular distribution of these two Cu forms.

  2. High-Resolution Secondary Ion Mass Spectrometry Reveals the Contrasting Subcellular Distribution of Arsenic and Silicon in Rice Roots

    National Research Council Canada - National Science Library

    Katie L. Moore; Markus Schröder; Zhongchang Wu; Barry G.H. Martin; Chris R. Hawes; Steve P. McGrath; Malcolm J. Hawkesford; Jian Feng Ma; Fang-Jie Zhao; Chris R.M. Grovenor

    2011-01-01

    .... In this study, the cellular and subcellular distributions of As and silicon (Si) in rice roots were investigated using high-pressure freezing, high-resolution secondary ion mass spectrometry, and transmission electron microscopy...

  3. Quantification of subcellular glycogen in resting human muscle: granule size, number, and location.

    Science.gov (United States)

    Marchand, I; Chorneyko, K; Tarnopolsky, M; Hamilton, S; Shearer, J; Potvin, J; Graham, T E

    2002-11-01

    A few qualitative investigations suggested that location of muscle glycogen (G) granules in specific sites may be associated with distinct metabolic roles. Similarly, it has been suggested that the acid-soluble and -insoluble G fractions (macro- and proglycogen, respectively) are different metabolic pools and also could exist as separate entities. We employed a transmission electron microscopic technique to quantify subcellular G particle size, number, and location in human vastus lateralis biopsies of 11 resting men. The intra- and interobserver variability for the various measures was generally etam and followed a continuous, normal distribution. This implies that proglycogen is not a distinct entity, but rather that pro- and macroglycogen are divisions of smaller and larger molecules. These results demonstrate a compartmentalized pattern of subcellular G deposition in human skeletal muscle for both the size and density of granules.

  4. Study of fractional ablative laser in surgical and post traumatic scar

    Directory of Open Access Journals (Sweden)

    Nagat Sobhy

    2012-07-01

    Full Text Available Introduction: Ablative, fractional lasers generate microscopic columns of coagulated tissue through the epidermis and dermis to evoke a wound healing response. In this study, we examined the efficacy and safety of fractional ablative 2940nm erbium: YAG laser in the treatment of surgical and post-traumatic scars. Fractional laser photothermolysis is the latest in the broad range of Er: YAG laser technique. This technique promises a novel means of providing treatments that would be as effective as traditional Er: YAG, while further reducing their down time and risk.Aim of the Work: The aim of this work is to assess the efficacy and safety of variable square pulse (VSP fractional Er: YAG laser for the treatment of surgical and post-traumatic scars; both clinically and histopathologically.Methods: Clinical studies were conducted on a range of surgical and post-traumatic scars with a 2940nm erbium: YAG fractional ablative laser varying energy, pulse widths, treatment passes, and number of treatments: twenty subjects, with Fitzpatrick skin types III-IV, received two to five treatments at one month interval and a follow up period for 3 months. Clinical and histopathological evaluation of the results was performed.Results: Almost all patients improved both clinically and histopathologically. Clinical improvement in scars according to investigator assessment: 40% of patients had excellent improvement of 76-100% (grade 3, 50% of patients had good improvement of 50-75% (grade 2, 10% had fair improvement of 26-49% (grade 1 at three month follow up. Histologic findings demonstrated remodeling of scar tissue with renewal and reorganization of collagen fibers in the dermis was noted two weeks post-treatment.Conclusion: These data illustrate the safety and efficacy of the 2940nm erbium:YAG fractional ablative laser in the treatment of surgical and post-traumatic scars with short down time period, and almost no incidence of complication.

  5. Why do some studies find that CPR fraction is not a predictor of survival?

    NARCIS (Netherlands)

    Wik, L.; Olsen, J.A.; Persse, D.; Sterz, F.; Lozano Jr, M.; Brouwer, M.A.; Westfall, M.; Souders, C.M.; Travis, D.T.; Herken, U.R.; Lerner, E.B.

    2016-01-01

    INTRODUCTION: An 80% chest compression fraction (CCF) during resuscitation is recommended. However, heterogeneous results in CCF studies were found during the 2015 Consensus on Science (CoS), which may be because chest compressions are stopped for a wide variety of reasons including providing

  6. A Study of the Hepatic Tolerance of the Ethyl Acetate Fraction of ...

    African Journals Online (AJOL)

    Purpose: In this study, the effect of the ethyl acetate fraction of the extract of Morinda morindoides (Baker) Milne-Redhead (Rubiaceae) on the tissue and metabolic integrity of rabbit liver was evaluated. Methods: Thirty rabbits (divided equally between male and female) were randomly distributed into five (5) groups of six (6) ...

  7. Experimental study of the viscosity of suspensions: effect of solid fraction, particle size and suspending liquid

    NARCIS (Netherlands)

    Konijn, B.J.; Sanderink, O.B.J.; Kruyt, Nicolaas P.

    2014-01-01

    The behaviour of nearly neutrally-buoyant suspensions has been studied experimentally, using a concentric-cylinder rheometer. The effect on the suspension viscosity of: (i) solid fraction, (ii) diameter of the solid, spherical particles, (iii) viscosity of the suspending liquid, and (iv) shear rate

  8. A study of the anti-inflammatory effects of the ethyl acetate fraction of ...

    African Journals Online (AJOL)

    ... optimize the practical efficacies of herbal medicines. Materials and Methods: In this study, the anti-inflammatory effects of the ethyl acetate fraction of the methanol extract of FF (FFE) were assessed by measuring NO and PGE2 production by and intracellular ROS and protein levels of iNOS and COX-2 in RAW 264.7 cells.

  9. A study of fractional Schrödinger equation composed of Jumarie ...

    Indian Academy of Sciences (India)

    2017-03-27

    Mar 27, 2017 ... [8] A Kilbas, H M Srivastava and J J Trujillo, Theory and appli- cations of fractional differential equations (North-Holland. Mathematics Studies, Elsevier Science, Amsterdam, The. Netherlands, 2006) p. 2014. [9] G Jumarie, Comput. Math. Appl. 51(9–10), 1367 (2006). [10] G M Mittag-Leffler, C. R. Acad. Sci.

  10. Immunocytochemical localization and subcellular site of lectin synthesis in developing wheat embryos

    Energy Technology Data Exchange (ETDEWEB)

    Raikhel, N.V.; Peumans, W.J.

    1986-04-01

    Appearance of wheat germ agglutinin (WGA) during wheat germ embryogenesis was studied using indirect immunocytochemical methods at the light and electron microscope levels. Developing embryos were labelled with (/sup 35/S) cysteine in pulse and pulse-chase experiments to study the synthesis and transport of the lectin to protein bodies (PB). The radical, and coleorhiza first accumulated WGA around 10 days post anthesis (DPA), while WGA was found in the epiblast and coleoptile 15 and 20 DPA respectively. At the subcellular level WGA can be seen first in a small developing PB which later fused with larger ones. WGA was distributed evenly throughout the PB. When tissue was pulse-labelled, fractionated on an isopycnic sucrose gradient and exposed to detergent, the incorporated radioactivity of released lectin coincided with the position of the endoplasmic reticulum (ER) marker enzyme NADH-cytochrome c reductase. Both radioactivity and enzyme activity shifted to a higher density in the presence of 2 mM Mg acetate, indicating that radioactive lectin was associated with the rough ER.

  11. Fractionated SRT using VMAT and Gamma Knife for brain metastases and gliomas--a planning study.

    Science.gov (United States)

    Huss, Marie; Barsoum, Pierre; Dodoo, Ernest; Sinclair, Georges; Toma-Dasu, Iuliana

    2015-11-08

    Stereotactic radiosurgery using Gamma Knife (GK) or linear accelerators has been used for decades to treat brain tumors in one fraction. A new positioning system, Extend™, was introduced by Elekta AB for fractionated stereotactic radiotherapy (SRT) with GK. Another option for fractionated SRT is advanced planning and delivery using linacs and volumetric modulated arc therapy (VMAT). This project aims to assess the performance of GK Extend™ for delivering fractionated SRT by comparing GK treatments plans for brain targets performed using Leksell GammaPlan (LGP) with VMAT treatment plans. Several targets were considered for the planning: simulated metastasis- and glioma-like targets surrounding an organ at risk (OAR), as well as three clinical cases of metastases. Physical parameters such as conformity, gradient index, dose to OARs, and brain volume receiving doses above the threshold associated with risk of damaging healthy tissue, were determined and compared for the treatment plans. The results showed that GK produced better dose distributions for target volumes below 15 cm3, while VMAT results in better dose conformity to the target and lower doses to the OARs in case of fractionated treatments for large or irregular volumes. The volume receiving doses above a threshold associated with increased risk of damage to normal brain tissue was also smaller for VMAT. The GK consistently performed better than VMAT in producing a lower dose-bath to the brain. The above is subjected only to margin-dependent fractionated radiotherapy (CTV/PTV). The results of this study could lead to clinically significant decisions regarding the choice of the radiotherapy technique for brain targets.

  12. Use of correspondence discriminant analysis to predict the subcellular location of bacterial proteins.

    Science.gov (United States)

    Perrière, Guy; Thioulouse, Jean

    2003-02-01

    Correspondence discriminant analysis (CDA) is a multivariate statistical method derived from discriminant analysis which can be used on contingency tables. We have used CDA to separate Gram negative bacteria proteins according to their subcellular location. The high resolution of the discrimination obtained makes this method a good tool to predict subcellular location when this information is not known. The main advantage of this technique is its simplicity. Indeed, by computing two linear formulae on amino acid composition, it is possible to classify a protein into one of the three classes of subcellular location we have defined. The CDA itself can be computed with the ADE-4 software package that can be downloaded, as well as the data set used in this study, from the Pôle Bio-Informatique Lyonnais (PBIL) server at http://pbil.univ-lyon1.fr.

  13. Subcellular Distribution of Glutathione Precursors in Arabidopsis thaliana

    Science.gov (United States)

    Koffler, Barbara Eva; Maier, Romana; Zechmann, Bernd

    2011-01-01

    Abstract Glutathione is an important antioxidant and has many important functions in plant development, growth and defense. Glutathione synthesis and degradation is highly compartment-specific and relies on the subcellular availability of its precursors, cysteine, glutamate, glycine and γ-glutamylcysteine especially in plastids and the cytosol which are considered as the main centers for glutathione synthesis. The availability of glutathione precursors within these cell compartments is therefore of great importance for successful plant development and defense. The aim of this study was to investigate the compartment-specific importance of glutathione precursors in Arabidopsis thaliana. The subcellular distribution was compared between wild type plants (Col-0), plants with impaired glutathione synthesis (glutathione deficient pad2-1 mutant, wild type plants treated with buthionine sulfoximine), and one complemented line (OE3) with restored glutathione synthesis. Immunocytohistochemistry revealed that the inhibition of glutathione synthesis induced the accumulation of the glutathione precursors cysteine, glutamate and glycine in most cell compartments including plastids and the cytosol. A strong decrease could be observed in γ-glutamylcysteine (γ-EC) contents in these cell compartments. These experiments demonstrated that the inhibition of γ-glutamylcysteine synthetase (GSH1) – the first enzyme of glutathione synthesis – causes a reduction of γ-EC levels and an accumulation of all other glutathione precursors within the cells. PMID:22050910

  14. Subcellular localization prediction through boosting association rules.

    Science.gov (United States)

    Yoon, Yongwook; Lee, Gary Geunbae

    2012-01-01

    Computational methods for predicting protein subcellular localization have used various types of features, including N-terminal sorting signals, amino acid compositions, and text annotations from protein databases. Our approach does not use biological knowledge such as the sorting signals or homologues, but use just protein sequence information. The method divides a protein sequence into short $k$-mer sequence fragments which can be mapped to word features in document classification. A large number of class association rules are mined from the protein sequence examples that range from the N-terminus to the C-terminus. Then, a boosting algorithm is applied to those rules to build up a final classifier. Experimental results using benchmark datasets show our method is excellent in terms of both the classification performance and the test coverage. The result also implies that the $k$-mer sequence features which determine subcellular locations do not necessarily exist in specific positions of a protein sequence. Online prediction service implementing our method is available at http://isoft.postech.ac.kr/research/BCAR/subcell.

  15. Experimental studies of equilibrium iron isotope fractionation in ferric aquo-chloro complexes

    Science.gov (United States)

    Hill, Pamela S.; Schauble, Edwin A.; Shahar, Anat; Tonui, Eric; Young, Edward D.

    2009-04-01

    Here we compare new experimental studies with theoretical predictions of equilibrium iron isotopic fractionation among aqueous ferric chloride complexes (Fe(H 2O) 63+, FeCl(H 2O) 52+, FeCl 2(H 2O) 4+, FeCl 3 (H 2O) 3, and FeCl 4-), using the Fe-Cl-H 2O system as a simple, easily-modeled example of the larger variety of iron-ligand compounds, such as chlorides, sulfides, simple organic acids, and siderophores. Isotopic fractionation ( 56Fe/ 54Fe) among naturally occuring iron-bearing species at Earth surface temperatures (up to ˜3‰) is usually attributed to redox effects in the environment. However, theoretical modeling of reduced isotopic partition functions among iron-bearing species in solution also predicts fractionations of similar magnitude due to non-redox changes in speciation (i.e., ligand bond strength and coordination number). In the present study, fractionations are measured in a series of low pH ([H +] = 5 M) solutions of ferric chloride (total Fe = 0.0749 mol/L) at chlorinities ranging from 0.5 to 5.0 mol/L. Advantage is taken of the unique solubility of FeCl 4- in immiscible diethyl ether to create a separate spectator phase, used to monitor changing fractionation in the aqueous solution. Δ 56Fe aq-eth = δ 56Fe (total Fe remaining in aqueous phase)-δ 56Fe (FeCl 4- in ether phase) is determined for each solution via MC-ICPMS analysis. Both experiments and theoretical calculations of Δ 56Fe aq-eth show a downward trend with increasing chlorinity: Δ 56Fe aq-eth is greatest at low chlorinity, where FeCl 2(H 2O) 4+ is the dominant species, and smallest at high chlorinity where FeCl 3(H 2O) 3 is dominant. The experimental Δ 56Fe aq-eth ranges from 0.8‰ at [Cl -] = 0.5 M to 0.0‰ at [Cl -] = 5.0 M, a decrease in aqueous-ether fractionation of 0.8‰. This is very close to the theoretically predicted decreases in Δ 56Fe aq-eth, which range from 1.0 to 0.7‰, depending on the ab initio model. The rate of isotopic exchange and attainment of

  16. Subcellular Redox Targeting: Bridging in Vitro and in Vivo Chemical Biology.

    Science.gov (United States)

    Long, Marcus J C; Poganik, Jesse R; Ghosh, Souradyuti; Aye, Yimon

    2017-03-17

    Networks of redox sensor proteins within discrete microdomains regulate the flow of redox signaling. Yet, the inherent reactivity of redox signals complicates the study of specific redox events and pathways by traditional methods. Herein, we review designer chemistries capable of measuring flux and/or mimicking subcellular redox signaling at the cellular and organismal level. Such efforts have begun to decipher the logic underlying organelle-, site-, and target-specific redox signaling in vitro and in vivo. These data highlight chemical biology as a perfect gateway to interrogate how nature choreographs subcellular redox chemistry to drive precision redox biology.

  17. Profiling study of the major and minor components of kaffir lime oil (Citrus hystrix DC.) in the fractional distillation process.

    Science.gov (United States)

    Warsito, Warsito; Palungan, Maimunah Hindun; Utomo, Edy Priyo

    2017-01-01

    Essential oil is consisting of complex component. It is divided into major and minor component. Therefore, this study aims to examine the distribution of major and minor components on Kaffir lime oil by using fractional distillation. Fractional distillation and distributional analysis of components within fractions have been performed on kaffir lime oil (Citrus hystrix DC.). Fractional distillation was performed by using PiloDist 104-VTU, column length of 2 m (number of plate 120), the system pressure was set on 5 and 10 mBar, while the reflux ratio varied on 10/10, 20/10 and 60/10, and the chemical composition analysis was done by using GC-MS. Chemical composition of the distillated lime oil consisted of mix-twigs and leaves that composed of 20 compounds, with five main components β-citronellal (46.40%), L-linalool (13.11%), β-citronellol (11.03%), citronelyl acetate (6.76%) and sabinen (5.91%). The optimum conditions for fractional distillation were obtained at 5 mBar pressure with reflux ratio of 10/10. Components of β -citronellal and L-linalool were distributed in the fraction-1 to fraction 9, hydrocarbon monoterpenes components were distributed only on the fraction-1 to fraction 4, while the oxygenated monoterpenes components dominated the fraction-5 to fraction-9. The highest level of β-citronellal was 84.86% (fraction-7), L-linalool 20.13% (fraction-5), sabinen 19.83% (fraction-1), and the component level of 4-terpeneol, β-citronellol and sitronelyl acetate respectively 7.16%; 12.27%; 5.22% (fraction-9).

  18. Parasites modify sub-cellular partitioning of metals in the gut of fish

    NARCIS (Netherlands)

    Oyoo-Okoth, E.; Admiraal, W.; Osano, O.; Kraak, M.H.S.; Gichuki, J.; Ogwai, C.

    2012-01-01

    Infestation of fish by parasites may influence metal accumulation patterns in the host. However, the subcellular mechanisms of these processes have rarely been studied. Therefore, this study determined how a cyprinid fish (Rastrineobola argentea) partitioned four metals (Cd, Cr, Zn and Cu) in the

  19. Study of the 125 GeV Standard Model Higgs Boson Partial Widths and Branching Fractions

    CERN Document Server

    Almeida, Leandro G; Pokorski, Stefan; Wells, James D

    2014-01-01

    The discovery of the Higgs boson, with mass known to better than the percent level, enables for the first time precision Higgs boson analyses. Toward this goal, we define an expansion formalism of the Higgs boson partial widths and branching fractions that facilitates such studies. This expansion yields the observables as a perturbative expansion around reference values of Standard Model input observables (quark masses, QCD coupling constant, etc.). We compute the coefficients of the expansion using state-of-the-art results. We also study the various sources of uncertainties in computing the partial widths and branching fractions more precisely. We discuss the impact of these results with efforts to discern new physics through precision Higgs boson studies.

  20. Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Dick Jeffrey M

    2009-07-01

    Full Text Available Abstract Background Protein subcellular localization and differences in oxidation state between subcellular compartments are two well-studied features of the the cellular organization of S. cerevisiae (yeast. Theories about the origin of subcellular organization are assisted by computational models that can integrate data from observations of compositional and chemical properties of the system. Presentation and implications of the hypothesis I adopt the hypothesis that the state of yeast subcellular organization is in a local energy minimum. This hypothesis implies that equilibrium thermodynamic models can yield predictions about the interdependence between populations of proteins and their subcellular chemical environments. Testing the hypothesis Three types of tests are proposed. First, there should be correlations between modeled and observed oxidation states for different compartments. Second, there should be a correspondence between the energy requirements of protein formation and the order the appearance of organelles during cellular development. Third, there should be correlations between the predicted and observed relative abundances of interacting proteins within compartments. Results The relative metastability fields of subcellular homologs of glutaredoxin and thioredoxin indicate a trend from less to more oxidizing as mitochondrion – cytoplasm – nucleus. Representing the overall amino acid compositions of proteins in 23 different compartments each with a single reference model protein suggests that the formation reactions for proteins in the vacuole (in relatively oxidizing conditions, ER and early Golgi (in relatively reducing conditions are relatively highly favored, while that for the microtubule is the most costly. The relative abundances of model proteins for each compartment inferred from experimental data were found in some cases to correlate with the predicted abundances, and both positive and negative correlations were

  1. Fractional Carbon Dioxide Laser for Keratosis Pilaris: A Single-Blind, Randomized, Comparative Study

    Directory of Open Access Journals (Sweden)

    Vasanop Vachiramon

    2016-01-01

    Full Text Available Objective. Keratosis pilaris (KP is a common condition which can frequently be cosmetically disturbing. Topical treatments can be used with limited efficacy. The objective of this study is to evaluate the effectiveness and safety of fractional carbon dioxide (CO2 laser for the treatment of KP. Patients and Methods. A prospective, randomized, single-blinded, intraindividual comparative study was conducted on adult patients with KP. A single session of fractional CO2 laser was performed to one side of arm whereas the contralateral side served as control. Patients were scheduled for follow-up at 4 and 12 weeks after treatment. Clinical improvement was graded subjectively by blinded dermatologists. Patients rated treatment satisfaction at the end of the study. Results. Twenty patients completed the study. All patients stated that the laser treatment improved KP lesions. At 12-week follow-up, 30% of lesions on the laser-treated side had moderate to good improvement according to physicians’ global assessment (p=0.02. Keratotic papules and hyperpigmentation appeared to respond better than the erythematous component. Four patients with Fitzpatrick skin type V developed transient pigmentary alteration. Conclusions. Fractional CO2 laser treatment may be offered to patients with KP. Dark-skinned patients should be treated with special caution.

  2. Using blocked fractional factorial designs to construct discrete choice experiments for healthcare studies.

    Science.gov (United States)

    Jaynes, Jessica; Wong, Weng-Kee; Xu, Hongquan

    2016-07-10

    Discrete choice experiments (DCEs) are increasingly used for studying and quantifying subjects preferences in a wide variety of healthcare applications. They provide a rich source of data to assess real-life decision-making processes, which involve trade-offs between desirable characteristics pertaining to health and healthcare and identification of key attributes affecting healthcare. The choice of the design for a DCE is critical because it determines which attributes' effects and their interactions are identifiable. We apply blocked fractional factorial designs to construct DCEs and address some identification issues by utilizing the known structure of blocked fractional factorial designs. Our design techniques can be applied to several situations including DCEs where attributes have different number of levels. We demonstrate our design methodology using two healthcare studies to evaluate (i) asthma patients' preferences for symptom-based outcome measures and (ii) patient preference for breast screening services. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  3. Comparison of testosterone fractions between Framingham Heart Study participants and Japanese participants

    OpenAIRE

    Taya, Masaki; Koh, Eitetsu; Izumi, Kouji; Iijima, Masashi; Maeda, Yuji; Matsushita, Tomohiko; Iwamoto, Teruaki; Namiki, Mikio

    2014-01-01

    Objectives: To determine testosterone fractions in Japanese men and to compare these values with those of Framingham Heart Study participants. Methods: We enrolled 498 healthy Japanese men. Total testosterone was assayed by liquid chromatography tandem mass spectrometry, sex hormone-binding globulin was assayed by immunoassay and free testosterone was calculated by a laboratory at the Boston Medical Center. Analog-based free testosterone and immunoassay-based total testosterone were determine...

  4. Toxicological studies on the purified protoberberine alkaloidal fraction of Enantia chlorantha Oliv (ANNONACEAE).

    Science.gov (United States)

    Moody, J O; Ogundipe, O D; Akang, E U U; Agbedana, E O

    2007-12-01

    We have examined the cumulative effects of the protoberberine alkaloidal fraction (AF) of the stein bark ethanolic extracts of Enantia chlorantha on some body tissues and organs as well as on certain biochemical and metabolic parameters in mice. Acute and sub-chronic toxicity studies of the alkaloidal fractions of Enantia chlorantha were carried out in 120 mice using oral and intraperitoneal administrations. Fatality was not recorded in mice injected intraperitonealy with 100 mg kg(-1) and 150 mg kg(-1) dose level but larger doses resulted in death and the mean lethal dose (LD50) toxicity studies showed neither behavioural/untoward reactions nor death in any of the animals. The histopathological examination of the test animals when compared with the control revealed that, the sub-chronic use of the alkaloidal fractions does not have any pathological effects (lesion) on the organs examined (the stomach, the kidney, the oesophagus and the liver) except the lungs which showed mild and moderate oedema. The biochemical and metabolic analysis of the mice plasma did not show any significant difference when the corresponding values for the test mice were compared with the control mice (P > 0.05) at the end of the 14 days treatment using both 20 mg kg(-1) and 2 mg kg(-1) dose levels. The results obtained in this study suggest the relative safety of short-term use of preparations containing E. chlorantha, a very popular antimalarial herbal remedy in Southern Nigeria.

  5. A study of fractional Schrödinger equation composed of Jumarie ...

    Indian Academy of Sciences (India)

    In this paper we have derived the fractional-order Schrödinger equation composed of Jumarie fractional derivative. The solution of this fractional-order Schrödinger equation is obtained in terms of Mittag–Leffler function with complex arguments, and fractional trigonometric functions. A few important properties of the ...

  6. Different subcellular locations of secretome components of Gram-positive bacteria

    NARCIS (Netherlands)

    Buist, Girbe; Ridder, Anja N. J. A.; Kok, Jan; Kuipers, Oscar P.

    2006-01-01

    Gram-positive bacteria contain different types of secretion systems for the transport of proteins into or across the cytoplasmic membrane. Recent studies on subcellular localization of specific components of these secretion systems and their substrates have shown that they can be present at various

  7. Foam fractionation as a tool to study the air-water interface structure-function relationship of wheat gluten hydrolysates.

    Science.gov (United States)

    Wouters, Arno G B; Rombouts, Ine; Schoebrechts, Nele; Fierens, Ellen; Brijs, Kristof; Blecker, Christophe; Delcour, Jan A

    2017-03-01

    Enzymatic hydrolysis of wheat gluten protein improves its solubility and produces hydrolysates with foaming properties which may find applications in food products. First, we here investigated whether foam-liquid fractionation can concentrate wheat gluten peptides with foaming properties. Foam and liquid fractions had high and very low foam stability (FS), respectively. In addition, foam fractions were able to decrease surface tension more pronouncedly than un-fractionated samples and liquid fractions, suggesting they are able to arrange themselves more efficiently at an interface. As a second objective, foam fractionation served as a tool to study the structural properties of the peptides, causing these differences in air-water interfacial behavior. Zeta potential and surface hydrophobicity measurements did not fully explain these differences but suggested that hydrophobic interactions at the air-water interface are more important than electrostatic interactions. RP-HPLC showed a large overlap between foam and liquid fractions. However, a small fraction of very hydrophobic peptides with relatively high average molecular mass was clearly enriched in the foam fraction. These peptides were also more concentrated in un-fractionated DH 2 hydrolysates, which had high FS, than in DH 6 hydrolysates, which had low FS. These peptides most likely play a key role in stabilizing the air-water interface. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Analytical study of fractional equations describing anomalous diffusion of energetic particles

    Science.gov (United States)

    Tawfik, A. M.; Fichtner, H.; Schlickeiser, R.; Elhanbaly, A.

    2017-06-01

    To present the main influence of anomalous diffusion on the energetic particle propagation, the fractional derivative model of transport is developed by deriving the fractional modified Telegraph and Rayleigh equations. Analytical solutions of the fractional modified Telegraph and the fractional Rayleigh equations, which are defined in terms of Caputo fractional derivatives, are obtained by using the Laplace transform and the Mittag-Leffler function method. The solutions of these fractional equations are given in terms of special functions like Fox’s H, Mittag-Leffler, Hermite and Hyper-geometric functions. The predicted travelling pulse solutions are discussed in each case for different values of fractional order.

  9. Olive oil and health effects: from epidemiological studies to the molecular mechanisms of phenolic fraction

    Directory of Open Access Journals (Sweden)

    Amiot Marie Josèphe

    2014-09-01

    Full Text Available Olive oil is a key component of the Mediterranean diet which is recognized to contribute to its health benefits. Recent prospective studies point towards a protective effect from an olive oil-rich diet in relation to the incidence of cardiovascular diseases and an improvement of cardiometabolic markers such as blood pressure, glycaemia and dyslipidemia, notably by reducing LDL cholesterol and LDL oxidation. The role of minor phenolic fraction was evidenced in intervention trials where lipid profiles showed greater improvement in participants receiving olive oil with higher phenolic content. The phenolic fraction of olive oil is composed of simple phenols (hydroxytyrosol, phenolic secoiridoids (oleuropein aglycone, lignans (pinoresinol, flavonoids and hydroxyisochromans. All these compounds have diverse biological activities that are described in the present review, supporting the protective effects of olive oil against degenerative diseases found in large cohorts monitored in Southern European countries.

  10. A speculative study of non-linear Arrhenius plot by using fractional calculus

    CERN Document Server

    Lemes, Nelson H T; Santos, José P C dos

    2016-01-01

    In this study, the Van't Hoff differential equation is taken under consideration by making use of fractional derivative tools. In this context, the nonlinear Arrhenius behaviour can be obtained and some experimental values of reaction rate as function of temperature were fitted, with the proposed model. The new model showed better performance to fit rate constant data for different kinetics process, when compared with Arrhenius law. In these case, the Van't Hoff differential equation with noniteger order found relative percentage error less that 3% within experimental error. The fractional order plays an important role in modeling temperature dependence of these kinetic processes. Thus it provides a new perspective in the handling of many problems (e.g., as solubility as function of temperature; temperature dependency of the viscosity and conductivity, etc).

  11. Analytical Study of Nonlinear Fractional-Order Integrodifferential Equation: Revisit Volterra's Population Model

    Directory of Open Access Journals (Sweden)

    Najeeb Alam Khan

    2012-01-01

    Full Text Available This paper suggests two component homotopy method to solve nonlinear fractional integrodifferential equations, namely, Volterra's population model. Padé approximation was effectively used in this method to capture the essential behavior of solutions for the mathematical model of accumulated effect of toxins on a population living in a closed system. The behavior of the solutions and the effects of different values of fractional-order α are indicated graphically. The study outlines significant features of this method as well as sheds some light on advantages of the method over the other. The results show that this method is very efficient, convenient, and can be adapted to fit a larger class of problems.

  12. Adipose derived stromal vascular fraction improves early tendon healing: an experimental study in rabbits

    Directory of Open Access Journals (Sweden)

    Mehdi Behfar

    2011-11-01

    Full Text Available Tendon never restores the complete biological and mechanical properties after healing. Bone marrow and recently adipose tissue have been used as the sources of mesenchymal stem cells, which have been proven to enhance tendon healing. Stromal vascular fraction (SVF, derived from adipose tissue by an enzymatic digestion, represents an alternative source of multipotent cells, which undergo differentiation into multiple lineages to be used in regenerative medicine. In the present study, we investigated potentials of this source on tendon healing. Twenty rabbits were divided into control and treatment groups. Five rabbits were used as donors of adipose tissue. The injury model was unilateral complete transection through the middle one third of deep digital flexor tendon. Immediately after suture repair, either fresh stromal vascular fraction from enzymatic digestion of adipose tissue or placebo was intratendinously injected into the suture site in treatments and controls, respectively. Cast immobilization was continued for two weeks after surgery. Animals were sacrificed at the third week and tendons underwent histological, immunohistochemical, and mechanical evaluations. By histology, improved fibrillar organization and remodeling of neotendon were observed in treatment group. Immunohistochemistry revealed an insignificant increase in collagen type III and I expression in treatments over controls. Mechanical testing showed significant increase in maximum load and energy absorption in SVF treated tendons. The present study showed that intratendinous injection of uncultured adipose derived stromal vascular fraction improved structural and mechanical properties of repaired tendon and it could be an effective modality for treating tendon laceration.

  13. 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.

  14. Characterization of Complex Fractionated Atrial Electrograms by Sample Entropy: An International Multi-Center Study

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    Eva Cirugeda–Roldán

    2015-10-01

    Full Text Available Atrial fibrillation (AF is the most commonly clinically-encountered arrhythmia. Catheter ablation of AF is mainly based on trigger elimination and modification of the AF substrate. Substrate mapping ablation of complex fractionated atrial electrograms (CFAEs has emerged to be a promising technique. To improve substrate mapping based on CFAE analysis, automatic detection algorithms need to be developed in order to simplify and accelerate the ablation procedures. According to the latest studies, the level of fractionation has been shown to be promisingly well estimated from CFAE measured during radio frequency (RF ablation of AF. The nature of CFAE is generally nonlinear and nonstationary, so the use of complexity measures is considered to be the appropriate technique for the analysis of AF records. This work proposes the use of sample entropy (SampEn, not only as a way to discern between non-fractionated and fractionated atrial electrograms (A-EGM, Entropy 2015, 17 7494 but also as a tool for characterizing the degree of A-EGM regularity, which is linked to changes in the AF substrate and to heart tissue damage. The use of SampEn combined with a blind parameter estimation optimization process enables the classification between CFAE and non-CFAE with statistical significance (p < 0:001, 0.89 area under the ROC, 86% specificity and 77% sensitivity over a mixed database of A-EGM combined from two independent CFAE signal databases, recorded during RF ablation of AF in two EU countries (542 signals in total. On the basis of the results obtained in this study, it can be suggested that the use of SampEn is suitable for real-time support during navigation of RF ablation of AF, as only 1.5 seconds of signal segments need to be analyzed.

  15. Characterization of RanBPM Molecular Determinants that Control Its Subcellular Localization

    Science.gov (United States)

    Salemi, Louisa M.; Loureiro, Sandra O.; Schild-Poulter, Caroline

    2015-01-01

    RanBPM/RanBP9 is a ubiquitous, nucleocytoplasmic protein that is part of an evolutionary conserved E3 ubiquitin ligase complex whose function and targets in mammals are still unknown. RanBPM itself has been implicated in various cellular processes that involve both nuclear and cytoplasmic functions. However, to date, little is known about how RanBPM subcellular localization is regulated. We have conducted a systematic analysis of RanBPM regions that control its subcellular localization using RanBPM shRNA cells to examine ectopic RanBPM mutant subcellular localization without interference from the endogenously expressed protein. We show that several domains and motifs regulate RanBPM nuclear and cytoplasmic localization. In particular, RanBPM comprises two motifs that can confer nuclear localization, one proline/glutamine-rich motif in the extreme N-terminus which has a dominant effect on RanBPM localization, and a second motif in the C-terminus which minimally contributes to RanBPM nuclear targeting. We also identified a nuclear export signal (NES) which mutation prevented RanBPM accumulation in the cytoplasm. Likewise, deletion of the central RanBPM conserved domains (SPRY and LisH/CTLH) resulted in the relocalization of RanBPM to the nucleus, suggesting that RanBPM cytoplasmic localization is also conferred by protein-protein interactions that promote its cytoplasmic retention. Indeed we found that in the cytoplasm, RanBPM partially colocalizes with microtubules and associates with α-tubulin. Finally, in the nucleus, a significant fraction of RanBPM is associated with chromatin. Altogether, these analyses reveal that RanBPM subcellular localization results from the combined effects of several elements that either confer direct transport through the nucleocytoplasmic transport machinery or regulate it indirectly, likely through interactions with other proteins and by intramolecular folding. PMID:25659156

  16. Cellular and subcellular localization of Marlin-1 in the brain

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    Luján Rafael

    2009-04-01

    Full Text Available Abstract Background Marlin-1 is a microtubule binding protein that associates specifically with the GABAB1 subunit in neurons and with members of the Janus kinase family in lymphoid cells. In addition, it binds the molecular motor kinesin-I and nucleic acids, preferentially single stranded RNA. Marlin-1 is expressed mainly in the central nervous system but little is known regarding its cellular and subcellular distribution in the brain. Results Here we have studied the localization of Marlin-1 in the rodent brain and cultured neurons combining immunohistochemistry, immunofluorescence and pre-embedding electron microscopy. We demonstrate that Marlin-1 is enriched in restricted areas of the brain including olfactory bulb, cerebral cortex, hippocampus and cerebellum. Marlin-1 is abundant in dendrites and axons of GABAergic and non-GABAergic hippocampal neurons. At the ultrastructural level, Marlin-1 is present in the cytoplasm and the nucleus of CA1 neurons in the hippocampus. In the cytoplasm it associates to microtubules in the dendritic shaft and occasionally with the Golgi apparatus, the endoplasmic reticulum (ER and dendritic spines. In the nucleus, clusters of Marlin-1 associate to euchromatin. Conclusion Our results demonstrate that Marlin-1 is expressed in discrete areas of the brain. They also confirm the microtubule association at the ultrastructural level in neurons. Together with the abundance of the protein in dendrites and axons they are consistent with the emerging role of Marlin-1 as an intracellular protein linking the cytoskeleton and transport. Our study constitutes the first detailed description of the cellular and subcellular distribution of Marlin-1 in the brain. As such, it will set the basis for future studies on the functional implications of Marlin-1 in protein trafficking.

  17. Cellular and subcellular localization of Marlin-1 in the brain.

    Science.gov (United States)

    Vidal, René L; Valenzuela, José I; Luján, Rafael; Couve, Andrés

    2009-04-22

    Marlin-1 is a microtubule binding protein that associates specifically with the GABAB1 subunit in neurons and with members of the Janus kinase family in lymphoid cells. In addition, it binds the molecular motor kinesin-I and nucleic acids, preferentially single stranded RNA. Marlin-1 is expressed mainly in the central nervous system but little is known regarding its cellular and subcellular distribution in the brain. Here we have studied the localization of Marlin-1 in the rodent brain and cultured neurons combining immunohistochemistry, immunofluorescence and pre-embedding electron microscopy. We demonstrate that Marlin-1 is enriched in restricted areas of the brain including olfactory bulb, cerebral cortex, hippocampus and cerebellum. Marlin-1 is abundant in dendrites and axons of GABAergic and non-GABAergic hippocampal neurons. At the ultrastructural level, Marlin-1 is present in the cytoplasm and the nucleus of CA1 neurons in the hippocampus. In the cytoplasm it associates to microtubules in the dendritic shaft and occasionally with the Golgi apparatus, the endoplasmic reticulum (ER) and dendritic spines. In the nucleus, clusters of Marlin-1 associate to euchromatin. Our results demonstrate that Marlin-1 is expressed in discrete areas of the brain. They also confirm the microtubule association at the ultrastructural level in neurons. Together with the abundance of the protein in dendrites and axons they are consistent with the emerging role of Marlin-1 as an intracellular protein linking the cytoskeleton and transport. Our study constitutes the first detailed description of the cellular and subcellular distribution of Marlin-1 in the brain. As such, it will set the basis for future studies on the functional implications of Marlin-1 in protein trafficking.

  18. Vacuoles in mammals: a subcellular structure indispensable for early embryogenesis.

    Science.gov (United States)

    Wada, Yoh

    2013-01-01

    A vacuole is a membrane-bound subcellular structure involved in intracellular digestion. Instead of the large "vacuolar" organelles that are found in plants and fungi, animal cells possess lysosomes that are smaller in size and are enriched with hydrolytic enzymes similar to those found in the vacuoles. Large vacuolar structures are often observed in highly differentiated mammalian tissues such as embryonic visceral endoderm and absorbing epithelium. Vacuoles/lysosomes share a conserved mechanism of biogenesis, and they are at the terminal of the endocytic pathways, Recent genetic studies of the mammalian orthologs of Vam/Vps genes, which have essential functions for vacuole assembly, revealed that the dynamics of vacuoles/lysosomes are important for tissue differentiation and patterning through regulation of various molecular signaling events in mammals.

  19. Subcellular Localization of Galloylated Catechins in Tea Plants (Camellia sinensis (L. O. Kuntze Assessed via Immunohistochemistry

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    Huanhuan eXu

    2016-05-01

    Full Text Available Galloylated catechins, as the main secondary metabolites in the tea plant, including (--epigallocatechin-3-gallate and (--epicatechin-3-gallate, comprise approximately three-quarters of all the tea plant catechins and have stronger effects than non-galloylated catechins, both on the product quality in tea processing and the pharmacological efficacy to human beings. The subcellular localization of galloylated catechins has been the primary focus of studies that assess biosynthesis and physiological functions. Classical histochemical localization staining reagents can not specifically detect galloylated catechins; thus, their subcellular localization remains controversial. In the present study, we generated a monoclonal antibody (mAb against galloylated catechins, which can be used for the subcellular localization of galloylated catechins in the tea plant by immunohistochemistry. Direct ELISA and ForteBio Octet Red 96 System assay indicated the mAb could recognize the galloylated catechins with high specificities and affinities. In addition, tea bud was ascertained as the optimal tissue for freezing microtomic sections for immunohistochemistry. What’s more, the high quality mAbs which exhibited excellent binding capability to galloylated catechins were utilised for the visualization of them via immunohistochemistry. Our findings demonstrated that vacuoles were the primary sites of localization of galloylated catechins at the subcellular level.

  20. Particle bombardment and subcellular protein localization analysis in the aquatic plant Egeria densa

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    Yasuhide Osaki

    2017-09-01

    Full Text Available Particle bombardment is a powerful and relatively easy method for transient expression of genes of interest in plant cells, especially those that are recalcitrant to other transformation methods. This method has facilitated numerous analyses of subcellular localization of fluorescent fusion protein constructs. Particle bombardment delivers genes to the first layer of plant tissue. In leaves of higher plants, epidermal cells are the first cell layer. Many studies have used the epidermal cell layer of onion bulb (Allium cepa as the experimental tissue, because these cells are relatively large. However, onion epidermal cells lack developed plastids (i.e., chloroplasts, thereby precluding subcellular localization analysis of chloroplastic proteins. In this study, we developed a protocol for particle bombardment of the aquatic plant Egeria densa, and showed that it is a useful system for subcellular localization analysis of higher plant proteins. E. densa leaflets contain only two cell layers, and cells in the adaxial layer are sufficiently large for observation. The cells in both layers contain well-developed chloroplasts. We fused fluorescent proteins to conventional plant localization signals for the nucleus, cytosol, mitochondria, peroxisome, and chloroplast, and used particle bombardment to transiently express these fusion constructs in E. densa leaves. The plant subcellular localization signals functioned normally and displayed the expected distributions in transiently transformed E. densa cells, and even chloroplastic structures could be clearly visualized.

  1. Fractionated Stereotactic Gamma Knife Radiosurgery for Large Brain Metastases: A Retrospective, Single Center Study.

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    Joo Whan Kim

    Full Text Available Stereotactic radiosurgery (SRS is widely used for brain metastases but has been relatively contraindicated for large lesions (>3 cm. In the present study, we analyzed the efficacy and toxicity of hypofractionated Gamma Knife radiosurgery to treat metastatic brain tumors for which surgical resection were not considered as the primary treatment option.Thirty-six patients, forty cases were treated with Gamma Knife-based fractionated SRS for three to four consecutive days with the same Leksell frame on their heads. The mean gross tumor volume was 18.3 cm³, and the median dose was 8 Gy at 50% isodose line with 3 fractions for three consecutive days (range, 5 to 11 Gy and 2 to 4 fractions for 2 to 4 consecutive days. Survival rates and prognostic factors were analyzed.The overall survival rate at one and two years was 66.7 and 33.1%, respectively. The median survival time was 16.2 months, and the local control rate was 90%. RTOG toxicity grade 1 was observed in 3 (8.3% patients, grade 2 in 1 (2.7% patient and grade 3 in 1 (2.7% patient respectively. Radiation necrosis was developed in 1 (2.7% patient. KPS scores and control of primary disease resulted in significant differences in survival.Our findings suggest that consecutive hypofractionated Gamma Knife SRS could be applied to large metastatic brain tumors with effective tumor control and low toxicity rates.

  2. Comparison of a fractional bipolar radiofrequency device and a fractional erbium-doped glass 1,550-nm device for the treatment of atrophic acne scars: a randomized split-face clinical study.

    Science.gov (United States)

    Rongsaard, Nopnarueporn; Rummaneethorn, Paisal

    2014-01-01

    A fractional erbium-doped glass 1,550-nm and a fractional bipolar radiofrequency (RF) device are effective in the treatment of atrophic acne scars. To compare the clinical effectiveness and side effects of fractional bipolar RF with those of fractional erbium-doped glass in atrophic acne scars treatment. Twenty Thai subjects with atrophic acne scars received three split-face monthly treatments, one side with fractional bipolar RF and the other with fractional erbium-doped glass. Three independent physicians and patients evaluated improvement in acne scars 4 weeks after the last treatment. Side effects were also recorded after each treatment. The study found significant improvement in acne scars after treatment with fractional bipolar RF and with a fractional erbium-doped glass device without a statistically significant difference between the two devices. The side effects of both devices were pain, transient facial erythema, and scab formation. The pain score with fractional erbium-doped glass was higher than that with fractional bipolar RF, but duration of scab shedding was shorter. One case had postinflammatory hyperpigmentation on only the side treated with fractional erbium-doped glass. Fractional bipolar RF and fractional erbium-doped glass have similar effectiveness for the treatment of atrophic acne scars. © 2013 by the American Society for Dermatologic Surgery, Inc. Published by Wiley Periodicals, Inc.

  3. Laserspritzer: a simple method for optogenetic investigation with subcellular resolutions.

    Science.gov (United States)

    Sun, Qian-Quan; Wang, Xinjun; Yang, Weiguo

    2014-01-01

    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.

  4. 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.

  5. Subcellular distribution of glutathione and cysteine in cyanobacteria

    Science.gov (United States)

    Tomašić, Ana; Horvat, Lucija; Fulgosi, Hrvoje

    2010-01-01

    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. PMID:20349253

  6. Subcellular Lipid Droplets in Vanilla Leaf Epidermis and Avocado Mesocarp Are Coated with Oleosins of Distinct Phylogenic Lineages1[OPEN

    Science.gov (United States)

    2016-01-01

    Subcellular lipid droplets (LDs) in diverse plant cells and species are coated with stabilizing oleosins of at least five phylogenic lineages and perform different functions. We examined two types of inadequately studied LDs for coated oleosins and their characteristics. The epidermis but not mesophyll of leaves of vanilla (Vanilla planifolia) and most other Asparagales species contained solitary and clustered LDs (avocado (Persea americana) and other Lauraceae species possessed large LDs, which likely function in attracting animals for seed dispersal. They contained transcripts of oleosin of a novel M phylogenic lineage. Each avocado mesocarp fatty cell possessed one to several large LDs (5 to 20 μm) and at their periphery, numerous small LDs (<0.5 μm). Immuno-confocal laser scanning microscopy revealed that oleosin was present mostly on the small LDs. LDs in isolated fractions coalesced rapidly, and the fraction contained oleosin and several other proteins and triacylglycerols as the main lipids. These two new types of oleosin-LDs exemplify the evolutionary plasticity of oleosins-LDs in generating novel functions in diverse cell types and species. PMID:27208281

  7. Sixth Graders Benefit from Educational Software when Learning about Fractions: A Controlled Classroom study

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    Susanne Scharnagl

    2014-01-01

    Full Text Available This study analyses the effectiveness of an educational web-based software package for teaching mathematics in schools. In all, 864 sixth graders and their teachers took part in the controlled study. Students learned the addition and subtraction of fractions with (intervention group; n = 469 or without (control group; n = 395 the support of the educational software. Compared to the controls, students who used the software showed better results in the post-test. Gains were dose dependent and particularly marked in high-ability students and students with lower scores of math anxiety.

  8. Study of the free volume fraction in polylactic acid (PLA) by thermal analysis

    Science.gov (United States)

    Abdallah, A.; Benrekaa, N.

    2015-10-01

    The poly (lactic acid) or polylactide (PLA) is a biodegradable polymer with high modulus, strength and thermoplastic properties. In this work, the evolution of various properties of PLA is studied, such as glass transition temperature, mechanical modules and elongation percentage with the aim of investigating the free volume fraction. To do so, two thermal techniques have been used: the dynamic mechanical analysis (DMA) and dilatometry. The results obtained by these techniques are combined to go back to the structural properties of the studied material.

  9. Multivalency Effect of TAT-Peptide-Functionalized Nanoparticle in Cellular Endocytosis and Subcellular Trafficking.

    Science.gov (United States)

    Dalal, Chumki; Jana, Nikhil R

    2017-04-13

    Although trans-activating transcription (TAT) peptide-functionalized nanoparticle/polymer/liposome is widely used for cellular transfection applications, the multivalency (number of attached peptide per particle) effect on cell uptake mechanism and subcellular targeting performance is largely unexplored. Here we show that multivalency of nanoparticle controls the cellular interaction, cellular entry/exit mechanism, and subcellular targeting performance. We have synthesized TAT-peptide functionalized quantum dot (QD) of 30-35 nm hydrodynamic diameter with varied multivalency from 10 to 75 (e.g., QD(TAT)10, QD(TAT)20, QD(TAT)40, QD(TAT)75) and studied the role of multivalency in endocytosis and subcellular trafficking. We found that both low and high multivalent nanoparticles enter into cell predominantly via lipid-raft mediated endocytosis but the higher multivalency of 40 and 75 induces vesicular trapping followed by exocytosis within 12 h. In contrast, lower multivalency of 10 and 20 offers efficient trafficking toward perinuclear region and Golgi apparatus. This work shows the functional role of nanoparticle multivalency in cellular uptake mechanism and importance of lower multivalency for efficient subcellular targeting.

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

    Science.gov (United States)

    Almagro Armenteros, José Juan; Sønderby, Casper Kaae; Sønderby, Søren Kaae; Nielsen, Henrik; Winther, Ole

    2017-11-01

    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 protein subcellular localization relying only on sequence information. At its core, the prediction model uses a recurrent neural network that processes the entire protein sequence and an attention mechanism identifying protein regions important for the subcellular localization. The model was trained and tested on a protein dataset extracted from one of the latest UniProt releases, in which experimentally annotated proteins follow more stringent criteria than previously. We demonstrate that our model achieves a good accuracy (78% for 10 categories; 92% for membrane-bound or soluble), outperforming 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://www.cbs.dtu.dk/services/DeepLoc/data.php. jjalma@dtu.dk.

  11. Biodynamics of copper oxide nanoparticles and copper ions in an oligochaete - Part II: Subcellular distribution following sediment exposure

    Energy Technology Data Exchange (ETDEWEB)

    Thit, Amalie, E-mail: athitj@ruc.dk [U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA 94025 (United States); Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000 (Denmark); Ramskov, Tina, E-mail: tramskov@hotmail.com [U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA 94025 (United States); Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000 (Denmark); Croteau, Marie-Noële, E-mail: mcroteau@usgs.gov [Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000 (Denmark); Selck, Henriette [U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA 94025 (United States); Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000 (Denmark)

    2016-11-15

    Highlights: • L. variegatus was exposed to sediment spiked with either aqueous Cu or nanoparticulate CuO. • Both aqueous and nanoparticulate Cu were marginally accumulated by L. variegatus. • Elimination of Cu accumulated from both forms was limited. • The subcellular distribution of accumulated Cu varied between Cu forms. • The use of a tracer, greater exposure concentration and duration are recommended. - Abstract: The use and likely incidental release of metal nanoparticles (NPs) is steadily increasing. Despite the increasing amount of published literature on metal NP toxicity in the aquatic environment, very little is known about the biological fate of NPs after sediment exposures. Here, we compare the bioavailability and subcellular distribution of copper oxide (CuO) NPs and aqueous Cu (Cu-Aq) in the sediment-dwelling worm Lumbriculus variegatus. Ten days (d) sediment exposure resulted in marginal Cu bioaccumulation in L. variegatus for both forms of Cu. Bioaccumulation was detected because isotopically enriched {sup 65}Cu was used as a tracer. Neither burrowing behavior or survival was affected by the exposure. Once incorporated into tissue, Cu loss was negligible over 10 d of elimination in clean sediment (Cu elimination rate constants were not different from zero). With the exception of day 10, differences in bioaccumulation and subcellular distribution between Cu forms were either not detectable or marginal. After 10 d of exposure to Cu-Aq, the accumulated Cu was primarily partitioned in the subcellular fraction containing metallothionein-like proteins (MTLP, ≈40%) and cellular debris (CD, ≈30%). Cu concentrations in these fractions were significantly higher than in controls. For worms exposed to CuO NPs for 10 d, most of the accumulated Cu was partitioned in the CD fraction (≈40%), which was the only subcellular fraction where the Cu concentration was significantly higher than for the control group. Our results indicate that L. variegatus

  12. Proteomic profiling of the outer membrane fraction of the obligate intracellular bacterial pathogen Ehrlichia ruminantium.

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    Amal Moumène

    Full Text Available The outer membrane proteins (OMPs of Gram-negative bacteria play a crucial role in virulence and pathogenesis. Identification of these proteins represents an important goal for bacterial proteomics, because it aids in vaccine development. Here, we have developed such an approach for Ehrlichia ruminantium, the obligate intracellular bacterium that causes heartwater. A preliminary whole proteome analysis of elementary bodies, the extracellular infectious form of the bacterium, had been performed previously, but information is limited about OMPs in this organism and about their role in the protective immune response. Identification of OMPs is also essential for understanding Ehrlichia's OM architecture, and how the bacterium interacts with the host cell environment. First, we developed an OMP extraction method using the ionic detergent sarkosyl, which enriched the OM fraction. Second, proteins were separated via one-dimensional electrophoresis, and digested peptides were analyzed via nano-liquid chromatographic separation coupled with mass spectrometry (LC-MALDI-TOF/TOF. Of 46 unique proteins identified in the OM fraction, 18 (39% were OMPs, including 8 proteins involved in cell structure and biogenesis, 4 in transport/virulence, 1 porin, and 5 proteins of unknown function. These experimental data were compared to the predicted subcellular localization of the entire E. ruminantium proteome, using three different algorithms. This work represents the most complete proteome characterization of the OM fraction in Ehrlichia spp. The study indicates that suitable subcellular fractionation experiments combined with straightforward computational analysis approaches are powerful for determining the predominant subcellular localization of the experimentally observed proteins. We identified proteins potentially involved in E. ruminantium pathogenesis, which are good novel targets for candidate vaccines. Thus, combining bioinformatics and proteomics, we

  13. Proteomic Profiling of the Outer Membrane Fraction of the Obligate Intracellular Bacterial Pathogen Ehrlichia ruminantium

    Science.gov (United States)

    Moumène, Amal; Marcelino, Isabel; Ventosa, Miguel; Gros, Olivier; Lefrançois, Thierry; Vachiéry, Nathalie

    2015-01-01

    The outer membrane proteins (OMPs) of Gram-negative bacteria play a crucial role in virulence and pathogenesis. Identification of these proteins represents an important goal for bacterial proteomics, because it aids in vaccine development. Here, we have developed such an approach for Ehrlichia ruminantium, the obligate intracellular bacterium that causes heartwater. A preliminary whole proteome analysis of elementary bodies, the extracellular infectious form of the bacterium, had been performed previously, but information is limited about OMPs in this organism and about their role in the protective immune response. Identification of OMPs is also essential for understanding Ehrlichia’s OM architecture, and how the bacterium interacts with the host cell environment. First, we developed an OMP extraction method using the ionic detergent sarkosyl, which enriched the OM fraction. Second, proteins were separated via one-dimensional electrophoresis, and digested peptides were analyzed via nano-liquid chromatographic separation coupled with mass spectrometry (LC-MALDI-TOF/TOF). Of 46 unique proteins identified in the OM fraction, 18 (39%) were OMPs, including 8 proteins involved in cell structure and biogenesis, 4 in transport/virulence, 1 porin, and 5 proteins of unknown function. These experimental data were compared to the predicted subcellular localization of the entire E. ruminantium proteome, using three different algorithms. This work represents the most complete proteome characterization of the OM fraction in Ehrlichia spp. The study indicates that suitable subcellular fractionation experiments combined with straightforward computational analysis approaches are powerful for determining the predominant subcellular localization of the experimentally observed proteins. We identified proteins potentially involved in E. ruminantium pathogenesis, which are good novel targets for candidate vaccines. Thus, combining bioinformatics and proteomics, we discovered new OMPs

  14. Using biased image analysis for improving unbiased stereological number estimation - a pilot simulation study of the smooth fractionator

    DEFF Research Database (Denmark)

    Gardi, Jonathan Eyal; Nyengaard, Jens Randel; Gundersen, Hans Jørgen Gottlieb

    2006-01-01

    The smooth fractionator was introduced in 2002. The combination of a smoothing protocol with a computer-aided stereology tool provides better precision and a lighter workload. This study uses simulation to compare fractionator sampling based on the smooth design, the commonly used systematic unif...

  15. Individual Differences in Students' Knowing and Learning about Fractions: Evidence from an In-Depth Qualitative Study

    Science.gov (United States)

    Bempeni, Maria; Vamvakoussi, Xenia

    2015-01-01

    We present the results of an in-depth qualitative study that examined ninth graders' conceptual and procedural knowledge of fractions as well as their approach to mathematics learning, in particular fraction learning. We traced individual differences, even extreme, in the way that students combine the two kinds of knowledge. We also provide…

  16. Effects of exogenous spermidine on subcellular distribution and chemical forms of cadmium in Typha latifolia L. under cadmium stress.

    Science.gov (United States)

    Tang, C F; Zhang, R Q; Wen, S Z; Li, C F; Guo, X F; Liu, Y G

    2009-01-01

    The effects of foliar spraying with spermidine (Spd) on the subcellular distribution and chemical speciation of Cd in Typha latifolia L. in hydroponic system were investigated. Increased Cd concentration in the medium caused an increase of Cd concentration in all tissues and all subcellular fractions, with the highest Cd level occurring in roots, followed by rhizomes and leaves and the greatest accumulation was in cell walls, soluble fraction and organelle containing fractions ranked next, respectively. The greatest amount of Cd was found in the extraction of 1 mol.L(-1) NaCl, followed by 2% HAC, deionized water, 80% ethanol, residues and the least in 0.6 mol.L(-1) HCl. The subcellular distribution and different chemical forms of Cd both decreased after Spd application and were more inhibited by 0.25 than 0.50 mmol.L(-1) Spd, especially in roots at 0.10 mmol.L(-1) Cd treatment. It could be suggested that the retention of Cd in roots, cell walls binding with metal, metal ion compartmentation in vacuoles and Cd forms existing in undissolved and integrated with pectates and protein play an important role in Cd detoxification and Spd could enhance the tolerance of cattail to Cd stress.

  17. Studies on composite solid propellant with tri-modal ammonium perchlorate containing an ultrafine fraction

    Directory of Open Access Journals (Sweden)

    K.V. Suresh Babu

    2017-08-01

    Full Text Available Composite solid propellant is prepared using tri-modal Ammonium perchlorate (AP containing coarse, fine and ultrafine fractions of AP with average particle size (APS 340, 40 and 5 μm respectively, in various compositions and their rheological, mechanical and burn rate characteristics are evaluated. The optimum combination of AP coarse to fine to ultrafine weight fraction was obtained by testing of series of propellant samples by varying the AP fractions at fixed solid loading. The concentration of aluminium was maintained constant throughout the experiments for ballistics requirement. The propellant formulation prepared using AP with coarse to fine to ultrafine ratio of 67:24:9 has lowest viscosity for the propellant paste and highest tensile strength due to dense packing as supported by the literature. A minimum modulus value was also observed at 9 wt. % of ultrafine AP concentration indicates the maximum solids packing density at this ratio of AP fractions. The burn rate is evaluated at different pressures to obtain pressure exponent. Incorporation of ultrafine fraction of AP in propellant increased burn rate without adversely affecting the pressure exponent. Higher solid loading propellants are prepared by increased AP concentration from 67 to 71 wt. % using AP with coarse to fine to ultrafine ratio of 67:24:9. Higher solid content up to 89 wt. % was achieved and hence increased solid motor performance. The unloading viscosity showed a trend with increased AP content and the propellant couldn't able to cast beyond 71 wt. % of AP. Mechanical properties were also studied and from the experiments noticed that % elongation decreased with increased AP content from 67 to 71 wt.%, whereas tensile strength and modulus increased. Burn rate increased with increased AP content and observed that pressure exponent also increased and it is high for the propellant containing with 71 wt.% of AP due to increased oxidiser to fuel ratio. Catalysed

  18. Enhancing membrane protein subcellular localization prediction by parallel fusion of multi-view features.

    Science.gov (United States)

    Yu, Dongjun; Wu, Xiaowei; Shen, Hongbin; Yang, Jian; Tang, Zhenmin; Qi, Yong; Yang, Jingyu

    2012-12-01

    Membrane proteins are encoded by ~ 30% in the genome and function importantly in the living organisms. Previous studies have revealed that membrane proteins' structures and functions show obvious cell organelle-specific properties. Hence, it is highly desired to predict membrane protein's subcellular location from the primary sequence considering the extreme difficulties of membrane protein wet-lab studies. Although many models have been developed for predicting protein subcellular locations, only a few are specific to membrane proteins. Existing prediction approaches were constructed based on statistical machine learning algorithms with serial combination of multi-view features, i.e., different feature vectors are simply serially combined to form a super feature vector. However, such simple combination of features will simultaneously increase the information redundancy that could, in turn, deteriorate the final prediction accuracy. That's why it was often found that prediction success rates in the serial super space were even lower than those in a single-view space. The purpose of this paper is investigation of a proper method for fusing multiple multi-view protein sequential features for subcellular location predictions. Instead of serial strategy, we propose a novel parallel framework for fusing multiple membrane protein multi-view attributes that will represent protein samples in complex spaces. We also proposed generalized principle component analysis (GPCA) for feature reduction purpose in the complex geometry. All the experimental results through different machine learning algorithms on benchmark membrane protein subcellular localization datasets demonstrate that the newly proposed parallel strategy outperforms the traditional serial approach. We also demonstrate the efficacy of the parallel strategy on a soluble protein subcellular localization dataset indicating the parallel technique is flexible to suite for other computational biology problems. The

  19. A formal ontology of subcellular neuroanatomy

    Directory of Open Access Journals (Sweden)

    Stephen D Larson

    2007-11-01

    Full Text Available The complexity of the nervous system requires high-resolution microscopy to resolve the detailed 3D structure of nerve cells and supracellular domains. The analysis of such imaging data to extract cellular surfaces and cell components often requires the combination of expert human knowledge with carefully engineered software tools. In an effort to make better tools to assist humans in this endeavor, create a more accessible and permanent record of their data, and to aid the process of constructing complex and detailed computational models, we have created a core of formalized knowledge about the structure of the nervous system and have integrated that core into several software applications. In this paper, we describe the structure and content of a formal ontology whose scope is the subcellular anatomy of the nervous system (SAO, covering nerve cells, their parts, and interactions between these parts. Many applications of this ontology to image annotation, content-based retrieval of structural data, and integration of shared data across scales and researchers are also described.

  20. Subcellular drug targeting, pharmacokinetics and bioavailability.

    Science.gov (United States)

    Leucuta, Sorin Emilian

    2014-02-01

    Effective treatment of diseases at the molecular level is possible by directing the drug substance (micromolecular, protein or peptide drugs, DNA, oligonucleotides, siRNA) with the aid of a specialized nanoparticulate carrier, for safe and effective transport to the specific site of action in the cytosol and its organelles including nuclear targeting. To achieve efficient cytosolic delivery of therapeutics or nuclear targeting, different drug delivery systems (DDS) have been developed (macromolecular drug conjugates, chemically or genetically modified proteins, and particulate drug carriers) capable of subcellular internalization overcoming the biological barriers, by passive targeting and especially by active targeting (receptor-targeted delivery). The success depends on the physicochemical nature of DDS, intracellular barriers that these systems need to overcome, the bioavailability of the bioactive drug, biodistribution, the intracellular pharmacokinetics and its influence on the pharmacodynamic effect. Models necessary for this purpose exist but they need to be more developed especially with quantitative treatments, after the development of the means of highlighting the evolution of the drug substance in biophase or at the level of the target cellular organelle by quantitative assays. It is expected that intracellularly targeted drug delivery approaches will be clinically useful using specialized DDSs belonging to the pharmaceutical nanotechnologies.

  1. cAMP signaling in subcellular compartments.

    Science.gov (United States)

    Lefkimmiatis, Konstantinos; Zaccolo, Manuela

    2014-09-01

    In the complex microcosm of a cell, information security and its faithful transmission are critical for maintaining internal stability. To achieve a coordinated response of all its parts to any stimulus the cell must protect the information received from potentially confounding signals. Physical segregation of the information transmission chain ensures that only the entities able to perform the encoded task have access to the relevant information. The cAMP intracellular signaling pathway is an important system for signal transmission responsible for the ancestral 'flight or fight' response and involved in the control of critical functions including frequency and strength of heart contraction, energy metabolism and gene transcription. It is becoming increasingly apparent that the cAMP signaling pathway uses compartmentalization as a strategy for coordinating the large number of key cellular functions under its control. Spatial confinement allows the formation of cAMP signaling "hot spots" at discrete subcellular domains in response to specific stimuli, bringing the information in proximity to the relevant effectors and their recipients, thus achieving specificity of action. In this report we discuss how the different constituents of the cAMP pathway are targeted and participate in the formation of cAMP compartmentalized signaling events. We illustrate a few examples of localized cAMP signaling, with a particular focus on the nucleus, the sarcoplasmic reticulum and the mitochondria. Finally, we discuss the therapeutic potential of interventions designed to perturb specific cAMP cascades locally. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. 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.

  3. Multimodal subcellular imaging with microcavity photoacoustic transducer.

    Science.gov (United States)

    Tan, Zhiliang; Tang, Zhilie; Wu, Yongbo; Liao, Yanfei; Dong, Wei; Guo, Lina

    2011-01-31

    Photoacoustic microscopy (PAM) is dominantly sensitive to the endogenous optical absorption compared with the confocal microscopy which images with scattering photons. PAM has similar structure such as optical transportation system, the optical scanning, and light source with the laser scanning confocal microscopy (LSCM). In order to match the PAM with LSCM, a special design microcavity photoacoustic (PA) transducer with high sensitivity is developed to detect the photoacoustic signals induced by modulated continuous wave (CW) laser. By employing a microcavity PA transducer, a PAM can be integrated with LSCM. Thus a simultaneous multimodal imaging can be obtained with the same laser source and optical system. The lateral resolutions of the PAM and the LSCM are both tested to be better than 1.25 μm. Then subcellular multimodal imaging can be achieved. Images from the two modes are corresponding with each other but functionally complementary. Combining PAM and LSCM provides more comprehensive information for the cytological test. This technique is demonstrated for imaging red-blood cells and meristematic cells.

  4. Acute toxicity profiling of the ethyl acetate fraction ofSwietenia macrophyllaseeds andin-vitroneuroprotection studies.

    Science.gov (United States)

    Sayyad, Mustak; Tiang, Ning; Kumari, Yatinesh; Goh, Bey Hing; Jaiswal, Yogini; Rosli, Rozita; Williams, Leonard; Shaikh, Mohd Farooq

    2017-02-01

    Swietenia macrophylla (SM) is a medicinally important plant found in tropical and subtropical regions of the world. The ethyl acetate fraction of the seeds of S. macrophylla (SMEAF) is reported to exhibit potent anticancer, antitumor, anti-inflammatory and antifeedant activities. Till date, there have been no studies reported on the acute oral toxicity profile of the ethyl acetate fraction of the seeds of SM. The objective of the present study was to determine the acute toxicity of SMEAF and evaluate the in - vitro neuroprotective activity of SMEAF using primary neuronal cell cultures. In acute oral toxicity study, the SMEAF did not produce any lethal signs of morbidity and mortality. Histo-pathological findings, support the safety of SMEAF, as there were no significant changes observed in any of the parameters studied. Based on the results obtained in MTT assay, we infer that SMEAF has a significant neuroprotective effect, as it increased the cell viability and exhibited protection to the neuronal cells against TBHP induced oxidative stress. Thus, SMEAF can be suggested for use in the development of herbal drug formulations with neuroprotective potential.

  5. 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.

  6. SPA Proteins Affect the Subcellular Localization of COP1 in the COP1/SPA Ubiquitin Ligase Complex during Photomorphogenesis.

    Science.gov (United States)

    Balcerowicz, Martin; Kerner, Konstantin; Schenkel, Christian; Hoecker, Ute

    2017-07-01

    The Arabidopsis ( Arabidopsis thaliana ) COP1/SPA ubiquitin ligase is a central repressor that suppresses light signaling in darkness by targeting positive regulators of the light response, mainly transcription factors, for degradation. Light inactivates COP1/SPA, in part by excluding COP1 from the nucleus. SPA proteins are essential cofactors of COP1, but their exact role in the COP1/SPA complex is thus far unknown. To unravel a potential role of SPA proteins in COP1 nucleocytoplasmic partitioning, we monitored the subcellular localization of COP1 in a spa1234 quadruple mutant ( spaQn ). We analyzed a YFP-COP1-expressing transgenic line and endogenous COP1 after subcellular fractionation. In dark-grown seedlings, both YFP-COP1 and endogenous COP1 accumulated in the nucleus in the absence and presence of SPA proteins, indicating that SPA proteins are not required for nuclear localization of COP1 in darkness. In contrast, in white light-grown seedlings, spaQn mutants failed to relocalize COP1 from the nucleus to the cytoplasm. Hence, SPA proteins are necessary for the light-controlled change in COP1 subcellular localization. We conclude that SPA proteins have a dual role: (1) they are required for light-responsiveness of COP1 subcellular localization, and (2) they promote COP1 activity in darkness in a fashion that is independent of the nuclear import/nuclear retention of COP1. © 2017 American Society of Plant Biologists. All Rights Reserved.

  7. Effect heat stress on subcellular localization of Ca2+ in tomato fruits

    Directory of Open Access Journals (Sweden)

    Grażyna Garbaczewska

    2014-01-01

    Full Text Available The aim of this paper was to compare the fruit cell ultrastructure and subcellular localization of Ca2+ after heat stress with the use of the potassium antimonate method (Slocum and Roux 1982, Tretyn et al. 1992. The tomato plants Robin cv., relatively tolerant to heat stress, were grown under uncontrolled greenhouse conditions to the stage of fruiting. The plants were placed for 20h in two temperature regimes: 23oC (optimal temperature or 40oC (heat stress in darkness, under water vapour saturated atmosphere. Immediately after heat stress the fruits were harvested to estimate water soluble and insoluble calcium contents and subcellular localization of Ca2+. After heating the concentration of calcium in tomato fruits increased about twice. In both temperature treatments the water soluble fractions were lower than insoluble ones at smaller differences between insoluble and soluble fractions after heat stress. The shapes and localization of Ca2+ detected with the use of potassium antimonate method show that in fruits of control plants the precipitates were numerous, small and of oval shape. They were dispersed in cytosol or adjoined to endoplasmic reticulum or to external membrane of chloroplast. In the fruit of heated plants the precipitates were irregular in shape, amorphous and singly dispersed in the cytosol. We observed also some cytological changes in the structure of membranes and organelles of the plants of both experimental treatments. The heat induced increase of calcium content and the changes in subcellular localization of Ca2+ under heat stress suggest that calcium ions may be involved in avoiding heat injury. The problem requires more detailed further investigations.

  8. HECTAR: a method to predict subcellular targeting in heterokonts

    National Research Council Canada - National Science Library

    Gschloessl, Bernhard; Guermeur, Yann; Cock, J Mark

    2008-01-01

    .... To understand the biology of these organisms, it is necessary to be able to predict the subcellular localisation of their proteins but this is not straightforward, particularly in photosynthetic...

  9. A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation.

    Directory of Open Access Journals (Sweden)

    Pei-Chi Yang

    2016-07-01

    Full Text Available Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain unique receptor-dependent functional responses. How exactly compartmentation is achieved, however, has remained a mystery for more than 40 years. In this study, we developed computational and mathematical models to represent a subcellular sarcomeric space in a cardiac myocyte with varying detail. We then used these models to predict the contributions of various mechanisms that establish subcellular cAMP microdomains. We used the models to test the hypothesis that phosphodiesterases act as functional barriers to diffusion, creating discrete cAMP signaling domains. We also used the models to predict the effect of a range of experimentally measured diffusion rates on cAMP compartmentation. Finally, we modeled the anatomical structures in a cardiac myocyte diad, to predict the effects of anatomical diffusion barriers on cAMP compartmentation. When we incorporated experimentally informed model parameters to reconstruct an in silico subcellular sarcomeric space with spatially distinct cAMP production sites linked to caveloar domains, the models predict that under realistic conditions phosphodiesterases alone were insufficient to generate significant cAMP gradients. This prediction persisted even when combined with slow cAMP diffusion. When we additionally considered the effects of anatomic barriers to diffusion that are expected in the cardiac myocyte dyadic space, cAMP compartmentation did occur, but only when diffusion was slow. Our model simulations suggest that additional mechanisms likely contribute to cAMP gradients occurring in submicroscopic domains. The difference between the physiological and pathological effects resulting from the production of cAMP may be a function of appropriate compartmentation of cAMP signaling. Therefore, understanding the contribution of factors that are responsible for coordinating the spatial and

  10. Sub-cellular force microscopy in single normal and cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Babahosseini, H. [VT MEMS Laboratory, The Bradley Department of Electrical and Computer Engineering, Blacksburg, VA 24061 (United States); Carmichael, B. [Nonlinear Intelligent Structures Laboratory, Department of Mechanical Engineering, University of Alabama, Tuscaloosa, AL 35487-0276 (United States); Strobl, J.S. [VT MEMS Laboratory, The Bradley Department of Electrical and Computer Engineering, Blacksburg, VA 24061 (United States); Mahmoodi, S.N., E-mail: nmahmoodi@eng.ua.edu [Nonlinear Intelligent Structures Laboratory, Department of Mechanical Engineering, University of Alabama, Tuscaloosa, AL 35487-0276 (United States); Agah, M., E-mail: agah@vt.edu [VT MEMS Laboratory, The Bradley Department of Electrical and Computer Engineering, Blacksburg, VA 24061 (United States)

    2015-08-07

    This work investigates the biomechanical properties of sub-cellular structures of breast cells using atomic force microscopy (AFM). The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity, and the relaxation time of sub-cellular structures. The triple-layered modeling results allow for determination and comparison of the biomechanical properties of the three major sub-cellular structures between normal and cancerous cells: the up plasma membrane/actin cortex, the mid cytoplasm/nucleus, and the low nuclear/integrin sub-domains. The results reveal that the sub-domains become stiffer and significantly more viscous with depth, regardless of cell type. In addition, there is a decreasing trend in the average elastic modulus and apparent viscosity of the all corresponding sub-cellular structures from normal to cancerous cells, which becomes most remarkable in the deeper sub-domain. The presented modeling in this work constitutes a unique AFM-based experimental framework to study the biomechanics of sub-cellular structures. - Highlights: • The cells are modeled as a triple-layered structure using Generalized Maxwell model. • The sub-domains include membrane/cortex, cytoplasm/nucleus, and nuclear/integrin. • Biomechanics of corresponding sub-domains are compared among normal and cancer cells. • Viscoelasticity of sub-domains show a decreasing trend from normal to cancer cells. • The decreasing trend becomes most significant in the deeper sub-domain.

  11. Subcellular targeting strategies for drug design and delivery.

    Science.gov (United States)

    Rajendran, Lawrence; Knölker, Hans-Joachim; Simons, Kai

    2010-01-01

    Many drug targets are localized to particular subcellular compartments, yet current drug design strategies are focused on bioavailability and tissue targeting and rarely address drug delivery to specific intracellular compartments. Insights into how the cell traffics its constituents to these different cellular locations could improve drug design. In this Review, we explore the fundamentals of membrane trafficking and subcellular organization, as well as strategies used by pathogens to appropriate these mechanisms and the implications for drug design and delivery.

  12. 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.

  13. Cadmium sensitivity, uptake, subcellular distribution and thiol induction in a marine diatom: Recovery from cadmium exposure

    Energy Technology Data Exchange (ETDEWEB)

    Wang Mengjiao [State Key Laboratory in Marine Pollution, Section of Marine Ecology and Biotechnology, Division of Life Science, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong); Wang Wenxiong, E-mail: wwang@ust.hk [State Key Laboratory in Marine Pollution, Section of Marine Ecology and Biotechnology, Division of Life Science, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong)

    2011-01-25

    Studies in the recovery from metal stress and the tolerance development to metal exposure of aquatic organisms are important for the understanding of epidemic pollution. In this study, the responses of a marine diatom, Thalassiosira nordenskioeldii, following recovery from environmental cadmium (Cd) stress were investigated. The diatoms were exposed to different concentrations of Cd for 7 days, and were then allowed different periods of time to recover. The Cd sensitivity increased after recovery from Cd stress, followed by a gradual restoration. The extent of restoration depended on both the recovery time and the environmental Cd stress during the exposure period. A complete restoration of Cd tolerance proved to be impossible for cells pre-exposed to High-Cd. The Cd cellular burden and subcellular Cd concentration decreased to the control level within the first day of recovery, indicating that the elevated sensitivity may have been due to the accumulation of functional damage caused by Cd exposure instead of a result of physical Cd accumulation. The rapid change in phytochelatins (PC) to both the increase in and the withdrawal of environmental Cd stress made it a good quantitative bioindicator of environmental Cd contamination. However, the relationships between Cd distribution in the metal sensitive fraction (MSF-Cd) or intracellular Cd to thiol ratio (intra-Cd/PC-SH) and the relative change in the median inhibition [Cd{sup 2+}] ([Cd{sup 2+}]-based-IC{sub 50}, i.e., Cd sensitivity) differed for the various exposure and recovery periods tested. Our study suggests that more attention should be given to the recovery of aquatic organisms from episodic metal exposure.

  14. Fundamental studies on kinetic isotope effect (KIE) of hydrogen isotope fractionation in natural gas systems

    Science.gov (United States)

    Ni, Y.; Ma, Q.; Ellis, G.S.; Dai, J.; Katz, B.; Zhang, S.; Tang, Y.

    2011-01-01

    Based on quantum chemistry calculations for normal octane homolytic cracking, a kinetic hydrogen isotope fractionation model for methane, ethane, and propane formation is proposed. The activation energy differences between D-substitute and non-substituted methane, ethane, and propane are 318.6, 281.7, and 280.2cal/mol, respectively. In order to determine the effect of the entropy contribution for hydrogen isotopic substitution, a transition state for ethane bond rupture was determined based on density function theory (DFT) calculations. The kinetic isotope effect (KIE) associated with bond rupture in D and H substituted ethane results in a frequency factor ratio of 1.07. Based on the proposed mathematical model of hydrogen isotope fractionation, one can potentially quantify natural gas thermal maturity from measured hydrogen isotope values. Calculated gas maturity values determined by the proposed mathematical model using ??D values in ethane from several basins in the world are in close agreement with similar predictions based on the ??13C composition of ethane. However, gas maturity values calculated from field data of methane and propane using both hydrogen and carbon kinetic isotopic models do not agree as closely. It is possible that ??D values in methane may be affected by microbial mixing and that propane values might be more susceptible to hydrogen exchange with water or to analytical errors. Although the model used in this study is quite preliminary, the results demonstrate that kinetic isotope fractionation effects in hydrogen may be useful in quantitative models of natural gas generation, and that ??D values in ethane might be more suitable for modeling than comparable values in methane and propane. ?? 2011 Elsevier Ltd.

  15. Subcellular targeting of nine calcium-dependent protein kinase isoforms from Arabidopsis

    Science.gov (United States)

    Dammann, Christian; Ichida, Audrey; Hong, Bimei; Romanowsky, Shawn M.; Hrabak, Estelle M.; Harmon, Alice C.; Pickard, Barbara G.; Harper, Jeffrey F.; Evans, M. L. (Principal Investigator)

    2003-01-01

    Calcium-dependent protein kinases (CDPKs) are specific to plants and some protists. Their activation by calcium makes them important switches for the transduction of intracellular calcium signals. Here, we identify the subcellular targeting potentials for nine CDPK isoforms from Arabidopsis, as determined by expression of green fluorescent protein (GFP) fusions in transgenic plants. Subcellular locations were determined by fluorescence microscopy in cells near the root tip. Isoforms AtCPK3-GFP and AtCPK4-GFP showed a nuclear and cytosolic distribution similar to that of free GFP. Membrane fractionation experiments confirmed that these isoforms were primarily soluble. A membrane association was observed for AtCPKs 1, 7, 8, 9, 16, 21, and 28, based on imaging and membrane fractionation experiments. This correlates with the presence of potential N-terminal acylation sites, consistent with acylation as an important factor in membrane association. All but one of the membrane-associated isoforms targeted exclusively to the plasma membrane. The exception was AtCPK1-GFP, which targeted to peroxisomes, as determined by covisualization with a peroxisome marker. Peroxisome targeting of AtCPK1-GFP was disrupted by a deletion of two potential N-terminal acylation sites. The observation of a peroxisome-located CDPK suggests a mechanism for calcium regulation of peroxisomal functions involved in oxidative stress and lipid metabolism.

  16. Ultra-low temperature studies of the even denominator fractional quantum Hall states

    Science.gov (United States)

    Samkharadze, Nodar

    We have constructed a specialized experimental setup with integrated magnetic field independent thermometry, which has enabled us to cool the charge carriers in two dimensional electron gases down to 5 mK, and reliably measure the temperature. Using this setup, we have conducted studies of nu=5/2 fractional quantum Hall state(FQHS) in so far unexplored regions of the parameter space. Using a sample with a tunable density, we observe, for the first time, an evidence of a transition at nu=5/2 filling factor. This transition takes place at the lowest density at which nu=5/2 state had been measured to date, around 6x1010cm-2. Using a different set of samples, we also demonstrate a consistent way to account for the disorder contribution to the energy gap of nu=5/2 FQHS for several samples of vastly different densities. This lets us quantify, for the first time, the dependence of the experimentally measured intrinsic gap at nu=5/2 on Landau level mixing alone. Finally, we have conducted an ultra-low temperature study of the fractional quantum Hall states in the 1/3mK, the magnetoresistance exhibits developing FQHS at nu=4/11; 5/13, 6/17 and 3/8. However, we find that at lower temperatures only the nu=4/11 and 5/13 develop incompressibility, while the nu=6/17 and 3/8 remain compressible.

  17. Energy recovery from organic fractions of municipal solid waste: A case study of Hyderabad city, Pakistan.

    Science.gov (United States)

    Safar, Korai M; Bux, Mahar R; Aslam, Uqaili M; Ahmed, Memon S; Ahmed, Lashari I

    2016-04-01

    Non-renewable energy sources have remained the choice of the world for centuries. Rapid growth in population and industrialisation have caused their shortage and environmental degradation by using them. Thus, at the present rate of consumption, they will not last very long. In this prospective, this study has been conducted. The estimation of energy in terms of biogas and heat from various organic fractions of municipal solid waste is presented and discussed. The results show that organic fractions of municipal solid waste possess methane potential in the range of 3%-22% and their heat capacity ranges from 3007 to 20,099 kJ kg(-1) Also, theoretical biogas potential of different individual fruit as well as vegetable components and mixed food waste are analysed and estimated in the range of 608-1244 m(3) t(-1) Further, the share of bioenergy from municipal solid waste in the total primary energy supply in Pakistan has been estimated to be 1.82%. About 8.43% of present energy demand of the country could be met from municipal solid waste. The study leads us to the conclusion that the share of imported energy (i.e. 0.1% of total energy supply) and reduction in the amount of energy from fossil fuels can be achieved by adopting a waste-to-energy system in the country. © The Author(s) 2016.

  18. Fractional correlation.

    Science.gov (United States)

    Mendlovic, D; Ozaktas, H M; Lohmann, A W

    1995-01-10

    Recently, optical interpretations of the fractional-Fourier-transform operator have been introduced. On the basis of this operator the fractional correlation operator is defined in two different ways that are both consistent with the definition of conventional correlation. Fractional correlation is not always a shift-invariant operation. This property leads to some new applications for fractional correlation as shift-variant image detection. A bulk-optics implementation of fractional correlation is suggested and demonstrated with computer simulations.

  19. Fractionation study in bioleached metallurgy wastes using six-step sequential extraction.

    Science.gov (United States)

    Krasnodebska-Ostrega, Beata; Pałdyna, Joanna; Kowalska, Joanna; Jedynak, Łukasz; Golimowski, Jerzy

    2009-08-15

    The stored metallurgy wastes contain residues from ore processing operations that are characterized by relatively high concentrations of heavy metals. The bioleaching process makes use of bacteria to recover elements from industrial wastes and to decrease potential risk of environmental contamination. Wastes were treated by solutions containing bacteria. In this work, the optimized six-stage sequential extraction procedure was applied for the fractionation of Ni, Cr, Fe, Mn, Cu and Zn in iron-nickel metallurgy wastes deposited in Southern Poland (Szklary). Fractionation and total concentrations of elements in wastes before and after various bioleaching treatments were studied. Analyses of the extracts were performed by ICP-MS and FAAS. To achieve the most effective bioleaching of Zn, Cr, Ni, Cu, Mn, Fe the usage of both autotrophic and heterotrophic bacteria in sequence, combined with flushing of the residue after bioleaching is required. 80-100% of total metal concentrations were mobilized after the proposed treatment. Wastes treated according to this procedure could be deposited without any risk of environmental contamination and additionally the metals could be recovered for industrial purposes.

  20. Subcellular boron and fluorine distributions with SIMS ion microscopy in BNCT and cancer research

    Energy Technology Data Exchange (ETDEWEB)

    Subhash Chandra

    2008-05-30

    The development of a secondary ion mass spectrometry (SIMS) based technique of Ion Microscopy in boron neutron capture therapy (BNCT) was the main goal of this project, so that one can study the subcellular location of boron-10 atoms and their partitioning between the normal and cancerous tissue. This information is fundamental for the screening of boronated drugs appropriate for neutron capture therapy of cancer. Our studies at Cornell concentrated mainly on studies of glioblastoma multiforme (GBM). The early years of the grant were dedicated to the development of cryogenic methods and correlative microscopic approaches so that a reliable subcellular analysis of boron-10 atoms can be made with SIMS. In later years SIMS was applied to animal models and human tissues of GBM for studying the efficacy of potential boronated agents in BNCT. Under this grant the SIMS program at Cornell attained a new level of excellence and collaborative SIMS studies were published with leading BNCT researchers in the U.S.

  1. Study of the branched hydrocarbon fraction of intramuscular lipids from Iberian dry-cured ham.

    Science.gov (United States)

    Petrón, M J; Tejeda, J F; Muriel, E; Ventanas, J; Antequera, T

    2005-01-01

    Branched hydrocarbons from the unsaponifiable lipid fraction of intramuscular fat from Iberian dry-cured hams were analyzed. Thirty-four hams were distributed into four groups according to the feed system of the pigs (extensive system "Montanera" and intensive system "Pienso") and genotype (Iberian and Iberian×Duroc). A total of 35 different hydrocarbons were identified in this study. Some differences were found in the levels of branched, cyclical and unsaturated hydrocarbons as a function of the diet of the pigs (3-hexyl-1,1-dimethyl cyclopentane, p<0.05; 3-octadecene, p<0.01; neophytadiene, p<0.001; 1-ethylundecyl benzene, p<0.01; cyclohexadecane, p<0.001; cyclotriacontane, p<0.05). However, the genotype had a limited effect in the level of branched hydrocarbons found. The study of branched hydrocarbons in intramuscular fat from dry-cured Iberian ham allows differentiation between the pigs management systems.

  2. Subcellular localization and internalization of the vasopressin V1B receptor.

    Science.gov (United States)

    Kashiwazaki, Aki; Fujiwara, Yoko; Tsuchiya, Hiroyoshi; Sakai, Nobuya; Shibata, Katsushi; Koshimizu, Taka-aki

    2015-10-15

    Only limited information is available on agonist-dependent changes in the subcellular localization of vasopressin V1B receptors. Our radioligand binding study of membrane preparations and intact cells revealed that a large fraction of the V1B receptor is located in the cytoplasm in unstimulated CHO cells, which is in contrast to the plasma membrane localization of the V1A and V2 receptors. Moreover, when the affinity of radiolabeled arginine-vasopressin ([3H]AVP) was compared between membrane preparations and intact cells, the affinity of [3H]AVP to the cell surface V1B receptors, but not the V1A receptors, was significantly reduced. Although the number and affinity of cell surface V1B receptors decreased, they became extensively internalized upon binding with [3H]AVP. Approximately 87% of cell surface-bound [3H]AVP was internalized and became resistant to acid wash during incubation with 1 nM [3H]AVP. By contrast, less ligand (35%) was internalized in the cells expressing the V1A receptor. Extensive internalization of the V1B receptors was partially attenuated by inhibitors of cytoskeletal proteins, siRNA against β-arrestin 2, or the removal of sodium chloride from the extracellular buffer, indicating that this internalization involves clathrin-coated pits. Together, these results indicate that the mechanism that regulates the number and affinity of V1B receptors in the plasma membrane is markedly distinct from the corresponding mechanisms for the V1A and V2 receptors and plays a critical role under stress conditions, when vasopressin release is augmented. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Single vs. multiple fraction regimens for palliative radiotherapy treatment of multiple myeloma. A prospective randomised study

    Energy Technology Data Exchange (ETDEWEB)

    Rudzianskiene, Milda; Inciura, Arturas; Gerbutavicius, Rolandas; Rudzianskas, Viktoras; Dambrauskiene, Ruta; Juozaityte, Elona [Lithuanian University of Health Sciences, Oncology Institute, Kaunas (Lithuania); Macas, Andrius [Lithuanian University of Health Sciences, Anaesthesiology Department, Kaunas (Lithuania); Simoliuniene, Renata [Lithuanian University of Health Sciences, Department of Physics, Mathematics and Biophysics, Kaunas (Lithuania); Kiavialaitis, Greta Emilia [University Hospital Zurich, Intitute of Anesthesiology, Zurich (Switzerland)

    2017-09-15

    To compare the impact of a single fraction (8 Gy x 1 fraction) and multifraction (3 Gy x 10 fractions) radiotherapy regimens on pain relief, recalcification and the quality of life (QoL) in patients with bone destructions due to multiple myeloma (MM). In all, 101 patients were included in a randomised prospective clinical trial: 58 patients were included in the control arm (3 Gy x 10 fractions) and 43 patients into the experimental arm (8 Gy x 1 fraction). The response rate was defined according to the International Consensus on Palliative Radiotherapy criteria. Recalcification was evaluated with radiographs. QoL questionnaires were completed before and 4 weeks after treatment. Pain relief was obtained in 81/101 patients (80.2%): complete response in 56 (69%) and partial in 25 patients (30.9%). No significant differences were observed in analgesic response between the groups. Significant factors for pain relief were female gender, age under 65, IgG MM type, presence of recalcification at the irradiated site. Recalcification was found in 32/101 patients (33.7%): complete in 17 (53.2%) and partial in 15 (46.2%). No significant differences were observed in recalcification between the groups. Significant factors for recalcification were Karnofsky index ≥ 60%, haemoglobin level ≤ 80 g/dl, MM stage II and analgesic response at the irradiated site. The QoL after radiotherapy was improved in the control group. The same analgesic and recalcification response was observed using two different radiotherapy regimens. Higher doses should be used to achieve a better QoL. (orig.) [German] Vergleich der einzeitigen vs. fraktionierten palliativen Radiotherapie in Bezug auf Schmerzlinderung, Knochenrekalzifizierung und Lebensqualitaet (QoL) bei Patienten mit multiplem Myelom (MM). In die randomisierte, prospektive Studie wurden 101 Patienten eingeschlossen: Die Kontrollgruppe (n = 58) erhielt eine fraktionierte (3 Gy x 10 Fraktionen) und die Experimentgruppe (n = 43) eine

  4. [Studies on the intradermal reactions with the fractions of Ascaris lumbricoides

    Science.gov (United States)

    Lee, Chan Wook

    1967-06-01

    INTRODUCTION : The studies on allergic reaction with the substances of Ascaris lumbricoides have long been studied by various worers; Conventry(1929), Campbell(1936), Sakei(1949), Miyakawa(1950), Ikeda(1952), Matsumoto and Imawari(1952), Morishita and Kobayashi(1953, 1954), Komiyayama(1954) and Yammoto(1956). Campbell(1936) and some other workers reported that the polysaccharides from ascaris produced the stronger intrademal reactions than protein fraction, though Yamamoto(1954) and others found the reverse results. On the other hand, Hosotani(1954) reported that the crude antigen or mixed antigen with polysaccharide and protein fraction of the ascaris produced the strongest skin reaction than with the other single fraction. As are shown in above reports, the intensity of the allergic reaction with the substances from ascaris is still remained under dipute. The reason might be due to the difference of the method of preparation, technique and evaluation. The aim of the present study is to elucidate the intensity of allergic reactivity fo protein and polysaccharide fration and mixed substance of two fractions and crude antigen of Ascaris lumbricoides. MATERIALS AND METHODS : A Intrdermal Test 1. Human Experiment. The intradermal test was performed on several groups of people. A: Ascaris lumbricoides egg positive cases among adult ages. B: Ascaris lumbricoides egg negative cases but who bad doubtful symptom. C: Ascaris lumbricoides egg negative cases but who had past history of ascaris infection. D: Ascaris lumbricoides egg negative cases and aged 3-8 months old. 2. Animal Experiment: Same breeds of 6 dogs were raised i cages of laboratory for 6 months, During the period, special attention was paid to keep them in parasite free conditon. The body weight was 10kg in average. B. Antigens. The adults worms of Ascaris lumbricoides, which were obtained during laparotomy, were first washed with sterilized saline solution. Each ascaris was placed in 50ml of saline solution

  5. Subcellular distribution of folate and folate binding protein in renal proximal tubules

    Energy Technology Data Exchange (ETDEWEB)

    Sharkey, C.; Hjelle, J.T.; Selhub, J.

    1986-03-01

    High affinity folate binding protein (FBP) found in brush border membranes derived from renal cortices is thought to be involved in the renal conservation of folate. To examine the mechanisms of folate recovery, the subcellular distribution of FBP and /sup 3/H-folate in rabbit renal proximal tubules (PT) was examined using analytical cell fractionation techniques. Tubules contain 3.41 +/- 0.32 picomoles FBP/mg protein (X +/- S.D.; n = 5). Postnuclear supernates (PNS) of PT were layered atop Percoll-sucrose gradients, centrifuged, fractions collected and assayed for various marker enzymes and FBP. Pooled fractions from such gradients were subsequently treated with digitonin and centrifuged in a stoichiometric manner with the activity of the microvillar enzyme, alanylaminopeptidase (AAP); excess FBP distributed with more buoyant particles. Infusion of /sup 3/H-folate into rabbit kidneys followed by tubule isolation and fractionation revealed a time dependent shift in distribution of radiolabel from the AAP-rich gradient fractions to a region containing more buoyant particles; radiolevel was not associated with lysosomal markers. EM-radioautography revealed grains over intracellular vesicles. These results are consistent with the hypothesis that folate is recovered by a process involving receptor-mediated endocytosis or transcytosis.

  6. In vitro and in vivo studies on radiobiological effects of prolonged fraction delivery time in A549 cells

    OpenAIRE

    Jiang, Ling; Xiong, Xiao-Peng; Hu, Chao-Su; Ou, Zhou-Luo; Zhu, Guo-Pei; Ying

    2012-01-01

    Intensity-modulated radiation therapy, when used in the clinic, prolongs fraction delivery time. Here we investigated both the in vivoand in vitroradiobiological effects on the A549 cell line, including the effect of different delivery times with the same dose on A549 tumor growth in nude mice. The in vitroeffects were studied with clonogenic assays, using linear-quadratic and incomplete repair models to fit the dose-survival curves. Fractionated irradiation of different doses was given at on...

  7. Fractional calculus approach to study temperature distribution within a spinning satellite

    Directory of Open Access Journals (Sweden)

    Jyotindra C. Prajapati

    2016-09-01

    Full Text Available This paper deals with the temperature distribution within spinning satellites and problem is formulated in terms of fractional differential equation. Applying fractional calculus approach, solution of this equation is obtained in terms of Wright generalized hypergeometric function, a generalization of exponential function.

  8. Sustainability assessment of oilseed fractionation processes: A case study on lupin seeds

    NARCIS (Netherlands)

    Berghout, J.A.M.; Pelgrom, P.J.M.; Schutyser, M.A.I.; Boom, R.M.; Goot, van der A.J.

    2015-01-01

    Traditional ingredient production focusses on high purity and yield, resulting in energy- and resource-intensive fractionation processes. We explored alternative fractionation routes for oilseeds by focussing on functionality and optimal resource use. Lupin seeds were taken as model material because

  9. Problem Solving as a Professional Development Strategy for Teachers: A Case Study with Fractions

    Science.gov (United States)

    Perdomo-Díaz, Josefa; Felmer, Patricio; Randolph, Valeria; González, Guillermo

    2017-01-01

    In this paper we present a professional development course designed to impact on teachers' mathematical knowledge for teaching fractions. The main features of the course are the use of i) problem solving activities related with mathematical knowledge for teaching fractions ii) peer discussions and iii) monitor's interventions focused on answering…

  10. The fraction of disability pensions attributable to smoking and obesity. Results from a 15-year follow-up study

    DEFF Research Database (Denmark)

    Lund, Thomas; Labriola, Merete; Feveile, Helene

    2010-01-01

    Objective The aim of this study was to estimate the fraction of permanent disability pensions among the working population in Denmark that can be attributed to differences in health behaviour. Methods A total of 8,287 employees were interviewed regarding health behaviour, work environment...... and general health. They were followed in a national register on granted disability pensions. Cox regression analysis was performed, and attributable fractions were calculated. Results The analysis showed a 48% and 79% risk increase for female heavy and moderate smokers, respectively (attributable fraction 19.......7%), and a 74% risk increase for BMI¿disability pension (attributable fraction 15.7%). Conclusions Smoking was an independent disability pension predictor regardless of age, work environment factors and baseline general health...

  11. Nonlinear fractional relaxation

    Indian Academy of Sciences (India)

    Nonlinear fractional equation; nonlinear fractional relaxation; -expansion. Abstract. We define a nonlinear model for fractional relaxation phenomena. We use -expansion method to analyse this model. By studying the fundamental solutions of this model we find that when → 0 the model exhibits a fast decay rate and ...

  12. Subcellular Localization of Galloylated Catechins in Tea Plants [Camellia sinensis (L.) O. Kuntze] Assessed via Immunohistochemistry

    OpenAIRE

    Xu, Huanhuan; Wang, Ya; Chen, Yana; Zhang, Pan; Zhao, Yi; Huang, Yewei; Wang, Xuanjun; Sheng, Jun

    2016-01-01

    Galloylated catechins, as the main secondary metabolites in the tea plant, including (-)-epigallocatechin-3-gallate and (-)-epicatechin-3-gallate, comprise approximately three-quarters of all the tea plant catechins and have stronger effects than non-galloylated catechins, both on the product quality in tea processing and the pharmacological efficacy to human beings. The subcellular localization of galloylated catechins has been the primary focus of studies that assess biosynthesis and physio...

  13. Towards further understanding on the antioxidative activities of Prunus persica fruit: A comparative study with four different fractions

    Science.gov (United States)

    Dhingra, Naveen; Sharma, Rajesh; Kar, Anand

    2014-11-01

    In the present study we have evaluated the antioxidant activities of different fractions (hexane, ethyl acetate, n-butanol and aqueous fractions) of Prunus persica fruit. For extraction simple warring blender method was employed and total phenolic and flavonoid contents were correlated with different antioxidant activities (total antioxidant, 2,2-diphenyl-1-picrylhydrazyl (DPPH), H2O2 scavenging, superoxide radical scavenging, iron chelating and their reducing power properties). Different in vitro antioxidant studies showed that ethyl acetate and n-butanol fractions had the maximum activities that were well correlated with total phenolic and flavonoid contents. Maximum yield (25.14 ± 2.2%) was obtained in its aqueous fraction. Both ethyl acetate and n-butanol fractions showed significant inhibitory effects on different antioxidant activities. A significantly high correlation coefficient existed between total antioxidant activities and with total phenolic as well as total flavonoid contents. It appears that ethyl acetate and n-butanol fractions of P. persica may serve as new potential sources of natural antioxidants and could be of therapeutic use in treating several diseases.

  14. Effects of Solid Fraction on Droplet Wetting and Vapor Condensation: A Molecular Dynamic Simulation Study.

    Science.gov (United States)

    Gao, Shan; Liao, Quanwen; Liu, Wei; Liu, Zhichun

    2017-10-31

    Recently, numerous studies focused on the wetting process of droplets on various surfaces at a microscale level. However, there are a limited number of studies about the mechanism of condensation on patterned surfaces. The present study performed the dynamic wetting behavior of water droplets and condensation process of water molecules on substrates with different pillar structure parameters, through molecular dynamic simulation. The dynamic wetting results indicated that droplets exhibit Cassie state, PW state, and Wenzel state successively on textured surfaces with decreasing solid fraction. The droplets possess a higher static contact angle and a smaller spreading exponent on textured surfaces than those on smooth surfaces. The condensation processes, including the formation, growth, and coalescence of a nanodroplet, are simulated and quantitatively recorded, which are difficult to be observed by experiments. In addition, a wetting transition and a dewetting transition were observed and analyzed in condensation on textured surfaces. Combining these simulation results with previous theoretical and experimental studies will guide us to understand the hypostasis and mechanism of the condensation more clearly.

  15. Study on the Potential Toxicity of a Thymoquinone-Rich Fraction Nanoemulsion in Sprague Dawley Tats

    Directory of Open Access Journals (Sweden)

    Maznah Ismail

    2013-06-01

    Full Text Available Toxicological studies constitute an essential part of the effort in developing an herbal medicine into a drug product. A newly developed thymoquinone-rich fraction nanoemulsion (TQRFNE has been prepared using a high pressure homogenizer. The purpose of this study was to investigate the potential acute toxicity of this nanoemulsion in Sprague Dawley rats. The acute toxicity studies were conducted as per the OECD guidelines 425, allowing for the use of test dose limit of 20 mL TQRFNE (containing 44.5 mg TQ/kg. TQRFNE and distilled water (DW as a control were administered orally to both sexes of rats on Day 0 and observed for 14 days. All the animals appeared normal, and healthy throughout the study. There was no observed mortality or any signs of toxicity during the experimental period. The effects of the TQRFNE and DW groups on general behavior, body weight, food and water consumption, relative organ weight, hematology, histopathology, and clinical biochemistry were measured. All the parameters measured were unaffected as compared to the control (DW group. The administration of 20 mL TQRFNE /kg was not toxic after an acute exposure.

  16. Experimental study on the relationship between average isotopic fractionation factor and evaporation rate

    Directory of Open Access Journals (Sweden)

    Tao WANG

    2010-12-01

    Full Text Available Isotopic fractionation is the foundation of tracing water cycle using hydrogen and oxygen isotopes. Isotopic fractionation factors in evaporation from free water body are mainly affected by temperature and relative humidity, and greatly vary with these atmospheric factors in a day. Evaporation rate can properly reveal the effects of atmospheric factors. Therefore, there should be a certain function relationship existing in isotopic fractionation factors and evaporation rate. An average isotopic fractionation factor was defined to describe isotopic differences between vapor and liquid phases in evaporation with time interval of hours or days. The relationship of average isotopic fractionation factor and evaporation based on isotopic mass balance was investigated through an evaporation pan experiment with no inflow. The experimental results showed that the isotopic compositions of residual water became more enrichment with time; the average isotopic fractionation factor was affected by air temperature, relative humidity and other atmospheric factors, and had a good functional relation with evaporation rate. The values of average isotopic fractionation factor could be easily calculated with the known of evaporation rate, the initial volume of water in pan and isotopic compositions of residual water.

  17. Ligand-binding properties and subcellular localization of maize cytokinin receptors

    Science.gov (United States)

    Lomin, Sergey N.; Yonekura-Sakakibara, Keiko; Romanov, Georgy A.; Sakakibara, Hitoshi

    2011-01-01

    The ligand-binding properties of the maize (Zea mays L.) cytokinin receptors ZmHK1, ZmHK2, and ZmHK3a have been characterized using cytokinin binding assays with living cells or membrane fractions. According to affinity measurements, ZmHK1 preferred N6-(Δ2-isopentenyl)adenine (iP) and had nearly equal affinities to trans-zeatin (tZ) and cis-zeatin (cZ). ZmHK2 preferred tZ and iP to cZ, while ZmHK3a preferred iP. Only ZmHK2 had a high affinity to dihydrozeatin (DZ). Analysis of subcellular fractions from leaves and roots of maize seedlings revealed specific binding of tZ in the microsome fraction but not in chloroplasts or mitochondria. In competitive binding assays with microsomes, tZ and iP were potent competitors of [3H]tZ while cZ demonstrated significantly lower affinity; adenine was almost ineffective. The binding specificities of microsomes from leaf and root cells for cytokinins were consistent with the expression pattern of the ZmHKs and our results on individual receptor properties. Aqueous two-phase partitioning and sucrose density-gradient centrifugation followed by immunological detection with monoclonal antibody showed that ZmHK1 was associated with the endoplasmic reticulum (ER). This was corroborated by observations of the subcellular localization of ZmHK1 fusions with green fluorescent protein in maize protoplasts. All these data strongly suggest that at least a part of cytokinin perception occurs in the ER. PMID:21778179

  18. Comparative study on efficacy and safety of 1550 nm Er:Glass fractional laser and fractional radiofrequency microneedle device for facial atrophic acne scar.

    Science.gov (United States)

    Chae, Woong Suk; Seong, Jun Young; Jung, Ha Na; Kong, Sook Hyun; Kim, Min Ho; Suh, Ho Seok; Choi, Yu Sung

    2015-06-01

    The 1550 nm Er:Glass fractional laser is widely used for the treatment of atrophic acne scar. A novel fractional radiofrequency microneedle device has recently emerged as an alternative for treating acne scars. To evaluate the clinical efficacy and safety of a Er:Glass fractional laser and fractional radiofrequency microneedle device in the treatment of facial atrophic acne scars and to assess the difference between the treatment modalities depending on facial compartment. A total of 40 patients were equally randomized into two groups. Each group of 20 patients received three treatments at 4-week interval using Er:Glass fractional laser or fractional radiofrequency microneedle device. Scar severity scores (ECCA grading scale) improved by a mean of 25.0% and 18.6% in groups A and B, respectively (both P acne scars improved in both groups without significant side effects. Additionally, the fractional laser was a more effective treatment option for acne scars, but the fractional radiofrequency microneedle device offered good adherence and short downtime. © 2015 Wiley Periodicals, Inc.

  19. Meaning of Fractions

    Science.gov (United States)

    Dewi, D. A. K.; Suryadi, D.; Suratno, T.; Mulyana, E.; Kurniawan, H.

    2017-02-01

    Introducing fractions is identical to divide an object. Suppose we divide the apple into two parts. One divided into two parts, the question arises whether one part can be called a half or not. Based on this activity, how can students give meaning to fractions. This study aims at designing a different fractions lesson by applying Didactical Design Research. In doing so, we undertook several research phases: 1) thinking what is fractions and why students should learn this concept; 2) designing didactical situation based on identified learning obstacles; and 3) reflecting retrospectively on the lesson design and its implementation as to redesign the fractions lesson. Our analysis revealed that most students held epistemological obstacles in giving meaning of fractions because they only know fractions as numbers that have numerator and denominator. By positioning ourselves as students, we discuss the ideal design to help students in constructing the meaning of fractions.

  20. Comparative study of two methods of fractionation bromelain from pineapple core extract (Ananas comosus)

    Science.gov (United States)

    Febriani, K.; Wahyuni, I.; Setiasih, S.; Hudiyono, S.

    2017-07-01

    The enzyme can be purified by fractional precipitation. This can be done by salt or organic solvent. In this research, purification of bromelain from pineapple core by fractional precipitation was done by 2 compounds, ammonium sulfate, and ethanol. Fractional precipitation by ammonium sulfate proved to be more effective as it yielded a higher specific activity. Specific activity by ethanol and ammonium sulfate is 4.6480 U/mg at 0-60 % saturation and 8.2243 U/mg at 50-80 % saturation.

  1. Study on the Business Cycle Model with Fractional-Order Time Delay under Random Excitation

    Directory of Open Access Journals (Sweden)

    Zifei Lin

    2017-07-01

    Full Text Available Time delay of economic policy and memory property in a real economy system is omnipresent and inevitable. In this paper, a business cycle model with fractional-order time delay which describes the delay and memory property of economic control is investigated. Stochastic averaging method is applied to obtain the approximate analytical solution. Numerical simulations are done to verify the method. The effects of the fractional order, time delay, economic control and random excitation on the amplitude of the economy system are investigated. The results show that time delay, fractional order and intensity of random excitation can all magnify the amplitude and increase the volatility of the economy system.

  2. 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).

  3. Fractional thermoelasticity

    CERN Document Server

    Povstenko, Yuriy

    2015-01-01

    This book is devoted to fractional thermoelasticity, i.e. thermoelasticity based on the heat conduction equation with differential operators of fractional order. Readers will discover how time-fractional differential operators describe memory effects and space-fractional differential operators deal with the long-range interaction. Fractional calculus, generalized Fourier law, axisymmetric and central symmetric problems and many relevant equations are featured in the book. The latest developments in the field are included and the reader is brought up to date with current research.  The book contains a large number of figures, to show the characteristic features of temperature and stress distributions and to represent the whole spectrum of order of fractional operators.  This work presents a picture of the state-of-the-art of fractional thermoelasticity and is suitable for specialists in applied mathematics, physics, geophysics, elasticity, thermoelasticity and engineering sciences. Corresponding sections of ...

  4. Asymmetrical flow field-flow fractionation with on-line detection for drug transfer studies: a feasibility study

    DEFF Research Database (Denmark)

    Hinna, A.; Steiniger, F.; Hupfeld, S.

    2014-01-01

    Knowledge about drug retention within colloidal carriers is of uppermost importance particularly if drug targeting is anticipated. The aim of the present study was to evaluate asymmetrical flow field-flow fractionation (AF4) with on-line UV/VIS drug quantification for its suitability to determine...... was found repeatable and robust. The employed combination of AF4 with multi-angle laser light scattering furthermore provided detailed size information of the eluting sample and thus allowed to detect instabilities and/or interactions between the donor and acceptor liposomes. Drug quantification by on...

  5. Time-frequency plane behavioural studies of harmonic and chirp functions with fractional Fourier transform (FRFT

    Directory of Open Access Journals (Sweden)

    Rajshree Mishra

    2009-12-01

    Full Text Available The behaviour of harmonic and chirp functions was studied on the time-frequency plane with the help of fractional Fourier transform (FRFT. Studies were also carried out through simulation with different numbers of samples of the functions. Variations were observed in the maximum side-lobe level (MSLL, half main-lobe width (HMLW and side-lobe fall-off rate (SLFOR of the functions. The parameters of these functions were compared with a similar set of parameters of some of the popular window functions. It can thus be concluded that in the time-frequency plane, the chirp function provides better spectral parameters than those of Boxcar window function with some particular values of rotational angle. A similar type of inference can also be drawn for the harmonic function in the time-frequency plane. Of course the rotational angle might vary in this case and a comparative analysis was carried out with Fejer window and the cosine-tip window functions. This study may prove to be helpful in replacing these existing window functions in a variety of applications where a particular parameter or group of parameters of the harmonic and chirp functions are found superior.

  6. HECTAR: a method to predict subcellular targeting in heterokonts.

    Science.gov (United States)

    Gschloessl, Bernhard; Guermeur, Yann; Cock, J Mark

    2008-09-23

    The heterokonts are a particularly interesting group of eukaryotic organisms; they include many key species of planktonic and coastal algae and several important pathogens. To understand the biology of these organisms, it is necessary to be able to predict the subcellular localisation of their proteins but this is not straightforward, particularly in photosynthetic heterokonts which possess a complex chloroplast, acquired as the result of a secondary endosymbiosis. This is because the bipartite target peptides that deliver proteins to these chloroplasts can be easily confused with the signal peptides of secreted proteins, causing currently available algorithms to make erroneous predictions. HECTAR, a subcellular targeting prediction method which takes into account the specific properties of heterokont proteins, has been developed to address this problem. HECTAR is a statistical prediction method designed to assign proteins to five different categories of subcellular targeting: Signal peptides, type II signal anchors, chloroplast transit peptides, mitochondrion transit peptides and proteins which do not possess any N-terminal target peptide. The recognition rate of HECTAR is 96.3%, with Matthews correlation coefficients ranging from 0.67 to 0.95. The method is based on a hierarchical architecture which implements the divide and conquer approach to identify the different possible target peptides one at a time. At each node of the hierarchy, the most relevant outputs of various existing subcellular prediction methods are combined by a Support Vector Machine. The HECTAR method is able to predict the subcellular localisation of heterokont proteins with high accuracy. It also efficiently predicts the subcellular localisation of proteins from cryptophytes, a group that is phylogenetically close to the heterokonts. A variant of HECTAR, called HECTARSEC, can be used to identify signal peptide and type II signal anchor sequences in proteins from any eukaryotic organism. Both

  7. HECTAR: A method to predict subcellular targeting in heterokonts

    Directory of Open Access Journals (Sweden)

    Guermeur Yann

    2008-09-01

    Full Text Available Abstract Background The heterokonts are a particularly interesting group of eukaryotic organisms; they include many key species of planktonic and coastal algae and several important pathogens. To understand the biology of these organisms, it is necessary to be able to predict the subcellular localisation of their proteins but this is not straightforward, particularly in photosynthetic heterokonts which possess a complex chloroplast, acquired as the result of a secondary endosymbiosis. This is because the bipartite target peptides that deliver proteins to these chloroplasts can be easily confused with the signal peptides of secreted proteins, causing currently available algorithms to make erroneous predictions. HECTAR, a subcellular targeting prediction method which takes into account the specific properties of heterokont proteins, has been developed to address this problem. Results HECTAR is a statistical prediction method designed to assign proteins to five different categories of subcellular targeting: Signal peptides, type II signal anchors, chloroplast transit peptides, mitochondrion transit peptides and proteins which do not possess any N-terminal target peptide. The recognition rate of HECTAR is 96.3%, with Matthews correlation coefficients ranging from 0.67 to 0.95. The method is based on a hierarchical architecture which implements the divide and conquer approach to identify the different possible target peptides one at a time. At each node of the hierarchy, the most relevant outputs of various existing subcellular prediction methods are combined by a Support Vector Machine. Conclusion The HECTAR method is able to predict the subcellular localisation of heterokont proteins with high accuracy. It also efficiently predicts the subcellular localisation of proteins from cryptophytes, a group that is phylogenetically close to the heterokonts. A variant of HECTAR, called HECTARSEC, can be used to identify signal peptide and type II signal

  8. Subcellular targeting domains of sphingomyelin synthase 1 and 2.

    Science.gov (United States)

    Yeang, Calvin; Ding, Tingbo; Chirico, William J; Jiang, Xian-Cheng

    2011-12-14

    Sphingomyelin synthase (SMS) sits at the crossroads of sphingomyelin (SM), ceramide, diacylglycerol (DAG) metabolism. It utilizes ceramide and phosphatidylcholine as substrates to produce SM and DAG, thereby regulating lipid messengers which play a role in cell survival and apoptosis. Furthermore, its product SM has been implicated in atherogenic processes such as retention of lipoproteins in the blood vessel intima. There are two mammalian sphingomyelin synthases: SMS1 and SMS2. SMS1 is found exclusively in the Golgi at steady state, whereas SMS2 exists in the Golgi and plasma membrane. Conventional motifs responsible for protein targeting to the plasma membrane or Golgi are either not present in, or unique to, SMS1 and SMS2. In this study, we examined how SMS1 and SMS2 achieve their respective subcellular localization patterns. Brefeldin A treatment prevented SMS1 and SMS2 from exiting the ER, demonstrating that they transit through the classical secretory pathway. We created truncations and chimeras of SMS1 and SMS2 to define their targeting signals. We found that SMS1 contains a C-terminal Golgi targeting signal and that SMS2 contains a C-terminal plasma membrane targeting signal.

  9. Subcellular localization of calcium deposits during zebrafish (Danio rerio) oogenesis.

    Science.gov (United States)

    Golpour, Amin; Pšenička, Martin; Niksirat, Hamid

    2016-01-01

    Calcium plays prominent roles in regulating a broad range of physiological events in reproduction. The aim of this study was to describe the subcellular distribution of calcium deposits during stages of oogenesis in zebrafish using a combined oxalate-pyroantimonate technique. The oocyte development of zebrafish was categorized into four stages: primary growth, cortical-alveolus, vitellogenic, and maturation, based on morphological criteria. Calcium deposits in the primary growth stage were detected in the cytoplasm, mitochondria, nucleus, and follicular cells. At the cortical-alveolus stage, calcium particles were transported from follicular cells and deposited in the cortical alveoli. In the vitellogenic stage, some cortical alveoli were compacted and transformed from flocculent electron-lucent to electron-dense objects with the progression of the stage. Calcium deposits were transformed from larger to smaller particles, coinciding with compaction of cortical alveoli. In the maturation stage, calcium deposits in all oocyte compartments decreased, with the exception of those in mitochondria. The proportion of area covered by calcium deposits in the mitochondria and cortical alveoli of oocytes at different stages of development was significantly different (poogenesis may contribute to better understanding of its role in oogenesis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Studies of technetium-99m nitridobisdithiocarboxylate leucocyte specific radiopharmaceutical: [{sup 99m}TcN(DTCX){sub 2}], DTCX=CH{sub 3}(CH{sub 2}){sub 8}CS{sub 2}. the cellular and subcellular distribution in human blood cells, and chemical behaviour. synthesis of the analogous rhenium-188 radiopharmaceutical

    Energy Technology Data Exchange (ETDEWEB)

    Demaimay, Florian; Roucoux, Alain E-mail: Alain.Roucoux@ensc-rennes.fr; Dazord, Leontine; Noiret, Nicolas; Moisan, Annick; Patin, Henri

    1999-02-01

    The distribution of the radiopharmaceutical ([{sup 99m}TcN(DTCX){sub 2}], DTCX=CH{sub 3}(CH{sub 2}){sub 8}CS{sub 2}) in the leucocyte population determinated by a density separation with double gradient Polymorphprep{sup TM} was studied. Microautoradiographic analysis showed a subcellular distribution of the radiomarker in human blood cells. This technique confirmed the observed lymphocyte selectivity (69%) and revealed that the uptake was predominantly cytoplasmic around the nucleus. A labeling mechanism by passive endocytosis could be proposed involving a required lipophilicity of the radiopharmaceutical for lymphocyte targeting. Finally, we describe the new synthesis with an efficient yield and radiochemical purity of the analogous radiopharmaceutical [{sup 188}ReN(DTCX){sub 2}].

  11. Subcellular distribution, modulation of antioxidant and stress-related genes response to arsenic in Brassica napus L.

    Science.gov (United States)

    Farooq, Muhammad A; Gill, Rafaqat A; Ali, Basharat; Wang, Jian; Islam, Faisal; Ali, Shafaqat; Zhou, Weijun

    2016-03-01

    Arsenic (As) is an environmental toxin pollutant that affects the numerous physiological processes of plants. In present study, two Brassica napus L. cultivars were subjected to various concentrations (0, 50, 100, and 200 µM) of As for 14 days, plants were examined for As subcellular distribution, photosynthesis parameters, oxidative stress, and ultrastructural changes under As-stress. Differential fraction analysis showed that significant amount of As was accumulated in the cell wall as compared to other organelles. Decline in photosynthetic efficiency under As stress was observed in term of reduced pigment contents and gas exchange parameters. Differential responses of antioxidants at both enzymatic and gene levels to higher As stress were more pronounced in cultivar ZS 758 as compared to Zheda 622. The qRT-PCR analysis showed that heat shock protein 90 (Hsp90) and metallothionein were over-expressed in As stressed B. napus plants. Disorganization of cell structure and the damages in different organelles were some of the obvious variations in cultivar Zheda 622 as compared to ZS 758.

  12. Scattering Study of a Modified Cusp Potential in Conformable Fractional Formalism

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Won Sang [Gyeongsang National University, Jinju (Korea, Republic of); Zarrinkamar, Saber [Islamic Azad University, Garmsar (Iran, Islamic Republic of); Zare, Soroush [Islamic Azad University North Tehran Branch, Tehran (Iran, Islamic Republic of); Hassanabadi, Hassan [Shahrood University of Technology, Shahrood (Iran, Islamic Republic of)

    2017-02-15

    The fractional Schr¨odinger equation is considered with a cusp interaction. Exact analytical solutions are obtained and thereby the scattering states as well as transmission and reflection coefficients are determined.

  13. Scattering study of a modified cusp potential in conformable fractional formalism

    Science.gov (United States)

    Chung, Won Sang; Zarrinkamar, Saber; Zare, Soroush; Hassanabadi, Hassan

    2017-02-01

    The fractional Schrödinger equation is considered with a cusp interaction. Exact analytical solutions are obtained and thereby the scattering states as well as transmission and reflection coefficients are determined.

  14. Fractional CO2 laser assisted delivery of topical anesthetics: A randomized controlled pilot study

    NARCIS (Netherlands)

    Meesters, Arne A.; Bakker, Myrna M.; de Rie, Menno A.; Wolkerstorfer, Albert

    2016-01-01

    Many dermatological procedures are performed under local anesthesia. Topical anesthesia requires prolonged occlusion and is often insufficient. Infiltration anesthesia is associated with discomfort. Pretreatment with an ablative fractional laser (AFXL) may enhance penetration of topical drugs,

  15. A Global Database of Soil Phosphorus Compiled from Studies Using Hedley Fractionation

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set provides concentrations of soil phosphorus (P) compiled from the peer-reviewed literature that cited the Hedley fractionation method (Hedley and...

  16. A Global Database of Soil Phosphorus Compiled from Studies Using Hedley Fractionation

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This data set provides concentrations of soil phosphorus (P) compiled from the peer-reviewed literature that cited the Hedley fractionation method (Hedley...

  17. Probing the subcellular localization of hopanoid lipids in bacteria using NanoSIMS.

    Directory of Open Access Journals (Sweden)

    David M Doughty

    Full Text Available The organization of lipids within biological membranes is poorly understood. Some studies have suggested lipids group into microdomains within cells, but the evidence remains controversial due to non-native imaging techniques. A recently developed NanoSIMS technique indicated that sphingolipids group into microdomains within membranes of human fibroblast cells. We extended this NanoSIMS approach to study the localization of hopanoid lipids in bacterial cells by developing a stable isotope labeling method to directly detect subcellular localization of specific lipids in bacteria with ca. 60 nm resolution. Because of the relatively small size of bacterial cells and the relative abundance of hopanoid lipids in membranes, we employed a primary (2H-label to maximize our limit of detection. This approach permitted the analysis of multiple stable isotope labels within the same sample, enabling visualization of subcellular lipid microdomains within different cell types using a secondary label to mark the growing end of the cell. Using this technique, we demonstrate subcellular localization of hopanoid lipids within alpha-proteobacterial and cyanobacterial cells. Further, we provide evidence of hopanoid lipid domains in between cells of the filamentous cyanobacterium Nostoc punctiforme. More broadly, our method provides a means to image lipid microdomains in a wide range of cell types and test hypotheses for their functions in membranes.

  18. 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.

  19. Estimation of population attributable fraction (PAF) for disease occurrence in a cohort study design.

    Science.gov (United States)

    Laaksonen, M A; Härkänen, T; Knekt, P; Virtala, E; Oja, H

    2010-03-30

    The population attributable fraction (PAF) is a useful measure for describing the expected change in an outcome if its risk factors are modified. Cohort studies allow researchers to assess the predictive value of the risk factor modification on the incidence of the outcome during a certain follow-up. Estimation of PAF for both mortality and morbidity in cohort studies with censored survival data has been developed in the recent years. So far, however, censoring due to death in the estimation of PAF for morbidity has been ignored, resulting in estimation of a quantity which is not relevant in practice as some people are likely to die during the follow-up. The risk factors related to the disease incidence may also be related to mortality, and modification of these risk factors is likely to delay the occurrence of both events. Thus, censoring due to death and the impact of risk factor modification must be considered when estimating PAF for disease incidence. We consider both and introduce two measures of disease burden: PAF for the incidence of disease during lifetime and PAF for the prevalence of disease in the population at a certain time. We demonstrate how consideration of censoring due to death changes the estimated PAF for disease incidence and its confidence interval. This underlines the importance of choosing a correct PAF measure depending on the outcome of interest and the risk factors of interest to obtain accurate and interpretable results.

  20. Histological studies of facial acne and atrophic acne scars treated with a bipolar fractional radiofrequency system.

    Science.gov (United States)

    Kaminaka, Chikako; Uede, Mikiko; Nakamura, Yasushi; Furukawa, Fukumi; Yamamoto, Yuki

    2014-05-01

    Various fractional radiofrequency (FRF) treatments have demonstrated significant beneficial effects and minor side-effects on atrophic acne scars and acne vulgaris by creating micro-thermal injuries in the skins. However, histological studies to identify the precise mechanism responsible for the success of bipolar FRF treatments are lacking. In this study, six human subjects with these diseases were histologically analyzed after treatment with a bipolar FRF system (eMatrix; Syneron, Yokneam, Israel) and the effects of multiple passes were compared. Histopathological results showed that two-pass FRF treatment created deeper dermal thermal injury zones compared to one-pass treatment. Periadnexal collagen was coagulated, as well as that in the sebaceous glands, as evaluated in all cases with two-pass FRF treatment. No severe side-effects were observed after treatment. Our experience suggests that the level of dermal thermal injury is directly related to the number of passes, and that a large benefit of this treatment for these diseases is the preservation of adnexal structures. © 2014 Japanese Dermatological Association.

  1. Study of antinociceptive effect of isolated fractions from Petiveria alliacea L. (tipi) in mice.

    Science.gov (United States)

    Gomes, Patrícia Bezerra; Oliveira, Maria Mirele da Silva; Nogueira, Carlos Renato Alves; Noronha, Emmanuelle Coelho; Carneiro, Lyvia Maria Vasconcelos; Bezerra, José Noberto Sousa; Neto, Manoel Andrade; Vasconcelos, Silvania Maria Mendes; Fonteles, Marta Maria França; Viana, Glauce Socorro Barros; de Sousa, Francisca Clea Florenço

    2005-01-01

    The acetate (FA), hexanic (FH), hydroalcoholic (FHA) and precipitated hydroalcoholic (FHAppt) fractions from the root of Petiveria alliacea L. were evaluated for antinociceptive effect using the abdominal constriction induced by acetic acid, hot-plate, formalin tests. The open field and rota rod tests were used to evaluate psychomotor function and myorelaxant activity. The fractions were administered intraperitoneally in mice at doses of 100 and 200 mg/kg. Inhibitions of abdominal constrictions were observed with all doses of the fractions, as compared to control. FH and FHAppt, at both doses, reduced the nociception produced by formalin in the 1st (0-5 min) and 2nd (20-25 min) phases, however FHA (100, 200 mg/kg) and FA 200 mg/kg presented significant inhibition on the 1st and 2nd phases, respectively, of this test. A reduction of the locomotor activity was observed in the open field test with all the fractions. These fractions failed to affect the motor coordination in the rota rod test. Results showed that the different fractions of Petiveria alliacea L. have different antinociceptive potentials as demonstrated in the experimental models of nociception in mice, supporting folk medicine use of this plant.

  2. Subcellular targeting and interactions among the Potato virus X TGB proteins.

    Science.gov (United States)

    Samuels, Timmy D; Ju, Ho-Jong; Ye, Chang-Ming; Motes, Christy M; Blancaflor, Elison B; Verchot-Lubicz, Jeanmarie

    2007-10-25

    Potato virus X (PVX) encodes three proteins named TGBp1, TGBp2, and TGBp3 which are required for virus cell-to-cell movement. To determine whether PVX TGB proteins interact during virus cell-cell movement, GFP was fused to each TGB coding sequence within the viral genome. Confocal microscopy was used to study subcellular accumulation of each protein in virus-infected plants and protoplasts. GFP:TGBp2 and TGBp3:GFP were both seen in the ER, ER-associated granular vesicles, and perinuclear X-bodies suggesting that these proteins interact in the same subdomains of the endomembrane network. When plasmids expressing CFP:TGBp2 and TGBp3:GFP were co-delivered to tobacco leaf epidermal cells, the fluorescent signals overlapped in ER-associated granular vesicles indicating that these proteins colocalize in this subcellular compartment. GFP:TGBp1 was seen in the nucleus, cytoplasm, rod-like inclusion bodies, and in punctate sites embedded in the cell wall. The puncta were reminiscent of previous reports showing viral proteins in plasmodesmata. Experiments using CFP:TGBp1 and YFP:TGBp2 or TGBp3:GFP showed CFP:TGBp1 remained in the cytoplasm surrounding the endomembrane network. There was no evidence that the granular vesicles contained TGBp1. Yeast two hybrid experiments showed TGBp1 self associates but failed to detect interactions between TGBp1 and TGBp2 or TGBp3. These experiments indicate that the PVX TGB proteins have complex subcellular accumulation patterns and likely cooperate across subcellular compartments to promote virus infection.

  3. Structural and functional plasticity of subcellular tethering, targeting and processing of RPGRIP1 by RPGR isoforms

    Directory of Open Access Journals (Sweden)

    Hemangi Patil

    2012-02-01

    Mutations affecting the retinitis pigmentosa GTPase regulator-interacting protein 1 (RPGRIP1 interactome cause syndromic retinal dystrophies. RPGRIP1 interacts with the retinitis pigmentosa GTPase regulator (RPGR through a domain homologous to RCC1 (RHD, a nucleotide exchange factor of Ran GTPase. However, functional relationships between RPGR and RPGRIP1 and their subcellular roles are lacking. We show by molecular modeling and analyses of RPGR disease-mutations that the RPGR-interacting domain (RID of RPGRIP1 embraces multivalently the shared RHD of RPGR1–19 and RPGRORF15 isoforms and the mutations are non-overlapping with the interface found between RCC1 and Ran GTPase. RPGR disease-mutations grouped into six classes based on their structural locations and differential impairment with RPGRIP1 interaction. RPGRIP1α1 expression alone causes its profuse self-aggregation, an effect suppressed by co-expression of either RPGR isoform before and after RPGRIP1α1 self-aggregation ensue. RPGR1–19 localizes to the endoplasmic reticulum, whereas RPGRORF15 presents cytosolic distribution and they determine uniquely the subcellular co-localization of RPGRIP1α1. Disease mutations in RPGR1–19, RPGRORF15, or RID of RPGRIP1α1, singly or in combination, exert distinct effects on the subcellular targeting, co-localization or tethering of RPGRIP1α1 with RPGR1–19 or RPGRORF15 in kidney, photoreceptor and hepatocyte cell lines. Additionally, RPGRORF15, but not RPGR1–19, protects the RID of RPGRIP1α1 from limited proteolysis. These studies define RPGR- and cell-type-dependent targeting pathways with structural and functional plasticity modulating the expression of mutations in RPGR and RPGRIP1. Further, RPGR isoforms distinctively determine the subcellular targeting of RPGRIP1α1, with deficits in RPGRORF15-dependent intracellular localization of RPGRIP1α1 contributing to pathomechanisms shared by etiologically distinct syndromic retinal dystrophies.

  4. Pendrin gene ablation alters ENaC subcellular distribution and open probability.

    Science.gov (United States)

    Pech, Vladimir; Wall, Susan M; Nanami, Masayoshi; Bao, Hui-Fang; Kim, Young Hee; Lazo-Fernandez, Yoskaly; Yue, Qiang; Pham, Truyen D; Eaton, Douglas C; Verlander, Jill W

    2015-07-15

    The present study explored whether the intercalated cell Cl(-)/HCO3(-) exchanger pendrin modulates epithelial Na(+) channel (ENaC) function by changing channel open probability and/or channel density. To do so, we measured ENaC subunit subcellular distribution by immunohistochemistry, single channel recordings in split open cortical collecting ducts (CCDs), as well as transepithelial voltage and Na(+) absorption in CCDs from aldosterone-treated wild-type and pendrin-null mice. Because pendrin gene ablation reduced 70-kDa more than 85-kDa γ-ENaC band density, we asked if pendrin gene ablation interferes with ENaC cleavage. We observed that ENaC-cleaving protease application (trypsin) increased the lumen-negative transepithelial voltage in pendrin-null mice but not in wild-type mice, which raised the possibility that pendrin gene ablation blunts ENaC cleavage, thereby reducing open probability. In mice harboring wild-type ENaC, pendrin gene ablation reduced ENaC-mediated Na(+) absorption by reducing channel open probability as well as by reducing channel density through changes in subunit total protein abundance and subcellular distribution. Further experiments used mice with blunted ENaC endocytosis and degradation (Liddle's syndrome) to explore the significance of pendrin-dependent changes in ENaC open probability. In mouse models of Liddle's syndrome, pendrin gene ablation did not change ENaC subunit total protein abundance, subcellular distribution, or channel density, but markedly reduced channel open probability. We conclude that in mice harboring wild-type ENaC, pendrin modulates ENaC function through changes in subunit abundance, subcellular distribution, and channel open probability. In a mouse model of Liddle's syndrome, however, pendrin gene ablation reduces channel activity mainly through changes in open probability. Copyright © 2015 the American Physiological Society.

  5. Cdc2/cyclin B1 regulates centrosomal Nlp proteolysis and subcellular localization.

    Science.gov (United States)

    Zhao, Xuelian; Jin, Shunqian; Song, Yongmei; Zhan, Qimin

    2010-11-01

    The formation of proper mitotic spindles is required for appropriate chromosome segregation during cell division. Aberrant spindle formation often causes aneuploidy and results in tumorigenesis. However, the underlying mechanism of regulating spindle formation and chromosome separation remains to be further defined. Centrosomal Nlp (ninein-like protein) is a recently characterized BRCA1-regulated centrosomal protein and plays an important role in centrosome maturation and spindle formation. In this study, we show that Nlp can be phosphorylated by cell cycle protein kinase Cdc2/cyclin B1. The phosphorylation sites of Nlp are mapped at Ser185 and Ser589. Interestingly, the Cdc2/cyclin B1 phosphorylation site Ser185 of Nlp is required for its recognition by PLK1, which enable Nlp depart from centrosomes to allow the establishment of a mitotic scaffold at the onset of mitosis . PLK1 fails to dissociate the Nlp mutant lacking Ser185 from centrosome, suggesting that Cdc2/cyclin B1 might serve as a primary kinase of PLK1 in regulating Nlp subcellular localization. However, the phosphorylation at the site Ser589 by Cdc2/cyclin B1 plays an important role in Nlp protein stability probably due to its effect on protein degradation. Furthermore, we show that deregulated expression or subcellular localization of Nlp lead to multinuclei in cells, indicating that scheduled levels of Nlp and proper subcellular localization of Nlp are critical for successful completion of normal cell mitosis, These findings demonstrate that Cdc2/cyclin B1 is a key regulator in maintaining appropriate degradation and subcellular localization of Nlp, providing novel insights into understanding on the role of Cdc2/cyclin B1 in mitotic progression.

  6. Fractional dosing of yellow fever vaccine to extend supply: a modelling study.

    Science.gov (United States)

    Wu, Joseph T; Peak, Corey M; Leung, Gabriel M; Lipsitch, Marc

    2016-12-10

    The ongoing yellow fever epidemic in Angola strains the global vaccine supply, prompting WHO to adopt dose sparing for its vaccination campaign in Kinshasa, Democratic Republic of the Congo, in July-August, 2016. Although a 5-fold fractional-dose vaccine is similar to standard-dose vaccine in safety and immunogenicity, efficacy is untested. There is an urgent need to ensure the robustness of fractional-dose vaccination by elucidation of the conditions under which dose fractionation would reduce transmission. We estimate the effective reproductive number for yellow fever in Angola using disease natural history and case report data. With simple mathematical models of yellow fever transmission, we calculate the infection attack rate (the proportion of population infected over the course of an epidemic) with various levels of transmissibility and 5-fold fractional-dose vaccine efficacy for two vaccination scenarios, ie, random vaccination in a hypothetical population that is completely susceptible, and the Kinshasa vaccination campaign in July-August, 2016, with different age cutoff for fractional-dose vaccines. We estimate the effective reproductive number early in the Angola outbreak was between 5·2 and 7·1. If vaccine action is all-or-nothing (ie, a proportion of vaccine recipients receive complete protection [VE] and the remainder receive no protection), n-fold fractionation can greatly reduce infection attack rate as long as VE exceeds 1/n. This benefit threshold becomes more stringent if vaccine action is leaky (ie, the susceptibility of each vaccine recipient is reduced by a factor that is equal to the vaccine efficacy). The age cutoff for fractional-dose vaccines chosen by WHO for the Kinshasa vaccination campaign (2 years) provides the largest reduction in infection attack rate if the efficacy of 5-fold fractional-dose vaccines exceeds 20%. Dose fractionation is an effective strategy for reduction of the infection attack rate that would be robust with a

  7. Spatial fractionation of the dose using neon and heavier ions: A Monte Carlo study.

    Science.gov (United States)

    Peucelle, C; Martínez-Rovira, I; Prezado, Y

    2015-10-01

    This work explores a new radiation therapy approach which might trigger a renewed use of neon and heavier ions to treat cancers. These ions were shown to be extremely efficient in radioresistant tumor killing. Unfortunately, the efficient region also extends into the normal tissue in front of the tumor. The strategy the authors propose is to profit from the well-established sparing effect of thin spatially fractionated beams, so that the impact on normal tissues might be minimized while a high tumor control is achieved. The main goal of this work is to provide a proof of concept of this new approach. With that aim, a dosimetric study was carried out as a first step to evaluate the interest of further explorations of this avenue. The gate/geant4 v.6.1 Monte Carlo simulation platform was employed to simulate arrays of rectangular minibeams (700 μm × 2 cm) of four ions (Ne, Si, Ar, and Fe). The irradiations were performed with a 2 cm-long spread-out Bragg peak centered at 7 cm-depth. Dose distributions in a water phantom were scored considering two minibeams center-to-center distances: 1400 and 3500 μm. Peak and valley doses, peak-to-valley dose ratios (PVDRs), beam penumbras, and relative contribution of nuclear fragments and electromagnetic processes were assessed as figures of merit. In addition, the type and proportion of the secondary nuclear fragments were evaluated in both peak and valley regions. Extremely high PVDR values (>100) and low valley doses were obtained. The higher the atomic number (Z) of the primary ion is, the lower the valleys and the narrower the penumbras. Although the yield of secondary nuclear products increases with Z, the actual dose being deposited by the secondary nuclear fragments in the valleys starts to be the dominant contribution at deeper points, helping in the sparing of proximal normal tissues. Additionally, a wider center-to-center distance leads to a minimized contribution of heavier secondary fragments in valleys. The

  8. Study on sedative effects of different fractions of Hop (Humulus lupulus L. extract compared with diazepam in rats

    Directory of Open Access Journals (Sweden)

    R Shishehgar

    2012-05-01

    Full Text Available Humulus lupulus is a medicinal plant which in Farsi is called "razak". The purpose of this research is, studying the sedative effects of polar, semi polar and non polar fractions extracted from Hop (Humulus lupulus. L in comparison with diazepam in the animal model of Rat. For conducting this research polar, semi polar and non polar fractions extracted from Hop based on the polarity of solvent. Then study continued with the injection of obtained extracts and other medicines to different groups of Wistar breed of rats. First group was injected with 100mg/kg of Polar fraction extract the second group, with 100mg/kg of Semipolar extract, the third group, with 100 mg/kg of non-polar extract of Humulus lupulus the fourth group with 2 mg/kg of Diazepam the fifth group with the same volume of DMSO used as solvent of injectable medicines an the sixth group was the control group and did not receive any drug. The method of injection was Intra peritoneal (IP form. Statistical diagrams and results showed a significant decreasing of anesthetic induction time and increasing of sleeping time of Ketamin induced anesthesia, after IP injection of the Polar fraction extract of Humulus lupulus. The results obtained showed that the polar-fraction extract of Humulus lupulus has more sufficient sedative effects than diazepam and other under studied groups.

  9. Internalization and subcellular fate of aptamer and peptide dual-functioned nanoparticles.

    Science.gov (United States)

    Gao, Huile; Yang, Zhi; Zhang, Shuang; Pang, Zhiqing; Jiang, Xinguo

    2014-06-01

    To evaluate the internalization and subcellular fate of AS1411 aptamer (for glioma targeting) and TGN peptide (for blood-brain barrier targeting)-modified nanoparticles (AsTNPs), which was important for optimizing targeted delivery systems and realizing the potential toxicity to cells. Organelles were labelled with specific markers. Several uptake inhibitors were used to determine the endocytosis pathways. Transmission electron microscopy (TEM) was utilized to directly observe the endocytosis procedure and subcellular fate of AsTNPs. Subcellular localization demonstrated that endosomes and mitochondria were involved in the uptake of AsTNPs by both C6 and bEnd.3 cells, however, lysosomes and Golgi apparatus were only involved in the internalization by C6 cells rather than bEnd.3 cells. Uptake mechanism study demonstrated the clathrin- and caveolae-mediated endocytosis were the main pathways in the uptake of AsTNPs by C6 and bEnd.3 cells. However, other pathways, including clathrin- and caveolae-independent endocytosis and macropinocytosis are also involved in the uptake by C6 cells and not by bEnd.3 cells. TEM directly demonstrated the involvement of these pathways. Particles could be found mostly in endosomes. Compared to unmodified nanoparticles, AsTNPs displayed different internalization pathways involved in several cell organelles.

  10. Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease*

    Science.gov (United States)

    da Palma, Joel Ramos; Burri, Dominique Julien; Oppliger, Joël; Salamina, Marco; Cendron, Laura; de Laureto, Patrizia Polverino; Seidah, Nabil Georges; Kunz, Stefan; Pasquato, Antonella

    2014-01-01

    The proprotein convertase subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P) plays crucial roles in cellular homeostatic functions and is hijacked by pathogenic viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P involves sequential autocatalytic processing of its N-terminal prodomain at sites B′/B followed by the herein newly identified C′/C sites. We found that SKI-1/S1P autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. In contrast to other zymogen proprotein convertases, all incompletely matured intermediates of SKI-1/S1P showed full catalytic activity toward cellular substrates, whereas optimal cleavage of viral glycoproteins depended on B′/B processing. Incompletely matured forms of SKI-1/S1P further process cellular and viral substrates in distinct subcellular compartments. Using a cell-based sensor for SKI-1/S1P activity, we found that 9 amino acid residues at the cleavage site (P1–P8) and P1′ are necessary and sufficient to define the subcellular location of processing and to determine to what extent processing of a substrate depends on SKI-1/S1P maturation. In sum, our study reveals novel and unexpected features of SKI-1/S1P zymogen activation and subcellular specificity of activity toward cellular and pathogen-derived substrates. PMID:25378398

  11. Inducible control of subcellular RNA localization using a synthetic protein-RNA aptamer interaction.

    Directory of Open Access Journals (Sweden)

    Brian J Belmont

    Full Text Available Evidence is accumulating in support of the functional importance of subcellular RNA localization in diverse biological contexts. In different cell types, distinct RNA localization patterns are frequently observed, and the available data indicate that this is achieved through a series of highly coordinated events. Classically, cis-elements within the RNA to be localized are recognized by RNA-binding proteins (RBPs, which then direct specific localization of a target RNA. Until now, the precise control of the spatiotemporal parameters inherent to regulating RNA localization has not been experimentally possible. Here, we demonstrate the development and use of a chemically-inducible RNA-protein interaction to regulate subcellular RNA localization. Our system is composed primarily of two parts: (i the Tet Repressor protein (TetR genetically fused to proteins natively involved in localizing endogenous transcripts; and (ii a target transcript containing genetically encoded TetR-binding RNA aptamers. TetR-fusion protein binding to the target RNA and subsequent localization of the latter are directly regulated by doxycycline. Using this platform, we demonstrate that enhanced and controlled subcellular localization of engineered transcripts are achievable. We also analyze rules for forward engineering this RNA localization system in an effort to facilitate its straightforward application to studying RNA localization more generally.

  12. Differential subcellular distribution of four phospholipase C isoforms and secretion of GPI-PLC activity.

    Science.gov (United States)

    Staudt, Emanuel; Ramasamy, Pathmanaban; Plattner, Helmut; Simon, Martin

    2016-12-01

    Phospholipase C (PLC) is an important enzyme of signal transduction pathways by generation of second messengers from membrane lipids. PLCs are also indicated to cleave glycosylphosphatidylinositol (GPI)-anchors of surface proteins thus releasing these into the environment. However, it remains unknown whether this enzymatic activity on the surface is due to distinct PLC isoforms in higher eukaryotes. Ciliates have, in contrast to other unicellular eukaryotes, multiple PLC isoforms as mammals do. Thus, Paramecium represents a perfect model to study subcellular distribution and potential surface activity of PLC isoforms. We have identified distinct subcellular localizations of four PLC isoforms indicating functional specialization. The association with different calcium release channels (CRCs) argues for distinct subcellular functions. They may serve as PI-PLCs in microdomains for local second messenger responses rather than free floating IP3. In addition, all isoforms can be found on the cell surface and they are found together with GPI-cleaved surface proteins in salt/ethanol washes of cells. We can moreover show them in medium supernatants of living cells where they have access to GPI-anchored surface proteins. Among the isoforms we cannot assign GPI-PLC activity to specific PLC isoforms; rather each PLC is potentially responsible for the release of GPI-anchored proteins from the surface. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. 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.

  14. A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Thomas eNägele

    2013-12-01

    Full Text Available During the last decade genome sequencing has experienced a rapid technological development resulting in numerous sequencing projects and applications in life science. In plant molecular biology, the availability of sequence data on whole genomes has enabled the reconstruction of metabolic networks. Enzymatic reactions are predicted by the sequence information. Pathways arise due to the participation of chemical compounds as substrates and products in these reactions. Although several of these comprehensive networks have been reconstructed for the genetic model plant Arabidopsis thaliana, the integration of experimental data is still challenging. Particularly the analysis of subcellular organization of plant cells limits the understanding of regulatory instances in these metabolic networks in vivo. In this study, we develop an approach for the functional integration of experimental high-throughput data into such large-scale networks. We present a subcellular metabolic network model comprising 524 metabolic intermediates and 548 metabolic interactions derived from a total of 2769 reactions. We demonstrate how to link the metabolite covariance matrix of different Arabidopsis thaliana accessions with the subcellular metabolic network model for the inverse calculation of the biochemical Jacobian, finally resulting in the calculation of a matrix which satisfies a Lyaponov equation involving a covariance matrix. In this way, differential strategies of metabolite compartmentation and involved reactions were identified in the accessions when exposed to low temperature.

  15. Subcellular distribution of non-muscle myosin IIb is controlled by FILIP through Hsc70.

    Directory of Open Access Journals (Sweden)

    Hideshi Yagi

    Full Text Available The neuronal spine is a small, actin-rich dendritic or somatic protrusion that serves as the postsynaptic compartment of the excitatory synapse. The morphology of the spine reflects the activity of the synapse and is regulated by the dynamics of the actin cytoskeleton inside, which is controlled by actin binding proteins such as non-muscle myosin. Previously, we demonstrated that the subcellular localization and function of myosin IIb are regulated by its binding partner, filamin-A interacting protein (FILIP. However, how the subcellular distribution of myosin IIb is controlled by FILIP is not yet known. The objective of this study was to identify potential binding partners of FILIP that contribute to its regulation of non-muscle myosin IIb. Pull-down assays detected a 70-kDa protein that was identified by mass spectrometry to be the chaperone protein Hsc70. The binding of Hsc70 to FILIP was controlled by the adenosine triphosphatase (ATPase activity of Hsc70. Further, FILIP bound to Hsc70 via a domain that was not required for binding non-muscle myosin IIb. Inhibition of ATPase activity of Hsc70 impaired the effect of FILIP on the subcellular distribution of non-muscle myosin IIb. Further, in primary cultured neurons, an inhibitor of Hsc70 impeded the morphological change in spines induced by FILIP. Collectively, these results demonstrate that Hsc70 interacts with FILIP to mediate its effects on non-muscle myosin IIb and to regulate spine morphology.

  16. Determination of fractional flow reserve (FFR) based on scaling laws: a simulation study

    Science.gov (United States)

    Wong, Jerry T.; Molloi, Sabee

    2008-07-01

    Fractional flow reserve (FFR) provides an objective physiological evaluation of stenosis severity. A technique that can measure FFR using only angiographic images would be a valuable tool in the cardiac catheterization laboratory. To perform this, the diseased blood flow can be measured with a first pass distribution analysis and the theoretical normal blood flow can be estimated from the total coronary arterial volume based on scaling laws. A computer simulation of the coronary arterial network was used to gain a better understanding of how hemodynamic conditions and coronary artery disease can affect blood flow, arterial volume and FFR estimation. Changes in coronary arterial flow and volume due to coronary stenosis, aortic pressure and venous pressure were examined to evaluate the potential use of flow and volume for FFR determination. This study showed that FFR can be estimated using arterial volume and a scaling coefficient corrected for aortic pressure. However, variations in venous pressure were found to introduce some error in FFR estimation. A relative form of FFR was introduced and was found to cancel out the influence of pressure on coronary flow, arterial volume and FFR estimation. The use of coronary flow and arterial volume for FFR determination appears promising.

  17. Isotope fractionation of sandy-soil water during evaporation - an experimental study.

    Science.gov (United States)

    Rao, Wen-Bo; Han, Liang-Feng; Tan, Hong-Bing; Wang, Shuai

    2017-06-01

    Soil samples containing water with known stable isotopic compositions were prepared. The soil water was recovered by using vacuum/heat distillation. The experiments were held under different conditions to control rates of water evaporation and water recovery. Recoveries, δ18O and δ2H values of the soil water were determined. Analyses of the data using a Rayleigh distillation model indicate that under the experimental conditions only loosely bound water is extractable in cases where the recovery is smaller than 100 %. Due to isotopic exchange between vapour and remaining water in the micro channels or capillaries of the soil matrix, isotopic fractionation may take place under near-equilibrium conditions. This causes the observed relationship between δ2H and δ18O of the extracted water samples to have a slope close to 8. The results of this study may indicate that, in arid zones when soil that initially contains water dries out, the slope of the relationship between δ2H and δ18O values should be close to 8. Thus, a smaller slope, as observed by some groundwater and soil water samples in arid zones, may be caused by evaporation of water before the water has entered the unsaturated zone.

  18. Comparison of non-ablative and ablative fractional laser treatments in a postoperative scar study.

    Science.gov (United States)

    Shin, Jung U; Gantsetseg, Dorjsuren; Jung, Jin Young; Jung, Inhee; Shin, Sungsik; Lee, Ju Hee

    2014-12-01

    Postoperative scarring after thyroidectomy is a problem for both patients and clinicians. Recently, both non-ablative and ablative fractional laser (NFL and AFL) systems have attracted attention as potential therapies for the revision of thyroidectomy scars. The present split-scar study was designed to directly compare the efficacy of these two methods for the treatment of post-thyroidectomy scars. Twenty females (mean age 42.1 years, range 22-55) with scarring 2-3 months post-thyroidectomy were enrolled in the study. One half of the scar (chosen at random) was treated with NFL and the other half was treated with AFL. In each case, two treatments were given at 2-month intervals. Clinical photographs were taken at baseline, before each treatment, and at the final 3-month evaluation. Independent clinician grading of improvement and patient satisfaction were measured on a quartile scale. Color (erythema and melanin indices) and scar hardness were measured at baseline and at three months post-treatment with a dermaspectrometer and durometer, respectively. The mean clinical improvement grades for AFL and NFL were highly similar, 2.45 ± 0.99 and 2.35 ± 0.85, respectively, without statistical significance (P = 0.752). However, NFL treatment resulted in statistically significant changes in erythema and pigmentation (P = 0.035 and P = 0.003, respectively), and skin hardness was significantly reduced after AFL treatment (P = 0.026). Clinical improvement was not significantly different between the two systems; however, AFL was better at reducing scar hardness whereas NFL was superior for lightening color. These data suggest that a study assessing the feasibility of a combined approach for the revision of post-thyroidectomy scarring might be warranted. © 2014 Wiley Periodicals, Inc.

  19. Adding structure to land cover - using fractional cover to study animal habitat use.

    Science.gov (United States)

    Bevanda, Mirjana; Horning, Ned; Reineking, Bjoern; Heurich, Marco; Wegmann, Martin; Mueller, Joerg

    2014-01-01

    Linking animal movements to landscape features is critical to identify factors that shape the spatial behaviour of animals. Habitat selection is led by behavioural decisions and is shaped by the environment, therefore the landscape is crucial for the analysis. Land cover classification based on ground survey and remote sensing data sets are an established approach to define landscapes for habitat selection analysis. We investigate an approach for analysing habitat use using continuous land cover information and spatial metrics. This approach uses a continuous representation of the landscape using percentage cover of a chosen land cover type instead of discrete classes. This approach, fractional cover, captures spatial heterogeneity within classes and is therefore capable to provide a more distinct representation of the landscape. The variation in home range sizes is analysed using fractional cover and spatial metrics in conjunction with mixed effect models on red deer position data in the Bohemian Forest, compared over multiple spatio-temporal scales. We analysed forest fractional cover and a texture metric within each home range showing that variance of fractional cover values and texture explain much of variation in home range sizes. The results show a hump-shaped relationship, leading to smaller home ranges when forest fractional cover is very homogeneous or highly heterogeneous, while intermediate stages lead to larger home ranges. The application of continuous land cover information in conjunction with spatial metrics proved to be valuable for the explanation of home-range sizes of red deer.

  20. Predicting Subcellular Localization of Proteins by Bioinformatic Algorithms

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2015-01-01

    When predicting the subcellular localization of proteins from their amino acid sequences, there are basically three approaches: signal-based, global property-based, and homology-based. Each of these has its advantages and drawbacks, and it is important when comparing methods to know which approac...

  1. Measurement of endogenous subcellular concentration of steroids in tissue

    NARCIS (Netherlands)

    Poortman, J.; Landeghem, A.A.J. van; Helmond-Agema, A.; Thussen, J.H.H.

    1984-01-01

    A reliable method for the extraction of steroid hormones from human uterine tissue and the subsequent measurement of these hormones in the subcellular compartments by radioimmunoassay is described. Extraction of radioactive steroid hormones from in vivo labelled human uterine tissue by different

  2. Lipidomics: analysis of the lipid composition of cells and subcellular organelles by electrospray ionization mass spectrometry.

    Science.gov (United States)

    Brügger, Britta

    2014-01-01

    Lipidomics aims to quantitatively define lipid classes, including their molecular species, in biological systems. Lipidomics has experienced rapid progress, mainly because of continuous technical advances in instrumentation that are now enabling quantitative lipid analyses with an unprecedented level of sensitivity and precision. The still-growing category of lipids includes a broad diversity of chemical structures with a wide range of physicochemical properties. Reflecting this diversity, different methods and strategies are being applied to the quantification of lipids. Here, I review state-of-the-art electrospray ionization tandem mass spectrometric approaches and direct infusion to quantitatively assess lipid compositions of cells and subcellular fractions. Finally, I discuss a few examples of the power of mass spectrometry-based lipidomics in addressing cell biological questions.

  3. Pilot in vivo animal study of bone regeneration by fractional Er: YAG-laser

    Science.gov (United States)

    Altshuler, Gregory B.; Belikov, Andrey V.; Shatilova, Ksenia V.; Yaremenko, Andrey I.; Zernitskiy, Alexander Y.; Zernitckaia, Ekaterina A.

    2016-04-01

    The histological structure of the rabbit parietal bone during its regeneration after fractional Er: YAG-laser (λ=2.94μm) treatment was investigated by hematoxylin and eosin (H&E) stain. In 48 days after fractional laser treatment, bone samples contained micro-cavities and fragments of necrotic tissue with empty cellular lacuna and coagulated protein of bone matrix. In this case, necrotic lesions appeared around the periphery of micro-cavities created by laser radiation. Fragmentation of detrital mass and partial substitution of micro-cavities with fatty bone marrow were observed in bone samples in 100 days after fractional laser treatment, in contrast to the earlier period. Partial filling of micro-cavities edges by fibrous tissue with presence of osteoblasts on their inner surface was observed in 100 days also, that indicates regenerative processes in the bone.

  4. Fractional factorial plans

    CERN Document Server

    Dey, Aloke

    2009-01-01

    A one-stop reference to fractional factorials and related orthogonal arrays.Presenting one of the most dynamic areas of statistical research, this book offers a systematic, rigorous, and up-to-date treatment of fractional factorial designs and related combinatorial mathematics. Leading statisticians Aloke Dey and Rahul Mukerjee consolidate vast amounts of material from the professional literature--expertly weaving fractional replication, orthogonal arrays, and optimality aspects. They develop the basic theory of fractional factorials using the calculus of factorial arrangements, thereby providing a unified approach to the study of fractional factorial plans. An indispensable guide for statisticians in research and industry as well as for graduate students, Fractional Factorial Plans features: * Construction procedures of symmetric and asymmetric orthogonal arrays. * Many up-to-date research results on nonexistence. * A chapter on optimal fractional factorials not based on orthogonal arrays. * Trend-free plans...

  5. Synthesis and subcellular location of peroxisomal membrane proteins in a peroxisome-deficient mutant of the yeast Hansenula polymorpha

    NARCIS (Netherlands)

    Sulter, G.J.; Vrieling, E.G.; Harder, W.; Veenhuis, M.

    We have studied the synthesis and subcellular location of peroxisomal membrane proteins (PMPs) in cells of a peroxisome-deficient (per) mutant of the methylotrophic yeast Hansenula polymorpha. Western blot analysis of methanol-induced cells of the per mutant, which had been growing in a continuous

  6. Comparison of cadmium absorption, translocation, subcellular distribution and chemical forms between two radish cultivars (Raphanus sativus L.).

    Science.gov (United States)

    Xin, Juan; Zhao, Xiaohu; Tan, Qiling; Sun, Xuecheng; Hu, Chengxiao

    2017-11-01

    Cadmium (Cd) absorption and accumulation vary greatly not only among plant species but also among cultivars within the same species. In order to better understand the mechanisms of Cd absorption, transportation and distribution, we examined the differences of Cd absorption, translocation, subcellular distribution and chemical forms between L19, a Cd-tolerant genotype, and H4, a Cd-sensitive genotype, using kinetic analysis and soil culture experiment. Kinetic assays showed that the different Cd concentrations between the two cultivars might be ascribed to root absorption and translocation from root to shoot. The investigations of subcellular distribution and chemical forms verified that Cd concentrations of all subcellular fractions in H4 were all higher than in L19. Meanwhile, most of the Cd was associated with cell walls in the root of H4, but the Cd in the root of L19 and leaf of the two cultivars was mainly stored in soluble fraction, which could be one possible mechanism of tolerance to Cd toxicity. In addition, Cd fractions extracted by 1M NaCl and 2% HAC were predominant in root and leaf of both cultivars and the concentrations and proportions extracted by water and 80% ethanol in root and 1M NaCl in leaf were all higher in H4 than in L19. These results indicate that the Cd in H4 is more active than L19, which could be responsible for the sensitivity of H4 to Cd damage. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Determination of scatter fractions of some materials by experimental studies and Monte Carlo calculations

    CERN Document Server

    Meric, N; Bor, D

    1999-01-01

    Scatter fractions have been determined experimentally for lucite, polyethylene, polypropylene, aluminium and copper of varying thicknesses using a polyenergetic broad X-ray beam of 67 kVp. Simulation of the experiment has been carried out by the Monte Carlo technique under the same input conditions. Comparison of the measured and predicted data with each other and with the previously reported values has been given. The Monte Carlo calculations have also been carried out for water, bakelite and bone to examine the dependence of scatter fraction on the density of the scatterer.

  8. Autophagosome Proteins LC3A, LC3B and LC3C Have Distinct Subcellular Distribution Kinetics and Expression in Cancer Cell Lines.

    Directory of Open Access Journals (Sweden)

    Michael I Koukourakis

    Full Text Available LC3s (MAP1-LC3A, B and C are structural proteins of autophagosomal membranes, widely used as biomarkers of autophagy. Whether these three LC3 proteins have a similar biological role in autophagy remains obscure. We examine in parallel the subcellular expression patterns of the three LC3 proteins in a panel of human cancer cell lines, as well as in normal MRC5 fibroblasts and HUVEC, using confocal microscopy and western blot analysis of cell fractions. In the cytoplasm, there was a minimal co-localization between LC3A, B and C staining, suggesting that the relevant autophagosomes are formed by only one out of the three LC3 proteins. LC3A showed a perinuclear and nuclear localization, while LC3B was equally distributed throughout the cytoplasm and localized in the nucleolar regions. LC3C was located in the cytoplasm and strongly in the nuclei (excluding nucleoli, where it extensively co-localized with the LC3A and the Beclin-1 autophagy initiating protein. Beclin 1 is known to contain a nuclear trafficking signal. Blocking nuclear export function by Leptomycin B resulted in nuclear accumulation of all LC3 and Beclin-1 proteins, while Ivermectin that blocks nuclear import showed reduction of accumulation, but not in all cell lines. Since endogenous LC3 proteins are used as major markers of autophagy in clinical studies and cell lines, it is essential to check the specificity of the antibodies used, as the kinetics of these molecules are not identical and may have distinct biological roles. The distinct subcellular expression patterns of LC3s provide a basis for further studies.

  9. Fractional CO(2) laser treatment vs autologous fat transfer in the treatment of acne scars: a comparative study.

    Science.gov (United States)

    Azzam, Omar A; Atta, Ahmed T; Sobhi, Rehab M; Mostafa, Pakinam I N

    2013-01-01

    Acne scars present a highly challenging and frustrating clinical problem. Fractional CO2 laser treatment has led to marked improvement in scars, and fat transfer, or fat grafting, has also recently proven very useful in regenerative medicine. To compare fractional CO2 laser treatment and fat grafting in the treatment of acne scars. Twenty patients were included in this study, 10 received 3 sessions of fractional CO2 laser therapy, and 10 received fat grafting. All patients were then followed up for 3 months, and results were assessed with digital photographs taken by a committee of 3 physicians, by a single-blinded physician, and by reports of patient satisfaction. In the fractional CO2 laser treatment group, under 20% of patients were graded as having excellent scar improvement, 0 as having marked scar improvement, under 10% as having mild scar improvement, and almost 70% as having moderate scar improvement. In the fat-grafting group, the scar and overall improvement were graded as 30% excellent, 30% marked, 20% moderate, and 20% mild. Fat grafting proved to be more effective in the treatment of acne scars than ablative fractional CO2 laser treatment. There were many points in its favor, the most significant being the clinical improvement in scars and texture. This supports the stem cell theory of adipose tissue in regenerative medicine.

  10. Fractional flow reserve versus angiography for guiding percutaneous coronary intervention in patients with multivessel coronary artery disease: 2-year follow-up of the FAME (Fractional Flow Reserve Versus Angiography for Multivessel Evaluation) study

    DEFF Research Database (Denmark)

    Pijls, Nico H J; Fearon, William F; Tonino, Pim A L

    2010-01-01

    The purpose of this study was to investigate the 2-year outcome of percutaneous coronary intervention (PCI) guided by fractional flow reserve (FFR) in patients with multivessel coronary artery disease (CAD)....

  11. Analytical Study of Fractional-Order Multiple Chaotic FitzHugh-Nagumo Neurons Model Using Multistep Generalized Differential Transform Method

    Directory of Open Access Journals (Sweden)

    Shaher Momani

    2014-01-01

    Full Text Available The multistep generalized differential transform method is applied to solve the fractional-order multiple chaotic FitzHugh-Nagumo (FHN neurons model. The algorithm is illustrated by studying the dynamics of three coupled chaotic FHN neurons equations with different gap junctions under external electrical stimulation. The fractional derivatives are described in the Caputo sense. Furthermore, we present figurative comparisons between the proposed scheme and the classical fourth-order Runge-Kutta method to demonstrate the accuracy and applicability of this method. The graphical results reveal that only few terms are required to deduce the approximate solutions which are found to be accurate and efficient.

  12. Oxygen extraction fraction mapping at 3 Tesla using an artificial neural network: A feasibility study.

    Science.gov (United States)

    Domsch, Sebastian; Mürle, Bettina; Weingärtner, Sebastian; Zapp, Jascha; Wenz, Frederik; Schad, Lothar R

    2018-02-01

    The oxygen extraction fraction (OEF) is an important biomarker for tissue-viability. MRI enables noninvasive estimation of the OEF based on the blood-oxygenation-level-dependent (BOLD) effect. Quantitative OEF-mapping is commonly applied using least-squares regression (LSR) to an analytical tissue model. However, the LSR method has not yet become clinically established due to the necessity for long acquisition times. Artificial neural networks (ANNs) recently have received increasing interest for robust curve-fitting and might pose an alternative to the conventional LSR method for reduced acquisition times. This study presents in vivo OEF mapping results using the conventional LSR and the proposed ANN method. In vivo data of five healthy volunteers and one patient with a primary brain tumor were acquired at 3T using a gradient-echo sampled spin-echo (GESSE) sequence. The ANN was trained with simulated BOLD data. In healthy subjects, the mean OEF was 36 ± 2% (LSR) and 40 ± 1% (ANN). The OEF variance within subjects was reduced from 8% to 6% using the ANN method. In the patient, both methods revealed a distinct OEF hotspot in the tumor area, whereas ANN showed less apparent artifacts in surrounding tissue. In clinical scan times, the ANN analysis enables OEF mapping with reduced variance, which could facilitate its integration into clinical protocols. Magn Reson Med 79:890-899, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  13. Validation Study of Image-Based Fractional Flow Reserve During Coronary Angiography.

    Science.gov (United States)

    Pellicano, Mariano; Lavi, Ifat; De Bruyne, Bernard; Vaknin-Assa, Hana; Assali, Abid; Valtzer, Orna; Lotringer, Yonit; Weisz, Giora; Almagor, Yaron; Xaplanteris, Panagiotis; Kirtane, Ajay J; Codner, Pablo; Leon, Martin B; Kornowski, Ran

    2017-09-01

    Fractional flow reserve (FFR), an index of the hemodynamic severity of coronary stenoses, is derived from invasive measurements and requires a pressure-monitoring guidewire and hyperemic stimulus. Angiography-derived FFR measurements (FFRangio) may have several advantages. The aim of this study is to assess the diagnostic performance and interobserver reproducibility of FFRangio in patients with stable coronary artery disease. FFRangio is a computational method based on rapid flow analysis for the assessment of FFR. FFRangio uses the patient's hemodynamic data and routine angiograms to generate a complete 3-dimensional coronary tree with color-coded FFR values at any epicardial location. Hyperemic flow ratio is derived from an automatic resistance-based lumped model of the entire coronary tree. A total of 203 lesions were analyzed in 184 patients from 4 centers. Values derived using FFRangio ranged from 0.5 to 0.97 (median 0.85) and correlated closely (Spearman ρ=0.90; P<0.001) with the invasive FFR measurements, which ranged from 0.5 to 1 (median 0.84). In Bland-Altman analyses, the 95% limits of agreement between these methods ranged from -0.096 to 0.112. Using an FFR cutoff value of 0.80, the sensitivity, specificity, and diagnostic accuracy of FFRangio were 88%, 95%, and 93%, respectively. The intraclass coefficient between 2 blinded operators was 0.962 with a 95% confidence interval from 0.950 to 0.971, P<0.001. There is a high concordance between FFRangio and invasive FFR. The color-coded display of FFR values during coronary angiography facilitates the integration of physiology and anatomy for decision making on revascularization in patients with stable coronary artery disease. URL: https://www.clinicaltrials.gov. Unique identifier: NCT03005028. © 2017 American Heart Association, Inc.

  14. Zn subcellular distribution in liver of goldfish (carassius auratus) with exposure to zinc oxide nanoparticles and mechanism of hepatic detoxification.

    Science.gov (United States)

    Fan, Wenhong; Li, Qian; Yang, Xiuping; Zhang, Li

    2013-01-01

    Zinc Oxide Nanoparticles (ZnO NPs) have attracted increasing concerns because of their widespread use and toxic potential. In this study, Zn accumulations in different tissues (gills, liver, muscle, and gut) of goldfish (Carassius auratus) after exposure to ZnO NPs were studied in comparison with bulk ZnO and Zn(2+). And the technique of subcellular partitioning was firstly used on the liver of goldfish to study the hepatic accumulation of ZnO NPs. The results showed that at sublethal Zn concentration (2 mg/L), bioaccumulation in goldfish was tissue-specific and dependent on the exposure materials. Compared with Zn(2+), the particles of bulk ZnO and the ZnO NPs appeared to aggregate in the environmentally contacted tissues (gills and gut), rather than transport to the internal tissues (liver and muscle). The subcellular distributions of liver differed for the three exposure treatments. After ZnO NPs exposure, Zn percentage in metal-rich granule (MRG) increased significantly, and after Zn(2+) exposure, it increased significantly in the organelles. Metallothionein-like proteins (MTLP) were the main target for Zn(2+), while MRG played dominant role for ZnO NPs. The different results of subcellular distributions revealed that metal detoxification mechanisms of liver for ZnO NPs, bulk ZnO, and Zn(2+) were different. Overall, subcellular partitioning provided an interesting start to better understanding of the toxicity of nano- and conventional materials.

  15. Gram-positive and gram-negative subcellular localization using rotation forest and physicochemical-based features

    Science.gov (United States)

    2015-01-01

    Background The functioning of a protein relies on its location in the cell. Therefore, predicting protein subcellular localization is an important step towards protein function prediction. Recent studies have shown that relying on Gene Ontology (GO) for feature extraction can improve the prediction performance. However, for newly sequenced proteins, the GO is not available. Therefore, for these cases, the prediction performance of GO based methods degrade significantly. Results In this study, we develop a method to effectively employ physicochemical and evolutionary-based information in the protein sequence. To do this, we propose segmentation based feature extraction method to explore potential discriminatory information based on physicochemical properties of the amino acids to tackle Gram-positive and Gram-negative subcellular localization. We explore our proposed feature extraction techniques using 10 attributes that have been experimentally selected among a wide range of physicochemical attributes. Finally by applying the Rotation Forest classification technique to our extracted features, we enhance Gram-positive and Gram-negative subcellular localization accuracies up to 3.4% better than previous studies which used GO for feature extraction. Conclusion By proposing segmentation based feature extraction method to explore potential discriminatory information based on physicochemical properties of the amino acids as well as using Rotation Forest classification technique, we are able to enhance the Gram-positive and Gram-negative subcellular localization prediction accuracies, significantly. PMID:25734546

  16. Study of the solubility of oil fractions in N-methylpyrrolidone and furfurol

    Energy Technology Data Exchange (ETDEWEB)

    Okhrimenko, N.V.; Baiburskaya, E.L.; Martynenko, A.G.

    1979-01-01

    Results of the one-stage purification and the purification in a pilot plant of distillates of 350-420 and 420-500/sup 0/ fractions by furfurol and N-methylpyrrolidone are presented. It is shown that N-methylpyrrolidone has high selectivity and dissolving capacity by comparison with furfurol.

  17. Phytochemical screening and anticonvulsant studies of ethyl acetate fraction of Globimetula braunii on laboratory animals

    Directory of Open Access Journals (Sweden)

    Musa Mumammad Aliyu

    2014-04-01

    Conclusions: These results suggest that the ethyl acetate fraction of Globimetula braunii leaves extract possesses psychoactive compound that may be useful in the management of petit mal epilepsy and lend credence to the ethnomedical use of the plant in the management of epilepsy.

  18. A FRACTIONATION STUDY OF MINERAL ELEMENTS IN RAW AND COOKED LEAF VEGETABLES CONSUMED IN SOUTHERN BRAZIL

    Directory of Open Access Journals (Sweden)

    Luciane Mie KAWASHIMA

    2009-07-01

    Full Text Available

    Five samplings of leaf vegetables widely consumed in Southern Brazil (lettuce, rucola, watercress, kale, chicory, Chinese cabbage, and cabbage were taken during the period of a year in food markets of the city of Campinas, Brazil. A selective extraction of potassium, sodium, calcium, magnesium, iron, manganese, copper, and zinc was conducted on the raw vegetables and four of the vegetables (kale, chicory, Chinese cabbage, and cabbage were also cooked briefly under dry heat for three minutes and submitted to the selective extraction. The extraction separated the minerals into fractions containing mineral elements bound to soluble complexes, bound to ligands solubilized by mild acidic oxidizing conditions, and bound to insoluble ligands under mild acidic oxidizing conditions. The minerals concentrations in each fraction were determined by flame atomic absorption spectrometry. The amount of K, Na, Ca, and Mg extractable at pH 7.0 (soluble fraction from raw vegetables varied between 22 to 75 % of the total content of the mineral present. The soluble fractions of minor elements such as Mn, Zn, and Fe varied from 0 to 100% in the raw vegetables. The brief cooking used besides causing negligible losses of the minerals also increased the solubility of the minerals by 44% to 200%. KEYWORDS: Leaf vegetables; soluble mineral elements in vegetables.

  19. Page 1 Studies on Tuber Hemicelluloses—I 313 Both the fractions ...

    Indian Academy of Sciences (India)

    Both the fractions are constituted from the same sugars and uronic acid, viz., xylose, glucose and glucuronic acid but in different proportions. In hemicellulose A2 the ratio of these components is 2:1:1, while in B, it is. 1 : 1 : 2. REFERENCES. 1. Rao, P. S., Beri, R. M. and J. Sci. & Ind. Res., 1952, 11 B, 127. Budhiraja, R. P. *.

  20. Ablative fractional laser therapy as treatment for Becker nevus: a randomized controlled pilot study

    NARCIS (Netherlands)

    Meesters, Arne A.; Wind, Bas S.; Kroon, Marije W.; Wolkerstorfer, Albert; van der Veen, J. P. Wietze; Nieuweboer-Krobotová, Ludmila; van der Wal, Allard C.; Bos, Jan D.; Beek, Johan F.

    2011-01-01

    Becker nevus (BN) is an uncommon pigment disorder characterized by hyperpigmentation and sometimes hypertrichosis. To date, no effective treatment has been available. We sought to assess efficacy and safety of ablative 10,600-nm fractional laser therapy (FLT) in the treatment of BN. Eleven patients

  1. Cell kill pattern and acute toxicity studies of the aqueous fraction of ...

    African Journals Online (AJOL)

    USER

    2010-08-02

    Aug 2, 2010 ... discussed in the context of the fact that P. biglobosa parts have been reported to be used extensively in the treatment of a wide variety of infections. Key words: Methanolic, aqueous fraction, Parkia biglobosa, bactericidal, slightly toxic. INTRODUCTION. Plants have traditionally provided a source of hope for.

  2. Experimental study of relationship between average isotopic fractionation factor and evaporation rate

    Directory of Open Access Journals (Sweden)

    Tao Wang

    2010-12-01

    Full Text Available Isotopic fractionation is the basis of tracing the water cycle using hydrogen and oxygen isotopes. Isotopic fractionation factors in water evaporating from free water bodies are mainly affected by temperature and relative humidity, and vary significantly with these atmospheric factors over the course of a day. The evaporation rate (E can reveal the effects of atmospheric factors. Therefore, there should be a certain functional relationship between isotopic fractionation factors and E. An average isotopic fractionation factor (α* was defined to describe isotopic differences between vapor and liquid phases in evaporation with time intervals of days. The relationship between α* and E based on the isotopic mass balance was investigated through an evaporation pan experiment with no inflow. The experimental results showed that the isotopic compositions of residual water were more enriched with time; α* was affected by air temperature, relative humidity, and other atmospheric factors, and had a strong functional relation with E. The values of α* can be easily calculated with the known values of E, the initial volume of water in the pan, and isotopic compositions of residual water.

  3. Cell kill pattern and acute toxicity studies of the aqueous fraction of ...

    African Journals Online (AJOL)

    The pattern and rate of kill of the aqueous fraction of the methanolic extract of the stem bark of Parkia biglobosa (WS) against three standard organisms of medical and pharmaceutical importance; Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853, as well as the ...

  4. Cell kill pattern and acute toxicity studies of the aqueous fraction of ...

    African Journals Online (AJOL)

    USER

    2010-08-02

    Aug 2, 2010 ... The pattern and rate of kill of the aqueous fraction of the methanolic extract of the stem bark of Parkia biglobosa (WS) against three standard organisms of medical and pharmaceutical importance;. Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC.

  5. Subcellular differences in handling Cu excess in three freshwater fish species contributes greatly to their differences in sensitivity to Cu

    Energy Technology Data Exchange (ETDEWEB)

    Eyckmans, Marleen, E-mail: marleen.eyckmans@ua.ac.be [Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Blust, Ronny; De Boeck, Gudrun [Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium)

    2012-08-15

    Since changes in metal distribution among tissues and subcellular fractions can provide insights in metal toxicity and tolerance, we investigated this partitioning of Cu in gill and liver tissue of rainbow trout (Oncorhynchus mykiss), common carp (Cyprinus carpio) and gibel carp (Carassius auratus gibelio). These fish species are known to differ in their sensitivity to Cu exposure with gibel carp being the most tolerant and rainbow trout the most sensitive. After an exposure to 50 {mu}g/l (0.79 {mu}M) Cu for 24 h, 3 days, 1 week and 1 month, gills and liver of control and exposed fish were submitted to a differential centrifugation procedure. Interestingly, there was a difference in accumulated Cu in the three fish species, even in control fishes. Where the liver of rainbow trout showed extremely high Cu concentrations under control conditions, the amount of Cu accumulated in their gills was much less than in common and gibel carp. At the subcellular level, the gills of rainbow trout appeared to distribute the additional Cu exclusively in the biologically active metal pool (BAM; contains heat-denaturable fraction and organelle fraction). A similar response could be seen in gill tissue of common carp, although the percentage of Cu in the BAM of common carp was lower compared to rainbow trout. Gill tissue of gibel carp accumulated more Cu in the biologically inactive metal pool (BIM compared to BAM; contains heat-stable fraction and metal-rich granule fraction). The liver of rainbow trout seemed much more adequate in handling the excess Cu (compared to its gills), since the storage of Cu in the BIM increased. Furthermore, the high % of Cu in the metal-rich granule fraction and heat-stable fraction in the liver of common carp and especially gibel carp together with the better Cu handling in gill tissue, pointed out the ability of the carp species to minimize the disadvantages related to Cu stress. The differences in Cu distribution at the subcellular level of gills

  6. A feasibility study: Selection of a personalized radiotherapy fractionation schedule using spatiotemporal optimization

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Minsun, E-mail: mk688@uw.edu; Stewart, Robert D. [Department of Radiation Oncology, University of Washington, Seattle, Washington 98195-6043 (United States); Phillips, Mark H. [Departments of Radiation Oncology and Neurological Surgery, University of Washington, Seattle, Washington 98195-6043 (United States)

    2015-11-15

    Purpose: To investigate the impact of using spatiotemporal optimization, i.e., intensity-modulated spatial optimization followed by fractionation schedule optimization, to select the patient-specific fractionation schedule that maximizes the tumor biologically equivalent dose (BED) under dose constraints for multiple organs-at-risk (OARs). Methods: Spatiotemporal optimization was applied to a variety of lung tumors in a phantom geometry using a range of tumor sizes and locations. The optimal fractionation schedule for a patient using the linear-quadratic cell survival model depends on the tumor and OAR sensitivity to fraction size (α/β), the effective tumor doubling time (T{sub d}), and the size and location of tumor target relative to one or more OARs (dose distribution). The authors used a spatiotemporal optimization method to identify the optimal number of fractions N that maximizes the 3D tumor BED distribution for 16 lung phantom cases. The selection of the optimal fractionation schedule used equivalent (30-fraction) OAR constraints for the heart (D{sub mean} ≤ 45 Gy), lungs (D{sub mean} ≤ 20 Gy), cord (D{sub max} ≤ 45 Gy), esophagus (D{sub max} ≤ 63 Gy), and unspecified tissues (D{sub 05} ≤ 60 Gy). To assess plan quality, the authors compared the minimum, mean, maximum, and D{sub 95} of tumor BED, as well as the equivalent uniform dose (EUD) for optimized plans to conventional intensity-modulated radiation therapy plans prescribing 60 Gy in 30 fractions. A sensitivity analysis was performed to assess the effects of T{sub d} (3–100 days), tumor lag-time (T{sub k} = 0–10 days), and the size of tumors on optimal fractionation schedule. Results: Using an α/β ratio of 10 Gy, the average values of tumor max, min, mean BED, and D{sub 95} were up to 19%, 21%, 20%, and 19% larger than those from conventional prescription, depending on T{sub d} and T{sub k} used. Tumor EUD was up to 17% larger than the conventional prescription. For fast proliferating

  7. Are Secondary School Students Still Hampered by the Natural Number Bias? A Reaction Time Study on Fraction Comparison Tasks

    Science.gov (United States)

    Van Hoof, Jo; Lijnen, Tristan; Verschaffel, Lieven; Van Dooren, Wim

    2013-01-01

    Rational numbers and particularly fractions are difficult for students. It is often claimed that the "natural number bias" underlies erroneous reasoning about rational numbers. This cross-sectional study investigated the natural number bias in first and fifth year secondary school students. Relying on dual process theory assumptions that…

  8. Interpretation of the Fractional Excretion of Sodium in the Absence of Acute Kidney Injury: A Cross-Sectional Study

    NARCIS (Netherlands)

    Schreuder, M.F.; Bokenkamp, A.; Wijk, J.A. van

    2017-01-01

    BACKGROUND/AIMS: The fractional excretion of sodium (FeNa) may be helpful in establishing the cause of acute renal failure. This study was performed to determine the influence of the glomerular filtration rate (GFR), sodium intake, and tubular function on FeNa in children without renal failure.

  9. Study on performance of double helical capacitance probe for water fraction measurement in multiphase flow

    Science.gov (United States)

    Ye, J.; Guo, L. J.; Zhou, H. L.

    2012-03-01

    A type of capacitance probe performance with two brass electrodes intertwined on the outer wall of insulation pipe like a double helix is investigated numerically in this paper, which can measure water fraction in air-oil-water two or three-phase flow in oil industry. The motivation of this paper is to optimize this kind of probe to improve its electric response and spatial resolution and so a 3-D numerical simulation using finite element method is employed to evaluate the effect of electrodes configuration of this capacitance probe on measuring water fraction in horizontal pipes. The electrostatic field of the probe is preliminarily analyzed referred to stratified flow of air-water two-phase flow regime. Several parameters are considered as main variables which have an important effect on the precision of the probe, such as central angle, position angle and length of the two electrodes. From the electrostatic field analysis, lumped capacitance between the two electrodes is obtained in every different electrode geometry model and the results of each model are compared to each other in order to select a better arrangement of the electrodes that has a better response to water fraction. And by using circuit simulation method, the numerical calculated lumped capacitance is transferred to voltage output through the circuit used in the experiment. The relationship between voltage and water fraction of calculated and experimental result are compared in order to test the reasonableness of the simulation. The results show that at high water fraction, the difference between numerical and measured data agrees very well.

  10. Associations of anthropometric characteristics with blood cholesterol fractions among adults. The Greek EPIC study.

    Science.gov (United States)

    Benetou, V; Bamia, C; Trichopoulos, D; Trichopoulou, A

    2006-08-01

    To explore the independent associations of body height, body mass index (BMI), waist circumference and hip circumference with high-density lipoprotein-cholesterol (HDL-cholesterol) and non-high-density lipoprotein-cholesterol (non-HDL-cholesterol), in a large general population sample. Cross sectional. Urban and rural areas throughout Greece. In total,10 837 volunteers, 2034 men and 8803 women, aged 25-82 years, participants in the European Prospective Investigation into Cancer and Nutrition study (EPIC), who have never smoked and never been treated for dyslipidemia. None. The effect of height on non-HDL-cholesterol was opposite but in absolute terms almost as important as that of BMI with no gender interaction. Among women, hip circumference was inversely associated with non-HDL-cholesterol (standardized coefficient bst = -1.11, with standard error (s.e.)=0.42) and positively with HDL-cholesterol (bst = 0.85, s.e.= 0.12) whereas, waist circumference was inversely associated with HDL-cholesterol (bst = -1.16, s.e.=0.13) and strongly positively with non-HDL-cholesterol (bst = 8.83, s.e.= 0.45). Among men, associations were generally weaker (in absolute terms by about 50%) and for hip circumference the association with non-HDL-cholesterol was actually non significantly positive. Height was inversely associated with HDL and non-HDL-cholesterol implicating early life phenomena in the regulation of these variables. Larger hip circumference among women had beneficial effects on blood cholesterol fractions by increasing HDL-cholesterol and reducing non-HDL-cholesterol, whereas among men the relevant effects were less clear cut. The detrimental consequences of large waist circumference on both HDL (reduction) and non-HDL-cholesterol (increase) were also particularly marked among women. The European Prospective Investigation into Cancer and Nutrition (EPIC) is coordinated by the International Agency for Research on Cancer (World Health Organization) and supported by the

  11. Comparison of testosterone fractions between Framingham Heart Study participants and Japanese participants.

    Science.gov (United States)

    Taya, Masaki; Koh, Eitetsu; Izumi, Kouji; Iijima, Masashi; Maeda, Yuji; Matsushita, Tomohiko; Iwamoto, Teruaki; Namiki, Mikio

    2014-07-01

    To determine testosterone fractions in Japanese men and to compare these values with those of Framingham Heart Study participants. We enrolled 498 healthy Japanese men. Total testosterone was assayed by liquid chromatography tandem mass spectrometry, sex hormone-binding globulin was assayed by immunoassay and free testosterone was calculated by a laboratory at the Boston Medical Center. Analog-based free testosterone and immunoassay-based total testosterone were determined by immunoassay. We compared mass spectrometry assay-based total testosterone and calculated free testosterone values in the Japanese participants with values in the American Framingham Heart Study third generation cohort. The mean serum mass spectrometry assay-based total testosterone, sex hormone-binding globulin, and calculated free testosterone values were 439.4 ± 167 ng/dL, 65.34 ± 30.61 nmol/L, and 58.75 ± 20.0 pg/mL, respectively. The correlation coefficients with age for mass spectrometry assay-based total testosterone, sex hormone-binding globulin, and calculated free testosterone were 0.0010, 0.5041, and -0.496, respectively. There were no age-related changes in mass spectrometry assay-based total testosterone values in healthy men (P = 0.981), whereas sex hormone-binding globulin and calculated free testosterone levels showed similar age-related changes (P free testosterone levels (8.24 ± 2.9 pg/mL) showed age-related changes (P testosterone levels (P = 0.828). Serum immunoassay-based total testosterone values (486.1 ± 162.5 ng/dL) correlated with serum mass spectrometry assay-based total testosterone values (r = 0.740, 95% confidence interval 0.6965-0.7781, P free testosterone and calculated free testosterone values showed a highly significant correlation (r = 0.706, 95% confidence interval 0.6587-0.7473, P free testosterone values were approximately 10% of the calculated free testosterone values. In contrast to the Framingham

  12. Subcellular distribution of calcium during spermatogenesis of zebrafish, Danio rerio.

    Science.gov (United States)

    Golpour, Amin; Pšenička, Martin; Niksirat, Hamid

    2017-08-01

    Calcium plays a variety of vital regulatory functions in many physiological and biochemical events in the cell. The aim of this study was to describe the ultrastructural distribution of calcium during different developmental stages of spermatogenesis in a model organism, the zebrafish (Danio rerio), using a combined oxalate-pyroantimonate technique. Samples were treated by potassium oxalate and potassium pyroantimonate during two fixation stages and examined using transmission electron microscopy to detect electron dense intracellular calcium. The subcellular distribution of intracellular calcium was characterized in spermatogonium, spermatocyte, spermatid, and spermatozoon stages. The area which is covered by intracellular calcium in different stages was quantified and compared using software. Isolated calcium deposits were mainly detectable in the cytoplasm and the nucleus of the spermatogonium and spermatocyte. In the spermatid, calcium was partially localized in the cytoplasm as isolated deposits. However, most calcium was transformed from isolated deposits into an unbound pool (free calcium) within the nucleus of the spermatid and the spermatozoon. Interestingly, in the spermatozoon, calcium was mainly localized in a form of an unbound pool which was detectable as an electron-dense mass within the nucleus. Also, sporadic calcium deposits were scattered in the midpiece and flagellum. The proportional area which was covered by intracellular calcium increased significantly from early to late stages of spermatogenesis. The extent of the area which was covered by intracellular calcium in the spermatozoon was the highest compared to earlier stages. Calcium deposits were also observed in the somatic cells (Sertoli, myoid, Leydig) of zebrafish testis. The notable changes in the distribution of intracellular calcium of germ cells during different developmental stages of zebrafish spermatogenesis suggest its different homeostasis and physiological functions during the

  13. Sub-cellular distribution and translocation of TRP channels.

    Science.gov (United States)

    Toro, Carlos A; Arias, Luis A; Brauchi, Sebastian

    2011-01-01

    Cellular electrical activity is the result of a highly complex processes that involve the activation of ion channel proteins. Ion channels make pores on cell membranes that rapidly transit between conductive and non-conductive states, allowing different ions to flow down their electrochemical gradients across cell membranes. In the case of neuronal cells, ion channel activity orchestrates action potentials traveling through axons, enabling electrical communication between cells in distant parts of the body. Somatic sensation -our ability to feel touch, temperature and noxious stimuli- require ion channels able to sense and respond to our peripheral environment. Sensory integration involves the summing of various environmental cues and their conversion into electrical signals. Members of the Transient Receptor Potential (TRP) family of ion channels have emerged as important mediators of both cellular sensing and sensory integration. The regulation of the spatial and temporal distribution of membrane receptors is recognized as an important mechanism for controlling the magnitude of the cellular response and the time scale on which cellular signaling occurs. Several studies have shown that this mechanism is also used by TRP channels to modulate cellular response and ultimately fulfill their physiological function as sensors. However, the inner-working of this mode of control for TRP channels remains poorly understood. The question of whether TRPs intrinsically regulate their own vesicular trafficking or weather the dynamic regulation of TRP channel residence on the cell surface is caused by extrinsic changes in the rates of vesicle insertion or retrieval remain open. This review will examine the evidence that sub-cellular redistribution of TRP channels plays an important role in regulating their activity and explore the mechanisms that control the trafficking of vesicles containing TRP channels.

  14. Stability of phospholipid vesicles studied by asymmetrical flow field-flow fractionation and capillary electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Yohannes, Gebrenegus [Laboratory of Analytical Chemistry, Department of Chemistry, P.O. Box 55, FIN-00014 University of Helsinki (Finland); Pystynen, Kati-Henna [Laboratory of Analytical Chemistry, Department of Chemistry, P.O. Box 55, FIN-00014 University of Helsinki (Finland); Riekkola, Marja-Liisa [Laboratory of Analytical Chemistry, Department of Chemistry, P.O. Box 55, FIN-00014 University of Helsinki (Finland); Wiedmer, Susanne K. [Laboratory of Analytical Chemistry, Department of Chemistry, P.O. Box 55, FIN-00014 University of Helsinki (Finland)]. E-mail: susanne.wiedmer@helsinki.fi

    2006-02-23

    The stability of zwitterionic phosphatidylcholine vesicles in the presence of 20 mol% phosphatidyl serine (PS), phosphatidic acid (PA), phosphatidyl inositol (PI), and diacylphosphatidyl glycerol (PG) phospholipid vesicles, and cholesterol or calcium chloride was investigated by asymmetrical flow field-flow fractionation (AsFlFFF). Large unilamellar vesicles (LUV, diameter 100 nm) prepared by extrusion at 25 deg. C were used. Phospholipid vesicles (liposomes) were stored at +4 and -18 deg. C over an extended period of time. Extruded egg yolk phosphatidylcholine (EPC) particle diameters at peak maximum and mean measured by AsFlFFF were 101 {+-} 3 nm and 122 {+-} 5 nm, respectively. No significant change in diameter was observed after storage at +4 deg. C for about 5 months. When the storage period was extended to about 8 months (250 days) larger destabilized aggregates were formed (172 and 215 nm at peak maximum and mean diameters, respectively). When EPC was stored at -18 deg. C, large particles with diameters of 700-800 nm were formed as a result of dehydration, aggregation, and fusion processes. In the presence of calcium chloride, EPC alone did not form large aggregates. Addition of 20 mol% of negatively charged phospholipids (PS, PA, PI, or PG) to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) vesicles increased the electrostatic interactions between calcium ion and the vesicles and large aggregates were formed. In the presence of cholesterol, large aggregates of about 250-350 nm appeared during storage at +4 and -18 deg. C for more than 1 day. The effect of liposome storage temperature on phospholipid coatings applied in capillary electrophoresis (CE) was studied by measuring the electroosmotic flow (EOF). EPC coatings with and without cholesterol, PS, or calcium chloride, prepared from liposomes stored at +25, +4, and -18 deg. C, were studied at 25 deg. C. The performances of the coatings were further evaluated with three uncharged compounds

  15. Distribution and Characterization of Antigens Found in Subcellular Fractions of African Trypanosomes.

    Science.gov (United States)

    1982-08-01

    report (Aug. 1981-Aug. 1982) the investigations described were firstly concerned with utilizing the information referenced above to permit the...measured for relative fluorescence. These details are ndicated in Fig. A. ii. Lecting affinity chromatography. Either lentil lectin seph- arose 4B or...course through the use of purified FPM antigens isolated using the methods previously detailed. D) CONCLUSIONS The Information obtained previously

  16. Evaluation on subcellular partitioning and biodynamics of pulse copper toxicity in tilapia reveals impacts of a major environmental disturbance.

    Science.gov (United States)

    Ju, Yun-Ru; Yang, Ying-Fei; Tsai, Jeng-Wei; Cheng, Yi-Hsien; Chen, Wei-Yu; Liao, Chung-Min

    2017-07-01

    Fluctuation exposure of trace metal copper (Cu) is ubiquitous in aquatic environments. The purpose of this study was to investigate the impacts of chronically pulsed exposure on biodynamics and subcellular partitioning of Cu in freshwater tilapia (Oreochromis mossambicus). Long-term 28-day pulsed Cu exposure experiments were performed to explore subcellular partitioning and toxicokinetics/toxicodynamics of Cu in tilapia. Subcellular partitioning linking with a metal influx scheme was used to estimate detoxification and elimination rates. A biotic ligand model-based damage assessment model was used to take into account environmental effects and biological mechanisms of Cu toxicity. We demonstrated that the probability causing 50% of susceptibility risk in response to pulse Cu exposure in generic Taiwan aquaculture ponds was ~33% of Cu in adverse physiologically associated, metabolically active pool, implicating no significant susceptibility risk for tilapia. We suggest that our integrated ecotoxicological models linking chronic exposure measurements with subcellular partitioning can facilitate a risk assessment framework that provides a predictive tool for preventive susceptibility reduction strategies for freshwater fish exposed to pulse metal stressors.

  17. Subcellular Targeting of VIP Boutons in Mouse Barrel Cortex is Layer-Dependent and not Restricted to Interneurons.

    Science.gov (United States)

    Zhou, Xiaojuan; Rickmann, Michael; Hafner, Georg; Staiger, Jochen F

    2017-11-01

    Neocortical vasoactive intestinal polypeptide (VIP) expressing cells are a diverse subpopulation of GABAergic interneurons issuing distinct axonal projections. They are known to inhibit other types of interneurons as well as excitatory principal neurons and possess a disinhibitory net effect in cortical circuits. In order to elucidate their targeting specificity, the output connectivity of VIP interneurons was studied at the subcellular level in barrel cortex of interneuron-specific Cre-driver mice, using pre- and postembedding electron microscopy. Systematically sampling VIP boutons across all layers, we found a substantial proportion of the innervated subcellular structures were dendrites (80%), with somata (13%), and spines (7%) being much less targeted. In layer VI, a high proportion of axosomatic synapses was found (39%). GABA-immunopositive ratio was quantified among the targets using statistically validated thresholds: only 37% of the dendrites, 7% of the spines, and 26% of the somata showed above-threshold immunogold labeling. For the main target structure "dendrite", a higher proportion of GABAergic subcellular profiles existed in deep than in superficial layers. In conclusion, VIP interneurons innervate non-GABAergic excitatory neurons and interneurons at their subcellular domains with layer-dependent specificity. This suggests a diverse output of VIP interneurons, which predicts multiple functionality in cortical circuitry beyond disinhibition. © The Author 2017. Published by Oxford University Press.

  18. A multiple information fusion method for predicting subcellular locations of two different types of bacterial protein simultaneously.

    Science.gov (United States)

    Chen, Jing; Xu, Huimin; He, Ping-An; Dai, Qi; Yao, Yuhua

    2016-01-01

    Subcellular localization prediction of bacterial protein is an important component of bioinformatics, which has great importance for drug design and other applications. For the prediction of protein subcellular localization, as we all know, lots of computational tools have been developed in the recent decades. In this study, we firstly introduce three kinds of protein sequences encoding schemes: physicochemical-based, evolutionary-based, and GO-based. The original and consensus sequences were combined with physicochemical properties. And elements information of different rows and columns in position-specific scoring matrix were taken into consideration simultaneously for more core and essence information. Computational methods based on gene ontology (GO) have been demonstrated to be superior to methods based on other features. Then principal component analysis (PCA) is applied for feature selection and reduced vectors are input to a support vector machine (SVM) to predict protein subcellular localization. The proposed method can achieve a prediction accuracy of 98.28% and 97.87% on a stringent Gram-positive (Gpos) and Gram-negative (Gneg) dataset with Jackknife test, respectively. At last, we calculate "absolute true overall accuracy (ATOA)", which is stricter than overall accuracy. The ATOA obtained from the proposed method is also up to 97.32% and 93.06% for Gpos and Gneg. From both the rationality of testing procedure and the success rates of test results, the current method can improve the prediction quality of protein subcellular localization. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. 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

  20. Tissue and subcellular distribution of CLIC1

    Directory of Open Access Journals (Sweden)

    Edwards John C

    2007-02-01

    Full Text Available Abstract Background CLIC1 is a chloride channel whose cellular role remains uncertain. The distribution of CLIC1 in normal tissues is largely unknown and conflicting data have been reported regarding the cellular membrane fraction in which CLIC1 resides. Results New antisera to CLIC1 were generated and were found to be sensitive and specific for detecting this protein. These antisera were used to investigate the distribution of CLIC1 in mouse tissue sections and three cultured cell lines. We find CLIC1 is expressed in the apical domains of several simple columnar epithelia including glandular stomach, small intestine, colon, bile ducts, pancreatic ducts, airway, and the tail of the epididymis, in addition to the previously reported renal proximal tubule. CLIC1 is expressed in a non-polarized distribution in the basal epithelial cell layer of the stratified squamous epithelium of the upper gastrointesitinal tract and the basal cells of the epididymis, and is present diffusely in skeletal muscle. Distribution of CLIC1 was examined in Panc1 cells, a relatively undifferentiated, non-polarized human cell line derived from pancreatic cancer, and T84 cells, a human colon cancer cell line which can form a polarized epithelium that is capable of regulated chloride transport. Digitonin extraction was used to distinguish membrane-inserted CLIC1 from the soluble cytoplasmic form of the protein. We find that digitonin-resistant CLIC1 is primarily present in the plasma membrane of Panc1 cells. In T84 cells, we find digitonin-resistant CLIC1 is present in an intracellular compartment which is concentrated immediately below the apical plasma membrane and the extent of apical polarization is enhanced with forskolin, which activates transepithelial chloride transport and apical membrane traffic in these cells. The sub-apical CLIC1 compartment was further characterized in a well-differentiated mouse renal proximal tubule cell line. The distribution of CLIC1 was

  1. High-Temperature Fractionation of Iron Isotopes During Metal Segregation From a Silicate Melt: Experimental Study of Kinetic and Equilibrium Fractionation

    Science.gov (United States)

    Roskosz, M.; Luais, B.; Watson, H.; Toplis, M. J.; Alexander, C. M.; Mysen, B. O.

    2005-12-01

    Advances in mass spectrometry make it possible to measure isotopic variations of iron in meteoritic and igneous materials. However, interpreting these data is hampered by a lack of theoretical and experimental knowledge concerning how Fe isotopes fractionate during magmatic processes. As a first step in this direction we have performed experiments in which metallic iron was reduced and segregated from a silicate melt at one bar as a function of f(O2) and time. The starting material was a glass of anorthite-diopside eutectic composition, to which 9 wt% Fe2O3 was added. Experiments were performed at 1500 circC and f(O2) in the range 10-0.7 to 10-8 bars. A proportion of this iron is extracted through formation of an alloy with the Pt-capsule in which the melt was held. The silicate and metallic portions were physically separated and bulk analyses of each fraction performed using standard MC-ICP-MS methods. Furthermore, a Cameca 6f ion microprobe was used to measure isotopic profiles in metallic samples, such that kinetic and equilibrium effects may be disentangled and quantified. Large isotopic variations are observed and attributed to kinetic fractionation during incorporation of iron into the initially Fe-free Pt-capsule. This process leads to the formation of isotopically light metal and a heavy silicate. For instance, in samples heat-treated for 24 hours, metal fractions have δ56Fe/54Fe from 0 to -2‰, whereas silicate fractions have δ56Fe/54Fe from 0 to 4.8‰. These values are positively correlated with the fraction of iron lost to the platinum. Ion-probe analyses and time-series experiments confirm that Fe isotopes are strongly fractionated during diffusion of Fe in the Pt,Fe alloy, and the observed profiles are used to calculate the diffusion coefficients of individual iron isotopes. With increasing time at fixed oxygen fugacity, iron in the alloy reaches a constant isotopic composition. At these conditions, assumed to represent equilibrium, iron in the

  2. Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus

    Directory of Open Access Journals (Sweden)

    Elena T. Herruzo

    2012-03-01

    Full Text Available Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip–surface forces such as the Lennard-Jones and Derjaguin–Muller–Toporov forces.

  3. Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus.

    Science.gov (United States)

    Herruzo, Elena T; Garcia, Ricardo

    2012-01-01

    Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip-surface forces such as the Lennard-Jones and Derjaguin-Muller-Toporov forces.

  4. Fractions composition study of the pyrolysis oil obtained from sewage sludge treatment plant.

    Science.gov (United States)

    Silva, R V S; Romeiro, G A; Veloso, M C C; Figueiredo, M K-K; Pinto, P A; Ferreira, A F; Gonçalves, M L A; Teixeira, A M; Damasceno, R N

    2012-01-01

    In this work the parameters of Low Temperature Conversion--LTC were applied in a centrifuged sludge from a sewage treatment plant located in Rio de Janeiro, Brazil. Before the conversion, the sludge was dried and analyzed by TGA to observe its behavior with increasing temperature. The chemical composition of the crude pyrolysis oil was analyzed by FTIR, 1H NMR and GC-MS. The results showed that the oil is a mixture of hydrocarbons, oxygenated and nitrogenated compounds. Using a catalytic treatment it was possible to fractionate the oil where the predominant constituents were hydrocarbons showing that the cracking was effective. An important result was the difference between the calorific value of dry sludge (10 MJ kg(-1)), the pyrolysis oil (36 MJ kg(-1)) and one of the fractions separated by catalytic cracking (40 MJ kg(-1)) when compared with commercial diesel (45 MJ kg(-1)). Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. Anti-inflammatory effects and chemical study of a flavonoid-enriched fraction from adlay bran.

    Science.gov (United States)

    Chen, Hong-Jhang; Chung, Cheng-Pei; Chiang, Wenchang; Lin, Yun-Lian

    2011-06-15

    Anti-inflammation-guided fractionation and purification were used to evaluate the bioactivity and components of adlay (Coix lachryma-jobi L. var. ma-yuen Stapf) bran. Results showed that the fraction with high phenolic and flavonoid contents from the ethanol extracts of adlay bran suppressed LPS-stimulated IL-6 and TNF-α secretions in a concentration-dependent manner in RAW 264.7 cells and murine peritoneal macrophages. Fifteen compounds, including a novel aurone derivative, two chromones, one dihydrochalcone, one chalcone, four flavanones, five flavones and one isoflavone, were isolated from the active fraction. The structure of the new compound was elucidated by spectroscopic methods, including 1D and 2D NMR and MS. All of the isolates are reported for the first time from adlay except naringenin. LC/MS was also provided as an analytical platform. Our results suggest that flavonoids in adlay bran, partially at least, contribute to its anti-inflammatory effect. Thus, adlay bran may be beneficial to the health of consumers. Copyright © 2010 Elsevier Ltd. All rights reserved.

  6. Interstitial photodynamic therapy and glioblastoma: light fractionation study on a preclinical model: preliminary results

    Science.gov (United States)

    Leroy, Henri-Arthur; Vermandel, Maximilien; Tétard, Marie-Charlotte; Lejeune, Jean-Paul; Mordon, Serge; Reyns, Nicolas

    2015-03-01

    Background Glioblastoma is a high-grade cerebral tumor with local recurrence and poor outcome. Photodynamic therapy (PDT) is a local treatment based on the light activation of a photosensitizer (PS) in the presence of oxygen to form cytotoxic species. Fractionation of light delivery may enhance treatment efficiency by restoring tissue oxygenation. Objectives To evaluate the efficiency of light fractionation using MRI imaging, including diffusion and perfusion, compared to histological data. Materials and Methods Thirty-nine "Nude" rats were grafted with human U87 cells into the right putamen. After PS precursor intake (5-ALA), an optic fiber was introduced into the tumor. The rats were randomized in three groups: without illumination, with monofractionated illumination and the third one with multifractionated light. Treatment effects were assessed with early MRI including diffusion and perfusion sequences. The animals were eventually sacrificed to perform brain histology. Results On MRI, we observed elevated diffusion values in the center of the tumor among treated animals, especially in multifractionated group. Perfusion decreased around the treatment site, all the more in the multifractionated group. Histology confirmed our MRI findings, with a more extensive necrosis and associated with a rarified angiogenic network in the treatment area, after multifractionated PDT. However, we observed more surrounding edema and neovascularization in the peripheral ring after multifractionated PDT. Conclusion Fractionated interstitial PDT induced specific tumoral lesions. The multifractionated scheme was more efficient, inducing increased tumoral necrosis, but it also caused significant peripheral edema and neovascularization. Diffusion and perfusion MRI imaging were able to predict the histological lesions.

  7. 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.

  8. Bioactive protein fraction DLBS1033 containing lumbrokinase isolated from Lumbricus rubellus: ex vivo, in vivo, and pharmaceutic studies.

    Science.gov (United States)

    Tjandrawinata, Raymond R; Trisina, Jessica; Rahayu, Puji; Prasetya, Lorentius Agung; Hanafiah, Aang; Rachmawati, Heni

    2014-01-01

    DLBS1033 is a bioactive protein fraction isolated from Lumbricus rubellus that tends to be unstable when exposed to the gastrointestinal environment. Accordingly, appropriate pharmaceutical development is needed to maximize absorption of the protein fraction in the gastrointestinal tract. In vitro, ex vivo, and in vivo stability assays were performed to study the stability of the bioactive protein fraction in gastric conditions. The bioactive protein fraction DLBS1033 was found to be unstable at low pH and in gastric fluid. The "enteric coating" formulation showed no leakage in gastric fluid-like medium and possessed a good release profile in simulated intestinal medium. DLBS1033 was absorbed through the small intestine in an intact protein form, confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) analysis. This result confirmed that an enteric coating formula using methacrylic acid copolymer could protect DLBS1033 from the acidic condition of the stomach by preventing the release of DLBS1033 in the stomach, while promoting its release when reaching the intestine. From the blood concentration-versus-time curve, (99m)Tc-DLBS1033 showed a circulation half-life of 70 minutes. This relatively long biological half-life supports its function as a thrombolytic protein. Thus, an enteric delivery system is considered the best approach for DLBS1033 as an oral thrombolytic agent.

  9. Preliminary study of the anti-inflammatory activity of hexane extract and fractions from Bursera simaruba (Linneo) Sarg. (Burseraceae) leaves.

    Science.gov (United States)

    Carretero, M E; López-Pérez, J L; Abad, M J; Bermejo, P; Tillet, S; Israel, A; Noguera-P, B

    2008-02-28

    Bursera simaruba (L.) Sarg. leaves hexane extracts display anti-inflammatory activity on the adjuvant-carrageenan-induced inflammation in rats. In order to isolate and identify the active compounds of the hexane extract, we performed a preliminary phytochemical study and a bioassay-directed fractionation using the carrageenan-induced paw oedema test in mice. From the nine fractions (A-I) obtained, of an initial chromatographic separation, fractions A and E (doses equivalents to 1.50 g dry plant/kg body weight) showed the strongest anti-inflammatory activity comparable to that of the reference drug phenylbutazone (80 mg/kg). The isolation and characterization of 3-methylene-7,11,15-trimethylhexadec-1-ene (neophytadiene) (1), ergost-5-en-3beta-ol (2), 24S-stigmast-5,22E-dien-3beta-ol (3), 24S-stigmast-5-en-3beta-ol (4) and alpha-amyrin (5), from these fractions is reported.

  10. A comparison study of steady-state vibrations with single fractional-order and distributed-order derivatives

    Directory of Open Access Journals (Sweden)

    Duan Jun-Sheng

    2017-12-01

    Full Text Available We conduct a detailed study and comparison for the one-degree-of-freedom steady-state vibrations under harmonic driving with a single fractional-order derivative and a distributed-order derivative. For each of the two vibration systems, we consider the stiffness contribution factor and damping contribution factor of the term of fractional derivatives, the amplitude and the phase difference for the response. The effects of driving frequency on these response quantities are discussed. Also the influences of the order α of the fractional derivative and the parameter γ parameterizing the weight function in the distributed-order derivative are analyzed. Two cases display similar response behaviors, but the stiffness contribution factor and damping contribution factor of the distributed-order derivative are almost monotonic change with the parameter γ, not exactly like the case of single fractional-order derivative for the order α. The case of the distributed-order derivative provides us more options for the weight function and parameters.

  11. Objective Clustering of Proteins Based on Subcellular Location Patterns

    Directory of Open Access Journals (Sweden)

    Xiang Chen

    2005-01-01

    Full Text Available The goal of proteomics is the complete characterization of all proteins. Efforts to characterize subcellular location have been limited to assigning proteins to general categories of organelles. We have previously designed numerical features to describe location patterns in microscope images and developed automated classifiers that distinguish major subcellular patterns with high accuracy (including patterns not distinguishable by visual examination. The results suggest the feasibility of automatically determining which proteins share a single location pattern in a given cell type. We describe an automated method that selects the best feature set to describe images for a given collection of proteins and constructs an effective partitioning of the proteins by location. An example for a limited protein set is presented. As additional data become available, this approach can produce for the first time an objective systematics for protein location and provide an important starting point for discovering sequence motifs that determine localization.

  12. 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

  13. Using the concept of Chou's pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy.

    Science.gov (United States)

    Jiang, Xiaoying; Wei, Rong; Zhang, Tongliang; Gu, Quan

    2008-01-01

    The function of protein is closely correlated with it subcellular location. Prediction of subcellular location of apoptosis proteins is an important research area in post-genetic era because the knowledge of apoptosis proteins is useful to understand the mechanism of programmed cell death. Compared with the conventional amino acid composition (AAC), the Pseudo Amino Acid composition (PseAA) as originally introduced by Chou can incorporate much more information of a protein sequence so as to remarkably enhance the power of using a discrete model to predict various attributes of a protein. In this study, a novel approach is presented to predict apoptosis protein solely from sequence based on the concept of Chou's PseAA composition. The concept of approximate entropy (ApEn), which is a parameter denoting complexity of time series, is used to construct PseAA composition as additional features. Fuzzy K-nearest neighbor (FKNN) classifier is selected as prediction engine. Particle swarm optimization (PSO) algorithm is adopted for optimizing the weight factors which are important in PseAA composition. Two datasets are used to validate the performance of the proposed approach, which incorporate six subcellular location and four subcellular locations, respectively. The results obtained by jackknife test are quite encouraging. It indicates that the ApEn of protein sequence could represent effectively the information of apoptosis proteins subcellular locations. It can at least play a complimentary role to many of the existing methods, and might become potentially useful tool for protein function prediction. The software in Matlab is available freely by contacting the corresponding author.

  14. Predicting subcellular location of proteins using integrated-algorithm method.

    Science.gov (United States)

    Cai, Yu-Dong; Lu, Lin; Chen, Lei; He, Jian-Feng

    2010-08-01

    Protein's subcellular location, which indicates where a protein resides in a cell, is an important characteristic of protein. Correctly assigning proteins to their subcellular locations would be of great help to the prediction of proteins' function, genome annotation, and drug design. Yet, in spite of great technical advance in the past decades, it is still time-consuming and laborious to experimentally determine protein subcellular locations on a high throughput scale. Hence, four integrated-algorithm methods were developed to fulfill such high throughput prediction in this article. Two data sets taken from the literature (Chou and Elrod, Protein Eng 12:107-118, 1999) were used as training set and test set, which consisted of 2,391 and 2,598 proteins, respectively. Amino acid composition was applied to represent the protein sequences. The jackknife cross-validation was used to test the training set. The final best integrated-algorithm predictor was constructed by integrating 10 algorithms in Weka (a software tool for tackling data mining tasks, http://www.cs.waikato.ac.nz/ml/weka/ ) based on an mRMR (Minimum Redundancy Maximum Relevance, http://research.janelia.org/peng/proj/mRMR/ ) method. It can achieve correct rate of 77.83 and 80.56% for the training set and test set, respectively, which is better than all of the 60 algorithms collected in Weka. This predicting software is available upon request.

  15. Bioactive protein fraction DLBS1033 containing lumbrokinase isolated from Lumbricus rubellus: ex vivo, in vivo, and pharmaceutic studies

    Directory of Open Access Journals (Sweden)

    Tjandrawinata RR

    2014-09-01

    Full Text Available Raymond R Tjandrawinata,1 Jessica Trisina,1 Puji Rahayu,1 Lorentius Agung Prasetya,1 Aang Hanafiah,2 Heni Rachmawati3 1Dexa Laboratories of Biomolecular Sciences, Dexa Medica, Cikarang, Indonesia; 2National Nuclear Energy Agency, Bandung, Indonesia; 3School of Pharmacy, Bandung Institute of Technology, Bandung, Indonesia Abstract: DLBS1033 is a bioactive protein fraction isolated from Lumbricus rubellus that tends to be unstable when exposed to the gastrointestinal environment. Accordingly, appropriate pharmaceutical development is needed to maximize absorption of the protein fraction in the gastrointestinal tract. In vitro, ex vivo, and in vivo stability assays were performed to study the stability of the bioactive protein fraction in gastric conditions. The bioactive protein fraction DLBS1033 was found to be unstable at low pH and in gastric fluid. The “enteric coating” formulation showed no leakage in gastric fluid–like medium and possessed a good release profile in simulated intestinal medium. DLBS1033 was absorbed through the small intestine in an intact protein form, confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE analysis. This result confirmed that an enteric coating formula using methacrylic acid copolymer could protect DLBS1033 from the acidic condition of the stomach by preventing the release of DLBS1033 in the stomach, while promoting its release when reaching the intestine. From the blood concentration–versus-time curve, 99mTc-DLBS1033 showed a circulation half-life of 70 minutes. This relatively long biological half-life supports its function as a thrombolytic protein. Thus, an enteric delivery system is considered the best approach for DLBS1033 as an oral thrombolytic agent. Keywords: bioactive protein fraction, enteric coated tablet, pharmacodynamic

  16. A Study of the Anti-Cancer Effects of the Hexane Fraction of the Methanol Extract of Forsythiae Fructus.

    Science.gov (United States)

    Lee, Se-Eun; Lim, Chiyeon; Ahn, Soon-Cheol; Cho, Suin

    2017-01-01

    Forsythiae Fructus (FF) is a well-known medicinal herb derived from the dried fruits of Forsythia suspensa (Thunb.) Vahl. (Oleaceae). Recently, bioactive compounds isolated from hydrophobic solvent fractions of FF have been reported to have anti-oxidant, antibacterial, and anti-cancer effects. Almost all herbal medicines are derived from water extracts, which suggests different extraction methods might enhance the practical efficacies of herbal medicines. In this study, the authors further investigated the most potential anti-cancer fraction, that is, the hexane fraction (FFH) of the methanol extract (FFM) of the dried fruits of Forsythia suspensa. FFH was investigated by measuring its effects on the viability and apoptotic death of PC-3 cells (a prostate cancer cell line), on the expression levels of Bcl-2, Bax, cytochrome c, procaspase-9, procaspase-3 and PARP, and caspase-3 activity. FFH significantly accelerated apoptotic cell death and decreased the protein levels of Bcl-2, procaspase-9, and procaspase-3. FFH can act as a pro-oxidative agent and induce the apoptosis of prostate cancer cells. Hexane fraction of the methanol extract of Forsythiae Fructus (FFH) at a concentration more than 50 µg/mL significantly reduced PC-3 cell viabilityFFH time and dose dependently elevated intracellular ROS levels and increased the proportion of cells arrested in the G0/G1 phaseFFH significantly accelerated apoptotic cell death and diminished the protein expression levels of Bcl-2, procaspase-9, and procaspase-3The protein expression levels of Bax, cytochrome c, and cleaved PARP were increased by FFH, and so was the caspase-3 activity. Abbreviations used: FF: Forsythiae Fructus; FFM: Methanol extract of Forsythiae Fructus; FFH: Hexane fraction of the methanol extract; DCFH-DA: 2',7'-dichlorodihydro-fluorescein diacetate.

  17. Environmental impact of toxic elements in red mud studied by fractionation and speciation procedures.

    Science.gov (United States)

    Milačič, Radmila; Zuliani, Tea; Ščančar, Janez

    2012-06-01

    Aluminum (Al) is mostly produced from bauxite ore, which contains up to 70% of Al(2)O(3) (alumina). Before alumina is refined to aluminum metal, it is purified by hot alkaline extraction. As a waste by-product red mud is formed. Due to its high alkalinity and large quantities, it represents a severe disposal problem. In Kidričevo (Slovenia), red mud was washed with water before disposal, and after drying, covered with soil. In Ajka (Hungary), the red mud slurry was collected directly in a containment structure, which burst caused a major accident in October 2010. In the present work the environmental impact of toxic elements in red mud from Kidričevo and Ajka were evaluated by applying a sequential extraction procedure and speciation analysis. The predominant red mud fraction was the insoluble residue; nevertheless, environmental concern was focused on the highly mobile water-soluble fraction of Al and Cr. Al in the water-soluble Ajka mud fraction was present exclusively in form of toxic [Al(OH)(4)](-), while Cr existed in its toxic hexavalent form. Comparative assessment to red mud from Kidričevo (Slovenia) with a lower alkalinity (pH 9) with that from Ajka demonstrated significantly lower Al solubility and the presence of only trace amounts of Cr(VI), confirming that disposal of neutralized mud is environmentally much more acceptable and carries a smaller risk of ecological accidents. Since during the Ajka accident huge amounts of biologically available Al and moderate Cr(VI) concentrations were released into the terrestrial and aquatic environments, monitoring of Al and Cr(VI) set free during remedial actions at the contaminated site is essential. Particular care should be taken to minimize the risk of release of soluble Al species and Cr(VI) into water supplies and surface waters. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Quantum-mechanical equilibrium isotopic fractionation correction to radiocarbon dating: a theory study.

    Science.gov (United States)

    Yuan, Jie; Liu, Yun

    This paper relates the quantum-mechanical equilibrium isotopic fractionation correction to the radiocarbon dating method by Eq. 9, and also shows the significant influence of temperature on the method. It is suggested that the correction is a function of the frequencies and temperature of a specific sample and these two variables can be evaluated theoretically by the ab initio quantum calculations and experimentally by analyzing the clumped-isotope ratios in it, respectively. This paper also suggests that the (14)C/(12)C ratio in the atmosphere in geological time can be calculated by Eq. 10.

  19. Analytical and numerical study of electroosmotic slip flows of fractional second grade fluids

    Science.gov (United States)

    Wang, Xiaoping; Qi, Haitao; Yu, Bo; Xiong, Zhen; Xu, Huanying

    2017-09-01

    This work investigates the unsteady electroosmotic slip flow of viscoelastic fluid through a parallel plate micro-channel under combined influence of electroosmotic and pressure gradient forcings with asymmetric zeta potentials at the walls. The generalized second grade fluid with fractional derivative was used for the constitutive equation. The Navier slip model with different slip coefficients at both walls was also considered. By employing the Debye-Hückel linearization and the Laplace and sin-cos-Fourier transforms, the analytical solutions for the velocity distribution are derived. And the finite difference method for this problem was also given. Finally, the influence of pertinent parameters on the generation of flow is presented graphically.

  20. A case study of nitrification and nitrite isotope fractionation in a eutrophic temperate river system

    Science.gov (United States)

    Jacob, Juliane; Dähnke, Kirstin; Sanders, Tina

    2014-05-01

    Stable isotopes of nitrate are often used to assess processing of nitrate in the water column of oceans, estuaries, and rivers. In all these environments, nitrate regeneration via nitrification is an important source of new nitrate. The bulk isotope effect of nitrification is hard to predict: It is a two-step-process by distinct groups of microorganisms oxidizing ammonium to nitrate via nitrite. Both processes have divergent isotope effects, and it is even more difficult to unravel these effects in natural environments, because nitrite usually does not accumulate and isotope analysis is not possible. During our routine sampling scheme at the River Elbe an exceptional flood occurred in June 2013, and nitrite and ammonium accumulated, allowing us to investigate isotope fractionation of nitrification in a natural river system. We measured nutrient concentrations, dual nitrate isotopes, δ15N-NO2, and, where possible, δ15N-NH4. Nitrate leached from catchment area, and δ15N-NO3 and δ18O-NO3 decreased from typical spring bloom values (9.0 o and 3.5 o respectively) to winter nitrate background values (7.4 o and 2.1 o respectively). This indicates that riverine assimilation was minimal during the flood. Ammonium and nitrite concentrations increased to 12.5 μM and 5.7 μM, respectively, which likely was due to remineralization and nitrification in the water column. Ammonium δ15N-NH4 values increased up to 12 o and nitrite δ15N-NO2 values ranged from -4.8 o and -14.2 ‰Nitrite oxidation and decreasing concentrations were coupled with a fractionation factor 15ɛ of -8.6 o following normal, and not inverse, isotope fractionation. This deviates from findings in pure cultures of nitrite-oxidizing bacteria. We assume that the mechanisms responsible for inverse fractionation apply in natural environment as well, but that the resulting trend in δ15N-NO2 is masked by dilution with fresh nitrite stemming from ammonium oxidation. Our data are a first approximation of the

  1. Can Kindergartners Do Fractions?

    Science.gov (United States)

    Cwikla, Julie

    2014-01-01

    Mathematics professor Julie Cwikla decided that she needed to investigate young children's understandings and see what precurricular partitioning notions young minds bring to the fraction table. Cwikla realized that only a handful of studies have examined how preschool-age and early elementary school-age students solve fraction problems (Empson…

  2. A Fractional Factorial Design to Study the Effect of Process Variables on the Preparation of Hyaluronidase Loaded PLGA Nanoparticles

    Directory of Open Access Journals (Sweden)

    K. Narayanan

    2014-01-01

    Full Text Available The present study was initiated to understand the effect of PLGA concentration, PVA concentration, internal-external phase ratio, homogenization speed, and homogenization time on mean particle size, zeta potential, and percentage drug encapsulation using fractional factorial design. Using PLGA (50-50 as the carrier, hyaluronidase loaded PLGA nanoparticles were prepared using double emulsion solvent evaporation technique. The particle size was analyzed by dynamic light scattering technique and protein content by Lowry method. The study showed that homogenization speed as an independent variable had maximum effect on particle size and zeta potential. Internal-external phase volume ratio had maximum effect on drug encapsulation. Mean particle size also had high dependency on the combined effect of PVA concentration and phase volume ratio. Using fractional factorial design particle size of <400 nm, zeta potential of <−30 mV, and percentage encapsulation of 15–18% were achieved.

  3. Study of antinociceptive effects on acute pain treated by bioactive fractions of Hyptis suaveolens

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    Azmathunnisa Begum

    2016-09-01

    Full Text Available Objective: To investigate the ethanolic extract and its fractions of Hyptis suaveolens (H. suaveolens for antinociceptive and central nervous system depressant effects. Methods: Dried and coarsely powdered aerial parts of plant material were extracted in 80% aqueous ethanol. Further extract was fractionated using solvents of varying polarity. Analgesic properties was assessed using acetic acid-induced writhing and hot plate test and locomotor activity were performed in mice using hole board test. Results: The petroleum ether and ethyl acetate extracts had produced significant analgesic properties and were found to be maximum when tested at 400 mg/kg. Both extracts significantly increased the latency time in hot plate test and the action was antagonised by naloxone. The naloxone was not able to alter H. suaveolens induced antinociceptive effect in writhing test. Conclusions: From the point of central nervous system depressant and good protective effect on chemical and thermal pain stimuli, it indicates that H. suaveolens might have resulted from activation of opioid and/or peripheral receptors.

  4. The batch fractionation of Juniperus communis L. essential oil: experimental study, mathematical simulation and process economy

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    Svetomir Ž. Milojević

    2010-07-01

    Full Text Available The separation in a batch vacuum column of the essential oil of common juniper berries (Juniperus communis L., from the southern part of Serbia was analyzed. The main goal of the analyzed separation process was to isolate several fractions from the essential oil which mainly contained α-pinene, sabinene and myrcene. These compounds contain about 65 mass% of the essential oil produced by hydrodistillation from the juniper berries originated from the southern part of Serbia. The results of experimental work in a laboratory column with 36 theoretical stages under vacuum (8.0-3.35 kPa was simulated using Aspen software, and a proposed mathematical model was used to analyze some other operating conditions for fractionation of juniper berry’s oil (number of plates: 25, 36 and 45 and reflux ratio: 2-10. According to the results of performed simulations, the most acceptable separation procedure which takes into account the prices of raw materials and distillate (α-pinene as well as consumed energy was proposed.

  5. Feasibility Studies on Static Pile Co Composting of Organic Fraction of Municipal Solid Waste With Dairy Waste Water

    OpenAIRE

    Manjula Gopinathan; Meenambal Thirumurthy

    2012-01-01

    Milk processing consumes a large amount of water and generates 6–10 liters of effluent per liter of milk processed. An effluent volume is approximately four times the volume of processed milk. Since the pollutants generated by industry are great losses of production, improvements in production efficiency are recommended to reduce pollutant loads. In this research a series of experimental studies were conducted with regard to bioconversion of organic fraction of municipal solid waste along wit...

  6. 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...

  7. Subcellular Characterization of Porcine Oocytes with Different Glucose-6-phosphate Dehydrogenase Activities

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    Bo Fu

    2015-12-01

    Full Text Available The in vitro maturation (IVM efficiency of porcine embryos is still low because of poor oocyte quality. Although brilliant cresyl blue positive (BCB+ oocytes with low glucose-6-phosphate dehydrogenase (G6PDH activity have shown superior quality than BCB negative (− oocytes with high G6PDH activity, the use of a BCB staining test before IVM is still controversial. This study aimed to shed more light on the subcellular characteristics of porcine oocytes after selection using BCB staining. We assessed germinal vesicle chromatin configuration, cortical granule (CG migration, mitochondrial distribution, the levels of acetylated lysine 9 of histone H3 (AcH3K9 and nuclear apoptosis features to investigate the correlation between G6PDH activity and these developmentally related features. A pattern of chromatin surrounding the nucleoli was seen in 53.0% of BCB+ oocytes and 77.6% of BCB+ oocytes showed peripherally distributed CGs. After IVM, 48.7% of BCB+ oocytes had a diffused mitochondrial distribution pattern. However, there were no significant differences in the levels of AcH3K9 in the nuclei of blastocysts derived from BCB+ and BCB− oocytes; at the same time, we observed a similar incidence of apoptosis in the BCB+ and control groups. Although this study indicated that G6PDH activity in porcine oocytes was correlated with several subcellular characteristics such as germinal vesicle chromatin configuration, CG migration and mitochondrial distribution, other features such as AcH3K9 level and nuclear apoptotic features were not associated with G6PDH activity and did not validate the BCB staining test. In using this test for selecting porcine oocytes, subcellular characteristics such as the AcH3K9 level and apoptotic nuclear features should also be considered. Adding histone deacetylase inhibitors or apoptosis inhibitors into the culture medium used might improve the efficiency of IVM of BCB+ oocytes.

  8. Proteomics: a subcellular look at spermatozoa

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    Yadav Satya P

    2011-03-01

    Full Text Available Abstract Background Male-factor infertility presents a vexing problem for many reproductively active couples. Many studies have focused on abnormal sperm parameters. Recent advances in proteomic techniques, especially in mass spectrometry, have aided in the study of sperm and more specifically, sperm proteins. The aim of this study was to review the current literature on the various proteomic techniques, and their usefulness in diagnosing sperm dysfunction and potential applications in the clinical setting. Methods Review of PubMed database. Key words: spermatozoa, proteomics, protein, proteome, 2D-PAGE, mass spectrometry. Results Recently employed proteomic methods, such as two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, and differential in gel electrophoresis, have identified numerous sperm-specific proteins. They also have provided a further understanding of protein function involved in sperm processes and for the differentiation between normal and abnormal states. In addition, studies on the sperm proteome have demonstrated the importance of post-translational modifications, and their ability to bring about physiological changes in sperm function. No longer do researchers believe that in order for them to elucidate the biochemical functions of genes, mere knowledge of the human genome sequence is sufficient. Moreover, a greater understanding of the physiological function of every protein in the tissue-specific proteome is essential in order to unravel the biological display of the human genome. Conclusion Recent advances in proteomic techniques have provided insight into sperm function and dysfunction. Several multidimensional separation techniques can be utilized to identify and characterize spermatozoa. Future developments in bioinformatics can further assist researchers in understanding the vast amount of data collected in proteomic studies. Moreover, such advances in proteomics may help to decipher metabolites

  9. Proteomics: a subcellular look at spermatozoa.

    Science.gov (United States)

    du Plessis, Stefan S; Kashou, Anthony H; Benjamin, David J; Yadav, Satya P; Agarwal, Ashok

    2011-03-22

    Male-factor infertility presents a vexing problem for many reproductively active couples. Many studies have focused on abnormal sperm parameters. Recent advances in proteomic techniques, especially in mass spectrometry, have aided in the study of sperm and more specifically, sperm proteins. The aim of this study was to review the current literature on the various proteomic techniques, and their usefulness in diagnosing sperm dysfunction and potential applications in the clinical setting. Review of PubMed database. Key words: spermatozoa, proteomics, protein, proteome, 2D-PAGE, mass spectrometry. Recently employed proteomic methods, such as two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, and differential in gel electrophoresis, have identified numerous sperm-specific proteins. They also have provided a further understanding of protein function involved in sperm processes and for the differentiation between normal and abnormal states. In addition, studies on the sperm proteome have demonstrated the importance of post-translational modifications, and their ability to bring about physiological changes in sperm function. No longer do researchers believe that in order for them to elucidate the biochemical functions of genes, mere knowledge of the human genome sequence is sufficient. Moreover, a greater understanding of the physiological function of every protein in the tissue-specific proteome is essential in order to unravel the biological display of the human genome. Recent advances in proteomic techniques have provided insight into sperm function and dysfunction. Several multidimensional separation techniques can be utilized to identify and characterize spermatozoa. Future developments in bioinformatics can further assist researchers in understanding the vast amount of data collected in proteomic studies. Moreover, such advances in proteomics may help to decipher metabolites which can act as biomarkers in the detection of sperm impairments and

  10. Arbitrage with fractional Gaussian processes

    Science.gov (United States)

    Zhang, Xili; Xiao, Weilin

    2017-04-01

    While the arbitrage opportunity in the Black-Scholes model driven by fractional Brownian motion has a long history, the arbitrage strategy in the Black-Scholes model driven by general fractional Gaussian processes is in its infancy. The development of stochastic calculus with respect to fractional Gaussian processes allowed us to study such models. In this paper, following the idea of Shiryaev (1998), an arbitrage strategy is constructed for the Black-Scholes model driven by fractional Gaussian processes, when the stochastic integral is interpreted in the Riemann-Stieltjes sense. Arbitrage opportunities in some fractional Gaussian processes, including fractional Brownian motion, sub-fractional Brownian motion, bi-fractional Brownian motion, weighted-fractional Brownian motion and tempered fractional Brownian motion, are also investigated.

  11. Analysis of the subcellular targeting of the smaller replicase protein of Pelargonium flower break virus.

    Science.gov (United States)

    Martínez-Turiño, Sandra; Hernández, Carmen

    2012-02-01

    Replication of all positive RNA viruses occurs in association with intracellular membranes. In many cases, the mechanism of membrane targeting is unknown and there appears to be no correlation between virus phylogeny and the membrane systems recruited for replication. Pelargonium flower break virus (PFBV, genus Carmovirus, family Tombusviridae) encodes two proteins, p27 and its read-through product p86 (the viral RNA dependent-RNA polymerase), that are essential for replication. Recent reports with other members of the family Tombusviridae have shown that the smaller replicase protein is targeted to specific intracellular membranes and it is assumed to determine the subcellular localization of the replication complex. Using in vivo expression of green fluorescent protein (GFP) fusions in plant and yeast cells, we show here that PFBV p27 localizes in mitochondria. The same localization pattern was found for p86 that contains the p27 sequence at its N-terminus. Cellular fractionation of p27GFP-expressing cells confirmed the confocal microscopy observations and biochemical treatments suggested a tight association of the protein to membranes. Analysis of deletion mutants allowed identification of two regions required for targeting of p27 to mitochondria. These regions mapped toward the N- and C-terminus of the protein, respectively, and could function independently though with distinct efficiency. In an attempt to search for putative cellular factors involved in p27 localization, the subcellular distribution of the protein was checked in a selected series of knockout yeast strains and the outcome of this approach is discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Sulfur isotope fractionation between fluid and andesitic melt: An experimental study

    Science.gov (United States)

    Fiege, Adrian; Holtz, François; Shimizu, Nobumichi; Mandeville, Charles W.; Behrens, Harald; Knipping, Jaayke L.

    2014-01-01

    Glasses produced from decompression experiments conducted by Fiege et al. (2014a) were used to investigate the fractionation of sulfur isotopes between fluid and andesitic melt upon magma degassing. Starting materials were synthetic glasses with a composition close to a Krakatau dacitic andesite. The glasses contained 4.55–7.95 wt% H2O, ∼140 to 2700 ppm sulfur (S), and 0–1000 ppm chlorine (Cl). The experiments were carried out in internally heated pressure vessels (IHPV) at 1030 °C and oxygen fugacities (fO2) ranging from QFM+0.8 log units up to QFM+4.2 log units (QFM: quartz–fayalite–magnetite buffer). The decompression experiments were conducted by releasing pressure (P) continuously from ∼400 MPa to final P of 150, 100, 70 and 30 MPa. The decompression rate (r) ranged from 0.01 to 0.17 MPa/s. The samples were annealed for 0–72 h (annealing time, tA) at the final P and quenched rapidly from 1030 °C to room temperature (T).The decompression led to the formation of a S-bearing aqueous fluid phase due to the relatively large fluid–melt partitioning coefficients of S. Secondary ion mass spectrometry (SIMS) was used to determine the isotopic composition of the glasses before and after decompression. Mass balance calculations were applied to estimate the gas–melt S isotope fractionation factor αg-m.No detectable effect of r and tA on αg-m was observed. However, SIMS data revealed a remarkable increase of αg-m from ∼0.9985 ± 0.0007 at >QFM+3 to ∼1.0042 ± 0.0042 at ∼QFM+1. Noteworthy, the isotopic fractionation at reducing conditions was about an order of magnitude larger than predicted by previous works. Based on our experimental results and on previous findings for S speciation in fluid and silicate melt a new model predicting the effect of fO2 on αg-m (or Δ34Sg–m) in andesitic systems at 1030 °C is proposed. Our experimental results as well as our modeling are of high importance for the interpretation of S isotope

  13. Mystery Fractions

    Science.gov (United States)

    Bhattacharyya, Sonalee; Namakshi, Nama; Zunker, Christina; Warshauer, Hiroko K.; Warshauer, Max

    2016-01-01

    Making math more engaging for students is a challenge that every teacher faces on a daily basis. These authors write that they are constantly searching for rich problem-solving tasks that cover the necessary content, develop critical-thinking skills, and engage student interest. The Mystery Fraction activity provided here focuses on a key number…

  14. Uncertain viscoelastic models with fractional order: A new spectral tau method to study the numerical simulations of the solution

    Science.gov (United States)

    Ahmadian, A.; Ismail, F.; Salahshour, S.; Baleanu, D.; Ghaemi, F.

    2017-12-01

    The analysis of the behaviors of physical phenomena is important to discover significant features of the character and the structure of mathematical models. Frequently the unknown parameters involve in the models are assumed to be unvarying over time. In reality, some of them are uncertain and implicitly depend on several factors. In this study, to consider such uncertainty in variables of the models, they are characterized based on the fuzzy notion. We propose here a new model based on fractional calculus to deal with the Kelvin-Voigt (KV) equation and non-Newtonian fluid behavior model with fuzzy parameters. A new and accurate numerical algorithm using a spectral tau technique based on the generalized fractional Legendre polynomials (GFLPs) is developed to solve those problems under uncertainty. Numerical simulations are carried out and the analysis of the results highlights the significant features of the new technique in comparison with the previous findings. A detailed error analysis is also carried out and discussed.

  15. Subcellular distribution of glycogen and decreased tetanic Ca2+ in fatigued single intact mouse muscle fibres

    Science.gov (United States)

    Nielsen, Joachim; Cheng, Arthur J; Ørtenblad, Niels; Westerblad, Håkan

    2014-01-01

    In skeletal muscle fibres, glycogen has been shown to be stored at different subcellular locations: (i) between the myofibrils (intermyofibrillar); (ii) within the myofibrils (intramyofibrillar); and (iii) subsarcolemmal. Of these, intramyofibrillar glycogen has been implied as a critical regulator of sarcoplasmic reticulum Ca2+ release. The aim of the present study was to test directly how the decrease in cytoplasmic free Ca2+ ([Ca2+]i) during repeated tetanic contractions relates to the subcellular glycogen distribution. Single fibres of mouse flexor digitorum brevis muscles were fatigued with 70 Hz, 350 ms tetani given at 2 s (high-intensity fatigue, HIF) or 10 s (low-intensity fatigue, LIF) intervals, while force and [Ca2+]i were measured. Stimulation continued until force decreased to 30% of its initial value. Fibres were then prepared for analyses of subcellular glycogen distribution by transmission electron microscopy. At fatigue, tetanic [Ca2+]i was reduced to 70 ± 4% and 54 ± 4% of the initial in HIF (P fibres, respectively. At fatigue, the mean inter- and intramyofibrillar glycogen content was 60–75% lower than in rested control fibres (P fibres showed a good correlation between the fatigue-induced decrease in tetanic [Ca2+]i and the reduction in intermyofibrillar (P = 0.051) and intramyofibrillar (P = 0.0008) glycogen. In conclusion, the fatigue-induced decrease in tetanic [Ca2+]i, and hence force, is accompanied by major reductions in inter- and intramyofibrillar glycogen. The stronger correlation between decreased tetanic [Ca2+]i and reduced intramyofibrillar glycogen implies that sarcoplasmic reticulum Ca2+ release critically depends on energy supply from the intramyofibrillar glycogen pool. PMID:24591577

  16. The restrictions covered in the distribution of fractional loads: a case study

    Directory of Open Access Journals (Sweden)

    Tassiana Vieira Santos

    2017-07-01

    Full Text Available As the economic crisis in Brazil advances, many transport companies on road charges, are losing ground in the market for lack of planning, quality services, high costs of transshipment and lack of information to its customers. More and more companies have been adjusting to market trends in order to become more competitive and improve their service levels, providing quality and punctual delivery and collections, for that they rely on technology and softwares to improve their performance and reduce costs on shipping. This article aims to analyze the constraints faced in the distribution of fractional loads, in a HUB operation, distribution and collection of a large company, acting as a support arm for this operation, in the metropolitan regions of São Paulo and how to present possible and  practical solutions from the techniques and concepts of distribution logistics aligned to technology of routing Road Show software, demonstrating how technical knowledge can add value to the business.

  17. Urinary Proteomics Pilot Study for Biomarker Discovery and Diagnosis in Heart Failure with Reduced Ejection Fraction

    DEFF Research Database (Denmark)

    Rossing, Kasper; Bosselmann, Helle Skovmand; Gustafsson, Finn

    2016-01-01

    Background Biomarker discovery and new insights into the pathophysiology of heart failure with reduced ejection fraction (HFrEF) may emerge from recent advances in high-throughput urinary proteomics. This could lead to improved diagnosis, risk stratification and management of HFrEF. Methods...... to determine a vast array of HFrEF-related urinary peptide biomarkers which might help improving our understanding and diagnosis of heart failure.......EF103 very accurately (area under the curve, AUC = 0.972) discriminated between HFrEF patients (N = 94, sensitivity = 93.6%) and control individuals with and without impaired renal function and hypertension (N = 552, specificity = 92.9%). Interestingly, HFrEF103 showed low sensitivity (12...

  18. Study of the branched hydrocarbon fraction of intramuscular lipids from Iberian fresh ham.

    Science.gov (United States)

    Tejeda, J F; Antequera, T; Martín, L; Ventanas, J; García, C

    2001-06-01

    Branched hydrocarbons from the unsaponifiable lipid fraction of the Biceps femoris muscle of Iberian pigs were analyzed. Fifty-five Iberian pigs were distributed to seven groups according to management system (short Montanera and long Montanera, i.e. fed on acorn and pasture for 55 and 75 days prior to slaughter, respectively, and Pienso, fed on a concentrate diet), and genetic type. A branched hydrocarbon, neophytadiene, was identified only in samples from the pigs fed on the extensive system, with higher levels being found in pigs from the long Montanera group, than in those from the short Montanera group; this compound was not found in the Pienso group. Genotype did not affect the level of branched hydrocarbons found.

  19. The Study of Fractional Order Controller with SLAM in the Humanoid Robot

    Directory of Open Access Journals (Sweden)

    Shuhuan Wen

    2014-01-01

    Full Text Available We present a fractional order PI controller (FOPI with SLAM method, and the proposed method is used in the simulation of navigation of NAO humanoid robot from Aldebaran. We can discretize the transfer function by the Al-Alaoui generating function and then get the FOPI controller by Power Series Expansion (PSE. FOPI can be used as a correction part to reduce the accumulated error of SLAM. In the FOPI controller, the parameters (Kp,Ki,  and  α need to be tuned to obtain the best performance. Finally, we compare the results of position without controller and with PI controller, FOPI controller. The simulations show that the FOPI controller can reduce the error between the real position and estimated position. The proposed method is efficient and reliable for NAO navigation.

  20. A study on the evolution of a community population by cumulative and fractional calculus approaches

    CERN Document Server

    Buyukkılıç, F; Demirhan, D

    2016-01-01

    Nowadays, in our globalized world,the local and intercountry movements of population have been increased. This situation makes it important for host countries to do right predictions for the future population of their native people as well as immigrant people. The knowledge of the attained number of accumulated population is necessary for future planning, concerning to education,health, job, housing, safety requirements, etc. In this work, for updating historically well known formulas of population dynamics of a community are revisited in the framework of compound growth and fractional calculus to get more realistic relations. Within this context, for a time t, the population evolution of a society which owns two different components is calculated. Concomitant relations have been developed to provide a comparison between the native population and the immigrant population that come into existence where at each time interval a colonial population is joined. Eventually at time t, the case where the native popula...

  1. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Chandra, Subhash [Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Snee Hall, Cornell University, Ithaca, NY 14853 (United States)], E-mail: sc40@cornell.edu

    2008-12-15

    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{sub 2}{sup +}) revealed local secondary ion signal enhancements correlated with the water image signals of {sup 19}(H{sub 3}O){sup +}. 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{sup +} and Na{sup +} in physiologically relevant concentrations. The high K

  3. Better compliance with hypofractionation vs. conventional fractionation in adjuvant breast cancer radiotherapy. Results of a single, institutional, retrospective study

    Energy Technology Data Exchange (ETDEWEB)

    Rudat, Volker; Nour, Alaa; Hammoud, Mohamed; Abou Ghaida, Salam [Saad Specialist Hospital, Department of Radiation Oncology, Al Khobar (Saudi Arabia)

    2017-05-15

    The aim of the study was to identify factors significantly associated with the occurrence of unintended treatment interruptions in adjuvant breast cancer radiotherapy. Patients treated with postoperative radiotherapy of the breast or chest wall between March 2014 and August 2016 were evaluated. The radiotherapy regimens and techniques applied were either conventional fractionation (CF; 28 daily fractions of 1.8 Gy or 25 fractions of 2.0 Gy) or hypofractionation (HF; 15 daily fractions of 2.67 Gy) with inverse planned intensity-modulated radiotherapy (IMRT) or three-dimensional planned conformal radiotherapy (3DCRT). Logistic regression analysis was used to identify factors associated with noncompliance. Noncompliance was defined as the missing of at least one scheduled radiotherapy fraction. In all, 19 of 140 (13.6%) patients treated with HF and 39 of 146 (26.7%) treated with CF experienced treatment interruptions. Of 23 factors tested, the fractionation regimen emerged as the only independent significant prognostic factor for noncompliance on multivariate analysis (CF; p = 0.007; odds ratio, 2.3; 95% confidence interval, 1.3-4.2). No statistically significant differences concerning the reasons for treatment interruptions could be detected between patients treated with CF or HF. HF is significantly associated with a better patient compliance with the prescribed radiotherapy schedule compared with CF. The data suggest that this finding is basically related to the shorter overall treatment time of HF. (orig.) [German] Ziel der Untersuchung war es, Faktoren zu identifizieren, die mit ungeplanten Behandlungsunterbrechungen bei der adjuvanten Strahlentherapie des Mammakarzinoms assoziiert sind. Es wurden Patienten untersucht, die eine adjuvante Strahlentherapie der Mamma oder Brustwand zwischen Maerz 2014 und August 2016 erhielten. Zur Anwendung kamen als Fraktionierungsprotokoll und strahlentherapeutische Technik eine konventionell fraktionierte (CF; 28 Fraktionen mit

  4. Iron-rich colloids as carriers of phosphorus in streams: A field-flow fractionation study.

    Science.gov (United States)

    Baken, Stijn; Regelink, Inge C; Comans, Rob N J; Smolders, Erik; Koopmans, Gerwin F

    2016-08-01

    Colloidal phosphorus (P) may represent an important fraction of the P in natural waters, but these colloids remain poorly characterized. In this work, we demonstrate the applicability of asymmetric flow field-flow fractionation (AF4) coupled to high resolution ICP-MS for the characterization of low concentrations of P-bearing colloids. Colloids from five streams draining catchments with contrasting properties were characterized by AF4-ICP-MS and by membrane filtration. All streams contain free humic substances (2-3 nm) and Fe-bearing colloids (3-1200 nm). Two soft water streams contain primary Fe oxyhydroxide-humic nanoparticles (3-6 nm) and aggregates thereof (up to 150 nm). In contrast, three harder water streams contain larger aggregates (40-1200 nm) which consist of diverse associations between Fe oxyhydroxides, humic substances, clay minerals, and possibly ferric phosphate minerals. Despite the diversity of colloids encountered in these contrasting streams, P is in most of the samples predominantly associated with Fe-bearing colloids (mostly Fe oxyhydroxides) at molar P:Fe ratios between 0.02 and 1.5. The molar P:Fe ratio of the waters explains the partitioning of P between colloids and truly dissolved species. Waters with a high P:Fe ratio predominantly contain truly dissolved species because the Fe-rich colloids are saturated with P, whereas waters with a low P:Fe ratio mostly contain colloidal P species. Overall, AF4-ICP-MS is a suitable technique to characterize the diverse P-binding colloids in natural waters. Such colloids may increase the mobility or decrease the bioavailability of P, and they therefore need to be considered when addressing the transport and environmental effects of P in catchments. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses.

    Directory of Open Access Journals (Sweden)

    Sandra Renier

    Full Text Available Genome-scale prediction of subcellular localization (SCL is not only useful for inferring protein function but also for supporting proteomic data. In line with the secretome concept, a rational and original analytical strategy mimicking the secretion steps that determine ultimate SCL was developed for Gram-positive (monoderm bacteria. Based on the biology of protein secretion, a flowchart and decision trees were designed considering (i membrane targeting, (ii protein secretion systems, (iii membrane retention, and (iv cell-wall retention by domains or post-translocational modifications, as well as (v incorporation to cell-surface supramolecular structures. Using Listeria monocytogenes as a case study, results were compared with known data set from SCL predictors and experimental proteomics. While in good agreement with experimental extracytoplasmic fractions, the secretomics-based method outperforms other genomic analyses, which were simply not intended to be as inclusive. Compared to all other localization predictors, this method does not only supply a static snapshot of protein SCL but also offers the full picture of the secretion process dynamics: (i the protein routing is detailed, (ii the number of distinct SCL and protein categories is comprehensive, (iii the description of protein type and topology is provided, (iv the SCL is unambiguously differentiated from the protein category, and (v the multiple SCL and protein category are fully considered. In that sense, the secretomics-based method is much more than a SCL predictor. Besides a major step forward in genomics and proteomics of protein secretion, the secretomics-based method appears as a strategy of choice to generate in silico hypotheses for experimental testing.

  6. Structural and functional plasticity of subcellular tethering, targeting and processing of RPGRIP1 by RPGR isoforms.

    Science.gov (United States)

    Patil, Hemangi; Guruju, Mallikarjuna R; Cho, Kyoung-In; Yi, Haiqing; Orry, Andrew; Kim, Hyesung; Ferreira, Paulo A

    2012-02-15

    Mutations affecting the retinitis pigmentosa GTPase regulator-interacting protein 1 (RPGRIP1) interactome cause syndromic retinal dystrophies. RPGRIP1 interacts with the retinitis pigmentosa GTPase regulator (RPGR) through a domain homologous to RCC1 (RHD), a nucleotide exchange factor of Ran GTPase. However, functional relationships between RPGR and RPGRIP1 and their subcellular roles are lacking. We show by molecular modeling and analyses of RPGR disease-mutations that the RPGR-interacting domain (RID) of RPGRIP1 embraces multivalently the shared RHD of RPGR(1-19) and RPGR(ORF15) isoforms and the mutations are non-overlapping with the interface found between RCC1 and Ran GTPase. RPGR disease-mutations grouped into six classes based on their structural locations and differential impairment with RPGRIP1 interaction. RPGRIP1α(1) expression alone causes its profuse self-aggregation, an effect suppressed by co-expression of either RPGR isoform before and after RPGRIP1α(1) self-aggregation ensue. RPGR(1-19) localizes to the endoplasmic reticulum, whereas RPGR(ORF15) presents cytosolic distribution and they determine uniquely the subcellular co-localization of RPGRIP1α(1). Disease mutations in RPGR(1) (-19), RPGR(ORF15), or RID of RPGRIP1α(1), singly or in combination, exert distinct effects on the subcellular targeting, co-localization or tethering of RPGRIP1α(1) with RPGR(1-19) or RPGR(ORF15) in kidney, photoreceptor and hepatocyte cell lines. Additionally, RPGR(ORF15), but not RPGR(1-19), protects the RID of RPGRIP1α(1) from limited proteolysis. These studies define RPGR- and cell-type-dependent targeting pathways with structural and functional plasticity modulating the expression of mutations in RPGR and RPGRIP1. Further, RPGR isoforms distinctively determine the subcellular targeting of RPGRIP1α(1,) with deficits in RPGR(ORF15)-dependent intracellular localization of RPGRIP1α(1) contributing to pathomechanisms shared by etiologically distinct syndromic

  7. Lung surface-active fraction as a model system for macromolecular ultrastructural studies with Crotalus atrox venom.

    Science.gov (United States)

    Frosolono, M F; Pawlowski, R; Charms, B L; Corbusier, C; Abrams, M; Jones, J

    1973-01-01

    The dog lung surface-active fraction and phosphatidylcholine constituents were subjected to hydrolysis by Crotalus atrox phospholipase A(2). Relative rates of hydrolysis were: dipalmitoyl glycerophosphorylcholine > phosphatidylcholine isolated from the surface-active fraction > phosphatidylcholine as an integral component of the intact surface-active macromolecular structure. Cholesterol markedly inhibited, whereas tripalmitin increased, the rate of hydrolysis with both pure phosphatidylcholine substrates. The effect of temperature on the velocity indicated the enzyme was most active when the substrates were in the gel state. These kinetic results, in conjunction with surface chemistry studies, can be interpreted to indicate that the phosphatidylcholine in the intact surface-active macromolecular particle is liquid crystalline due to molecular interactions with other constituents. Gas-liquid chromatographic analysis of the 2-lysophosphatidylcholines and fatty acids produced from the enzymatic hydrolysis of the intact surface-active fraction indicated that palmitoyl residues were more accessible to the enzyme, perhaps because they occupied positions near the surface of the particle.

  8. A study on fractional erbium glass laser therapy versus chemical peeling for the treatment of melasma in female patients

    Directory of Open Access Journals (Sweden)

    Neerja Puri

    2013-01-01

    Full Text Available Introduction: Melasma is a commonly acquired hypermelanosis and a common dermatologic skin disease that occurs on sun-exposed areas of face. Aims: To assess the efficacy and safety of non-ablative 1,550 nm Erbium glass fractional laser therapy and compare results with those obtained with chemical peeling. Materials and Methods: We selected 30 patients of melasma aged between 20 years and 50 years for the study. The patients were divided into two groups of 15 patients each. Group I patients were subjected to four sessions of 1,550 nm Erbium glass non-ablative fractional laser at 3 weeks interval. In group II patients, four sessions of chemical peeling with 70% glycolic acid was performed. Results: After 12 weeks of treatment, percentage reduction in Melasma Area and Severity Index (MASI score was seen in 62.9% in the laser group and 58.7% in the peels group. Conclusion: It was observed that 1,550 nm fractional laser is as effective as 70% glycolic acid peel in reducing MASI score in patients with melasma.

  9. A retrospective study of the management of Chinese melasma patients using a 1927 nm fractional thulium fiber laser.

    Science.gov (United States)

    Ho, Stephanie G Y; Yeung, C K; Chan, Nicola P Y; Shek, Samantha Y; Chan, Henry H L

    2013-08-01

    A new fractional photothermolysis device is used in our retrospective study to treat melasma in Chinese patients. To evaluate the efficacy and safety of the 1927 nm fractional thulium fiber laser in the treatment of melasma in Chinese patients. Eleven melasma patients who received treatment between November 2009 and May 2010 were included. Photographic images at baseline and follow-up were assessed for clinical efficacy and complications by two independent and blinded physicians. Questionnaires were also completed by patients. Significant MASI improvements were seen at 1 week, 1 month and 2 months, but not at 3 months. Patients' degree of satisfaction was high. Significant improvement in skin texture and pore size was seen for up to 2 months and improvement in wrinkles for up to a month. There was no change in skin laxity. Main adverse effects seen were erythema, edema, and crusting in the early days. One patient developed PIH. The novel 1927 nm fractional thulium fiber laser is safe and effective in the management of melasma in Chinese patients for up to 2 months. It is also useful in photo-rejuvenation. Complications were limited to erythema and edema in the early days, and transient PIH.

  10. Ablative CO2 fractional resurfacing in treatment of thermal burn scars: an open-label controlled clinical and histopathological study.

    Science.gov (United States)

    El-Zawahry, Bakr M; Sobhi, Rehab M; Bassiouny, Dalia A; Tabak, Sahar A

    2015-12-01

    Burn scars can cause permanent disfiguring problems with limited treatments available. To assess and correlate the clinical and histopathological effects of fractional CO2 laser on thermal burns in a controlled study. Fifteen patients 11 with hypertrophic and four with keloidal scars received three CO2 fractional laser sessions every 4-6 weeks. Half of the scar was untreated as a control. Clinical evaluation by Vancouver, PSOAS scores, and photography before, monthly, and 3 months after the last laser session was performed. Ten patients were evaluated histopathologically by standard H&E, Masson trichrome, and Elastica von Gieson special stains. Hypertrophic scars (HTSs) showed textural improvement and a significant decrease of Vancouver, POSAS observer, and patient scores by the end of follow-up period in the laser-treated area (P = 0.011, 0.017 and 0.018, respectively) unlike keloidal scars. Histopathology revealed significant decrease in scar thickness in HTSs only (P < 0.001) as well as a significant decrease in collagen bundle thickness and density in the upper dermis in both types of scars. Fractional CO2 laser is a possible safe and effective modality for the treatment of hypertrophic burn scars with improvement achieved both clinically and histopathologically. © 2015 Wiley Periodicals, Inc.

  11. A Growth Curve Model with Fractional Polynomials for Analysing Incomplete Time-Course Data in Microarray Gene Expression Studies

    Directory of Open Access Journals (Sweden)

    Qihua Tan

    2011-01-01

    Full Text Available Identifying the various gene expression response patterns is a challenging issue in expression microarray time-course experiments. Due to heterogeneity in the regulatory reaction among thousands of genes tested, it is impossible to manually characterize a parametric form for each of the time-course pattern in a gene by gene manner. We introduce a growth curve model with fractional polynomials to automatically capture the various time-dependent expression patterns and meanwhile efficiently handle missing values due to incomplete observations. For each gene, our procedure compares the performances among fractional polynomial models with power terms from a set of fixed values that offer a wide range of curve shapes and suggests a best fitting model. After a limited simulation study, the model has been applied to our human in vivo irritated epidermis data with missing observations to investigate time-dependent transcriptional responses to a chemical irritant. Our method was able to identify the various nonlinear time-course expression trajectories. The integration of growth curves with fractional polynomials provides a flexible way to model different time-course patterns together with model selection and significant gene identification strategies that can be applied in microarray-based time-course gene expression experiments with missing observations.

  12. In vitro and in vivo studies on radiobiological effects of prolonged fraction delivery time in A549 cells.

    Science.gov (United States)

    Jiang, Ling; Xiong, Xiao-Peng; Hu, Chao-Su; Ou, Zhou-Luo; Zhu, Guo-Pei; Ying, Hong-Mei

    2013-03-01

    Intensity-modulated radiation therapy, when used in the clinic, prolongs fraction delivery time. Here we investigated both the in vivoand in vitroradiobiological effects on the A549 cell line, including the effect of different delivery times with the same dose on A549 tumor growth in nude mice. The in vitroeffects were studied with clonogenic assays, using linear-quadratic and incomplete repair models to fit the dose-survival curves. Fractionated irradiation of different doses was given at one fraction per day, simulating a clinical dose-time-fractionation pattern. The longer the interval between the exposures, the more cells survived. To investigate the in vivoeffect, we used sixty-four nude mice implanted with A549 cells in the back legs, randomly assigned into eight groups. A 15 Gy radiation dose was divided into different subfractions. The maximum and minimum tumor diameters were recorded to determine tumor growth. Tumor growth was delayed for groups with prolonged delivery time (40 min) compared to the group receiving a single dose of 15 Gy (Pdelivery time had delayed growth compared to those with a 40 min delivery time [20' (7.5 Gy × 2 F) vs 40' (7.5 Gy × 2 F), P= 0.035; 20' (3 Gy × 5 F) vs 40' (3 Gy × 5 F); P= 0.054; 20' (1.67 Gy × 9 F) vs 40' (1.67 Gy × 9 F), P= 0.028]. A prolonged delivery time decreased the radiobiological effects, so we strongly recommend keeping the delivery time as short as possible.

  13. Fraction Reduction through Continued Fractions

    Science.gov (United States)

    Carley, Holly

    2011-01-01

    This article presents a method of reducing fractions without factoring. The ideas presented may be useful as a project for motivated students in an undergraduate number theory course. The discussion is related to the Euclidean Algorithm and its variations may lead to projects or early examples involving efficiency of an algorithm.

  14. The CORONIS Trial. International study of caesarean section surgical techniques: a randomised fractional, factorial trial

    Directory of Open Access Journals (Sweden)

    2007-10-01

    Full Text Available Abstract Background Caesarean section is one of the most commonly performed operations on women throughout the world. Rates have increased in recent years – about 20–25% in many developed countries. Rates in other parts of the world vary widely. A variety of surgical techniques for all elements of the caesarean section operation are in use. Many have not yet been rigorously evaluated in randomised controlled trials, and it is not known whether any are associated with better outcomes for women and babies. Because huge numbers of women undergo caesarean section, even small differences in post-operative morbidity rates between techniques could translate into improved health for substantial numbers of women, and significant cost savings. Design CORONIS is a multicentre, fractional, factorial randomised controlled trial and will be conducted in centres in Argentina, Ghana, India, Kenya, Pakistan and Sudan. Women are eligible if they are undergoing their first or second caesarean section through a transverse abdominal incision. Five comparisons will be carried out in one trial, using a 2 × 2 × 2 × 2 × 2 fractional factorial design. This design has rarely been used, but is appropriate for the evaluation of several procedures which will be used together in clinical practice. The interventions are: • Blunt versus sharp abdominal entry • Exteriorisation of the uterus for repair versus intra-abdominal repair • Single versus double layer closure of the uterus • Closure versus non-closure of the peritoneum (pelvic and parietal • Chromic catgut versus Polyglactin-910 for uterine repair The primary outcome is death or maternal infectious morbidity (one or more of the following: antibiotic use for maternal febrile morbidity during postnatal hospital stay, antibiotic use for endometritis, wound infection or peritonitis or further operative procedures; or blood transfusion. The sample size required is 15,000 women in total; at least 7,586 women

  15. Fractional Number Operator and Associated Fractional Diffusion Equations

    Science.gov (United States)

    Rguigui, Hafedh

    2018-03-01

    In this paper, we study the fractional number operator as an analog of the finite-dimensional fractional Laplacian. An important relation with the Ornstein-Uhlenbeck process is given. Using a semigroup approach, the solution of the Cauchy problem associated to the fractional number operator is presented. By means of the Mittag-Leffler function and the Laplace transform, we give the solution of the Caputo time fractional diffusion equation and Riemann-Liouville time fractional diffusion equation in infinite dimensions associated to the fractional number operator.

  16. Sedimentation field flow fractionation and flow field flow fractionation as tools for studying the aging effects of WO₃ colloids for photoelectrochemical uses.

    Science.gov (United States)

    Contado, Catia; Argazzi, Roberto

    2011-07-08

    WO₃ colloidal suspensions obtained through a simple sol-gel procedure were subjected to a controlled temperature aging process whose time evolution in terms of particle mass and size distribution was followed by sedimentation field flow fractionation (SdFFF) and flow field flow fractionation (FlFFF). The experiments performed at a temperature of 60 °C showed that in a few hours the initially transparent sol of WO₃ particles, whose size was less than 25 nm, undergoes a progressive size increase allowing nanoparticles to reach a maximum equivalent spherical size of about 130 nm after 5 h. The observed shift in particle size distribution maxima (SdFFF), the broadening of the curves (FlFFF) and the SEM-TEM observations suggest a mixed mechanism of growth-aggregation of initial nanocrystals to form larger particles. The photoelectrochemical properties of thin WO₃ films obtained from the aged suspensions at regular intervals, were tested in a biased photoelectrocatalytic cell with 1M H₂SO₄ under solar simulated irradiation. The current-voltage polarization curves recorded in the potential range 0-1.8 V (vs. SCE) showed a diminution of the maximum photocurrent from 3.7 mA cm⁻² to 2.8 mA cm⁻² with aging times of 1h and 5h, respectively. This loss of performance was mainly attributed to the reduction of the electroactive surface area of the sintered particles as suggested by the satisfactory linear correlation between the integrated photocurrent and the cyclic voltammetry cathodic wave area of the W(VI)→W(V) process measured in the dark. Copyright © 2010 Elsevier B.V. All rights reserved.

  17. Efficacy of minimal ablative fractional Er: YAG laser in the treatment of acne scars: A retrospective study

    Directory of Open Access Journals (Sweden)

    Erol Koç

    2015-06-01

    Full Text Available Background: Acne scar is a complication of inflammatory acne due to the damage of skin. Various therapeutic modalities have been used for the treatment of acne scars. Among these treatments, minimal ablative fractional Er: YAG (Erbium: yttrium-aluminum-garnet laser is a popular treatment modality for the improvement of acne scars. In this study, we restrospectively analysed efficiency and tolerability of minimal ablative fractional Er: YAG laser therapy in the treatment of acne scars. Materials and Methods: Seventy one patients with acne scars treated with minimal ablative fractional Er: YAG laser in our clinic between November 2011 and April 2013 were retrospectively evaluated. Treatment parameters, demographic features and before and after pictures of the lesions were investigated from patients’ records in order to evaluate efficency of Er: YAG laser therapy. Patients’ photographs before and after treatment were compared. Clinical response was graded according to the percentage improvement. Side effects observed during treatment and in follow-up visits were evaluated from patients’ records. Results: Acne scar types included in the study were icepick (n=32, 45.1%, rolling (n=24, 33.9%, shallow boxed (n=7, 9.8% and deep boxed (n=8, 11.2%. Clinical improvement rates evaluated as 1.4% minimal, 38.1% moderate, 47.8% good and 2.7% excellent. Adverse effects were 16.8% erythema that lasted more 3 days, 4.2% postinflammatory hyperpigmentation and 7.0% acne aggravation. Clinical improvement (3.2, good-excellent and patient satisfaction rates (2.6, good-excellent for icepick type scars were very high. Similarly in shallow boxed scar types clinical improvement (2.8, good and patient satisfaction rates (2.6, good-excellent were high. However, in rolling scars and deep boxed scars clinical improvement rates were low. Conclusion: Minimal ablative fractional Er: YAG laser therapy is an effective and safe treatment option for acne scars, especially, in

  18. A Study on Overestimating a Given Fraction Defective by an Imperfect Inspector

    Directory of Open Access Journals (Sweden)

    Moon Hee Yang

    2014-01-01

    Full Text Available It has been believed that even an imperfect inspector with nonzero inspection errors could either overestimate or underestimate a given FD (fraction defective with a 50 : 50 chance. What happens to the existing inspection plans, if an imperfect inspector overestimates a known FD, when it is very low? We deal with this fundamental question, by constructing four mathematical models, under the assumptions that an infinite sequence of items with a known FD is given to an imperfect inspector with nonzero inspection errors, which can be constant and/or randomly distributed with a uniform distribution. We derive four analytical formulas for computing the probability of overestimation (POE and prove that an imperfect inspector overestimates a given FD with more than 50%, if the FD is less than a value termed as a critical FD. Our mathematical proof indicates that the POE approaches one when FD approaches zero under our assumptions. Hence, if a given FD is very low, commercial inspection plans should be revised with the POE concept in the near future, for the fairness of commercial trades.

  19. A CFD modeling study in an urban street canyon for ultrafine particles and population exposure: The intake fraction approach.

    Science.gov (United States)

    Habilomatis, George; Chaloulakou, Archontoula

    2015-10-15

    Air quality in street canyons is of major importance, since the highest pollution levels are often encountered in these microenvironments. The canyon effect (reduced natural ventilation) makes them "hot spots" for particulate pollution contributing to adverse health effects for the exposed population. In this study we tried to characterize the influence of UFP (ultrafine particle) emissions from traffic on population exposure in an urban street canyon, by applying the intake fraction (iF) approach. One month long measurements of UFP levels have been monitored and used for the need of this study. We applied a three dimensional computational fluid dynamic (CFD) model based on real measurements for the simulation of UFP levels. We used infiltration factors, evaluated on a daily basis for the under study area, to estimate the indoor UFP levels. As a result the intake fraction for the pedestrians, residents and office workers is in the range of (1E-5)-(1E-4). The street canyon is mostly residential justifying partially the higher value of intake fraction for residents (1E-4). The above iF value is on the same order of magnitude with the corresponding one evaluated in a relative street canyon study. The total iF value in this microenvironment is one order of magnitude higher than ours, explained partially by the different use and activities. Two specific applications of iF to assess prioritization among emission sources and environmental justice issues are also examined. We ran a scenario with diesel and gasoline cars and diesel fueled vehicle seems to be a target source to improve overall iF. Our application focus on a small residential area, typical of urban central Athens, in order to evaluate high resolution iF. The significance of source-exposure relationship study in a micro scale is emphasized by recent research. Copyright © 2015 Elsevier B.V. All rights reserved.

  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...... localization in an oscillatory fashion unitemporally with Ca2+ oscillations, whereas a Ca2+-binding deficient mutant of ALG-2 did not redistribute. Using tagged ALG-2 as bait we identified its novel target protein Sec31A and based on the partial colocalization of endogenous ALG-2 and Sec31A we propose that ALG...

  1. rAAV-mediated subcellular targeting of optogenetic tools in retinal ganglion cells in vivo.

    Science.gov (United States)

    Wu, Chaowen; Ivanova, Elena; Zhang, Yi; Pan, Zhuo-Hua

    2013-01-01

    Expression of optogenetic tools in surviving inner retinal neurons to impart retinal light sensitivity has been a new strategy for restoring vision after photoreceptor degeneration. One potential approach for restoring retinal light sensitivity after photoreceptor degeneration is to express optogenetic tools in retinal ganglion cells (RGCs). For this approach, restoration of ON and OFF center-surround receptive fields in RGCs, a key feature of visual information processing, may be important. A possible solution is to differentially express depolarizing and hyperpolarizing optogenetic tools, such as channelrhodopsin-2 and halorhodopsin, to the center and peripheral regions of the RGC dendritic field by using protein targeting motifs. Recombinant adeno-associated virus (rAAV) vectors have proven to be a powerful vehicle for in vitro and in vivo gene delivery, including in the retina. Therefore, the search for protein targeting motifs that can achieve rAAV-mediated subcellular targeted expression would be particularly valuable for developing therapeutic applications. In this study, we identified two protein motifs that are suitable for rAAV-mediated subcellular targeting for generating center-surround receptive fields while reducing the axonal expression in RGCs. Resulting morphological dendritic field and physiological response field by center-targeting were significantly smaller than those produced by surround-targeting. rAAV motif-mediated protein targeting could also be a valuable tool for studying physiological function and clinical applications in other areas of the central nervous system.

  2. Mutational analyses of the signals involved in the subcellular location of DSCR1

    Directory of Open Access Journals (Sweden)

    Henrique-Silva Flávio

    2002-09-01

    Full Text Available Abstract Background Down syndrome is the most frequent genetic disorder in humans. Rare cases involving partial trisomy of chromosome 21 allowed a small chromosomal region common to all carriers, called Down Syndrome Critical Region (DSCR, to be determined. The DSCR1 gene was identified in this region and is expressed preferentially in the brain, heart and skeletal muscle. Recent studies have shown that DSCR1 belongs to a family of proteins that binds and inhibits calcineurin, a serine-threonine phosphatase. The work reported on herein consisted of a study of the subcellular location of DSCR1 and DSCR1-mutated forms by fusion with a green fluorescent protein, using various cell lines, including human. Results The protein's location was preferentially nuclear, independently of the isoform, cell line and insertion in the GFP's N- or C-terminal. A segment in the C-terminal, which is important in the location of the protein, was identified by deletion. On the other hand, site-directed mutational analyses have indicated the involvement of some serine and threonine residues in this event. Conclusion In this paper, we discuss the identification of amino acids which can be important for subcellular location of DSCR1. The involvement of residues that are prone to phosphorylation suggests that the location and function of DSCR1 may be regulated by kinases and/or phosphatases.

  3. A preliminary study of iron isotope fractionation in marine invertebrates (chitons, Mollusca) in near-shore environments

    Science.gov (United States)

    Emmanuel, S.; Schuessler, J. A.; Vinther, J.; Matthews, A.; von Blanckenburg, F.

    2014-10-01

    Chitons (Mollusca) are marine invertebrates that produce radulae (teeth or rasping tongues) containing high concentrations of biomineralized magnetite and other iron-bearing minerals. As Fe isotope signatures are influenced by redox processes and biological fractionation, Fe isotopes in chiton radulae might be expected to provide an effective tracer of ambient oceanic conditions and biogeochemical cycling. Here, in a pilot study to measure Fe isotopes in marine invertebrates, we examine Fe isotopes in modern marine chiton radulae collected from different locations in the Atlantic and Pacific oceans to assess the range of isotopic values, and to test whether or not the isotopic signatures reflect seawater values. Values of δ56Fe (relative to IRMM-014) in chiton teeth range from -1.90 to 0.00 ‰ (±0.05‰ (2σ) uncertainty in δ56Fe), probably reflecting a combination of geographical control and biological fractionation processes. Comparison with published local surface seawater Fe isotope data shows a consistent negative offset of chiton teeth Fe isotope compositions relative to seawater. Strikingly, two different species from the same locality in the North Pacific (Puget Sound, Washington, USA) have distinct isotopic signatures. Tonicella lineata, which feeds on red algae in the sublittoral zone, has a mean δ56Fe of -0.65 ± 0.26‰ (2σ, 3 specimens), while Mopalia muscosa, which feeds on both green and red algae in the eulittoral zone, shows lighter isotopic values with a mean δ56Fe of -1.47 ± 0.98‰ (2σ, 5 specimens). Three possible pathways are proposed to account for the different isotopic signatures: (i) physiologically controlled processes within the chitons that lead to species-dependent fractionation; (ii) diet-controlled variability due to different Fe isotope fractionation in the red and green algal food sources; and (iii) environmentally controlled fractionation that causes variation in the isotopic signatures of bioavailable Fe in the different

  4. Mathematical modeling of sub-cellular asymmetry of fat-dachsous heterodimer for generation of planar cell polarity.

    Directory of Open Access Journals (Sweden)

    Mohit Kumar Jolly

    Full Text Available Planar Cell Polarity (PCP is an evolutionarily conserved characteristic of animal tissues marked by coordinated polarization of cells or structures in the plane of a tissue. In insect wing epithelium, for instance, PCP is characterized by en masse orientation of hairs orthogonal to its apical-basal axis and pointing along the proximal-distal axis of the organ. Directional cue for PCP has been proposed to be generated by complex sets of interactions amongst three proteins - Fat (Ft, Dachsous (Ds and Four-jointed (Fj. Ft and Ds are two atypical cadherins, which are phosphorylated by Fj, a Golgi kinase. Ft and Ds from adjacent cells bind heterophilically via their tandem cadherin repeats, and their binding affinities are regulated by Fj. Further, in the wing epithelium, sub-cellular levels of Ft-Ds heterodimers are seen to be elevated at the distal edges of individual cells, prefiguring their PCP. Mechanisms generating this sub-cellular asymmetry of Ft-Ds heterodimer in proximal and distal edges of cells, however, have not been resolved yet. Using a mathematical modeling approach, here we provide a framework for generation of this sub-cellular asymmetry of Ft-Ds heterodimer. First, we explain how the known interactions within Ft-Ds-Fj system translate into sub-cellular asymmetry of Ft-Ds heterodimer. Second, we show that this asymmetric localization of Ft-Ds heterodimer is lost when tissue-level gradient of Fj is flattened, or when phosphorylation of Ft by Fj is abolished, but not when tissue-level gradient of Ds is flattened or when phosphorylation of Ds is abrogated. Finally, we show that distal enrichment of Ds also amplifies Ft-Ds asymmetry. These observations reveal that gradient of Fj expression, phosphorylation of Ft by Fj and sub-cellular distal accumulation of Ds are three critical elements required for generating sub-cellular asymmetry of Ft-Ds heterodimer. Our model integrates the known experimental data and presents testable predictions

  5. Precise Photodynamic Therapy of Cancer via Subcellular Dynamic Tracing of Dual-loaded Upconversion Nanophotosensitizers

    National Research Council Canada - National Science Library

    Yulei Chang; Xiaodan Li; Li Zhang; Lu Xia; Xiaomin Liu; Cuixia Li; Youlin Zhang; Langping Tu; Bin Xue; Huiying Zhao; Hong Zhang; Xianggui Kong

    2017-01-01

    ...) light have led to substantial progress in improving photodynamic therapy (PDT) of cancer. For a successful PDT, subcellular organelles are promising therapeutic targets for reaching a satisfactory efficacy...

  6. 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

    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...... 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...

  7. Urinary Proteomics Pilot Study for Biomarker Discovery and Diagnosis in Heart Failure with Reduced Ejection Fraction.

    Directory of Open Access Journals (Sweden)

    Kasper Rossing

    Full Text Available Biomarker discovery and new insights into the pathophysiology of heart failure with reduced ejection fraction (HFrEF may emerge from recent advances in high-throughput urinary proteomics. This could lead to improved diagnosis, risk stratification and management of HFrEF.Urine samples were analyzed by on-line capillary electrophoresis coupled to electrospray ionization micro time-of-flight mass spectrometry (CE-MS to generate individual urinary proteome profiles. In an initial biomarker discovery cohort, analysis of urinary proteome profiles from 33 HFrEF patients and 29 age- and sex-matched individuals without HFrEF resulted in identification of 103 peptides that were significantly differentially excreted in HFrEF. These 103 peptides were used to establish the support vector machine-based HFrEF classifier HFrEF103. In a subsequent validation cohort, HFrEF103 very accurately (area under the curve, AUC = 0.972 discriminated between HFrEF patients (N = 94, sensitivity = 93.6% and control individuals with and without impaired renal function and hypertension (N = 552, specificity = 92.9%. Interestingly, HFrEF103 showed low sensitivity (12.6% in individuals with diastolic left ventricular dysfunction (N = 176. The HFrEF-related peptide biomarkers mainly included fragments of fibrillar type I and III collagen but also, e.g., of fibrinogen beta and alpha-1-antitrypsin.CE-MS based urine proteome analysis served as a sensitive tool to determine a vast array of HFrEF-related urinary peptide biomarkers which might help improving our understanding and diagnosis of heart failure.

  8. Comparison of Radiation-Induced Bystander Effect in QU-DB Cells after Acute and Fractionated Irradiation: An In Vitro Study.

    Science.gov (United States)

    Soleymanifard, Shokouhozaman; Bahreyni Toossi, Mohammad Taghi; Kamran Samani, Roghayeh; Mohebbi, Shokoufeh

    2016-01-01

    Radiation effects induced in non-irradiated cells are termed radiation-induced bystander effects (RIBE). The present study intends to examine the RIBE response of QU-DB bystander cells to first, second and third radiation fractions and compare their cumulative outcome with an equal, single acute dose. This experimental study irradiated three groups of target cells for one, two and three times with(60)Co gamma rays. One hour after irradiation, we transferred their culture media to non-irradiated (bystander) cells. We used the cytokinesis block micronucleus assay to evaluate RIBE response in the bystander cells. The numbers of micronuclei generated in bystander cells were determined. RIBE response to single acute doses increased up to 4 Gy, then decreased, and finally at the 8 Gy dose disappeared. The second and third fractions induced RIBE in bystander cells, except when RIBE reached to the maximum level at the first fraction. We split the 4 Gy acute dose into two fractions, which decreased the RIBE response. However, fractionation of 6 Gy (into two fractions of 3 Gy or three fractions of 2 Gy) had no effect on RIBE response. When we split the 8 Gy acute dose into two fractions we observed RIBE, which had disappeared following the single 8 Gy dose. The impact of dose fractionation on RIBE induced in QU-DB cells de- pended on the RIBE dose-response relationship. Where RIBE increased proportion- ally with the dose, fractionation reduced the RIBE response. In contrast, at high dos- es where RIBE decreased proportionally with the dose, fractionation either did not change RIBE (at 6 Gy) or increased it (at 8 Gy).

  9. Study on the distribution of organic carbon in soil fractions and its reaction potential of binding the pesticides

    Science.gov (United States)

    Chowdhury, Ashim

    2010-05-01

    STUDY ON THE DISTRIBUTION OF ORGANIC CARBON IN SOIL FRACTIONS AND ITS REACTION POTENTIAL OF BINDING THE PESTICIDES **SUMITRA ROY1, SANKHAJIT ROY1, *ASHIM CHOWDHURY2, SASWATI PRADHAN2 and PETER BURAUEL3 1Department of Agricultural Chemicals, Bidhan Chandra Krishi Viswavidyalay, Mohanpur, West Bengal, India. 2Department of Agricultural Chemistry and Soil Science, University of Calcutta, West Bengal, India. 3Institute of Chemical Dynamics & Geosphere, FZ-Juelich, Germany. *Correspondence: ashimkly@hotmail.com **Research work carried out as DAAD Sandwich research fellow at FZ- Juelich, Germany Soil is the ultimate sink of all selectively applied pesticides. In addition to the basic physicochemical data of an active ingredient, the fate of the various compounds is largely determined by the type of application. Finally, pesticide and their metabolites, as well as structural elements, remain in the native carbon reserves of the soil or are sorbed & fixed to clay minerals and clay- humus complexes. Soil organic matter (SOM) and the soil microbial community are the crucial components which regulate soil processes and contribute towards the stability of the soil ecosystem. It is an energy source for biological mineralization processes, functions as a buffer and participates in chemical reaction. Knowledge is essential to understand the extent to which the SOM influences the mobilization and immobilization processes of foreign substance in soil and the substance transport and pollutant decomposition in soil. The freshly incorporated organic matter undergoes mineralization and the non mineralized carbon fraction is of special relevance with respect to soil stability in general and decisive for the fate and particular the persistence of xenobiotics in soil. The biological and physicochemical interactions establishing equilibrium between the organic matter bound, fixed or complexed to the soil matrix and that dissolve in the soil solution must be understood in detail to realize

  10. Analytical study of exact solutions of the nonlinear Korteweg-de Vries equation with space-time fractional derivatives

    Science.gov (United States)

    Liu, Jiangen; Zhang, Yufeng

    2018-01-01

    This paper gives an analytical study of dynamic behavior of the exact solutions of nonlinear Korteweg-de Vries equation with space-time local fractional derivatives. By using the improved (G‧ G )-expansion method, the explicit traveling wave solutions including periodic solutions, dark soliton solutions, soliton solutions and soliton-like solutions, are obtained for the first time. They can better help us further understand the physical phenomena and provide a strong basis. Meanwhile, some solutions are presented through 3D-graphs.

  11. Engineering an effective Mn-binding MRI reporter protein by subcellular targeting.

    Science.gov (United States)

    Bartelle, Benjamin B; Mana, Miyeko D; Suero-Abreu, Giselle A; Rodriguez, Joe J; Turnbull, Daniel H

    2015-12-01

    Manganese (Mn) is an effective contrast agent and biologically active metal, which has been widely used for Mn-enhanced MRI (MEMRI). The purpose of this study was to develop and test a Mn binding protein for use as a genetic reporter for MEMRI. The bacterial Mn-binding protein, MntR was identified as a candidate reporter protein. MntR was engineered for expression in mammalian cells, and targeted to different subcellular organelles, including the Golgi Apparatus where cellular Mn is enriched. Transfected HEK293 cells and B16 melanoma cells were tested in vitro and in vivo, using immunocytochemistry, MR imaging and relaxometry. Subcellular targeting of MntR to the cytosol, endoplasmic reticulum and Golgi apparatus was verified with immunocytochemistry. After targeting to the Golgi, MntR expression produced robust R1 changes and T1 contrast in cells, in vitro and in vivo. Co-expression with the divalent metal transporter DMT1, a previously described Mn-based reporter, further enhanced contrast in B16 cells in culture, but in the in vivo B16 tumor model tested was not significantly better than MntR alone. This second-generation reporter system both expands the capabilities of genetically encoded reporters for imaging with MEMRI and provides important insights into the mechanisms of Mn biology which create endogenous MEMRI contrast. © 2014 Wiley Periodicals, Inc.

  12. Characterization of Subcellular Responses Induced by Exposure of Microbubbles to Astrocytes.

    Science.gov (United States)

    Sun, Shan; Kanagaraj, Johnwesly; Cho, Lindsey; Kang, Dongkoo; Xiao, Shu; Cho, Michael

    2015-10-01

    Blast traumatic brain injury (bTBI) has now been identified to associate with adverse health consequences among combat veterans. Post-traumatic stress disorder linked with explosive blasts, for example, may result from such brain injury. The fundamental questions about the nature, diagnosis, and long-term consequences of bTBI and causative relationship to post-traumatic stress disorder remain elusive, however. A better understanding of brain tissue injury requires elucidation of potential mechanisms. One such mechanism may be generation of microcavitation bubbles in the brain after an explosive blast and their subsequent interaction with brain cells. Using a controlled electrical discharge system, we have successfully generated shock waves (∼10 MPa) and microbubbles (20-30 μm) in the cell culture of mouse astrocytes. Detachment of astrocytes from the substrate after exposure to microbubbles was observed, and it depended on repetitive exposures. Of the cells that survived the initial assault, several subcellular changes were monitored and determined using fluorescent microscopy, including cell viability, cytoskeletal reorganization, changes in focal adhesion, membrane permeability, and potential onset of apoptosis. While the astrocytes impacted by the shock wave only demonstrated essentially unaltered cellular behavior, the astrocytes exposed to microbubbles exhibited significantly different responses, including production of reactive oxygen species by collapse of microbubbles. In the present study, we characterized and report for the first time the altered biophysical and subcellular properties in astrocytes in response to exposure to the combination of shock waves and microbubbles.

  13. Subcellular and cellular locations of nitric-oxide synthase isoforms as determinants of health and disease

    Science.gov (United States)

    Villanueva, Cleva; Giulivi, Cecilia

    2010-01-01

    The effects of nitric oxide in biological systems depend on its steady-state concentration and where it is being produced. The organ where nitric oxide is produced is relevant, and within the organ, which types of cells are actually contributing to this production seem to play a major determinant of its effect. Subcellular compartmentalization of specific nitric-oxide synthase enzymes has been shown to play a major role in health and disease. Pathophysiological conditions affect the cellular expression and localization of nitric oxide synthases, which in turn alter organ cross talk. In this study, we described the compartmentalization of nitric oxide in organs, cells and subcellular organelles, and how its localization relates to several relevant clinical conditions. Understanding the complexity of the compartmentalization of nitric oxide production and the implications of this compartmentalization in terms of cellular targets and downstream effects will eventually contribute toward the development of better strategies for treating or preventing pathological events associated with the increase, inhibition or mislocalization of nitric oxide production. PMID:20388537

  14. Prediction of subcellular location apoptosis proteins with ensemble classifier and feature selection.

    Science.gov (United States)

    Gu, Quan; Ding, Yong-Sheng; Jiang, Xiao-Ying; Zhang, Tong-Liang

    2010-04-01

    Apoptosis proteins have a central role in the development and the homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death. The function of an apoptosis protein is closely related to its subcellular location. It is crucial to develop powerful tools to predict apoptosis protein locations for rapidly increasing gap between the number of known structural proteins and the number of known sequences in protein databank. In this study, amino acids pair compositions with different spaces are used to construct feature sets for representing sample of protein feature selection approach based on binary particle swarm optimization, which is applied to extract effective feature. Ensemble classifier is used as prediction engine, of which the basic classifier is the fuzzy K-nearest neighbor. Each basic classifier is trained with different feature sets. Two datasets often used in prior works are selected to validate the performance of proposed approach. The results obtained by jackknife test are quite encouraging, indicating that the proposed method might become a potentially useful tool for subcellular location of apoptosis protein, or at least can play a complimentary role to the existing methods in the relevant areas. The supplement information and software written in Matlab are available by contacting the corresponding author.

  15. Changes in chemical forms, subcellular distribution, and thiol compounds involved in Pb accumulation and detoxification in Athyrium wardii (Hook.).

    Science.gov (United States)

    Zhao, Li; Li, Tingxuan; Yu, Haiying; Chen, Guangdeng; Zhang, Xizhou; Zheng, Zicheng; Li, Jinxing

    2015-08-01

    Athyrium wardii is one of the dominant plant species flourishing on the Pb-Zn mine tailings in Sichuan Province, China. A greenhouse pot experiment was conducted to evaluate the chemical forms, subcellular distribution, and thiol compounds in A. wardii under different Pb treatments. The results showed that plants of the mining ecotype (ME) of A. wardii were more tolerant to Pb than those of the non-mining ecotype (NME) in spite of accumulation of higher Pb concentrations. The Pb concentrations in shoots and roots of the ME were 3.2∼8.6 times and 3.0∼24.6 times higher than those of the NME, respectively. The ME was more efficient in Pb uptake than the NME. Moreover, 27.8∼39.0% of the total Pb in ME was sodium chloride (NaCl) extractable and 38.0∼48.5% was acetic acid (HAc) extractable, whereas only a minority of total Pb was in ethanol and H2O extractable. In subcellular level, 77.4∼88.8% of total Pb was stored in the cell walls of ME and 9.0∼18.9% in soluble fractions. Increasing Pb concentrations enhanced sequestration of Pb into the cell walls and soluble fractions of ME tissues to protect organelles against Pb. Synthesis of non-protein thiols (NP-SH) and phytochelatins (PCs) in roots of ME significantly enhanced in response to Pb stress, and significant increases in glutathione (GSH) were observed in shoots of ME. Higher levels of NP-SH, GSH, and PCs were observed in roots of the ME comparing with NME, especially under high Pb treatments. The results indicated that Pb was localized mainly in cell wall and soluble fraction of ME plants with low biological activity by cell wall deposition and vacuolar compartmentalization, which might be the important adapted Pb detoxification mechanisms of ME.

  16. Genetically targeted fluorogenic macromolecules for subcellular imaging and cellular perturbation.

    Science.gov (United States)

    Magenau, Andrew J D; Saurabh, Saumya; Andreko, Susan K; Telmer, Cheryl A; Schmidt, Brigitte F; Waggoner, Alan S; Bruchez, Marcel P

    2015-10-01

    The alteration of cellular functions by anchoring macromolecules to specified organelles may reveal a new area of therapeutic potential and clinical treatment. In this work, a unique phenotype was evoked by influencing cellular behavior through the modification of subcellular structures with genetically targetable macromolecules. These fluorogen-functionalized polymers, prepared via controlled radical polymerization, were capable of exclusively decorating actin, cytoplasmic, or nuclear compartments of living cells expressing localized fluorgen-activating proteins. The macromolecular fluorogens were optimized by establishing critical polymer architecture-biophysical property relationships which impacted binding rates, binding affinities, and the level of internalization. Specific labeling of subcellular structures was realized at nanomolar concentrations of polymer, in the absence of membrane permeabilization or transduction domains, and fluorogen-modified polymers were found to bind to protein intact after delivery to the cytosol. Cellular motility was found to be dependent on binding of macromolecular fluorogens to actin structures causing rapid cellular ruffling without migration. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. A retrospective study of the effectiveness of hemostatic radiotherapy with conventional fractionation in patients with advanced cancer

    Directory of Open Access Journals (Sweden)

    Nomoto S

    2015-12-01

    Full Text Available The aim of this study was to assess the efficacy of hemostatic radiotherapy (HRT in patients with advanced cancer. Eighteen patients with advanced cancer treated with HRT at the Fukuoka University and Kyushu Rosai Hospitals in Japan between July 2010 and February 2015 were retrospectively assessed. The hemostatic effect of tumor-related bleeding was assessed by the clinical course of bleeding, laboratory data, the endoscopic study, and the number of blood transfusion units (BTRUs for one month before and after HRT. The median follow-up time was 2.6 months (range, 0.7 to 36.2 months. The median age of the patients was 77 years (range, 51 to 93. The primary diseases with tumor-related bleeding included gastric cancer, urinary bladder cancer, gynecological cancer, prostate cancer, non-small-cell lung cancer, and breast cancer. The median overall survival time was three months, and the one year survival rate was 22.9% of all patients. The HRT regimens ranged from 30 Gy in 10 fractions to 40 Gy in 20 fractions. In all patients, the anemia grade and the number of BTRUs decreased for 1 month after RT. The percentage of patients who were diagnosed as “successful” for hemostasis was 83% (15 of 18 patients. HRT is therefore strongly suggested as effective for the control of tumor-related bleeding in patients with advanced cancer. The optimal radiation doses and fractions are controversial; however, this treatment should be offered for patients with a poor life expectancy.

  18. Evaluation of Isolated Fractions of Aloe vera Gel Materials on Indinavir Pharmacokinetics: In vitro and in vivo Studies.

    Science.gov (United States)

    Wallis, Lonette; Malan, Maides; Gouws, Chrisna; Steyn, Dewald; Ellis, Suria; Abay, Efrem; Wiesner, Lubbe; Otto, Daniel P; Hamman, Josias

    2016-01-01

    Aloe vera is a plant with a long history of traditional medicinal use and is consumed in different products, sometimes in conjunction with prescribed medicines. A. vera gel has shown the ability to modulate drug absorption in vitro. The aim of this study was to fractionate the precipitated polysaccharide component of A. vera gel based on molecular weight and to compare their interactions with indinavir pharmacokinetics. Crude polysaccharides were precipitated from a solution of A. vera gel and was fractionated by means of centrifugal filtration through membranes with different molecular weight cut-off values (i.e. 300 KDa, 100 KDa and 30 KDa). Marker molecules were quantified in the aloe leaf materials by means of nuclear magnetic resonance spectroscopy and the average molecular weight was determined by means of gel filtration chromatography linked to multi-angle-laser-light scattering and refractive index detection. The effect of the aloe leaf materials on the transepithelial electrical resistance (TEER) of Caco-2 cell monolayers as well as indinavir metabolism in LS180 cells was measured. The bioavailability of indinavir in the presence and absence of the aloe leaf materials was determined in Sprague-Dawley rats. All the aloe leaf materials investigated in this study reduced the TEER of Caco-2 cell monolayers, inhibited indinavir metabolism in LS 180 cells to different extents and changed the bioavailability parameters of indinavir in rats compared to that of indinavir alone. These indinavir pharmacokinetic modulation effects were not dependent on the presence of aloverose and also not on the average molecular weight of the isolated fractions.

  19. Simplified fractional Fourier transforms.

    Science.gov (United States)

    Pei, S C; Ding, J J

    2000-12-01

    The fractional Fourier transform (FRFT) has been used for many years, and it is useful in many applications. Most applications of the FRFT are based on the design of fractional filters (such as removal of chirp noise and the fractional Hilbert transform) or on fractional correlation (such as scaled space-variant pattern recognition). In this study we introduce several types of simplified fractional Fourier transform (SFRFT). Such transforms are all special cases of a linear canonical transform (an affine Fourier transform or an ABCD transform). They have the same capabilities as the original FRFT for design of fractional filters or for fractional correlation. But they are simpler than the original FRFT in terms of digital computation, optical implementation, implementation of gradient-index media, and implementation of radar systems. Our goal is to search for the simplest transform that has the same capabilities as the original FRFT. Thus we discuss not only the formulas and properties of the SFRFT's but also their implementation. Although these SFRFT's usually have no additivity properties, they are useful for the practical applications. They have great potential for replacing the original FRFT's in many applications.

  20. Fractional 1,550 nm Ytterbium/Erbium fiber laser in the treatment of lichen amyloidosis: clinical and histological study.

    Science.gov (United States)

    Panchaprateep, Ratchathorn; Tusgate, Sai; Munavalli, Girish S; Noppakun, Nopadon

    2015-03-01

    Lichen amyloidosis is characterized by amyloid deposition in the papillary dermis, presenting clinically with intensely pruritic hyperkeratotic papules. Various treatment modalities have been used but the results are generally unsatisfactory. Several studies show that non-ablative fractional lasers can be used to treat depositional diseases due to their capability of inducing transepidermal elimination of the dermal content. To investigate the efficacy and safety of a non-ablative fractional 1,550 nm Yttrium/Erbium fiber laser for the treatment of lichen amyloidosis. Ten subjects with a clinical and histological diagnosis of lichen amyloidosis were treated with fractional non-ablative laser using a 7-cm tip, with the parameter of 30 mJ/cm2 and 1,000 microscopic treatment zones (MTZ)/cm2 for three sessions at 4-week intervals. Clinical improvement (in terms of global improvement score, brownish/hyperpigmentation, thickness, and number of papules) was evaluated using a quartile grading scale at baseline, and 4, 12, and 24 weeks after the last treatment. Itch score and subjective satisfaction rates were also assessed. Adverse events were recorded, and pain was scored using a visual analog scale (VAS). Histologic changes were observed using standard staining with hematoxylin and eosin, as well as special stains of alkaline congo red and crystal violet at baseline and 4 weeks after treatment. At 4 and 24 weeks after treatment, the lichen amyloid lesions had statistically significantly improved in all aspects compared to baseline (P = 0.01 and P = 0.016, respectively; Wilcoxon signed-rank test). However, partial recurrence was reported in 2 out of 10 subjects. All subjects rated itching symptom significantly improved after only the first treatment (P material deposition in the papillary dermis. There was no amyloid material deposition noted in two out of eight histopathology studies. The non-ablative fractional 1,550 nm Ytterbium/Erbium fiber laser is

  1. N-terminal acetylation by NatC is not a general determinant for substrate subcellular localization in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Henriette Aksnes

    Full Text Available N-terminal acetylation has been suggested to play a role in the subcellular targeting of proteins, in particular those acetylated by the N-terminal acetyltransferase complex NatC. Based on previous positional proteomics data revealing N-terminal acetylation status and the predicted NAT substrate classes, we selected 13 suitable NatC substrates for subcellular localization studies in Saccharomyces cerevisiae. Fluorescence microscopy analysis of GFP-tagged candidates in the presence or absence of the NatC catalytic subunit Naa30 (Mak3 revealed unaltered localization patterns for all 13 candidates, thus arguing against a general role for the N-terminal acetyl group as a localization determinant. Furthermore, all organelle-localized substrates indicated undisrupted structures, thus suggesting that absence of NatC acetylation does not have a vast effect on organelle morphology in yeast.

  2. Mapping the subcellular localization of Fe3O4@TiO2 nanoparticles by X-ray Fluorescence Microscopy

    Science.gov (United States)

    Yuan, Y.; Chen, S.; Gleber, S. C.; Lai, B.; Brister, K.; Flachenecker, C.; Wanzer, B.; Paunesku, T.; Vogt, S.; Woloschak, G. E.

    2013-10-01

    The targeted delivery of Fe3O4@TiO2 nanoparticles to cancer cells is an important step in their development as nanomedicines. We have synthesized nanoparticles that can bind the Epidermal Growth Factor Receptor, a cell surface protein that is overexpressed in many epithelial type cancers. In order to study the subcellular distribution of these nanoparticles, we have utilized the sub-micron resolution of X-ray Fluorescence Microscopy to map the location of Fe3O4@TiO2 NPs and other trace metal elements within HeLa cervical cancer cells. Here we demonstrate how the higher resolution of the newly installed Bionanoprobe at the Advanced Photon Source at Argonne National Laboratory can greatly improve our ability to distinguish intracellular nanoparticles and their spatial relationship with subcellular compartments.

  3. 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......-a-go-go-related gene-1 (ERG1), was investigated in the adult rat heart. Confocal immunofluorescence microscopy of atrial and ventricular cells revealed that whereas KCNQ1 labeling was detected in both the peripheral sarcolemma and a structure transversing the myocytes, ERG1 immunoreactivity was confined to the latter....... Immunoelectron microscopy of atrial and ventricular myocytes showed that the ERG1 channel was primarily expressed in the transverse tubular system and its entrance, whereas KCNQ1 was detected in both the peripheral sarcolemma and in the T tubules. Thus, whereas ERG1 displays a very restricted subcellular...

  4. Different fractionation schedules of radiotherapy in locally advanced head and neck malignancy: A prospective randomized study to compare the results of treatment and toxicities of different protocols

    Directory of Open Access Journals (Sweden)

    Dipanjan Majumder

    2013-01-01

    Full Text Available Context: Altered fractionated radiotherapy may have better result than conventional radiotherapy and concomitant chemoradiotherapy to treat locally advanced head and neck cancers. Aims: Evaluation of the response and toxicities in different fractionated radiotherapy schedules in locally advanced head and neck cancer. Materials and Methods: Sixty four histologically proved patients of locally advanced head and neck cancer were included in the study according to protocol and were randomized into three arms. Arm A (n = 21 received 66 Gy in 33 fractions (5 fractions/week from Monday to Friday single fraction daily in 6½ weeks along with concomitant chemotherapy (injection Cisplatin 30 mg/m 2 intravenous once weekly for 6 weeks. Arm B (n = 21 received 66 Gy in 33 fractions (6 fractions per week single fraction daily in 5½ weeks, and arm C ( n = 22 received late hyperfractionation after 3 weeks; 30 Gy in 15 fractions in 3 weeks followed by 1.4 Gy twice daily (time gap between 2 fractions were 6 hours for 15 days with a total of 72 Gy in 6 weeks. Response to treatment, compliance, and toxicities were compared in all the three arms. Statistical Analysis Used: Frequency table and chi square tests done. Results: Baseline data were comparable in all the three arms. Complete response in arm A, arm B, and arm C were 15%, 26.315%, and 23.81%, respectively ( P = 0.339. Grade 1 Neutropenia in arm A was 15%, arm B was 26.32%, and arm C was nil (P = 0.0486. Conclusion: Altered fractionation and concurrent chemoradiation showed similar response with comparable acute toxicities except nutropenia, which was significantly higher in arm B.

  5. 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

  6. Use of polar and nonpolar fractions as additional information sources for studying thermoxidized virgin olive oils by FTIR

    Directory of Open Access Journals (Sweden)

    Tena, N.

    2014-09-01

    Full Text Available Fourier transform infrared (FTIR spectroscopy has been proposed to study the degradation of virgin olive oils (VOO in samples undergoing thermoxidation. The polar and nonpolar fractions of oxidized oils have been analyzed by FTIR to provide further information on the minor spectral changes taking place during thermoxidation. This information assists in the interpretation of the spectra of the samples. For this purpose polar and nonpolar fractions of 47 VOO samples thermoxidized (190 °C in a fryer were analyzed by FTIR. The time-course change of the band area assigned to single cis double bonds was explained by their correlation with the decrease in oleic acid (adjusted-R2=0.93. The bands assigned to the hydroxyl groups and the first overtone of ester groups was better studied in the spectra collected for the polar and nonpolar fractions, respectively. The bands assigned to peroxide, epoxy, tertiary alcohols and fatty acids were clearly observed in the spectra of the polar fraction while they are not noticeable in the spectra of the oils.La espectroscopía de infrarrojos por transformada de Fourier (FTIR se ha propuesto para estudiar la degradación de los aceites de oliva vírgenes (AOV sujetas a termoxidación. Las fracciones polares y no polares de aceites oxidados se analizaron mediante FTIR para obtener más información sobre los cambios espectrales menores que tienen lugar durante la termoxidación. Esa información ayuda en la interpretación de los espectros de las muestras puras. Con este objetivo, fracciones polares y no polares de 47 AOV termoxidados (190 °C en una freidora se analizaron mediante FTIR. La banda asignada a dobles enlaces cis se explica por su correlación con la disminución de ácido oleico (R2-ajustado=0,93. Las bandas asignadas a los grupos hidroxilos y del primer sobretono de los grupos éster se estudió mejor en los espectros recogidos para la fracción polar y no polar, respectivamente. Grupos asignados a per

  7. Fractional calculus in bioengineering.

    Science.gov (United States)

    Magin, Richard L

    2004-01-01

    Fractional calculus (integral and differential operations of noninteger order) is not often used to model biological systems. Although the basic mathematical ideas were developed long ago by the mathematicians Leibniz (1695), Liouville (1834), Riemann (1892), and others and brought to the attention of the engineering world by Oliver Heaviside in the 1890s, it was not until 1974 that the first book on the topic was published by Oldham and Spanier. Recent monographs and symposia proceedings have highlighted the application of fractional calculus in physics, continuum mechanics, signal processing, and electromagnetics, but with few examples of applications in bioengineering. This is surprising because the methods of fractional calculus, when defined as a Laplace or Fourier convolution product, are suitable for solving many problems in biomedical research. For example, early studies by Cole (1933) and Hodgkin (1946) of the electrical properties of nerve cell membranes and the propagation of electrical signals are well characterized by differential equations of fractional order. The solution involves a generalization of the exponential function to the Mittag-Leffler function, which provides a better fit to the observed cell membrane data. A parallel application of fractional derivatives to viscoelastic materials establishes, in a natural way, hereditary integrals and the power law (Nutting/Scott Blair) stress-strain relationship for modeling biomaterials. In this review, I will introduce the idea of fractional operations by following the original approach of Heaviside, demonstrate the basic operations of fractional calculus on well-behaved functions (step, ramp, pulse, sinusoid) of engineering interest, and give specific examples from electrochemistry, physics, bioengineering, and biophysics. The fractional derivative accurately describes natural phenomena that occur in such common engineering problems as heat transfer, electrode/electrolyte behavior, and sub

  8. The subcellular fate of cadmium and zinc in the scallop Chlamys nobilis during waterborne and dietary metal exposure

    Energy Technology Data Exchange (ETDEWEB)

    Pan Ke [Department of Biology, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong); Wang Wenxiong [Department of Biology, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong)], E-mail: wwang@ust.hk

    2008-12-11

    Subcellular metal distribution has received increasing attention in aquatic toxicology studies, but the relationship between metal distribution and metal biokinetics remains largely unexplored. A series of short-term experiments on different concentrations of dissolved and dietary metals and on metal elimination were conducted to investigate the dynamics of subcellular distribution of Cd and Zn in the scallop Chlamys nobilis, a bivalve species that is known to accumulate very high concentrations of Cd and Zn in its tissues. Our results showed that, in general, both Cd and Zn were sequestered in insoluble forms (organelles, metal-rich granules, and cellular debris). The main binding pool for the newly acquired metals was organelles for Cd and cellular debris for Zn. Metallothionein-like protein (MTLP) was the most important storage pool for Cd in the scallops. Storage in the non-toxic form both in organelles and MTLP instead of through exocytosis was the major detoxification strategy to control Cd and accounted for the low efflux rate of Cd from scallops. In contrast to Cd, the main binding pool for Zn was cellular debris. Significant changes were found in the scallops when they were challenged with different concentrations of metals in the aqueous and food phases. Such changes provide important information on how scallops handle metals when there is increasing metal uptake. The redistribution of Zn among each subcellular compartment was much faster than the redistribution of Cd, suggesting an effective regulation mechanism for Zn in scallops. Thus, knowing subcellular metal distribution helps in studying the toxicity of both waterborne and dietborne metals.

  9. A randomized study of accelerated fractionation radiotherapy with and without mitomycin C in the treatment of locally advanced head and neck cancer

    DEFF Research Database (Denmark)

    Ezzat, M.; Shouman, T.; Zaza, K.

    2005-01-01

    Objectives: This single-institution study evaluates the feasibility of accelerated fractionation radiotherapy (AF) with and without mitomycin C (MMC) in the treatment of locally advanced head and neck cancer. Patients and Methods: Between May 1998 and October 2001, sixty patients with locally...... advanced stage III and IV of head and neck cancer were randomized into three treatment arms: (1) conventional fractionation radiotherapy (CF) (5 fractions per week); (2) accelerated fractionation radiotherapy (AF) (6 fractions per week); and (3) AF plus Mitomycin C (MMC). Results: The 2-year overall...... survival (OS) of the whole group was 21%. The OS according to treatment arm was 23%, 20%, and 28% in CF, AF, and AF+MMC arms respectively (pMMC respectively (p=0...

  10. Internalization and Subcellular Trafficking of Poly-l-lysine Dendrimers Are Impacted by the Site of Fluorophore Conjugation.

    Science.gov (United States)

    Avaritt, Brittany R; Swaan, Peter W

    2015-06-01

    Internalization and intracellular trafficking of dendrimer-drug conjugates play an important role in achieving successful drug delivery. In this study, we aimed to elucidate the endocytosis mechanisms and subcellular localization of poly-l-lysine (PLL) dendrimers in Caco-2 cells. We also investigated the impact of fluorophore conjugation on cytotoxicity, uptake, and transepithelial transport. Oregon green 514 (OG) was conjugated to PLL G3 at either the dendrimer periphery or the core. Chemical inhibitors of clathrin-, caveolin-, cholesterol-, and dynamin-mediated endocytosis pathways and macropinocytosis were employed to establish internalization mechanisms, while colocalization with subcellular markers was used to determine dendrimer trafficking. Cell viability, internalization, and uptake were all influenced by the site of fluorophore conjugation. Uptake was found to be highly dependent on cholesterol- and dynamin-mediated endocytosis as well as macropinocytosis. Dendrimers were trafficked to endosomes and lysosomes, and subcellular localization was impacted by the fluorophore conjugation site. The results of this study indicate that PLL dendrimers exploit multiple pathways for cellular entry, and internalization and trafficking can be impacted by conjugation. Therefore, design of dendrimer-drug conjugates requires careful consideration to achieve successful drug delivery.

  11. Fractional Derivative as Fractional Power of Derivative

    OpenAIRE

    Tarasov, Vasily E.

    2007-01-01

    Definitions of fractional derivatives as fractional powers of derivative operators are suggested. The Taylor series and Fourier series are used to define fractional power of self-adjoint derivative operator. The Fourier integrals and Weyl quantization procedure are applied to derive the definition of fractional derivative operator. Fractional generalization of concept of stability is considered.

  12. Adenovirus E1A proteins direct subcellular redistribution of Nek9, a NimA-related kinase.

    Science.gov (United States)

    Pelka, Peter; Scimè, Anthony; Mandalfino, Christina; Joch, Monica; Abdulla, Parween; Whyte, Peter

    2007-07-01

    A monoclonal antibody raised against adenovirus E1A-associated cellular proteins recognized Nek9, a NimA-related protein kinase. Subcellular fractionation and immunofluorescence indicated that Nek9 was primarily cytoplasmic with a small portion located in the nucleus whereas E1A was primarily nuclear. Although co-immunoprecipitation experiments indicated that nuclear Nek9 interacted, directly or indirectly, with E1A, the major effect of E1A was to diminish the amount of Nek9 in the nucleus suggesting that E1A alters the subcellular distribution of Nek9 and that the interaction is transient. A Nek9 deletion mutant lacking a central RCC1-like domain interacted stably with E1A and accumulated in the nucleus in the presence of E1A, possibly representing an intermediate stage of the normally transient Nek9/E1A interaction. The interaction of Nek9 with E1A was dependent on the N-terminal sequences of E1A. Attempts to stably overexpress either Nek9 or the kinase-inactive mutant in various cell lines were unsuccessful; however, the presence of E1A allowed stable overexpression of both proteins. These results suggest that E1A disrupts a nuclear function of Nek9.

  13. Subcellular Localization of HIV-1 gag-pol mRNAs Regulates Sites of Virion Assembly.

    Science.gov (United States)

    Becker, Jordan T; Sherer, Nathan M

    2017-03-15

    Full-length unspliced human immunodeficiency virus type 1 (HIV-1) RNAs serve dual roles in the cytoplasm as mRNAs encoding the Gag and Gag-Pol capsid proteins as well as genomic RNAs (gRNAs) packaged by Gag into virions undergoing assembly at the plasma membrane (PM). Because Gag is sufficient to drive the assembly of virus-like particles even in the absence of gRNA binding, whether viral RNA trafficking plays an active role in the native assembly pathway is unknown. In this study, we tested the effects of modulating the cytoplasmic abundance or distribution of full-length viral RNAs on Gag trafficking and assembly in the context of single cells. Increasing full-length viral RNA abundance or distribution had little-to-no net effect on Gag assembly competency when provided in trans In contrast, artificially tethering full-length viral RNAs or surrogate gag-pol mRNAs competent for Gag synthesis to non-PM membranes or the actin cytoskeleton severely reduced net virus particle production. These effects were explained, in large part, by RNA-directed changes to Gag's distribution in the cytoplasm, yielding aberrant subcellular sites of virion assembly. Interestingly, RNA-dependent disruption of Gag trafficking required either of two cis-acting RNA regulatory elements: the 5' packaging signal (Psi) bound by Gag during genome encapsidation or, unexpectedly, the Rev response element (RRE), which regulates the nuclear export of gRNAs and other intron-retaining viral RNAs. Taken together, these data support a model for native infection wherein structural features of the gag-pol mRNA actively compartmentalize Gag to preferred sites within the cytoplasm and/or PM.IMPORTANCE The spatial distribution of viral mRNAs within the cytoplasm can be a crucial determinant of efficient translation and successful virion production. Here we provide direct evidence that mRNA subcellular trafficking plays an important role in regulating the assembly of human immunodeficiency virus type 1 (HIV

  14. Studies on serum protein fractions of patients with uterine cervical cancer undergoing radiotherapy. Relationship between changes in serum protein fractions and prognosis

    Energy Technology Data Exchange (ETDEWEB)

    Onizuka, Keiichiro; Yamada, Hiroki; Uwada, Osamu; Umemura, Yoshiro; Kuroki, Masaomi; Tateyama, Hiromichi (Miyazaki Prefectural Hospital (Japan)); Migita, Shunsuke

    1994-09-01

    The correlation between changes in serum protein fractions and patient prognosis was evaluated. The subjects were 84 patients with uterine cervical cancer treated with combined external pelvic irradiation and intracavitary irradiation using a remote afterloading system (RALS). Twenty one normal women served as controls. Serum levels of 23 protein components were determined before and after radiotherapy. All patients were followed up for 4 to 8 years after radiotherapy. Pretreatment serum levels of prealbumin (Prealb), [alpha][sub 2]HS glycoprotein ([alpha][sub 2]HS), [alpha][sub 2]-plasmin inhibitor ([alpha][sub 2]PI), transferrin (Tf), plasminogen (Pmg), albumin (Alb), IgM, and hemopexin (Hx) were significantly lower in the group of cervical cancer patients than the control group; and serum levels of [alpha][sub 1]-antichymotrypsin ([alpha][sub 1]X), haptoglobin (Hp), C9, fibrinogen (Fib), ceruloplasmin (Cp), [alpha][sub 1]-acid glycoprotein ([alpha][sub 1]AG), [alpha][sub 1]-antitrypsin ([alpha][sub 1]AT), and C4 were elevated. At the completion of radiotherapy, HP, C4, and Fib levels were significantly lower than those before radiotherapy; Prealb, [alpha][sub 2]HS, and [alpha][sub 2]PI were elevated. In patients who survived 4 years and 8 years, pretreatment levels of Cp, [alpha][sub 1]AG, Hp, and C9 were significantly reduced and Tf was elevated, as compared with those who died within 4 years. In those who survived more than 4 years, posttreatment levels of [alpha][sub 1]AT, Hp, [alpha][sub 1]X, Cp, and C9 were significantly reduced, although the serum level of C4 was elevated. Survival positively correlated with pretreatment levels of Tf, Pmg, and [alpha][sub 1]AT, but negatively correlated with AT III, Cp, C1Inh, IgA, [alpha][sub 1]AG, and C9. For posttreatment levels, it positively correlated with Pmg, C4, Prealb, Alb, [alpha][sub 2]M, and Hp, but negatively correlated with Tf, [alpha][sub 2]PI, AT III, [alpha][sub 1]AT, C1Inh, C9, and IgA. (N.K.).

  15. Discrete fractional calculus

    CERN Document Server

    Goodrich, Christopher

    2015-01-01

    This text provides the first comprehensive treatment of the discrete fractional calculus. Experienced researchers will find the text useful as a reference for discrete fractional calculus and topics of current interest. Students who are interested in learning about discrete fractional calculus will find this text to provide a useful starting point. Several exercises are offered at the end of each chapter and select answers have been provided at the end of the book. The presentation of the content is designed to give ample flexibility for potential use in a myriad of courses and for independent study. The novel approach taken by the authors includes a simultaneous treatment of the fractional- and integer-order difference calculus (on a variety of time scales, including both the usual forward and backwards difference operators). The reader will acquire a solid foundation in the classical topics of the discrete calculus while being introduced to exciting recent developments, bringing them to the frontiers of the...

  16. Rate of dehydration, state of subcellular organisation and nature of cryoprotection are critical factors contributing to the variable success of cryopreservation: studies on recalcitrant zygotic embryos of Haemanthus montanus.

    Science.gov (United States)

    Sershen; Berjak, Patricia; Pammenter, N W; Wesley-Smith, James

    2012-01-01

    Effects of sequential procedures required for cryopreservation of embryos excised from the recalcitrant seeds of Haemanthus montanus were assessed ultrastructurally and in conjunction with respiratory activity and the rate of protein synthesis. Fresh material (water content, 5.05 ± 0.92 g g(-1) dry mass) afforded ultrastructural evidence of considerable metabolic activity, borne out by respiratory rates. Neither exposure to glycerol nor sucrose as penetrating and non-penetrating cryoprotectants, respectively, brought about degradative changes, although increased vacuolation and autophagy accompanied both, while respiratory and protein synthetic activity were not adversely affected. Glycerol-cryoprotected embryos flash dried to water contents >0.4 g g(-1) showed organised ultrastructural features and considerable autophagy consistent with metabolic activity, and although respiratory activity was lower, protein synthesis rate was enhanced relative to fresh material. However, at water contents Success, assessed as ≥50% axes forming seedlings after cryogen exposure, was obtained only when glycerol-cryoprotected embryos at water contents >0.4 g g(-1)-in which the degree of vacuolation remained moderate-were rapidly cooled. The outcomes of this study are considered particularly in terms of the stresses imposed by prolonged, relatively slow dehydration and ultimate water contents, on embryos showing considerable metabolic activity.

  17. Left Ventricular Longitudinal Systolic Function in Septic Shock Patients with Normal Ejection Fraction: A Case-control Study.

    Science.gov (United States)

    Zhang, Hong-Min; Wang, Xiao-Ting; Zhang, Li-Na; He, Wei; Zhang, Qing; Liu, Da-Wei

    2017-05-20

    Septic cardiomyopathy is a common finding in septic shock patients. The accepted definition of septic cardiomyopathy is often based on the left ventricular ejection fraction (LVEF). The aim of this study was to determine whether the left ventricular longitudinal systolic function was more sensitive than the LVEF in heart function appraisal of septic shock patients. This was a case-control study conducted at a 40-bed Intensive Care Unit (ICU) of Peking Union Medical College Hospital. Septic shock patients admitted to the ICU were consecutively enrolled in the study group from March 1, 2016 to September 1, 2016. The control group was selected from nonsepsis patients who were admitted to the ICU and were comparable to the study group. Transthoracic echocardiography was performed to obtain the LVEF measurement, mitral annular plane systolic excursion (MAPSE), tissue Doppler velocity measurement of mitral annulus (Sa), and tricuspid annular plane systolic excursion. The study group consisted of 45 septic shock patients. Another 45 nonsepsis patients were selected as the control group. There was no difference in the LVEF between the two groups (64.6% vs. 67.2%, t= -1.426, P= 0.161). MAPSE in the study group was much lower than in the control group (1.2 cm vs. 1.5 cm, t= -4.945, Pstudy group was also lower than in the control group (10.2 cm/s vs. 11.8 cm/s, t = -2.796, P= 0.014). Compared to the LVEF, longitudinal systolic function might be more sensitive in the detection of cardiac depression in septic shock patients. In the heart function appraisal of septic shock patients with a normal ejection fraction, more attention should be given to longitudinal function parameters such as MAPSE and Sa.

  18. Meta-analysis of diffusion tensor imaging studies shows altered fractional anisotropy occurring in distinct brain areas in association with depression.

    LENUS (Irish Health Repository)

    Murphy, Melissa L

    2011-09-01

    Fractional anisotropy anomalies occurring in the white matter tracts in the brains of depressed patients may reflect microstructural changes underlying the pathophysiology of this disorder. We conducted a meta-analysis of fractional anisotropy abnormalities occurring in major depressive disorder using voxel-based diffusion tensor imaging studies. Using the Embase, PubMed and Google Scholar databases, 89 relevant data sets were identified, of which 7 (including 188 patients with major depressive disorder and 221 healthy controls) met our inclusion criteria. Authors were contacted to retrieve any additional data required. Coordinates were extracted from clusters of significant white matter fractional anisotropy differences between patients and controls. Relevant demographic, clinical and methodological variables were extracted from each study or obtained directly from authors. The meta-analysis was carried out using Signed Differential Mapping. Patients with depression showed decreased white matter fractional anisotropy values in the superior longitudinal fasciculus and increased fractional anisotropy values in the fronto-occipital fasciculus compared to controls. Using quartile and jackknife sensitivity analysis, we found that reduced fractional anisotropy in the left superior longitudinal fasciculus was very stable, with increases in the right fronto-occipital fasciculus driven by just one study. In conclusion, our meta-analysis revealed a significant reduction in fractional anisotropy values in the left superior longitudinal fasciculus, which may ultimately play an important role in the pathology of depression.

  19. Meta-analysis of diffusion tensor imaging (DTI) studies shows altered fractional anisotropy occurring in distinct brain areas in association with depression

    LENUS (Irish Health Repository)

    Murphy, Melissa L

    2011-09-27

    Abstract Fractional anisotropy anomalies occurring in the white matter tracts in the brains of depressed patients may reflect microstructural changes underlying the pathophysiology of this disorder. We conducted a meta-analysis of fractional anisotropy abnormalities occurring in major depressive disorder using voxel-based diffusion tensor imaging studies. Using the Embase, PubMed and Google Scholar databases, 89 relevant data sets were identified, of which 7 (including 188 patients with major depressive disorder and 221 healthy controls) met our inclusion criteria. Authors were contacted to retrieve any additional data required. Coordinates were extracted from clusters of significant white matter fractional anisotropy differences between patients and controls. Relevant demographic, clinical and methodological variables were extracted from each study or obtained directly from authors. The meta-analysis was carried out using Signed Differential Mapping. Patients with depression showed decreased white matter fractional anisotropy values in the superior longitudinal fasciculus and increased fractional anisotropy values in the fronto-occipital fasciculus compared to controls. Using quartile and jackknife sensitivity analysis, we found that reduced fractional anisotropy in the left superior longitudinal fasciculus was very stable, with increases in the right fronto-occipital fasciculus driven by just one study. In conclusion, our meta-analysis revealed a significant reduction in fractional anisotropy values in the left superior longitudinal fasciculus, which may ultimately play an important role in the pathology of depression.

  20. 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.

  1. Functional analysis of Plasmodium vivax VIR proteins reveals different subcellular localizations and cytoadherence to the ICAM-1 endothelial receptor.

    Science.gov (United States)

    Bernabeu, M; Lopez, F J; Ferrer, M; Martin-Jaular, L; Razaname, A; Corradin, G; Maier, A G; Del Portillo, H A; Fernandez-Becerra, C

    2012-03-01

    The subcellular localization and function of variant subtelomeric multigene families in Plasmodium vivax remain vastly unknown. Among them, the vir superfamily is putatively involved in antigenic variation and in mediating adherence to endothelial receptors. In the absence of a continuous in vitro culture system for P. vivax, we have generated P. falciparum transgenic lines expressing VIR proteins to infer location and function. We chose three proteins pertaining to subfamilies A (VIR17), C (VIR14) and D (VIR10), with domains and secondary structures that predictably traffic these proteins to different subcellular compartments. Here, we showed that VIR17 remained inside the parasite and around merozoites, whereas VIR14 and VIR10 were exported to the membrane of infected red blood cells (iRBCs) in an apparent independent pathway of Maurer's clefts. Remarkably, VIR14 was exposed at the surface of iRBCs and mediated adherence to different endothelial receptors expressed in CHO cells under static conditions. Under physiological flow conditions, however, cytoadherence was only observed to ICAM-1, which was the only receptor whose adherence was specifically and significantly inhibited by antibodies against conserved motifs of VIR proteins. Immunofluorescence studies using these antibodies also showed different subcellular localizations of VIR proteins in P. vivax-infected reticulocytes from natural infections. These data suggest that VIR proteins are trafficked to different cellular compartments and functionally demonstrates that VIR proteins can specifically mediate cytoadherence to the ICAM-1 endothelial receptor. © 2011 Blackwell Publishing Ltd.

  2. pH and salinity evolution of Europa's brines: Raman spectroscopy study of fractional precipitation at 1 and 300 bar.

    Science.gov (United States)

    Muñoz-Iglesias, Victoria; Bonales, Laura J; Prieto-Ballesteros, Olga

    2013-08-01

    Several lines of evidence indicate the existence of salty liquid water below the icy surface of the satellite Europa. Depending on the chemical composition of the original interior brines, minerals that precipitate will be varied as will be the resulting physicochemical parameters of the evolving solutions such as pH and salinity. These parameters are determinants apropos to the study of the possible habitability of the satellite. In this work, experiments of fractional precipitation by cooling of several brines with different chemical composition (acid, alkaline, and neutral) were performed at 1 and 300 bar. The gradual decrease in temperature leads to mineral precipitation and changes in salinity and pH values. During the experiment, Raman spectroscopy was used to analyze quantitatively the variation of the salt concentration in the aqueous solutions. The obtained laboratory data indicate the manner in which cryomagma differentiation might occur on Europa. These endogenous processes of differentiation require planetary energy, which seems to have been plentiful during Europa's geological history. Ultimately, the dissipation of part of that energy is translated to a higher complexity of the cryopetrology in Europa's crust. From the results, we conclude that fractional differentiation processes of briny cryomagmas produce several types of igneous salty mineral suites on icy moons.

  3. PILOT STUDY: An international comparison of mass fraction purity assignment of theophylline: CCQM Pilot Study CCQM-P20.e (Theophylline)

    Science.gov (United States)

    Westwood, S.; Josephs, R.; Daireaux, A.; Wielgosz, R.; Davies, S.; Kang, M.; Ting, H.; Phillip, R.; Malz, F.; Shimizu, Y.; Frias, E.; Pérez, M.; Apps, P.; Fernandes-Whaley, M.; DeVos, B.; Wiangnon, K.; Ruangrittinon, N.; Wood, S.; Duewer, D.; Schantz, M.; Bedner, M.; Hancock, D.; Esker, J.

    2009-01-01

    Under the auspices of the Organic Analysis Working Group (OAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM) a laboratory comparison, CCQM-P20.e, was coordinated by the Bureau International de Poids et Mesures (BIPM) in 2006/2007. Nine national measurement institutes, two expert laboratories and the BIPM participated in the comparison. Participants were required to assign the mass fraction of theophylline present as the main component in two separate study samples (CCQM-P20.e.1 and CCQM-P20.e.2). CCQM-P20.e.1 consisted of a high-purity theophylline material obtained from a commercial supplier. CCQM-P20.e.2 consisted of theophylline to which known amounts of the related structure compounds theobromine and caffeine were added in a homogenous, gravimetrically controlled fashion. For the CCQM-P20.e.2 sample it was possible to estimate gravimetric reference values both for the main component and for the two spiked impurities. In addition to assigning the mass fraction content of theophylline for both materials, participants were requested but not obliged to provide mass fraction estimates for the minor components they identified in each sample. The results reported by the study participants for the mass fraction content of theophylline in both materials showed good levels of agreement both with each other and with the gravimetric reference value assigned to the CCQM-P20.e.2 material. There was also satisfactory agreement overall, albeit at higher levels of uncertainty, in the quantification data reported for the minor components present in both samples. In the few cases where a significant deviation was observed from the consensus values reported by the comparison participants or gravimetric reference values where these where available, they appeared to arise from the use of non-optimal chromatographic separation conditions. The results demonstrate the feasibility for laboratories to assign mass fraction content with associated absolute expanded

  4. Dermal toxicity studies of technical polychlorinated biphenyls and fractions thereof in rabbits

    NARCIS (Netherlands)

    Vos, J.G.; Beems, R.B.

    A significant difference in toxicity between 3 polychlorinated biphenyl (PCB) preparations was found in a prior study: Clophen A 60 and Phenoclor DP6 showing the highest, Aroclor 1260 the lowest, toxicity (Vos and Koeman, 1970). A subsequent study revealed the presence of tetra- and

  5. Subcellular location and species specificity of pipecolate degradation

    Energy Technology Data Exchange (ETDEWEB)

    Mihalik, S.J.; Rhead, W.J.

    1986-03-05

    Defects in pipecolic acid (PA) catabolism are characteristic of several inherited metabolic diseases including hyperpipecolic acidemia, Zellweger's Syndrome, neonatal-onset adrenoleukodystrophy, and infantile Refsum's disease. In the latter three diseases, peroxisomes are abnormal. The authors have studied the subcelluar distribution of the PA degradation to determine a mammalian model for the normal pathway. Crude light and heavy mitochondrial fractions (including lysosomes and peroxisomes) from kidney cortex or liver were separated on Percoll gradients. Individual fractions were then incubated at 37/sup 0/C with 3H-2,3,4,5,6 L-PA. Using ion exchange chromatography, the production of 3H ..cap alpha..-aminoadipic acid (AAA) and 3H-H2O were quantitated. AAA production paralleled the activity of the mitochondrial marker enzyme, glutamate dehydrogenase, in the rabbit, guinea pig, dog, pig, and sheep. 3H-AAA production ranged from 382 to 13,900 pmol/mg prot/h. Guinea pig kidney cortex exhibited highest specific activity. The mitochondrial enzyme was absent from human liver (n=3) and liver and kidney cortex from rat, mouse, and monkey. In these tissues, the activity followed the pattern of the peroxisomal core enzyme, urate oxidase.

  6. Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns

    Directory of Open Access Journals (Sweden)

    Alicia Lundby

    2012-08-01

    Full Text Available Lysine acetylation is a major posttranslational modification involved in a broad array of physiological functions. Here, we provide an organ-wide map of lysine acetylation sites from 16 rat tissues analyzed by high-resolution tandem mass spectrometry. We quantify 15,474 modification sites on 4,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals that the subcellular acetylation distribution is tissue-type dependent and that acetylation targets tissue-specific pathways involved in fundamental physiological processes. We compare lysine acetylation patterns for rat as well as human skeletal muscle biopsies and demonstrate its general involvement in muscle contraction. Furthermore, we illustrate that acetylation of fructose-bisphosphate aldolase and glycerol-3-phosphate dehydrogenase serves as a cellular mechanism to switch off enzymatic activity.

  7. Silicon modifies root anatomy, and uptake and subcellular distribution of cadmium in young maize plants.

    Science.gov (United States)

    Vaculík, Marek; Landberg, Tommy; Greger, Maria; Luxová, Miroslava; Stoláriková, Miroslava; Lux, Alexander

    2012-07-01

    Silicon (Si) has been shown to ameliorate the negative influence of cadmium (Cd) on plant growth and development. However, the mechanism of this phenomenon is not fully understood. Here we describe the effect of Si on growth, and uptake and subcellular distribution of Cd in maize plants in relation to the development of root tissues. Young maize plants (Zea mays) were cultivated for 10 d hydroponically with 5 or 50 µm Cd and/or 5 mm Si. Growth parameters and the concentrations of Cd and Si were determined in root and shoot by atomic absorption spectrometry or inductively coupled plasma mass spectroscopy. The development of apoplasmic barriers (Casparian bands and suberin lamellae) and vascular tissues in roots were analysed, and the influence of Si on apoplasmic and symplasmic distribution of (109)Cd applied at 34 nm was investigated between root and shoot. Si stimulated the growth of young maize plants exposed to Cd and influenced the development of Casparian bands and suberin lamellae as well as vascular tissues in root. Si did not affect the distribution of apoplasmic and symplasmic Cd in maize roots, but considerably decreased symplasmic and increased apoplasmic concentration of Cd in maize shoots. Differences in Cd uptake of roots and shoots are probably related to the development of apoplasmic barriers and maturation of vascular tissues in roots. Alleviation of Cd toxicity by Si might be attributed to enhanced binding of Cd to the apoplasmic fraction in maize shoots.

  8. Kinetic study on unsaponifiable fraction changes and lactose hydrolysis during storage of Mozzarella di Bufala Campana PDO cheese.

    Science.gov (United States)

    Manzi, Pamela; Pizzoferrato, Laura

    2009-01-01

    Cholesterol, vitamin E and vitamin A isomers, components of the unsaponifiable fraction, and lactose contents in Mozzarella di Bufala Campana PDO cheese have been studied during storage in different conditions: at 6-8 degrees C, and at room temperature (traditional habits). During cold storage there were no significant differences in the unsaponifiable compounds, while during storage at room temperature an increase of the 13-cis isomer and a decrease of all-trans-retinol were observed. Trans/cis-retinol isomerization, expressed as the Degree of Retinol Isomerization (13-cis/all-trans%) showed an increase in all samples during storage at room temperature following a linear correlation. The decrease of lactose content during storage was studied by a first-order differential relaxation equation. Apart from the traditional habits, consumers should be aware that, during storage at room temperature, the most important changes in the considered nutrients occur. These changes can be negative (vitamin A reduction) but also positive (lactose reduction).

  9. In Vitro Study on Glucose Utilization Capacity of Bioactive Fractions of Houttuynia cordata in Isolated Rat Hemidiaphragm and Its Major Phytoconstituent.

    Science.gov (United States)

    Kumar, Manish; Prasad, Satyendra K; Hemalatha, Siva

    2016-01-01

    Objective. The whole plant of Houttuynia cordata has been reported to have potent antihyperglycemic activity. Therefore, the present study was undertaken to investigate the glucose utilization capacity of bioactive fractions of ethanol extract of Houttuynia cordata (HC) in isolated rat hemidiaphragm. Methods. All the fractions, that is, aqueous (AQ), hexane (HEX), chloroform (CHL), and ethyl acetate (EA), obtained from ethanol extract of H. cordata were subjected to phytochemical standardization use in quercetin as a marker with the help of HPTLC. Further, glucose utilization capacity by rat hemidiaphragm was evaluated in 12 different sets of in vitro experiments. In the study, different fractions from H. cordata as mentioned above were evaluated, where insulin was used as standard and quercetin as a biological standard. Results. Among all the tested fractions, AQ and EA significantly increased glucose uptake by isolated rat hemidiaphragm compared to negative control. Moreover, AQ fractions enhanced the uptake of glucose significantly (p fractions may be attributed to the presence of quercetin, which was found to be 7.1 and 3.2% w/w, respectively, in both the fractions.

  10. In Vitro Study on Glucose Utilization Capacity of Bioactive Fractions of Houttuynia cordata in Isolated Rat Hemidiaphragm and Its Major Phytoconstituent

    Directory of Open Access Journals (Sweden)

    Manish Kumar

    2016-01-01

    Full Text Available Objective. The whole plant of Houttuynia cordata has been reported to have potent antihyperglycemic activity. Therefore, the present study was undertaken to investigate the glucose utilization capacity of bioactive fractions of ethanol extract of Houttuynia cordata (HC in isolated rat hemidiaphragm. Methods. All the fractions, that is, aqueous (AQ, hexane (HEX, chloroform (CHL, and ethyl acetate (EA, obtained from ethanol extract of H. cordata were subjected to phytochemical standardization use in quercetin as a marker with the help of HPTLC. Further, glucose utilization capacity by rat hemidiaphragm was evaluated in 12 different sets of in vitro experiments. In the study, different fractions from H. cordata as mentioned above were evaluated, where insulin was used as standard and quercetin as a biological standard. Results. Among all the tested fractions, AQ and EA significantly increased glucose uptake by isolated rat hemidiaphragm compared to negative control. Moreover, AQ fractions enhanced the uptake of glucose significantly (p<0.05 and was found to be more effective than insulin. Conclusions. The augmentation in glucose uptake by hemidiaphragm in presence of AQ and EA fractions may be attributed to the presence of quercetin, which was found to be 7.1 and 3.2% w/w, respectively, in both the fractions.

  11. A prospective, split-face, randomized study of the efficacy and safety of a novel fractionated intense pulsed light treatment for melasma in Asians.

    Science.gov (United States)

    Yun, Woo Jin; Lee, Sang Min; Han, Ji Su; Lee, Sang Hyung; Chang, Seo Youn; Haw, Sik; Lee, Jung Bok; Won, Chong Hyun; Lee, Mi Woo; Choi, Jee Ho; Chang, Sung Eun

    2015-01-01

    Intense pulsed light (IPL) has been reported to effectively treat melasma in previous studies, but an aggravation of pigmentation was noted. Fractionated IPL is a novel technique in which microsecond-domain fractionated pulses are delivered to the target area. To compare the safety and efficacy of low-fluency, frequently scheduled fractionated IPL and conventional IPL for melasma treatment. This was a 14-week, split-face study in which 30 Asian women were treated with weekly fractionated IPL on one side of the face and biweekly conventional IPL on the other side. The non-inferiority of a weekly fractionated IPL regimen to a biweekly conventional IPL regimen was verified by a lower margin of the 95% confidence interval for the difference in the Melasma Area and Severity Index (MASI) change from baseline of 2.61 for each side. This value was greater than the previously determined non-inferiority margin of -2.68 (P IPL side, the modified MASI score decreased continuously, but in the conventional IPL group, the MASI score rebounded during the treatment course. Fractionated IPL shows moderate efficacy as a melasma treatment and is therefore a good alternative to conventional IPL as there is no indication of melasma exacerbation. Fractionated IPL can also be used as a maintenance treatment for melasma.

  12. Fractional complex transform for fractional differential equations

    National Research Council Canada - National Science Library

    Lİ, Zheng Biao; HE, Ji Huan

    2010-01-01

    Fractional complex transform is proposed to convert fractional differential equations into ordinary differential equations, so that all analytical methods devoted to advanced calculus can be easily...

  13. Metal-induced stress in bivalves living along a gradient of Cd contamination: relating sub-cellular metal distribution to population-level responses

    Energy Technology Data Exchange (ETDEWEB)

    Perceval, Olivier [Groupe de recherche interuniversitaire en limnologie (GRIL), Departement de sciences biologiques, Universite de Montreal, C.P. 6128, Succursale Centre-ville, Montreal, Que., H3C 3J7 (Canada)], E-Mail: olivier.perceval@umontreal.ca; Couillard, Yves [Division de l' evaluation des Produits Chimiques, Environnement Canada, Place Vincent Massey, 351 Bd Saint-Joseph, Hull, Que., K1A 0H3 (Canada); Pinel-Alloul, Bernadette [Groupe de recherche interuniversitaire en limnologie (GRIL), Departement de sciences biologiques, Universite de Montreal, C.P. 6128, Succursale Centre-ville, Montreal, Que., H3C 3J7 (Canada); Giguere, Anik [INRS-ETE, Universite du Quebec, C.P. 7500, 2800 rue Einstein, Sainte-Foy, Que., G1V 4C7 (Canada); Campbell, Peter G.C. [INRS-ETE, Universite du Quebec, C.P. 7500, 2800 rue Einstein, Sainte-Foy, Que., G1V 4C7 (Canada)

    2004-09-20

    The use of biomarkers to assess the impacts of contaminants on aquatic ecosystems has noticeably increased over the past few years. Few of these studies, however, have contributed to the prediction of ecologically significant effects (i.e., at the population or community levels). The present field study was designed to evaluate the potential of metallothionein (MT) and sub-cellular metal partitioning measurements for predicting toxic effects at higher levels of the biological organization in freshwater bivalves (Pyganodon grandis) chronically exposed to Cd. For that purpose, we quantitatively sampled P. grandis populations in the littoral zone of nine lakes on the Precambrian Canadian Shield during two consecutive summers (1998 and 1999); lakes were characterized by contrasting Cd levels but similar trophic status. We tested relationships between the population status of P. grandis (i.e., growth parameters, density, biomass, secondary production, turnover ratio and cumulative fecundity) and (i) ambient Cd concentrations, (ii) sub-organismal responses (MT concentrations in the gill cytosol of individuals and Cd concentrations in three metal-ligand pools identified as M-HMW, the high molecular weight pool, M-MT, the metallothionein-like pool and M-LMW, the low molecular weight pool) and (iii) ecological confounding factors (food resources, presence of host fishes for the obligatory parasitic larval stage of P. grandis). Our results show that littoral density, live weight, dry viscera biomass, production and cumulative fecundity decreased with increasing concentrations of the free-cadmium ion in the environment (Pearson's r ranging from -0.63 to -0.78). On the other hand, theoretical maximum shell lengths (L{sub {infinity}}) in our populations were related to both the dissolved Ca concentration and food quality (sestonic C and N concentrations). Overall, Cd concentrations in the gill cytosolic HMW pool of the individual molluscs were the biomarker response that

  14. Fractional Processes and Fractional-Order Signal Processing Techniques and Applications

    CERN Document Server

    Sheng, Hu; Qiu, TianShuang

    2012-01-01

    Fractional processes are widely found in science, technology and engineering systems. In Fractional Processes and Fractional-order Signal Processing, some complex random signals, characterized by the presence of a heavy-tailed distribution or non-negligible dependence between distant observations (local and long memory), are introduced and examined from the ‘fractional’ perspective using simulation, fractional-order modeling and filtering and realization of fractional-order systems. These fractional-order signal processing (FOSP) techniques are based on fractional calculus, the fractional Fourier transform and fractional lower-order moments. Fractional Processes and Fractional-order Signal Processing: • presents fractional processes of fixed, variable and distributed order studied as the output of fractional-order differential systems; • introduces FOSP techniques and the fractional signals and fractional systems point of view; • details real-world-application examples of FOSP techniques to demonstr...

  15. Dynamic subcellular localization of a respiratory complex controls bacterial respiration.

    Science.gov (United States)

    Alberge, François; Espinosa, Leon; Seduk, Farida; Sylvi, Léa; Toci, René; Walburger, Anne; Magalon, Axel

    2015-06-16

    Respiration, an essential process for most organisms, has to optimally respond to changes in the metabolic demand or the environmental conditions. The branched character of their respiratory chains allows bacteria to do so by providing a great metabolic and regulatory flexibility. Here, we show that the native localization of the nitrate reductase, a major respiratory complex under anaerobiosis in Escherichia coli, is submitted to tight spatiotemporal regulation in response to metabolic conditions via a mechanism using the transmembrane proton gradient as a cue for polar localization. These dynamics are critical for controlling the activity of nitrate reductase, as the formation of polar assemblies potentiates the electron flux through the complex. Thus, dynamic subcellular localization emerges as a critical factor in the control of respiration in bacteria.

  16. Isotope Fractionation in Methane Reactions Studied by Gas Chromatography and Liquid Scintillation

    DEFF Research Database (Denmark)

    Andersen, Bertel Lohmann; Bidoglio, G.; Leip, A.

    1997-01-01

    Determination of C-14-marked methane by gas chromatography and liquid scintillation counting is shown to be useful in studies of isotope effects. Data on the specific activity is used to separate the contributions of (CH4)-C-14, and (CH4)-C-12 to the gas-chromatographic peak area. As an application...

  17. Silicon isotope fractionation between rice plants and nutrient solution and its significance to the study of the silicon cycle

    Science.gov (United States)

    Ding, T. P.; Tian, S. H.; Sun, L.; Wu, L. H.; Zhou, J. X.; Chen, Z. Y.

    2008-12-01

    The silicon isotope fractionation between rice plant and nutrient solution was studied experimentally. Rice plants were grown to maturity with the hydroponic culture in a naturally lit glasshouse. The nutrient solution was sampled for 14 times during the whole rice growth period. The rice plants were collected at various growth stages and different parts of the plants were sampled separately. The silica contents of the samples were determined by the gravimetric method and the silicon isotope compositions were measured using the SiF 4 method. In the growth process, the silicon content in the nutrient solution decreased gradually from 16 mM at starting stage to 0.1-0.2 mM at harvest and the amount of silica in single rice plant increased gradually from 0.00013 g at start to 4.329 g at harvest. Within rice plant the SiO 2 fraction in roots reduced continuously from 0.23 at the seedling stage, through 0.12 at the tiller stage, 0.05 at the jointing stage, 0.023 at the heading stage, to 0.009 at the maturity stage. Accordingly, the fraction of SiO 2 in aerial parts increased from 0.77, through 0.88, 0.95, 0.977, to 0.991 for the same stages. The silicon content in roots decreased from the jointing stage, through the heading stage, to the maturity stage, parallel to the decrease of silicon content in the nutrient solution. At the maturity stage, the silicon content increased from roots, through stem and leaves, to husks, but decreased drastically from husks to grains. These observations show that transpiration and evaporation may play an important role in silica transportation and precipitation within rice plants. It was observed that the δ30Si of the nutrient solution increased gradually from -0.1‰ at start to 1.5‰ at harvest, and the δ30Si of silicon absorbed by bulk rice plant increased gradually from -1.72‰ at start to -0.08‰ at harvest, reflecting the effect of the kinetic silicon isotope fractionation during silicon absorption by rice plants from nutrient

  18. Subcellular localization and displacement by diuretics of the peripheral benzodiazepine binding site (PBS) from rat kidney

    Energy Technology Data Exchange (ETDEWEB)

    Lukeman, S.; Fanestil, D.

    1986-03-05

    Although the PBS has been identified in many organs, its function and cellular location are speculative. Using rapid filtration, binding of (/sup 3/H)RO 5-4864 (*RO) (.75 nM) was assessed in four subcellular fractions (.3 mg/ml) derived from depapillated rat kidney by differential centrifugation: N (450g x 2 min), O (13,000 x 10), P (105,000 x 30), and S. The binding distribution was: N-18%, O-74%, P-6%, and S-2%. Marker enzyme analysis revealed that O was enriched in mitochondria (M), lysosomes (L), peroxisomes (P), and endoplasmic reticulum (ER), but not plasma membrane, and that N contained small amounts (10-15%) of markers for the above. Repeated washing of O removed ER enzymes but preserved *RO binding. O was further fractionated with centrifugation (57,000g x 4 hr) on a linear sucrose gradient (18-65%); *RO binding then comigrated with M but not P and L markers. Centrifugation of isolated M (5500 x 10 min) on another linear sucrose gradient (37-65%) gave low and high density bands, which contained 65% and 35% of *RO binding activity, resp. *RO binding in O was specific, saturable, reversible, and inhibited by diuretics. Inhibitors with the highest potency were indacrinone (K/sub d/ = 35 ..mu..M), hydrochlorothiazide (100 ..mu..M), and ethacrynic acid (325 ..mu..M). Low potency inhibitors (K/sub d/ greater than or equal to 1 mM) included amiloride, triamterene, furosemide, bumetanide, and ozolinone.

  19. Prolactin-induced Subcellular Targeting of GLUT1 Glucose Transporter in Living Mammary Epithelial Cells.

    Science.gov (United States)

    Riskin, Arieh; Mond, Yehudit

    2015-10-26

    Studying the biological pathways involved in mammalian milk production during lactation could have many clinical implications. The mammary gland is unique in its requirement for transport of free glucose into the cell for the synthesis of lactose, the primary carbohydrate in milk. To study GLUT1 trafficking and subcellular targeting in living mammary epithelial cells (MEC) in culture. Immunocytochemistry was used to study GLUT1 hormonally regulated subcellular targeting in human MEC (HMEC). To study GLUT1 targeting and recycling in living mouse MEC (MMEC) in culture, we constructed fusion proteins of GLUT1 and green fluorescent protein (GFP) and expressed them in CIT3 MMEC. Cells were maintained in growth medium (GM), or exposed to secretion medium (SM), containing prolactin. GLUT1 in HMEC localized primarily to the plasma membrane in GM. After exposure to prolactin for 4 days, GLUT1 was targeted intracellularly and demonstrated a perinuclear distribution, co-localizing with lactose synthetase. The dynamic trafficking of GFP-GLUT1 fusion proteins in CIT3 MMEC suggested a basal constitutive GLUT1 recycling pathway between an intracellular pool and the cell surface that targets most GLUT1 to the plasma membrane in GM. Upon exposure to prolactin in SM, GLUT1 was specifically targeted intracellularly within 90-110 minutes. Our studies suggest intracellular targeting of GLUT1 to the central vesicular transport system upon exposure to prolactin. The existence of a dynamic prolactin-induced sorting machinery for GLUT1 could be important for transport of free glucose into the Golgi for lactose synthesis during lactation.

  20. Uptake and subcellular distribution of triclosan in typical hydrophytes under hydroponic conditions.

    Science.gov (United States)

    He, Yupeng; Nie, Enguang; Li, Chengming; Ye, Qingfu; Wang, Haiyan

    2017-01-01

    The increasing discharge of pharmaceuticals and personal care products (PPCPs) into the environment has generated serious public concern. The recent awareness of the environmental impact of this emerging class of pollutants and their potential adverse effects on human health have been documented in many reports. However, information regarding uptake and intracellular distribution of PPCPs in hydrophytes under hydroponic conditions, and potential human exposure is very limited. A laboratory experiment was conducted using 14C-labeled triclosan (TCS) to investigate uptake and distribution of TCS in six aquatic plants (water spinach, purple perilla, cress, penny grass, cane shoot, and rice), and the subcellular distribution of 14C-TCS was determined in these plants. The results showed that the uptake and removal rate of TCS from nutrient solution by hydrophytes followed the order of cress (96%) > water spinach (94%) > penny grass (87%) > cane shoot (84%) > purple perilla (78%) > rice (63%) at the end of incubation period (192 h). The range of 14C-TCS content in the roots was 94.3%-99.0% of the added 14C-TCS, and the concentrations in roots were 2-3 orders of magnitude greater than those in shoots. Furthermore, the subcellular fraction-concentration factor (3.6 × 102-2.6 × 103 mL g-1), concentration (0.58-4.47 μg g-1), and percentage (30%-61%) of 14C-TCS in organelles were found predominantly greater than those in cell walls and/or cytoplasm. These results indicate that for these plants, the roots are the primary storage for TCS, and within plant cells organelles are the major domains for TCS accumulation. These findings provide a better understanding of translocation and accumulation of TCS in aquatic plants at the cellular level, which is valuable for environmental and human health assessments of TCS. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Drive tube 60009 - A chemical study of magnetic separates of size fractions from five strata. [lunar soil analysis

    Science.gov (United States)

    Blanchard, D. P.; Jacobs, J. W.; Brannon, J. C.; Brown, R. W.

    1976-01-01

    Each bulk soil and both the magnetic and nonmagnetic components of the 90-150 micron and below 20 micron fractions of five soils from drive tube 60009 were analyzed. Samples were analyzed for FeO, Na2O, Sc, Cr, Co, Ni, Hf, Ta, Th, La, Ce, Sm, Eu, Tb, Yb, and Lu by neutron activation analysis. Several samples were fused and analyzed for major elements by electron microprobe analysis. Compositional variations are not systematically related to depth. The compositions of the five soils studied are well explained by a two-component mixing model whose end members are a submature Apollo 16-type soil and an extremely immature anorthositic material similar to 60025. There is evidence that the anorthositic component had received a small amount of exposure before these soils were mixed. After mixing, the soils received little exposure suggesting mixing and deposition on a rapid time scale.

  2. Triplet fraction buildup effect of the DNA-YOYO complex studied with fluorescence correlation spectroscopy.

    Science.gov (United States)

    Shimizu, Masafumi; Sasaki, Satoshi; Kinjo, Masataka

    2007-07-01

    DNA fragments of various lengths and YOYO-1 iodide (YOYO) were mixed at various ratios, and fluorescence was measured using fluorescence correlation spectroscopy. The number of substantially emitting YOYO molecules binding to the DNA and the binding intervals between the YOYO molecules were estimated for DNA-YOYO complexes of various lengths. In the present study, we found an interesting phenomenon: triplet buildup. Because fluorophores that fall into the triplet state do not emit fluorescence, a part of the dark period can be recovered by emitting photons from other excited YOYO molecules in the same DNA strings in the confocal elements. The remaining dark period can be considered to be the total miss-emission rate. Estimates of the total miss-emission rate are important for calculation of the length and amount of DNA.

  3. Co-digestion performance of organic fraction of municipal solid waste with leachate: Preliminary studies.

    Science.gov (United States)

    Guven, Huseyin; Akca, Mehmet Sadik; Iren, Erol; Keles, Fatih; Ozturk, Izzet; Altinbas, Mahmut

    2017-05-04

    The main aim of the study was to evaluate the co-digestion performance of OFMSW with different wastes. Leachate, reverse osmosis (RO) concentrate collected from a leachate treatment facility and dewatered sewage sludge taken from a wastewater treatment plant (WWTP) were used for co-digestion in this paper. An extra effort was made to observe the effect of leachate inclusion in the co-digestion. In the study, the mono-digestion of OFMSW, leachate, RO concentrate and sewage sludge as well as digestion of 7 different waste mixtures were carried out for this objective. The experiments were carried out for approximately 50days under mesophilic conditions. The highest methane yield was 785L CH4/kg VSadded in the reactor, which had only OFMSW. While the methane yield derived from OFMSW was found higher than previous studies, methane yield of leachate was found to be 110L CH4/kg VSadded, which was lower than findings in the literature. The mono-substrate of OFMSW was followed by the reactor of having waste mixture of leachate+sewage sludge+OFMSW+water (C7) with 391L CH4/kg VSadded, which was the only combination included water. In order to understand the effect of leachate and water inclusions on co-digestion, two separate waste combinations; leachate+sewage sludge+OFMSW+water (C7) and leachate+sewage sludge+OFMSW (C1) were prepared that had different amounts of leachate but same amounts of other wastes. The methane yield of leachate+sewage sludge+OFMSW+water (C7) indicated that addition of some water instead of leachate could stimulate biogas production. Methane yield of this reactor was found to be 71% higher than the waste combination of leachate+sewage sludge+OFMSW (C1). It could be thought that the high amount of non-biodegradable matters in leachate could be responsible for lower methane yield in leachate+sewage sludge+OFMSW (C1) reactor. Methane yields of the reactors showed that co-digestion of OFMSW and leachate could be a solution not only for treatment of

  4. Analyses élémentaires (carbone,hydrogène,oxygène,azote,soufre des fractions lourdes du pétrole. Elemental Analysis (Carbon,Hydrogen,Oxygen,Nitrogen,Sulfur of Heavy Oil Fractions Bibliographic Study

    Directory of Open Access Journals (Sweden)

    Barbelet M.

    2006-11-01

    Full Text Available La détermination des éléments carbone, hydrogène, oxygène, azote, soufre est essentielle pour la connaissance des fractions lourdes du pétrole. Cette étude bibliographique présente les principales méthodes d'analyse élémentaire utilisées dans ce domaine. On décrit les méthodes de minéralisation, de détection, et l'évolution suivie depuis plusieurs années dans l'automatisation des dosages. Determining, carbon, hydrogen, oxygen, nitrogen and sulfer elements is essential for understanding heavy oil fractions. This bibliographic study describes the leading elemental analysis methods used in this field. Mineralization and detection methods are described, and the development of titra-tion automation in recent years is reviewed.

  5. Preliminary study on element mass fraction determination on catfish samples from Paraguay

    Energy Technology Data Exchange (ETDEWEB)

    Moreira, Edson G.; Catharino, Marilia G.M.; Vasconcellos, Marina B.A., E-mail: emoreira@ipen.br, E-mail: mbvascon@ipen.br, E-mail: mariliasemmler@uol.com.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Frutos, Sixto A.; Insaurralde, Mario S., E-mail: tony8013@hotmail.com, E-mail: insaurraldemar9@hotmail.com [Universidad Nacional de Asuncion (FCV/UNA), San Lorenzo (Paraguay). Facultad de Ciencias Veterinarias. Departamento de Pesca y Acuicultura

    2013-07-01

    South American catfish (Pseudoplatystoma), commonly known in Spanish as atigrado or surubi and in Portuguese as surubim or pintado is a large fish that typically reaches 1 m long and weighs 60 kg to 80 kg and may be found at the basins of the Amazon, the Sao Francisco and de la Plata rivers, usually in riverbeds and deep wells. Being a much appreciated fish for human consumption, it is quite sought after by fishermen who have been contributing to the reduction of the stocks. This fact attracted the attention of the Paraguayan authorities to the point of imposing restrictions to free fishing and commercialization. This study aims to assist the conservation efforts towards this fish by investigating its exposure to possible pollutants. Preliminary results on element determination on six samples of catfish from Paraguayan rivers are presented. Cs, Co, Fe, Se and Zn were determined by applying an Instrumental Neutron Activation Analysis method. While these element levels were lower than the legislation for human consumption, the elements As, Cr e La were not detected in the samples as they are below the detection limit of the method employed. Atomic Absorption Spectrometry was used to investigate the presence of Cd, Hg and Pb in the samples. Hg was detected in the samples while Cd and Pb were below the detection limit of the method. (author)

  6. Comparative study of the paracasein fraction of two ewe's milk cheese varieties.

    Science.gov (United States)

    Panteli, Maria; Zoidou, Evangelia; Moatsou, Golfo

    2015-11-01

    The aim of the present work was to assess the characteristics of the paracasein of two ewe's milk cheese varieties using various concentrations of urea and EDTA to solubilise caseins and calcium. The solubilised paracasein elements were evaluated by means of RP-HPLC and AAS. For this purpose cheeses with different physical and biochemical characteristics, i.e. Feta (53.1% moisture and pH 4.32) and Graviera Kritis (33.2% moisture and pH 5.54) were analysed. Soluble calcium of Feta was 71% of total calcium much higher than the 25% in Graviera. Treatment with 4 m urea fully solubilised Feta paracasein, whereas 6 m urea was needed to solubilise caseins from Graviera. Caseins were released from both cheeses by 100 mm EDTA. Solubilisation of paracasein induced by urea or EDTA was not significantly affected (P cheese. Similarly to urea, EDTA induced significantly (P cheeses was solubilised by 50 mm EDTA while the release of casein was poor, confirming the important role of types of interactions other than protein-calcium bonds in the paracasein network. Hydrophobic interactions, hydrogen bonds and electrostatic attractions, contributed substantially to the paracasein stability of both cheese types. The interactions of αs1-casein with calcium played a more significant role in Graviera cheese than in Feta. Finally, the present study demonstrated that the profile of bonds and interactions within the cheese paracasein network was dynamicly configured by the conditions of cheese manufacture.

  7. Impacts of BDE209 addition on Pb uptake, subcellular partitioning and gene toxicity in earthworm (Eisenia fetida)

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Wei, E-mail: wzhang@ecust.edu.cn [State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237 (China); School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237 (China); Liu, Kou; Li, Jing; Liang, Jun; Lin, Kuangfei [State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, Shanghai 200237 (China); School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai 200237 (China)

    2015-12-30

    Highlights: • 10 or 100 μg g{sup −1} BDE209 addition caused histological changes in Pb-exposed earthworms’ body wall. • Strong histopathological effects with BDE209 addition confirmed the enhanced Pb bioavailability. • The presence of higher levels of BDE209 altered subcellular partitioning of Pb in earthworm. • Co-exposure to Pb and BDE209 declined SOD and CAT gene transcripts synergistically. • BDE209 addition elicited up-regulation of Hsp90 gene expression compared to Pb exposure alone. - Abstract: Lead (Pb) and decabromodiphenyl ether (BDE209) are the mainly co-existed contaminants at e-waste recycling sites. The potential toxicity of Pb (250 μg g{sup −1}) to earthworm Eisenia fetida in the presence of BDE209 (1, 10 and 100 μg g{sup −1}) was determined during 14-d incubation period. Compared to Pb treatment alone, the co-exposure with 1 μg g{sup −1} BDE209 barely affected Pb uptake, subcellular partitioning and gene expression; however, histopathological changes in earthworms’ body wall (epidermal, circular and longitudinal muscles) demonstrated that 10 and 100 μg g{sup −1} BDE209 additions enhanced Pb uptake and altered its subcellular partitioning, indicating that Pb redistributed from fractions E (cell debris) and D (metal-rich granules) to fraction C (cytosols); Additionally, BDE209 supply significantly inhibited (p < 0.05) the induction of SOD (superoxide dismutase) and CAT (catalase) gene expressions (maximum down-regulation 59% for SOD gene at Pb + 100 μg g{sup −1} BDE209 and 89% for CAT gene at Pb + 10 μg g{sup −1} BDE209), while facilitated (p < 0.05) Hsp90 (heat shock protein 90) gene expression with maximum induction rate of 120% after exposure to Pb + 10 μg g{sup −1} BDE209. These findings illustrate the importance of considering environmental BDE209 co-exposure when assessing Pb bioaccumulation and toxicity in multi-contaminated soil ecosystems.

  8. A Randomized Controlled Pilot Study on Ablative Fractional CO2 Laser for Consecutive Patients Presenting With Various Scar Types

    NARCIS (Netherlands)

    van Drooge, Anne Margreet; Vrijman, Charlotte; van der Veen, Wietze; Wolkerstorfer, Albert

    2015-01-01

    BACKGROUND Although ablative fractional laser is the gold standard for acne scars, evidence is still lacking for other types of scars. OBJECTIVE To evaluate the efficacy and safety of the ablative fractional 10,600-nm CO2 laser in the treatment of various scar types. MATERIALS AND METHODS The

  9. Introducing the Improved Heaviside Approach to Partial Fraction Decomposition to Undergraduate Students: Results and Implications from a Pilot Study

    Science.gov (United States)

    Man, Yiu-Kwong

    2012-01-01

    Partial fraction decomposition is a useful technique often taught at senior secondary or undergraduate levels to handle integrations, inverse Laplace transforms or linear ordinary differential equations, etc. In recent years, an improved Heaviside's approach to partial fraction decomposition was introduced and developed by the author. An important…

  10. Fractional vector calculus for fractional advection dispersion

    Science.gov (United States)

    Meerschaert, Mark M.; Mortensen, Jeff; Wheatcraft, Stephen W.

    2006-07-01

    We develop the basic tools of fractional vector calculus including a fractional derivative version of the gradient, divergence, and curl, and a fractional divergence theorem and Stokes theorem. These basic tools are then applied to provide a physical explanation for the fractional advection-dispersion equation for flow in heterogeneous porous media.

  11. In situ spatiotemporal mapping of flow fields around seeded stem cells at the subcellular length scale.

    Directory of Open Access Journals (Sweden)

    Min Jae Song

    2010-09-01

    Full Text Available A major hurdle to understanding and exploiting interactions between the stem cell and its environment is the lack of a tool for precise delivery of mechanical cues concomitant to observing sub-cellular adaptation of structure. These studies demonstrate the use of microscale particle image velocimetry (μ-PIV for in situ spatiotemporal mapping of flow fields around mesenchymal stem cells, i.e. murine embryonic multipotent cell line C3H10T1/2, at the subcellular length scale, providing a tool for real time observation and analysis of stem cell adaptation to the prevailing mechanical milieu. In the absence of cells, computational fluid dynamics (CFD predicts flow regimes within 12% of μ-PIV measures, achieving the technical specifications of the chamber and the flow rates necessary to deliver target shear stresses at a particular height from the base of the flow chamber. However, our μ-PIV studies show that the presence of cells per se as well as the density at which cells are seeded significantly influences local flow fields. Furthermore, for any given cell or cell seeding density, flow regimes vary significantly along the vertical profile of the cell. Hence, the mechanical milieu of the stem cell exposed to shape changing shear stresses, induced by fluid drag, varies with respect to proximity of surrounding cells as well as with respect to apical height. The current study addresses a previously unmet need to predict and observe both flow regimes as well as mechanoadaptation of cells in flow chambers designed to deliver precisely controlled mechanical signals to live cells. An understanding of interactions and adaptation in response to forces at the interface between the surface of the cell and its immediate local environment may be key for de novo engineering of functional tissues from stem cell templates as well as for unraveling the mechanisms underlying multiscale development, growth and adaptation of organisms.

  12. In Situ Spatiotemporal Mapping of Flow Fields around Seeded Stem Cells at the Subcellular Length Scale

    Science.gov (United States)

    Song, Min Jae; Dean, David; Knothe Tate, Melissa L.

    2010-01-01

    A major hurdle to understanding and exploiting interactions between the stem cell and its environment is the lack of a tool for precise delivery of mechanical cues concomitant to observing sub-cellular adaptation of structure. These studies demonstrate the use of microscale particle image velocimetry (μ-PIV) for in situ spatiotemporal mapping of flow fields around mesenchymal stem cells, i.e. murine embryonic multipotent cell line C3H10T1/2, at the subcellular length scale, providing a tool for real time observation and analysis of stem cell adaptation to the prevailing mechanical milieu. In the absence of cells, computational fluid dynamics (CFD) predicts flow regimes within 12% of μ-PIV measures, achieving the technical specifications of the chamber and the flow rates necessary to deliver target shear stresses at a particular height from the base of the flow chamber. However, our μ-PIV studies show that the presence of cells per se as well as the density at which cells are seeded significantly influences local flow fields. Furthermore, for any given cell or cell seeding density, flow regimes vary significantly along the vertical profile of the cell. Hence, the mechanical milieu of the stem cell exposed to shape changing shear stresses, induced by fluid drag, varies with respect to proximity of surrounding cells as well as with respect to apical height. The current study addresses a previously unmet need to predict and observe both flow regimes as well as mechanoadaptation of cells in flow chambers designed to deliver precisely controlled mechanical signals to live cells. An understanding of interactions and adaptation in response to forces at the interface between the surface of the cell and its immediate local environment may be key for de novo engineering of functional tissues from stem cell templates as well as for unraveling the mechanisms underlying multiscale development, growth and adaptation of organisms. PMID:20862249

  13. 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

  14. Transformation of heavy metal fractionation under changing environments: a case study of a drainage system in an e-waste dismantling community.

    Science.gov (United States)

    Damrongsiri, Seelawut

    2018-02-14

    The change in environmental conditions during the transportation of contaminated soil and sediment was expected to affect the transformation of heavy metal fractionation. This study disclosed the serious contamination of copper (Cu), lead (Pb), and zinc (Zn) in the sewer sediment of an e-waste dismantling community in Thailand which may be caused by flushed contaminated soil and e-waste fragments. Two environmental conditions were simulated to observe the transformation of heavy metal fractionation. The anoxic sewer condition was induced using high substrate and sulfate in a closed container. The aeration of anoxic contaminated sediment was applied to simulate the transformation to an oxidative environment. The BCR sequential extraction was applied for heavy metal fractionation in this study. The study results exhibited that when heavy metal contaminated soil was transferred into this induced anoxic condition, fractionation was redistributed based on the chemical change of system that tends to be associated into F3 (oxidizable fraction) > F2 (reducible fraction) > F1 (acid soluble/exchangeable fraction). Cu exhibited the outstanding capability association to F3. The iron sulfide was not observed as usual due to its lower capability than Cu, Pb, and Zn. When contaminated sediment was transported to a more oxidative environment, the heavy metals fractionation would be redistributed again among those new environment media. It is noteworthy that F3 of Cu was stable even in oxic conditions. F2 of Fe was not developed by this oxic condition, possibly because its dehydration process was limited. The redistribution under an oxic environment became F1 > F2 > F3 indicating their more available form. This transformation was imperative and should be taken into account in heavy metal contaminated site management and control.

  15. A fractional factorial field experiment to study the decomposition of municipal solid wastes stored in wrapped bales.

    Science.gov (United States)

    Markidis, Ioannis; Komilis, Dimitrios; Tsagas, Fotios; Petalas, Anastasios

    2013-01-30

    Wrapped bales can be temporarily used to store municipal solid wastes (MSW) prior to treatment or final disposal. The degree of transformation of wastes within the bales can determine the method to treat MSW after their storage. Goal of the research described in this paper was to monitor the decomposition of the organic fraction of MSW stored in wrapped bales. The monitoring was based on the momentary volumetric concentrations of O(2), CO(2) and CH(4) that were regularly measured in the centre of 23 low density polyethylene (LDPE) wrapped bales over a 617-day period. The field experiment was designed at two levels and four factors, based on the principles of fractional factorial designs. The factors that were studied were: shredding, waste particle size and waste density, thickness of wrapping layers, and type of wrapping film. Two bales were randomly chosen and opened after one year of storage and their solid contents were analysed. Results indicate that carbon dioxide was the prevalent decomposition gaseous product that started from around 80% (v/v) and gradually diminished to around 20%. A non-steady methanogenic phase was established after 150 days from initial wrapping and lasted for approximately 150 days. Methane concentration never exceeded 17%, on average, in the interior of the bales. A 40% dry mass reduction was measured after one year of storage in two bales that contained 74% organics. The factorial analysis revealed that particle size/density and film type were the two main factors that significantly affected methane and carbon dioxide generation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. Subcellular targeting of Salmonella virulence proteins by host-mediated S-palmitoylation.

    Science.gov (United States)

    Hicks, Stuart W; Charron, Guillaume; Hang, Howard C; Galán, Jorge E

    2011-07-21

    Several pathogenic bacteria utilize type III secretion systems (TTSS) to deliver into host cells bacterial virulence proteins with the capacity to modulate a variety of cellular pathways. Once delivered into host cells, the accurate targeting of bacterial effectors to specific locations is critical for their proper function. However, little is known about the mechanisms these virulence effectors use to reach their subcellular destination. Here we show that the Salmonella TTSS effector proteins SspH2 and SseI are localized to the plasma membrane of host cells, a process dependent on S-palmitoylation of a conserved cysteine residue within their N-terminal domains. We also show that effector protein lipidation is mediated by a specific subset of host-cell palmitoyltransferases and that lipidation is critical for effector function. This study describes a remarkable mechanism by which a pathogen exploits host-cell machinery to properly target its virulence factors. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. MECHANISMS OF DAMAGING EFFECT OF MANGENESE IN TOXIC CONCENTRATIONS ON CELLULAR AND SUBCELLULAR LEVELS

    Directory of Open Access Journals (Sweden)

    Goncharenko A. V.

    2012-11-01

    Full Text Available Influence of subtoxic concentration of manganese chloride in dose equal to LD 50 on condition of plasmatic membranes (model: erythrocytes and functional activity of cell power (model: the isolated liver mitochondrion of rats was studied. It was established that manganese chloride in fixed concentration caused authentic augmentation of sorption capacity of erythrocytes towards alcian blue, influenced increasing of their spontaneous haemolysis and activation of peroxide oxidation of lipids. In experiment on the isolated mitochondrion it was proved that manganese chloride caused dissociation of an oxidizing phosphorusling and complete inhibition of respiration in concentrations of 3 and 4,5mM. These dependences testify that subtoxic concentration of manganese can damage the cell energy. Thus, this pilot research indicated damaging effect of manganese on cellular (erythrocytes and subcellular (mitochondrion levels which are realized through external functioning of membrane structures and deprived them from restoration.

  18. Separation and purification of soluble polymers and cell wall fractions from wheat, rye and hull less barley endosperm flours for structure-nutrition studies.

    Science.gov (United States)

    Comino, Penny; Shelat, Kinnari; Collins, Helen; Lahnstein, Jelle; Gidley, Michael J

    2013-12-11

    The nutritional values associated with the cell walls of cereal endosperm flours are due to a combination of solubilized arabinoxylan and (1-3,1-4)-β-d-glucan as well as residual nonsolubilized cell wall material. In order to investigate structure-nutrition relationships, an appropriate method for the complete functional and structural characterization of cell wall polysaccharides in various cereal endosperm flours is described. This involves the separation of soluble polymers and the residual cell wall fraction without using organic solvents, and the fractionation of soluble polymers into arabinoxylan- and (1-3,1-4)-β-d-glucan-rich fractions for subsequent analysis. This methodology is applied to endosperm flours from wheat, hull-less barley and rye, and could be extended to include studies on the effects of food processing with respect to yield and characteristics of the three fractions in order to better understand the structural basis for nutritional functionality.

  19. Meadow based Fraction Theory

    OpenAIRE

    Bergstra, Jan A.

    2015-01-01

    In the context of an involutive meadow a precise definition of fractions is formulated and on that basis formal definitions of various classes of fractions are given. The definitions follow the fractions as terms paradigm. That paradigm is compared with two competing paradigms for storytelling on fractions: fractions as values and fractions as pairs.

  20. 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)

  1. A novel approach for protein subcellular location prediction using amino acid exposure

    Science.gov (United States)

    2013-01-01

    Background Proteins perform their functions in associated cellular locations. Therefore, the study of protein function can be facilitated by predictions of protein location. Protein location can be predicted either from the sequence of a protein alone by identification of targeting peptide sequences and motifs, or by homology to proteins of known location. A third approach, which is complementary, exploits the differences in amino acid composition of proteins associated to different cellular locations, and can be useful if motif and homology information are missing. Here we expand this approach taking into account amino acid composition at different levels of amino acid exposure. Results Our method has two stages. For stage one, we trained multiple Support Vector Machines (SVMs) to score eukaryotic protein sequences for membership to each of three categories: nuclear, cytoplasmic and extracellular, plus extra category nucleocytoplasmic, accounting for the fact that a large number of proteins shuttles between those two locations. In stage two we use an artificial neural network (ANN) to propose a category from the scores given to the four locations in stage one. The method reaches an accuracy of 68% when using as input 3D-derived values of amino acid exposure. Calibration of the method using predicted values of amino acid exposure allows classifying proteins without 3D-information with an accuracy of 62% and discerning proteins in different locations even if they shared high levels of identity. Conclusions In this study we explored the relationship between residue exposure and protein subcellular location. We developed a new algorithm for subcellular location prediction that uses residue exposure signatures. Our algorithm uses a novel approach to address the multiclass classification problem. The algorithm is implemented as web server 'NYCE’ and can be accessed at http://cbdm.mdc-berlin.de/~amer/nyce. PMID:24283794

  2. Comparison of PIXE and SXRF for kinetic studies in cell pharmacology of platinum and gold compounds

    Energy Technology Data Exchange (ETDEWEB)

    Sommer, F. (Faculte de Medecine de Creteil (France). Lab. de Biophysique Laboratoire d' Analyse par Activation Pierre-Sue - Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France)); Chevallier, P. (Paris-6 Univ., 75 (France)); Tapiero, H. (Hopital Paul-Brousse, 94 - Villejuif (France)); Massiot, P.; Piccot, D. (Laboratoire d' Analyse par Activation Pierre-Sue - Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France)); Galle, P. (Faculte de Medecine de Creteil (France). Lab. de Biophysique); Silvestro, L. (Turin Univ. (Italy). Facolta di Medicina); Arizti, P. (Universidad Pais Vasco, Leioa (Spain). Facultad de Medicina)

    1991-01-01

    The analytical conditions in PIXE and SXRF are studied in order to optimize the detection of platinum and gold compounds in the cell and in their subcellular fractions. Calibration curves, reproducibility and detection limits were obtained with both techniques and compared. The best detection limit was achieved with SXRF. Preliminary data on the cellular pharmacokinetics of cisplatinum and gold selective distribution in nuclei were obtained by the above techniques. (author).

  3. Mannitol increases renal blood flow and maintains filtration fraction and oxygenation in postoperative acute kidney injury: a prospective interventional study

    Science.gov (United States)

    2012-01-01

    Introduction Acute kidney injury (AKI), which is a major complication after cardiovascular surgery, is associated with significant morbidity and mortality. Diuretic agents are frequently used to improve urine output and to facilitate fluid management in these patients. Mannitol, an osmotic diuretic, is used in the perioperative setting in the belief that it exerts reno-protective properties. In a recent study on uncomplicated postcardiac-surgery patients with normal renal function, mannitol increased glomerular filtration rate (GFR), possibly by a deswelling effect on tubular cells. Furthermore, experimental studies have previously shown that renal ischemia causes an endothelial cell injury and dysfunction followed by endothelial cell edema. We studied the effects of mannitol on renal blood flow (RBF), glomerular filtration rate (GFR), renal oxygen consumption (RVO2), and extraction (RO2Ex) in early, ischemic AKI after cardiac surgery. Methods Eleven patients with AKI were studied during propofol sedation and mechanical ventilation 2 to 6 days after complicated cardiac surgery. All patients had severe heart failure treated with one (100%) or two (73%) inotropic agents and intraaortic balloon pump (36%). Systemic hemodynamics were measured with a pulmonary artery catheter. RBF and renal filtration fraction (FF) were measured by the renal vein thermo-dilution technique and by renal extraction of chromium-51-ethylenediaminetetraacetic acid (51Cr-EDTA), respectively. GFR was calculated as the product of FF and renal plasma flow RBF × (1-hematocrit). RVO2 and RO2Ex were calculated from arterial and renal vein blood samples according to standard formulae. After control measurements, a bolus dose of mannitol, 225 mg/kg, was given, followed by an infusion at a rate of 75 mg/kg/h for two 30-minute periods. Results Mannitol did not affect cardiac index or cardiac filling pressures. Mannitol increased urine flow by 61% (P Mannitol increased the RBF/cardiac output (CO

  4. Predicting human protein subcellular locations by the ensemble of multiple predictors via protein-protein interaction network with edge clustering coefficients.

    Directory of Open Access Journals (Sweden)

    Pufeng Du

    Full Text Available One of the fundamental tasks in biology is to identify the functions of all proteins to reveal the primary machinery of a cell. Knowledge of the subcellular locations of proteins will provide key hints to reveal their functions and to understand the intricate pathways that regulate biological processes at the cellular level. Protein subcellular location prediction has been extensively studied in the past two decades. A lot of methods have been developed based on protein primary sequences as well as protein-protein interaction network. In this paper, we propose to use the protein-protein interaction network as an infrastructure to integrate existing sequence based predictors. When predicting the subcellular locations of a given protein, not only the protein itself, but also all its interacting partners were considered. Unlike existing methods, our method requires neither the comprehensive knowledge of the protein-protein interaction network nor the experimentally annotated subcellular locations of most proteins in the protein-protein interaction network. Besides, our method can be used as a framework to integrate multiple predictors. Our method achieved 56% on human proteome in absolute-true rate, which is higher than the state-of-the-art methods.

  5. Robust classification of subcellular location patterns in high resolution 3D fluorescence microscope images.

    Science.gov (United States)

    Chen, Xiang; Murphy, Robert

    2004-01-01

    Knowledge of a protein's subcellular location is essential to a complete understanding of its functions. Automated interpretation methods for protein location patterns are needed for proteomics projects, and we have previously described systems for classifying the major subcellular patterns in cultured mammalian cells. We describe here the calculation of improved 3D Haralick texture features, which yielded a near-perfect classification accuracy when combined with 3D morphological and edge features. In particular, a set of 7 features achieved 98% overall accuracy for classifying 10 major subcellular location patterns in HeLa cells.

  6. Human cell structure-driven model construction for predicting protein subcellular location from biological images.

    Science.gov (United States)

    Shao, Wei; Liu, Mingxia; Zhang, Daoqiang

    2016-01-01

    The systematic study of subcellular location pattern is very important for fully characterizing the human proteome. Nowadays, with the great advances in automated microscopic imaging, accurate bioimage-based classification methods to predict protein subcellular locations are highly desired. All existing models were constructed on the independent parallel hypothesis, where the cellular component classes are positioned independently in a multi-class classification engine. The important structural information of cellular compartments is missed. To deal with this problem for developing more accurate models, we proposed a novel cell structure-driven classifier construction approach (SC-PSorter) by employing the prior biological structural information in the learning model. Specifically, the structural relationship among the cellular components is reflected by a new codeword matrix under the error correcting output coding framework. Then, we construct multiple SC-PSorter-based classifiers corresponding to the columns of the error correcting output coding codeword matrix using a multi-kernel support vector machine classification approach. Finally, we perform the classifier ensemble by combining those multiple SC-PSorter-based classifiers via majority voting. We evaluate our method on a collection of 1636 immunohistochemistry images from the Human Protein Atlas database. The experimental results show that our method achieves an overall accuracy of 89.0%, which is 6.4% higher than the state-of-the-art method. The dataset and code can be downloaded from https://github.com/shaoweinuaa/. dqzhang@nuaa.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Protein subcellular location pattern classification in cellular images using latent discriminative models.

    Science.gov (United States)

    Li, Jieyue; Xiong, Liang; Schneider, Jeff; Murphy, Robert F

    2012-06-15

    Knowledge of the subcellular location of a protein is crucial for understanding its functions. The subcellular pattern of a protein is typically represented as the set of cellular components in which it is located, and an important task is to determine this set from microscope images. In this article, we address this classification problem using confocal immunofluorescence images from the Human Protein Atlas (HPA) project. The HPA contains images of cells stained for many proteins; each is also stained for three reference components, but there are many other components that are invisible. Given one such cell, the task is to classify the pattern type of the stained protein. We first randomly select local image regions within the cells, and then extract various carefully designed features from these regions. This region-based approach enables us to explicitly study the relationship between proteins and different cell components, as well as the interactions between these components. To achieve these two goals, we propose two discriminative models that extend logistic regression with structured latent variables. The first model allows the same protein pattern class to be expressed differently according to the underlying components in different regions. The second model further captures the spatial dependencies between the components within the same cell so that we can better infer these components. To learn these models, we propose a fast approximate algorithm for inference, and then use gradient-based methods to maximize the data likelihood. In the experiments, we show that the proposed models help improve the classification accuracies on synthetic data and real cellular images. The best overall accuracy we report in this article for classifying 942 proteins into 13 classes of patterns is about 84.6%, which to our knowledge is the best so far. In addition, the dependencies learned are consistent with prior knowledge of cell organization. http://murphylab.web.cmu.edu/software/.

  8. Diverse subcellular localizations of the insect CMP-sialic acid synthetases.

    Science.gov (United States)

    Di, Wu; Fujita, Akiko; Hamaguchi, Kayo; Delannoy, Philippe; Sato, Chihiro; Kitajima, Ken

    2017-04-01

    The occurrence and biological importance of sialic acid (Sia) and its metabolic enzymes in insects have been studied using Drosophila melanogaster. The most prominent feature of D. melanogaster CMP-Sia synthetase (DmCSS) is its Golgi-localization, contrasted with nuclear localization of vertebrate CSSs. However, it remains unclear if the Golgi-localization is common to other insect CSSs and why it happens. To answer these questions, Aedes aegypti (mosquito) CSS (AaCSS) and Tribolium castaneum (beetle) CSS (TcCSS) were cloned and characterized for their activity and subcellular localization. Our new findings show: (1) AaCSS and TcCSS share a common overall structure with DmCSS in terms of evolutionarily conserved motifs and the absence of the C-terminal domain typical to vertebrate CSSs; (2) when expressed in mammalian and insect cells, AaCSS and TcCSS showed in vivo and in vitro CSS activities, similar to DmCSS. In contrast, when expressed in bacteria, they lacked CSS activity because the N-terminal hydrophobic region appeared to induce protein aggregation; (3) when expressed in Drosophila S2 cells, AaCSS and TcCSS were predominantly localized in the ER, but not in the Golgi. Surprisingly, DmCSS was mainly secreted into the culture medium, although partially detected in Golgi. Consistent with these results, the N-terminal hydrophobic regions of AaCSS and TcCSS functioned as a signal peptide to render them soluble in the ER, while the N-terminus of DmCSS functioned as a membrane-spanning region of type II transmembrane proteins whose cytosolic KLK sequence functioned as an ER export signal. Accordingly, the differential subcellular localization of insect CSSs are distinctively more diverse than previously recognized. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. 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.

  10. Efficacy of punch elevation combined with fractional carbon dioxide laser resurfacing in facial atrophic acne scarring: A randomized split-face clinical study

    Directory of Open Access Journals (Sweden)

    Gita Faghihi

    2015-01-01

    Full Text Available Background: A number of treatments for reducing the appearance of acne scars are available, but general guidelines for optimizing acne scar treatment do not exist. The aim of this study was to compare the clinical effectiveness and side effects of fractional carbon dioxide (CO 2 laser resurfacing combined with punch elevation with fractional CO 2 laser resurfacing alone in the treatment of atrophic acne scars. Materials and Methods: Forty-two Iranian subjects (age range 18-55 with Fitzpatrick skin types III to IV and moderate to severe atrophic acne scars on both cheeks received randomized split-face treatments: One side received fractional CO 2 laser treatment and the other received one session of punch elevation combined with two sessions of laser fractional CO 2 laser treatment, separated by an interval of 1 month. Two dermatologists independently evaluated improvement in acne scars 4 and 16 weeks after the last treatment. Side effects were also recorded after each treatment. Results: The mean ± SD age of patients was 23.4 ± 2.6 years. Clinical improvement of facial acne scarring was assessed by two dermatologists blinded to treatment conditions. No significant difference in evaluation was observed 1 month after treatment (P = 0.56. Their evaluation found that fractional CO 2 laser treatment combined with punch elevation had greater efficacy than that with fractional CO 2 laser treatment alone, assessed 4 months after treatment (P = 0.02. Among all side effects, coagulated crust formation and pruritus at day 3 after fractional CO 2 laser treatment was significant on both treatment sides (P < 0.05. Conclusion: Concurrent use of fractional laser skin resurfacing with punch elevation offers a safe and effective approach for the treatment of acne scarring.

  11. Distribution of mitochondrial enzymes between the perikaryal and synaptic fractions of immature and adult rat brain

    Energy Technology Data Exchange (ETDEWEB)

    Dienel, G.; Ryder, E.; Greengard, O.

    1977-01-01

    The subcellular distribution of mitochondrial enzymes was studied in cerebral hemispheres of 15-day-old and adult rats. At both ages the synaptosomal fraction contained very little glutamate dehydrogenase (EC 1.4.1.2) but significant amounts of succinate dehydrogenase (EC 1.3.99.1), glutaminase (EC 3.5.1.2), hexokinase (EC 2.7.1.1), malate NADP dehydrogenase (EC 1.1.1.40) and ..beta..-hydroxybutyrate dehydrogenase (EC 1.1.1.30). In immature brain, in the fraction enriched with free (perikaryal) mitochondria, the concentrations of these enzymes were 9.5, 1.8, 2.0, 0.92, 1.5, and 2.1 times higher, respectively, than in the synaptosomes. The increase with age in succinate dehydrogenase and glutaminase was restricted to free mitochondria while hexokinase and malate NADP dehydrogenase accumulated and ..beta..-hydroxybutyrate dehydrogenase diminished in both fractions. In adult brain, too, where the above ratios became 7.5, 5.2, 3.5, 0.84, 1.4, and 2.0, respectively, the concentrations of enzymes relative to each other distinguished clearly between free and synaptic mitochondria. The results substantiate previously noted signs of mitochondrial heterogeneity in adult brain, and extend them to immature brain. The chemical composition, the quantitative pattern of enzymes, of free and synaptic mitochondria is clearly different, and undergoes separate changes during postnatal differentiation.

  12. Study of fractionation and potential mobility of metal from the Guadalquivir estuary: changes in mobility with time and influence of the aznalcollar mining spill.

    Science.gov (United States)

    Morillo, José; Usero, José; Gracia, Ignacio

    2005-07-01

    This study analyzed the evolution of metal levels in surface sediments from the Guadalquivir estuary between 1997 and 2002 and assessed the impact of the April 1998 Aznalcollar tailings dam failure and subsequent cleanup on metal concentrations in surface sediments. We also analyzed metal distribution with time in five chemical fractions of the surface sediments: exchangable, carbonate, reducible, oxidizable, and residual. This work showed that the April 1998 Aznalcollar tailings dam failure caused a considerable increase in the concentrations of Cd, Zn, Cu, and Pb in the surface sediments of the Guadalquivir estuary. It was also found there was a change in the distribution of Cd, Zn, Cu, and Pb between the chemical fractions of the sediment after the failure of the dam. There were increases in the percentages of Cd in the carbonate fraction, of Zn and Pb in the reducible fraction, and of Cu in the oxidizable fraction, whereas the percentages of these elements associated with the residual fraction decreased. In 1999, there was a decrease in the metal concentrations in the surface sediments from the Guadalquivir estuary, and by 2000 the chemical distribution and metal levels had returned to levels similar those before the dam failure.

  13. The Local Fractional Bootstrap

    DEFF Research Database (Denmark)

    Bennedsen, Mikkel; Hounyo, Ulrich; Lunde, Asger

    new resampling method, the local fractional bootstrap, relies on simulating an auxiliary fractional Brownian motion that mimics the fine properties of high frequency differe