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Sample records for cell cycle-dependent variations

  1. Cell-cycle-dependent regulation of cell motility and determination of the role of Rac1

    DEFF Research Database (Denmark)

    Walmod, Peter S.; Hartmann-Petersen, Rasmus; Prag, S.

    2004-01-01

    was accompanied by changes in morphology reflecting the larger volume of cells in G2 than in G1. Furthermore, L-cells and HeLa-cells appeared to be less adherent in the G2 phase. Transfection of L-cells with constitutively active Rac1 led to a general increase in the speed and rate of diffusion in G2 to levels...... comparable to those of control cells in G1. In contrast, transfection with dominant-negative Rac1 reduced cell speed and resulted in cellular displacements, which were identical in G1 and G2. These observations indicate that migration of cultured cells is regulated in a cell-cycle-dependent manner......, and that an enhancement of Rac1 activity is sufficient for a delay of the reduced cell displacement otherwise seen in G2....

  2. Cell cycle-dependent differentiation dynamics balances growth and endocrine differentiation in the pancreas

    DEFF Research Database (Denmark)

    Kim, Yung Hae; Larsen, Hjalte List; Rué, Paul

    2015-01-01

    Organogenesis relies on the spatiotemporal balancing of differentiation and proliferation driven by an expanding pool of progenitor cells. In the mouse pancreas, lineage tracing at the population level has shown that the expanding pancreas progenitors can initially give rise to all endocrine...... differentiation process is consistent with a simple model of cell cycle-dependent stochastic priming of progenitors to endocrine fate. The findings provide insights to define control parameters to optimize the generation of β-cells in vitro....

  3. Cell cycle dependency of 67gallium uptake and cytotoxicity in human cell lines of hematological malignancies.

    Science.gov (United States)

    Van Leeuwen-Stok, E A; Jonkhoff, A R; Visser-Platier, A W; Dräger, L M; Teule, G J; Huijgens, P C; Schuurhuis, G J

    1998-11-01

    67Gallium (67Ga) is a radionuclide which accumulates in hematological malignancies and is used for diagnostic imaging. We investigated in this in vitro study the cell cycle dependency of cellular uptake and cytotoxicity of 67Ga. Cell cycle synchronization of cells was achieved by counterflow centrifugal elutriation and the use of cytostatic drugs. The human lymphoma cell lines U-937 and U-715 were used and in elutriation experiments we also used the leukemic cell line HL-60. The transferrin receptor (CD71) expression, 67Ga uptake and cell proliferation inhibition were the parameters measured. We also studied cytotoxicity in various schedules for combination of 67Ga and drugs and the residual proliferative capacity was measured. The CD71 expression in the three cell lines increased from 106-177% on S phase cells and from 118-233% on G2M cells, as compared to the G0/G1 cell fraction. The 67Ga uptake varied from 108-127% for S cells and 128-139% for G2M cells. The drugs chosen induced cell cycle phase accumulation in S and/or G2M phase during preincubation. 67Ga preincubation induced accumulation in the G2M phase. Almost all combinations of 67Ga and drugs resulted in a non-interactive effect, except for methotrexate which resulted in an antagonistic effect. No preferential effect of any of the incubation schemes was seen. CD71 expression and 67Ga uptake were increased in S and G2M cells. Combination of 67Ga with drugs which arrest cells in these cell cycle phases did not result in a change in cytotoxicity. However, these results implicate that 67Ga and the cytostatic drugs tested except for methotrexate might be used together or sequentially in therapy.

  4. Cell cycle dependent association of EBP50 with protein phosphatase 2A in endothelial cells.

    Directory of Open Access Journals (Sweden)

    Anita Boratkó

    Full Text Available Ezrin-radixin-moesin (ERM-binding phosphoprotein 50 (EBP50 is a phosphorylatable PDZ domain-containing adaptor protein that is abundantly expressed in epithelium but was not yet studied in the endothelium. We report unusual nuclear localization of EBP50 in bovine pulmonary artery endothelial cells (BPAEC. Immunofluorescent staining and cellular fractionation demonstrated that EBP50 is present in the nuclear and perinuclear region in interphase cells. In the prophase of mitosis EBP50 redistributes to the cytoplasmic region in a phosphorylation dependent manner and during mitosis EBP50 co-localizes with protein phosphatase 2A (PP2A. Furthermore, in vitro wound healing of BPAEC expressing phospho-mimic mutant of EBP50 was accelerated indicating that EBP50 is involved in the regulation of the cell division. Cell cycle dependent specific interactions were detected between EBP50 and the subunits of PP2A (A, C, and Bα with immunoprecipitation and pull-down experiments. The interaction of EBP50 with the Bα containing form of PP2A suggests that this holoenzyme of PP2A can be responsible for the dephosphorylation of EBP50 in cytokinesis. Moreover, the results underline the significance of EBP50 in cell division via reversible phosphorylation of the protein with cyclin dependent kinase and PP2A in normal cells.

  5. Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure.

    Science.gov (United States)

    Grand, Ralph S; Pichugina, Tatyana; Gehlen, Lutz R; Jones, M Beatrix; Tsai, Peter; Allison, Jane R; Martienssen, Robert; O'Sullivan, Justin M

    2014-11-10

    Successful progression through the cell cycle requires spatial and temporal regulation of gene transcript levels and the number, positions and condensation levels of chromosomes. Here we present a high resolution survey of genome interactions in Schizosaccharomyces pombe using synchronized cells to investigate cell cycle dependent changes in genome organization and transcription. Cell cycle dependent interactions were captured between and within S. pombe chromosomes. Known features of genome organization (e.g. the clustering of telomeres and retrotransposon long terminal repeats (LTRs)) were observed throughout the cell cycle. There were clear correlations between transcript levels and chromosomal interactions between genes, consistent with a role for interactions in transcriptional regulation at specific stages of the cell cycle. In silico reconstructions of the chromosome organization within the S. pombe nuclei were made by polymer modeling. These models suggest that groups of genes with high and low, or differentially regulated transcript levels have preferred positions within the S. pombe nucleus. We conclude that the S. pombe nucleus is spatially divided into functional sub-nuclear domains that correlate with gene activity. The observation that chromosomal interactions are maintained even when chromosomes are fully condensed in M phase implicates genome organization in epigenetic inheritance and bookmarking. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Cell cycle-dependent microtubule-based dynamic transport of cytoplasmic dynein in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Takuya Kobayashi

    Full Text Available BACKGROUND: Cytoplasmic dynein complex is a large multi-subunit microtubule (MT-associated molecular motor involved in various cellular functions including organelle positioning, vesicle transport and cell division. However, regulatory mechanism of the cell-cycle dependent distribution of dynein has not fully been understood. METHODOLOGY/PRINCIPAL FINDINGS: Here we report live-cell imaging of cytoplasmic dynein in HeLa cells, by expressing multifunctional green fluorescent protein (mfGFP-tagged 74-kDa intermediate chain (IC74. IC74-mfGFP was successfully incorporated into functional dynein complex. In interphase, dynein moved bi-directionally along with MTs, which might carry cargos such as transport vesicles. A substantial fraction of dynein moved toward cell periphery together with EB1, a member of MT plus end-tracking proteins (+TIPs, suggesting +TIPs-mediated transport of dynein. In late-interphase and prophase, dynein was localized at the centrosomes and the radial MT array. In prometaphase and metaphase, dynein was localized at spindle MTs where it frequently moved from spindle poles toward chromosomes or cell cortex. +TIPs may be involved in the transport of spindle dyneins. Possible kinetochore and cortical dyneins were also observed. CONCLUSIONS AND SIGNIFICANCE: These findings suggest that cytoplasmic dynein is transported to the site of action in preparation for the following cellular events, primarily by the MT-based transport. The MT-based transport may have greater advantage than simple diffusion of soluble dynein in rapid and efficient transport of the limited concentration of the protein.

  7. Cell-cycle-dependent efficacy of photodynamic therapy with ATX-S10(Na).

    Science.gov (United States)

    Sano, Munetaka; Furuta, Takahisa; Takahira, Kenichiro; Kajimura, Masayoshi; Hanai, Hiroyuki; Kohno, Eiji; Hirano, Toru; Hishida, Akira

    2005-01-01

    Photodynamic therapy (PDT) is a useful strategy for treating various cancers. Details of the mechanisms of PDT have not been made clear yet. We intended to study the efficacy of PDT in relation to the cell cycle. HeLa S3 cells were synchronized by the thymidine block method. Cells in different cell cycle phases after release were treated with the water-soluble photosensitizer, ATX-S10(Na). The cellular viability after PDT was determined by the MTT assay. Intracellular levels of ATX-S10(Na) in different cell cycle phases were also determined. We found that cells in the S and G(2)/M phases were hypersensitive to PDT with ATX-S10(Na) in comparison with those in the G(1) phase, and that cellular levels of ATX-S10(Na) were increased in cells in the S and G(2)/M phases compared to those in the G(1) phase. We conclude that cellular ATX-S10(Na) levels differ among the different cell cycle phases, which is associated with the cell-cycle-dependent efficacy of PDT with ATX-S10(Na).

  8. Cell cycle-dependent alteration in NAC1 nuclear body dynamics and morphology

    International Nuclear Information System (INIS)

    Wu, Pei-Hsun; Hung, Shen-Hsiu; Ren, Tina; Tseng, Yiider; Shih, Ie-Ming

    2011-01-01

    NAC1, a BTB/POZ family member, has been suggested to participate in maintaining the stemness of embryonic stem cells and has been implicated in the pathogenesis of human cancer. In ovarian cancer, NAC1 upregulation is associated with disease aggressiveness and with the development of chemoresistance. Like other BTB/POZ proteins, NAC1 forms discrete nuclear bodies in non-dividing cells. To investigate the biological role of NAC1 nuclear bodies, we characterized the expression dynamics of NAC1 nuclear bodies during different phases of the cell cycle. Fluorescence recovery after photobleaching assays revealed that NAC1 was rapidly exchanged between the nucleoplasm and NAC1 nuclear bodies in interphase cells. The number of NAC1 bodies significantly increased and their size decreased in the S phase as compared to the G 0 /G 1 and G 2 phases. NAC1 nuclear bodies disappeared and NAC1 became diffuse during mitosis. NAC1 nuclear bodies reappeared immediately after completion of mitosis. These results indicate that a cell cycle-dependent regulatory mechanism controls NAC1 body formation in the nucleus and suggest that NAC1 body dynamics are associated with mitosis or cytokinesis

  9. The CHR Promoter Element Controls Cell Cycle-Dependent Gene Transcription and Binds the DREAM and MMB Complexes

    OpenAIRE

    Müller, Gerd A.; Quaas, Marianne; Schümann, Michael; Krause, Eberhard; Fischer, Martin; Engeland, Kurt; Padi, Megha; Litovchick, Larisa; DeCaprio, James A.

    2011-01-01

    Cell cycle-dependent gene expression is often controlled on the transcriptional level. Genes like \\(cyclin B, CDC2\\) and \\(CDC25C\\) are regulated by cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) promoter elements mainly through repression in \\(G_0/G_1\\). It had been suggested that E2F4 binding to CDE sites is central to transcriptional regulation. However, some promoters are only controlled by a CHR. We identify the DREAM complex binding to the CHR of mouse and...

  10. Cell cycle-dependent SUMO-1 conjugation to nuclear mitotic apparatus protein (NuMA)

    International Nuclear Information System (INIS)

    Seo, Jae Sung; Kim, Ha Na; Kim, Sun-Jick; Bang, Jiyoung; Kim, Eun-A; Sung, Ki Sa; Yoon, Hyun-Joo; Yoo, Hae Yong; Choi, Cheol Yong

    2014-01-01

    Highlights: •NuMA is modified by SUMO-1 in a cell cycle-dependent manner. •NuMA lysine 1766 is the primary target site for SUMOylation. •SUMOylation-deficient NuMA induces multiple spindle poles during mitosis. •SUMOylated NuMA induces microtubule bundling. -- Abstract: Covalent conjugation of proteins with small ubiquitin-like modifier 1 (SUMO-1) plays a critical role in a variety of cellular functions including cell cycle control, replication, and transcriptional regulation. Nuclear mitotic apparatus protein (NuMA) localizes to spindle poles during mitosis, and is an essential component in the formation and maintenance of mitotic spindle poles. Here we show that NuMA is a target for covalent conjugation to SUMO-1. We find that the lysine 1766 residue is the primary NuMA acceptor site for SUMO-1 conjugation. Interestingly, SUMO modification of endogenous NuMA occurs at the entry into mitosis and this modification is reversed after exiting from mitosis. Knockdown of Ubc9 or forced expression of SENP1 results in impairment of the localization of NuMA to mitotic spindle poles during mitosis. The SUMOylation-deficient NuMA mutant is defective in microtubule bundling, and multiple spindles are induced during mitosis. The mitosis-dependent dynamic SUMO-1 modification of NuMA might contribute to NuMA-mediated formation and maintenance of mitotic spindle poles during mitosis

  11. Cell cycle-dependent SUMO-1 conjugation to nuclear mitotic apparatus protein (NuMA)

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Jae Sung; Kim, Ha Na; Kim, Sun-Jick; Bang, Jiyoung; Kim, Eun-A; Sung, Ki Sa [Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Yoon, Hyun-Joo [TissueGene Inc. 9605 Medical Center Dr., Rockville, MD 20850 (United States); Yoo, Hae Yong [Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University, Seoul 135-710 (Korea, Republic of); Choi, Cheol Yong, E-mail: choicy@skku.ac.kr [Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2014-01-03

    Highlights: •NuMA is modified by SUMO-1 in a cell cycle-dependent manner. •NuMA lysine 1766 is the primary target site for SUMOylation. •SUMOylation-deficient NuMA induces multiple spindle poles during mitosis. •SUMOylated NuMA induces microtubule bundling. -- Abstract: Covalent conjugation of proteins with small ubiquitin-like modifier 1 (SUMO-1) plays a critical role in a variety of cellular functions including cell cycle control, replication, and transcriptional regulation. Nuclear mitotic apparatus protein (NuMA) localizes to spindle poles during mitosis, and is an essential component in the formation and maintenance of mitotic spindle poles. Here we show that NuMA is a target for covalent conjugation to SUMO-1. We find that the lysine 1766 residue is the primary NuMA acceptor site for SUMO-1 conjugation. Interestingly, SUMO modification of endogenous NuMA occurs at the entry into mitosis and this modification is reversed after exiting from mitosis. Knockdown of Ubc9 or forced expression of SENP1 results in impairment of the localization of NuMA to mitotic spindle poles during mitosis. The SUMOylation-deficient NuMA mutant is defective in microtubule bundling, and multiple spindles are induced during mitosis. The mitosis-dependent dynamic SUMO-1 modification of NuMA might contribute to NuMA-mediated formation and maintenance of mitotic spindle poles during mitosis.

  12. The Single Cell Proteome Project - Cell-Cycle Dependent Protein Expression in Breast Cancer Cell Lines

    National Research Council Canada - National Science Library

    Dovichi, Norman J

    2005-01-01

    .... Capillary sieving electrophoresis and capillary micellar electrophoresis were used to characterize proteins in single cells in one-dimensional separations, while the two techniques were combined...

  13. Cell cycle-dependent activity of the volume- and Ca2+-activated anion currents in Ehrlich lettre ascites cells

    DEFF Research Database (Denmark)

    Klausen, Thomas Kjaer; Bergdahl, Andreas; Christophersen, Palle

    2007-01-01

    Recent evidence implicates the volume-regulated anion current (VRAC) and other anion currents in control or modulation of cell cycle progression; however, the precise involvement of anion channels in this process is unclear. Here, Cl- currents in Ehrlich Lettre Ascites (ELA) cells were monitored......+ in the pipette), was unaltered from G0 to G1, but decreased in early S phase. A novel high-affinity anion channel inhibitor, the acidic di-aryl-urea NS3728, which inhibited both VRAC and CaCC, attenuated ELA cell growth, suggesting a possible mechanistic link between cell cycle progression and cell cycle......-dependent changes in the capacity for conductive Cl- transport. It is suggested that in ELA cells, entrance into the S phase requires an increase in VRAC activity and/or an increased potential for regulatory volume decrease (RVD), and at the same time a decrease in CaCC magnitude....

  14. The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes.

    Science.gov (United States)

    Müller, Gerd A; Quaas, Marianne; Schümann, Michael; Krause, Eberhard; Padi, Megha; Fischer, Martin; Litovchick, Larisa; DeCaprio, James A; Engeland, Kurt

    2012-02-01

    Cell cycle-dependent gene expression is often controlled on the transcriptional level. Genes like cyclin B, CDC2 and CDC25C are regulated by cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) promoter elements mainly through repression in G(0)/G(1). It had been suggested that E2F4 binding to CDE sites is central to transcriptional regulation. However, some promoters are only controlled by a CHR. We identify the DREAM complex binding to the CHR of mouse and human cyclin B2 promoters in G(0). Association of DREAM and cell cycle-dependent regulation is abrogated when the CHR is mutated. Although E2f4 is part of the complex, a CDE is not essential but can enhance binding of DREAM. We show that the CHR element is not only necessary for repression of gene transcription in G(0)/G(1), but also for activation in S, G(2) and M phases. In proliferating cells, the B-myb-containing MMB complex binds the CHR of both promoters independently of the CDE. Bioinformatic analyses identify many genes which contain conserved CHR elements in promoters binding the DREAM complex. With Ube2c as an example from that screen, we show that inverse CHR sites are functional promoter elements that can bind DREAM and MMB. Our findings indicate that the CHR is central to DREAM/MMB-dependent transcriptional control during the cell cycle.

  15. CXCR3 surface expression in human airway epithelial cells: cell cycle dependence and effect on cell proliferation.

    Science.gov (United States)

    Aksoy, Mark O; Yang, Yi; Ji, Rong; Reddy, P J; Shahabuddin, Syed; Litvin, Judith; Rogers, Thomas J; Kelsen, Steven G

    2006-05-01

    We recently demonstrated that human bronchial epithelial cells (HBEC) constitutively express the CXC chemokine receptor CXCR3, which when activated, induces directed cell migration. The present study in HBEC examined the relative expression of the CXCR3 splice variants CXCR3-A and -B, cell cycle dependence of CXCR3 expression, and the effects of the CXCR3 ligand, the interferon-gamma-inducible CXC chemokine I-TAC/CXCL11, on DNA synthesis and cell proliferation. Both CXCR3-A and -B mRNA, assessed by real-time RT-PCR, were expressed in normal HBEC (NHBEC) and the HBEC line 16-HBE. However, CXCR3-B mRNA was 39- and 6-fold greater than CXCR3-A mRNA in NHBEC and 16-HBE, respectively. Although most HBEC (>80%) assessed by flow cytometry and immunofluorescence microscopy contained intracellular CXCR3, only a minority (75%) were in the S + G(2)/M phases of the cell cycle. Stimulation of CXCR3 with I-TAC enhanced thymidine incorporation and cell proliferation and increased p38 and ERK1/2 phosphorylation. These data indicate that 1) human airway epithelial cells primarily express CXCR3-B mRNA, 2) surface expression of CXCR3 is largely confined to the S + G(2)/M phases of the cell cycle, and 3) activation of CXCR3 induces DNA synthesis, cell proliferation, and activation of MAPK pathways. We speculate that activation of CXCR3 exerts a mitogenic effect in HBEC, which may be important during airway mucosal injury in obstructive airway diseases such as asthma and chronic obstructive pulmonary disease.

  16. Cell-cycle-dependent Xenopus TRF1 recruitment to telomere chromatin regulated by Polo-like kinase

    Science.gov (United States)

    Nishiyama, Atsuya; Muraki, Keiko; Saito, Motoki; Ohsumi, Keita; Kishimoto, Takeo; Ishikawa, Fuyuki

    2006-01-01

    Telomeres are regulated by a homeostatic mechanism that includes telomerase and telomeric repeat binding proteins, TRF1 and TRF2. Recently, it has been hypothesized that telomeres assume distinct configurations in a cell-cycle-dependent manner, although direct biochemical evidence is lacking. Here we demonstrated that Xenopus TRF1 (xTRF1) associates with telomere chromatin specifically in mitotic Xenopus egg extracts, and dissociates from it upon mitotic exit. Both the N-terminal TRF-homology (TRFH) domain and the linker region connecting the TRFH domain and the C-terminal Myb domain are required for this cell-cycle-dependent association of xTRF1 with chromatin. In contrast, Xenopus TRF2 (xTRF2) associates with chromatin throughout the cell cycle. We showed that Polo-like kinase (Plx1) phosphorylates xTRF1 in vitro. Moreover, the mitotic xTRF1–chromatin association was significantly impaired when Plx1 was immunodepleted from the extracts. Finally, high telomerase activities were detected in association with replicating interphase chromatin compared with mitotic chromatin. These results indicate that telomere chromatin is actively regulated by cell-cycle-dependent processes, and provide an insight for understanding how telomeres undergo DNA metabolisms during the cell cycle. PMID:16424898

  17. Isolation of cell cycle-dependent gamma ray-sensitive Chinese hamster ovary cell

    International Nuclear Information System (INIS)

    Stamato, T.D.; Weinstein, R.; Giaccia, A.; Mackenzie, L.

    1983-01-01

    A technique for the isolation of gamma ray-sensitive Chinese hamster ovary (CHO) cell mutants is described, which uses nylon cloth replica plating and photography with dark-field illumination to directly monitor colonies for growth after gamma irradiation. Two gamma ray-sensitive mutants were isolated using this method. One of these cells (XR-1) had a two-slope survival curve: an initial steep slope and then a flattening of the curve at about 10% survival. Subsequently, it was found that this cell is sensitive to gamma irradiation in G1, early S, and late G2 phases of the cell cycle, whereas in the resistant phase (late S phase) its survival approaches that of the parental cells. The D37 in the sensitive G1 period is approximately 30 rads, compared with 300 rads of the parental cell. This mutant cell is also sensitive to killing by the DNA breaking agent, bleomycin, but is relatively insensitive to UV light and ethyl methane sulfonate, suggesting that the defect is specific for agents that produce DNA strand breakage

  18. Cell-cycle-dependent Xenopus TRF1 recruitment to telomere chromatin regulated by Polo-like kinase

    OpenAIRE

    Nishiyama, Atsuya; Muraki, Keiko; Saito, Motoki; Ohsumi, Keita; Kishimoto, Takeo; Ishikawa, Fuyuki

    2006-01-01

    Telomeres are regulated by a homeostatic mechanism that includes telomerase and telomeric repeat binding proteins, TRF1 and TRF2. Recently, it has been hypothesized that telomeres assume distinct configurations in a cell-cycle-dependent manner, although direct biochemical evidence is lacking. Here we demonstrated that Xenopus TRF1 (xTRF1) associates with telomere chromatin specifically in mitotic Xenopus egg extracts, and dissociates from it upon mitotic exit. Both the N-terminal TRF-homology...

  19. Backup pathways of NHEJ in cells of higher eukaryotes: Cell cycle dependence

    International Nuclear Information System (INIS)

    Iliakis, George

    2009-01-01

    DNA double-strand breaks (DSBs) induced by ionizing radiation (IR) in cells of higher eukaryotes are predominantly repaired by a pathway of non-homologous end joining (NHEJ) utilizing Ku, DNA-PKcs, DNA ligase IV, XRCC4 and XLF/Cernunnos (D-NHEJ) as central components. Work carried out in our laboratory and elsewhere shows that when this pathway is chemically or genetically compromised, cells do not shunt DSBs to homologous recombination repair (HRR) but instead use another form of NHEJ operating as a backup (B-NHEJ). Here I review our efforts to characterize this repair pathway and discuss its dependence on the cell cycle as well as on the growth conditions. I present evidence that B-NHEJ utilizes ligase III, PARP-1 and histone H1. When B-NHEJ is examined throughout the cell cycle, significantly higher activity is observed in G2 phase that cannot be attributed to HRR. Furthermore, the activity of B-NHEJ is compromised when cells enter the plateau phase of growth. Together, these observations uncover a repair pathway with unexpected biochemical constitution and interesting cell cycle and growth factor regulation. They generate a framework for investigating the mechanistic basis of HRR contribution to DSB repair.

  20. Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

    DEFF Research Database (Denmark)

    Frenkel-Morgenstern, Milana; Danon, Tamar; Christian, Thomas

    2012-01-01

    The cell cycle is a temporal program that regulates DNA synthesis and cell division. When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-optimal codons. Moreover, genes encoding proteins that cycle...... at the protein level exhibit non-optimal codon preferences. Remarkably, cell cycle-regulated genes expressed in different phases display different codon preferences. Here, we show empirically that transfer RNA (tRNA) expression is indeed highest in the G2 phase of the cell cycle, consistent with the non...... that non-optimal (wobbly) matching codons influence protein synthesis during the cell cycle. We describe a new mathematical model that shows how codon usage can give rise to cell-cycle regulation. In summary, our data indicate that cells exploit wobbling to generate cell cycle-dependent dynamics...

  1. Cell cycle-dependent O-GlcNAc modification of tobacco histones and their interaction with the tobacco lectin.

    Science.gov (United States)

    Delporte, Annelies; De Zaeytijd, Jeroen; De Storme, Nico; Azmi, Abdelkrim; Geelen, Danny; Smagghe, Guy; Guisez, Yves; Van Damme, Els J M

    2014-10-01

    The Nicotiana tabacum agglutinin or Nictaba is a nucleocytoplasmic lectin that is expressed in tobacco after the plants have been exposed to jasmonate treatment or insect herbivory. Nictaba specifically recognizes GlcNAc residues. Recently, it was shown that Nictaba is interacting in vitro with the core histone proteins from calf thymus. Assuming that plant histones - similar to their animal counterparts - undergo O-GlcNAcylation, this interaction presumably occurs through binding of the lectin to the O-GlcNAc modification present on the histones. Hereupon, the question was raised whether this modification also occurs in plants and if it is cell cycle dependent. To this end, histones were purified from tobacco BY-2 suspension cells and the presence of O-GlcNAc modifications was checked. Concomitantly, O-GlcNAcylation of histone proteins was studied. Our data show that similar to animal histones plant histones are modified by O-GlcNAc in a cell cycle-dependent fashion. In addition, the interaction between Nictaba and tobacco histones was confirmed using lectin chromatography and far Western blot analysis. Collectively these findings suggest that Nictaba can act as a modulator of gene transcription through its interaction with core histones. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  2. Cell cycle dependent x-ray-induced death in Chlamydomonas reinhardi

    International Nuclear Information System (INIS)

    Gruber, H.E.; Nachtwey, D.S.

    1976-01-01

    Light-dark (L-D) synchronized Chlamydomonas grow during a 12-hr light period and divide by a series of mitoses into 4 or 8 daughter cells during the early part of the following 12-hr dark period. Sensitivity to the lethal effects of 9108 R X-irradiation varies throughout the L-D cycle. Mortality rises from 20 percent at the 1st hour to 40 percent at the 9th hour, to 70 percent at the onset of the dark; it reaches a peak of about 85 percent at about the 14th hour, just before the first cytokinesis, and then returns to a level of about 45 percent when cell division has been completed (after data correction for multiplicity of targets per colony-forming unit). Most lethally affected cells complete at least one set of divisions (into 4 or 8 daughter cells) before they die; however, exposure shortly before the first nuclear division results in two sets of divisions before death, suggesting that these cells were committed in some way at the time of irradiation to divide again 24 hr later. Some single cells exposed prior to cytokinesis exhibit mixed-colony formation: About half of their progeny die and half survive, indicating that prior to cytokinesis there are perhaps two radiation-sensitive ''targets'' per cell

  3. Cell cycle-dependent mobility of Cdc45 determined in vivo by fluorescence correlation spectroscopy.

    Directory of Open Access Journals (Sweden)

    Ronan Broderick

    Full Text Available Eukaryotic DNA replication is a dynamic process requiring the co-operation of specific replication proteins. We measured the mobility of eGFP-Cdc45 by Fluorescence Correlation Spectroscopy (FCS in vivo in asynchronous cells and in cells synchronized at the G1/S transition and during S phase. Our data show that eGFP-Cdc45 mobility is faster in G1/S transition compared to S phase suggesting that Cdc45 is part of larger protein complex formed in S phase. Furthermore, the size of complexes containing Cdc45 was estimated in asynchronous, G1/S and S phase-synchronized cells using gel filtration chromatography; these findings complemented the in vivo FCS data. Analysis of the mobility of eGFP-Cdc45 and the size of complexes containing Cdc45 and eGFP-Cdc45 after UVC-mediated DNA damage revealed no significant changes in diffusion rates and complex sizes using FCS and gel filtration chromatography analyses. This suggests that after UV-damage, Cdc45 is still present in a large multi-protein complex and that its mobility within living cells is consistently similar following UVC-mediated DNA damage.

  4. Cell Cycle Dependent Expression of Plk1 in Synchronized Porcine Fetal Fibroblasts

    Czech Academy of Sciences Publication Activity Database

    Anger, Martin; Kues, W. A.; Klíma, Jiří; Mielenz, M.; Kubelka, Michal; Motlík, Jan; Ešner, M.; Dvořák, P.; Carnwath, J. W.; Niemann, H.

    2003-01-01

    Roč. 65, č. 3 (2003), s. 245-253 ISSN 1040-452X R&D Projects: GA MŠk LN00A065 Grant - others:FIRCA(XX) R03-TW-05530-01 Institutional research plan: CEZ:AV0Z5045916 Keywords : Plk1 * serum deprivation * cell cycle Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.543, year: 2003

  5. The DREAM complex: master coordinator of cell cycle-dependent gene expression.

    Science.gov (United States)

    Sadasivam, Subhashini; DeCaprio, James A

    2013-08-01

    The dimerization partner, RB-like, E2F and multi-vulval class B (DREAM) complex provides a previously unsuspected unifying role in the cell cycle by directly linking p130, p107, E2F, BMYB and forkhead box protein M1. DREAM mediates gene repression during the G0 phase and coordinates periodic gene expression with peaks during the G1/S and G2/M phases. Perturbations in DREAM complex regulation shift the balance from quiescence towards proliferation and contribute to the increased mitotic gene expression levels that are frequently observed in cancers with a poor prognosis.

  6. Genome-wide analysis reveals a cell cycle-dependent mechanism controlling centromere propagation.

    Science.gov (United States)

    Erhardt, Sylvia; Mellone, Barbara G; Betts, Craig M; Zhang, Weiguo; Karpen, Gary H; Straight, Aaron F

    2008-12-01

    Centromeres are the structural and functional foundation for kinetochore formation, spindle attachment, and chromosome segregation. In this study, we isolated factors required for centromere propagation using genome-wide RNA interference screening for defects in centromere protein A (CENP-A; centromere identifier [CID]) localization in Drosophila melanogaster. We identified the proteins CAL1 and CENP-C as essential factors for CID assembly at the centromere. CID, CAL1, and CENP-C coimmunoprecipitate and are mutually dependent for centromere localization and function. We also identified the mitotic cyclin A (CYCA) and the anaphase-promoting complex (APC) inhibitor RCA1/Emi1 as regulators of centromere propagation. We show that CYCA is centromere localized and that CYCA and RCA1/Emi1 couple centromere assembly to the cell cycle through regulation of the fizzy-related/CDH1 subunit of the APC. Our findings identify essential components of the epigenetic machinery that ensures proper specification and propagation of the centromere and suggest a mechanism for coordinating centromere inheritance with cell division.

  7. Cell cycle-dependent DNA damage signaling induced by ICRF-193 involves ATM, ATR, CHK2, and BRCA1

    International Nuclear Information System (INIS)

    Park, Iha; Avraham, Hava Karsenty

    2006-01-01

    Topoisomerase II is essential for cell proliferation and survival and has been a target of various anticancer drugs. ICRF-193 has long been used as a catalytic inhibitor to study the function of topoisomerase II. Here, we show that ICRF-193 treatment induces DNA damage signaling. Treatment with ICRF-193 induced G2 arrest and DNA damage signaling involving γ-H2AX foci formation and CHK2 phosphorylation. DNA damage by ICRF-193 was further demonstrated by formation of the nuclear foci of 53BP1, NBS1, BRCA1, MDC1, and FANCD2 and increased comet tail moment. The DNA damage signaling induced by ICRF-193 was mediated by ATM and ATR and was restricted to cells in specific cell cycle stages such as S, G2, and mitosis including late and early G1 phases. Downstream signaling of ATM and ATR involved the phosphorylation of CHK2 and BRCA1. Altogether, our results demonstrate that ICRF-193 induces DNA damage signaling in a cell cycle-dependent manner and suggest that topoisomerase II might be essential for the progression of the cell cycle at several stages including DNA decondensation

  8. Cell cycle-dependent SUMO-1 conjugation to nuclear mitotic apparatus protein (NuMA).

    Science.gov (United States)

    Seo, Jae Sung; Kim, Ha Na; Kim, Sun-Jick; Bang, Jiyoung; Kim, Eun-A; Sung, Ki Sa; Yoon, Hyun-Joo; Yoo, Hae Yong; Choi, Cheol Yong

    2014-01-03

    Covalent conjugation of proteins with small ubiquitin-like modifier 1 (SUMO-1) plays a critical role in a variety of cellular functions including cell cycle control, replication, and transcriptional regulation. Nuclear mitotic apparatus protein (NuMA) localizes to spindle poles during mitosis, and is an essential component in the formation and maintenance of mitotic spindle poles. Here we show that NuMA is a target for covalent conjugation to SUMO-1. We find that the lysine 1766 residue is the primary NuMA acceptor site for SUMO-1 conjugation. Interestingly, SUMO modification of endogenous NuMA occurs at the entry into mitosis and this modification is reversed after exiting from mitosis. Knockdown of Ubc9 or forced expression of SENP1 results in impairment of the localization of NuMA to mitotic spindle poles during mitosis. The SUMOylation-deficient NuMA mutant is defective in microtubule bundling, and multiple spindles are induced during mitosis. The mitosis-dependent dynamic SUMO-1 modification of NuMA might contribute to NuMA-mediated formation and maintenance of mitotic spindle poles during mitosis. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Cell-Cycle-Dependent Reconfiguration of the DNA Methylome during Terminal Differentiation of Human B Cells into Plasma Cells

    Directory of Open Access Journals (Sweden)

    Gersende Caron

    2015-11-01

    Full Text Available Molecular mechanisms underlying terminal differentiation of B cells into plasma cells are major determinants of adaptive immunity but remain only partially understood. Here we present the transcriptional and epigenomic landscapes of cell subsets arising from activation of human naive B cells and differentiation into plasmablasts. Cell proliferation of activated B cells was linked to a slight decrease in DNA methylation levels, but followed by a committal step in which an S phase-synchronized differentiation switch was associated with an extensive DNA demethylation and local acquisition of 5-hydroxymethylcytosine at enhancers and genes related to plasma cell identity. Downregulation of both TGF-β1/SMAD3 signaling and p53 pathway supported this final step, allowing the emergence of a CD23-negative subpopulation in transition from B cells to plasma cells. Remarkably, hydroxymethylation of PRDM1, a gene essential for plasma cell fate, was coupled to progression in S phase, revealing an intricate connection among cell cycle, DNA (hydroxymethylation, and cell fate determination.

  10. The central role of CDE/CHR promoter elements in the regulation of cell cycle-dependent gene transcription.

    Science.gov (United States)

    Müller, Gerd A; Engeland, Kurt

    2010-02-01

    The cell cycle-dependent element (CDE) and the cell cycle genes homology region (CHR) control the transcription of genes with maximum expression in G(2) phase and in mitosis. Promoters of these genes are repressed by proteins binding to CDE/CHR elements in G(0) and G(1) phases. Relief from repression begins in S phase and continues into G(2) phase and mitosis. Generally, CDE sites are located four nucleotides upstream of CHR elements in TATA-less promoters of genes such as Cdc25C, Cdc2 and cyclin A. However, expression of some other genes, such as human cyclin B1 and cyclin B2, has been shown to be controlled only by a CHR lacking a functional CDE. To date, it is not fully understood which proteins bind to and control CDE/CHR-containing promoters. Recently, components of the DREAM complex were shown to be involved in CDE/CHR-dependent transcriptional regulation. In addition, the expression of genes regulated by CDE/CHR elements is mostly achieved through CCAAT-boxes, which bind heterotrimeric NF-Y proteins as well as the histone acetyltransferase p300. Importantly, many CDE/CHR promoters are downregulated by the tumor suppressor p53. In this review, we define criteria for CDE/CHR-regulated promoters and propose to distinguish two classes of CDE/CHR-regulated genes. The regulation through transcription factors potentially binding to the CDE/CHR is discussed, and recently discovered links to central pathways regulated by E2F, the pRB family and p53 are highlighted.

  11. Cell cycle-dependent expression of Dub3, Nanog and the p160 family of nuclear receptor coactivators (NCoAs in mouse embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Siem van der Laan

    Full Text Available Pluripotency of embryonic stem cells (ESC is tightly regulated by a network of transcription factors among which the estrogen-related receptor β (Esrrb. Esrrb contributes to the relaxation of the G1 to S-phase (G1/S checkpoint in mouse ESCs by transcriptional control of the deubiquitylase Dub3 gene, contributing to Cdc25A persistence after DNA damage. We show that in mESCs, Dub3 gene expression is cell cycle regulated and is maximal prior G1/S transition. In addition, following UV-induced DNA damage in G1, Dub3 expression markedly increases in S-phase also suggesting a role in checkpoint recovery. Unexpectedly, we also observed cell cycle-regulation of Nanog expression, and not Oct4, reaching high levels prior to G1/S transition, finely mirroring Cyclin E1 fluctuations. Curiously, while Esrrb showed only limited cell-cycle oscillations, transcript levels of the p160 family of nuclear receptor coactivators (NCoAs displayed strong cell cycle-dependent fluctuations. Since NCoAs function in concert with Esrrb in transcriptional activation, we focussed on NCoA1 whose levels specifically increase prior onset of Dub3 transcription. Using a reporter assay, we show that NCoA1 potentiates Esrrb-mediated transcription of Dub3 and we present evidence of protein interaction between the SRC1 splice variant NCoA1 and Esrrb. Finally, we show a differential developmental regulation of all members of the p160 family during neural conversion of mESCs. These findings suggest that in mouse ESCs, changes in the relative concentration of a coactivator at a given cell cycle phase, may contribute to modulation of the transcriptional activity of the core transcription factors of the pluripotent network and be implicated in cell fate decisions upon onset of differentiation.

  12. FasL and FADD delivery by a glioma-specific and cell cycle-dependent HSV-1 amplicon virus enhanced apoptosis in primary human brain tumors

    Directory of Open Access Journals (Sweden)

    Lam Paula Y

    2010-10-01

    Full Text Available Abstract Background Glioblastoma multiforme is the most malignant cancer of the brain and is notoriously difficult to treat due to the highly proliferative and infiltrative nature of the cells. Herein, we explored the combination treatment of pre-established human glioma xenograft using multiple therapeutic genes whereby the gene expression is regulated by both cell-type and cell cycle-dependent transcriptional regulatory mechanism conferred by recombinant HSV-1 amplicon vectors. Results We demonstrated for the first time that Ki67-positive proliferating primary human glioma cells cultured from biopsy samples were effectively induced into cell death by the dual-specific function of the pG8-FasL amplicon vectors. These vectors were relatively stable and exhibited minimal cytotoxicity in vivo. Intracranial implantation of pre-transduced glioma cells resulted in better survival outcome when compared with viral vectors inoculated one week post-implantation of tumor cells, indicating that therapeutic efficacy is dependent on the viral spread and mode of viral vectors administration. We further showed that pG8-FasL amplicon vectors are functional in the presence of commonly used treatment regimens for human brain cancer. In fact, the combined therapies of pG8-FasL and pG8-FADD in the presence of temozolomide significantly improved the survival of mice bearing intracranial high-grade gliomas. Conclusion Taken together, our results showed that the glioma-specific and cell cycle-dependent HSV-1 amplicon vector is potentially useful as an adjuvant therapy to complement the current gene therapy strategy for gliomas.

  13. Cell-cycle dependent expression of a translocation-mediated fusion oncogene mediates checkpoint adaptation in rhabdomyosarcoma.

    Directory of Open Access Journals (Sweden)

    Ken Kikuchi

    2014-01-01

    Full Text Available Rhabdomyosarcoma is the most commonly occurring soft-tissue sarcoma in childhood. Most rhabdomyosarcoma falls into one of two biologically distinct subgroups represented by alveolar or embryonal histology. The alveolar subtype harbors a translocation-mediated PAX3:FOXO1A fusion gene and has an extremely poor prognosis. However, tumor cells have heterogeneous expression for the fusion gene. Using a conditional genetic mouse model as well as human tumor cell lines, we show that that Pax3:Foxo1a expression is enriched in G2 and triggers a transcriptional program conducive to checkpoint adaptation under stress conditions such as irradiation in vitro and in vivo. Pax3:Foxo1a also tolerizes tumor cells to clinically-established chemotherapy agents and emerging molecularly-targeted agents. Thus, the surprisingly dynamic regulation of the Pax3:Foxo1a locus is a paradigm that has important implications for the way in which oncogenes are modeled in cancer cells.

  14. Curcumin and trans-resveratrol exert cell cycle-dependent radioprotective or radiosensitizing effects as elucidated by the PCC and G2-assay

    Energy Technology Data Exchange (ETDEWEB)

    Sebastià, N., E-mail: natividad.sebastia@uv.es [Radiation Protection Service, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Montoro, A. [Radiation Protection Service, Universitary and Politechnic Hospital La Fe, Valencia (Spain); Grupo de Investigación Biomédica en Imagen GIBI230, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Unidad Mixta de Investigación en Endocrinología, Nutrición y Dietética Clínica, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Hervás, D. [Biostatistics Unit, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Pantelias, G.; Hatzi, V.I. [Institute of Nuclear and Radiological Sciences and Technology, Energy and Safety, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, Athens (Greece); Soriano, J.M. [Grupo de Investigación Biomédica en Imagen GIBI230, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Unidad Mixta de Investigación en Endocrinología, Nutrición y Dietética Clínica, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Department of Preventive Medicine and Public Health, Faculty of Pharmacy, University of Valencia, Burjassot, Valencia (Spain); Villaescusa, J.I. [Radiation Protection Service, Universitary and Politechnic Hospital La Fe, Valencia (Spain); and others

    2014-08-15

    Highlights: • Curcumin and trans-resveratrol can exert radioprotective or radiosensitizing effects. • The mechanisms underlying such dual action were elucidated using the PCC and G2-assay. • Radioprotection occurs in non-cycling cells exposed to curcumin and resveratrol. • Radiosensitization occurs in cycling cells exposed to the chemicals. • G2-checkpoint abrogation by the chemicals underlies the radiosensitizing mechanism. - Abstract: Curcumin and trans-resveratrol are well-known antioxidant polyphenols with radiomodulatory properties, radioprotecting non-cancerous cells while radiosensitizing tumor cells. This dual action may be the result of their radical scavenging properties and their effects on cell-cycle checkpoints that are activated in response to radiation-induced chromosomal damage. It could be also caused by their effect on regulatory pathways with impact on detoxification enzymes, the up-regulation of endogenous protective systems, and cell-cycle-dependent processes of DNA damage. This work aims to elucidate the mechanisms underlying the dual action of these polyphenols and investigates under which conditions they exhibit radioprotecting or radiosensitizing properties. The peripheral blood lymphocyte test system was used, applying concentrations ranging from 1.4 to 140 μM curcumin and 2.2 to 220 μM trans-resveratrol. The experimental design focuses first on their radioprotective effects in non-cycling lymphocytes, as uniquely visualized using cell fusion-mediated premature chromosome condensation, excluding, thus, cell-cycle interference to repair processes and activation of checkpoints. Second, the radiosensitizing potential of these chemicals on the induction of chromatid breaks in cultured lymphocytes following G2-phase irradiation was evaluated by a standardized G2-chromosomal radiosensitivity predictive assay. This assay uses caffeine for G2-checkpoint abrogation and it was applied to obtain an internal control for radiosensitivity

  15. Cell cycle dependent oscillatory expression of estrogen receptor-α links Pol II elongation to neoplastic transformation.

    Science.gov (United States)

    Vantaggiato, Cristina; Tocchetti, Marta; Cappelletti, Vera; Gurtner, Aymone; Villa, Alessandro; Daidone, Maria Grazia; Piaggio, Giulia; Maggi, Adriana; Ciana, Paolo

    2014-07-01

    Decades of studies provided a detailed view of the mechanism of estrogen receptor-α (ERα) regulated gene transcription and the physio-pathological relevance of the genetic programs controlled by this receptor in a variety of tissues. However, still limited is our knowledge on the regulation of ERα synthesis. Preliminary observations showed that the expression of ERα is cell cycle regulated. Here, we have demonstrated that a well described polymorphic sequence in the first intron of ERα (PvuII and XbaI) has a key role in regulating the ERα content in cycling cells. We have shown that the RNA Pol II (Pol II) elongation is blocked at the polymorphic site and that the proto-oncogene c-MYB modulates the release of the pausing polymerase. It is well known that the two SNPs are associated to an increased risk, progression, survival and mortality of endocrine-related cancers, here we have demonstrated that the c-MYB-dependent release of Pol II at a specific phase of the cell cycle is facilitated by the px haplotype, thus leading to a higher ERα mitogenic signal. In breast cancer, this mechanism is disrupted when the hormone refractory phenotype is established; therefore, we propose this oscillator as a novel target for the development of therapies aimed at sensitizing breast cancer resistant to hormonal treatments. Because PvuII and XbaI were associated to a broad range physio-pathological conditions beside neoplastic transformation, we expect that the ERα oscillator contributes to the regulation of the estrogen signal in several tissues.

  16. p53 and cell cycle dependent transcription of kinesin family member 23 (KIF23 is controlled via a CHR promoter element bound by DREAM and MMB complexes.

    Directory of Open Access Journals (Sweden)

    Martin Fischer

    Full Text Available The microtubule-dependent molecular motor KIF23 (Kinesin family member 23 is one of two components of the centralspindlin complex assembled during late stages of mitosis. Formation of this complex is known as an essential step for cytokinesis. Here, we identified KIF23 as a new transcriptional target gene of the tumor suppressor protein p53. We showed that p53 reduces expression of KIF23 on the mRNA as well as the protein level in different cell types. Promoter reporter assays revealed that this repression results from downregulation of KIF23 promoter activity. CDK inhibitor p21(WAF1/CIP1 was shown to be necessary to mediate p53-dependent repression. Furthermore, we identified the highly conserved cell cycle genes homology region (CHR in the KIF23 promoter to be strictly required for p53-dependent repression as well as for cell cycle-dependent expression of KIF23. Cell cycle- and p53-dependent regulation of KIF23 appeared to be controlled by differential binding of DREAM and MMB complexes to the CHR element. With this study, we describe a new mechanism for transcriptional regulation of KIF23. Considering the strongly supporting function of KIF23 in cytokinesis, its p53-dependent repression may contribute to the prevention of uncontrolled cell growth.

  17. Cell Cycle-dependent Changes in Localization and Phosphorylation of the Plasma Membrane Kv2.1 K+ Channel Impact Endoplasmic Reticulum Membrane Contact Sites in COS-1 Cells.

    Science.gov (United States)

    Cobb, Melanie M; Austin, Daniel C; Sack, Jon T; Trimmer, James S

    2015-12-04

    The plasma membrane (PM) comprises distinct subcellular domains with diverse functions that need to be dynamically coordinated with intracellular events, one of the most impactful being mitosis. The Kv2.1 voltage-gated potassium channel is conditionally localized to large PM clusters that represent specialized PM:endoplasmic reticulum membrane contact sites (PM:ER MCS), and overexpression of Kv2.1 induces more exuberant PM:ER MCS in neurons and in certain heterologous cell types. Localization of Kv2.1 at these contact sites is dynamically regulated by changes in phosphorylation at one or more sites located on its large cytoplasmic C terminus. Here, we show that Kv2.1 expressed in COS-1 cells undergoes dramatic cell cycle-dependent changes in its PM localization, having diffuse localization in interphase cells, and robust clustering during M phase. The mitosis-specific clusters of Kv2.1 are localized to PM:ER MCS, and M phase clustering of Kv2.1 induces more extensive PM:ER MCS. These cell cycle-dependent changes in Kv2.1 localization and the induction of PM:ER MCS are accompanied by increased mitotic Kv2.1 phosphorylation at several C-terminal phosphorylation sites. Phosphorylation of exogenously expressed Kv2.1 is significantly increased upon metaphase arrest in COS-1 and CHO cells, and in a pancreatic β cell line that express endogenous Kv2.1. The M phase clustering of Kv2.1 at PM:ER MCS in COS-1 cells requires the same C-terminal targeting motif needed for conditional Kv2.1 clustering in neurons. The cell cycle-dependent changes in localization and phosphorylation of Kv2.1 were not accompanied by changes in the electrophysiological properties of Kv2.1 expressed in CHO cells. Together, these results provide novel insights into the cell cycle-dependent changes in PM protein localization and phosphorylation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Cell Cycle-Dependent Expression of Adeno-Associated Virus 2 (AAV2) Rep in Coinfections with Herpes Simplex Virus 1 (HSV-1) Gives Rise to a Mosaic of Cells Replicating either AAV2 or HSV-1.

    Science.gov (United States)

    Franzoso, Francesca D; Seyffert, Michael; Vogel, Rebecca; Yakimovich, Artur; de Andrade Pereira, Bruna; Meier, Anita F; Sutter, Sereina O; Tobler, Kurt; Vogt, Bernd; Greber, Urs F; Büning, Hildegard; Ackermann, Mathias; Fraefel, Cornel

    2017-08-01

    Adeno-associated virus 2 (AAV2) depends on the simultaneous presence of a helper virus such as herpes simplex virus 1 (HSV-1) for productive replication. At the same time, AAV2 efficiently blocks the replication of HSV-1, which would eventually limit its own replication by diminishing the helper virus reservoir. This discrepancy begs the question of how AAV2 and HSV-1 can coexist in a cell population. Here we show that in coinfected cultures, AAV2 DNA replication takes place almost exclusively in S/G 2 -phase cells, while HSV-1 DNA replication is restricted to G 1 phase. Live microscopy revealed that not only wild-type AAV2 (wtAAV2) replication but also reporter gene expression from both single-stranded and double-stranded (self-complementary) recombinant AAV2 vectors preferentially occurs in S/G 2 -phase cells, suggesting that the preference for S/G 2 phase is independent of the nature of the viral genome. Interestingly, however, a substantial proportion of S/G 2 -phase cells transduced by the double-stranded but not the single-stranded recombinant AAV2 vectors progressed through mitosis in the absence of the helper virus. We conclude that cell cycle-dependent AAV2 rep expression facilitates cell cycle-dependent AAV2 DNA replication and inhibits HSV-1 DNA replication. This may limit competition for cellular and viral helper factors and, hence, creates a biological niche for either virus to replicate. IMPORTANCE Adeno-associated virus 2 (AAV2) differs from most other viruses, as it requires not only a host cell for replication but also a helper virus such as an adenovirus or a herpesvirus. This situation inevitably leads to competition for cellular resources. AAV2 has been shown to efficiently inhibit the replication of helper viruses. Here we present a new facet of the interaction between AAV2 and one of its helper viruses, herpes simplex virus 1 (HSV-1). We observed that AAV2 rep gene expression is cell cycle dependent and gives rise to distinct time

  19. Regulation of store-operated Ca{sup 2+} entry activity by cell cycle dependent up-regulation of Orai2 in brain capillary endothelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Kito, Hiroaki [Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya (Japan); Department of Pharmacology, Division of Pathological Sciences, Kyoto Pharmaceutical University, Kyoto (Japan); Yamamura, Hisao; Suzuki, Yoshiaki; Yamamura, Hideto [Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya (Japan); Ohya, Susumu [Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya (Japan); Department of Pharmacology, Division of Pathological Sciences, Kyoto Pharmaceutical University, Kyoto (Japan); Asai, Kiyofumi [Department of Molecular Neurobiology, Graduate School of Medical Sciences, Nagoya City University, Nagoya (Japan); Imaizumi, Yuji, E-mail: yimaizum@phar.nagoya-cu.ac.jp [Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya (Japan)

    2015-04-10

    Store-operated Ca{sup 2+} entry (SOCE) via Orai1 and STIM1 complex is supposed to have obligatory roles in the regulation of cellular functions of vascular endothelial cells, while little is known about the contribution of Orai2. Quantitative PCR and Western blot analyses indicated the expression of Orai2 and STIM2, in addition to Orai1 and STIM1 in bovine brain capillary endothelial cell line, t-BBEC117. During the exponential growth of t-BBEC117, the knockdown of Orai1 and STIM1 significantly reduced the SOCE activity, whereas Orai2 and STIM2 siRNAs had no effect. To examine whether endogenous SOCE activity contributes to the regulation of cell cycle progression, t-BBEC117 were synchronized using double thymidine blockage. At the G2/M phase, Ca{sup 2+} influx via SOCE was decreased and Orai2 expression was increased compared to the G0/G1 phase. When Orai2 was knocked down at the G2/M phase, the decrease in SOCE was removed, and cell proliferation was partly attenuated. Taken together, Orai1 significantly contributes to cell proliferation via the functional expression, which is presumably independent of the cell cycle phases. In construct, Orai2 is specifically up-regulated during the G2/M phase, negatively modulates the SOCE activity, and may contribute to the regulation of cell cycle progression in brain capillary endothelial cells. - Highlights: • Orai1 is essential for SOCE activity in brain capillary endothelial cells (BCECs). • Cell cycle independent expression of Orai1 regulated SOCE and cell proliferation. • Orai2 was up-regulated only at G2/M phase and this consequently reduced SOCE. • Orai2 as well as Orai1 is a key player controlling SOCE and proliferation in BCECs.

  20. Regulation of store-operated Ca2+ entry activity by cell cycle dependent up-regulation of Orai2 in brain capillary endothelial cells

    International Nuclear Information System (INIS)

    Kito, Hiroaki; Yamamura, Hisao; Suzuki, Yoshiaki; Yamamura, Hideto; Ohya, Susumu; Asai, Kiyofumi; Imaizumi, Yuji

    2015-01-01

    Store-operated Ca 2+ entry (SOCE) via Orai1 and STIM1 complex is supposed to have obligatory roles in the regulation of cellular functions of vascular endothelial cells, while little is known about the contribution of Orai2. Quantitative PCR and Western blot analyses indicated the expression of Orai2 and STIM2, in addition to Orai1 and STIM1 in bovine brain capillary endothelial cell line, t-BBEC117. During the exponential growth of t-BBEC117, the knockdown of Orai1 and STIM1 significantly reduced the SOCE activity, whereas Orai2 and STIM2 siRNAs had no effect. To examine whether endogenous SOCE activity contributes to the regulation of cell cycle progression, t-BBEC117 were synchronized using double thymidine blockage. At the G2/M phase, Ca 2+ influx via SOCE was decreased and Orai2 expression was increased compared to the G0/G1 phase. When Orai2 was knocked down at the G2/M phase, the decrease in SOCE was removed, and cell proliferation was partly attenuated. Taken together, Orai1 significantly contributes to cell proliferation via the functional expression, which is presumably independent of the cell cycle phases. In construct, Orai2 is specifically up-regulated during the G2/M phase, negatively modulates the SOCE activity, and may contribute to the regulation of cell cycle progression in brain capillary endothelial cells. - Highlights: • Orai1 is essential for SOCE activity in brain capillary endothelial cells (BCECs). • Cell cycle independent expression of Orai1 regulated SOCE and cell proliferation. • Orai2 was up-regulated only at G2/M phase and this consequently reduced SOCE. • Orai2 as well as Orai1 is a key player controlling SOCE and proliferation in BCECs

  1. Decreased radioiodine uptake of FRTL-5 cells after {sup 131}I incubation in vitro: molecular biological investigations indicate a cell cycle-dependent pathway

    Energy Technology Data Exchange (ETDEWEB)

    Meller, Birgit; Deisting, Wibke; Baehre, Manfred [University of Luebeck, Clinic of Radiology and Nuclear Medicine, Luebeck (Germany); Gaspar, Erzsebet; Wenzel, Bjoern E. [University of Luebeck, Clinic of Internal Medicine I, Luebeck (Germany); Czarnocka, Barbara [Medical Centre of Postgraduate Education, Department of Clinical Biochemistry and Molecular Biology, Warsaw (Poland)

    2008-06-15

    In radioiodine therapy the 'stunning phenomenon' is defined as a reduction of radioiodine uptake after diagnostic application of {sup 131}I. In the current study, we established an in vitro model based on the 'Fisher rat thyrocyte cell line no. 5' (FRTL-5) to investigate the stunning. TSH-stimulated FRTL-5 cells were incubated with {sup 131}I. Time-dependent {sup 131}I uptake and the viability of FRTL-5 cells were evaluated at 4-144 h after radioiodine application. All data was corrected for number of viable cells, half life and {sup 131}I concentration. Sodium iodide symporter (NIS) and the housekeeping gene ({beta}-actin, GAPDH) levels were quantified by quantitative polymerase chain reaction (qPCR). Additionally, immunohistochemical staining (IHC) of NIS on the cell membrane was carried out. FRTL-5 monolayer cell cultures showed a specific maximum uptake of {sup 131}I 24-48 h after application. Significantly decreased {sup 131}I uptake values were observed after 72-144 h. The decrease in radioiodine uptake was correlated with decreasing mRNA levels of NIS and housekeeping genes. In parallel, unlike in controls, IHC staining of NIS on FRTL-5 cells declined significantly after {sup 131}I long-term incubation. It could be demonstrated that during {sup 131}I incubation of FRTL-5 cells, radioiodine uptake decreased significantly. Simultaneously decreasing levels of NIS mRNA and protein expression suggest a NIS-associated mechanism. Since mRNA levels of housekeeping genes decreased, too, the reduced NIS expression might be provoked by a cell cycle arrest. Our investigations recommend the FRTL-5 model as a valuable tool for further molecular biological investigations of the stunning phenomenon. (orig.)

  2. Estrogen Receptor Beta Displays Cell Cycle-Dependent Expression and Regulates the G1 Phase through a Non-Genomic Mechanism in Prostate Carcinoma Cells

    Directory of Open Access Journals (Sweden)

    Antoni Hurtado

    2008-01-01

    Full Text Available Background: It is well known that estrogens regulate cell cycle progression, but the specific contributions and mechanisms of action of the estrogen receptor beta (ERβ remain elusive.

  3. Distinct kinetics of DNA repair protein accumulation at DNA lesions and cell cycle-dependent formation of gammaH2AX- and NBS1-positive repair foci

    Czech Academy of Sciences Publication Activity Database

    Suchánková, Jana; Kozubek, Stanislav; Legartová, Soňa; Sehnalová, Petra; Kuntzinger, T.; Bártová, Eva

    2015-01-01

    Roč. 107, č. 12 (2015), s. 440-454 ISSN 0248-4900 R&D Projects: GA ČR(CZ) GBP302/12/G157; GA ČR(CZ) GA13-07822S Institutional support: RVO:68081707 Keywords : Cell cycle * DNA repair * Interphase Subject RIV: BO - Biophysics Impact factor: 2.552, year: 2015

  4. Human DNA-binding peptidyl-prolyl cis/trans isomerase Par14 is cell cycle dependently expressed and associates with chromatin in vivo.

    Science.gov (United States)

    Saningong, Akuma D; Bayer, Peter

    2015-02-03

    Par14, a member of the parvulin family of peptidyl-prolyl cis-trans isomerases that is involved in rRNA processing, microtubule formation and the glucose metabolism and has been suggested to play a role in chromatin remodeling on basis of sequence and structural identities to HMG proteins. Par14 is enriched in the nucleus and binds to double-stranded DNA in vitro. By means of sub-nuclear biochemical fractionations, we demonstrate that cellular Par14 is associated with chromatin 3-fold higher than with the nuclear matrix in vivo. Par14 is released from the chromatin fraction after treatment with DNase I and elutes at high NaCl concentrations from the nucleic acid-binding fraction. Using qRT-PCR and western blotting we demonstrate that Par14 is up-regulated during the S and G2/M phases in synchronised human foreskin fibroblasts cells. In the light of our results, Par14 can be described as an endogenous non-histone chromatin protein, which binds DNA in vivo. We propose that Par14 is involved in a DNA-dependent activity such as transcription.

  5. Harnessing cell-to-cell variations to probe bacterial structure and biophysics

    Science.gov (United States)

    Cass, Julie A.

    Advances in microscopy and biotechnology have given us novel insights into cellular biology and physics. While bacteria were long considered to be relatively unstructured, the development of fluorescence microscopy techniques, and spatially and temporally resolved high-throughput quantitative studies, have uncovered that the bacterial cell is highly organized, and its structure rigorously maintained. In this thesis I will describe our gateTool software, designed to harness cell-to-cell variations to probe bacterial structure, and discuss two exciting aspects of structure that we have employed gateTool to investigate: (i) chromosome organization and the cellular mechanisms for controlling DNA dynamics, and (ii) the study of cell wall synthesis, and how the genes in the synthesis pathway impact cellular shape. In the first project, we develop a spatial and temporal mapping of cell-cycle-dependent chromosomal organization, and use this quantitative map to discover that chromosomal loci segregate from midcell with universal dynamics. In the second project, I describe preliminary time- lapse and snapshot imaging analysis suggesting phentoypical coherence across peptidoglycan synthesis pathways.

  6. Quantifying Cell-to-Cell Variations in Lithium Ion Batteries

    Directory of Open Access Journals (Sweden)

    Shriram Santhanagopalan

    2012-01-01

    Full Text Available Lithium ion batteries have conventionally been manufactured in small capacities but large volumes for consumer electronics applications. More recently, the industry has seen a surge in the individual cell capacities, as well as the number of cells used to build modules and packs. Reducing cell-to-cell and lot-to-lot variations has been identified as one of the major means to reduce the rejection rate when building the packs as well as to improve pack durability. The tight quality control measures have been passed on from the pack manufactures to the companies building the individual cells and in turn to the components. This paper identifies a quantitative procedure utilizing impedance spectroscopy, a commonly used tool, to determine the effects of material variability on the cell performance, to compare the relative importance of uncertainties in the component properties, and to suggest a rational procedure to set quality control specifications for the various components of a cell, that will reduce cell-to-cell variability, while preventing undue requirements on uniformity that often result in excessive cost of manufacturing but have a limited impact on the cells' performance.

  7. Temporal Variation in Single-Cell Power-Law Rheology Spans the Ensemble Variation of Cell Population.

    Science.gov (United States)

    Cai, PingGen; Takahashi, Ryosuke; Kuribayashi-Shigetomi, Kaori; Subagyo, Agus; Sueoka, Kazuhisa; Maloney, John M; Van Vliet, Krystyn J; Okajima, Takaharu

    2017-08-08

    Changes in the cytoskeletal organization within cells can be characterized by large spatial and temporal variations in rheological properties of the cell (e.g., the complex shear modulus G ∗ ). Although the ensemble variation in G ∗ of single cells has been elucidated, the detailed temporal variation of G ∗ remains unknown. In this study, we investigated how the rheological properties of individual fibroblast cells change under a spatially confined environment in which the cell translational motion is highly restricted and the whole cell shape remains unchanged. The temporal evolution of single-cell rheology was probed at the same measurement location within the cell, using atomic force microscopy-based oscillatory deformation. The measurements reveal that the temporal variation in the power-law rheology of cells is quantitatively consistent with the ensemble variation, indicating that the cell system satisfies an ergodic hypothesis in which the temporal statistics are identical to the ensemble statistics. The autocorrelation of G ∗ implies that the cell mechanical state evolves in the ensemble of possible states with a characteristic timescale. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. Variation in traction forces during cell cycle progression.

    Science.gov (United States)

    Vianay, Benoit; Senger, Fabrice; Alamos, Simon; Anjur-Dietrich, Maya; Bearce, Elizabeth; Cheeseman, Bevan; Lee, Lisa; Théry, Manuel

    2018-02-01

    Tissue morphogenesis results from the interplay between cell growth and mechanical forces. While the impact of geometrical confinement and mechanical forces on cell proliferation has been fairly well characterised, the inverse relationship is much less understood. Here, we investigated how traction forces vary during cell cycle progression. Cell shape was constrained on micropatterned substrates in order to distinguish variations in cell contractility from cell size increase. We performed traction force measurements of asynchronously dividing cells expressing a cell-cycle reporter, to obtain measurements of contractile forces generated during cell division. We found that forces tend to increase as cells progress through G1, before reaching a plateau in S phase, and then decline during G2. While cell size increases regularly during cell cycle progression, traction forces follow a biphasic behaviour based on specific and opposite regulation of cell contractility during early and late growth phases. These results highlight the key role of cellular signalling in the regulation of cell contractility, independently of cell size and shape. Non-monotonous variations of cell contractility during cell cycle progression are likely to impact the mechanical regulation of tissue homoeostasis in a complex and non-linear manner. © 2018 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

  9. The Variation of Electrochemical Cell Potentials with Temperature

    Science.gov (United States)

    Peckham, Gavin D.; McNaught, Ian J.

    2011-01-01

    Electrochemical cell potentials have no simple relationship with temperature but depend on the interplay between the sign and magnitude of the isothermal temperature coefficient, dE[degrees]/dT, and on the magnitude of the reaction quotient, Q. The variations in possible responses of standard and non-standard cell potentials to changes in the…

  10. Diurnal Variations of Human Circulating Cell-Free Micro-RNA.

    Directory of Open Access Journals (Sweden)

    Niels H H Heegaard

    Full Text Available A 24-hour light and dark cycle-dependent rhythmicity pervades physiological processes in virtually all living organisms including humans. These regular oscillations are caused by external cues to endogenous, independent biological time-keeping systems (clocks. The rhythm is reflected by gene expression that varies in a circadian and specific fashion in different organs and tissues and is regulated largely by dynamic epigenetic and post-transcriptional mechanisms. This leads to well-documented oscillations of specific electrolytes, hormones, metabolites, and plasma proteins in blood samples. An emerging, important class of gene regulators is short single-stranded RNA (micro-RNA, miRNA that interferes post-transcriptionally with gene expression and thus may play a role in the circadian variation of gene expression. MiRNAs are promising biomarkers by virtue of their disease-specific tissue expression and because of their presence as stable entities in the circulation. However, no studies have addressed the putative circadian rhythmicity of circulating, cell-free miRNAs. This question is important both for using miRNAs as biological markers and for clues to miRNA function in the regulation of circadian gene expression. Here, we investigate 92 miRNAs in plasma samples from 24 young male, healthy volunteers repeatedly sampled 9 times during a 24-hour stay in a regulated environment. We demonstrate that a third (26/79 of the measurable plasma miRNAs (using RT-qPCR on a microfluidic system exhibit a rhythmic behavior and are distributed in two main phase patterns. Some of these miRNAs weakly target known clock genes and many have strong targets in intracellular MAPK signaling pathways. These novel findings highlight the importance of considering bio-oscillations in miRNA biomarker studies and suggest the further study of a set of specific circulating miRNAs in the regulation and functioning of biological clocks.

  11. Joint modeling of cell and nuclear shape variation

    Science.gov (United States)

    Johnson, Gregory R.; Buck, Taraz E.; Sullivan, Devin P.; Rohde, Gustavo K.; Murphy, Robert F.

    2015-01-01

    Modeling cell shape variation is critical to our understanding of cell biology. Previous work has demonstrated the utility of nonrigid image registration methods for the construction of nonparametric nuclear shape models in which pairwise deformation distances are measured between all shapes and are embedded into a low-dimensional shape space. Using these methods, we explore the relationship between cell shape and nuclear shape. We find that these are frequently dependent on each other and use this as the motivation for the development of combined cell and nuclear shape space models, extending nonparametric cell representations to multiple-component three-dimensional cellular shapes and identifying modes of joint shape variation. We learn a first-order dynamics model to predict cell and nuclear shapes, given shapes at a previous time point. We use this to determine the effects of endogenous protein tags or drugs on the shape dynamics of cell lines and show that tagged C1QBP reduces the correlation between cell and nuclear shape. To reduce the computational cost of learning these models, we demonstrate the ability to reconstruct shape spaces using a fraction of computed pairwise distances. The open-source tools provide a powerful basis for future studies of the molecular basis of cell organization. PMID:26354424

  12. Business Cycle Dependent Unemployment Benefits with Wealth Heterogeneity and Precautionary Savings

    DEFF Research Database (Denmark)

    Kristoffersen, Mark Strøm

    In the wake of the financial and economic crisis the discussion about social insurance and optimal stabilization policies has re-blossomed. This paper adds to the literature by studying the effects of a business cycle dependent level of unemployment benefits in a model with labor market matching......, wealth heterogeneity, precautionary savings, and aggregate fluctuations in productivity. The results are ambiguous: both procyclical and countercyclical unemployment benefits can increase welfare relative to business cycle invariant benefits. Procyclical benefits are beneficial due to countercyclicality...

  13. Quantifying Cell-to-Cell Variation in Power-Law Rheology

    Science.gov (United States)

    Cai, PingGen; Mizutani, Yusuke; Tsuchiya, Masahiro; Maloney, John M.; Fabry, Ben; Van Vliet, Krystyn J.; Okajima, Takaharu

    2013-01-01

    Among individual cells of the same source and type, the complex shear modulus G∗ exhibits a large log-normal distribution that is the result of spatial, temporal, and intrinsic variations. Such large distributions complicate the statistical evaluation of pharmacological treatments and the comparison of different cell states. However, little is known about the characteristic features of cell-to-cell variation. In this study, we investigated how this variation depends on the spatial location within the cell and on the actin filament cytoskeleton, the organization of which strongly influences cell mechanics. By mechanically probing fibroblasts arranged on a microarray, via atomic force microscopy, we observed that the standard deviation σ of G∗ was significantly reduced among cells in which actin filaments were depolymerized. The parameter σ also exhibited a subcellular spatial dependence. Based on our findings regarding the frequency dependence of σ of the storage modulus G′, we proposed two types of cell-to-cell variation in G′ that arise from the purely elastic and the frequency-dependent components in terms of the soft glassy rheology model of cell deformability. We concluded that the latter inherent cell-to-cell variation can be reduced greatly by disrupting actin networks, by probing at locations within the cell nucleus boundaries distant from the cell center, and by measuring at high loading frequencies. PMID:24010652

  14. Biomechanics of Meniscus Cells: Regional Variation and Comparison to Articular Chondrocytes and Ligament Cells

    OpenAIRE

    Sanchez-Adams, Johannah; Athanasiou, Kyriacos A.

    2012-01-01

    Central to understanding mechanotransduction in the knee meniscus is the characterization of meniscus cell mechanics. In addition to biochemical and geometric differences, the inner and outer regions of the meniscus contain cells that are distinct in morphology and phenotype. This study investigated the regional variation in meniscus cell mechanics in comparison to articular chondrocytes and ligament cells. It was found that the meniscus contains two biomechanically distinct cell populations,...

  15. Cell cycle dependent expression of Plk 1 in synchronized porcine fetal fibroblasts

    Czech Academy of Sciences Publication Activity Database

    Anger, M.; Kues, W. A.; Klíma, J.; Mielenz, M.; Kubelka, M.; Motlík, J.; Ešner, M.; Dvořák, Petr; Carnwath, J. W.; Niemann, H.

    2003-01-01

    Roč. 65, - (2003), s. 245-253 ISSN 1040-452X R&D Projects: GA MŠk LN00A065 Institutional research plan: CEZ:AV0Z5039906 Keywords : serum deprivation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.543, year: 2003

  16. Batch variation between branchial cell cultures: An analysis of variance

    DEFF Research Database (Denmark)

    Hansen, Heinz Johs. Max; Grosell, M.; Kristensen, L.

    2003-01-01

    We present in detail how a statistical analysis of variance (ANOVA) is used to sort out the effect of an unexpected batch-to-batch variation between cell cultures. Two separate cultures of rainbow trout branchial cells were grown on permeable filtersupports ("inserts"). They were supposed...... to be simple duplicates for testing the effect of two induced factors-apical or basolateral addition of radioactive precursors and different apical media-on the incorporation of 14C-acetate and 32Pphosphate intotissue lipids. Unfortunately, they did not altogether give the same result. By accepting this fact...... and introducing the observed difference between batches as one of the factors in an expanded three-dimensional ANOVA, we were able to overcome an otherwisecrucial lack of sufficiently reproducible duplicate values. We could thereby show that the effect of changing the apical medium was much more marked when...

  17. Daily variation in radiosensitivity of circulating blood cells and bone marrow cell density in mice

    International Nuclear Information System (INIS)

    Tabatabai, R.N.

    1984-01-01

    Mice on a 12/12 light/dark cycle were bled during a twenty-four hour period each week for eight weeks to establish daily values of circulating blood cells. No significant daily variation was found in total red blood cells, hematocrit, or percentage of reticulocytes. A significant (P < 0.001) daily variation was found in total white blood cells, with the minimum occurring at 8 PM and the maximum occurring during the daylight hours from 8 a.m. to 2 p.m. Mice were then exposed to 0 R, 20 R, 50 R, or 100 R of x-radiation to determine what dose significantly reduces the total white cell count in circulating blood. It was found that 100 R significantly (P < .05) reduces the total white cell count over a four week period post-exposure. To determine if circulating blood cells and bone marrow cells show a diurnal radiosensitivity, mice were exposed to 100 R or 200 R of x-radiation at noon or midnight. Hematocrits, reticulocyte and white blood cell counts, daily white blood cell rhythm, and bone marrow cell density indicate that these mice were more radiosensitive at night

  18. Systematic regional variations in Purkinje cell spiking patterns.

    Directory of Open Access Journals (Sweden)

    Jianqiang Xiao

    Full Text Available In contrast to the uniform anatomy of the cerebellar cortex, molecular and physiological studies indicate that significant differences exist between cortical regions, suggesting that the spiking activity of Purkinje cells (PCs in different regions could also show distinct characteristics. To investigate this possibility we obtained extracellular recordings from PCs in different zebrin bands in crus IIa and vermis lobules VIII and IX in anesthetized rats in order to compare PC firing characteristics between zebrin positive (Z+ and negative (Z- bands. In addition, we analyzed recordings from PCs in the A2 and C1 zones of several lobules in the posterior lobe, which largely contain Z+ and Z- PCs, respectively. In both datasets significant differences in simple spike (SS activity were observed between cortical regions. Specifically, Z- and C1 PCs had higher SS firing rates than Z+ and A2 PCs, respectively. The irregularity of SS firing (as assessed by measures of interspike interval distribution was greater in Z+ bands in both absolute and relative terms. The results regarding systematic variations in complex spike (CS activity were less consistent, suggesting that while real differences can exist, they may be sensitive to other factors than the cortical location of the PC. However, differences in the interactions between SSs and CSs, including the post-CS pause in SSs and post-pause modulation of SSs, were also consistently observed between bands. Similar, though less strong trends were observed in the zonal recordings. These systematic variations in spontaneous firing characteristics of PCs between zebrin bands in vivo, raises the possibility that fundamental differences in information encoding exist between cerebellar cortical regions.

  19. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

    DEFF Research Database (Denmark)

    Hou, Yong; Wu, Kui; Shi, Xulian

    2015-01-01

    BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleoti......BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate...

  20. A Technique for Designing Variation Resilient Subthreshold Sram Cell

    Directory of Open Access Journals (Sweden)

    Aminul Islam

    2013-04-01

    Full Text Available This paper presents a technique for designing a variability aware subthreshold SRAM cell. The architecture of the proposed cell is similar to the standard read-decoupled 8-transistor (RD8T SRAM cell with the exception that the access FETS are replaced with transmission gates (TGs. In this work, various design metrics are assessed and compared with RD8T SRAM cell. The proposed design offers 2.14× and 1.75× improvement in TRA (read access time and TWA (write access time respectively compared with RD8T. It proves its robustness against process variations by featuring narrower spread in TRA distribution (2.35× and TWA distribution (3.79× compared with RD8T. The proposed bitcell offers 1.16× higher read current (IREAD and 1.64× lower bitline leakage current (ILEAK respectively compared with RD8T. It also shows its robustness by offering 1.34× (1.58× tighter spread in IREAD (ILEAK compared with RD8T. It exhibits 1.42× larger IREAD to ILEAK ratio. It shows 2.2× higher frequency @ 250 mV with read bitline capacitance of 10 fF. Besides, the proposed bitcell achieves same read stability and write-ability as that of RD8T at the cost of 3 extra transistors. The leakage power of the proposed design is close to that of RD8T.   ABSTRAK: Kertas kerja ini membentangkan teknik merekabentuk sel bawah ambang SRAM yang bolehubah. Senibina sel yang dicadangkan adalah sama dengan sel SRAM 8-transistor (RD8T “pisahan-bacaan” piawai kecuali FET akses  digantikan dengan sel pintu transmisi (TGs. Di dalam kajian ini, beberapa metrik rekabentuk dinilai dan dibandingkan dengan sel RD8T SRAM. Rekabentuk yang dicadangkan menawarkan  peningkatan 2.14× dan 1.75×  dalam TRA (masa akses baca dan TWA (masa akses tulis berbanding dengan RD8T. Ia membuktikan kekukuhan variasi proses dengan menampilkan tebaran yang lebih sempit dalam pengagihan TRA (2.35 × dan pengagihan TWA (3.79 × berbanding dengan RD8T. Sel-Bit yang dicadangkan mempunyai arus baca 1.16

  1. Ion-swimming speed variation of Vibrio cholerae cells

    Indian Academy of Sciences (India)

    In the present work we report the variation in swimming speed of Vibrio cholerae with respect to the change in concentration of sodium ions in the medium. We have also studied the variation in swimming speed with respect to temperature. We find that the swimming speed initially shows a linear increase with the increase of ...

  2. Quantitative variations of CD4 + CD25 + cells in Peking duckwhite ...

    African Journals Online (AJOL)

    Purpose: To develop a chimera via microinjection of poultry xenogeneic bone marrow mesenchymal stem cells (BMMSCs), and to assess its immune tolerance based on variations in proportion of CD4+CD25+ cells in CD4+ cells (specific CD4+CD25+ cells). Methods: BMMSCs were flush out from femurs and tibias of ...

  3. Ethnic variation of the histological subtypes of renal cell carcinoma ...

    African Journals Online (AJOL)

    E.V. Ezenwa

    Malays with the papillary cell subtype, and also in the Chinese population the highest mortality rate was found in cases with the papillary cell subtype (16.9%). Conclusion: The commonest histological subtype of RCC in each of the studied ethnic groups in Singapore is clear cell carcinoma. However, most of the cancer ...

  4. Variations of cell performance in ITO-free organic solar cells with increasing cell areas

    International Nuclear Information System (INIS)

    Yeo, Jun-Seok; Yun, Jin-Mun; Kim, Junkyung; Na, Seok-In; Kim, Seok-Soon; Kim, Dong-Yu

    2011-01-01

    This study examined the effects of a cell area on the cell performances in ITO-free organic solar cells (OSCs) based on poly(3-hexylthiophene) (P3HT) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C 61 (PCBM). Highly conductive poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) films with two different sheet resistances (R sh ) were used as polymeric transparent anodes for cost-effective ITO-free OSCs. Changes in the power conversion efficiency (PCE), the fill factor (FF), the short-circuit current (J sc ), and the open-circuit voltage (V oc ) that resulted from changing the cell area or sheet resistance of transparent electrodes were systematically investigated. With increasing cell area from 4.5 to 49.5 mm 2 , the device performance of ITO-free OSCs was continuously decreased mainly due to the decrease in the FF and the series resistance (R s ). In addition, the performance of OSCs was critically dependent on R sh of the PEDOT:PSS electrode. Upon reducing R sh of the polymer anode from ∼200 to ∼90 Ω/□, the FF and PCE showed better values at an identical large cell area and exhibited a relieved cell performance degradation with increasing cell area, suggesting that the sheet resistance of transparent electrodes is a dominant factor to limit cell efficiencies in practical large-area solar cells

  5. A Unique cis-Encoded Small Noncoding RNA Is Regulating Legionella pneumophila Hfq Expression in a Life Cycle-Dependent Manner

    Directory of Open Access Journals (Sweden)

    Giulia Oliva

    2017-01-01

    Full Text Available Legionella pneumophila is an environmental bacterium that parasitizes protozoa, but it may also infect humans, thereby causing a severe pneumonia called Legionnaires’ disease. To cycle between the environment and a eukaryotic host, L. pneumophila is regulating the expression of virulence factors in a life cycle-dependent manner: replicating bacteria do not express virulence factors, whereas transmissive bacteria are highly motile and infective. Here we show that Hfq is an important regulator in this network. Hfq is highly expressed in transmissive bacteria but is expressed at very low levels in replicating bacteria. A L. pneumophila hfq deletion mutant exhibits reduced abilities to infect and multiply in Acanthamoeba castellanii at environmental temperatures. The life cycle-dependent regulation of Hfq expression depends on a unique cis-encoded small RNA named Anti-hfq that is transcribed antisense of the hfq transcript and overlaps its 5′ untranslated region. The Anti-hfq sRNA is highly expressed only in replicating L. pneumophila where it regulates hfq expression through binding to the complementary regions of the hfq transcripts. This results in reduced Hfq protein levels in exponentially growing cells. Both the small noncoding RNA (sRNA and hfq mRNA are bound and stabilized by the Hfq protein, likely leading to the cleavage of the RNA duplex by the endoribonuclease RNase III. In contrast, after the switch to transmissive bacteria, the sRNA is not expressed, allowing now an efficient expression of the hfq gene and consequently Hfq. Our results place Hfq and its newly identified sRNA anti-hfq in the center of the regulatory network governing L. pneumophila differentiation from nonvirulent to virulent bacteria.

  6. Identification of structural DNA variations in human cell cultures after long-term passage.

    Science.gov (United States)

    Pavlova, G V; Vergun, A A; Rybalkina, E Y; Butovskaya, P R; Ryskov, A P

    2015-01-01

    Random amplified polymorphic DNA (RAPD) analysis was adapted for genomic identification of cell cultures and evaluation of DNA stability in cells of different origin at different culture passages. DNA stability was observed in cultures after no more than 5 passages. Adipose-derived stromal cells demonstrated increased DNA instability. RAPD fragments from different cell lines after different number of passages were cloned and sequenced. The chromosomal localization of these fragments was identified and single-nucleotide variations in RAPD fragments isolated from cell lines after 8-12 passages were revealed. Some of them had permanent localization, while most variations demonstrated random distribution and can be considered as de novo mutations.

  7. Clinical Relevance of Gene Copy Number Variation in Metastatic Clear Cell Renal Cell Carcinoma.

    Science.gov (United States)

    Nouhaud, François-Xavier; Blanchard, France; Sesboue, Richard; Flaman, Jean-Michel; Sabourin, Jean-Christophe; Pfister, Christian; Di Fiore, Frédéric

    2018-02-23

    Gene copy number variations (CNVs) have been reported to be frequent in renal cell carcinoma (RCC), with potential prognostic value for some. However, their clinical utility, especially to guide treatment of metastatic disease remains to be established. Our objectives were to assess CNVs on a panel of selected genes and determine their clinical relevance in patients who underwent treatment of metastatic RCC. The genetic assessment was performed on frozen tissue samples of clear cell metastatic RCC using quantitative multiplex polymerase chain reaction of short fluorescent fragment method to detect CNVs on a panel of 14 genes of interest. The comparison of the electropherogram obtained from both tumor and normal renal adjacent tissue allowed for CNV identification. The clinical, biologic, and survival characteristics were assessed for their associations with the most frequent CNVs. Fifty patients with clear cell metastatic RCC were included. The CNV rate was 21.4%. The loss of CDKN2A and PLG was associated with a higher tumor stage (P relevance, especially those located on CDKN2A, PLG, and ALDOB, in a homogeneous cohort of patients with clear cell metastatic RCC. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Regular cell design approach considering lithography-induced process variations

    OpenAIRE

    Gómez Fernández, Sergio

    2014-01-01

    The deployment delays for EUVL, forces IC design to continue using 193nm wavelength lithography with innovative and costly techniques in order to faithfully print sub-wavelength features and combat lithography induced process variations. The effect of the lithography gap in current and upcoming technologies is to cause severe distortions due to optical diffraction in the printed patterns and thus degrading manufacturing yield. Therefore, a paradigm shift in layout design is mandatory towards ...

  9. The impact of diurnal variation on induced sputum cell counts in healthy adults.

    Science.gov (United States)

    Davidson, Warren J; Wong, Lisa E; The, Stephanie; Leigh, Richard

    2013-03-28

    Induced sputum cell counts are a non-invasive, reliable method for evaluating the presence, type, and degree of inflammation in the airways of the lungs. Current reference values for induced sputum cell counts in healthy adults do not account for the effects of circadian rhythm, including diurnal variation. The objective of this study was to describe the diurnal variation in induced sputum cell counts, compared between early morning and late afternoon, in healthy adult individuals. 100 healthy adult subjects with no history of lung disease and normal bronchial reactivity proceeded with induced sputum testing at 7 am and 4 pm on different days. The order of testing was randomized. The cytotechnologist preparing and performing the cell counts was blinded to the sample collection time and subject characteristics. 65 subjects were included in the final analyses. There was no significant change in the total and differential sputum cell counts between the 7 am and 4 pm collections. There was good inter-observer agreement with respect to differential sputum cell count interpretation. This is the largest study to assess the variation in induced sputum cell counts in healthy adult subjects at different times of the day. We found no significant change in total and differential sputum cell counts between the 7 am and 4 pm collection time points. This is in contrast to studies in asthmatics that demonstrated a circadian variation in sputum cell counts and other markers of inflammation, suggesting that fluctuations in airway inflammatory cells during the day are a disease-specific effect.

  10. Cell age dependent variations in oxidative protective enzymes

    International Nuclear Information System (INIS)

    Blakely, E.A.; Chang, P.Y.; Lommel, L.; Tobias, C.A.

    1986-01-01

    Activity levels of antioxidant enzymes were correlated before and after heavy-ion exposures with cellular radiosensitivity. In preliminary feasibility experiments with human T-1 cells relatively high antioxidant enzyme levels were shown in the unirradiated G 1 phase prior to the normal DNA synthetic phase. Endogenous cellular levels of three antioxidant enzymes were measured at various times in the unirradiated human T-1 cell division cycle. The enzymes measured were: catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSHPX). Unlike the case in Chinese hamster V79 cells the early data with the synchronized human cell show that in very early G 1 phase (e.g., approximately 1.5 hours after mitotic selection) there are significant peaks in the levels (U/mg cell protein) of both CAT and SOD. Both enzymes show increases as the unirradiated cells progressed from mitosis into G 1 phase while the levels of GSHPX measured in duplicate samples were somewhat more variable than was the case for the other two enzymes. Studies were made in collaboration with the Armed Forces Radiobiology Research Institute

  11. Variation in RNA virus mutation rates across host cells.

    Directory of Open Access Journals (Sweden)

    Marine Combe

    2014-01-01

    Full Text Available It is well established that RNA viruses exhibit higher rates of spontaneous mutation than DNA viruses and microorganisms. However, their mutation rates vary amply, from 10(-6 to 10(-4 substitutions per nucleotide per round of copying (s/n/r and the causes of this variability remain poorly understood. In addition to differences in intrinsic fidelity or error correction capability, viral mutation rates may be dependent on host factors. Here, we assessed the effect of the cellular environment on the rate of spontaneous mutation of the vesicular stomatitis virus (VSV, which has a broad host range and cell tropism. Luria-Delbrück fluctuation tests and sequencing showed that VSV mutated similarly in baby hamster kidney, murine embryonic fibroblasts, colon cancer, and neuroblastoma cells (approx. 10(-5 s/n/r. Cell immortalization through p53 inactivation and oxygen levels (1-21% did not have a significant impact on viral replication fidelity. This shows that previously published mutation rates can be considered reliable despite being based on a narrow and artificial set of laboratory conditions. Interestingly, we also found that VSV mutated approximately four times more slowly in various insect cells compared with mammalian cells. This may contribute to explaining the relatively slow evolution of VSV and other arthropod-borne viruses in nature.

  12. Metabolic network capacity of Escherichia coli for Krebs cycle-dependent proline hydroxylation.

    Science.gov (United States)

    Theodosiou, Eleni; Frick, Oliver; Bühler, Bruno; Schmid, Andreas

    2015-07-29

    Understanding the metabolism of the microbial host is essential for the development and optimization of whole-cell based biocatalytic processes, as it dictates production efficiency. This is especially true for redox biocatalysis where metabolically active cells are employed because of the cofactor/cosubstrate regenerative capacity endogenous in the host. Recombinant Escherichia coli was used for overproducing proline-4-hydroxylase (P4H), a dioxygenase catalyzing the hydroxylation of free L-proline into trans-4-hydroxy-L-proline with a-ketoglutarate (a-KG) as cosubstrate. In this whole-cell biocatalyst, central carbon metabolism provides the required cosubstrate a-KG, coupling P4H biocatalytic performance directly to carbon metabolism and metabolic activity. By applying both experimental and computational biology tools, such as metabolic engineering and (13)C-metabolic flux analysis ((13)C-MFA), we investigated and quantitatively described the physiological, metabolic, and bioenergetic response of the whole-cell biocatalyst to the targeted bioconversion and identified possible metabolic bottlenecks for further rational pathway engineering. A proline degradation-deficient E. coli strain was constructed by deleting the putA gene encoding proline dehydrogenase. Whole-cell biotransformations with this mutant strain led not only to quantitative proline hydroxylation but also to a doubling of the specific trans-4-L-hydroxyproline (hyp) formation rate, compared to the wild type. Analysis of carbon flux through central metabolism of the mutant strain revealed that the increased a-KG demand for P4H activity did not enhance the a-KG generating flux, indicating a tightly regulated TCA cycle operation under the conditions studied. In the wild type strain, P4H synthesis and catalysis caused a reduction in biomass yield. Interestingly, the ΔputA strain additionally compensated the associated ATP and NADH loss by reducing maintenance energy demands at comparably low glucose

  13. Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

    Directory of Open Access Journals (Sweden)

    Theodoros I. Roumeliotis

    2017-08-01

    Full Text Available Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labeling to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the functional consequences of somatic genomic variants. The robust quantification of over 9,000 proteins and 11,000 phosphopeptides on average enabled the de novo construction of a functional protein correlation network, which ultimately exposed the collateral effects of mutations on protein complexes. CRISPR-cas9 deletion of key chromatin modifiers confirmed that the consequences of genomic alterations can propagate through protein interactions in a transcript-independent manner. Lastly, we leveraged the quantified proteome to perform unsupervised classification of the cell lines and to build predictive models of drug response in colorectal cancer. Overall, we provide a deep integrative view of the functional network and the molecular structure underlying the heterogeneity of colorectal cancer cells.

  14. Menstrual Cycle Dependent Variability for Serum Tumor Markers CEA, AFP, CA 19-9, CA 125 and CA 15-3 in Healthy Women

    Directory of Open Access Journals (Sweden)

    Ayşe Binnur Erbağci

    1999-01-01

    Full Text Available Information on menstrual cycle dependent variation of tumor markers in healthy women is a subject of diagnostic efficiency and has an impact in elucidating the normal function of these markers. In this study midfollicular and midluteal concentrations of serum CEA, AFP, CA 19-9, CA 125, CA 15-3 and their relations with LH, FSH, prolactin, estradiol and progesterone were evaluated during ovulatory cycles in a group of 23 healthy female individuals. Samples were collected on the 7th and 21st day of the same menstrual cycle. Tumor marker and hormone concentrations were determined with chemiluminescence or electrochemiluminescence EIA methods. A significant phase-dependent difference was observed for CA 15-3, midluteal concentrations (mean ± SEM; 26.33 ± 1.56 U/ml higher than the midfollicular (mean ± SEM; 19.27 ± 1.49 U/ml concentrations (p < 0.001. But an obvious difference for other tumor markers investigated did not exist. Significant correlations of follicular and luteal CA 125 levels with body mass index of the subjects were observed (r:0.52, p < 0.05 and r:0.57, p < 0.005, respectively.

  15. Ethnic variation of the histological subtypes of renal cell carcinoma ...

    African Journals Online (AJOL)

    Introduction: The purpose of this study is to determine how the histological subtypes of renal cell carcinoma (RCC) vary among the heterogeneous Singaporean population and how this affects the survival rate. Patients and methods: The data analyzed in this retrospective study of the histological subtypes of RCC cases ...

  16. Single nucleotide variations in cultured cancer cells: Effect of mismatch repair.

    Science.gov (United States)

    Panyutin, Igor G; Panyutin, Irina V; Powell-Castilla, Ian; Felix, Laura; Neumann, Ronald D

    2017-10-01

    We assessed single nucleotide variations (SNVs) between individual cells in two cancer cell lines; DU145, from brain metastasis of prostate tumor with deficient mismatch repair; and HT1080, a fibrosarcoma cell line. Clones of individual cells were isolated, and sequenced using Ion Ampliseq comprehensive cancer panel that covered the exomes of 409 oncogenes and tumor suppressor genes. Five clones of DU145 and four clones of HT1080 cells were analyzed. We found from 7 to 12 unique SNVs between DU145 clones, while HT1080 clones showed no more than one unique SNV. We then sub-cloned individual cells from some of these isolated clones of DU145 and HT1080 cells. The sub-clones were expanded from a single cell to approximately one million cells after about 20 cell divisions. The sub-clones of DU145 cells had from one to four new unique SNVs within the sequenced regions. No unique SNVs were found between sub-clones of HT1080 cells. Our data demonstrate that the extent of genetic variation at the single nucleotide level in cultured cancer cells is significantly affected by the status of the DNA mismatch repair system. Published by Elsevier B.V.

  17. Donor Dependent Variations in Hematopoietic Differentiation among Embryonic and Induced Pluripotent Stem Cell Lines.

    Directory of Open Access Journals (Sweden)

    Olivier Féraud

    Full Text Available Hematopoiesis generated from human embryonic stem cells (ES and induced pluripotent stem cells (iPS are unprecedented resources for cell therapy. We compared hematopoietic differentiation potentials from ES and iPS cell lines originated from various donors and derived them using integrative and non-integrative vectors. Significant differences in differentiation toward hematopoietic lineage were observed among ES and iPS. The ability of engraftment of iPS or ES-derived cells in NOG mice varied among the lines with low levels of chimerism. iPS generated from ES cell-derived mesenchymal stem cells (MSC reproduce a similar hematopoietic outcome compared to their parental ES cell line. We were not able to identify any specific hematopoietic transcription factors that allow to distinguish between good versus poor hematopoiesis in undifferentiated ES or iPS cell lines. There is a relatively unpredictable variation in hematopoietic differentiation between ES and iPS cell lines that could not be predicted based on phenotype or gene expression of the undifferentiated cells. These results demonstrate the influence of genetic background in variation of hematopoietic potential rather than the reprogramming process.

  18. Inter-donor variation in cell subset specific immune signaling responses in healthy individuals.

    Science.gov (United States)

    Longo, Diane M; Louie, Brent; Wang, Ena; Pos, Zoltan; Marincola, Francesco M; Hawtin, Rachael E; Cesano, Alessandra

    2012-01-01

    Single cell network profiling (SCNP) is a multi-parameter flow cytometry based approach that allows for the simultaneous interrogation of intracellular signaling pathways in multiple cell subpopulations within heterogeneous tissues, without the need for individual cell subset isolation. Thus, the technology is extremely well-suited for characterizing the multitude of interconnected signaling pathways and immune cell subpopulations that regulate the function of the immune system. Recently, SCNP was applied to generate a functional map of the healthy human immune cell signaling network by profiling immune signaling pathways downstream of 12 immunomodulators in 7 distinct immune cell subsets within peripheral blood mononuclear cells (PBMCs) from 60 healthy donors. In the study reported here, the degree of inter-donor variation in the magnitude of the immune signaling responses was analyzed. The highest inter-donor differences in immune signaling pathway activity occurred following perturbation of the immune signaling network, rather than in basal signaling. When examining the full panel of immune signaling responses, as one may expect, the overall degree of inter-donor variation was positively correlated (r = 0.727) with the magnitude of node response (i.e. a larger median signaling response was associated with greater inter-donor variation). However, when examining the degree of heterogeneity across cell subpopulations for individual signaling nodes, cell subset specificity in the degree of inter-donor variation was observed for several nodes. For such nodes, relatively weak correlations between inter-donor variation and the magnitude of the response were observed. Further, within the phenotypically distinct subpopulations, a fraction of the immune signaling responses had bimodal response profiles in which (a) only a portion of the cells had elevated phospho-protein levels following modulation and (b) the proportion of responsive cells varied by donor. These data

  19. Genomic variations in the counterpart normal controls of lung squamous cell carcinomas.

    Science.gov (United States)

    Qu, Liwei; Zhou, Bo; Wang, Guizhen; Zhou, Guangbiao

    2017-11-28

    Lung squamous cell carcinoma (LUSC) causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas.We then called genomic variations specific to the normal lung tissues through filtering the genomic sequence of the normal lung tissues against that of the paired tumors, the reference human genome, the dbSNP138 common germline variants, and the variations derived from sequencing artifacts. To expand these observations, the whole exome sequences of 478 counterpart normal controls (CNCs) and paired LUSCs of The Cancer Genome Atlas (TCGA) dataset were analyzed. Sixteen genomic variations were called in the three normal lung tissues. These variations were confirmed by Sanger capillary sequencing. A mean of 0.5661 exonic variations/Mb and 7.7887 altered genes per sample were identified in the CNC genome sequences of TCGA. In these CNCs, C:G→T:A transitions, which are the genomic signatures of tobacco carcinogen N-methyl-N-nitro-N-nitrosoguanidine, were the predominant nucleotide changes. Twenty five genes in CNCs had a variation rate that exceeded 2%, including ARSD (18.62%), MUC4 (8.79%), and RBMX (7.11%). CNC variations in CTAGE5 and USP17L7 were associated with the poor prognosis of patients with LUSC. Our results uncovered previously unreported genomic variations in CNCs, rather than LUSCs, that may be involved in the development of LUSC.

  20. Effects of common germ-line genetic variation in cell cycle genes on ovarian cancer survival

    DEFF Research Database (Denmark)

    Song, H.; Hogdall, E.; Ramus, S.J.

    2008-01-01

    PURPOSE: Somatic alterations have been shown to correlate with ovarian cancer prognosis and survival, but less is known about the effects on survival of common inherited genetic variation. Of particular interest are genes involved in cell cycle pathways, which regulate cell division and could...... plausibly influence clinical characteristics of multiple tumors types. EXPERIMENTAL DESIGN: We examined associations between common germ-line genetic variation in 14 genes involved in cell cycle pathway (CCND1, CCND2, CCND3, CCNE1, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CDK2, CDK4, CDK6, and RB1....... CONCLUSION: It is unlikely that common variants in cell cycle pathways examined above associated with moderate effect in survival after diagnosis of ovarian cancer. Much larger studies will be needed to exclude common variants with small effects Udgivelsesdato: 2008/2/15...

  1. Biophysical Variation within the M1 Type of Ganglion Cell Photoreceptor

    Directory of Open Access Journals (Sweden)

    Alan J. Emanuel

    2017-10-01

    Full Text Available Intrinsically photosensitive retinal ganglion cells of the M1 type encode environmental irradiance for functions that include circadian and pupillary regulation. Their distinct role, morphology, and molecular markers indicate that they are stereotyped circuit elements, but their physiological uniformity has not been investigated in a systematic fashion. We have profiled the biophysical parameters of mouse M1s and found that extreme variation is their hallmark. Most parameters span 1–3 log units, and the full range is evident in M1s that innervate brain regions serving divergent functions. Biophysical profiles differ among cells possessing similar morphology and between neighboring M1s recorded simultaneously. Variation in each parameter is largely independent of that in others, allowing for flexible individualization. Accordingly, a common stimulus drives heterogeneous spike outputs across cells. By contrast, a population of directionally selective retinal ganglion cells appeared physiologically uniform under similar conditions. Thus, M1s lack biophysical constancy and send diverse signals downstream.

  2. Copy number and nucleotide variation of the LILR family of myelomonocytic cell activating and inhibitory receptors

    OpenAIRE

    López-Álvarez, María R.; Jones, Des C.; Jiang, Wei; Traherne, James A.; Trowsdale, John

    2013-01-01

    Leukocyte immunoglobulin-like receptors (LILR) are cell surface molecules that regulate the activities of myelomonocytic cells through the balance of inhibitory and activation signals. LILR genes are located within the leukocyte receptor complex (LRC) on chromosome 19q13.4 adjacent to KIR genes, which are subject to allelic and copy number variation (CNV). LILRB3 (ILT5) and LILRA6 (ILT8) are highly polymorphic receptors with similar extracellular domains. LILRB3 contains inhibitory ITIM motif...

  3. Development of small scale cell culture models for screening poloxamer 188 lot-to-lot variation.

    Science.gov (United States)

    Peng, Haofan; Hall, Kaitlyn M; Clayton, Blake; Wiltberger, Kelly; Hu, Weiwei; Hughes, Erik; Kane, John; Ney, Rachel; Ryll, Thomas

    2014-01-01

    Shear protectants such as poloxamer 188 play a critical role in protecting cells during cell culture bioprocessing. Lot-to-lot variation of poloxamer 188 was experienced during a routine technology transfer across sites of similar scale and equipment. Cell culture medium containing a specific poloxamer 188 lot resulted in an unusual drop in cell growth, viability, and titer during manufacturing runs. After switching poloxamer lots, culture performance returned to the expected level. In order to control the quality of poloxamer 188 and thus maintain better consistency in manufacturing, multiple small scale screening models were developed. Initially, a 5L bioreactor model was established to evaluate cell damage by high sparge rates with different poloxamer 188 lots. Subsequently, a more robust, simple, and efficient baffled shake flask model was developed. The baffled shake flask model can be performed in a high throughput manner to investigate the cell damage in a bubbling environment. The main cause of the poor performance was the loss of protection, rather than toxicity. It was also suggested that suspicious lots can be identified using different cell line and media. The screening methods provide easy, yet remarkable models for understanding and controlling cell damage due to raw material lot variation as well as studying the interaction between poloxamer 188 and cells. © 2014 American Institute of Chemical Engineers.

  4. Sex and estrous cycle-dependent rapid protein kinase signaling actions of estrogen in distal colonic cells.

    LENUS (Irish Health Repository)

    O'Mahony, Fiona

    2008-10-01

    Previous studies from our laboratory demonstrated that 17beta-estradiol (E2) rapidly inhibits Cl(-) secretion in rat and human distal colonic epithelium. The inhibition has been shown to occur via targeting of a basolateral K(+) channel identified as the KCNQ1 (KvLQT1) channel. E2 indirectly modulates the channel activity via a cascade of second messengers which are rapidly phosphorylated in response to E2. The anti-secretory mechanism may be the manner by which E2 induces fluid retention in the intestine during periods of high circulating plasma E2. Here we review the sex-dependent and estrous cycle regulation of this novel rapid response to E2. The inhibition of KCNQ1 channel activity and Cl(-) secretion will be of interest in the future in the investigation of the retentive effects of estrogen in female tissue and also in the study of secretory disorders and drugable targets of the intestine.

  5. A new epigenetic marker: The replication-coupled, cell cycle-dependent, dual modification of the histone H4 tail

    Czech Academy of Sciences Publication Activity Database

    Fidlerová, Helena; Kalinová, Jana; Blechová, Miroslava; Velek, Jiří; Raška, Ivan

    2009-01-01

    Roč. 167, č. 1 (2009), s. 76-82 ISSN 1047-8477 R&D Projects: GA ČR(CZ) GA304/06/1691 Grant - others:GA MŠk(CZ) LC535 Program:LC Institutional research plan: CEZ:AV0Z50110509; CEZ:AV0Z40550506 Keywords : epigenetics * H4K16 * H4K20 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.673, year: 2009

  6. Effect of design variations on AMTEC cell efficiency, and of operating parameters on performance OSC cell design

    International Nuclear Information System (INIS)

    Schock, A.; Noravian, H.; Kumar, V.; Or, C.

    1997-01-01

    A companion paper presented here described an OSC-derived methodology for the coupled thermal, fluid flow, and electrical analyses of AMTEC cells with multiple Beta Alumina Solid Electrolyte (BASE) tubes, and illustrated its application to a specific cell design. The present paper describes parametric results obtained by applying the same procedure to 39 variations of that cell design to determine the effect of 24 individual design variables on cell performance. For each of the 24 design variables, OSC performed detailed analyses of two designs that were identical except for that variable. This served to isolate the effect of that variable on the cell's power, efficiency, and critical temperatures. The paper presents the results of those analyses, and explains the reasons for the design decisions made by OSC. Subsequently, it describes the results of parametric analyses to determine the effect of temperature margin, input thermal power, and output voltage on the cell's critical temperatures and performance

  7. Detection of Cell Wall Chemical Variation in Zea Mays Mutants Using Near-Infrared Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Buyck, N.; Thomas, S.

    2001-01-01

    Corn stover is regarded as the prime candidate feedstock material for commercial biomass conversion in the United States. Variations in chemical composition of Zea mays cell walls can affect biomass conversion process yields and economics. Mutant lines were constructed by activating a Mu transposon system. The cell wall chemical composition of 48 mutant families was characterized using near-infrared (NIR) spectroscopy. NIR data were analyzed using a multivariate statistical analysis technique called Principal Component Analysis (PCA). PCA of the NIR data from 349 maize leaf samples reveals 57 individuals as outliers on one or more of six Principal Components (PCs) at the 95% confidence interval. Of these, 19 individuals from 16 families are outliers on either PC3 (9% of the variation) or PC6 (1% of the variation), the two PCs that contain information about cell wall polymers. Those individuals for which altered cell wall chemistry is confirmed with wet chemical analysis will then be subjected to fermentation analysis to determine whether or not biomass conversion process kinetics, yields and/or economics are significantly affected. Those mutants that provide indications for a decrease in process cost will be pursued further to identify the gene(s) responsible for the observed changes in cell wall composition and associated changes in process economics. These genes will eventually be incorporated into maize breeding programs directed at the development of a truly dual use crop.

  8. Changes in hemoglobin-oxygen affinity with shape variations of red blood cells

    Science.gov (United States)

    Chowdhury, Aniket; Dasgupta, Raktim; Majumder, Shovan K.

    2017-10-01

    Shape variations of red blood cells (RBCs) are known to occur upon exposure to various drugs or under diseased conditions. The commonly observed discocytic RBCs can be transformed to echinocytic or stomatocytic shape under such conditions. Raman spectra of the three major shape variations, namely discocyte, echinocyte, and stomatocyte, of RBCs were studied while subjecting the cells to oxygenated and deoxygenated conditions. Analysis of the recorded spectra suggests an increased level of hemoglobin (Hb)-oxygen affinity for the echinocytes. Also, some level of Hb degradation could be noticed for the deoxygenated echinocytes. The effects may arise from a reduced level of intracellular adenosine triphosphate in echinocytic cells and an increased fraction of submembrane Hb.

  9. Detection and Measurement of the Intracellular Calcium Variation in Follicular Cells

    Directory of Open Access Journals (Sweden)

    Ana M. Herrera-Navarro

    2014-01-01

    Full Text Available This work presents a new method for measuring the variation of intracellular calcium in follicular cells. The proposal consists in two stages: (i the detection of the cell’s nuclei and (ii the analysis of the fluorescence variations. The first stage is performed via watershed modified transformation, where the process of labeling is controlled. The detection process uses the contours of the cells as descriptors, where they are enhanced with a morphological filter that homogenizes the luminance variation of the image. In the second stage, the fluorescence variations are modeled as an exponential decreasing function, where the fluorescence variations are highly correlated with the changes of intracellular free Ca2+. Additionally, it is introduced a new morphological called medium reconstruction process, which helps to enhance the data for the modeling process. This filter exploits the undermodeling and overmodeling properties of reconstruction operators, such that it preserves the structure of the original signal. Finally, an experimental process shows evidence of the capabilities of the proposal.

  10. Passage Variation of PC12 Cells Results in Inconsistent Susceptibility to Externally Induced Apoptosis.

    Science.gov (United States)

    Kinarivala, Nihar; Shah, Kaushik; Abbruscato, Thomas J; Trippier, Paul C

    2017-01-18

    The PC12 cell line is a widely used in vitro model for screening the neuroprotective activity of small molecule libraries. External insult due to serum deprivation or addition of etoposide induces cell death by apoptosis. While this screening method is commonly used in early stage drug discovery no protocol accounting for cell passage number effect on neuroprotective activity has been disclosed. We herein report that passage variation results in false-positive/false-negative identification of neuroprotective compounds; undifferentiated PC12 cells with high passage number are less sensitive to injury induced by serum-deprivation or etoposide treatment. In contrast, NGF differentiated PC12 cells of later passage number are more sensitive to injury induced by etoposide than lower passage number but only after 72 h. Passage number also affects the adherence phenotype of the PC12 cells, complicating screening assays. We report an optimized protocol for screening the neuroprotective activity of small molecules in PC12 cells, which accounts for passage number variations.

  11. Effect of commercial enzymes on berry cell wall deconstruction in the context of intravineyard ripeness variation under winemaking conditions

    DEFF Research Database (Denmark)

    Gao, Yu; Fangel, Jonatan Ulrik; Willats, William George Tycho

    2016-01-01

    Significant intravineyard variation in grape berry ripening occurs within vines and between vines. However, no cell wall data are available on such variation. Here we used a checkerboard panel design to investigate ripening variation in pooled grape bunches for enzyme-assisted winemaking...... positively influence the consistency of winemaking and provides a foundation for further research into the relationship between grape berry cell wall architecture and enzyme formulations....

  12. Variation of DNA damage levels in peripheral blood mononuclear cells isolated in different laboratories

    DEFF Research Database (Denmark)

    Godschalk, Roger W L; Ersson, Clara; Stępnik, Maciej

    2014-01-01

    collected in the same way and processed using the same blood isolation procedure. The inter-laboratory variation was the prominent contributor to the overall variation. The inter-laboratory coefficient of variation decreased for both DNA strand breaks (from 68 to 26%) and FPG sensitive sites (from 57 to 12......This study investigated the levels of DNA strand breaks and formamidopyrimidine DNA glycosylase (FPG) sensitive sites, as assessed by the comet assay, in peripheral blood mononuclear cells (PBMC) from healthy women from five different countries in Europe. The laboratory in each country (referred......%) by standardisation of the primary comet assay endpoint with calibration curve samples. The level of DNA strand breaks in the samples from two of the centres (0.56-0.61 lesions/10(6) bp) was significantly higher compared with the other three centres (0.41-0.45 lesions/10(6) bp). In contrast, there was no difference...

  13. Variation of Peripheral Blood Mononuclear Cell RNA Quality in Archived Samples.

    Science.gov (United States)

    Kozlakidis, Zisis; Mant, Christine; Abdinur, Fartun; Cope, Andrew; Steiner, Szabi; Peakman, Mark; Hayday, Adrian; Cason, John

    2011-09-01

    The Infectious Diseases BioBank (IDB) has consistently archived peripheral blood mononuclear cell (PBMNC) RNA for transcriptome analyses. RNA is particularly labile, and hence, these samples provide a sensitive indicator for assessing the IDB's quality-assurance measures. Independent analyses of 104 PBMNC RNA specimens from 26 volunteers revealed that the mean RNA integrity number (RIN) was high (9.02), although RIN ranged between scores of 7 and 10. This variation of RIN values was not associated with ischemic time, PBMNC quality, number of samples processed per day, self-medication after immunization, freezer location, donor characteristics, differential white blood cell counts, or daily variation in RNA extractions (all P>0.05). RIN values were related to the date of collection, with those processed during mid-summer having highest RIN scores (P=0.0001). Amongst specimens with the lowest RIN scores, no common feature could be identified. Thus, no technical explanation for the variation in RNA quality could be ascertained and these may represent normal physiological variations. These data provide strong evidence that current IDB protocols for the isolation and preservation PBMNC RNA are robust.

  14. Heterogeneity in cancer cells: variation in drug response in different primary and secondary colorectal cancer cell lines in vitro.

    Science.gov (United States)

    Arul, Melanie; Roslani, April Camilla; Cheah, Swee Hung

    2017-05-01

    Tumor heterogeneity may give rise to differential responses to chemotherapy drugs. Therefore, unraveling tumor heterogeneity has an implication for biomarker discovery and cancer therapeutics. To test this phenomenon, we investigated the differential responses of three secondary colorectal cancer cell lines of different origins (HCT116, HT29, and SW620 cells) and four novel primary cell lines obtained from different colorectal cancer patients to 5-fluorouracil (5-FU) and oxaliplatin (L-OHP) and explored the differences in gene expression among the primary cell lines in response to exposure to cytotoxic drugs. Cells were exposed to different doses of 5-FU and L-OHP separately or in combinations of equitoxic drug or equimolar drug ratios (median effect of Chou-Talalay principle). Cell viability was assessed using MTT assay and the respective IC 50 values were determined. Changes in gene expression in primary cell lines after exposure to the same drug doses were compared using real-time PCR array. The sensitivities (IC 50 ) of different cell lines, both secondary and primary, to 5-FU and L-OHP were significantly different, whether in monotherapy or combined treatment. Primary cell lines needed higher doses to reach IC 50 . There were variations in gene expression among the primary cell lines of different chemosensitivities to the challenge of the same combined dose of 5-FU and L-OHP. The results confirm the heterogeneous nature of colorectal cancer cells from different patient tumors. Studies using primary cancer cells established from patient's tumors rather than secondary cell lines will more closely reflect the actual character of the disease.

  15. Microfluidic-Based Measurement Method of Red Blood Cell Aggregation under Hematocrit Variations.

    Science.gov (United States)

    Kang, Yang Jun

    2017-09-06

    Red blood cell (RBC) aggregation and erythrocyte sedimentation rate (ESR) are considered to be promising biomarkers for effectively monitoring blood rheology at extremely low shear rates. In this study, a microfluidic-based measurement technique is suggested to evaluate RBC aggregation under hematocrit variations due to the continuous ESR. After the pipette tip is tightly fitted into an inlet port, a disposable suction pump is connected to the outlet port through a polyethylene tube. After dropping blood (approximately 0.2 mL) into the pipette tip, the blood flow can be started and stopped by periodically operating a pinch valve. To evaluate variations in RBC aggregation due to the continuous ESR, an EAI (Erythrocyte-sedimentation-rate Aggregation Index) is newly suggested, which uses temporal variations of image intensity. To demonstrate the proposed method, the dynamic characterization of the disposable suction pump is first quantitatively measured by varying the hematocrit levels and cavity volume of the suction pump. Next, variations in RBC aggregation and ESR are quantified by varying the hematocrit levels. The conventional aggregation index (AI) is maintained constant, unrelated to the hematocrit values. However, the EAI significantly decreased with respect to the hematocrit values. Thus, the EAI is more effective than the AI for monitoring variations in RBC aggregation due to the ESR. Lastly, the proposed method is employed to detect aggregated blood and thermally-induced blood. The EAI gradually increased as the concentration of a dextran solution increased. In addition, the EAI significantly decreased for thermally-induced blood. From this experimental demonstration, the proposed method is able to effectively measure variations in RBC aggregation due to continuous hematocrit variations, especially by quantifying the EAI.

  16. Microfluidic-Based Measurement Method of Red Blood Cell Aggregation under Hematocrit Variations

    Science.gov (United States)

    2017-01-01

    Red blood cell (RBC) aggregation and erythrocyte sedimentation rate (ESR) are considered to be promising biomarkers for effectively monitoring blood rheology at extremely low shear rates. In this study, a microfluidic-based measurement technique is suggested to evaluate RBC aggregation under hematocrit variations due to the continuous ESR. After the pipette tip is tightly fitted into an inlet port, a disposable suction pump is connected to the outlet port through a polyethylene tube. After dropping blood (approximately 0.2 mL) into the pipette tip, the blood flow can be started and stopped by periodically operating a pinch valve. To evaluate variations in RBC aggregation due to the continuous ESR, an EAI (Erythrocyte-sedimentation-rate Aggregation Index) is newly suggested, which uses temporal variations of image intensity. To demonstrate the proposed method, the dynamic characterization of the disposable suction pump is first quantitatively measured by varying the hematocrit levels and cavity volume of the suction pump. Next, variations in RBC aggregation and ESR are quantified by varying the hematocrit levels. The conventional aggregation index (AI) is maintained constant, unrelated to the hematocrit values. However, the EAI significantly decreased with respect to the hematocrit values. Thus, the EAI is more effective than the AI for monitoring variations in RBC aggregation due to the ESR. Lastly, the proposed method is employed to detect aggregated blood and thermally-induced blood. The EAI gradually increased as the concentration of a dextran solution increased. In addition, the EAI significantly decreased for thermally-induced blood. From this experimental demonstration, the proposed method is able to effectively measure variations in RBC aggregation due to continuous hematocrit variations, especially by quantifying the EAI. PMID:28878199

  17. Fractional variational problems and particle in cell gyrokinetic simulations with fuzzy logic approach for tokamaks

    Directory of Open Access Journals (Sweden)

    Rastović Danilo

    2009-01-01

    Full Text Available In earlier Rastovic's papers [1] and [2], the effort was given to analyze the stochastic control of tokamaks. In this paper, the deterministic control of tokamak turbulence is investigated via fractional variational calculus, particle in cell simulations, and fuzzy logic methods. Fractional integrals can be considered as approximations of integrals on fractals. The turbulent media could be of the fractal structure and the corresponding equations should be changed to include the fractal features of the media.

  18. Genetic and Nongenetic Determinants of Cell Growth Variation Assessed by High-Throughput Microscopy

    Science.gov (United States)

    Ziv, Naomi; Siegal, Mark L.; Gresham, David

    2013-01-01

    In microbial populations, growth initiation and proliferation rates are major components of fitness and therefore likely targets of selection. We used a high-throughput microscopy assay, which enables simultaneous analysis of tens of thousands of microcolonies, to determine the sources and extent of growth rate variation in the budding yeast (Saccharomyces cerevisiae) in different glucose environments. We find that cell growth rates are regulated by the extracellular concentration of glucose as proposed by Monod (1949), but that significant heterogeneity in growth rates is observed among genetically identical individuals within an environment. Yeast strains isolated from different geographic locations and habitats differ in their growth rate responses to different glucose concentrations. Inheritance patterns suggest that the genetic determinants of growth rates in different glucose concentrations are distinct. In addition, we identified genotypes that differ in the extent of variation in growth rate within an environment despite nearly identical mean growth rates, providing evidence that alleles controlling phenotypic variability segregate in yeast populations. We find that the time to reinitiation of growth (lag) is negatively correlated with growth rate, yet this relationship is strain-dependent. Between environments, the respirative activity of individual cells negatively correlates with glucose abundance and growth rate, but within an environment respirative activity and growth rate show a positive correlation, which we propose reflects differences in protein expression capacity. Our study quantifies the sources of genetic and nongenetic variation in cell growth rates in different glucose environments with unprecedented precision, facilitating their molecular genetic dissection. PMID:23938868

  19. Somatic Variation of T-Cell Receptor Genes Strongly Associate with HLA Class Restriction.

    Directory of Open Access Journals (Sweden)

    Paul L Klarenbeek

    Full Text Available Every person carries a vast repertoire of CD4+ T-helper cells and CD8+ cytotoxic T cells for a healthy immune system. Somatic VDJ recombination at genomic loci that encode the T-cell receptor (TCR is a key step during T-cell development, but how a single T cell commits to become either CD4+ or CD8+ is poorly understood. To evaluate the influence of TCR sequence variation on CD4+/CD8+ lineage commitment, we sequenced rearranged TCRs for both α and β chains in naïve T cells isolated from healthy donors and investigated gene segment usage and recombination patterns in CD4+ and CD8+ T-cell subsets. Our data demonstrate that most V and J gene segments are strongly biased in the naïve CD4+ and CD8+ subsets with some segments increasing the odds of being CD4+ (or CD8+ up to five-fold. These V and J gene associations are highly reproducible across individuals and independent of classical HLA genotype, explaining ~11% of the observed variance in the CD4+ vs. CD8+ propensity. In addition, we identified a strong independent association of the electrostatic charge of the complementarity determining region 3 (CDR3 in both α and β chains, where a positively charged CDR3 is associated with CD4+ lineage and a negatively charged CDR3 with CD8+ lineage. Our findings suggest that somatic variation in different parts of the TCR influences T-cell lineage commitment in a predominantly additive fashion. This notion can help delineate how certain structural features of the TCR-peptide-HLA complex influence thymic selection.

  20. Single-cell paired-end genome sequencing reveals structural variation per cell cycle

    Science.gov (United States)

    Voet, Thierry; Kumar, Parveen; Van Loo, Peter; Cooke, Susanna L.; Marshall, John; Lin, Meng-Lay; Zamani Esteki, Masoud; Van der Aa, Niels; Mateiu, Ligia; McBride, David J.; Bignell, Graham R.; McLaren, Stuart; Teague, Jon; Butler, Adam; Raine, Keiran; Stebbings, Lucy A.; Quail, Michael A.; D’Hooghe, Thomas; Moreau, Yves; Futreal, P. Andrew; Stratton, Michael R.; Vermeesch, Joris R.; Campbell, Peter J.

    2013-01-01

    The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis. PMID:23630320

  1. Regional variations in HDL metabolism in human fat cells: effect of cell size

    International Nuclear Information System (INIS)

    Despres, J.; Fong, B.S.; Julien, P.; Jimenez, J.; Angel, A.

    1987-01-01

    Abdominal obesity is related to reduced plasma high-density lipoprotein (HDL) cholesterol, and both are associated with cardiovascular disease risk. The authors have observed that plasma membranes from abdominal subcutaneous adipocytes have a greater HDL binding capacity than omental fat cell plasma membranes. The present study examined whether these binding characteristics could be due to differences in fat cell size or cholesterol concentration between the two adipose depots. Abdominal subcutaneous and deep omental fat were obtained from massively obese patients at surgery. Subcutaneous abdominal fat cells were significantly larger and their cellular cholesterol content greater than omental adipocytes. The uptake of HDL by collagenase-isolated fat cells was studied by incubating the cells for 2 h at 37 0 C with 10 μg/ml 125 I-HDL 2 or 125 I-HDL 3 . In both depots, the cellular uptake of 125 I-HDL 2 and 125 I-HDL 3 was specifically inhibited by addition of 25-fold excess unlabeled HDL and a close correlation was observed between the cellular uptake of 125 I-HDL 2 and 125 I-HDL 3 . In obese patients, the uptake of 125 I-HDL was higher in subcutaneous cells than in omental cells. The cellular 125 I-HDL uptake was significantly correlated with adipocyte size and fat cell cholesterol content but not with adipocyte cholesterol concentration. These results suggest that the higher HDL uptake observed in subcutaneous cells compared with omental cells in obesity is the result of differences in adipocyte size rather than differences in the cholesterol concentration (cholesterol-to-triglyceride ratio). The increased interaction of HDL with hypertrophied abdominal adipocytes may play an important role in determining the lipid composition of HDL in obesity

  2. Variation of Neisseria gonorrhoeae lipooligosaccharide directs dendritic cell-induced T helper responses.

    Directory of Open Access Journals (Sweden)

    Sandra J van Vliet

    2009-10-01

    Full Text Available Gonorrhea is one of the most prevalent sexually transmitted diseases in the world. A naturally occurring variation of the terminal carbohydrates on the lipooligosaccharide (LOS molecule correlates with altered disease states. Here, we investigated the interaction of different stable gonoccocal LOS phenotypes with human dendritic cells and demonstrate that each variant targets a different set of receptors on the dendritic cell, including the C-type lectins MGL and DC-SIGN. Neisseria gonorrhoeae LOS phenotype C constitutes the first bacterial ligand to be described for the human C-type lectin receptor MGL. Both MGL and DC-SIGN are locally expressed at the male and female genital area, the primary site of N. gonorrhoeae infection. We show that targeting of different C-type lectins with the N. gonorrhoeae LOS variants results in alterations in dendritic cell cytokine secretion profiles and the induction of distinct adaptive CD4(+ T helper responses. Whereas N. gonorrhoeae variant A with a terminal N-acetylglucosamine on its LOS was recognized by DC-SIGN and induced significantly more IL-10 production, phenotype C, carrying a terminal N-acetylgalactosamine, primarily interacted with MGL and skewed immunity towards the T helper 2 lineage. Together, our results indicate that N. gonorrhoeae LOS variation allows for selective manipulation of dendritic cell function, thereby shifting subsequent immune responses in favor of bacterial survival.

  3. Variation in the uptake of nanoparticles by monolayer cultured cells using high resolution MeV ion beam imaging

    International Nuclear Information System (INIS)

    Tao, Ye; Mi, Zhaohong; Vanga, Sudheer Kumar; Chen, Ce-Belle; Bettiol, Andrew A.; Watt, Frank

    2015-01-01

    Gold nanoparticle uptake by cells is being increasingly studied because of its potential in biomedical applications. In this work, we show how scanning transmission ion microscopy can be employed to visualize and quantify 50 nm gold nanoparticles taken up by individual cells. Preliminary studies have indicated that the cellular content of gold nanoparticles exhibits a wide variation (up to a factor of 10) among individual cells. This cell-to-cell variation can affect the efficiency of utilizing gold nanoparticles for therapeutic or diagnostic purposes

  4. Impact of process variations and long term degradation on 6T-SRAM cells

    Directory of Open Access Journals (Sweden)

    Th. Fischer

    2007-06-01

    Full Text Available In modern deep-submicron CMOS technologies voltage scaling can not keep up with the scaling of the dimensions of transistors. Therefore the electrical fields inside the transistors are not constant anymore, while scaling down the device area. The rising electrical fields bring up reliability problems, such as hot carrier injection. Also other long term degradation mechanisms like Negative Bias Temperature Instability (NBTI come into the focus of circuit design.

    Along with process device parameter variations (threshold voltage, mobility, variations due to the degradation of devices form a big challenge for designers to build circuits that both yield high under the influence of process variations and remain functional with respect to long term device drift.

    In this work we present the influence of long term degradation and process variations on the performance of SRAM core-cells and parametric yield of SRAM arrays. For different use cases we show the performance degradation depending on temperature and supply voltage.

  5. Genetics of single-cell protein abundance variation in large yeast populations

    Science.gov (United States)

    Albert, Frank W.; Treusch, Sebastian; Shockley, Arthur H.; Bloom, Joshua S.; Kruglyak, Leonid

    2014-02-01

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or several genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL). Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power. Consequently, many eQTL are probably missed, especially those with smaller effects. Furthermore, most studies use messenger RNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics reported unexpected differences between eQTL and protein QTL (pQTL) for the same genes, but these studies have been even more limited in scope. Here we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyces cerevisiae. We measure single-cell protein abundance through the use of green fluorescent protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high versus low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci that we detected were clustered in `hotspots' that influence multiple proteins, and some hotspots were found to influence more than half of the proteins that we examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell

  6. Analysis of cell line variation in biochemical production of protoporphyrin IX

    Science.gov (United States)

    Gibbs, Summer L.; Chen, Bin; O'Hara, Julia A.; Hoopes, P. Jack; Hasan, Tayyaba; Pogue, Brian W.

    2006-02-01

    Protoporphyrin IX (PpIX) is produced via the heme synthesis pathway by the cell following administration of aminolevulinic acid (ALA). ALA synthase, the enzyme that produces ALA in the cell from glycine and succinyl-coenzyme A, is inhibited in a feedback mechanism by heme and thus is the rate limiting enzyme in the heme synthesis pathway. Since ALA is administered systemically, the rate limiting step that naturally exists in the cells is bypassed, however it is currently unclear why cells have different rate limiting steps in the ALA-PpIX synthesis pathway, and more specifically which types of cancer cells are most productive. It has been determined that when the same amount of ALA is administered to a wide panel of cancer cells in vitro that vastly differing amounts of PpIX are produced. The steps for the ALA-PpIX pathway occur in and around the mitochondria of the cell, but interestingly no correlation is seen between PpIX production and mitochondrial content of the cell, following ALA administration. However, total cell area shows positive correlation with PpIX production. Administration of the iron chelator, 1,2-dimethyl-3-hydroxy-4-pyridone (L1) in combination with ALA allows the final step in the heme synthesis pathway, conversion of PpIX to heme, to be delayed and thus increases the detectable amount of PpIX in each cell line. The cell lines that have the lowest PpIX production following administration of ALA alone show the largest increase in production following the combined administration of ALA and L1. PpIX fluorescence is thought to be a measure of cellular activity and the goal of the current study was to determine which cell lines would be the most promising targets for fluorescence detection or monitoring response to therapy. The results indicate that the cells with larger size and larger numbers of mitochondria may be good potential targets for this therapy. While this conclusion may appear obvious, it is not universally true, and cellular specific

  7. PVC bacteria: variation of, but not exception to, the Gram-negative cell plan.

    Science.gov (United States)

    Devos, Damien P

    2014-01-01

    Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacteria have features that differentiate them from classical Gram-negative (G-) bacteria. One such feature is their complex endomembrane system. Based on the difference of membrane organization and compartment identity, PVC bacteria were proposed to form an exception to the bacterial G- cell plan. Here I argue that all PVC membranes are derived from G- membranes, and that their organization and the compartments they form are similar to those of G- bacteria. I suggest that PVC membrane organization should be evaluated within a G- framework and as a variation of it. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Variation in pestivirus growth in testicle primary cell culture is more dependent on the individual cell donor than cattle breed.

    Science.gov (United States)

    Weber, Matheus N; Bauermann, Fernando V; Gómez-Romero, Ninnet; Herring, Andy D; Canal, Cláudio W; Neill, John D; Ridpath, Julia F

    2017-03-01

    The causes of bovine respiratory disease complex (BRDC) are multifactorial and include infection with both viral and bacterial pathogens. Host factors are also involved as different breeds of cattle appear to have different susceptibilities to BRDC. Infection with bovine pestiviruses, including bovine viral diarrhea virus 1 (BVDV1), BVDV2 and 'HoBi'-like viruses, is linked to the development of BRDC. The aim of the present study was to compare the growth of different bovine pestiviruses in primary testicle cell cultures obtained from taurine, indicine and mixed taurine and indicine cattle breeds. Primary cells strains, derived from testicular tissue, were generated from three animals from each breed. Bovine pestivirus strains used were from BVDV-1a, BVDV-1b, BVDV-2a and 'HoBi'-like virus. Growth was compared by determining virus titers after one passage in primary cells. All tests were run in triplicate. Virus titers were determined by endpoint dilution and RT-qPCR. Statistical analysis was performed using one way analysis of variance (ANOVA) followed by the Tukey's Multiple Comparison Test (P˂0.05). Significant differences in virus growth did not correlate with cattle breed. However, significant differences were observed between cells derived from different individuals regardless of breed. Variation in the replication of virus in primary cell strains may reflect a genetic predisposition that favors virus replication.

  9. Resistance to malaria through structural variation of red blood cell invasion receptors.

    Science.gov (United States)

    Leffler, Ellen M; Band, Gavin; Busby, George B J; Kivinen, Katja; Le, Quang Si; Clarke, Geraldine M; Bojang, Kalifa A; Conway, David J; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bougouma, Edith C; Mangano, Valentina D; Modiano, David; Sirima, Sodiomon B; Achidi, Eric; Apinjoh, Tobias O; Marsh, Kevin; Ndila, Carolyne M; Peshu, Norbert; Williams, Thomas N; Drakeley, Chris; Manjurano, Alphaxard; Reyburn, Hugh; Riley, Eleanor; Kachala, David; Molyneux, Malcolm; Nyirongo, Vysaul; Taylor, Terrie; Thornton, Nicole; Tilley, Louise; Grimsley, Shane; Drury, Eleanor; Stalker, Jim; Cornelius, Victoria; Hubbart, Christina; Jeffreys, Anna E; Rowlands, Kate; Rockett, Kirk A; Spencer, Chris C A; Kwiatkowski, Dominic P

    2017-06-16

    The malaria parasite Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy-number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently increased in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. Copyright © 2017, American Association for the Advancement of Science.

  10. Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing

    Science.gov (United States)

    Sahoo, Malaya K.; Tan, Susanna K.; Chen, Sharon F.; Kapusinszky, Beatrix; Concepcion, Katherine R.; Kjelson, Lynn; Mallempati, Kalyan; Farina, Heidi M.; Fernández-Viña, Marcelo; Tyan, Dolly; Grimm, Paul C.; Anderson, Matthew W.; Concepcion, Waldo

    2015-01-01

    BK virus (BKV) infection causing end-organ disease remains a formidable challenge to the hematopoietic cell transplant (HCT) and kidney transplant fields. As BKV-specific treatments are limited, immunologic-based therapies may be a promising and novel therapeutic option for transplant recipients with persistent BKV infection. Here, we describe a whole-genome, deep-sequencing methodology and bioinformatics pipeline that identify BKV variants across the genome and at BKV-specific HLA-A2-, HLA-B0702-, and HLA-B08-restricted CD8 T-cell epitopes. BKV whole genomes were amplified using long-range PCR with four inverse primer sets, and fragmentation libraries were sequenced on the Ion Torrent Personal Genome Machine (PGM). An error model and variant-calling algorithm were developed to accurately identify rare variants. A total of 65 samples from 18 pediatric HCT and kidney recipients with quantifiable BKV DNAemia underwent whole-genome sequencing. Limited genetic variation was observed. The median number of amino acid variants identified per sample was 8 (range, 2 to 37; interquartile range, 10), with the majority of variants (77%) detected at a frequency of <5%. When normalized for length, there was no statistical difference in the median number of variants across all genes. Similarly, the predominant virus population within samples harbored T-cell epitopes similar to the reference BKV strain that was matched for the BKV genotype. Despite the conservation of epitopes, low-level variants in T-cell epitopes were detected in 77.7% (14/18) of patients. Understanding epitope variation across the whole genome provides insight into the virus-immune interface and may help guide the development of protocols for novel immunologic-based therapies. PMID:26202116

  11. Few single nucleotide variations in exomes of human cord blood induced pluripotent stem cells.

    Directory of Open Access Journals (Sweden)

    Rui-Jun Su

    Full Text Available The effect of the cellular reprogramming process per se on mutation load remains unclear. To address this issue, we performed whole exome sequencing analysis of induced pluripotent stem cells (iPSCs reprogrammed from human cord blood (CB CD34(+ cells. Cells from a single donor and improved lentiviral vectors for high-efficiency (2-14% reprogramming were used to examine the effects of three different combinations of reprogramming factors: OCT4 and SOX2 (OS, OS and ZSCAN4 (OSZ, OS and MYC and KLF4 (OSMK. Five clones from each group were subject to whole exome sequencing analysis. We identified 14, 11, and 9 single nucleotide variations (SNVs, in exomes, including untranslated regions (UTR, in the five clones of OSMK, OS, and OSZ iPSC lines. Only 8, 7, and 4 of these, respectively, were protein-coding mutations. An average of 1.3 coding mutations per CB iPSC line is remarkably lower than previous studies using fibroblasts and low-efficiency reprogramming approaches. These data demonstrate that point nucleotide mutations during cord blood reprogramming are negligible and that the inclusion of genome stabilizers like ZSCAN4 during reprogramming may further decrease reprogramming-associated mutations. Our findings provide evidence that CB is a superior source of cells for iPSC banking.

  12. Plasticity in variation of xylem and phloem cell characteristics of Norway spruce under different local conditions

    Directory of Open Access Journals (Sweden)

    Jozica eGricar

    2015-09-01

    Full Text Available There is limited information on intra-annual plasticity of secondary tissues of tree species growing under different environmental conditions. To increase the knowledge about the plasticity of secondary growth, which allows trees to adapt to specific local climatic regimes, we examined climate–radial growth relationships of Norway spruce (Picea abies (L. H. Karst. from three contrasting locations in the temperate climatic zone by analyzing tree-ring widths for the period 1932–2010, and cell characteristics in xylem and phloem increments formed in the years 2009–2011. Variation in the structure of xylem and phloem increments clearly shows that plasticity in seasonal dynamics of cambial cell production and cell differentiation exists on xylem and phloem sides. Anatomical characteristics of xylem and phloem cells are predominantly site-specific characteristics, because they varied among sites but were fairly uniform among years in trees from the same site. Xylem and phloem tissues formed in the first part of the growing season seemed to be more stable in structure, indicating their priority over latewood and late phloem for tree performance. Long-term climate and radial growth analyses revealed that growth was in general less dependent on precipitation than on temperature; however, growth sensitivity to local conditions differed among the sites. Only partial dependence of radial growth of spruce on climatic factors on the selected sites confirms its strategy to adapt the structure of wood and phloem increments to function optimally in local conditions.

  13. A dense voltage-mode Josephson memory cell insensitive to systematic variations in critical current density

    International Nuclear Information System (INIS)

    Bradley, P.; Van Duzer, T.

    1985-01-01

    A destructive read-out (DRO) memory cell using three Josephson junctions has been devised whose operation depends only on the ratio of critical currents and application of the proper read/write voltages. The effects of run-to-run and across-thewafer variations in I /SUB c/ are minimized since all three junctions for a given cell are quite close to each other. Additional advantages are: immunity from flux trapping, high circuit density, and fast switching. Since destructive read-out is generally undesirable, a self-rewriting scheme is necessary. Rows and columns of cells with drivers and sense circuits, as well as small memory arrays and decoders have been simulated on SPICE. Power dissipation of cells and bias circuits for a 1K-bit RAM is estimated at about 2 mW. Inclusion of peripheral circuitry raises this by as much as a factor of five depending on the driving scheme and speed desired. Estimated access time is appreciably less than a nanosecond. Preliminary experimental investigations are reported

  14. Variations in Glycogen Synthesis in Human Pluripotent Stem Cells with Altered Pluripotent States

    Science.gov (United States)

    Chen, Richard J.; Zhang, Guofeng; Garfield, Susan H.; Shi, Yi-Jun; Chen, Kevin G.; Robey, Pamela G.; Leapman, Richard D.

    2015-01-01

    Human pluripotent stem cells (hPSCs) represent very promising resources for cell-based regenerative medicine. It is essential to determine the biological implications of some fundamental physiological processes (such as glycogen metabolism) in these stem cells. In this report, we employ electron, immunofluorescence microscopy, and biochemical methods to study glycogen synthesis in hPSCs. Our results indicate that there is a high level of glycogen synthesis (0.28 to 0.62 μg/μg proteins) in undifferentiated human embryonic stem cells (hESCs) compared with the glycogen levels (0 to 0.25 μg/μg proteins) reported in human cancer cell lines. Moreover, we found that glycogen synthesis was regulated by bone morphogenetic protein 4 (BMP-4) and the glycogen synthase kinase 3 (GSK-3) pathway. Our observation of glycogen bodies and sustained expression of the pluripotent factor Oct-4 mediated by the potent GSK-3 inhibitor CHIR-99021 reveals an altered pluripotent state in hPSC culture. We further confirmed glycogen variations under different naïve pluripotent cell growth conditions based on the addition of the GSK-3 inhibitor BIO. Our data suggest that primed hPSCs treated with naïve growth conditions acquire altered pluripotent states, similar to those naïve-like hPSCs, with increased glycogen synthesis. Furthermore, we found that suppression of phosphorylated glycogen synthase was an underlying mechanism responsible for altered glycogen synthesis. Thus, our novel findings regarding the dynamic changes in glycogen metabolism provide new markers to assess the energetic and various pluripotent states in hPSCs. The components of glycogen metabolic pathways offer new assays to delineate previously unrecognized properties of hPSCs under different growth conditions. PMID:26565809

  15. Sunspot cycle-dependent changes in the distribution of GSE latitudinal angles of IMF observed near 1 AU

    Science.gov (United States)

    Felix Pereira, B.; Girish, T. E.

    2004-05-01

    The solar cycle variations in the characteristics of the GSE latitudinal angles of the Interplanetary Magnetic Field ($\\theta$GSE) observed near 1 AU have been studied for the period 1967-2000. It is observed that the statistical parameters mean, standard deviation, skewness and kurtosis vary with sunspot cycle. The $\\theta$GSE distribution resembles the Gaussian curve during sunspot maximum and is clearly non-Gaussian during sunspot minimum. The width of the $\\theta$GSE distribution is found to increase with sunspot activity, which is likely to depend on the occurrence of solar transients. Solar cycle variations in skewness are ordered by the solar polar magnetic field changes. This can be explained in terms of the dependence of the dominant polarity of the north-south component of IMF in the GSE system near 1 AU on the IMF sector polarity and the structure of the heliospheric current sheet.

  16. Beat-to-Beat Variation in Periodicity of Local Calcium Releases Contributes to Intrinsic Variations of Spontaneous Cycle Length in Isolated Single Sinoatrial Node Cells.

    Directory of Open Access Journals (Sweden)

    Oliver Monfredi

    Full Text Available Spontaneous, submembrane local Ca(2+ releases (LCRs generated by the sarcoplasmic reticulum in sinoatrial nodal cells, the cells of the primary cardiac pacemaker, activate inward Na(+/Ca(2+-exchange current to accelerate the diastolic depolarization rate, and therefore to impact on cycle length. Since LCRs are generated by Ca(2+ release channel (i.e. ryanodine receptor openings, they exhibit a degree of stochastic behavior, manifested as notable cycle-to-cycle variations in the time of their occurrence.The present study tested whether variation in LCR periodicity contributes to intrinsic (beat-to-beat cycle length variability in single sinoatrial nodal cells.We imaged single rabbit sinoatrial nodal cells using a 2D-camera to capture LCRs over the entire cell, and, in selected cells, simultaneously measured action potentials by perforated patch clamp.LCRs begin to occur on the descending part of the action potential-induced whole-cell Ca(2+ transient, at about the time of the maximum diastolic potential. Shortly after the maximum diastolic potential (mean 54±7.7 ms, n = 14, the ensemble of waxing LCR activity converts the decay of the global Ca(2+ transient into a rise, resulting in a late, whole-cell diastolic Ca(2+ elevation, accompanied by a notable acceleration in diastolic depolarization rate. On average, cells (n = 9 generate 13.2±3.7 LCRs per cycle (mean±SEM, varying in size (7.1±4.2 µm and duration (44.2±27.1 ms, with both size and duration being greater for later-occurring LCRs. While the timing of each LCR occurrence also varies, the LCR period (i.e. the time from the preceding Ca(2+ transient peak to an LCR's subsequent occurrence averaged for all LCRs in a given cycle closely predicts the time of occurrence of the next action potential, i.e. the cycle length.Intrinsic cycle length variability in single sinoatrial nodal cells is linked to beat-to-beat variations in the average period of individual LCRs each cycle.

  17. Variations in insulin responsiveness in rat fat cells are due to metabolic differences rather than insulin binding

    DEFF Research Database (Denmark)

    Hansen, Finn Mølgård; Nilsson, Poul; Sonne, Ole

    1983-01-01

    -insulin to fat cells. Insulin binding was not correlated to the plasma insulin level which however was reflected in the lipoprotein lipase activity in the adipose tissue. In conclusion, these results indicate that variations in insulin responsiveness in fat cells are due to alterations in cellular metabolism...

  18. Regional variations in Paneth cell antimicrobial peptide expression along the mouse intestinal tract

    Directory of Open Access Journals (Sweden)

    Bevins Charles L

    2008-07-01

    Full Text Available Abstract Background Enteric antimicrobial peptides secreted from Paneth cells, including α-defensins (in mice named cryptdins, are key effector molecules of innate immunity in the small intestine. The importance of Paneth cells α-defensins emerged from studies of enteric bacterial infection in genetically modified mice, as well as from recent studies linking reduced levels of these α-defensins to Crohn's disease localized to the ileum. However, analysis of expression of Paneth cell α-defensins is incomplete. We therefore performed a comprehensive evaluation of the distribution of antimicrobial molecules along the mouse small intestinal tract to identify potential variations in regional expression. Results In conventionally reared mice, the repertoire of Paneth cell antimicrobials differs between duodenum and ileum. In contrast to the uniform expression of most Paneth cell antimicrobials, both cryptdin 4 and cryptdin-related sequences (CRS 4C peptides were expressed at progressively increasing amounts (101- and 104-fold, respectively comparing duodenum and ileum. In tissues other than the small intestine, expression of CRS peptides was noted in thymus and caecum. Most Paneth cell products were also produced in the small intestine of germ-free mice at levels similar to those in controls, however CRS4C and RegIIIγ had reduced levels in the former (3- and 8-fold, respectively. No significant changes in expression levels of Paneth cell antimicrobial peptides was observed after oral challenge with either Salmonella enterica serovar typhimurium or Listeria monocytogenes, supporting current notions on the constitutive nature of this defensive system. Conclusion The repertoire of antimicrobial peptides changes along the small intestinal tract, and a subset of these molecules are up-regulated upon colonization, but not in response to enteric bacterial pathogens. The changes detected upon colonization suggest that Paneth cell antimicrobial peptides

  19. Comparison of Cultivars and Seasonal Variation in Blueberry (Vaccinium Species) Leaf Extract on Adult T-Cell Leukemia Cell Line Growth Suppression

    OpenAIRE

    Kai, Hisahiro; Fuse, Takuichi; Kunitake, Hisato; Morishita, Kazuhiro; Matsuno, Koji

    2014-01-01

    The inhibitory effects of blueberry leaves on the proliferation of adult T-cell leukemia (ATL) cell lines have previously been reported. A comparison of blueberry leaf extracts from different cultivars and seasonal variation were investigated regarding their effects on ATL cell line proliferation. The inhibitory effects of 80% ethanol leaf extracts from different blueberry cultivars collected from April to December in 2006 or 2008 were evaluated using two ATL cell lines. The bioactivities of ...

  20. Copy number and nucleotide variation of the LILR family of myelomonocytic cell activating and inhibitory receptors.

    Science.gov (United States)

    López-Álvarez, María R; Jones, Des C; Jiang, Wei; Traherne, James A; Trowsdale, John

    2014-02-01

    Leukocyte immunoglobulin-like receptors (LILR) are cell surface molecules that regulate the activities of myelomonocytic cells through the balance of inhibitory and activation signals. LILR genes are located within the leukocyte receptor complex (LRC) on chromosome 19q13.4 adjacent to KIR genes, which are subject to allelic and copy number variation (CNV). LILRB3 (ILT5) and LILRA6 (ILT8) are highly polymorphic receptors with similar extracellular domains. LILRB3 contains inhibitory ITIM motifs and LILRA6 is coupled to an adaptor with activating ITAM motifs. We analysed the sequences of the extracellular immunoglobulin domain-encoding regions of LILRB3 and LILRA6 in 20 individuals, and determined the copy number of these receptors, in addition to those of other members of the LILR family. We found 41 polymorphic sites within the extracellular domains of LILRB3 and LILRA6. Twenty-four of these sites were common to both receptors. LILRA6, but not LILRB3, exhibited CNV. In 20 out of 48 human cell lines from the International Histocompatibility Working Group, LILRA6 was deleted or duplicated. The only other LILR gene exhibiting genomic aberration was LILRA3, in this case due to a partial deletion.

  1. Genetic variation in MHC proteins is associated with T cell receptor expression biases

    Science.gov (United States)

    Sharon, Eilon; Sibener, Leah V.; Battle, Alexis; Fraser, Hunter B.; Garcia, K. Christopher; Pritchard, Jonathan K.

    2016-01-01

    Within each individual, a highly diverse T cell receptor (TCR) repertoire interacts with peptides presented by major histocompatibility complex (MHC) molecules. Despite extensive research, it remains controversial whether germline-encoded TCR-MHC contacts promote TCR-MHC specificity and if so, whether there exist differences in TCR V-gene compatibilities with different MHC alleles. We applied eQTL mapping to test for associations between genetic variation and TCR V-gene usage in a large human cohort. We report strong trans associations between variation in the MHC locus and TCR V-gene usage. Fine mapping of the association signals reveals specific amino acids in MHC genes that bias V-gene usage, many of which contact or are spatially proximal to the TCR or peptide. Hence, these MHC variants, several of which are linked to autoimmune diseases, can directly affect TCR-MHC interaction. These results provide the first examples of trans-QTLs mediated by protein-protein interactions, and are consistent with intrinsic TCR-MHC specificity. PMID:27479906

  2. Diurnal Variations of Human Circulating Cell-Free Micro-RNA

    DEFF Research Database (Denmark)

    Heegaard, Niels H H; Carlsen, Anting Liu; Lilje, Berit

    2016-01-01

    . An emerging, important class of gene regulators is short single-stranded RNA (micro-RNA, miRNA) that interferes post-transcriptionally with gene expression and thus may play a role in the circadian variation of gene expression. MiRNAs are promising biomarkers by virtue of their disease-specific tissue...... expression and because of their presence as stable entities in the circulation. However, no studies have addressed the putative circadian rhythmicity of circulating, cell-free miRNAs. This question is important both for using miRNAs as biological markers and for clues to miRNA function in the regulation...... expression that varies in a circadian and specific fashion in different organs and tissues and is regulated largely by dynamic epigenetic and post-transcriptional mechanisms. This leads to well-documented oscillations of specific electrolytes, hormones, metabolites, and plasma proteins in blood samples...

  3. Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins

    DEFF Research Database (Denmark)

    Tyanova, S.; Frishman, D.; Cox, J.

    2013-01-01

    of the cell division cycle we investigate how the variation of the amount of phosphorylation correlates with the protein structure in the vicinity of the modified site. We find two distinct phosphorylation site groups: intrinsically disordered regions tend to contain sites with dynamically varying levels...... that includes a temporal dimension. By contrast, structural properties of identified phosphorylation sites have so far been investigated in a static, non-quantitative way. Here we combine for the first time dynamic properties of the phosphoproteome with protein structural features. At six time points...... in the latter. Furthermore, these preferences scale with the degree of disorderedness, from regular to irregular and to disordered structures. Our results suggest that the structural organization of the region in which a phosphorylation site resides may serve as an additional control mechanism. They also imply...

  4. Power optimized variation aware dual-threshold SRAM cell design technique

    Directory of Open Access Journals (Sweden)

    Aminul Islam

    2011-02-01

    Full Text Available Aminul Islam1, Mohd Hasan21Department of Electronics and Communication Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India; 2Department of Electronics Engineering, Aligarh Muslim University, Aligarh, Uttar Pradesh, IndiaAbstract: Bulk complementary metal-oxide semiconductor (CMOS technology is facing enormous challenges at channel lengths below 45 nm, such as gate tunneling, device mismatch, random dopant fluctuations, and mobility degradation. Although multiple gate transistors and strained silicon devices overcome some of the bulk CMOS problems, it is sensible to look for revolutionary new materials and devices to replace silicon. It is obvious that future technology materials should exhibit higher mobility, better channel electrostatics, scalability, and robustness against process variations. Carbon nanotube-based technology is very promising because it has most of these desired features. There is a need to explore the potential of this emerging technology by designing circuits based on this technology and comparing their performance with that of existing bulk CMOS technology. In this paper, we propose a low-power variation-immune dual-threshold voltage carbon nanotube field effect transistor (CNFET-based seven-transistor (7T static random access memory (SRAM cell. The proposed CNFET-based 7T SRAM cell offers ~1.2× improvement in standby power, ~1.3× improvement in read delay, and ~1.1× improvement in write delay. It offers narrower spread in write access time (1.4× at optimum energy point [OEP] and 1.2× at 1 V. It features 56.3% improvement in static noise margin and 40% improvement in read static noise margin. All the simulation measurements are taken at proposed OEP decided by the optimum results obtained after extensive simulation on HSPICE (high-performance simulation program with integrated circuit emphasis environment.Keywords: carbon nanotube field effect transistor (CNFET, chirality vector, random dopant

  5. Identification of copy number variations and translocations in cancer cells from Hi-C data.

    Science.gov (United States)

    Chakraborty, Abhijit; Ay, Ferhat

    2017-10-18

    Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities (e.g., copy number variations (CNVs) and translocations) altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e.g., Hi-C), which are originally developed for decoding the 3D structure of the chromatin, provide a great opportunity to simultaneously identify the locations of genomic rearrangements and to investigate the 3D genome organization in cancer cells. Even though Hi-C data has been used for validating known rearrangements, computational methods that can distinguish rearrangement signals from the inherent biases of Hi-C data and from the actual 3D conformation of chromatin, and can precisely detect rearrangement locations de novo have been missing. In this work, we characterize how intra and inter-chromosomal Hi-C contacts are distributed for normal and rearranged chromosomes to devise a new set of algorithms (i) to identify genomic segments that correspond to CNV regions such as amplifications and deletions (HiCnv), (Nurtdinov et al.) to call inter-chromosomal translocations and their boundaries (HiCtrans) from Hi-C experiments, and (iii) to simulate Hi-C data from genomes with desired rearrangements and abnormalities (AveSim) in order to select optimal parameters for and to benchmark the accuracy of our methods. Our results on 10 different cancer cell lines with Hi-C data show that we identify a total number of 105 amplifications and 45 deletions together with 90 translocations, whereas we identify virtually no such events for two karyotypically normal cell lines. Our CNV predictions correlate very well with whole genome sequencing (WGS) data among chromosomes

  6. Variation Principles and Applications in the Study of Cell Structure and Aging

    Science.gov (United States)

    Economos, Angelos C.; Miquel, Jaime; Ballard, Ralph C.; Johnson, John E., Jr.

    1981-01-01

    In this report we have attempted to show that "some reality lies concealed in biological variation". This "reality" has its principles, laws, mechanisms, and rules, only a few of which we have sketched. A related idea we pursued was that important information may be lost in the process of ignoring frequency distributions of physiological variables (as is customary in experimental physiology and gerontology). We suggested that it may be advantageous to expand one's "statistical field of vision" beyond simple averages +/- standard deviations. Indeed, frequency distribution analysis may make visible some hidden information not evident from a simple qualitative analysis, particularly when the effect of some external factor or condition (e.g., aging, dietary chemicals) is being investigated. This was clearly illustrated by the application of distribution analysis in the study of variation in mouse liver cellular and fine structure, and may be true of fine structural studies in general. In living systems, structure and function interact in a dynamic way; they are "inseparable," unlike in technological systems or machines. Changes in fine structure therefore reflect changes in function. If such changes do not exceed a certain physiologic range, a quantitative analysis of structure will provide valuable information on quantitative changes in function that may not be possible or easy to measure directly. Because there is a large inherent variation in fine structure of cells in a given organ of an individual and among individuals, changes in fine structure can be analyzed only by studying frequency distribution curves of various structural characteristics (dimensions). Simple averages +/- S.D. do not in general reveal all information on the effect of a certain factor, because often this effect is not uniform; on the contrary, this will be apparent from distribution analysis because the form of the curves will be affected. We have also attempted to show in this chapter that

  7. Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli

    KAUST Repository

    Sakata, Katsumi

    2016-10-24

    Soybean (Glycine max) is sensitive to flooding stress, and flood damage at the seedling stage is a barrier to growth. We constructed two mathematical models of the soybean metabolic network, a control model and a flooded model, from metabolic profiles in soybean plants. We simulated the metabolic profiles with perturbations before and after the flooding stimulus using the two models. We measured the variation of state that the system could maintain from a state–space description of the simulated profiles. The results showed a loss of variation of state during the flooding response in the soybean plants. Loss of variation of state was also observed in a human myelomonocytic leukaemia cell transcriptional network in response to a phorbol-ester stimulus. Thus, we detected a loss of variation of state under external stimuli in two biological systems, regardless of the regulation and stimulus types. Our results suggest that a loss of robustness may occur concurrently with the loss of variation of state in biological systems. We describe the possible applications of the quantity of variation of state in plant genetic engineering and cell biology. Finally, we present a hypothetical “external stimulus-induced information loss” model of biological systems.

  8. Incorporation of the Pore Size Variation to Modeling of the Elastic Behavior of Metallic Open-Cell Foams

    Directory of Open Access Journals (Sweden)

    Ćwieka K.

    2017-03-01

    Full Text Available In the present paper we present the approach for modeling of the elastic behavior of open-cell metallic foams concerning non-uniform pore size distribution. This approach combines design of foam structures and numerical simulations of compression tests using finite element method (FEM. In the design stage, Laguerre-Voronoi tessellations (LVT were performed on several sets of packed spheres with defined variation of radii, bringing about a set of foam structures with porosity ranging from 74 to 98% and different pore size variation quantified by the coefficient of pore volume variation, CV(V, from 0.5 to 2.1. Each structure was numerically subjected to uni-axial compression test along three directions within the elastic region. Basing on the numerical response, the effective Young’s modulus, Eeff, was calculated for each structure. It is shown that the Eeff is not only dependent on the porosity but also on the pore size variation.

  9. Genome-wide association study for milk somatic cell score in holstein cattle using copy number variation as markers.

    Science.gov (United States)

    Durán Aguilar, M; Román Ponce, S I; Ruiz López, F J; González Padilla, E; Vásquez Peláez, C G; Bagnato, A; Strillacci, M G

    2017-02-01

    Mastitis, the most common and expensive disease in dairy cows, implies significant losses in the dairy industry worldwide. Many efforts have been made to improve genetic mastitis resistance in dairy populations, but low heritability of this trait made this process not as effective as desired. The purpose of this study was to identify genomic regions explaining genetic variation of somatic cell count using copy number variations (CNVs) as markers in the Holstein population, genotyped with the Illumina BovineHD BeadChip. We found 24 and 47 copy number variation regions significantly associated with estimated breeding values for somatic cell score (SCS_EBVs) using SVS 8.3.1 and PennCNV-CNVRuler software, respectively. The association analysis performed with these two software allowed the identification of 18 candidate genes (TERT, NOTCH1, SLC6A3, CLPTM1L, PPARα, BCL-2, ABO, VAV2, CACNA1S, TRAF2, RELA, ELF3, DBH, CDK5, NF2, FASN, EWSR1 and MAP3K11) that result classified in the same functional cluster. These genes are also part of two gene networks, whose genes share the 'stress', 'cell death', 'inflammation' and 'immune response' GO terms. Combining CNV detection/association analysis based on two different algorithms helps towards a more complete identification of genes linked to phenotypic variation of the somatic cell count. © 2016 Blackwell Verlag GmbH.

  10. Variation of Red Blood Cell Distribution Width and Mean Platelet Volume after Moderate Endurance Exercise

    Directory of Open Access Journals (Sweden)

    Giuseppe Lippi

    2014-01-01

    Full Text Available Although physical exercise strongly influences several laboratory parameters, data about the hematological changes after medium distance running are scarce. We studied 31 middle-trained athletes (mean training regimen 217±32 min/week who performed a 21.1 km, half-marathon run. Blood samples were collected before the run, at the end, and 3 and 20 hours thereafter. The complete blood count was performed on Advia 2120 and included red blood cell (RBC, reticulocyte, and platelet counts; hemoglobin; mean corpuscular volume (MCV; mean corpuscular hemoglobin (MCH; reticulocyte haemoglobin content (Ret CHR; RBC distribution width (RDW, mean platelet volume (MPV. No significant variations were observed for MCH and Ret CHR. The RBC, reticulocyte, and hemoglobin values modestly decreased after the run. The MCV significantly increased at the end of running but returned to baseline 3 hours thereafter. The RDW constantly increased, reaching a peak 20 hours after the run. The platelet count and MPV both increased after the run and returned to baseline 3 hours thereafter. These results may have implications for definition of reference ranges and antidoping testing, and may also contribute to explaining the relationship between endurance exercise and mortality, since previous studies reported that RDW and MPV may be significantly associated with cardiovascular disease.

  11. Phosphorylation variation during the cell cycle scales with structural propensities of proteins.

    Directory of Open Access Journals (Sweden)

    Stefka Tyanova

    Full Text Available Phosphorylation at specific residues can activate a protein, lead to its localization to particular compartments, be a trigger for protein degradation and fulfill many other biological functions. Protein phosphorylation is increasingly being studied at a large scale and in a quantitative manner that includes a temporal dimension. By contrast, structural properties of identified phosphorylation sites have so far been investigated in a static, non-quantitative way. Here we combine for the first time dynamic properties of the phosphoproteome with protein structural features. At six time points of the cell division cycle we investigate how the variation of the amount of phosphorylation correlates with the protein structure in the vicinity of the modified site. We find two distinct phosphorylation site groups: intrinsically disordered regions tend to contain sites with dynamically varying levels, whereas regions with predominantly regular secondary structures retain more constant phosphorylation levels. The two groups show preferences for different amino acids in their kinase recognition motifs - proline and other disorder-associated residues are enriched in the former group and charged residues in the latter. Furthermore, these preferences scale with the degree of disorderedness, from regular to irregular and to disordered structures. Our results suggest that the structural organization of the region in which a phosphorylation site resides may serve as an additional control mechanism. They also imply that phosphorylation sites are associated with different time scales that serve different functional needs.

  12. Variations in insulin responsiveness in rat fat cells are due to metabolic differences rather than insulin binding

    DEFF Research Database (Denmark)

    Hansen, Finn Mølgård; Nilsson, Poul; Sonne, Ole

    1983-01-01

    to fat cells. Insulin binding was not correlated to the plasma insulin level which however was reflected in the lipoprotein lipase activity in the adipose tissue. In conclusion, these results indicate that variations in insulin responsiveness in fat cells are due to alterations in cellular metabolism......Insulin resistance was studied by comparing insulin response and insulin binding in four groups of rats. Glucose metabolism in isolated fat cells from male Wistar rats weighing 340 g was less responsive to a supramaximal dose of insulin than glucose metabolism in fat cells from rats weighing 200 g....... Induction of streptozotocin-diabetes in rats weighing 200 g resulted in a marked decrease in the insulin responsiveness of fat cells. Ventromedial hypothalamic lesions of 340 g rats had the opposite effect and restored the insulin responsiveness of fat cells. The responsiveness in the four groups...

  13. Digital reconstruction of the cell body in dense neural circuits using a spherical-coordinated variational model

    Science.gov (United States)

    Quan, Tingwei; Li, Jing; Zhou, Hang; Li, Shiwei; Zheng, Ting; Yang, Zhongqing; Luo, Qingming; Gong, Hui; Zeng, Shaoqun

    2014-05-01

    Mapping the neuronal circuits is essential to understand brain function. Recent technological advancements have made it possible to acquire the brain atlas at single cell resolution. Digital reconstruction of the neural circuits down to this level across the whole brain would significantly facilitate brain studies. However, automatic reconstruction of the dense neural connections from microscopic image still remains a challenge. Here we developed a spherical-coordinate based variational model to reconstruct the shape of the cell body i.e. soma, as one of the procedures for this purpose. When intuitively processing the volumetric images in the spherical coordinate system, the reconstruction of somas with variational model is no longer sensitive to the interference of the complicated neuronal morphology, and could automatically and robustly achieve accurate soma shape regardless of the dense spatial distribution, and diversity in cell size, and morphology. We believe this method would speed drawing the neural circuits and boost brain studies.

  14. Somatic Variation of T-Cell Receptor Genes Strongly Associate with HLA Class Restriction

    NARCIS (Netherlands)

    Klarenbeek, Paul L.; Doorenspleet, Marieke E.; Esveldt, Rebecca E. E.; van Schaik, Barbera D. C.; Lardy, Neubury; van Kampen, Antoine H. C.; Tak, Paul P.; Plenge, Robert M.; Baas, Frank; de Bakker, Paul I. W.; de Vries, Niek

    2015-01-01

    Every person carries a vast repertoire of CD4+ T-helper cells and CD8+ cytotoxic T cells for a healthy immune system. Somatic VDJ recombination at genomic loci that encode the T-cell receptor (TCR) is a key step during T-cell development, but how a single T cell commits to become either CD4+ or CD8+

  15. Cell-free mitochondrial DNA copy number variation in head and neck squamous cell carcinoma: A study of non-invasive biomarker from Northeast India.

    Science.gov (United States)

    Kumar, Manish; Srivastava, Shilpee; Singh, Seram Anil; Das, Anup Kumar; Das, Ganesh Chandra; Dhar, Bishal; Ghosh, Sankar Kumar; Mondal, Rosy

    2017-10-01

    Head and neck squamous cell carcinoma is the most commonly diagnosed cancer worldwide. The lifestyle, food habits, and customary practices manifest the Northeast Indian population toward higher susceptibility to develop head and neck squamous cell carcinoma. Here, we have investigated the association of smoke and smokeless tobacco, and alcohol with copy number variation of cell-free mitochondrial DNA and cell-free nuclear DNA in cases and controls. Cell-free DNA from plasma was isolated from 50 head and neck squamous cell carcinoma cases and 50 controls with informed written consent using QIAamp Circulating Nucleic Acid Kit. Real-time polymerase chain reaction was done for copy number variation in cell-free mitochondrial DNA and cell-free nuclear DNA. Receiver operating characteristic curve analysis was performed to evaluate the diagnostic application between the two study groups using clinicopathological parameters. The levels of cell-free nuclear DNA and cell-free mitochondrial DNA of cases in association with smoke and smokeless tobacco, alcohol with smoking (p mitochondrial DNA (cutoff: 19.84 raw Ct; sensitivity: 84%; specificity: 100%; p mitochondrial DNA: 29,103,476.15 genomic equivalent/mL) and controls (cell-free nuclear DNA: 1650.9 genomic equivalent/mL and cell-free mitochondrial DNA: 9,189,312.54 genomic equivalent/mL), respectively. Our result indicates that the cell-free mitochondrial DNA content is highly associated with smoke and smokeless tobacco, betel quid chewing, and alcohol which shows greater promises, holding the key characteristics of diagnostic biomarkers, that is, minimal invasiveness, high specificity, and sensitivity.

  16. Variation of radiation sensitivity of Friend Erythroleukemia cells cultured in the presence of the differentiation inducer DMSO

    International Nuclear Information System (INIS)

    Einspenner, M.; Boulton, J.E.; Borsa, J.

    1984-01-01

    Differentiation of Friend erythroleukemia cells (FELC) was induced with 1.5% dimethyl sulfoxide (DMSO) in the culture medium. Cell growth, erythroid differentiation, and radiosensitivity of the proliferative capacity of the cells were measured and compared to a noninduced control culture of identical age. Induced cells first appeared on Day 2 after DMSO addition, and increased to a maximum of 80 to 90% of the cell population on Day 5, whereas in the control culture, induction was less than 2% of the cells. Radiosensitivity of the cells in the induced culture relative to that of cells in the control culture, showed an age-dependent variation. On days 1 and 2 after DMSO addition, the cells in the induced culture were less radiosensitive than those in the control culture. At later times, this relationship was reversed, and between days 3 and 5 the clonable cells in the induced culture were less radiosensitive than those in the control culture. These results suggest that the metabolic events associated with commitment of FELC to differentiate affect their ability to cope with the radiation-induced lesions underlying the loss of division capacity

  17. Business Cycle Dependent Unemployment Insurance

    DEFF Research Database (Denmark)

    Andersen, Torben M.; Svarer, Michael

    argument. Since benefits may be less distortionary in a recession than a boom, it follows that counter-cyclical benefits reduce average distortions compared to state independent benefits. We show that optimal (utilitarian) benefits are counter-cyclical and may reduce the structural (average) unemployment...

  18. cgCorrect: a method to correct for confounding cell-cell variation due to cell growth in single-cell transcriptomics

    Science.gov (United States)

    Blasi, Thomas; Buettner, Florian; Strasser, Michael K.; Marr, Carsten; Theis, Fabian J.

    2017-06-01

    Accessing gene expression at a single-cell level has unraveled often large heterogeneity among seemingly homogeneous cells, which remains obscured when using traditional population-based approaches. The computational analysis of single-cell transcriptomics data, however, still imposes unresolved challenges with respect to normalization, visualization and modeling the data. One such issue is differences in cell size, which introduce additional variability into the data and for which appropriate normalization techniques are needed. Otherwise, these differences in cell size may obscure genuine heterogeneities among cell populations and lead to overdispersed steady-state distributions of mRNA transcript numbers. We present cgCorrect, a statistical framework to correct for differences in cell size that are due to cell growth in single-cell transcriptomics data. We derive the probability for the cell-growth-corrected mRNA transcript number given the measured, cell size-dependent mRNA transcript number, based on the assumption that the average number of transcripts in a cell increases proportionally to the cell’s volume during the cell cycle. cgCorrect can be used for both data normalization and to analyze the steady-state distributions used to infer the gene expression mechanism. We demonstrate its applicability on both simulated data and single-cell quantitative real-time polymerase chain reaction (PCR) data from mouse blood stem and progenitor cells (and to quantitative single-cell RNA-sequencing data obtained from mouse embryonic stem cells). We show that correcting for differences in cell size affects the interpretation of the data obtained by typically performed computational analysis.

  19. Natural allelic variation defines a role for ATMYC1: trichome cell fate determination.

    Directory of Open Access Journals (Sweden)

    V Vaughan Symonds

    2011-06-01

    Full Text Available The molecular nature of biological variation is not well understood. Indeed, many questions persist regarding the types of molecular changes and the classes of genes that underlie morphological variation within and among species. Here we have taken a candidate gene approach based on previous mapping results to identify the gene and ultimately a polymorphism that underlies a trichome density QTL in Arabidopsis thaliana. Our results show that natural allelic variation in the transcription factor ATMYC1 alters trichome density in A. thaliana; this is the first reported function for ATMYC1. Using site-directed mutagenesis and yeast two-hybrid experiments, we demonstrate that a single amino acid replacement in ATMYC1, discovered in four ecotypes, eliminates known protein-protein interactions in the trichome initiation pathway. Additionally, in a broad screen for molecular variation at ATMYC1, including 72 A. thaliana ecotypes, a high-frequency block of variation was detected that results in >10% amino acid replacement within one of the eight exons of the gene. This sequence variation harbors a strong signal of divergent selection but has no measurable effect on trichome density. Homologs of ATMYC1 are pleiotropic, however, so this block of variation may be the result of natural selection having acted on another trait, while maintaining the trichome density role of the gene. These results show that ATMYC1 is an important source of variation for epidermal traits in A. thaliana and indicate that the transcription factors that make up the TTG1 genetic pathway generally may be important sources of epidermal variation in plants.

  20. Variation in assessment of oxidatively damaged DNA in mononuclear blood cells by the comet assay with visual scoring

    DEFF Research Database (Denmark)

    Forchhammer, Lykke; Bräuner, Elvira Vaclavik; Folkmann, Janne Kjaersgaard

    2008-01-01

    The comet assay is popular for assessments of genotoxicity, but the comparison of results between studies is challenging because of differences in experimental procedures and reports of DNA damage in different units. We investigated the variation of DNA damage in mononuclear blood cells (MNBCs......) measured by the comet assay with focus on the variation related to alkaline unwinding and electrophoresis time, number of cells scored, as well as the putative benefits of transforming the primary end points to common units by the use of reference standards and calibration curves. Eight experienced......, our results indicate that inter-investigator difference in scoring is a strong determinant of DNA damage levels measured by the comet assay....

  1. No evidence that genetic variation in the myeloid-derived suppressor cell pathway influences ovarian cancer survival

    DEFF Research Database (Denmark)

    Sucheston-Campbell, Lara E; Cannioto, Rikki; Clay, Alyssa I

    2017-01-01

    BACKGROUND: The precise mechanism by which the immune system is adversely affected in cancer patients remains poorly understood, but the accumulation of immune suppressive/pro-tumorigenic myeloid-derived suppressor cells (MDSCs) is thought to be one prominent mechanism contributing to immunologic...... tolerance of malignant cells in epithelial ovarian cancer (EOC). To this end, we hypothesized genetic variation in MDSC pathway genes would be associated with survival after EOC diagnoses. METHODS: We measured the hazard of death due to EOC within 10 years of diagnosis, overall and by invasive subtype...

  2. Variation in dicer gene is associated with increased survival in T-cell lymphoma.

    Directory of Open Access Journals (Sweden)

    Xi Li

    Full Text Available Dicer, an endonuclease in RNase III family, is essential for the RNA interference (RNAi pathway. Aberrant expression of Dicer has been shown in various cancers including some subtypes of T cell lymphoma (TCL, which influences patient prognosis. A single-nucleotide polymorphism (SNP rs3742330A>G has been identified in the Dicer gene, located in the 3' untranslated region (3' UTR that is important for mRNA transcript stability. We investigated whether rs3742330 is associated with the survival in 163 TCL patients. Significant association between Dicer rs3742330 and TCL survival were found. Patients carrying the GG genotype (n = 12 had a significantly increased overall survival (OS compared with those carrying the GA and AA genotypes (n = 70 and n = 81, respectively; p = 0.031. Moreover, the significant association was maintained for patients with mature T type (n = 134; p = 0.026. In multivariate Cox-regression analysis, rs3742330 proved to be an independent predictor for OS, together with the commonly used International Prognostic Index (IPI and BAFF rs9514828, another SNP we have previously reported to be associated with TCL survival, with hazard ratios (HRs for patient death rate of 8.956 (95% CI, 1.210 to 66.318; p = 0.032 for the GA genotype and 10.145 (95% CI, 1.371 to 75.084; p = 0.023 for the AA genotype. Furthermore, we observed cumulative effects of Dicer rs3742330 and BAFF rs9514828 on TCL survival. Compared with patients carrying zero unfavorable genotype, those carrying one and two unfavorable genotypes had an increased risk of death with a HR of 7.104 (95% CI, 0.969-53.086; p = 0.054 and 14.932 (95% CI, 1.950-114.354; p = 0.009, respectively, with a significant dose-response trend (p(trend  = 0.004. In conclusion, Dicer rs3742330 is associated with TCL survival, suggesting that genetic variation might play a role in predicting prognosis of TCL patients.

  3. Variation of mechanical behavior of β-TCP/collagen two phase composite scaffold with mesenchymal stem cell in vitro.

    Science.gov (United States)

    Arahira, Takaaki; Todo, Mitsugu

    2016-08-01

    The primary aim of this study is to characterize the variational behavior of the compressive mechanical property of bioceramic-based scaffolds using stem cells during the cell culture period. β-Tricalcium phosphate (TCP)/collagen two phase composites and β-TCP scaffolds were fabricated using the polyurethane template technique and a subsequent freeze-drying method. Rat bone-marrow mesenchymal stem cells (rMSCs) were then cultured in these scaffolds for up to 28 days. Compression tests of the scaffolds with rMSCs were periodically conducted. Biological properties, such as the cell number, alkaline phosphatase (ALP) activity, and gene expressions of osteogenesis, were evaluated. The microstructural change due to cell growth and the formation of extracellular matrices was examined using a field-emission scanning electron microscope. The compressive property was then correlated with the biological properties and microstructures to understand the mechanism of the variational behavior of the macroscopic mechanical property. The porous collagen structure in the β-TCP scaffold effectively improved the structural stability of the composite scaffold, whereas the β-TCP scaffold exhibited structural instability with the collapse of the porous structure when immersed in a culture medium. The β-TCP/collagen composite scaffold exhibited higher ALP activity and more active generation of osteoblastic markers than the β-TCP scaffold. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Seasonal and clonal variation in cellulose microfibril orientation during cell wall formation of tracheids in Cryptomeria japonica.

    Science.gov (United States)

    Jyske, Tuula; Fujiwara, Takeshi; Kuroda, Katsushi; Iki, Taiichi; Zhang, Chunhua; Jyske, Tuomas K; Abe, Hisashi

    2014-08-01

    To investigate the biological mechanism by which trees control the changes in microfibril (MF) orientation among secondary cell wall layers of conifer tracheids, we studied seasonal variation in the orientation of newly deposited MFs during tracheid cell wall development in Japanese cedar (Cryptomeria japonica D. Don) trees growing in Central Japan (36°36'N, 140°39'E). Sample blocks were repeatedly collected from four 16-year-old clones of different origins during the growing season of 2010 to investigate the hypotheses that changes in cellulose MF orientation between wall layers exhibited seasonal and clonal differences. The progressive change in the orientation of newly deposited MFs on the primary and secondary cell wall layers of tracheids was detected by field-emission-scanning electron microscopy. Tracheid production and differentiation was studied by light microscopy. We observed a decreasing trend in the orientation of deposited MFs from earlywood to latewood in the S2 and S1 layers, where MFs appeared in a Z-helix. In contrast, no seasonal pattern in the orientation of the MFs in the S-helix was observed. Minor clonal variation was observed in the phenology of tracheid production and differentiation. We concluded that a seasonal decreasing trend in the orientation of the MFs in the Z-helix in S1 and S2 was present, whereas the MFs in other layers exhibited minor random variations. Thus, the orientation of the MFs in S2 was affected by seasonal factors, whereas the MFs in other layers were more intrinsically controlled. The within-ring variations in the MF orientation and thus the resulting average MF angle might also be related to genotypic differences in the tracheid production and differentiation rate. However, our results do not exclude other intrinsic and environmental regulations in the change in MF orientation, which remains a topic for future studies. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions

  5. Genetic and environmental factors contribute to variation in cell wall composition in mature desi chickpea (Cicer arietinum L.) cotyledons.

    Science.gov (United States)

    Wood, Jennifer A; Tan, Hwei-Ting; Collins, Helen M; Yap, Kuok; Khor, Shi Fang; Lim, Wai Li; Xing, Xiaohui; Bulone, Vincent; Burton, Rachel A; Fincher, Geoffrey B; Tucker, Matthew R

    2018-03-13

    Chickpea (Cicer arietinum L.) is an important nutritionally rich legume crop that is consumed worldwide. Prior to cooking, desi chickpea seeds are most often dehulled and cleaved to release the split cotyledons, referred to as dhal. Compositional variation between desi genotypes has a significant impact on nutritional quality and downstream processing, and this has been investigated mainly in terms of starch and protein content. Studies in pulses such as bean and lupin have also implicated cell wall polysaccharides in cooking time variation, but the underlying relationship between desi chickpea cotyledon composition and cooking performance remains unclear. Here, we utilized a variety of chemical and immunohistological assays to examine details of polysaccharide composition, structure, abundance, and location within the desi chickpea cotyledon. Pectic polysaccharides were the most abundant cell wall components, and differences in monosaccharide and glycosidic linkage content suggest both environmental and genetic factors contribute to cotyledon composition. Genotype-specific differences were identified in arabinan structure, pectin methylesterification, and calcium-mediated pectin dimerization. These differences were replicated in distinct field sites and suggest a potentially important role for cell wall polysaccharides and their underlying regulatory machinery in the control of cooking time in chickpea. © 2018 The Authors. Plant, Cell & Environment Published by John Wiley & Sons Ltd.

  6. Biochemical Variations in Cytolytic Activity of Ortho- and Paramyxoviruses in Human Lung Tumor Cell Culture.

    Science.gov (United States)

    Zhirnov, O P

    2017-09-01

    Human lung cancer cells (Calu-3 line) were studied for the development of apoptosis, necrosis, and autophagy in response to infection with ortho- and paramyxoviruses. Biochemical pathways underlying various mechanisms of cell death differed for different viruses. When infected with murine Sendai paramyxovirus, Calu-3 cells demonstrated typical necrotic features such as cell swelling (but not shrinkage), lack of chromatin DNA laddering, of caspase 3 and 8 activation, and of apoptotic cleavage of poly(ADP-ribose) polymerase (PARP) protein; an activation of antiapoptotic protein kinase Akt was also revealed. In contrast, infection with avian influenza virus A/FPV/Rostock/34 (H7N1 subtype) or Newcastle disease virus (NDV, avian paramyxovirus) caused the development of typical apoptotic markers such as cell shrinkage, ladder-type chromosomal DNA fragmentation, caspase 3 and 8 activation, and proteolytic cleavage of PARP in the absence of Akt activation. Notably, no upregulation of p53 protein phosphorylation was observed in all infected cells, which indicates that p53 is not involved in the virus-induced death of Calu-3 cells. Cell death caused by the influenza virus was accompanied by overstimulation of autophagy, whereas no stimulation of autophagy was observed in the NDV-infected cells. Infection with Sendai virus caused moderate stimulation of autophagy, which suggests that the mechanism of the virus-induced cell death and the balance between autophagy and cell death in infected cancer cells depend on the virus type and might significantly differ even for closely related viruses. Therefore, an optimal strategy for oncolytic virus-mediated destruction of tumor cells in cancer patients requires selection of the most appropriate oncolytic virus based on the mechanism of its cytolytic action in a particular type of tumor.

  7. Cell cycle-dependent changes in localization of a 210-kDa microtubule-interacting protein in .I.Leishmania./I..

    Czech Academy of Sciences Publication Activity Database

    Libusová, Lenka; Dráberová, Eduarda; Juliano, C.; Viklický, Vladimír; Fiori, P. L.; Cappuccinelli, P.; Dráber, Petr

    2001-01-01

    Roč. 266, č. 2 (2001), s. 270-278 ISSN 0014-4827 R&D Projects: GA ČR GA304/00/0553; GA AV ČR IAA5052004 Keywords : microtubule-associated proteins * Leishmania-antibody Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.096, year: 2001

  8. Modelling and simulation of double chamber microbial fuel cell. Cell voltage, power density and temperature variation with process parameters

    Energy Technology Data Exchange (ETDEWEB)

    Shankar, Ravi; Mondal, Prasenjit; Chand, Shri [Indian Institute of Technology Roorkee, Uttaranchal (India). Dept. of Chemical Engineering

    2013-11-01

    In the present paper steady state models of a double chamber glucose glutamic acid microbial fuel cell (GGA-MFC) under continuous operation have been developed and solved using Matlab 2007 software. The experimental data reported in a recent literature has been used for the validation of the models. The present models give prediction on the cell voltage and cell power density with 19-44% errors, which is less (up to 20%) than the errors on the prediction of cell voltage made in some recent literature for the same MFC where the effects of the difference in pH and ionic conductivity between anodic and cathodic solutions on cell voltage were not incorporated in model equations. It also describes the changes in anodic and cathodic chamber temperature due to the increase in substrate concentration and cell current density. Temperature profile across the membrane thickness has also been studied. (orig.)

  9. Variations in Humanized and Defined Culture Conditions Supporting Derivation of New Human Embryonic Stem Cell Lines

    DEFF Research Database (Denmark)

    Fletcher, Judy M; Ferrier, Patricia M; Gardner, John O

    2006-01-01

    The evolution of "humanized" (i.e., free of animal sourced reagents) and ultimately chemically defined culture systems for human embryo stem cell (hESC) isolation and culture is of importance to improving their efficacy and safety in research and therapeutic applications. This can be achieved...... serum-free medium (SFM) containing only human sourced and recombinant protein. Further, outgrowth of embryonic cells from whole blastocysts in both media could be achieved for up to 1 week without reliance on feeder cells. All variant conditions sustained undifferentiated cell status, a stable karyotype......, with a transitional requirement for human feeder cells. This represents another sequential step in the generation of therapeutic grade stem cells with reduced risk of zoonotic pathogen transmission....

  10. RNA-Seq Highlights High Clonal Variation in Monoclonal Antibody Producing CHO Cells

    DEFF Research Database (Denmark)

    Orellana, Camila A.; Marcellin, Esteban; Palfreyman, Robin W.

    2018-01-01

    The development of next-generation sequencing technologies has opened new opportunities to better characterize complex eukaryotic cells. Chinese hamster ovary (CHO) cells play a primary role in therapeutic protein production, with currently five of the top ten blockbuster drugs produced in CHO....... However, engineering superior CHO cells with improved production features has had limited success to date and cell lines are still developed through the generation and screening of large strain pools. Here, we applied RNA sequencing to contrast a high and a low monoclonal antibody producing cell line......-regulation of genes encoding secreted glycoproteins is found to be the most significant change. The large number of significant differences even between subclones challenges the notion of identifying and manipulating a few key genes to generate high production CHO cell lines....

  11. Physiological responses of wild type and putrescine-overproducing transgenic cells of poplar to variations in the form and concentration of nitrogen in the medium

    Science.gov (United States)

    Rakesh Minocha; Jae Soon Lee; Stephanie Long; Pratiksha Bhatnagar; Subhash C. Minocha

    2004-01-01

    We determined: (a) the physiological consequences of overproduction of putrescine in transgenic poplar (Populus nigra x mnrimoviczir) cells expressing an omithine decarboxylase transgene; and (b) effects of variation in nitrogen (N) concentration of the medium on cellular polyamine concentration in transgenic and non-transgenic cells. Cells grown in...

  12. Association of activating KIR copy number variation of NK cells with containment of SIV replication in rhesus monkeys.

    Directory of Open Access Journals (Sweden)

    Ina Hellmann

    2011-12-01

    Full Text Available While the contribution of CD8⁺ cytotoxic T lymphocytes to early containment of HIV-1 spread is well established, a role for NK cells in controlling HIV-1 replication during primary infection has been uncertain. The highly polymorphic family of KIR molecules expressed on NK cells can inhibit or activate these effector cells and might therefore modulate their activity against HIV-1-infected cells. In the present study, we investigated copy number variation in KIR3DH loci encoding the only activating KIR receptor family in rhesus monkeys and its effect on simian immunodeficiency virus (SIV replication during primary infection in rhesus monkeys. We observed an association between copy numbers of KIR3DH genes and control of SIV replication in Mamu-A*01⁻ rhesus monkeys that express restrictive TRIM5 alleles. These findings provide further evidence for an association between NK cells and the early containment of SIV replication, and underscore the potential importance of activating KIRs in stimulating NK cell responses to control SIV spread.

  13. Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes.

    Science.gov (United States)

    Astolfi, P A; Salamini, F; Sgaramella, V

    2010-09-01

    Theoretical and experimental evidences support the hypothesis that the genomes and the epigenomes may be different in the somatic cells of complex organisms. In the genome, the differences range from single base substitutions to chromosome number; in the epigenome, they entail multiple postsynthetic modifications of the chromatin. Somatic genome variations (SGV) may accumulate during development in response both to genetic programs, which may differ from tissue to tissue, and to environmental stimuli, which are often undetected and generally irreproducible. SGV may jeopardize physiological cellular functions, but also create novel coding and regulatory sequences, to be exposed to intraorganismal Darwinian selection. Genomes acknowledged as comparatively poor in genes, such as humans', could thus increase their pristine informational endowment. A better understanding of SGV will contribute to basic issues such as the "nature vs nurture" dualism and the inheritance of acquired characters. On the applied side, they may explain the low yield of cloning via somatic cell nuclear transfer, provide clues to some of the problems associated with transdifferentiation, and interfere with individual DNA analysis. SGV may be unique in the different cells types and in the different developmental stages, and thus explain the several hundred gaps persisting in the human genomes "completed" so far. They may compound the variations associated to our epigenomes and make of each of us an "(epi)genomic" mosaic. An ensuing paradigm is the possibility that a single genome (the ephemeral one assembled at fertilization) has the capacity to generate several different brains in response to different environments.

  14. Viscosity-dependent variations in the cell shape and swimming manner of Leptospira.

    Science.gov (United States)

    Takabe, Kyosuke; Tahara, Hajime; Islam, Md Shafiqul; Affroze, Samia; Kudo, Seishi; Nakamura, Shuichi

    2017-02-01

    Spirochaetes are spiral or flat-wave-shaped Gram-negative bacteria that have periplasmic flagella between the peptidoglycan layer and outer membrane. Rotation of the periplasmic flagella transforms the cell body shape periodically, allowing the cell to swim in aqueous environments. Because the virulence of motility-deficient mutants of pathogenic species is drastically attenuated, motility is thought to be an essential virulence factor in spirochaetes. However, it remains unknown how motility practically contributes to the infection process. We show here that the cell body configuration and motility of the zoonotic spirochaete Leptospira changes depending on the viscosity of the medium. Leptospira swim and reverse the swimming direction by transforming the cell body. Motility analysis showed that the frequency of cell shape transformation was increased by increasing the viscosity of the medium. The increased cell body transformation induced highly frequent reversal of the swimming direction. A simple kinetic model based on the experimental results shows that the viscosity-induced increase in reversal limits cell migration, resulting in the accumulation of cells in high-viscosity regions. This behaviour could facilitate the colonization of the spirochaete on host tissues covered with mucosa.

  15. Dissecting Regional Variations in Stress Fiber Mechanics in Living Cells with Laser Nanosurgery

    Energy Technology Data Exchange (ETDEWEB)

    Tanner, Kandice; Boudreau, Aaron; Bissell, Mina J; Kumar, Sanjay

    2010-03-02

    The ability of a cell to distribute contractile stresses across the extracellular matrix in a spatially heterogeneous fashion underlies many cellular behaviors, including motility and tissue assembly. Here we investigate the biophysical basis of this phenomenon by using femtosecond laser nanosurgery to measure the viscoelastic recoil and cell-shape contributions of contractile stress fibers (SFs) located in specific compartments of living cells. Upon photodisruption and recoil, myosin light chain kinase-dependent SFs located along the cell periphery display much lower effective elasticities and higher plateau retraction distances than Rho-associated kinase-dependent SFs located in the cell center, with severing of peripheral fibers uniquely triggering a dramatic contraction of the entire cell within minutes of fiber irradiation. Image correlation spectroscopy reveals that when one population of SFs is pharmacologically dissipated, actin density flows toward the other population. Furthermore, dissipation of peripheral fibers reduces the elasticity and increases the plateau retraction distance of central fibers, and severing central fibers under these conditions triggers cellular contraction. Together, these findings show that SFs regulated by different myosin activators exhibit different mechanical properties and cell shape contributions. They also suggest that some fibers can absorb components and assume mechanical roles of other fibers to stabilize cell shape.

  16. Cell cycle stage dependent variations in drug-induced topoisomerase II mediated DNA cleavage and cytotoxicity

    International Nuclear Information System (INIS)

    Estey, E.; Adlakha, R.C.; Hittelman, W.N.; Zwelling, L.A.

    1987-01-01

    The DNA cleavage produced by 4'-(9-acridinylamino)methanesulfon-m-anisidide (m-AMSA) in mammalian cells is putatively mediated by topoisomerase II. The authors found that in synchronized HeLa cells the frequency of such cleavage was 4-15-fold greater in mitosis than in S while the DNA of G 1 and G 2 cells exhibited an intermediate susceptibility to cleavage. The hypersensitivity of mitotic DNA to m-AMSA-induced cleavage was acquired relatively abruptly in late G 2 and was lost similarly abruptly in early G 1 . The susceptibility of mitotic cells to m-AMSA-induced DNA cleavage was not clearly paralleled by an increase in topoisomerase II activity in 350 mM NaCl extracts from mitotic cells compared to similar extracts from cells in G 1 , S, or G 2 . Furthermore, equal amounts of decatenating activity from cells in mitosis and S produced equal amounts of m-AMSA-induced cleavage of simian virus 40 (SV40) DNA; i.e., the interaction between m-AMSA and extractable enzyme was similar in mitosis and S. The DNA of mitotic cells was also hypersensitive to cleavage by 4'-demethylepipodophyllotoxin 4-(4,6-O-ethylidene-β-D-glucopyranoside) (etoposide), a drug that produces topoisomerase II mediated DNA cleavage without binding to DNA. Cell cycle stage dependent fluctuations in m-AMSA-induced DNA cleavage may result from fluctuations in the structure of chromatin per se that occur during the cell cycle. Surprisingly, cell cycle stage dependent differences in m-AMSA-induced DNA cleavage did not correlate with differences in the susceptibility to the cytotoxic effects of the drug. In fact, cells in S were most sensitive to these effects. These results are an exception to the previously observed parallel between the susceptibility of mammalian cells to drug-induced DNA cleavage and the susceptibility of the cells to drug-induced cytotoxicity and indicate the complexity of any relationship between the two phenomena

  17. EXPERIMENTAL STUDY ON THE VARIATION OF DEGRADED SILICON SOLAR CELLS PARAMETER

    Directory of Open Access Journals (Sweden)

    DAVUD MOSTAFA TOBNAGHI

    2017-09-01

    Full Text Available In the lifetime and under ordinary working conditions, solar cells prone to the effects of aging and their electrical parameters are degrading continually. In this paper, to simulate and accelerate the effects of aging, solar cells were exposed to the different doses of gamma radiation, since gamma radiation and aging produces similar effects in semiconducting devices. The current-voltage characteristics and spectral photo current of mono-crystalline solar cells were studied before and after the gamma irradiation. Experimental results showed that the gamma radiation causes a significant Reduction in the short circuit current (Isc and efficiency (η while the open circuit voltage (Voc is slightly reduced. The spectral photo current shows that, by increasing irradiation dose, reducing the current occurred at lower wavelengths and defects is mainly inflicted to region close to the surface of solar cells. Obtained results could lead to novel designs of silicon solar cells with purpose of increasing their possible applications.

  18. Pyrrolizidine alkaloid variation in Jacobaea plants: from plant organ to cell level

    OpenAIRE

    Nuringtyas, Tri Rini

    2013-01-01

    The aim of this thesis is to understand the diversity of pyrrolizidine alkaloids (PAs) in Jacobaea plants with respect to their spatial distribution and its consequences for generalist insects. Chapter 2 reports on the role of endophytes in the production of PAs in Jacobaea. Plants were treated with different systemic fungicides to eliminate endophytic fungi and the effect on PA concentration and composition was determined. Chapter 3, 4 and 5 deal with the variation of PA distribution at orga...

  19. Aging has the opposite effect on cAMP and cGMP circadian variations in rat Leydig cells.

    Science.gov (United States)

    Baburski, Aleksandar Z; Sokanovic, Srdjan J; Andric, Silvana A; Kostic, Tatjana S

    2017-05-01

    The Leydig cell physiology displays a circadian rhythm driven by a complex interaction of the reproductive axis hormones and circadian system. The final output of this regulatory process is circadian pattern of steroidogenic genes expression and testosterone production. Aging gradually decreases robustness of rhythmic testosterone secretion without change in pattern of LH secretion. Here, we analyzed effect of aging on circadian variation of cAMP and cGMP signaling in Leydig cells. Results showed opposite effect of aging on cAMP and cGMP daily variation. Reduced amplitude of cAMP circadian oscillation was probably associated with changed expression of genes involved in cAMP production (increased circadian pattern of Adcy7, Adcy9, Adcy10 and decreased Adcy3); cAMP degradation (increased Pde4a, decreased Pde8b, canceled rhythm of Pde4d, completely reversed circadian pattern of Pde7b and Pde8a); and circadian expression of protein kinase A subunits (Prkac/PRKAC and Prkar2a). Aging stimulates expression of genes responsible for cGMP production (Nos2, Gucy1a3 and Gucy1b3/GUCYB3) and degradation (Pde5a, Pde6a and Pde6h) but the overall net effect is elevation of cGMP circadian oscillations in Leydig cells. In addition, the expression of cGMP-dependent kinase, Prkg1/PRKG1 is up-regulated. It seems that aging potentiate cGMP- and reduce cAMP-signaling in Leydig cells. Since both signaling pathways affect testosterone production and clockwork in the cells, further insights into these signaling pathways will help to unravel disorders linked to the circadian timing system, aging and reproduction.

  20. Detuning related coupler kick variation of a superconducting nine-cell 1.3 GHz cavity

    Science.gov (United States)

    Hellert, Thorsten; Dohlus, Martin

    2018-04-01

    Superconducting TESLA-type cavities are widely used to accelerate electrons in long bunch trains, such as in high repetition rate free electron lasers. The TESLA cavity is equipped with two higher order mode couplers and a fundamental power coupler (FPC), which break the axial symmetry of the cavity. The passing electrons therefore experience axially asymmetrical coupler kicks, which depend on the transverse beam position at the couplers and the rf phase. The resulting emittance dilution has been studied in detail in the literature. However, the kick induced by the FPC depends explicitly on the ratio of the forward to the backward traveling waves at the coupler, which has received little attention. The intention of this paper is to present the concept of discrete coupler kicks with a novel approach of separating the field disturbances related to the standing wave and a reflection dependent part. Particular attention is directed to the role of the penetration depth of the FPC antenna, which determines the loaded quality factor of the cavity. The developed beam transport model is compared to dedicated experiments at FLASH and European XFEL. Both the observed transverse coupling and detuning related coupler kick variations are in good agreement with the model. Finally, the expected trajectory variations due to coupler kick variations at European XFEL are investigated and results of numerical studies are presented.

  1. A framework to quantify karyotype variation associated with CHO cell line instability at a single-cell level.

    Science.gov (United States)

    Baik, Jong Youn; Lee, Kelvin H

    2017-05-01

    Chinese hamster ovary (CHO) cells, the major mammalian host cells for biomanufacturing of therapeutic proteins, have been extensively investigated to enhance productivity and product quality. However, cell line instability resulting in unexpected changes in productivity or product quality continues to be a challenge. Based on previous reports about causes and characteristics of production instability, we hypothesized that chromosomal rearrangements due to genomic instability are associated with production instability and that these events can be characterized. We developed a production instability model using secreted alkaline phosphatase (SEAP)-expressing CHO cells (CHO-SEAP) as well as a framework to quantify chromosomal rearrangements by karyotyping. In the absence of methotrexate (MTX), CHO-SEAP cells exhibited a slightly increased growth rate, a significantly decreased specific productivity, and changes in the chromosomal rearrangement ratio of seven chromosomes. In contrast, when MTX was re-introduced, the growth rate and SEAP productivity reversed to the initial values, demonstrating the reversibility of production instability in CHO-SEAP cells. Fluorescence in situ hybridization analysis identified that the SEAP genes were incorporated in the chromosomal rearrangement (insertion) part of the der(Z9) chromosome. Karyotype analysis indicated that the insertion ratio of the der(Z9) chromosome decreased in the CHO-SEAP cells grown without MTX, demonstrating a correlation between chromosomal rearrangement and production instability. Our results support a mechanism for production instability, wherein a randomly generated chromosomal rearrangement (or genotype) results in cells with a growth advantage that is also associated with non (or low)-producing traits. As a result, the non-producing cells grow faster and thereby outgrow the producing population. Biotechnol. Bioeng. 2017;114: 1045-1053. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  2. Impact of blood processing variations on Natural Killer cell frequency, activation, chemokine receptor expression and function

    Science.gov (United States)

    Naranbhai, Vivek; Bartman, Pat; Ndlovu, Dudu; Ramkalawon, Pamela; Ndung’u, Thumbi; Wilson, Douglas; Altfeld, Marcus; Carr, William H

    2011-01-01

    Understanding the role of natural killer (NK) cells in human disease pathogenesis is crucial and necessitates study of patient samples directly ex vivo. Manipulation of whole blood by density gradient centrifugation or delays in sample processing due to shipping, however, may lead to artifactual changes in immune response measures. Here, we assessed the impact of density gradient centrifugation and delayed processing of both whole blood and peripheral blood mononuclear cells (PBMC) at multiple timepoints (2–24 hrs) on flow cytometric measures of NK cell frequency, activation status, chemokine receptor expression, and effector functions. We found that density gradient centrifugation activated NK cells and modified chemokine receptor expression. Delays in processing beyond 8 hours activated NK cells in PBMC but not in whole blood. Likewise, processing delays decreased chemokine receptor (CCR4 and CCR7) expression in both PBMC and whole blood. Finally, delays in processing PBMC were associated with a decreased ability of NK cells to degranulate (as measured by CD107a expression) or secrete cytokines (IFN-γ and TNF-α). In summary, our findings suggest that density gradient centrifugation and delayed processing of PBMC can alter measures of clinically relevant NK cell characteristics including effector functions; and therefore should be taken into account in designing clinical research studies. PMID:21255578

  3. Variation in sensitizing effect of caffeine in human tumour cell lines after γ-irradiation

    International Nuclear Information System (INIS)

    Valenzuela, M.T.; Almodovar, M.R. de; Mateos, S.; McMillan, T.J.

    2000-01-01

    We have investigated whether the protective role of the G2 checkpoint has increasing importance when the p53-dependent G1 checkpoint is inactivated. We have studied the differential effect of caffeine by clonogenic assays and flow cytometry in three human tumour cell lines with different functionality of p53 protein. The radiosensitizing effect of caffeine (2 mM) expressed itself as a significant decrease in surviving fraction at 2 Gy and a significant increase in α-values in RT112 and TE671, both with non-functional p53. However, no radiosensitizing effect was seen in cells with a normal p53 function (MCF-7 BUS). Two millimoles of caffeine also caused important changes in the cell cycle progression after irradiation. MCF-7 BUS showed a G1 arrest after irradiation and an early G2 arrest but those cells that reached the second G2 did not arrest significantly. In contrast, TE671 exhibited radiosensitization by caffeine, no G1 arrest, a G2 arrest in those cells irradiated in G2, no significant accumulation in the second G2 but an overall delay in release from the first cell cycle, which could be abrogated by caffeine. RT112 was similar to TE671 except that the emphasis in a G2 arrest was shifted from the block in cells irradiated in G2 to those irradiated at other cell cycle phases. The data presented confirm that p53 status can be a significant determinant of the efficacy of caffeine as radiosensitizer in these tumour cell lines, and document the importance of the G2 checkpoint in this effect. (author)

  4. Genotype, development and tissue-derived variation of cell-wall properties in the lignocellulosic energy crop Miscanthus.

    Science.gov (United States)

    da Costa, Ricardo M F; Lee, Scott J; Allison, Gordon G; Hazen, Samuel P; Winters, Ana; Bosch, Maurice

    2014-10-01

    Species and hybrids of the genus Miscanthus contain attributes that make them front-runners among current selections of dedicated bioenergy crops. A key trait for plant biomass conversion to biofuels and biomaterials is cell-wall quality; however, knowledge of cell-wall composition and biology in Miscanthus species is limited. This study presents data on cell-wall compositional changes as a function of development and tissue type across selected genotypes, and considers implications for the development of miscanthus as a sustainable and renewable bioenergy feedstock. Cell-wall biomass was analysed for 25 genotypes, considering different developmental stages and stem vs. leaf compositional variability, by Fourier transform mid-infrared spectroscopy and lignin determination. In addition, a Clostridium phytofermentans bioassay was used to assess cell-wall digestibility and conversion to ethanol. Important cell-wall compositional differences between miscanthus stem and leaf samples were found to be predominantly associated with structural carbohydrates. Lignin content increased as plants matured and was higher in stem tissues. Although stem lignin concentration correlated inversely with ethanol production, no such correlation was observed for leaves. Leaf tissue contributed significantly to total above-ground biomass at all stages, although the extent of this contribution was genotype-dependent. It is hypothesized that divergent carbohydrate compositions and modifications in stem and leaf tissues are major determinants for observed differences in cell-wall quality. The findings indicate that improvement of lignocellulosic feedstocks should encompass tissue-dependent variation as it affects amenability to biological conversion. For gene-trait associations relating to cell-wall quality, the data support the separate examination of leaf and stem composition, as tissue-specific traits may be masked by considering only total above-ground biomass samples, and sample

  5. Variation of radiation-sensitivity of neural stem and progenitor cell populations within the developing mouse brain

    International Nuclear Information System (INIS)

    Etienne, Olivier; Roque, Telma; Haton, Celine; Boussin, Francois D.

    2012-01-01

    We investigated the DNA damage response (DDR) of fetal neural stem and progenitor cells (NSPC), since exposure to ionizing radiation can severely impair the brain development. We compared apoptosis induction in the dorsal tel-encephalon and the lateral ganglionic eminences (LGE) of mouse embryos after an in utero irradiation. We used two thymidine analogs, together with the physical position of nuclei within brain structures, to determine the fate of irradiated NSPC. NSPC did not activate an apparent protein 21(p21)- dependent G1/S checkpoint within the LGE as their counterparts within the dorsal tel-encephalon. However, the levels of radiation induced apoptosis differed between the two tel-encephalic regions, due to the high radiation sensitivity of intermediate progenitors of the LGE. Besides radial glial cells, that function as neural stem cells, were more resistant and were reoriented toward self-renewing within hours following irradiation. The lack of the p21-dependent-cell cycle arrest at the G1/S transition appears to be a general feature of NSPC in the developing brain. However, we found variation of radiation response in function of the types of NSPC. Factors involved in DDR and those involved in the regulation of neurogenesis are intricately linked in determining the cell fate after irradiations. (authors)

  6. DNA damage follows repair factor depletion and portends genome variation in cancer cells after pore migration

    OpenAIRE

    Irianto, Jerome; Xia, Yuntao; Pfeifer, Charlotte R.; Athirasala, Avathamsa; Ji, Jiazheng; Alvey, Cory; Tewari, Manu; Bennett, Rachel; Harding, Shane M.; Liu, Andrea; Greenberg, Roger A.; Discher, Dennis E.

    2016-01-01

    Migration through micron-size constrictions has been seen to rupture the nucleus, release nuclear-localized GFP, and cause localized accumulations of ectopic 53BP1 – a DNA repair protein. Here, constricted migration of two human cancer cell types and primary mesenchymal stem cells (MSC) increases DNA breaks throughout the nucleoplasm as assessed by endogenous damage markers and by electrophoretic ‘comet’ measurements. Migration also causes multiple DNA repair proteins to segregate away from D...

  7. Copper variation in Cu(In,Ga)Se{sub 2} solar cells with indium sulphide buffer layer

    Energy Technology Data Exchange (ETDEWEB)

    Spiering, S., E-mail: stefanie.spiering@zsw-bw.de [Zentrum für Sonnenenergie- und Wasserstoff-Forschung (ZSW) Baden-Wuerttemberg, Industriestrasse 6, 70565 Stuttgart (Germany); Paetel, S.; Kessler, F. [Zentrum für Sonnenenergie- und Wasserstoff-Forschung (ZSW) Baden-Wuerttemberg, Industriestrasse 6, 70565 Stuttgart (Germany); Igalson, M.; Abdel Maksoud, H. [Warsaw University of Technology (WUT), Faculty of Physics, Koszykowa 75, 00-662 Warszawa (Poland)

    2015-05-01

    In the manufacturing of Cu(In,Ga)Se{sub 2} (CIGS) thin film solar cells the application of a buffer layer on top of the absorber is essential to obtain high efficiency devices. Regarding the roll-to-roll production of CIGS cells and modules a vacuum deposition process for the buffer is preferable to the conventional cadmium sulphide buffer deposited in a chemical bath. Promising results have already been achieved for the deposition of indium sulphide buffer by different vacuum techniques. The solar device performance is very sensitive to the conditions at the absorber-buffer heterojunction. In view of optimization we investigated the influence of the Cu content in the absorber on the current-voltage characteristics. In this work the integral copper content was varied between 19 and 23 at.% in CIGS on glass substrates. An improvement of the cell performance by enhanced open circuit voltage was observed for a reduction to ~ 21 at.% when thermally evaporated indium sulphide was applied as the buffer layer. The influence of stoichiometry deviations on the transport mechanism and secondary barriers in the device was studied using detailed dark and light current-voltage analysis and admittance spectroscopy and compared to the reference CdS-buffered cells. We conclude that the composition of the absorber in the interface region affects current transport in In{sub x}S{sub y}-buffered and CdS-buffered cells in different ways hence optimal Cu content in those two types of devices is different. - Highlights: • Influence of Cu-variation in CIGS cells with In{sub x}S{sub y} buffer layer on cell performance • Enhanced efficiency by slight reduction of Cu-content to 21 at.% • Contribution of tunnelling-enhanced interface recombination for higher Cu-content.

  8. Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer

    Science.gov (United States)

    Hampras, Shalaka S.; Sucheston-Campbell, Lara E.; Cannioto, Rikki; Chang-Claude, Jenny; Modugno, Francesmary; Dörk, Thilo; Hillemanns, Peter; Preus, Leah; Knutson, Keith L.; Wallace, Paul K.; Hong, Chi-Chen; Friel, Grace; Davis, Warren; Nesline, Mary; Pearce, Celeste L.; Kelemen, Linda E.; Goodman, Marc T.; Bandera, Elisa V.; Terry, Kathryn L.; Schoof, Nils; Eng, Kevin H.; Clay, Alyssa; Singh, Prashant K.; Joseph, Janine M.; Aben, Katja K.H.; Anton-Culver, Hoda; Antonenkova, Natalia; Baker, Helen; Bean, Yukie; Beckmann, Matthias W.; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A.; Brooks-Wilson, Angela; Bruinsma, Fiona; Butzow, Ralf; Campbell, Ian G.; Carty, Karen; Cook, Linda S.; Cramer, Daniel W.; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; Dennis, Joe; Despierre, Evelyn; Dicks, Ed; Doherty, Jennifer A.; du Bois, Andreas; Dürst, Matthias; Easton, Doug; Eccles, Diana; Edwards, Robert P.; Ekici, Arif B.; Fasching, Peter A.; Fridley, Brooke L.; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G.; Glasspool, Rosalind; Gronwald, Jacek; Harrington, Patricia; Harter, Philipp; Hasmad, Hanis Nazihah; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A.T.; Hogdall, Claus; Hogdall, Estrid; Hosono, Satoyo; Iversen, Edwin S.; Jakubowska, Anna; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y.; Kellar, Melissa; Kelley, Joseph L.; Kiemeney, Lambertus A.; Klapdor, Rüdiger; Kolomeyevskaya, Nonna; Krakstad, Camilla; Kjaer, Susanne K.; Kruszka, Bridget; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D.; Lee, Alice W.; Lele, Shashikant; Leminen, Arto; Lester, Jenny; Levine, Douglas A.; Liang, Dong; Lissowska, Jolanta; Liu, Song; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F.A.G.; Matsuo, Keitaro; McGuire, Valeria; McLaughlin, John R.; McNeish, Ian; Menon, Usha; Moes-Sosnowska, Joanna; Narod, Steven A.; Nedergaard, Lotte; Nevanlinna, Heli; Nickels, Stefan; Olson, Sara H.; Orlow, Irene; Weber, Rachel Palmieri; Paul, James; Pejovic, Tanja; Pelttari, Liisa M.; Perkins, Barbara; Permuth-Wey, Jenny; Pike, Malcolm C.; Plisiecka-Halasa, Joanna; Poole, Elizabeth M.; Risch, Harvey A.; Rossing, Mary Anne; Rothstein, Joseph H.; Rudolph, Anja; Runnebaum, Ingo B.; Rzepecka, Iwona K.; Salvesen, Helga B.; Schernhammer, Eva; Schmitt, Kristina; Schwaab, Ira; Shu, Xiao-Ou; Shvetsov, Yurii B; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C.; Tangen, Ingvild L.; Teo, Soo-Hwang; Thompson, Pamela J.; Timorek, Agnieszka; Tsai, Ya-Yu; Tworoger, Shelley S.; Tyrer, Jonathan; van Altena, Anna M.; Vergote, Ignace; Vierkant, Robert A.; Walsh, Christine; Wang-Gohrke, Shan; Wentzensen, Nicolas; Whittemore, Alice S.; Wicklund, Kristine G.; Wilkens, Lynne R.; Wu, Anna H.; Wu, Xifeng; Woo, Yin-Ling; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Gayther, Simon A.; Ramus, Susan J.; Sellers, Thomas A.; Schildkraut, Joellen M.; Phelan, Catherine M.; Berchuck, Andrew; Chenevix-Trench, Georgia; Cunningham, Julie M.; Pharoah, Paul P.; Ness, Roberta B.; Odunsi, Kunle; Goode, Ellen L.; Moysich, Kirsten B.

    2016-01-01

    Background Regulatory T (Treg) cells, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and, thus, variants in genes encoding Treg cell immune molecules could be associated with ovarian cancer. Methods In a population of 15,596 epithelial ovarian cancer (EOC) cases and 23,236 controls, we measured genetic associations of 1,351 SNPs in Treg cell pathway genes with odds of ovarian cancer and tested pathway and gene-level associations, overall and by histotype, for the 25 genes, using the admixture likelihood (AML) method. The most significant single SNP associations were tested for correlation with expression levels in 44 ovarian cancer patients. Results The most significant global associations for all genes in the pathway were seen in endometrioid (p = 0.082) and clear cell (p = 0.083), with the most significant gene level association seen with (p = 0.001) and clear cell EOC. Gene associations with histotypes at< 0.05 included:(p = 0.005 and = 0.008, serous and high-grade serous, respectively), (p = 0.035, endometrioid and mucinous), (p = 0.03, mucinous), (p = 0.022, clear cell), (p = 0.021 endometrioid) and (p = 0.017 and = 0.025, endometrioid and mucinous, respectively). Conclusions Common inherited gene variation in Treg cell pathways shows some evidence of germline genetic contribution to odds of EOC that varies by histologic subtype and may be associated with mRNA expression of immune-complex receptor in EOC patients. PMID:27533245

  9. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

    Science.gov (United States)

    Astle, William J; Elding, Heather; Jiang, Tao; Allen, Dave; Ruklisa, Dace; Mann, Alice L; Mead, Daniel; Bouman, Heleen; Riveros-Mckay, Fernando; Kostadima, Myrto A; Lambourne, John J; Sivapalaratnam, Suthesh; Downes, Kate; Kundu, Kousik; Bomba, Lorenzo; Berentsen, Kim; Bradley, John R; Daugherty, Louise C; Delaneau, Olivier; Freson, Kathleen; Garner, Stephen F; Grassi, Luigi; Guerrero, Jose; Haimel, Matthias; Janssen-Megens, Eva M; Kaan, Anita; Kamat, Mihir; Kim, Bowon; Mandoli, Amit; Marchini, Jonathan; Martens, Joost H A; Meacham, Stuart; Megy, Karyn; O'Connell, Jared; Petersen, Romina; Sharifi, Nilofar; Sheard, Simon M; Staley, James R; Tuna, Salih; van der Ent, Martijn; Walter, Klaudia; Wang, Shuang-Yin; Wheeler, Eleanor; Wilder, Steven P; Iotchkova, Valentina; Moore, Carmel; Sambrook, Jennifer; Stunnenberg, Hendrik G; Di Angelantonio, Emanuele; Kaptoge, Stephen; Kuijpers, Taco W; Carrillo-de-Santa-Pau, Enrique; Juan, David; Rico, Daniel; Valencia, Alfonso; Chen, Lu; Ge, Bing; Vasquez, Louella; Kwan, Tony; Garrido-Martín, Diego; Watt, Stephen; Yang, Ying; Guigo, Roderic; Beck, Stephan; Paul, Dirk S; Pastinen, Tomi; Bujold, David; Bourque, Guillaume; Frontini, Mattia; Danesh, John; Roberts, David J; Ouwehand, Willem H; Butterworth, Adam S; Soranzo, Nicole

    2016-11-17

    Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains. Finally, through Mendelian randomization, we provide evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations between blood cell indices and cardiovascular disease may be non-causal. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways.

    Directory of Open Access Journals (Sweden)

    Martin H Schaefer

    2014-06-01

    Full Text Available Many proteins and signaling pathways are present in most cell types and tissues and yet perform specialized functions. To elucidate mechanisms by which these ubiquitous pathways are modulated, we overlaid information about cross-cell line protein abundance and variability, and evolutionary conservation onto functional pathway components and topological layers in the pathway hierarchy. We found that the input (receptors and the output (transcription factors layers evolve more rapidly than proteins in the intermediary transmission layer. In contrast, protein expression variability decreases from the input to the output layer. We observed that the differences in protein variability between the input and transmission layer can be attributed to both the network position and the tendency of variable proteins to physically interact with constitutively expressed proteins. Differences in protein expression variability and conservation are also accompanied by the tendency of conserved and constitutively expressed proteins to acquire somatic mutations, while germline mutations tend to occur in cell type-specific proteins. Thus, conserved core proteins in the transmission layer could perform a fundamental role in most cell types and are therefore less tolerant to germline mutations. In summary, we propose that the core signal transmission machinery is largely modulated by a variable input layer through physical protein interactions. We hypothesize that the bow-tie organization of cellular signaling on the level of protein abundance variability contributes to the specificity of the signal response in different cell types.

  11. Variations in sensitivity of synchronized Chinese hamster cells to oxic and anoxic X-ray exposures

    International Nuclear Information System (INIS)

    Siracka, E.; Littbrand, B.; Clifton, K.H.; Revesz, L.

    1975-01-01

    V-79 Chinese hamster cells in monolayer cultures on glass surfaces were synchronized by treatment with hydroxyurea and then exposed at different times to X-rays in air or in oxygen-free argon. Survival determinations indicated that the oxygen enhancement ratio (OER) as expressed by the ratio of the respective D 0 values varied over a narrow range in the different phases of the cell cycle. These changes resulted from cyclic alterations in both aerobic and anaerobic D 0 values, possibly in n values. (author)

  12. Estimation of physical activity levels using cell phone questionnaires: a comparison with accelerometry for evaluation of between-subject and within-subject variations.

    Science.gov (United States)

    Bexelius, Christin; Sandin, Sven; Trolle Lagerros, Ylva; Litton, Jan-Eric; Löf, Marie

    2011-09-25

    Physical activity promotes health and longevity. Further elaboration of the role of physical activity for human health in epidemiological studies on large samples requires accurate methods that are easy to use, cheap, and possible to repeat. The use of telecommunication technologies such as cell phones is highly interesting in this respect. In an earlier report, we showed that physical activity level (PAL) assessed using a cell phone procedure agreed well with corresponding estimates obtained using the doubly labeled water method. However, our earlier study indicated high within-subject variation in relation to between-subject variations in PAL using cell phones, but we could not assess if this was a true variation of PAL or an artifact of the cell phone technique. Our objective was to compare within- and between-subject variations in PAL by means of cell phones with corresponding estimates using an accelerometer. In addition, we compared the agreement of daily PAL values obtained using the cell phone questionnaire with corresponding data obtained using an accelerometer. PAL was measured both with the cell phone questionnaire and with a triaxial accelerometer daily during a 2-week study period in 21 healthy Swedish women (20 to 45 years of age and BMI from 17.7 kg/m² to 33.6 kg/m²). The results were evaluated by fitting linear mixed effect models and descriptive statistics and graphs. With the accelerometer, 57% (95% confidence interval [CI] 40%-66%) of the variation was within subjects, while with the cell phone, within-subject variation was 76% (95% CI 59%-83%). The day-to-day variations in PAL observed using the cell phone questions agreed well with the corresponding accelerometer results. Both the cell phone questionnaire and the accelerometer showed high within-subject variations. Furthermore, day-to-day variations in PAL within subjects assessed using the cell phone agreed well with corresponding accelerometer values. Consequently, our cell phone

  13. New genetic variation of Aedes albopictus densovirus isolated from mosquito C6/36 cell line.

    Science.gov (United States)

    Sangdee, Kusavadee; Pattanakitsakul, Sa-Nga

    2012-09-01

    Densovirus (DNV) is a small single-stranded DNA, non-enveloped virus belonging to the subfamily Densovirinae of the Parvoviridae family. This group of invertebrate viruses infects exclusively insects. Two of the major densoviruses, Aedes aegypti (AaeDNV) and Ae. albopictus (AalDNV), infect mosquitoes that carry viruses responsible for two important public health diseases, namely, dengue hemorrhagic fever and yellow fever. The present study describes cloning, sequencing and phylogenetic analysis of a new densovirus, AalDNV-4, from infected Ae. albopictus C6/36 cell line. The total nucleotide sequence (3.9 kb) of AalDNV-4 was obtained from sequencing of DNA fragments, and is 98% homologous to the initial AalDNV previously isolated, and distinguishable from other AalDNVs reported earlier. This full-length viral genome contains a 40-bp deletion at the left terminal region, 12 substitutions and 3 indels. Phylogenetic analysis of AalDNV-4 genome indicates that this virus is more closely related to the original AalDNV found in C6/36 cell line than to AaeDNV isolated from other mosquitoes. It was concluded that AalDNV-4 may have been derived from the original DNV found in the C6/36 cell line and has transferred worldwide from the exchange of this cell line among laboratories.

  14. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

    NARCIS (Netherlands)

    Astle, William J.; Elding, Heather; Jiang, Tao; Allen, Dave; Ruklisa, Dace; Mann, Alice L.; Mead, Daniel; Bouman, Heleen; Riveros-Mckay, Fernando; Kostadima, Myrto A.; Lambourne, John J.; Sivapalaratnam, Suthesh; Downes, Kate; Kundu, Kousik; Bomba, Lorenzo; Berentsen, Kim; Bradley, John R.; Daugherty, Louise C.; Delaneau, Olivier; Freson, Kathleen; Garner, Stephen F.; Grassi, Luigi; Guerrero, Jose; Haimel, Matthias; Janssen-Megens, Eva M.; Kaan, Anita; Kamat, Mihir; Kim, Bowon; Mandoli, Amit; Marchini, Jonathan; Martens, Joost H. A.; Meacham, Stuart; Megy, Karyn; O'Connell, Jared; Petersen, Romina; Sharifi, Nilofar; Sheard, Simon M.; Staley, James R.; Tuna, Salih; van der Ent, Martijn; Walter, Klaudia; Wang, Shuang-Yin; Wheeler, Eleanor; Wilder, Steven P.; Iotchkova, Valentina; Moore, Carmel; Sambrook, Jennifer; Stunnenberg, Hendrik G.; Di Angelantonio, Emanuele; Kaptoge, Stephen; Kuijpers, Taco W.; Carrillo-de-Santa-Pau, Enrique; Juan, David; Rico, Daniel; Valencia, Alfonso; Chen, Lu; Ge, Bing; Vasquez, Louella; Kwan, Tony; Garrido-Martín, Diego; Watt, Stephen; Yang, Ying; Guigo, Roderic; Beck, Stephan; Paul, Dirk S.; Pastinen, Tomi; Bujold, David; Bourque, Guillaume; Frontini, Mattia; Danesh, John; Roberts, David J.; Ouwehand, Willem H.; Butterworth, Adam S.; Soranzo, Nicole

    2016-01-01

    Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell,

  15. Interspecific variation of intracellular localization and postirradiation movement of Ku70-protein in fibroblastic cells

    International Nuclear Information System (INIS)

    Endoh, Daiji; Hayashi, Masanobu; Okui, Toyo; Kawase, Shiro; Kon, Yasushiro

    2003-01-01

    Ku (Ku70 and Ku80) Proteins are known as components of DNA-dependent protein kinase (DNA-PK) and play an important role for DNA repair. We previously reported that more than 70% of Ku proteins were located in cytoplasm of rat cells, the Ku proteins moved into nuclei of normal rat cells after X-irradiation, Ku proteins also moved into nuclei after X-irradiation but were not retained in nucleus of radiosensitive LEC rat cells. While reports have been shown about mechanisms on nuclear localization of Ku proteins, how Ku proteins export from nucleus is poorly understood. Here we show that C-terminal region of Ku70 protein is important for its cytoplasmic localization. When transfected into LEC rat cells, exogenous intact Ku70 (1-609) tagged with enhanced green fluorescent protein (EGFP-Ku70) localized mainly in the cytoplasm, whereas C-terminal-deletion mutant of Ku70 (1-593) tagged with EGFP (EGFP-Ku70D) was mainly localized in the nucleus. After X-irradiation, the endogenous intact EGFP-Ku70 once moved into nucleus, but returned into the cytoplasm. On the other hand, EGFP-Ku70D was retained in nucleus for two hours after X-irradiation. These results suggest that C-terminal region of Ku70 is included in the postirradiation nuclear export. Next, we investigated the intracellular localization of Ku70 proteins and the movement after X-irradiation of fibroblastic cells prepared from some mammalian species. Ku70 proteins were localized in nucleus and the postirradiation-extranuclear transport was not observed in human and African green monkey cells. On the other hand, Ku70 proteins were mainly localized in cytoplasm and moved into nucleus in mouse, Chinese hamster, Golden hamster, cotton rat, squirrel, cat and dog cells. These results may show that alternatively Ku70 protein is localized in the cytoplasm or nucleus depends on species and translocation of cytoplasmic Ku70 into nucleus is a response against low dose irradiation in fibroblasts of rodents, cats and dogs

  16. Common genetic variations in cell cycle and DNA repair pathways associated with pediatric brain tumor susceptibility

    DEFF Research Database (Denmark)

    Fahmideh, Maral Adel; Lavebratt, Catharina; Schüz, Joachim

    2016-01-01

    Knowledge on the role of genetic polymorphisms in the etiology of pediatric brain tumors (PBTs) is limited. Therefore, we investigated the association between single nucleotide polymorphisms (SNPs), identified by candidate gene-association studies on adult brain tumors, and PBT risk. The study...... cycle and DNA repair pathways variations associated with susceptibility to adult brain tumors also seem to be associated with PBT risk, suggesting pediatric and adult brain tumors might share similar etiological pathways....... to PBTs, whereas ERCC1rs3212986 may increase risk of these tumors. Moreover, stratified analyses indicated CHAF1Ars243341, CHAF1Ars2992, and XRCC1rs25487 were associated with a decreased risk of astrocytoma subtype. Furthermore, an increased risk of non-astrocytoma subtype associated with EGFRrs9642393...

  17. Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations

    International Nuclear Information System (INIS)

    Tsai, Yi-Chien; Chiao, Chun-Hui; Chang, Ian Yi-Feng; Chen, Dow-Tien; Liu, Tze-Tze; Hua, Kate; Chang, Chuan-Hsiung; Hsu, Ming-Ta

    2011-01-01

    We have previously identified large megabase-sized hypomethylated zones in the genome of the breast cancer cell line MCF-7 using the TspRI-ExoIII technique. In this report, we used a more convenient high throughput method for mapping the hypomethylated zones in a number of human tumor genomes simultaneously. The method was validated by the bisulfite sequencing of 39 randomly chosen sites in a demethylated domain and by bisulfite genome-wide sequencing of the MCF-7 genome. This showed that the genomes of the various tumor cell lines, as well as some primary tumors, exhibit common hypomethylated domains. Interestingly, these hypomethylated domains are correlated with low CpG density distribution genome-wide, together with the histone H3K27Me3 landscape. Furthermore, they are inversely correlated with the H3K9Ac landscape and gene expression as measured in MCF-7 cells. Treatment with drugs resulted in en-bloc changes to the methylation domains. A close examination of the methylation domains found differences between non-invasive and invasive tumors with respect to tumorigenesis related genes. Taken together these results suggest that the human genome is organized in epigenomic domains that contain various different types of genes and imply that there are cis- and trans-regulators that control these domain-wide epigenetic changes and hence gene expression in the human genome. The hypomethylated domains are located in gene deserts that contain mainly tissue-specific genes and therefore we hypothesize that tumor cells keep these regions demethylated and silenced in order to save energy and resources and allow higher levels of cell proliferation and better survival (a thrifty tumor genome hypothesis)

  18. Candida albicans CUG mistranslation is a mechanism to create cell surface variation.

    Science.gov (United States)

    Miranda, Isabel; Silva-Dias, Ana; Rocha, Rita; Teixeira-Santos, Rita; Coelho, Carolina; Gonçalves, Teresa; Santos, Manuel A S; Pina-Vaz, Cidália; Solis, Norma V; Filler, Scott G; Rodrigues, Acácio G

    2013-08-30

    In the human fungal pathogen Candida albicans, the CUG codon is translated 97% of the time as serine and 3% of the time as leucine, which potentially originates an array of proteins resulting from the translation of a single gene. Genes encoding cell surface proteins are enriched in CUG codons; thus, CUG mistranslation may influence the interactions of the organism with the host. To investigate this, we compared a C. albicans strain that misincorporates 28% of leucine at CUGs with a wild-type parental strain. The first strain displayed increased adherence to inert and host molecules. In addition, it was less susceptible to phagocytosis by murine macrophages, probably due to reduced exposure of cell surface β-glucans. To prove that these phenotypes occurred due to serine/leucine exchange, the C. albicans adhesin and invasin ALS3 was expressed in Saccharomyces cerevisiae in its two natural isoforms (Als3p-Leu and Als3p-Ser). The cells with heterologous expression of Als3p-Leu showed increased adherence to host substrates and flocculation. We propose that CUG mistranslation has been maintained during the evolution of C. albicans due to its potential to generate cell surface variability, which significantly alters fungus-host interactions. The translation of genetic information into proteins is a highly accurate cellular process. In the human fungal pathogen Candida albicans, a unique mistranslation event involving the CUG codon occurs. The CUG codon is mainly translated as serine but can also be translated as leucine. Leucine and serine are two biochemically distinct amino acids, hydrophobic and hydrophilic, respectively. The increased rate of leucine incorporation at CUG decoding triggers C. albicans virulence attributes, such as morphogenesis, phenotypic switching, and adhesion. Here, we show that CUG mistranslation masks the fungal cell wall molecule β-glucan that is normally recognized by the host immune system, delaying its response. Furthermore, we demonstrate

  19. Weibull strength variations between room temperature and high temperature Ni-3YSZ half-cells

    DEFF Research Database (Denmark)

    Curran, Declan; Frandsen, Henrik Lund; Hendriksen, Peter Vang

    2013-01-01

    and 800°C in a reducing atmosphere. The strength of an as sintered half-cell was also measured at room temperature for comparison. Weibull analysis was performed on large sample sets of 30 for statistical viability. The Weibull strength and elastic modulus of the room temperature tested reduced samples...... show a decrease of approximately 33% and 51% respectively, when compared to the oxidized samples tested at room temperature. When tested at elevated temperatures both Weibull strength and elastic modulus decrease further when compared to the room temperature reduced samples. However these further...... efficiency, increased degradation and/or the complete termination of a functioning stack. This paper investigates the effects of temperature on the mechanical strength of 3% yttria-stabilised zirconia half-cells. Strength was measured using a four-point bend method at room temperature and at 600°C, 700°C...

  20. Candida albicans CUG Mistranslation Is a Mechanism To Create Cell Surface Variation

    OpenAIRE

    Miranda, Isabel; Silva-Dias, Ana; Rocha, Rita; Teixeira-Santos, Rita; Coelho, Carolina; Gon?alves, Teresa; Santos, Manuel A. S.; Pina-Vaz, Cid?lia; Solis, Norma V.; Filler, Scott G.; Rodrigues, Ac?cio G.

    2013-01-01

    ABSTRACT In the human fungal pathogen Candida albicans, the CUG codon is translated 97% of the time as serine and 3% of the time as leucine, which potentially originates an array of proteins resulting from the translation of a single gene. Genes encoding cell surface proteins are enriched in CUG codons; thus, CUG mistranslation may influence the interactions of the organism with the host. To investigate this, we compared a C.?albicans strain that misincorporates 28% of leucine at CUGs with a ...

  1. Intratumour variation of biomarker expression by immunohistochemistry in resectable non-small cell lung cancer

    DEFF Research Database (Denmark)

    Jakobsen, Jan Nyrop; Santoni-Rugiu, Eric; Ravn, Jesper

    2013-01-01

    truly reflect the pattern of biomarker expression. It may also be an important factor in chemo resistance, as tumours with heterogeneous biomarker expression may potentially harbour chemo resistant tumour clones. MATERIALS AND METHODS: Immunohistochemical evaluation of the expression of excision repair...... intratumour heterogeneity in 33-87% of tumours examined. This heterogeneity may influence results in studies investigating the therapeutic impact of predictive biomarkers in non-small cell lung cancer (NSCLC)....

  2. Analyzing clonal variation of monoclonal antibody-producing CHO cell lines using an in silico metabolomic platform.

    Directory of Open Access Journals (Sweden)

    Atefeh Ghorbaniaghdam

    Full Text Available Monoclonal antibody producing Chinese hamster ovary (CHO cells have been shown to undergo metabolic changes when engineered to produce high titers of recombinant proteins. In this work, we have studied the distinct metabolism of CHO cell clones harboring an efficient inducible expression system, based on the cumate gene switch, and displaying different expression levels, high and low productivities, compared to that of the parental cells from which they were derived. A kinetic model for CHO cell metabolism was further developed to include metabolic regulation. Model calibration was performed using intracellular and extracellular metabolite profiles obtained from shake flask batch cultures. Model simulations of intracellular fluxes and ratios known as biomarkers revealed significant changes correlated with clonal variation but not to the recombinant protein expression level. Metabolic flux distribution mostly differs in the reactions involving pyruvate metabolism, with an increased net flux of pyruvate into the tricarboxylic acid (TCA cycle in the high-producer clone, either being induced or non-induced with cumate. More specifically, CHO cell metabolism in this clone was characterized by an efficient utilization of glucose and a high pyruvate dehydrogenase flux. Moreover, the high-producer clone shows a high rate of anaplerosis from pyruvate to oxaloacetate, through pyruvate carboxylase and from glutamate to α-ketoglutarate, through glutamate dehydrogenase, and a reduced rate of cataplerosis from malate to pyruvate, through malic enzyme. Indeed, the increase of flux through pyruvate carboxylase was not driven by an increased anabolic demand. It is in fact linked to an increase of the TCA cycle global flux, which allows better regulation of higher redox and more efficient metabolic states. To the best of our knowledge, this is the first time a dynamic in silico platform is proposed to analyze and compare the metabolomic behavior of different CHO

  3. Variation of Hydroxyapatite Content in Soft Gelatin Affects Mesenchymal Stem Cell Differentiation

    Directory of Open Access Journals (Sweden)

    Fahsai Kantawong

    2016-01-01

    Full Text Available Gelatin is a common material used in tissue engineering and hydroxyapatite (HA has a composition and structure similar to natural bone mineral. HA is also used to increase the adhesion ability of scaffolds. The physical and mechanical properties of gelatin, together with the chemical properties of HA, can affect cell differentiation. The main purpose of this study is to investigate the gene expression of human mesenchymal stem cells (HMSCs upon culturing on gelatin composite with HA. Low amounts of HA were introduced into the gelatin in order to modulate properties of gelatin. Three types of hydrogel were fabricated by glutaraldehyde crosslinking before lyophilization to produce the porous 3D structure: (1 pure gelatin, (2 0.5 mg/ml HA in gelatin, and (3 1 mg/ml HA in gelatin. The fabricated hydrogels were used as scaffolds to cultivate HMSCs for two periods - 24 hours and 3 weeks. The results showed that all types of fabricated hydrogels could be used to cultivate HMSCs. Changes of gene expressions indicated that the HMSCs cultured on the 1 mg/ml HA in gelatin showed neuronal lineage-specific differentiation.

  4. The biological default state of cell proliferation with variation and motility, a fundamental principle for a theory of organisms.

    Science.gov (United States)

    Soto, Ana M; Longo, Giuseppe; Montévil, Maël; Sonnenschein, Carlos

    2016-10-01

    The principle of inertia is central to the modern scientific revolution. By postulating this principle Galileo at once identified a pertinent physical observable (momentum) and a conservation law (momentum conservation). He then could scientifically analyze what modifies inertial movement: gravitation and friction. Inertia, the default state in mechanics, represented a major theoretical commitment: there is no need to explain uniform rectilinear motion, rather, there is a need to explain departures from it. By analogy, we propose a biological default state of proliferation with variation and motility. From this theoretical commitment, what requires explanation is proliferative quiescence, lack of variation, lack of movement. That proliferation is the default state is axiomatic for biologists studying unicellular organisms. Moreover, it is implied in Darwin's "descent with modification". Although a "default state" is a theoretical construct and a limit case that does not need to be instantiated, conditions that closely resemble unrestrained cell proliferation are readily obtained experimentally. We will illustrate theoretical and experimental consequences of applying and of ignoring this principle. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Estrous cycle-dependent changes of Fas expression in the bovine corpus luteum: influence of keratin 8/18 intermediate filaments and cytokines

    Directory of Open Access Journals (Sweden)

    Duncan Alice

    2012-10-01

    Full Text Available Abstract Background Fas expression and Fas-induced apoptosis are mechanisms attributed to the selective destruction of cells of the corpus luteum (CL during luteal regression. In certain cell-types, sensitivity to these death-inducing mechanisms is due to the loss or cleavage of keratin-containing intermediate filaments. Specifically, keratin 8/18 (K8/K18 filaments are hypothesized to influence cell death in part by regulating Fas expression at the cell surface. Methods Here, Fas expression on bovine luteal cells was quantified by flow cytometry during the early (Day 5, postovulation and late stages (Days 16–18, postovulation of CL function, and the relationship between Fas expression, K8/K18 filament expression and cytokine-induced cell death in vitro was evaluated. Results Both total and cell surface expression of Fas on luteal cells was greater for early versus late stage bovine CL (89% vs. 44% of cells for total Fas; 65% vs.18% of cells for cell surface Fas; respectively, P0.05, n=4 CL/stage, despite evidence these conditions increased Fas expression on HepG2 cells (P0.05 or stage of CL (P>0.05, n= 4 CL/stage on this outcome. Conclusion In conclusion, we rejected our null hypothesis that the cell surface expression of Fas does not differ between luteal cells of early and late stage CL. The results also did not support the idea that K8/K18 filaments influence the expression of Fas on the surface of bovine luteal cells. Potential downstream effects of these filaments on death signaling, however, remain a possibility. Importantly, the elevated expression of Fas observed on cells of early stage bovine CL compared to late stage bovine CL raises a provocative question concerning the physiological role(s of Fas in the corpus luteum, particularly during early luteal development.

  6. In-depth assessment of within-individual and inter-individual variation in the B cell receptor repertoire

    Directory of Open Access Journals (Sweden)

    Jacob Daniel Galson

    2015-10-01

    Full Text Available High-throughput sequencing of the B cell receptor (BCR repertoire can provide rapid characterization of the B cell response in a wide variety of applications in health, after vaccination and in infectious, inflammatory and immune-driven disease, and is starting to yield clinical applications. However, the interpretation of repertoire data is compromised by a lack of studies to assess the intra and inter-individual variation in the BCR repertoire over time in healthy individuals. We applied a standardized isotype-specific BCR repertoire deep sequencing protocol to a single highly sampled participant, and then evaluated the method in 10 further participants to comprehensively describe such variation. We assessed total repertoire metrics of mutation, diversity, VJ gene usage and isotype subclass usage, as well as tracking specific BCR sequence clusters. There was good assay reproducibility (both in PCR amplification and biological replicates, but we detected striking fluctuations in the repertoire over time that we hypothesize may be due to subclinical immune activation. Repertoire properties were unique for each individual, which could partly be explained by a decrease in IgG2 with age, and genetic differences at the immunoglobulin locus. There was a small repertoire of public clusters (0.5, 0.3 and 1.4% of total IgA, IgG and IgM clusters respectively, which was enriched for expanded clusters containing sequences with suspected specificity towards antigens that should have been historically encountered by all participants through prior immunization or infection. We thus provide baseline BCR repertoire information that can be used to inform future study design, and aid in interpretation of results from these studies. Furthermore our results indicate that BCR repertoire studies could be used to track changes in the public repertoire in and between populations that might relate to population immunity against infectious diseases, and identify the

  7. Association between genetic variation within vitamin D receptor-DNA binding sites and risk of basal cell carcinoma.

    Science.gov (United States)

    Lin, Yuan; Chahal, Harvind S; Wu, Wenting; Cho, Hyunje G; Ransohoff, Katherine J; Dai, Hongji; Tang, Jean Y; Sarin, Kavita Y; Han, Jiali

    2017-05-01

    An increasing number of studies have reported a protective association between vitamin D and cancer risk. The vitamin D endocrine system regulates transcriptional programs involved in inflammation, cell growth and differentiation through the binding of vitamin D receptor (VDR) to specific VDR elements. However, limited attention has been given to the role of variation within VDR binding sites in the development of basal cell carcinoma (BCC). Across 2,776 previously identified VDR binding sites, we identified 2,540 independent single-nucleotide polymorphisms (SNPs) and examined their associations with BCC risk in a genome-wide association meta-analysis totaling 17,187 BCC cases and 287,054 controls from two data sets. After multiple testing corrections, we identified two SNPs at new loci (rs16917546 at 10q21.1: odds ratio (OR) = 1.06, p = 3.16 × 10 -7 and rs79824801 at 12q13.3: OR = 1.10, p = 1.88 × 10 -5 ) for the first time as independently related to BCC risk in meta-analysis; and both SNPs were nominally significant in two data sets. In addition, the SNP rs3769823 within VDR binding site at a previously reported BCC susceptibility locus (2q33.1, rs13014235) also exhibited a significant association (OR = 1.12, p = 3.99 × 10 -18 ). A mutually adjusted model suggested that rs3769823 explained the signal in this region. Our findings support the hypothesis that inherited common variation in VDR binding sites affects the development of BCC. © 2017 UICC.

  8. Genetic variations in T-cell activation and effector pathways modulate alloimmune responses after allogeneic hematopoietic stem cell transplantation in patients with hematologic malignancies

    Science.gov (United States)

    Xiao, Haowen; Luo, Yi; Lai, Xiaoyu; Fu, Shan; Shi, Jimin; Tan, Yamin; He, Jingsong; Xie, Wanzhuo; Zheng, Weiyan; Wang, Li-Mengmeng; Zhang, Lifei; Liu, Lizhen; Ye, Xiujin; Yu, Xiaohong; Cai, Zhen; Lin, Maofang; Huang, He

    2012-01-01

    Background Recently, several important polymorphisms have been identified in T-cell activation and effector pathway genes and have been reported to be associated with inter-patient variability in alloimmune responses. The present study was designed to assess the impact of these genetic variations on the outcomes of allogeneic hematopoietic stem cell transplantation. Design and Methods We first investigated ten single nucleotide polymorphisms in six genes, CD28, inducible co-stimulator, cytotoxic T-lymphocyte antigen 4, granzyme B, Fas and Fas ligand, in 138 pairs of patients and their unrelated donors and a second cohort of 102 pairs of patients and their HLA-identical sibling donors. Results We observed that patients receiving stem cells from a donor with the cytotoxic T-lymphocyte antigen 4 gene CT60 variant allele (AA genotype) had a reduced incidence of grades II–IV acute graft-versus-host disease; however, they experienced early cytomegalovirus infection and relapsed more frequently, which suggested an interaction between the donor cytotoxic T-lymphocyte antigen 4 gene CT60 AA genotype and reduced T-cell alloreactivity. Furthermore, an unrelated donor with the granzyme B +55 variant genotype (AA) was an independent risk factor for development of grades II–IV acute graft-versus-host disease (P=0.024, RR=1.811). Among patients with acute myelogenous leukemia, those with the Fas -670 TT genotype were at higher risk of relapse (P=0.003, RR=3.823). The presence of these susceptible alleles in the donor and/or patient resulted in worse overall survival (54.9% versus 69.5%, P=0.029). Conclusions Our data suggest that genotype analysis of T-cell activation and effector pathway genes can be used for risk assessment for patients with hematologic malignancies before hematopoietic stem cell transplantation. PMID:22733023

  9. Identification and genetic characterization of maize cell wall variation for improved biorefinery feedstock characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Pauly, Markus [UC Berkeley; Hake, Sarah [USDA Albany

    2013-10-31

    The objectives of this program are to 1) characterize novel maize mutants with altered cell walls for enhanced biorefinery characteristics and 2) find quantitative trait loci (QTLs) related to biorefinery characteristics by taking advantage of the genetic diversity of maize. As a result a novel non-transgenic maize plant (cal1) has been identified, whose stover (leaves and stalk) contain more glucan in their walls leading to a higher saccharification yield, when subjected to a standard enzymatic digestion cocktail. Stacking this trait with altered lignin mutants yielded evene higher saccharification yields. Cal-1 mutants do not show a loss of kernel and or biomass yield when grown in the field . Hence, cal1 biomass provides an excellent feedstock for the biofuel industry.

  10. Within and between population variation in epidermal club cell investment in a freshwater prey fish: a cautionary tale for evolutionary ecologists.

    Directory of Open Access Journals (Sweden)

    Aditya K Manek

    Full Text Available Many prey fishes possess large club cells in their epidermis. The role of these cells has garnered considerable attention from evolutionary ecologists. These cells likely form part of the innate immune system of fishes, however, they also have an alarm function, releasing chemical cues that serve to warn nearby conspecifics of danger. Experiments aimed at understanding the selection pressures leading to the evolution of these cells have been hampered by a surprisingly large intraspecific variation in epidermal club cell (ECC investment. The goal of our current work was to explore the magnitude and nature of this variation in ECC investment. In a field survey, we documented large differences in ECC investment both within and between several populations of minnows. We then tested whether we could experimentally reduce variation in mean ECC number by raising fish under standard laboratory conditions for 4 weeks. Fish from different populations responded very differently to being held under standard laboratory conditions; some populations showed an increase in ECC investment while others remained unchanged. More importantly, we found some evidence that we could reduce within population variation in ECC investment through time, but could not reduce among-population variation in mean ECC investment. Given the large variation we observed in wild fish and our limited ability to converge mean cell number by holding the fish under standard conditions, we caution that future studies may be hard pressed to find subtle effects of various experimental manipulations; this will make elucidating the selection pressures leading to the evolution of the cells challenging.

  11. MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells.

    Science.gov (United States)

    Liu, Zongzhi; Li, Ao; Schulz, Vincent; Chen, Min; Tuck, David

    2010-06-01

    Genotyping platforms such as single nucleotide polymorphism (SNP) arrays are powerful tools to study genomic aberrations in cancer samples. Allele specific information from SNP arrays provides valuable information for interpreting copy number variation (CNV) and allelic imbalance including loss-of-heterozygosity (LOH) beyond that obtained from the total DNA signal available from array comparative genomic hybridization (aCGH) platforms. Several algorithms based on hidden Markov models (HMMs) have been designed to detect copy number changes and copy-neutral LOH making use of the allele information on SNP arrays. However heterogeneity in clinical samples, due to stromal contamination and somatic alterations, complicates analysis and interpretation of these data. We have developed MixHMM, a novel hidden Markov model using hidden states based on chromosomal structural aberrations. MixHMM allows CNV detection for copy numbers up to 7 and allows more complete and accurate description of other forms of allelic imbalance, such as increased copy number LOH or imbalanced amplifications. MixHMM also incorporates a novel sample mixing model that allows detection of tumor CNV events in heterogeneous tumor samples, where cancer cells are mixed with a proportion of stromal cells. We validate MixHMM and demonstrate its advantages with simulated samples, clinical tumor samples and a dilution series of mixed samples. We have shown that the CNVs of cancer cells in a tumor sample contaminated with up to 80% of stromal cells can be detected accurately using Illumina BeadChip and MixHMM. The MixHMM is available as a Python package provided with some other useful tools at http://genecube.med.yale.edu:8080/MixHMM.

  12. MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells.

    Directory of Open Access Journals (Sweden)

    Zongzhi Liu

    Full Text Available BACKGROUND: Genotyping platforms such as single nucleotide polymorphism (SNP arrays are powerful tools to study genomic aberrations in cancer samples. Allele specific information from SNP arrays provides valuable information for interpreting copy number variation (CNV and allelic imbalance including loss-of-heterozygosity (LOH beyond that obtained from the total DNA signal available from array comparative genomic hybridization (aCGH platforms. Several algorithms based on hidden Markov models (HMMs have been designed to detect copy number changes and copy-neutral LOH making use of the allele information on SNP arrays. However heterogeneity in clinical samples, due to stromal contamination and somatic alterations, complicates analysis and interpretation of these data. METHODS: We have developed MixHMM, a novel hidden Markov model using hidden states based on chromosomal structural aberrations. MixHMM allows CNV detection for copy numbers up to 7 and allows more complete and accurate description of other forms of allelic imbalance, such as increased copy number LOH or imbalanced amplifications. MixHMM also incorporates a novel sample mixing model that allows detection of tumor CNV events in heterogeneous tumor samples, where cancer cells are mixed with a proportion of stromal cells. CONCLUSIONS: We validate MixHMM and demonstrate its advantages with simulated samples, clinical tumor samples and a dilution series of mixed samples. We have shown that the CNVs of cancer cells in a tumor sample contaminated with up to 80% of stromal cells can be detected accurately using Illumina BeadChip and MixHMM. AVAILABILITY: The MixHMM is available as a Python package provided with some other useful tools at http://genecube.med.yale.edu:8080/MixHMM.

  13. Seasonal variation in cell proliferation and cell migration in the brain of adult red-sided garter snakes (Thamnophis sirtalis parietalis).

    Science.gov (United States)

    Maine, Ashley R; Powers, Sean D; Lutterschmidt, Deborah I

    2014-01-01

    Plasticity in the adult central nervous system has been described in all vertebrate classes as well as in some invertebrate groups. However, the limited taxonomic diversity represented in the current neurogenesis literature limits our ability to assess the functional significance of adult neurogenesis for natural behaviors as well as the evolution of its regulatory mechanisms. In the present study, we used free-ranging red-sided garter snakes (Thamnophis sirtalis parietalis) to test the hypothesis that seasonal shifts in physiology and behavior are associated with seasonal variation in postembryonic neurogenesis. Specifically, we used the thymidine analog 5-bromo-2'-deoxyuridine (BrdU) to determine if the rates of cell proliferation in the adult brain vary between male snakes collected during spring and fall at 1, 5, and 10 days post-BrdU treatment. To assess rates of cell migration within the brain, we further categorized BrdU-labeled cells according to their location within the ventricular zone or parenchymal region. BrdU-labeled cells were localized mainly within the lateral, dorsal, and medial cortex, septal nucleus, nucleus sphericus, preoptic area, and hypothalamus. In all regions, the number of BrdU-labeled cells in the ventricular zone was higher in the fall compared to spring. In the parenchymal region, a significantly higher number of labeled cells was also observed during the fall, but only within the nucleus sphericus and the combined preoptic area/hypothalamus. The immunoreactive cell number did not vary significantly with days post-BrdU treatment in either season or in any brain region. While it is possible that the higher rates of cell proliferation in the fall simply reflect increased growth of all body tissues, including the brain, our data show that seasonal changes in cell migration into the parenchyma are region specific. In red-sided garter snakes and other reptiles, the dorsal and medial cortex is important for spatial navigation and memory

  14. High-Dimensional Phenotypic Mapping of Human Dendritic Cells Reveals Interindividual Variation and Tissue Specialization.

    Science.gov (United States)

    Alcántara-Hernández, Marcela; Leylek, Rebecca; Wagar, Lisa E; Engleman, Edgar G; Keler, Tibor; Marinkovich, M Peter; Davis, Mark M; Nolan, Garry P; Idoyaga, Juliana

    2017-12-19

    Given the limited efficacy of clinical approaches that rely on ex vivo generated dendritic cells (DCs), it is imperative to design strategies that harness specialized DC subsets in situ. This requires delineating the expression of surface markers by DC subsets among individuals and tissues. Here, we performed a multiparametric phenotypic characterization and unbiased analysis of human DC subsets in blood, tonsil, spleen, and skin. We uncovered previously unreported phenotypic heterogeneity of human cDC2s among individuals, including variable expression of functional receptors such as CD172a. We found marked differences in DC subsets localized in blood and lymphoid tissues versus skin, and a striking absence of the newly discovered Axl + DCs in the skin. Finally, we evaluated the capacity of anti-receptor monoclonal antibodies to deliver vaccine components to skin DC subsets. These results offer a promising path for developing DC subset-specific immunotherapies that cannot be provided by transcriptomic analysis alone. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Genetic variation and epigenetic modification of the prodynorphin gene in peripheral blood cells in alcoholism.

    Science.gov (United States)

    D'Addario, Claudio; Shchetynsky, Klementy; Pucci, Mariangela; Cifani, Carlo; Gunnar, Agneta; Vukojević, Vladana; Padyukov, Leonid; Terenius, Lars

    2017-06-02

    Dynorphins are critically involved in the development, maintenance and relapse of alcoholism. Alcohol-induced changes in the prodynorphin gene expression may be influenced by both gene polymorphisms and epigenetic modifications. The present study of human alcoholics aims to evaluate DNA methylation patterns in the prodynorphin gene (PDYN) promoter and to identify single nucleotide polymorphisms (SNPs) associated with alcohol dependence and with altered DNA methylation. Genomic DNA was isolated from peripheral blood cells of alcoholics and healthy controls, and DNA methylation was studied in the PDYN promoter by bisulfite pyrosequencing. In alcoholics, DNA methylation increased in three of the seven CpG sites investigated, as well as in the average of the seven CpG sites. Data stratification showed lower increase in DNA methylation levels in individuals reporting craving and with higher levels of alcohol consumption. Association with alcoholism was observed for rs2235751 and the presence of the minor allele G was associated with reduced DNA methylation at PDYN promoter in females and younger subjects. Genetic and epigenetic factors within PDYN are related to risk for alcoholism, providing further evidence of its involvement on ethanol effects. These results might be of relevance for developing new biomarkers to predict disease trajectories and therapeutic outcome. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Variation of power generation at different buffer types and conductivities in single chamber microbial fuel cells

    KAUST Repository

    Nam, Joo-Youn

    2010-01-15

    Microbial fuel cells (MFCs) are operated with solutions containing various chemical species required for the growth of electrochemically active microorganisms including nutrients and vitamins, substrates, and chemical buffers. Many different buffers are used in laboratory media, but the effects of these buffers and their inherent electrolyte conductivities have not been examined relative to current generation in MFCs. We investigated the effect of several common buffers (phosphate, MES, HEPES, and PIPES) on power production in single chambered MFCs compared to a non-buffered control. At the same concentrations the buffers produced different solution conductivities which resulted in different ohmic resistances and power densities. Increasing the solution conductivities to the same values using NaCl produced comparable power densities for all buffers. Very large increases in conductivity resulted in a rapid voltage drop at high current densities. Our results suggest that solution conductivity at a specific pH for each buffer is more important in MFC studies than the buffer itself given relatively constant pH conditions. Based on our analysis of internal resistance and a set neutral pH, phosphate and PIPES are the most useful buffers of those examined here because pH was maintained close to the pKa of the buffer, maximizing the ability of the buffer to contribute to increase current generation at high power densities. © 2009 Elsevier B.V. All rights reserved.

  17. Variation of power generation at different buffer types and conductivities in single chamber microbial fuel cells.

    Science.gov (United States)

    Nam, Joo-Youn; Kim, Hyun-Woo; Lim, Kyeong-Ho; Shin, Hang-Sik; Logan, Bruce E

    2010-01-15

    Microbial fuel cells (MFCs) are operated with solutions containing various chemical species required for the growth of electrochemically active microorganisms including nutrients and vitamins, substrates, and chemical buffers. Many different buffers are used in laboratory media, but the effects of these buffers and their inherent electrolyte conductivities have not been examined relative to current generation in MFCs. We investigated the effect of several common buffers (phosphate, MES, HEPES, and PIPES) on power production in single chambered MFCs compared to a non-buffered control. At the same concentrations the buffers produced different solution conductivities which resulted in different ohmic resistances and power densities. Increasing the solution conductivities to the same values using NaCl produced comparable power densities for all buffers. Very large increases in conductivity resulted in a rapid voltage drop at high current densities. Our results suggest that solution conductivity at a specific pH for each buffer is more important in MFC studies than the buffer itself given relatively constant pH conditions. Based on our analysis of internal resistance and a set neutral pH, phosphate and PIPES are the most useful buffers of those examined here because pH was maintained close to the pK(a) of the buffer, maximizing the ability of the buffer to contribute to increase current generation at high power densities. Copyright 2009 Elsevier B.V. All rights reserved.

  18. Elucidating the effects of arginine and lysine on a monoclonal antibody C-terminal lysine variation in CHO cell cultures.

    Science.gov (United States)

    Zhang, Xintao; Tang, Hongping; Sun, Ya-Ting; Liu, Xuping; Tan, Wen-Song; Fan, Li

    2015-08-01

    C-terminal lysine variants are commonly observed in monoclonal antibodies (mAbs) and found sensitive to process conditions, especially specific components in culture medium. The potential roles of media arginine (Arg) and lysine (Lys) in mAb heavy chain C-terminal lysine processing were investigated by monitoring the lysine variant levels under various Arg and Lys concentrations. Both Arg and Lys were found to significantly affect lysine variant level. Specifically, lysine variant level increased from 18.7 to 31.8 % when Arg and Lys concentrations were increased from 2 to 10 mM. Since heterogeneity of C-terminal lysine residues is due to the varying degree of proteolysis by basic carboxypeptidases (Cps), enzyme (basic Cps) level, pH conditions, and product (Arg and Lys) inhibition, which potentially affect the enzymatic reaction, were investigated under various Arg and Lys conditions. Enzyme level and pH conditions were found not to account for the different lysine variant levels, which was evident from the minimal variation in transcription level and intracellular pH. On the other hand, product inhibition effect of Arg and Lys on basic Cps was evident from the notable intracellular and extracellular Arg and Lys concentrations comparable with Ki values (inhibition constant) of basic Cps and further confirmed by cell-free assays. Additionally, a kinetic study of lysine variant level during the cell culture process enabled further characterization of the C-terminal lysine processing.

  19. Variation in Definitive Therapy for Localized Non-Small Cell Lung Cancer Among National Comprehensive Cancer Network Institutions

    Energy Technology Data Exchange (ETDEWEB)

    Valle, Luca F. [Geisel School of Medicine at Dartmouth College, Dartmouth College, Hanover, New Hampshire (United States); Jagsi, Reshma [Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan (United States); Bobiak, Sarah N.; Zornosa, Carrie [National Comprehensive Cancer Network, Fort Washington, Pennsylvania (United States); D' Amico, Thomas A. [Department of Surgery, Division of Thoracic Surgery, Duke Cancer Institute, Durham, North Carolina (United States); Pisters, Katherine M. [Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Dexter, Elisabeth U. [Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York (United States); Niland, Joyce C. [Department of Information Sciences, City of Hope Comprehensive Cancer Center, Duarte, California (United States); Hayman, James A. [Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan (United States); Kapadia, Nirav S., E-mail: Nirav.S.Kapadia@hitchcock.org [Department of Radiation Oncology, Dartmouth-Hitchcock Norris Cotton Cancer Center, Lebanon, New Hampshire (United States); Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, New Hampshire (United States)

    2016-02-01

    Purpose: This study determined practice patterns in the staging and treatment of patients with stage I non-small cell lung cancer (NSCLC) among National Comprehensive Cancer Network (NCCN) member institutions. Secondary aims were to determine trends in the use of definitive therapy, predictors of treatment type, and acute adverse events associated with primary modalities of treatment. Methods and Materials: Data from the National Comprehensive Cancer Network Oncology Outcomes Database from 2007 to 2011 for US patients with stage I NSCLC were used. Main outcome measures included patterns of care, predictors of treatment, acute morbidity, and acute mortality. Results: Seventy-nine percent of patients received surgery, 16% received definitive radiation therapy (RT), and 3% were not treated. Seventy-four percent of the RT patients received stereotactic body RT (SBRT), and the remainder received nonstereotactic RT (NSRT). Among participating NCCN member institutions, the number of surgeries-to-RT course ratios varied between 1.6 and 34.7 (P<.01), and the SBRT-to-NSRT ratio varied between 0 and 13 (P=.01). Significant variations were also observed in staging practices, with brain imaging 0.33 (0.25-0.43) times as likely and mediastinoscopy 31.26 (21.84-44.76) times more likely for surgical patients than for RT patients. Toxicity rates for surgical and for SBRT patients were similar, although the rates were double for NSRT patients. Conclusions: The variations in treatment observed among NCCN institutions reflects the lack of level I evidence directing the use of surgery or SBRT for stage I NSCLC. In this setting, research of patient and physician preferences may help to guide future decision making.

  20. Individual variation of the genetic response to bisphenol a in human foreskin fibroblast cells derived from cryptorchidism and hypospadias patients.

    Directory of Open Access Journals (Sweden)

    Xian-Yang Qin

    Full Text Available BACKGROUND/PURPOSE: We hypothesized that polymorphic differences among individuals might cause variations in the effect that environmental endocrine disruptors (EEDs have on male genital malformations (MGMs. In this study, individual variation in the genetic response to low-dose bisphenol A (BPA was investigated in human foreskin fibroblast cells (hFFCs derived from child cryptorchidism (CO and hypospadias (HS patients. METHODOLOGY/PRINCIPAL FINDINGS: hFFCs were collected from control children without MGMs (n=5 and child CO and HS patients (n=8 and 21, respectively. BPA exposure (10 nM was found to inhibit matrix metalloproteinase-11 (MMP11 expression in the HS group (0.74-fold, P=0.0034 but not in the control group (0.93-fold, P=0.84 and CO group (0.94-fold, P=0.70. Significantly lower levels of MMP11 expression were observed in the HS group compared with the control group (0.80-fold, P=0.0088 and CO group (0.79-fold, P=0.039 in response to 10 nM BPA. The effect of single-nucleotide polymorphism rs5000770 (G>A, located within the aryl hydrocarbon receptor nuclear translocator 2 (ARNT2 locus, on individual sensitivity to low-dose BPA was investigated in the HS group. A significant difference in neurotensin receptor 1 (NTSR1 expression in response to 10 nM BPA was observed between AA and AG/GG groups (n=6 and 15, respectively. P=0.031. However, no significant difference in ARNT2 expression was observed (P=0.18. CONCLUSIONS/SIGNIFICANCE: This study advances our understanding of the specificity of low-dose BPA effects on human reproductive health. Our results suggest that genetic variability among individuals affects susceptibility to the effects of EEDs exposure as a potential cause of HS.

  1. The Impact of Quality Variations on Patients Undergoing Surgery for Renal Cell Carcinoma: A National Cancer Database Study.

    Science.gov (United States)

    Lawson, Keith A; Saarela, Olli; Abouassaly, Robert; Kim, Simon P; Breau, Rodney H; Finelli, Antonio

    2017-09-01

    Despite efforts to define metrics assessing hospital-level quality for renal cell carcinoma (RCC) surgical care there remains a paucity of real-world data validating their ability to benchmark performance. Consequently, whether poor performance on hospital-level quality indicators is associated with inferior patient outcomes remains unknown. To determine hospital-level variations in RCC surgical quality after adjusting for differences in patient- and tumor-specific factors. Further, to determine associations between hospital-level quality performance and surgical volume, academic affiliation, and patient mortality. RCC patients undergoing surgery in the USA and Puerto Rico (2004-2014) were identified from the National Cancer Database. Hospital-level quality of care was assessed according to disease-specific process and outcome quality indicators. Case-mix adjusted hospital benchmarking was performed using indirect standardization methodology and multivariable regression models. A composite measure of quality, the Renal Cancer Quality Score (RC-QS), was subsequently derived and associations between RC-QS and surgical volume, academic affiliation, and patient mortality were determined. Over 1100 hospitals were benchmarked for quality, with 10-31% identified as providing poor care for a given quality indicator. Lower RC-QS hospitals had smaller referral volumes and were less academic compared with higher RC-QS hospitals (pexist, as captured by the RC-QS. Superior quality is associated with improved patient outcomes, including mortality benefit. The RC-QS serves as a benchmarking tool for RCC quality that can provide audit level feedback to hospitals and policymakers for quality improvement. We benchmarked hospital performance across quality indicators for kidney cancer surgical care. Overall, large variations in quality exist, with high volume academic hospitals demonstrating superior performance and improved patient survival. These data can inform hospitals and

  2. Quantitative Assessment of Intra-Patient Variation in CD4+ T Cell Counts in Stable, Virologically-Suppressed, HIV-Infected Subjects.

    Science.gov (United States)

    Gordon, Claire L; Cheng, Allen C; Cameron, Paul U; Bailey, Michael; Crowe, Suzanne M; Mills, John

    2015-01-01

    Counts of absolute CD4+ T lymphocytes (CD4+ T cells) are known to be highly variable in untreated HIV-infected individuals, but there are no data in virologically-suppressed individuals. We investigated CD4+ T cell variability in stable, virologically-suppressed, HIV-1 infected adults on combination antiretroviral therapy (cART). From a large hospital database we selected patients with stable virological suppression on cART for >3 years with >10 CD4+ T cell measurements performed over a further >2 years; and a control group of 95 patients not on cART. We identified 161 HIV-infected patients on cART without active HCV or HBV infection, with stable virological suppression for a median of 6.4 years. Over the study period 88 patients had reached a plateau in their absolute CD4+ T cell counts, while 65 patients had increasing and 8 patients had decreasing absolute CD4+ T cell counts. In patients with plateaued CD4+ T cell counts, variability in absolute CD4+ T cell counts was greater than in percent CD4+ T cells (median coefficient of variation (CV) 16.6% [IQR 13.8-20.1%] and CV 9.6% [IQR 7.4-13.0%], respectively). Patients with increasing CD4+ T cell counts had greater variability in absolute CD4+ T cell counts than those with plateaued CD4 T cell counts (CV 19.5% [IQR 16.1-23.8%], pcounts; this variation can be of clinical relevance especially around CD4+ thresholds. However, the variation seen in individuals on cART is substantially less than in untreated subjects.

  3. Large-scale evaluation of common variation in regulatory T cell-related genes and ovarian cancer outcome.

    Science.gov (United States)

    Charbonneau, Bridget; Moysich, Kirsten B; Kalli, Kimberly R; Oberg, Ann L; Vierkant, Robert A; Fogarty, Zachary C; Block, Matthew S; Maurer, Matthew J; Goergen, Krista M; Fridley, Brooke L; Cunningham, Julie M; Rider, David N; Preston, Claudia; Hartmann, Lynn C; Lawrenson, Kate; Wang, Chen; Tyrer, Jonathan; Song, Honglin; deFazio, Anna; Johnatty, Sharon E; Doherty, Jennifer A; Phelan, Catherine M; Sellers, Thomas A; Ramirez, Starr M; Vitonis, Allison F; Terry, Kathryn L; Van Den Berg, David; Pike, Malcolm C; Wu, Anna H; Berchuck, Andrew; Gentry-Maharaj, Aleksandra; Ramus, Susan J; Diergaarde, Brenda; Shen, Howard; Jensen, Allan; Menkiszak, Janusz; Cybulski, Cezary; Lubiłski, Jan; Ziogas, Argyrios; Rothstein, Joseph H; McGuire, Valerie; Sieh, Weiva; Lester, Jenny; Walsh, Christine; Vergote, Ignace; Lambrechts, Sandrina; Despierre, Evelyn; Garcia-Closas, Montserrat; Yang, Hannah; Brinton, Louise A; Spiewankiewicz, Beata; Rzepecka, Iwona K; Dansonka-Mieszkowska, Agnieszka; Seibold, Petra; Rudolph, Anja; Paddock, Lisa E; Orlow, Irene; Lundvall, Lene; Olson, Sara H; Hogdall, Claus K; Schwaab, Ira; du Bois, Andreas; Harter, Philipp; Flanagan, James M; Brown, Robert; Paul, James; Ekici, Arif B; Beckmann, Matthias W; Hein, Alexander; Eccles, Diana; Lurie, Galina; Hays, Laura E; Bean, Yukie T; Pejovic, Tanja; Goodman, Marc T; Campbell, Ian; Fasching, Peter A; Konecny, Gottfried; Kaye, Stanley B; Heitz, Florian; Hogdall, Estrid; Bandera, Elisa V; Chang-Claude, Jenny; Kupryjanczyk, Jolanta; Wentzensen, Nicolas; Lambrechts, Diether; Karlan, Beth Y; Whittemore, Alice S; Culver, Hoda Anton; Gronwald, Jacek; Levine, Douglas A; Kjaer, Susanne K; Menon, Usha; Schildkraut, Joellen M; Pearce, Celeste Leigh; Cramer, Daniel W; Rossing, Mary Anne; Chenevix-Trench, Georgia; Pharoah, Paul D P; Gayther, Simon A; Ness, Roberta B; Odunsi, Kunle; Sucheston, Lara E; Knutson, Keith L; Goode, Ellen L

    2014-04-01

    The presence of regulatory T cells (Treg) in solid tumors is known to play a role in patient survival in ovarian cancer and other malignancies. We assessed inherited genetic variations via 749 tag single-nucleotide polymorphisms (SNP) in 25 Treg-associated genes (CD28, CTLA4, FOXP3, IDO1, IL10, IL10RA, IL15, 1L17RA, IL23A, IL23R, IL2RA, IL6, IL6R, IL8, LGALS1, LGALS9, MAP3K8, STAT5A, STAT5B, TGFB1, TGFB2, TGFB3, TGFBR1, TGRBR2, and TGFBR3) in relation to ovarian cancer survival. We analyzed genotype and overall survival in 10,084 women with invasive epithelial ovarian cancer, including 5,248 high-grade serous, 1,452 endometrioid, 795 clear cell, and 661 mucinous carcinoma cases of European descent across 28 studies from the Ovarian Cancer Association Consortium (OCAC). The strongest associations were found for endometrioid carcinoma and IL2RA SNPs rs11256497 [HR, 1.42; 95% confidence interval (CI), 1.22-1.64; P = 5.7 × 10(-6)], rs791587 (HR, 1.36; 95% CI, 1.17-1.57; P = 6.2 × 10(-5)), rs2476491 (HR, = 1.40; 95% CI, 1.19-1.64; P = 5.6 × 10(-5)), and rs10795763 (HR, 1.35; 95% CI, 1.17-1.57; P = 7.9 × 10(-5)), and for clear cell carcinoma and CTLA4 SNP rs231775 (HR, 0.67; 95% CI, 0.54-0.82; P = 9.3 × 10(-5)) after adjustment for age, study site, population stratification, stage, grade, and oral contraceptive use. The rs231775 allele associated with improved survival in our study also results in an amino acid change in CTLA4 and previously has been reported to be associated with autoimmune conditions. Thus, we found evidence that SNPs in genes related to Tregs seem to play a role in ovarian cancer survival, particularly in patients with clear cell and endometrioid epithelial ovarian cancer.

  4. Genome-wide copy number variation pattern analysis and a classification signature for non-small cell lung cancer.

    Science.gov (United States)

    Qiu, Zhe-Wei; Bi, Jia-Hao; Gazdar, Adi F; Song, Kai

    2017-07-01

    The accurate classification of non-small cell lung carcinoma (NSCLC) into lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) is essential for both clinical practice and lung cancer research. Although the standard WHO diagnosis of NSCLC on biopsy material is rapid and economic, more than 13% of NSCLC tumors in the USA are not further classified. The purpose of this study was to analyze the genome-wide pattern differences in copy number variations (CNVs) and to develop a CNV signature as an adjunct test for the routine histopathologic classification of NSCLCs. We investigated the genome-wide CNV differences between these two tumor types using three independent patient datasets. Approximately half of the genes examined exhibited significant differences between LUAD and LUSC tumors and the corresponding non-malignant tissues. A new classifier was developed to identify signature genes out of 20 000 genes. Thirty-three genes were identified as a CNV signature of NSCLC. Using only their CNV values, the classification model separated the LUADs from the LUSCs with an accuracy of 0.88 and 0.84, respectively, in the training and validation datasets. The same signature also classified NSCLC tumors from their corresponding non-malignant samples with an accuracy of 0.96 and 0.98, respectively. We also compared the CNV patterns of NSCLC tumors with those of histologically similar tumors arising at other sites, such as the breast, head, and neck, and four additional tumors. Of greater importance, the significant differences between these tumors may offer the possibility of identifying the origin of tumors whose origin is unknown. © 2017 Wiley Periodicals, Inc.

  5. Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells

    DEFF Research Database (Denmark)

    Pedersen, Natasja Wulff; Chandran, P. Anoop; Qian, Yu

    2017-01-01

    Manual analysis of flow cytometry data and subjective gate-border decisions taken by individuals continue to be a source of variation in the assessment of antigen-specific T cells when comparing data across laboratories, and also over time in individual labs. Therefore, strategies to provide auto...

  6. Threshold voltage variation depending on single grain boundary and stored charges in an adjacent cell for vertical silicon–oxide–nitride–oxide–silicon NAND flash memory

    Science.gov (United States)

    Oh, Hyeongwan; Kim, Jiwon; Baek, Rock-Hyun; Lee, Jeong-Soo

    2018-04-01

    The effects of single grain boundary (SGB) position and stored electron charges in an adjacent cell in silicon–oxide–nitride–oxide–silicon (SONOS) structures on the variations of threshold voltage (V th) were investigated using technology computer-aided design (TCAD) simulation. As the bit line voltage increases, the SGB position causing the maximum V th variation was shifted from the center to the source side in the channel, owing to the drain-induced grain barrier lowering effect. When the SGB is located in the spacer region, the potential interaction from both the SGB and the stored electron charges in the adjacent cell becomes significant and thus resulting in larger V th variation. In contrast, when the SGB is located at the center of the channel, the peak position of potential barrier is shifted to the center, so that the influence of the adjacent cell is diminished. As the gate length is scaled down to 20 nm, the influence of stored charges in adjacent cells becomes significant, resulting in larger V th variations.

  7. Correlation among genetic variations of c-MET in Chinese patients with non-small cell lung cancer.

    Science.gov (United States)

    Duan, Jianchun; Yang, Xiaodan; Zhao, Jun; Zhuo, Minglei; Wang, Zhijie; An, Tongtong; Bai, Hua; Wang, Jie

    2018-01-05

    The purpose of our research was to determine the correlation of amplification, protein expression and somatic mutation of c-MET in IIIb-IV stage NSCLC (Non-small cell lung cancer). We also explored correlation of c-MET variation with clinical outcome. c-MET expression was observed in 28.6% (56/196) cases, and among those 13.8% (27/196) were shown to be FISH positive. Only 2.67% patients in this study carried the c-MET mutation. Cases with c-MET FISH positive were all IHC positive ,but in IHC positive cases, only half were FISH positive. Among patients with IHC 2+ staining, 35.5% was FISH positive, while cases with IHC 3+ staining,64% was FISH positive. Both protein expression and copy number of c-MET did not significantly correlate with clinical prognosis in these patients treated with EGFR-TKIs. IHC could be used as a preliminary screening method for c-MET copy number amplification and should be confirmed by FISH only in IHC positive case which facilitate selection of ALK or MET inhibitor therapy. c-MET gene copy number, protein expression and somatic mutation for exon 14 were detected by fluorescent- In-Situ -Hybridization (FISH), Immunohistochemistry (IHC), and Denaturing-High-Performance-Liquid-Chromatography (DHPLC), respectively, in 196 NSCLC patients. The relationship between c-MET abnormalities and clinical outcome of targeted therapy was analyzed by McNemar's test.

  8. Estrous cycle-dependent neural plasticity in the caudal brainstem in the female golden hamster : Ultrastructural and immunocytochemical studies of axo-dendritic relationships and dynamic remodeling

    NARCIS (Netherlands)

    Gerrits, P. O.; Kortekaas, R.; Veening, J. G.; de Weerd, H.; Algra, A.; Mouton, L. J.; van der Want, J. J. L.

    2008-01-01

    During the short four-day estrous cycle of the female hamster various behavioral (lordosis, vocalization and aggression) and autonomic adaptations occur. Presumably, these changes are under ovarian control. Recently, we described a distinct estrogen receptor-alpha immunoreactive (ER-alpha-IR) cell

  9. Estrous cycle-dependent neural plasticity in the caudal brainstem in the female golden hamster: ultrastructural and immunocytochemical studies of axo-dendritic relationships and dynamic remodeling.

    NARCIS (Netherlands)

    Gerrits, P.O.; Kortekaas, R.; Veening, J.G.; Weerd, H. de; Algra, A.; Mouton, L.J.; Want, J.J. van der

    2008-01-01

    During the short four-day estrous cycle of the female hamster various behavioral (lordosis, vocalization and aggression) and autonomic adaptations occur. Presumably, these changes are under ovarian control. Recently, we described a distinct estrogen receptor-alpha immunoreactive (ER-alpha-IR) cell

  10. Morphological and photosynthetic variations in the process of spermatia formation from vegetative cells in Porphyra yezoensis Ueda (Bangiales, Rhodophyta) and their responses to desiccation.

    Science.gov (United States)

    Yang, Rui-Ling; Zhou, Wei; Shen, Song-Dong; Wang, Guang-Ce; He, Lin-Wen; Pan, Guang-Hua

    2012-05-01

    Porphyra yezoensis has a macroscopic foliage gametophyte phase with only a single cell layer, and is ideally suited for the study of the sexual differentiation process, from the vegetative cell to the spermatia. Firstly, we compared variations in the responses of the vegetative and male sectors to desiccation. Later, cell tracking experiments were carried out during the formation of spermatia from vegetative cells. The two sectors showed similar tolerance to desiccation, and the formation of spermatia from vegetative cells was independent of the degree of desiccation. Both light and scanning electron microscopy (SEM) observations of the differentiation process showed that the formation of spermatia could be divided into six phases: the one-cell, two-cell, four-cell, eight-cell, pre-release and spermatia phases. Photomicrographs of Fluorescent Brightener staining showed that the released spermatia had no cell walls. Photosynthetic data showed that there was a significant rise in Y(II) in the four-cell phase, indicating an increase in photosynthetic efficiency of PSII during this phase. We propose that this photosynthetic rise may be substantial and provide the increased energy needed for the formation and release of spermatia in P. yezoensis.

  11. Histologic processing artifacts and inter-pathologist variation in measurement of inked margins of canine mast cell tumors.

    Science.gov (United States)

    Kiser, Patti K; Löhr, Christiane V; Meritet, Danielle; Spagnoli, Sean T; Milovancev, Milan; Russell, Duncan S

    2018-02-01

    Although quantitative assessment of margins is recommended for describing excision of cutaneous malignancies, there is poor understanding of limitations associated with this technique. We described and quantified histologic artifacts in inked margins and determined the association between artifacts and variance in histologic tumor-free margin (HTFM) measurements based on a novel grading scheme applied to 50 sections of normal canine skin and 56 radial margins taken from 15 different canine mast cell tumors (MCTs). Three broad categories of artifact were 1) tissue deformation at inked edges, 2) ink-associated artifacts, and 3) sectioning-associated artifacts. The most common artifacts in MCT margins were ink-associated artifacts, specifically ink absent from an edge (mean prevalence: 50%) and inappropriate ink coloring (mean: 45%). The prevalence of other artifacts in MCT skin was 4-50%. In MCT margins, frequency-adjusted kappa statistics found fair or better inter-rater reliability for 9 of 10 artifacts; intra-rater reliability was moderate or better in 9 of 10 artifacts. Digital HTFM measurements by 5 blinded pathologists had a median standard deviation (SD) of 1.9 mm (interquartile range: 0.8-3.6 mm; range: 0-6.2 mm). Intraclass correlation coefficients demonstrated good inter-pathologist reliability in HTFM measurement (κ = 0.81). Spearman rank correlation coefficients found negligible correlation between artifacts and HTFM SDs ( r ≤ 0.3). These data confirm that although histologic artifacts commonly occur in inked margin specimens, artifacts are not meaningfully associated with variation in HTFM measurements. Investigators can use the grading scheme presented herein to identify artifacts associated with tissue processing.

  12. Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells

    Directory of Open Access Journals (Sweden)

    Natasja Wulff Pedersen

    2017-07-01

    Full Text Available Manual analysis of flow cytometry data and subjective gate-border decisions taken by individuals continue to be a source of variation in the assessment of antigen-specific T cells when comparing data across laboratories, and also over time in individual labs. Therefore, strategies to provide automated analysis of major histocompatibility complex (MHC multimer-binding T cells represent an attractive solution to decrease subjectivity and technical variation. The challenge of using an automated analysis approach is that MHC multimer-binding T cell populations are often rare and therefore difficult to detect. We used a highly heterogeneous dataset from a recent MHC multimer proficiency panel to assess if MHC multimer-binding CD8+ T cells could be analyzed with computational solutions currently available, and if such analyses would reduce the technical variation across different laboratories. We used three different methods, FLOw Clustering without K (FLOCK, Scalable Weighted Iterative Flow-clustering Technique (SWIFT, and ReFlow to analyze flow cytometry data files from 28 laboratories. Each laboratory screened for antigen-responsive T cell populations with frequency ranging from 0.01 to 1.5% of lymphocytes within samples from two donors. Experience from this analysis shows that all three programs can be used for the identification of high to intermediate frequency of MHC multimer-binding T cell populations, with results very similar to that of manual gating. For the less frequent populations (<0.1% of live, single lymphocytes, SWIFT outperformed the other tools. As used in this study, none of the algorithms offered a completely automated pipeline for identification of MHC multimer populations, as varying degrees of human interventions were needed to complete the analysis. In this study, we demonstrate the feasibility of using automated analysis pipelines for assessing and identifying even rare populations of antigen-responsive T cells and discuss

  13. Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells.

    Science.gov (United States)

    Pedersen, Natasja Wulff; Chandran, P Anoop; Qian, Yu; Rebhahn, Jonathan; Petersen, Nadia Viborg; Hoff, Mathilde Dalsgaard; White, Scott; Lee, Alexandra J; Stanton, Rick; Halgreen, Charlotte; Jakobsen, Kivin; Mosmann, Tim; Gouttefangeas, Cécile; Chan, Cliburn; Scheuermann, Richard H; Hadrup, Sine Reker

    2017-01-01

    Manual analysis of flow cytometry data and subjective gate-border decisions taken by individuals continue to be a source of variation in the assessment of antigen-specific T cells when comparing data across laboratories, and also over time in individual labs. Therefore, strategies to provide automated analysis of major histocompatibility complex (MHC) multimer-binding T cells represent an attractive solution to decrease subjectivity and technical variation. The challenge of using an automated analysis approach is that MHC multimer-binding T cell populations are often rare and therefore difficult to detect. We used a highly heterogeneous dataset from a recent MHC multimer proficiency panel to assess if MHC multimer-binding CD8 + T cells could be analyzed with computational solutions currently available, and if such analyses would reduce the technical variation across different laboratories. We used three different methods, FLOw Clustering without K (FLOCK), Scalable Weighted Iterative Flow-clustering Technique (SWIFT), and ReFlow to analyze flow cytometry data files from 28 laboratories. Each laboratory screened for antigen-responsive T cell populations with frequency ranging from 0.01 to 1.5% of lymphocytes within samples from two donors. Experience from this analysis shows that all three programs can be used for the identification of high to intermediate frequency of MHC multimer-binding T cell populations, with results very similar to that of manual gating. For the less frequent populations (analysis. In this study, we demonstrate the feasibility of using automated analysis pipelines for assessing and identifying even rare populations of antigen-responsive T cells and discuss the main properties, differences, and advantages of the different methods tested.

  14. Seasonal variation of cell proliferation and apoptosis in the efferent ductules and epididymis of the Neotropical bat Artibeus lituratus (Chiroptera, Phyllostomidae).

    Science.gov (United States)

    Campolina-Silva, Gabriel H; Hess, Rex A; Oliveira, Cleida A

    2018-02-07

    The balance between cell proliferation and apoptosis is important for maintenance of male fertility, being influenced by a variety of stimuli including androgens and estrogens. However, studies concerning regulation of these processes along the male reproductive tract under physiological conditions are scarce. Therefore, in this study, we investigated the profile of cell proliferation and apoptosis in the efferent ductules and epididymis of the Neotropical bat Artibeus lituratus, a seasonal breeder that presents natural variation in components of the androgen and estrogen responsive systems along the circannual cycle. Low rates of cell proliferation and apoptosis were found in the efferent ductules and epididymis of A. lituratus during the reproductive period, as few epithelial cells were positive for MCM7 (proliferation marker) and cleaved caspase-3 or TUNEL (apoptosis markers). In contrast, during the regressive period, the rate of both proliferating and apoptotic cells was significantly higher in the epithelium lining the efferent ductules as well as throughout the epididymis. The increased proliferative activity at this phase was positively correlated with the expression of estrogen receptor alpha (ERα), whereas the variation in apoptosis appears to be unrelated to the local expression of androgen and estrogen receptors. Together, these data suggest that cell proliferation and apoptosis are differentially modulated in the efferent ductules and epididymis of A. lituratus during the annual reproductive cycle, and support the hypothesis that ERα may be important in preparing the male reproductive tract for sexual recrudescence. Copyright © 2018 Elsevier Inc. All rights reserved.

  15. Phosphatidylserine exposure on stored red blood cells as a parameter for donor-dependent variation in product quality

    NARCIS (Netherlands)

    Dinkla, S.; Peppelman, M.; Raadt, J. van der; Atsma, F.; Novotny, V.M.J.; Kraaij, M.G.J. van; Joosten, I.; Bosman, G.J.C.G.M.

    2014-01-01

    BACKGROUND: Exposure of phosphatidylserine on the outside of red blood cells contributes to recognition and removal of old and damaged cells. The fraction of phosphatidylserine-exposing red blood cells varies between donors, and increases in red blood cell concentrates during storage. The

  16. Radiosensitivity variations in human tumor cell lines exposed in vitro to p(66)/Be neutrons or 60Co γ-rays

    International Nuclear Information System (INIS)

    Slabbert, J.P.; Theron, T.; Serafin, A.; Jones, D.T.L.; Boehm, L.; Schmitt, G.

    1996-01-01

    Neutron therapy should be beneficial to patients with tumor types which are resistant to photons but relatively sensitive to high-LET radiation. In this work the potential therapeutic gain of a clinical neutron beam is evaluated by quantifying the variations in radiosensitivity of different cell lines to neutrons and photons. Different cell lines were exposed in vitro to p(66)/Be neutrons or 60 Co γ-rays. Micronuclei frequencies in binucleated cells and surviving fractions were determined for each cell type. Following exposure to either 1 or 1.5 Gy neutrons, micronuclei frequencies were significantly correlated with that observed for 2 Gy photons. A weak but significant correlation between the variation in neutron RBE values, determined from survival curve inactivation parameters and the mean inactivation doses for photon exposures, was also established. It is concluded that although neutron and photon sensitivities are related, the use of this high energy neutron source may constitute a potential therapeutic gain for tumor types that can be identified as very resistant to photons. Considering that a definitive oxygen gain factor has been established for this neutron beam the observed therapeutic gain is expected to be further enhanced in tumors where hypoxia protects cells from conventional radiation damage. (orig.) [de

  17. Gibberellin-Regulation and Genetic Variations in Leaf Elongation for Tall Fescue in Association with Differential Gene Expression Controlling Cell Expansion.

    Science.gov (United States)

    Xu, Qian; Krishnan, Sanalkumar; Merewitz, Emily; Xu, Jichen; Huang, Bingru

    2016-07-26

    Leaf elongation rate (LER) is an important factor controlling plant growth and productivity. The objective of this study was to determine whether genetic variation in LER for a fast-growing ('K-31'), and a dwarf cultivar ('Bonsai') of tall fescue (Festuca arundinacea) and gibberellic acid (GA) regulation of LER were associated with differential expression of cell-expansion genes. Plants were treated with GA3, trinexapac-ethyl (TE) (GA inhibitor), or water (untreated control) in a hydroponic system. LER of 'K-31' was 63% greater than that of 'Bonsai', which corresponded with 32% higher endogenous GA4 content in leaf and greater cell elongation and production rates under the untreated control condition. Exogenous application of GA3 significantly enhanced LER while TE treatment inhibited leaf elongation due to GA3-stimulation or TE-inhibition of cell elongation and production rate in leaves for both cultivars. Real-time quantitative polymerase chain reaction analysis revealed that three α-expansins, one β-expansin, and three xyloglucan endotransglycosylase (XET) genes were associated with GA-stimulation of leaf elongation, of which, the differential expression of EXPA4 and EXPA7 was related to the genotypic variation in LER of two cultivars. Those differentially-expressed expansin and XET genes could play major roles in genetic variation and GA-regulated leaf elongation in tall fescue.

  18. Balanced transcription of cell division genes in Bacillus subtilis as revealed by single cell analysis

    NARCIS (Netherlands)

    Trip, Erik Nico; Veening, Jan-Willem; Stewart, Eric J.; Errington, Jeff; Scheffers, Dirk-Jan

    2013-01-01

    Cell division in bacteria is carried out by a set of conserved proteins that all have to function at the correct place and time. A cell cycle-dependent transcriptional programme drives cell division in bacteria such as Caulobacter crescentus. Whether such a programme exists in the Gram-positive

  19. VARIATIONS IN RADIATION SENSITIVITY AND REPAIR AMONG DIFFERENT HEMATOPOIETIC STEM-CELL SUBSETS FOLLOWING FRACTIONATED-IRRADIATION

    NARCIS (Netherlands)

    DOWN, JD; BOUDEWIJN, A; VANOS, R; THAMES, HD; PLOEMACHER, RE

    1995-01-01

    The radiation dose-survival of various hematopoietic cell subsets in murine bone marrow (BM) was determined in the cobblestone area forming cell (CAFC) assay under conditions of single-, split-, and multiple-dose irradiation. A greater recovery in cell survival with decreasing dose per fraction, or

  20. Effects of Integrating and Non-Integrating Reprogramming Methods on Copy Number Variation and Genomic Stability of Human Induced Pluripotent Stem Cells.

    Science.gov (United States)

    Kang, Xiangjin; Yu, Qian; Huang, Yuling; Song, Bing; Chen, Yaoyong; Gao, Xingcheng; He, Wenyin; Sun, Xiaofang; Fan, Yong

    2015-01-01

    Human-induced pluripotent stem cells (iPSCs) are derived from differentiated somatic cells using defined factors and provide a renewable source of autologous cells for cell therapy. Many reprogramming methods have been employed to generate human iPSCs, including the use of integrating vectors and non-integrating vectors. Maintenance of the genomic integrity of iPSCs is highly desirable if the cells are to be used in clinical applications. Here, using the Affymetrix Cytoscan HD array, we investigated the genomic aberration profiles of 19 human cell lines: 5 embryonic stem cell (ESC) lines, 6 iPSC lines derived using integrating vectors ("integrating iPSC lines"), 6 iPSC lines derived using non-integrating vectors ("non-integrating iPSC lines"), and the 2 parental cell lines from which the iPSCs were derived. The genome-wide copy number variation (CNV), loss of heterozygosity (LOH) and mosaicism patterns of integrating and non-integrating iPSC lines were investigated. The maximum sizes of CNVs in the genomes of the integrating iPSC lines were 20 times higher than those of the non-integrating iPSC lines. Moreover, the total number of CNVs was much higher in integrating iPSC lines than in other cell lines. The average numbers of novel CNVs with a low degree of overlap with the DGV and of likely pathogenic CNVs with a high degree of overlap with the ISCA (International Symposium on Computer Architecture) database were highest in integrating iPSC lines. Different single nucleotide polymorphisms (SNP) calls revealed that, using the parental cell genotype as a reference, integrating iPSC lines displayed more single nucleotide variations and mosaicism than did non-integrating iPSC lines. This study describes the genome stability of human iPSCs generated using either a DNA-integrating or non-integrating reprogramming method, of the corresponding somatic cells, and of hESCs. Our results highlight the importance of using a high-resolution method to monitor genomic aberrations

  1. Effects of Integrating and Non-Integrating Reprogramming Methods on Copy Number Variation and Genomic Stability of Human Induced Pluripotent Stem Cells.

    Directory of Open Access Journals (Sweden)

    Xiangjin Kang

    Full Text Available Human-induced pluripotent stem cells (iPSCs are derived from differentiated somatic cells using defined factors and provide a renewable source of autologous cells for cell therapy. Many reprogramming methods have been employed to generate human iPSCs, including the use of integrating vectors and non-integrating vectors. Maintenance of the genomic integrity of iPSCs is highly desirable if the cells are to be used in clinical applications. Here, using the Affymetrix Cytoscan HD array, we investigated the genomic aberration profiles of 19 human cell lines: 5 embryonic stem cell (ESC lines, 6 iPSC lines derived using integrating vectors ("integrating iPSC lines", 6 iPSC lines derived using non-integrating vectors ("non-integrating iPSC lines", and the 2 parental cell lines from which the iPSCs were derived. The genome-wide copy number variation (CNV, loss of heterozygosity (LOH and mosaicism patterns of integrating and non-integrating iPSC lines were investigated. The maximum sizes of CNVs in the genomes of the integrating iPSC lines were 20 times higher than those of the non-integrating iPSC lines. Moreover, the total number of CNVs was much higher in integrating iPSC lines than in other cell lines. The average numbers of novel CNVs with a low degree of overlap with the DGV and of likely pathogenic CNVs with a high degree of overlap with the ISCA (International Symposium on Computer Architecture database were highest in integrating iPSC lines. Different single nucleotide polymorphisms (SNP calls revealed that, using the parental cell genotype as a reference, integrating iPSC lines displayed more single nucleotide variations and mosaicism than did non-integrating iPSC lines. This study describes the genome stability of human iPSCs generated using either a DNA-integrating or non-integrating reprogramming method, of the corresponding somatic cells, and of hESCs. Our results highlight the importance of using a high-resolution method to monitor genomic

  2. Osteoblast adhesion, migration, and proliferation variations on chemically patterned nanocrystalline diamond films evaluated by live-cell imaging.

    Science.gov (United States)

    Broz, Antonin; Ukraintsev, Egor; Kromka, Alexander; Rezek, Bohuslav; Hubalek Kalbacova, Marie

    2017-05-01

    Cell fate modulation by adapting the surface of a biocompatible material is nowadays a challenge in implantology, tissue engineering as well as in construction of biosensors. Nanocrystalline diamond (NCD) thin films are considered promising in these fields due to their extraordinary physical and chemical properties and diverse ways in which they can be modified structurally and chemically. The initial cell distribution, the rate of cell adhesion, distance of cell migration and also the cell proliferation are influenced by the NCD surface termination. Here, we use real-time live-cell imaging to investigate the above-mentioned processes on oxidized NCD (NCD-O) and hydrogenated NCD (NCD-H) to elucidate cell preference to the NCD-O especially on surfaces with microscopic surface termination patterns. Cells adhere more slowly and migrate farther on NCD-H than on NCD-O. Cells seeded with a fetal bovine serum (FBS) supplement in the medium move across the surface prior to adhesion. In the absence of FBS, the cells adhere immediately, but still exhibit different migration and proliferation on NCD-O/H regions. We discuss the impact of these effects on the formation of cell arrays on micropatterned NCD. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1469-1478, 2017. © 2017 Wiley Periodicals, Inc.

  3. Celiac disease T-cell epitopes from gamma-gliadins: immunoreactivity depends on the genome of origin, transcript frequency, and flanking protein variation

    Directory of Open Access Journals (Sweden)

    Salentijn Elma MJ

    2012-06-01

    Full Text Available Abstract Background Celiac disease (CD is caused by an uncontrolled immune response to gluten, a heterogeneous mixture of wheat storage proteins. The CD-toxicity of these proteins and their derived peptides is depending on the presence of specific T-cell epitopes (9-mer peptides; CD epitopes that mediate the stimulation of HLA-DQ2/8 restricted T-cells. Next to the thoroughly characterized major T-cell epitopes derived from the α-gliadin fraction of gluten, γ-gliadin peptides are also known to stimulate T-cells of celiac disease patients. To pinpoint CD-toxic γ-gliadins in hexaploid bread wheat, we examined the variation of T-cell epitopes involved in CD in γ-gliadin transcripts of developing bread wheat grains. Results A detailed analysis of the genetic variation present in γ-gliadin transcripts of bread wheat (T. aestivum, allo-hexaploid, carrying the A, B and D genome, together with genomic γ-gliadin sequences from ancestrally related diploid wheat species, enabled the assignment of sequence variants to one of the three genomic γ-gliadin loci, Gli-A1, Gli-B1 or Gli-D1. Almost half of the γ-gliadin transcripts of bread wheat (49% was assigned to locus Gli-D1. Transcripts from each locus differed in CD epitope content and composition. The Gli-D1 transcripts contained the highest frequency of canonical CD epitope cores (on average 10.1 per transcript followed by the Gli-A1 transcripts (8.6 and the Gli-B1 transcripts (5.4. The natural variants of the major CD epitope from γ-gliadins, DQ2-γ-I, showed variation in their capacity to induce in vitro proliferation of a DQ2-γ-I specific and HLA-DQ2 restricted T-cell clone. Conclusions Evaluating the CD epitopes derived from γ-gliadins in their natural context of flanking protein variation, genome specificity and transcript frequency is a significant step towards accurate quantification of the CD toxicity of bread wheat. This approach can be used to predict relative levels of CD toxicity of

  4. The dosage optimization of He-Ne laser energy as a candidate for photodynamic therapy of cancer cells with exogenous photosensitizer variations

    Science.gov (United States)

    Apsari, R.; Maghfiroh, I.; Setyawati, H.; Winarno; Arifianto, D.; Zaidan, A.

    2017-05-01

    The aim of this research was to find out the most effective energy dose of laser energy per unit area irradiated to the subject, used in T47D cancer cell photodynamic therapy. The experiment used three variations of energy doses and two exogenous photosensitizers. The laser used was the He-Ne laser with a wavelength of 632 nm. Laser exposure on the T47D cancer cells was conducted in vitro at a distance of 1 cm with energy doses of 30.4 J/cm2, 18.8 J/cm2, and 30.4 J/cm2. The photosensitizers used in the experiment were chlorophylls isolated from sour-sop leaves and Protoporphyrin IX (PpIX). The concentration of photosensitizers which is not toxic to cells, based on the toxicity test, is 300 ppm for chlorophylls and 350 ppm for PpIX. At the energy dose of 30.4 J/cm2, the percentage of cell death was 96.25% with chlorophyll addition, while with PpIX addition, the percentage was 81.62%. At the same energy dose, cell death in apoptosis was 95.78% with chlorophyll addition and 80.56% with PpIX addition. Based on the result of this research, it was revealed that the energy dose of He-Ne laser output of 30.4 J/cm2 was the most effective energy dose between the energy dose variation that could yield T47D cell death in an apoptosis way.

  5. HIV Sequence Variation Associated With env Antisense Adoptive T-cell Therapy in the hNSG Mouse Model

    OpenAIRE

    Mukherjee, Rithun; Plesa, Gabriela; Sherrill-Mix, Scott; Richardson, Max W; Riley, James L; Bushman, Frederic D

    2010-01-01

    The first use of lentiviral vectors in humans involved transduction of mature T-cells with an human immunodeficiency virus (HIV)–derived env antisense (envAS) vector to protect cells from HIV infection. In that study, only a minority of the patient T-cell population could be gene-modified, raising the question of whether the altered cells could affect replicating HIV populations. We investigated this using humanized NOD/SCID IL-2Rγnull (hNSG) mice reconstituted with ~4–11% envAS-modified huma...

  6. Investigation into Variation of Endogenous Metabolites in Bone Marrow Cells and Plasma in C3H/He Mice Exposed to Benzene

    Science.gov (United States)

    Sun, Rongli; Zhang, Juan; Yin, Lihong; Pu, Yuepu

    2014-01-01

    Benzene is identified as a carcinogen. Continued exposure of benzene may eventually lead to damage to the bone marrow, accompanied by pancytopenia, aplastic anemia or leukemia. This paper explores the variations of endogenous metabolites to provide possible clues for the molecular mechanism of benzene-induced hematotoxicity. Liquid chromatography coupled with time of flight-mass spectrometry (LC-TOF-MS) and principal component analysis (PCA) was applied to investigate the variation of endogenous metabolites in bone marrow cells and plasma of male C3H/He mice. The mice were injected subcutaneously with benzene (0, 300, 600 mg/day) once daily for seven days. The body weights, relative organ weights, blood parameters and bone marrow smears were also analyzed. The results indicated that benzene caused disturbances in the metabolism of oxidation of fatty acids and essential amino acids (lysine, phenylalanine and tyrosine) in bone marrow cells. Moreover, fatty acid oxidation was also disturbed in plasma and thus might be a common disturbed metabolic pathway induced by benzene in multiple organs. This study aims to investigate the underlying molecular mechanisms involved in benzene hematotoxicity, especially in bone marrow cells. PMID:24658442

  7. Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer

    NARCIS (Netherlands)

    Hampras, S.S.; Sucheston-Campbell, L.E.; Cannioto, R.; Chang-Claude, J.; Modugno, F.; Dork, T.; Hillemanns, P.; Preus, L.; Knutson, K.L.; Wallace, P.K.; Hong, C.C.; Friel, G.; Davis, W.; Nesline, M.; Pearce, C.L.; Kelemen, L.E.; Goodman, M.T.; Bandera, E.V.; Terry, K.L.; Schoof, N.; Eng, K.H.; Clay, A.; Singh, P.K.; Joseph, J.M.; Aben, K.K.H.; Anton-Culver, H.; Antonenkova, N.; Baker, H.; Bean, Y.; Beckmann, M.W.; Bisogna, M.; Bjorge, L.; Bogdanova, N.; Brinton, L.A.; Brooks-Wilson, A.; Bruinsma, F.; Butzow, R.; Campbell, I.G.; Carty, K.; Cook, L.S.; Cramer, D.W; Cybulski, C.; Dansonka-Mieszkowska, A.; Dennis, J.; Despierre, E.; Dicks, E.; Doherty, J.A.; Bois, A. du; Durst, M.; Easton, D.; Eccles, D.; Edwards, R.P.; Ekici, A.B.; Fasching, P.A.; Fridley, B.L.; Gao, Y.T.; Gentry-Maharaj, A.; Giles, G.G.; Glasspool, R.; Gronwald, J.; Harrington, P.; Harter, P.; Hasmad, H.N.; Hein, A.; Heitz, F.; Hildebrandt, M.A.T.; Hogdall, C.; Hogdall, E.; Hosono, S.; Iversen, E.S.; Jakubowska, A.; Jensen, A.; Ji, B.T.; Karlan, B.Y.; Kellar, M.; Kelley, J.L.; Kiemeney, L.A.L.M.; Klapdor, R.; Kolomeyevskaya, N.; Krakstad, C.; Kjaer, S.K.; Kruszka, B.; Kupryjanczyk, J.; Lambrechts, D.; Lambrechts, S.; Le, N.D.; Lee, A.W.; Lele, S.; Leminen, A.; Lester, J.; Levine, D.A.; Liang, D.; Lissowska, J.; Liu, S.; Lu, K.; Lubinski, J.; Lundvall, L.; Massuger, L.F.A.G.; Matsuo, K.; McGuire, V.; et al.,

    2016-01-01

    BACKGROUND: Regulatory T (Treg) cells, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and, thus, variants in genes encoding Treg cell immune molecules could be associated with ovarian cancer. METHODS: In a population of 15,596 epithelial ovarian cancer (EOC) cases and

  8. Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer

    DEFF Research Database (Denmark)

    Hampras, Shalaka S; Sucheston-Campbell, Lara E; Cannioto, Rikki

    2016-01-01

    BACKGROUND: Regulatory T (Treg) cells, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and, thus, variants in genes encoding Treg cell immune molecules could be associated with ovarian cancer. METHODS: In a population of 15,596 epithelial ovarian cancer (EOC) cases a...

  9. Chromosome copy number variation in telomerized human bone marrow stromal cells; insights for monitoring safe ex-vivo expansion of adult stem cells

    DEFF Research Database (Denmark)

    Burns, Jorge S.; Harkness, Linda; Aldahmash, Abdullah

    2017-01-01

    Adult human bone marrow stromal cells (hBMSC) cultured for cell therapy require evaluation of potency and stability for safe use. Chromosomal aberrations upsetting genomic integrity in such cells have been contrastingly described as "Limited" or "Significant". Previously reported stepwise acquisi...

  10. Studying the effect of spectral variations intensity of the incident solar radiation on the Si solar cells performance

    Directory of Open Access Journals (Sweden)

    Ahmed Elsayed Ghitas

    2012-12-01

    Full Text Available Solar spectral variation is important in characterization of photovoltaic devices. We present results of an experimental investigation of the effects of the daily spectral variation on the device performance of multicrystalline silicon photovoltaic module. The investigation concentrate on the analysis of outdoor solar spectral measurements carried out at 1 min intervals on clear sky days. Short circuit current and open circuit voltage have been measured to describe the module electrical performance. We have shown that the shift in the solar spectrum towards infrared has a negative impact on the device performance of the module. The spectral bands in the visible region contribute more to the short circuit current than the bands in the infrared region while the ultraviolet region contributes least. The quantitative effect of the spectral variation on the performance of the photovoltaic module is reflected on their respective device performance parameters. The decrease in the visible and the increase in infrared of the radiation spectra account for the decreased current collection and hence power of the module.

  11. Age-related declines and disease-associated variation in immune cell telomere length in a wild mammal.

    Directory of Open Access Journals (Sweden)

    Christopher Beirne

    Full Text Available Immunosenescence, the deterioration of immune system capability with age, may play a key role in mediating age-related declines in whole-organism performance, but the mechanisms that underpin immunosenescence are poorly understood. Biomedical research on humans and laboratory models has documented age and disease related declines in the telomere lengths of leukocytes ('immune cells', stimulating interest their having a potentially general role in the emergence of immunosenescent phenotypes. However, it is unknown whether such observations generalise to the immune cell populations of wild vertebrates living under ecologically realistic conditions. Here we examine longitudinal changes in the mean telomere lengths of immune cells in wild European badgers (Meles meles. Our findings provide the first evidence of within-individual age-related declines in immune cell telomere lengths in a wild vertebrate. That the rate of age-related decline in telomere length appears to be steeper within individuals than at the overall population level raises the possibility that individuals with short immune cell telomeres and/or higher rates of immune cell telomere attrition may be selectively lost from this population. We also report evidence suggestive of associations between immune cell telomere length and bovine tuberculosis infection status, with individuals detected at the most advanced stage of infection tending to have shorter immune cell telomeres than disease positive individuals. While male European badgers are larger and show higher rates of annual mortality than females, we found no evidence of a sex difference in either mean telomere length or the average rate of within-individual telomere attrition with age. Our findings lend support to the view that age-related declines in the telomere lengths of immune cells may provide one potentially general mechanism underpinning age-related declines in immunocompetence in natural populations.

  12. Inter-experiment variation and dependence on culture conditions in assaying the chemosensitivity of human small cell lung cancer cell lines

    DEFF Research Database (Denmark)

    Roed, H; Christensen, I B; Vindeløv, L L

    1987-01-01

    Sensitivity of five human small cell lung cancer cell lines to doxorubicin was assessed by a double layer agar technique using two different bottom-layers. Neither of the bottom-layers provided proportionality between numbers of cells plated and numbers of colonies, but they were correlated...... by a logarithmic function. Even after correction for lack of proportionality the two assay systems provided significantly different dose-response curves. The stability of the chemosensitivity was tested after 25-30 weeks continuous in vitro culture or prolonged storage in liquid nitrogen. One cell line underwent...... significant changes after continuous in vitro culture whereas the cell lines tested after prolonged storage in liquid nitrogen showed only minor changes. It is concluded that instead of considering the concentration necessary to achieve a certain degree of cell kill (e.g. ID50) in one experiment on one cell...

  13. Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer

    DEFF Research Database (Denmark)

    Edsgard, Stefan Daniel; Dalgaard, Marlene Danner; Weinhold, Nils

    2013-01-01

    Testicular germ cell cancer (TGCC) is one of the most heritable forms of cancer. Previous genome-wide association studies have focused on single nucleotide polymorphisms, largely ignoring the influence of copy number variants (CNVs). Here we present a genome-wide study of CNV on a cohort of 212...... of rare CNVs related to cell migration (false-discovery rate = 0.021, 1.8% of cases and 1.1% of controls). Dysregulation during migration of primordial germ cells has previously been suspected to be a part of TGCC development and this set of multiple rare variants may thereby have a minor contribution...

  14. Variations in DNA synthesis and mitotic indices in hepatocytes and sinusoid litoral cells of adult intact male mouse along a circadian time span.

    Science.gov (United States)

    Surur, J M; Moreno, F R; Badrán, A F; Llanos, J M

    1985-01-01

    Variations of DNA synthesis (DNAS) and mitotic indices along a circadian time span are described in the hepatocyte and sinusoid litoral cell populations of adult intact male mouse liver. Standardized (light from 0600 to 1800) mice were killed in groups of six to nine animals, every 2-4 hr along a circadian time span. Hepatocytes show significant peaks in the synthesis of DNA and the mitotic activity at 0200 and 1400, respectively. These results correspond to those previously described by us in young immature liver, regenerating liver and hepatomas. The phase differences between these peaks and the differences between their absolute values are discussed. Also considered are the practical consequences of our findings for experimental design. The curve of DNA synthesis of sinusoid litoral cells show a peak at 0200. The mitotic index show a bimodal waveform with peaks at 0800 and 2000. The existence of four different cell populations composing the so called sinusoid litoral cells and also the migration into and out of the liver of some macrophages considered as litoral (Kupffer) cells in our counts, makes interpretation of the curves somewhat complicated and deserves further analysis.

  15. Bovine conceptus of Bos indicus produced by somatic cell nuclear transfer and parthenogenesis present morphological variations since the blastocyst stage

    Directory of Open Access Journals (Sweden)

    F.D. Oliveira

    2015-12-01

    Full Text Available In cattle, embryo development is characterized by the appearance of two distinct cell layers, the trophectoderm and the inner cell mass. The latter will undergo differentiation to form the embryonic disc consisting of the epiblast and hypoblast. The aim of this study was to ultrastructurally characterize the bovine embryo from different in vitro production techniques, with emphasis on trophectoderm and inner cell mass cells. Bovine embryos on day 7 (conception = D1 of pregnancy, derived via in vitro production techniques, were fixed for light and transmission electron microscopy processing. Results suggested that embryos produced by nuclear transfer of somatic cells and parthenogenesis showed significant changes in macroscopic and microscopic structure. Size was reduced, and the inner cell mass had no defined shape. Furthermore, organelles responsible for the absorption processes, communication, growth, and cellular metabolism were fewer and had changes in shape, when compared to results in embryos produced by in vitrofertilization. We concluded that embryos produced by parthenogenesis and SCNT exhibit morphological differences when compared with IVF embryos, such as undeveloped blastocoel, poorly defined distribution of ICM, and morphological differences in organelles.

  16. Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information

    DEFF Research Database (Denmark)

    Edsgärd, D; Scheel, M; Hansen, N T

    2011-01-01

    To search for disease-related copy number variations (CNVs) in families with a high frequency of germ cell tumours (GCT), we analysed 16 individuals from four families by array comparative genomic hybridization (aCGH) and applied an integrative systems biology algorithm that prioritizes risk...... GCT patients and 200 healthy controls. Observed CNV frequencies of 1.9% among cases and 1.5% amongst controls were not significantly different and this was further confirmed by CNV data extracted from a genome-wide analysis of 189 cases and 380 controls, where similar frequencies of 2.2% were observed....... Collectively, the findings show that a heterozygous loss at the RLN1 locus is not a genetic factor mediating high population-wide risk for testicular germ cell tumour, but do not exclude a contribution of this aberration in some cases of cancer. The preliminary expression data suggest a possible role...

  17. Conspicuous variation of the lattice unit cell in the pavonite homologous series and its relation with cation/anion occupational modulations

    Energy Technology Data Exchange (ETDEWEB)

    Perez-Mato, J.M., E-mail: jm.perez-mato@ehu.es [Dpto. de Física de la Materia Condensada, Facultad de Ciencia y Tecnología, UPV/EHU, Apartado 644, 48080 Bilbao (Spain); Elcoro, Luis [Dpto. de Física de la Materia Condensada, Facultad de Ciencia y Tecnología, UPV/EHU, Apartado 644, 48080 Bilbao (Spain); Makovicky, Emil [Department of Geography and Geology, University of Copenhagen, Øster Voldgade 10, DK-1350 Copenhagen K (Denmark); Topa, Dan [Department of Materials Research and Physics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Petříček, Václav [Institute of Physics, Academy of Sciences of the Czech Republic v.v.i., Na Slovance 2, 182 21 Praha 8 (Czech Republic); Madariaga, Gotzon [Dpto. de Física de la Materia Condensada, Facultad de Ciencia y Tecnología, UPV/EHU, Apartado 644, 48080 Bilbao (Spain)

    2013-06-01

    Highlights: ► Strong non-uniform variation of unit cell parameters in the pavonite homologous series. ► Conspicuous unit cell variation due to an underlying sub-lattice with cation/anion occupation. ► A modulated model common to the whole series using the superspace formalism proposed. ► Model successfully applied to the {sup 7}P pavonite Ag{sub 3}(Bi,Pb){sub 7}S{sub 12}. ► The model can be applied in a predictive way to other members of the family. - Abstract: The pavonites is a homologous series of sulfosalts with galena-like modules of variable size. A survey of their unit cells reveals that they are severely constrained by the metrics of an underlying common average sublattice. The unit cell of any compound of the series accommodates with high precision an integer number of approximately equal subcells. This explains a peculiar non-uniform variation of the unit cell parameters within the series and evidences that the interface between the galena-like modules, despite having a very different topology, approximately maintains the subperiodicity of the modules, and must therefore be subject to strong steric restrictions. It also implies that cations and anions occupy the nodes of the observed common underlying average sublattice according to a striking alternate cation/anion occupational modulation. This is the starting point for a description of these materials as modulated structures, which can make a proficient use of the approximate atomic positional non-crystallographic correlations caused by their modular character. Under this approach only four parameters suffice to define a realistic approximate model of any member of the series. A full structural characterization of any of the compounds only requires the determination of additional small/smooth modulations. As an example, the case of the {sup 7}P pavonite Ag{sub 3}Bi{sub 6.2}Pb{sub 0.8}S{sub 12}, is analyzed.

  18. {delta}-ALAD activity variations in red blood cells in response to lead accumulation in rock doves (Columba livia)

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, M.; Tejedor, M.C. [Universidad de Alcala de Henares (Spain)

    1992-10-01

    The enzyme {delta}-aminolevulinic acid dehydratase ({delta}-ALAD, E.C. 4.2.1.24), catalyses the second step of the haeme biosynthetic pathway and is required to maintain the haemoglobin and cytochrome content in red cells. {delta}-ALAD is not only found in bone marrow cells, the major site of haeme synthesis, but also in circulating erythrocytes and other tissues. An inverse correlation was found between {delta}-ALAD activity in red blood cells and lead concentration in the blood. The degree of {delta}-ALAD inhibition in erythrocytes has been widely accepted as a standard bioassay to detect acute and chronic lead exposure in humans and in avians. The value of this parameter as an indicator for environmental lead has been often reported in doves and Scanlon. In lead-treated rats, an increase in {delta}-ALAD activity in bone marrow cells and in blood samples was shown by radioimmunoassay at 5 and 9 days after the treatment. Similarly, the amount of {delta}-ALAD seems to be more sensitive to lead in avian species than in mammals, the usefulness of blood {delta}-ALAD activity as an index of lead exposure has already been questioned by Hutton in the pigeon and by Jaffe et al. in humans. The present investigation studied the toxic effects of lead on rock dove red blood cell {delta}-ALAD activity in two situations: in doves treated with lead acetate in the laboratory and in doves exposed to the environment of Alcala de Henares. The final lead blood concentrations were lower in the environmental than in the laboratory doves. {delta}-ALAD activity in bone marrow cells and the relationships between lead accumulation and enzyme activity in red cells, are examined. 20 refs., 5 figs., 1 tab.

  19. Effects of clonal variation on growth, metabolism, and productivity in response to trophic factor stimulation: a study of Chinese hamster ovary cells producing a recombinant monoclonal antibody.

    Science.gov (United States)

    Dahodwala, Hussain; Nowey, Mark; Mitina, Tatyana; Sharfstein, Susan T

    2012-01-01

    The growth, metabolism, and productivity of five Chinese hamster ovary (CHO) clones were explored in response to stimulation with insulin (5 mg/L) and LONG(®)R(3)IGF-I (20 μg/L or 100 μg/L). All five clones were derived from the same parental CHO cell line (DG44) and produced the same recombinant monoclonal antibody, with varying specific productivities. There was no uniform response among the clones to stimulation with the different trophic factors. One of the high productivity clones (clone D) exhibited significantly better growth in response to LONG(®)R(3)IGF-I; whereas the other clones showed equivalent or slightly better growth in the presence of insulin. Three out of the five clones had higher specific productivities in the presence of insulin (although not statistically significant); one was invariant, and the final clone exhibited slightly higher specific productivity in the presence of LONG(®)R(3)IGF-I. Total product titers exhibited moderate variation between culture conditions, again with neither trophic factor being clearly superior. Overall product titers were affected by variations in both integrated viable cell density and specific productivity. Nutrient uptake and metabolite generation patterns varied strongly between clones and much less with culture conditions. These results point to the need for careful clonal analysis when selecting clones, particularly for platform processes where media and culture conditions are predetermined.

  20. Variations in Target Volume Definition for Postoperative Radiotherapy in Stage III Non-Small-Cell Lung Cancer: Analysis of an International Contouring Study

    International Nuclear Information System (INIS)

    Spoelstra, Femke; Senan, Suresh; Le Pechoux, Cecile; Ishikura, Satoshi; Casas, Francesc; Ball, David; Price, Allan; De Ruysscher, Dirk; Soernsen de Koste, John R. van

    2010-01-01

    Purpose: Postoperative radiotherapy (PORT) in patients with completely resected non-small-cell lung cancer with mediastinal involvement is controversial because of the failure of earlier trials to demonstrate a survival benefit. Improved techniques may reduce toxicity, but the treatment fields used in routine practice have not been well studied. We studied routine target volumes used by international experts and evaluated the impact of a contouring protocol developed for a new prospective study, the Lung Adjuvant Radiotherapy Trial (Lung ART). Methods and Materials: Seventeen thoracic radiation oncologists were invited to contour their routine clinical target volumes (CTV) for 2 representative patients using a validated CD-ROM-based contouring program. Subsequently, the Lung ART study protocol was provided, and both cases were contoured again. Variations in target volumes and their dosimetric impact were analyzed. Results: Routine CTVs were received for each case from 10 clinicians, whereas six provided both routine and protocol CTVs for each case. Routine CTVs varied up to threefold between clinicians, but use of the Lung ART protocol significantly decreased variations. Routine CTVs in a postlobectomy patient resulted in V 20 values ranging from 12.7% to 54.0%, and Lung ART protocol CTVs resulted in values of 20.6% to 29.2%. Similar results were seen for other toxicity parameters and in the postpneumectomy patient. With the exception of upper paratracheal nodes, protocol contouring improved coverage of the required nodal stations. Conclusion: Even among experts, significant interclinician variations are observed in PORT fields. Inasmuch as contouring variations can confound the interpretation of PORT results, mandatory quality assurance procedures have been incorporated into the current Lung ART study.

  1. Variation in U.V. primary fluorescence-intensity of vital cells depending on 60Co γ-radiation dose

    International Nuclear Information System (INIS)

    Merkle, K.

    1978-01-01

    Using impulse-cytofluorophotometry in the ultra-violet spectral region it has been shown on vital, unstained Ehrlich ascites tumour cells that the primary fluorescence intensity of this tumour was on day 11 after transplantation 20 per cent higher than on day 8. Storage of the vital cells for 25 min at 20 0 C had no effect on this result. When the cells were exposed to 60 Co γ-radiation on day 6, a new stable fluorescence level was established after 20 hours. Measurements of the primary fluorescence intensity depending on dose have shown a significant rise starting from 75 rad at 48 hours after irradiation. The fluorescence intensity rose by 42.5 per cent of the control value at 3000 rad, but only by 31.5 per cent on exposure to 4000 rad. (author)

  2. Elucidating Batch-to-Batch Variation Caused by Homocoupled Side Products in Solution-Processable Organic Solar Cells

    DEFF Research Database (Denmark)

    Vangerven, Tim; Verstappen, Pieter; Patil, Nilesh

    2016-01-01

    on the impact of homocouplings on device performance is, however, still lacking as is a profound understanding of the underlying causes of the device deterioration. For differentiating the combined effect of molecular weight and homocouplings in polymer solar cells, a systematic study on a small molecule system......Conjugated polymers and small molecules based on alternating electron-donating (D) and electron-accepting (A) building blocks have led to state-of-the-art organic solar cell materials governing efficiencies beyond 10%. Unfortunately, the connection of D and A building blocks via cross......-coupling reactions does not always proceed as planned, which can result in the generation of side products containing D-D or A-A homocoupling motifs. Previous studies have reported a reduced performance in polymer and small molecule solar cells when such defect structures are present. A general consensus...

  3. Variation in the excitability of developed D. discoideum cells as a function of agar concentration in the substrate

    Science.gov (United States)

    Oikawa, Noriko; Bae, Albert; Amselem, Gabriel; Bodenschatz, Eberhard

    2010-03-01

    In the absence of nutrients, Dictyostelium discoideum cells enter a developmental cycle--they signal each other, aggregate, and ultimately form fruiting bodies. During the signaling stage, the cells relay waves of cyclic adenosine 3',5' monophosphate (cAMP). We observed a transition from spiral to circular patterns in the signaling wave, depending on the agar concentration of the substrate. In this talk we will present the changes in the times for the onset of signaling and synchronization versus agar concentration, as measured by spectral entropy. We also will discuss the origin of these effects.

  4. Killer-cell Immunoglobulin-like Receptor gene linkage and copy number variation analysis by droplet digital PCR.

    Science.gov (United States)

    Roberts, Chrissy H; Jiang, Wei; Jayaraman, Jyothi; Trowsdale, John; Holland, Martin J; Traherne, James A

    2014-01-01

    The Killer-cell Immunoglobulin-like Receptor (KIR) gene complex has considerable biomedical importance. Patterns of polymorphism in the KIR region include variability in the gene content of haplotypes and diverse structural arrangements. Droplet digital PCR (ddPCR) was used to identify different haplotype motifs and to enumerate KIR copy number variants (CNVs). ddPCR detected a variety of KIR haplotype configurations in DNA from well-characterized cell lines. Mendelian segregation of ddPCR-estimated KIR2DL5 CNVs was observed in Gambian families and CNV typing of other KIRs was shown to be accurate when compared to an established quantitative PCR method.

  5. Polymorphic variation in the androgen receptor gene: association with risk of testicular germ cell cancer and metastatic disease

    DEFF Research Database (Denmark)

    Västermark, Åke; Giwercman, Yvonne Lundberg; Hagströmer, Oskar

    2011-01-01

    Increasing incidence of testicular germ cell cancer (TGCC) is most probably related to environment and lifestyle. However, an underlying genetic predisposition may play a role and since sex steroids are assumed to be important for the rise and progression of TGCC, a study of androgen receptor (AR...... of endocrine disruptors. From a biological point of view, our findings strengthen the hypothesis of the importance of androgen action in the aetiology and pathogenesis of testicular malignancy. Future studies should focus on the impact of sex hormones on foetal germ cell development and the interaction between...

  6. Effects of water turbulence on variations in cell ultrastructure and metabolism of amino acids in the submersed macrophyte, Elodea nuttallii (Planch.) H. St. John.

    Science.gov (United States)

    Atapaththu, K S S; Miyagi, A; Atsuzawa, K; Kaneko, Y; Kawai-Yamada, M; Asaeda, T

    2015-09-01

    The interactions between macrophytes and water movement are not yet fully understood, and the causes responsible for the metabolic and ultrastructural variations in plant cells as a consequence of turbulence are largely unknown. In the present study, growth, metabolism and ultrastructural changes were evaluated in the aquatic macrophyte Elodea nuttallii, after exposure to turbulence for 30 days. The turbulence was generated with a vertically oscillating horizontal grid. The turbulence reduced plant growth, plasmolysed leaf cells and strengthened cell walls, and plants exposed to turbulence accumulated starch granules in stem chloroplasts. The size of the starch granules increased with the magnitude of the turbulence. Using capillary electrophoresis-mass spectrometry (CE-MS), analysis of the metabolome found metabolite accumulation in response to the turbulence. Asparagine was the dominant amino acid that was concentrated in stressed plants, and organic acids such as citrate, ascorbate, oxalate and γ-amino butyric acid (GABA) also accumulated in response to turbulence. These results indicate that turbulence caused severe stress that affected plant growth, cell ultrastructure and some metabolic functions of E. nuttallii. Our findings offer insights to explain the effects of water movement on the functions of aquatic plants. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

  7. Conformational variation of surface class II MHC proteins during myeloid dendritic cell differentiation accompanies structural changes in lysosomal MIIC

    Czech Academy of Sciences Publication Activity Database

    Potolicchio, I.; Chitta, S.; Xu, X.; Fonseca, D.; Crisi, G.; Hořejší, Václav; Strominger, J. L.; Stern, L. J.; Raposo, G.; Santambrogio, L.

    2005-01-01

    Roč. 175, č. 8 (2005), s. 4935-4947 ISSN 0022-1767 Institutional research plan: CEZ:AV0Z50520514 Keywords : MHC II * HLA-DR * dendritic cell Subject RIV: EC - Immunology Impact factor: 6.387, year: 2005

  8. Variations in gene and protein expression in canine chondrodystrophic nucleus pulposus cells following long-term three-dimensional culture.

    Directory of Open Access Journals (Sweden)

    Munetaka Iwata

    Full Text Available Intervertebral disc (IVD degeneration greatly affects quality of life. The nucleus pulposus (NP of chondrodystrophic dog breeds (CDBs is similar to the human NP, because the cells disappear with age and are replaced by fibrochondrocyte-like cells. However, because IVD develops as early as within the first year of life, we used canines as a model to investigate in vitro the mechanisms underlying IVD degeneration. Specifically, we evaluated the potential of a three-dimensional (3D culture of healthy NP as an in vitro model system to investigate the mechanisms of IVD degeneration. Agarose hydrogels were populated with healthy NP cells from beagles after performing magnetic resonance imaging, and mRNA expression profiles and pericellular extracellular matrix (ECM protein distribution were determined. After 25 days of 3D culture, there was a tendency for redifferentiation into the native NP phenotype, and mRNA levels of Col2A1, COMP, and CK18 were not significantly different from those of freshly isolated cells. Our findings suggest that long-term 3D culture promoted chondrodystrophic NP redifferentiation through reconstruction of the pericellular microenvironment. Further, lipopolysaccharide (LPS induced expression of TNF-α, MMP3, MMP13, VEGF, and PGES mRNA in the 3D cultures, creating a molecular milieu that mimics that of degenerated NP. These results suggest that this in vitro model represents a reliable and cost-effective tool for evaluating new therapies for disc degeneration.

  9. Numerical variation of cell lysosomes of the proximal convoluted tubules of mice Kidneys submitted to different X-ray doses

    International Nuclear Information System (INIS)

    Silva Lapa, R. de C.R. da; Pacheco, I.P.; Segreto, C.

    1984-01-01

    The number of cell lysosomes of the proximal convoluted tubules of mice Kidneys (Mus musculus) before and after whole-body irradiation with different X-ray doses is confronted. The mice were sacrificed after 72 hours and the cortex fragments were conduct to electron microscopy. A statistically significant numerical reduction of the lysosomas was observed in 72 hours. (M.A.C.) [pt

  10. Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci

    NARCIS (Netherlands)

    Paul, D.S.; Albers, C.A.; Rendon, A.; Voss, K.; Stephens, J.; Akkerman, J.W.; Algra, A.; Al-Hussani, A.; Allayee, H.; Anni, F.; Asselbergs, F.W.; Attwood, A.; Balkau, B.; Bandinelli, S.; Bastardot, F.; Basu, S.; Baumeister, S.E.; Beckmann, J.; Benyamin, B.; Biino, G.; Bis, J.C.; Bomba, L.; Bonnefond, A.; Boomsma, D.I.; Bradley, J.R.; Cambien, F.; Ciullo, M.; Cookson, W.O.; Cucca, F.; Cvejic, A.; d'Adamo, A.P.; Danesh, J.; Danjou, F.; Das, D.; Davies, G.; de Bakker, P.I.; de Boer, R.A.; de Geus, E.J.C.; Deary, I.J.; Dedoussis, G.V.; Dimitriou, M.; Dina, C.; Döring, A.; Elling, U.; Ellinghaus, D.; Elliott, P.; Engström, G.; Erdmann, J.; Esko, T.; Evans, D.M.; Eyjolfsson, G.I.; Falchi, M.; Feng, W.W.; Ferreira, M.A.; Ferrucci, L.; Fischer, K.; Folsom, A.R.; Fortina, P.; Franke, A.; Franke, L.; Frazer, I.H.; Froguel, P.; Galanello, R.; Ganesh, S.; Garner, S.F.; Gasparini, P.; Genser, B.; Gibson, Q.D.; Gieger, C.; Girotto, G.; Glazer, N.L.; Gögele, M.; Goodall, A.H.; Greinacher, A.; Gudbjartsson, D.F.; Hammond, C.J.; Harris, S.E.; Hartiala, J.; Hartikainen, A.L.; Hazen, S.L.; Heckbert, S.R.; Hedblad, B.; Hengstenberg, C.; Hersch, M.; Hicks, A.A.; Holm, H.; Hottenga, J.J.; Illig, T.; Järvelin, M.R.; Jolley, J.; Jupe, S.; Kähönen, M.; Kamatani, N.; Kanoni, S.; Kema, I.P.; Kemp, J.P.; Khadake, J.; Khaw, K.T.; Kleber, M.E.; Kooner, J.S.; Kovacs, P.; Kühnel, B.; Kyrtsonis, M.C.; Labrune, Y.; Lagou, V.; Langenberg, C.; Lehtimäki, T.; Li, X.; Liang, L.; Lloyd-Jones, H.; Loos, R.J.; Lopez, L.M.; Lumley, T.; Lyytikäinen, L.P.; Maerz, W.; Mägi, R.; Mangino, M.; Martin, N.G.; Maschio, A.; Mateo Leach, I.; McKnight, B.; Meacham, S.; Medland, S.E.; Meisinger, C.; Melander, O.; Memari, Y.; Metspalu, A.; Miller, K.; Mitchell, B.D.; Moffatt, M.F.; Montgomery, G.W.; Moore, C.; Murgia, F.; Nakamura, Y.; Nauck, M.; Navis, G.; Nolte, I.M.; Nöthlings, U.; Nutile, T.; Okada, Y.; Olafsson, I.; Onundarson, P.T.; O'Reilly, P.F.; Parracciani, D.; Parsa, A.; Penninger, J.M.; Penninx, B.W.J.H.; Pirastu, M.; Pirastu, N.; Pistis, G.; Porcu, E.; Portas, L.; Porteous, D.J.; Pouta, A.; Pramstaller, P.P.; Prokopenko, I.; Psaty, B.M.; Pullat, J.; Radhakrishnan, A.; Raitakari, O.; Ramirez-Solis, R.; Ried, J.S.; Ring, S.M.; Robino, A.; Rotter, J.I.; Ruggiero, D.; Ruokonen, A.; Sala, C.; Saluments, A.; Samani, N.J.; Sambrook, J.; Sanna, S.; Schlessinger, D.; Schmidt, C.O.; Schreiber, S; Schunkert, H.; Scott, J.; Sehmi, J.; Serbanovic-Canic, J.; Shin, S.Y.; Shuldiner, A.R.; Sladek, R.; Smit, J.H.; Smith, G.D.; Smith, J.G.; Smith, N.L.; Snieder, H.; Sorice, R.; Spector, T.D.; Starr, J.M.; Stefansson, K.; Stemple, D.; Stumvoll, M.; Sulem, P.; Takahashi, A.; Tan, S.T.; Tanaka, T.; Tang, C.; Tang, W.; Tang, W.H.; Taylor, K.; Tenesa, A.; Teumer, A.; Thein, S.; Thorsteinsdottir, U.; Toniolo, D.; Tönjes, A.; Traglia, M.; Uda, M.; Ulivi, S.; van der Schoot, E.; van Gilst, W.H.; van Pelt, L.J.; van Veldhuisen, D.J.; Verweij, N.; Visscher, P.M.; Völker, U.; Vollenweider, P.; Wareham, N.J.; Wernisch, L.; Westra, H.J.; Whitfield, J.B.; Wichmann, H.E.; Wiggins, K.L.; Willemsen, G.; Winkelmann, B.R.; Wirnsberger, G.; Wolffenbuttel, B.H.; Yang, J.; Yang, T.P.; Zhang, J.H.; Zhao, J.H.; Zitting, P.; Zwaginga, JJ; van der Harst, P.; Chambers, J.C.; Soranzo, N.; Ouwehand, W.H.; Deloukas, P.

    2013-01-01

    Nearly three-quarters of the 143 genetic signals associated with platelet and erythrocyte phenotypes identified by metaanalyses of genome-wide association (GWA) studies are located at non-protein-coding regions. Here, we assessed the role of candidate regulatory variants associated with cell

  11. Inositol Pyrophosphate Profiling of Two HCT116 Cell Lines Uncovers Variation in InsP8 Levels.

    Directory of Open Access Journals (Sweden)

    Chunfang Gu

    Full Text Available The HCT116 cell line, which has a pseudo-diploid karotype, is a popular model in the fields of cancer cell biology, intestinal immunity, and inflammation. In the current study, we describe two batches of diverged HCT116 cells, which we designate as HCT116NIH and HCT116UCL. Using both gel electrophoresis and HPLC, we show that HCT116UCL cells contain 6-fold higher levels of InsP8 than HCT116NIH cells. This observation is significant because InsP8 is one of a group of molecules collectively known as 'inositol pyrophosphates' (PP-InsPs-highly 'energetic' and conserved regulators of cellular and organismal metabolism. Variability in the cellular levels of InsP8 within divergent HCT116 cell lines could have impacted the phenotypic data obtained in previous studies. This difference in InsP8 levels is more remarkable for being specific; levels of other inositol phosphates, and notably InsP6 and 5-InsP7, are very similar in both HCT116NIH and HCT116UCL lines. We also developed a new HPLC procedure to record 1-InsP7 levels directly (for the first time in any mammalian cell line; 1-InsP7 comprised <2% of total InsP7 in HCT116NIH and HCT116UCL lines. The elevated levels of InsP8 in the HCT116UCL lines were not due to an increase in expression of the PP-InsP kinases (IP6Ks and PPIP5Ks, nor to a decrease in the capacity to dephosphorylate InsP8. We discuss how the divergent PP-InsP profiles of the newly-designated HCT116NIH and HCT116UCL lines should be considered an important research opportunity: future studies using these two lines may uncover new features that regulate InsP8 turnover, and may also yield new directions for studying InsP8 function.

  12. Cell size variations of large granular lymphocyte leukemia: Implication of a small cell subtype of granular lymphocyte leukemia with STAT3 mutations.

    Science.gov (United States)

    Tanahashi, Takahiro; Sekiguchi, Nodoka; Matsuda, Kazuyuki; Takezawa, Yuka; Ito, Toshiro; Kobayashi, Hikaru; Ichikawa, Naoaki; Nishina, Sayaka; Senoo, Noriko; Sakai, Hitoshi; Nakazawa, Hideyuki; Ishida, Fumihiro

    2016-06-01

    Large granular lymphocyte leukemia (LGL-L) has been morphologically defined as a group of lymphoproliferative disorders, including T-cell large granular lymphocytic leukemia (T-LGL-L), chronic lymphoproliferative disorders of NK cells (CLPD-NK) and aggressive NK cell leukemia. We investigated the morphological features of LGL leukemic cells in 26 LGL-L patients in order to elucidate relationships with current classifications and molecular backgrounds. LGL-L cells were mostly indistinguishable from normal LGL. Patients with STAT3 SH2 domain mutations showed significantly smaller cells compared with patients without STAT3 mutations. Four patients with T-LGL-L showed smaller granular lymphocytes with a median diameter of less than 13μm, which were rarely seen in normal subjects. This small subtype of T-LGL-L was recognized among rather young patients and was associated with D661Y mutations in the STAT3 gene SH2 domain. In addition, all of them showed anemia including two cases with pure red cell aplasia. These results suggest the heterogeneity of T-LGL-L and a specific subtype with small variants of T-LGL-L. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Dynamics of intracellular ionic concentrations in single living cells using videomicrofluorometry: application to pHi variations

    Science.gov (United States)

    Viallet, Pierre M.; Yassine, Mohamed; Salmon, Jean-Marie; Vigo, Jean

    1996-01-01

    The intracellular concentration of ions such as H+, Mg2+, Ca2+, is known to monitor the activity of many fundamental enzymes. Furthermore these ions are generally considered as intracellular messengers involved in the transduction of extracellular signals. Recent technological progress, occulting the physicochemical properties of the probe, led to the feeling that accurate data on microvolumes are instantly accessible. Unfortunately fluorescent probes are supposed to fill up conflicting requirements for ionic affinity, absence of fading and intracellular calibration. Such a situation generally precludes the use of the simplest methods of data acquisition and treatment. This paper is based on the use of microspectrofluorometry, resolution of single cell complex fluorescence spectrum, and videomicrofluorometry. The methods of data handling allow us to demonstrate that most of the problems met in intracellular calibration come from the fighting of cells against the modification of the extracellular pH. Using these techniques allows us to restrict the need of comparison between results in cuvettes and intracellular results to the physiological pH range. A consequence of such an approach is that the effect with time of known concentrations of amiloride and nigericin on pHi became accessible. Data is presented allowing us to get information on the behavior of the ionic channels and/or cation/H+ exchangers involved in the pHi regulation. Such a method leads the way to direct investigations and monitoring of the different processes of regulation of the intracellular ionic concentrations in different cell lines at the level of single cells. Using different specific modifiers (activators or blocking agents) and convenient specific fluorescent probes, the efficiency of such pathways is expected to be checked at will. Compared to the patch clamp techniques, the method can be extended to the study of pathways located on the inner cell membranes.

  14. Combining multivariate analysis and monosaccharide composition modeling to identify plant cell wall variations by Fourier Transform Near Infrared spectroscopy

    Directory of Open Access Journals (Sweden)

    Smith-Moritz Andreia M

    2011-08-01

    Full Text Available Abstract We outline a high throughput procedure that improves outlier detection in cell wall screens using FT-NIR spectroscopy of plant leaves. The improvement relies on generating a calibration set from a subset of a mutant population by taking advantage of the Mahalanobis distance outlier scheme to construct a monosaccharide range predictive model using PLS regression. This model was then used to identify specific monosaccharide outliers from the mutant population.

  15. Variations in Western blot banding patterns of human T-cell lymphotropic virus type III/lymphadenopathy-associated virus.

    OpenAIRE

    Burke, D S; Redfield, R R; Putman, P; Alexander, S S

    1987-01-01

    Serum samples from 27 patients infected with human T-cell lymphotropic virus type III (14 with acquired immune deficiency syndrome [AIDS] and 13 with AIDS-related complex) were examined for antibodies to viral proteins by the Western blot method and with four different commercial solid-phase enzyme-linked immunosorbent assays (ELISAs). Virus-specific bands on blots at molecular masses of 64, 55, 53, 41, 31, 24, and 17 kilodaltons were observed. Rank correlation matrices were calculated to rel...

  16. Osteoblast adhesion, migration, and proliferation variations on chemically patterned nanocrystalline diamond films evaluated by live-cell imaging

    Czech Academy of Sciences Publication Activity Database

    Brož, Antonín; Ukraintsev, Egor; Kromka, Alexander; Rezek, Bohuslav; Kalbáčová, M.H.

    2017-01-01

    Roč. 105, č. 5 (2017), s. 1469-1478 ISSN 1549-3296 R&D Projects: GA ČR(CZ) GA14-04790S; GA MZd(CZ) NV15-32497A Institutional support: RVO:67985823 ; RVO:68378271 Keywords : live-cell imaging * osteoblasts * adhesion * proliferation * migration * patterned surface Subject RIV: EI - Biotechnology ; Bionics OBOR OECD: Biomaterials (as related to medical implants, devices, sensors) Impact factor: 3.076, year: 2016

  17. Heterogeneity of Purkinje cell simple spike-complex spike interactions: zebrin- and non-zebrin-related variations.

    Science.gov (United States)

    Tang, Tianyu; Xiao, Jianqiang; Suh, Colleen Y; Burroughs, Amelia; Cerminara, Nadia L; Jia, Linjia; Marshall, Sarah P; Wise, Andrew K; Apps, Richard; Sugihara, Izumi; Lang, Eric J

    2017-08-01

    Cerebellar Purkinje cells (PCs) generate two types of action potentials, simple and complex spikes. Although they are generated by distinct mechanisms, interactions between the two spike types exist. Zebrin staining produces alternating positive and negative stripes of PCs across most of the cerebellar cortex. Thus, here we compared simple spike-complex spike interactions both within and across zebrin populations. Simple spike activity undergoes a complex modulation preceding and following a complex spike. The amplitudes of the pre- and post-complex spike modulation phases were correlated across PCs. On average, the modulation was larger for PCs in zebrin positive regions. Correlations between aspects of the complex spike waveform and simple spike activity were found, some of which varied between zebrin positive and negative PCs. The implications of the results are discussed with regard to hypotheses that complex spikes are triggered by rises in simple spike activity for either motor learning or homeostatic functions. Purkinje cells (PCs) generate two types of action potentials, called simple and complex spikes (SSs and CSs). We first investigated the CS-associated modulation of SS activity and its relationship to the zebrin status of the PC. The modulation pattern consisted of a pre-CS rise in SS activity, and then, following the CS, a pause, a rebound, and finally a late inhibition of SS activity for both zebrin positive (Z+) and negative (Z-) cells, though the amplitudes of the phases were larger in Z+ cells. Moreover, the amplitudes of the pre-CS rise with the late inhibitory phase of the modulation were correlated across PCs. In contrast, correlations between modulation phases across CSs of individual PCs were generally weak. Next, the relationship between CS spikelets and SS activity was investigated. The number of spikelets/CS correlated with the average SS firing rate only for Z+ cells. In contrast, correlations across CSs between spikelet numbers and the

  18. The use of reverse phase protein arrays (RPPA) to explore protein expression variation within individual renal cell cancers.

    Science.gov (United States)

    O'Mahony, Fiach C; Nanda, Jyoti; Laird, Alexander; Mullen, Peter; Caldwell, Helen; Overton, Ian M; Eory, Lel; O'Donnell, Marie; Faratian, Dana; Powles, Thomas; Harrison, David J; Stewart, Grant D

    2013-01-22

    Currently there is no curative treatment for metastatic clear cell renal cell cancer, the commonest variant of the disease. A key factor in this treatment resistance is thought to be the molecular complexity of the disease. Targeted therapy such as the tyrosine kinase inhibitor (TKI)-sunitinib have been utilized, but only 40% of patients will respond, with the overwhelming majority of these patients relapsing within 1 year. As such the question of intrinsic and acquired resistance in renal cell cancer patients is highly relevant. In order to study resistance to TKIs, with the ultimate goal of developing effective, personalized treatments, sequential tissue after a specific period of targeted therapy is required, an approach which had proved successful in chronic myeloid leukaemia. However the application of such a strategy in renal cell carcinoma is complicated by the high level of both inter- and intratumoral heterogeneity, which is a feature of renal cell carcinoma as well as other solid tumors. Intertumoral heterogeneity due to transcriptomic and genetic differences is well established even in patients with similar presentation, stage and grade of tumor. In addition it is clear that there is great morphological (intratumoral) heterogeneity in RCC, which is likely to represent even greater molecular heterogeneity. Detailed mapping and categorization of RCC tumors by combined morphological analysis and Fuhrman grading allows the selection of representative areas for proteomic analysis. Protein based analysis of RCC is attractive due to its widespread availability in pathology laboratories; however, its application can be problematic due to the limited availability of specific antibodies. Due to the dot blot nature of the Reverse Phase Protein Arrays (RPPA), antibody specificity must be pre-validated; as such strict quality control of antibodies used is of paramount importance. Despite this limitation the dot blot format does allow assay miniaturization, allowing

  19. Epigenetic dynamics across the cell cycle

    DEFF Research Database (Denmark)

    Kheir, Tony Bou; Lund, Anders H.

    2010-01-01

    Progression of the mammalian cell cycle depends on correct timing and co-ordination of a series of events, which are managed by the cellular transcriptional machinery and epigenetic mechanisms governing genome accessibility. Epigenetic chromatin modifications are dynamic across the cell cycle...... a correct inheritance of epigenetic chromatin modifications to daughter cells. In this chapter, we summarize the current knowledge on the dynamics of epigenetic chromatin modifications during progression of the cell cycle....

  20. Neonatal plasmacytoid dendritic cells (pDCs display subset variation but can elicit potent anti-viral innate responses.

    Directory of Open Access Journals (Sweden)

    Xiaoming Zhang

    Full Text Available Neonates are highly susceptible to infectious diseases and defective antiviral pDC immune responses have been proposed to contribute to this phenomenon. Isolated cord blood pDCs innately responded to a variety of TLR7 and TLR9 dependent viruses, including influenza A virus (IAV, human immunodeficiency virus (HIV or herpes-simplex virus (HSV by efficiently producing IFN-α, TNF-α as well as chemokines. Interestingly, following activation by CpGA, but not viruses, cord pDCs tend to survive less efficiently. We found that a hallmark of pDCs in neonates is an extended CD2+pDCs compartment compared to adult pDCs without affecting the antiviral IFN-α response. Within CD2+pDCs, we identified a subpopulation expressing CD5 and responsible for IL-12p40 production, however this population is significantly decreased in cord blood compared to adult blood. Therefore, neonatal pDCs clearly display variation in phenotype and subset composition, but without major consequences for their antiviral responses.

  1. Branched multifunctional polyether polyketals: variation of ketal group structure enables unprecedented control over polymer degradation in solution and within cells.

    Science.gov (United States)

    Shenoi, Rajesh A; Narayanannair, Jayaprakash K; Hamilton, Jasmine L; Lai, Benjamin F L; Horte, Sonja; Kainthan, Rajesh K; Varghese, Jos P; Rajeev, Kallanthottathil G; Manoharan, Muthiah; Kizhakkedathu, Jayachandran N

    2012-09-12

    Multifunctional biocompatible and biodegradable nanomaterials incorporating specific degradable linkages that respond to various stimuli and with defined degradation profiles are critical to the advancement of targeted nanomedicine. Herein we report, for the first time, a new class of multifunctional dendritic polyether polyketals containing different ketal linkages in their backbone that exhibit unprecedented control over degradation in solution and within the cells. High-molecular-weight and highly compact poly(ketal hydroxyethers) (PKHEs) were synthesized from newly designed α-epoxy-ω-hydroxyl-functionalized AB(2)-type ketal monomers carrying structurally different ketal groups (both cyclic and acyclic) with good control over polymer properties by anionic ring-opening multibranching polymerization. Polymer functionalization with multiple azide and amine groups was achieved without degradation of the ketal group. The polymer degradation was controlled primarily by the differences in the structure and torsional strain of the substituted ketal groups in the main chain, while for polymers with linear (acyclic) ketal groups, the hydrophobicity of the polymer may play an additional role. This was supported by the log P values of the monomers and the hydrophobicity of the polymers determined by fluorescence spectroscopy using pyrene as the probe. A range of hydrolysis half-lives of the polymers at mild acidic pH values was achieved, from a few minutes to a few hundred days, directly correlating with the differences in ketal group structures. Confocal microscopy analyses demonstrated similar degradation profiles for PKHEs within live cells, as seen in solution and the delivery of fluorescent marker to the cytosol. The cell viability measured by MTS assay and blood compatibility determined by complement activation, platelet activation, and coagulation assays demonstrate that PKHEs and their degradation products are highly biocompatible. Taken together, these data

  2. Wall ingrowth deposition in phloem parenchyma transfer cells in Arabidopsis: Heteroblastic variations and a potential role in pathogen defence.

    Science.gov (United States)

    Nguyen, Suong T T; McCurdy, David W

    2017-06-03

    Transfer cell (TCs) develop unique wall ingrowth networks which amplify plasma membrane surface area and thus maximize nutrient transporter density at key anatomic sites for nutrient exchange within plants and their external environment. These sites fall into 4 main groups corresponding to 4 categories of trans-membrane flux: absorption/secretion of solutes from or to the external environment, and absorption/secretion of solutes from or to internal, extra-cytoplasmic compartments. Research on TC biology over recent decades has demonstrated correlations between wall ingrowth deposition in TCs and enhanced transport capacity in many major agricultural species such as pea, fava bean, cotton and maize. Consequently, there is general consensus that the existence of wall ingrowth morphology implies an augmentation in membrane transport capacity. However, this may not be entirely applicable for phloem parenchyma (PP) TCs in Arabidopsis. Our recent survey of PP TC abundance and distribution in Arabidopsis veins indicated that PP TC development reflects heteroblastic status. A consequence of this observation is the suggestion that PP TCs, or at least wall ingrowth deposition in these cells, potentially act as a physical barrier to defend access of invading pathogens to sugar-rich sieve elements rather than solely in facilitating the export of photoassimilate from collection phloem in leaves.

  3. Microbiological quality and somatic cell count in bulk milk of dromedary camels (Camelus dromedarius): descriptive statistics, correlations, and factors of variation.

    Science.gov (United States)

    Nagy, P; Faye, B; Marko, O; Thomas, S; Wernery, U; Juhasz, J

    2013-09-01

    The objectives of the present study were to monitor the microbiological quality and somatic cell count (SCC) of bulk tank milk at the world's first large-scale camel dairy farm for a 2-yr period, to compare the results of 2 methods for the enumeration of SCC, to evaluate correlation among milk quality indicators, and to determine the effect of specific factors (year, season, stage of lactation, and level of production) on milk quality indicators. The study was conducted from January 2008 to January 2010. Total viable count (TVC), coliform count (CC), California Mastitis Test (CMT) score, and SCC were determined from daily bulk milk samples. Somatic cell count was measured by using a direct microscopic method and with an automatic cell counter. In addition, production parameters [total daily milk production (TDM, kg), number of milking camels (NMC), average milk per camel (AMC, kg)] and stage of lactation (average postpartum days, PPD) were recorded for each test day. A strong correlation (r=0.33) was found between the 2 methods for SCC enumeration; however, values derived using the microscopic method were higher. The geometric means of SCC and TVC were 394×10(3) cells/mL and 5,157 cfu/mL during the observation period, respectively. Somatic cell count was >500×10(3) cells/mL on 14.6% (106/725) and TVC was >10×10(3) cfu/mL on 4.0% (30/742) of the test days. Both milk quality indicators had a distinct seasonal pattern. For log SCC, the mean was lowest in summer and highest in autumn. The seasonal pattern of log TVC was slightly different, with the lowest values being recorded during the spring. The monthly mean TVC pattern showed a clear difference between years. Coliform count was <10 cfu/mL in most of the samples (709/742, 95.6%). A positive correlation was found between log SCC and log TVC (r=0.32), between log SCC and CMT score (r=0.26), and between log TVC and CC in yr 1 (r=0.30). All production parameters and stage of lactation showed strong seasonal

  4. Trade-off between carbon emission and effluent quality of activated sludge processes under seasonal variations of wastewater temperature and mean cell retention time.

    Science.gov (United States)

    Guo, Jingbo; Fu, Xin; Andrés Baquero, G; Sobhani, Reza; Nolasco, Daniel A; Rosso, Diego

    2016-03-15

    Over the seasonal cycles, the mean cell retention time (MCRT) of the activated sludge process is varied to compensate the wastewater temperature variations. The effects of these variations on the carbon footprint (CFP) and effluent quality index (EQI) of a conventional activated sludge (CAS) process and a nitrification/denitrification (NDN) process were quantified. The carbon emission included both biogenic and non-biogenic carbon. Carbon emissions of wasted biosolids management were also addressed. Our results confirmed that the effluent quality indicated by EQI was not necessarily improved by increasing MCRT. Higher MCRT increased the carbon emission and reduced excess sludge production, which decreased the potential for biogas energy recovery. The NDN process was preferable to the CAS process from the perspective of effluent quality. This consideration extended to the whole plant CFP if the N2O emitted during NDN was limited ([N2O]intensity (γ) derived from CFP and EQI, our work provides a quantitative tool for decision makers evaluating process alternatives when there is a trade-off between carbon emission and effluent quality. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Cell growth and lipid accumulation of a microalgal mutant Scenedesmus sp. Z-4 by combining light/dark cycle with temperature variation.

    Science.gov (United States)

    Ma, Chao; Zhang, Yan-Bo; Ho, Shih-Hsin; Xing, De-Feng; Ren, Nan-Qi; Liu, Bing-Feng

    2017-01-01

    The light/dark cycle is one of the most important factors affecting the microalgal growth and lipid accumulation. Biomass concentration and lipid productivity could be enhanced by optimization of light/dark cycles, and this is considered an effective control strategy for microalgal cultivation. Currently, most research on effects of light/dark cycles on algae is carried out under autotrophic conditions and little information is about the effects under mixotrophic cultivation. At the same time, many studies related to mixotrophic cultivation of microalgal strains, even at large scale, have been performed to obtain satisfactory biomass and lipid production. Therefore, it is necessary to investigate cellular metabolism under autotrophic and mixotrophic conditions at different light/dark cycles. Even though microalgal lipid production under optimal environmental factors has been reported by some researchers, the light/dark cycle and temperature are regarded as separate parameters in their studies. In practical cases, light/dark cycling and temperature variation during the day occur simultaneously. Therefore, studies about the combined effects of light/dark cycles and temperature variation on microalgal lipid production are of practical value, potentially providing significant guidelines for large-scale microalgal cultivation under natural conditions. In this work, cell growth and lipid accumulation of an oleaginous microalgal mutant, Scenedesmus sp. Z-4, were investigated at five light/dark cycles (0 h/24 h, 8 h/16 h, 12 h/12 h, 16 h/8 h, and 24 h/0 h) in batch culture. The results showed that the optimal light/dark cycle was 12 h/12 h, when maximum lipid productivity rates of 56.8 and 182.6 mg L -1  day -1 were obtained under autotrophic and mixotrophic cultivation, respectively. Poor microalgal growth and lipid accumulation appeared in the light/dark cycles of 0 h/24 h and 24 h/0 h under autotrophic condition. Prolonging the light duration was

  6. The state of cell block variation and satisfaction in the era of molecular diagnostics and personalized medicine

    Directory of Open Access Journals (Sweden)

    John P Crapanzano

    2014-01-01

    Full Text Available Background: In the recent past, algorithms and recommendations to standardize the morphological, immunohistochemical and molecular classification of lung cancers on cytology specimens have been proposed, and several organizations have recommended cell blocks (CBs as the preferred modality for molecular testing. Based on the literature, there are several different techniques available for CB preparation-suggesting that there is no standard. The aim of this study was to conduct a survey of CB preparation techniques utilized in various practice settings and analyze current issues, if any. Materials and Methods: A single E-mail with a link to an electronic survey was distributed to members of the American Society of Cytopathology and other pathologists. Questions pertaining to the participants′ practice setting and CBs-volume, method, quality and satisfaction-were included. Results: Of 95 respondents, 90/95 (94% completed the survey and comprise the study group. Most participants practice in a community hospital/private practice (44% or academic center (41%. On average, 14 CBs (range 0-50; median 10 are prepared by a laboratory daily. Over 10 methods are utilized: Plasma thrombin (33%, HistoGel (27%, Cellient automated cell block system (8% and others (31% respectively. Forty of 90 (44% respondents are either unsatisfied or sometimes satisfied with their CB quality, with low-cellular yield being the leading cause of dissatisfaction. There was no statistical significance between the three most common CB preparation methods and satisfaction with quality. Discussion: Many are dissatisfied with their current method of CB preparation, and there is no consistent method to prepare CBs. In today′s era of personalized medicine with an increasing array of molecular tests being applied to cytological specimens, there is a need for a standardized protocol for CB optimization to enhance cellularity.

  7. Short communication: Influence of the sampling device on somatic cell count variation in cow milk samples (by official recording)

    Energy Technology Data Exchange (ETDEWEB)

    Fouz, R.; Vilar, M.J.; Yus, E.; Sanjuán, M.L.; Diéguez, F.J.

    2016-11-01

    The objective of this study was to investigate the variability in cow´s milk somatic cell counts (SCC) depending on the type of milk meter used by dairy farms for official milk recording. The study was performed in 2011 and 2012 in the major cattle area of Spain. In total, 137,846 lactations of Holstein-Friesian cows were analysed at 1,912 farms. A generalised least squares regression model was used for data analysis. The model showed that the milk meter had a substantial effect on the SCC for individual milk samples obtained for official milk recording. The results suggested an overestimation of the SCC in milk samples from farms that had electronic devices in comparison with farms that used portable devices and underestimation when volumetric meters are used. A weak positive correlation was observed between the SCC and the percentage of fat in individual milk samples. The results underline the importance of considering this variable when using SCC data from milk recording in the dairy herd improvement program or in quality milk programs. (Author)

  8. Arabinoxylo-Oligosaccharides and Inulin Impact Inter-Individual Variation on Microbial Metabolism and Composition, Which Immunomodulates Human Cells.

    Science.gov (United States)

    Van den Abbeele, Pieter; Taminiau, Bernard; Pinheiro, Iris; Duysburgh, Cindy; Jacobs, Heidi; Pijls, Loek; Marzorati, Massimo

    2018-02-07

    Fecal batch fermentations coupled to cocultures of epithelial cells and macrophages were used to compare how arabinoxylo-oligosaccharides (AXOS) and inulin modulate gut microbial activity and composition of three different human donors and subsequently the epithelial permeability and immune response. Both inulin and AXOS decreased the pH during incubation (-1.5 pH units), leading to increased productions of acetate, propionate, and butyrate. Differences in terms of metabolites production could be linked to specific microbial alterations at genus level upon inulin/AXOS supplementation (i.e., Bifidobacterium, Bacteroides, Prevotella and unclassified Erysipelotrichaceae), as shown by 16S-targeted Illumina sequencing. Both products stimulated gut barrier and immune function with increases in TEER, NF-KB, IL-10, and IL-6. Ingredients with different structures selectively modulate the microbiota of a specific donor leading to differential changes at metabolic level. The extent of this effect is donor specific and is linked to a final specific modulation of the host's immune system.

  9. Sequence variation of Vanabin2-like vanadium-binding proteins in blood cells of the vanadium-accumulating ascidian Ascidia sydneiensis samea.

    Science.gov (United States)

    Ueki, Tatsuya; Satake, Makoto; Kamino, Kei; Michibata, Hitoshi

    2008-01-01

    The blood cells of ascidians accumulate extremely high levels of the transition metal vanadium. We previously isolated four vanadium-binding proteins (Vanabins 1-4) and a homologous protein (VanabinP) from the vanadium-rich ascidian Ascidia sydneiensis samea. In the present study, we identified cDNAs encoding five different Vanabin2-related proteins in A. sydneiensis samea blood cells. It was notable that the sequences of the encoded proteins vary from that of Vanabin2 at up to 14 specific positions, while both the polypeptide length and the 18 cysteine residues were completely conserved. The most divergent protein, named 14MT, differed from Vanabin2 at all 14 positions. Using immobilized metal-ion affinity chromatography, we found that Vanabin2 and 14MT have the same metal-ion selectivity, but the overall affinity of 14MT for VO(2+) is higher than that of Vanabin2. Binding number for VO(2+) ions was the same between Vanabin2 and 14MT as assessed by gel filtration. These results suggested that sequence variations were under strict evolutionary constraints and high-affinity binding sites for VO(2+) are conserved among Vanabin2 variants.

  10. Variational principles

    CERN Document Server

    Moiseiwitsch, B L

    2004-01-01

    This graduate-level text's primary objective is to demonstrate the expression of the equations of the various branches of mathematical physics in the succinct and elegant form of variational principles (and thereby illuminate their interrelationship). Its related intentions are to show how variational principles may be employed to determine the discrete eigenvalues for stationary state problems and to illustrate how to find the values of quantities (such as the phase shifts) that arise in the theory of scattering. Chapter-by-chapter treatment consists of analytical dynamics; optics, wave mecha

  11. Should variation of serum lipid levels be considered a risk factor for the development of basal cell carcinoma?

    Science.gov (United States)

    Zamanian, Abbas; Rokni, Ghasem Rahmatpour; Ansar, Akram; Mobasher, Pezhman; Jazi, Ghazaleh Ahmadi

    2014-01-01

    Basal cell carcinoma (BCC) is the most common cutaneous neoplasm in human beings. Ultraviolet radiation is one of the most important predisposing factors for BCC. Although some recent investigations have shown a high serum level of phospholipids in actinic keratosis and BCC, this subject is still debated and needs approval. This study aimed to evaluate the association between serum lipid level and development of cutaneous BCC. In this case-control study, lipid profile including triglyceride (TG), Cholesterol (CHOL), high-density lipoprotein (HDL) and low-density lipoprotein (LDL) were measured in 30 patients with BCC and 30 healthy controls. Data were analyzed by descriptive statistical tests including t tests and Chi square test. This study shows that the mean age of the case and control groups were 63.93 ± 12.09 and 61.57 ± 21.1 years (mean ± SD), respectively. The average amount of triglyceride, cholesterol, HDL and LDL in the BCC patients were 139.73 ± 69.11 mg/dl, 179.20 ± 43.42 mg/dl, 39.40 ± 9.30 mg/dl and 110.70 ± 34.13 mg/dl, respectively, whereas these amounts in the control group were 141.83 ± 80.41 mg/dl, 173.60 ± 96.32 mg/dl, 36.97 ± 6.35 mg/dl, 110.70 ± 34.13 mg/dl and 104.87 ± 30.85 mg/dl, respectively. No significant difference was found in the lipid profile of the case and control groups (P > 0.05%). This study shows that the serum lipid levels in patients with BCC has no significant difference in comparison with the control group and, therefore, relevance between BCC and serum lipid level is not proven. Further studies with a larger sample size are necessary for evaluating this subject.

  12. Discovery of Black Dye Crystal Structure Polymorphs: Implications for Dye Conformational Variation in Dye-Sensitized Solar Cells.

    Science.gov (United States)

    Cole, Jacqueline M; Low, Kian Sing; Gong, Yun

    2015-12-23

    We present the discovery of a new crystal structure polymorph (1) and pseudopolymorph (2) of the Black Dye, one of the world's leading dyes for dye-sensitized solar cells, DSSCs (10.4% device performance efficiency). This reveals that Black Dye molecules can adopt multiple low-energy conformers. This is significant since it challenges existing models of the Black Dye···TiO2 adsorption process that renders a DSSC working electrode; these have assumed a single molecular conformation that refers to the previously reported Black Dye crystal structure (3). The marked structural differences observed between 1, 2, and 3 make the need for modeling multiple conformations more acute. Additionally, the ordered form of the Black Dye (1) provides a more appropriate depiction of its anionic structure, especially regarding its anchoring group and NCS bonding descriptions. The tendency toward NCS ligand isomerism, evidenced via the disordered form 2, has consequences for electron injection and electron recombination in Black Dye embedded DSSC devices. Dyes 2 and 3 differ primarily by the absence or presence of a solvent of crystallization, respectively; solvent environment effects on the dye are thereby elucidated. This discovery of multiple Black Dye conformers from diffraction, with atomic-level definition, complements recently reported nanoscopic evidence for multiple dye conformations existing at a dye···TiO2 interface, for a chemically similar DSSC dye; those results emanated from imaging and spectroscopy, but were unresolved at the submolecular level. Taken together, these findings lead to the general notion that multiple dye conformations should be explicitly considered when modeling dye···TiO2 interfaces in DSSCs, at least for ruthenium-based dye complexes.

  13. Intrinsic Sex-Linked Variations in Osteogenic and Adipogenic Differentiation Potential of Bone Marrow Multipotent Stromal Cells.

    Science.gov (United States)

    Bragdon, Beth; Burns, Robert; Baker, Amelia H; Belkina, Anna C; Morgan, Elise F; Denis, Gerald V; Gerstenfeld, Louis C; Schlezinger, Jennifer J

    2015-02-01

    Bone formation and aging are sexually dimorphic. Yet, definition of the intrinsic molecular differences between male and female multipotent mesenchymal stromal cells (MSCs) in bone is lacking. This study assessed sex-linked differences in MSC differentiation in 3-, 6-, and 9-month-old C57BL/6J mice. Analysis of tibiae showed that female mice had lower bone volume fraction and higher adipocyte content in the bone marrow compared to age-matched males. While both males and females lost bone mass in early aging, the rate of loss was higher in males. Similar expression of bone- and adipocyte-related genes was seen in males and females at 3 and 9 months, while at 6 months, females exhibited a twofold greater expression of these genes. Under osteogenic culture conditions, bone marrow MSCs from female 3- and 6-month-old mice expressed similar levels of bone-related genes, but significantly greater levels of adipocyte-related genes, than male MSCs. Female MSCs also responded to rosiglitazone-induced suppression of osteogenesis at a 5-fold lower (10 nM) concentration than male MSCs. Female MSCs grown in estrogen-stripped medium showed similar responses to rosiglitazone as MSCs grown in serum containing estrogen. MSCs from female mice that had undergone ovariectomy before sexual maturity also were sensitive to rosiglitazone-induced effects on osteogenesis. These results suggest that female MSCs are more sensitive to modulation of differentiation by PPARγ and that these differences are intrinsic to the sex of the animal from which the MSCs came. These results also may explain the sensitivity of women to the deleterious effects of rosiglitazone on bone. © 2014 Wiley Periodicals, Inc.

  14. Copy number variation analysis implicates the cell polarity gene glypican 5 as a human spina bifida candidate gene

    Science.gov (United States)

    Bassuk, Alexander G.; Muthuswamy, Lakshmi B.; Boland, Riley; Smith, Tiffany L.; Hulstrand, Alissa M.; Northrup, Hope; Hakeman, Matthew; Dierdorff, Jason M.; Yung, Christina K.; Long, Abby; Brouillette, Rachel B.; Au, Kit Sing; Gurnett, Christina; Houston, Douglas W.; Cornell, Robert A.; Manak, J. Robert

    2013-01-01

    Neural tube defects (NTDs) are common birth defects of complex etiology. Family and population-based studies have confirmed a genetic component to NTDs. However, despite more than three decades of research, the genes involved in human NTDs remain largely unknown. We tested the hypothesis that rare copy number variants (CNVs), especially de novo germline CNVs, are a significant risk factor for NTDs. We used array-based comparative genomic hybridization (aCGH) to identify rare CNVs in 128 Caucasian and 61 Hispanic patients with non-syndromic lumbar-sacral myelomeningocele. We also performed aCGH analysis on the parents of affected individuals with rare CNVs where parental DNA was available (42 sets). Among the eight de novo CNVs that we identified, three generated copy number changes of entire genes. One large heterozygous deletion removed 27 genes, including PAX3, a known spina bifida-associated gene. A second CNV altered genes (PGPD8, ZC3H6) for which little is known regarding function or expression. A third heterozygous deletion removed GPC5 and part of GPC6, genes encoding glypicans. Glypicans are proteoglycans that modulate the activity of morphogens such as Sonic Hedgehog (SHH) and bone morphogenetic proteins (BMPs), both of which have been implicated in NTDs. Additionally, glypicans function in the planar cell polarity (PCP) pathway, and several PCP genes have been associated with NTDs. Here, we show that GPC5 orthologs are expressed in the neural tube, and that inhibiting their expression in frog and fish embryos results in NTDs. These results implicate GPC5 as a gene required for normal neural tube development. PMID:23223018

  15. Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations

    Directory of Open Access Journals (Sweden)

    Liang Muh-Lii

    2010-02-01

    Full Text Available Abstract Background Intracranial pediatric germ cell tumors (GCTs are rare and heterogeneous neoplasms and vary in histological differentiation, prognosis and clinical behavior. Germinoma and mature teratoma are GCTs that have a good prognosis, while other types of GCTs, termed nongerminomatous malignant germ cell tumors (NGMGCTs, are tumors with an intermediate or poor prognosis. The second group of tumors requires more extensive drug and irradiation treatment regimens. The mechanisms underlying the differences in incidence and prognosis of the various GCT subgroups are unclear. Results We identified a distinct mRNA profile correlating with GCT histological differentiation and prognosis, and also present in this study the first miRNA profile of pediatric primary intracranial GCTs. Most of the differentially expressed miRNAs were downregulated in germinomas, but miR-142-5p and miR-146a were upregulated. Genes responsible for self-renewal (such as POU5F1 (OCT4, NANOG and KLF4 and the immune response were abundant in germinomas, while genes associated with neuron differentiation, Wnt/β-catenin pathway, invasiveness and epithelial-mesenchymal transition (including SNAI2 (SLUG and TWIST2 were abundant in NGMGCTs. Clear transcriptome segregation based on patient survival was observed, with malignant NGMGCTs being closest to embryonic stem cells. Chromosome copy number variations (CNVs at cytobands 4q13.3-4q28.3 and 9p11.2-9q13 correlated with GCT malignancy and clinical risk. Six genes (BANK1, CXCL9, CXCL11, DDIT4L, ELOVL6 and HERC5 within 4q13.3-4q28.3 were more abundant in germinomas. Conclusions Our results integrate molecular profiles with clinical observations and provide insights into the underlying mechanisms causing GCT malignancy. The genes, pathways and microRNAs identified have the potential to be novel therapeutic targets.

  16. Variations in brain DNA

    Directory of Open Access Journals (Sweden)

    Jesus eAvila

    2014-11-01

    Full Text Available It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain.

  17. Fimbrial phase variation

    DEFF Research Database (Denmark)

    Khandige, Surabhi; Møller-Jensen, Jakob

    2016-01-01

    Surface fimbriae of pathogenic Escherichia coli facilitate sensing, adhesion and even invasion of host epithelial cells. While it is known that the pathogen has the potential to express a plethora of fimbrial variants susceptible to rapid phase ON/OFF variation, it is an open question...... if the fimbrial diversity seen at the population level is the product of random stochasticity or a concerted effort based on active communication. Here we discuss the possibility of a mechanism alternative to a stochastic fimbrial phase variation model affecting the dynamics of a heterogeneous population....

  18. Probing the functional impact of sequence variation on p53-DNA interactions using a novel microsphere assay for protein-DNA binding with human cell extracts.

    Directory of Open Access Journals (Sweden)

    Maher A Noureddine

    2009-05-01

    Full Text Available The p53 tumor suppressor regulates its target genes through sequence-specific binding to DNA response elements (REs. Although numerous p53 REs are established, the thousands more identified by bioinformatics are not easily subjected to comparative functional evaluation. To examine the relationship between RE sequence variation -- including polymorphisms -- and p53 binding, we have developed a multiplex format microsphere assay of protein-DNA binding (MAPD for p53 in nuclear extracts. Using MAPD we measured sequence-specific p53 binding of doxorubicin-activated or transiently expressed p53 to REs from established p53 target genes and p53 consensus REs. To assess the sensitivity and scalability of the assay, we tested 16 variants of the p21 target sequence and a 62-multiplex set of single nucleotide (nt variants of the p53 consensus sequence and found many changes in p53 binding that are not captured by current computational binding models. A group of eight single nucleotide polymorphisms (SNPs was examined and binding profiles closely matched transactivation capability tested in luciferase constructs. The in vitro binding characteristics of p53 in nuclear extracts recapitulated the cellular in vivo transactivation capabilities for eight well-established human REs measured by luciferase assay. Using a set of 26 bona fide REs, we observed distinct binding patterns characteristic of transiently expressed wild type and mutant p53s. This microsphere assay system utilizes biologically meaningful cell extracts in a multiplexed, quantitative, in vitro format that provides a powerful experimental tool for elucidating the functional impact of sequence polymorphism and protein variation on protein/DNA binding in transcriptional networks.

  19. iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types

    Directory of Open Access Journals (Sweden)

    Athanasia D. Panopoulos

    2017-04-01

    Full Text Available Summary: Large-scale collections of induced pluripotent stem cells (iPSCs could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines. : Working as part of the NHLBI NextGen consortium, Panopoulos and colleagues report the derivation and characterization of 222 publicly available iPSCs from ethnically diverse individuals with corresponding genomic data including SNP arrays, RNA-seq, and whole-genome sequencing. This collection provides a powerful resource to investigate the function of genetic variants. Keywords: iPSCORE, iPSC, GWAS, molecular traits, physiological traits, cardiac disease, NHLBI Next Gen, LQT2, KCNH2, iPSC-derived cardiomyocytes

  20. Association in a Chinese population of a genetic variation in the early B-cell factor 1 gene with coronary artery disease.

    Science.gov (United States)

    Li, Yafei; Xie, Zhiyong; Chen, Lei; Yan, Jianjun; Ma, Yao; Wang, Liansheng; Chen, Zhong

    2017-02-10

    Early B-cell factor 1 (EBF1) is a transcription factor expressed primarily during early B cell development. Previous studies have shown EBF1 regulates blood glucose and lipid metabolism in mice with diabetes and central adiposity. Recently, a genetic variation (rs36071027) located in an EBF1 gene intron was associated with carotid artery intima-media thickness. However, whether this polymorphism is actually linked with coronary artery disease (CAD) and its severity remains unclear. This study includes 293 CAD cases and 262 controls without CAD. All participants were devided into two groups based on their coronary angiography results. A polymerase chain reaction-ligase detection reaction was used to identify genotypes at rs36071027, and CAD patients were further divided into subgroups with one-, two-, or three-vessel stenosis reflective of CAD severity. The frequency of the rs36071027 TT genotype was significantly higher in CAD cases versus controls (4.8% vs. 1.5%, 95% CI: 1.13-10.81 P = 0.029). Subjects with a variant genotype T allele had an increased risk of CAD compared to C allele carriers (additive model: 95% CI: 1.13-2.23, P = 0.008). After adjustment for cardiovascular risk factors, analysis of the additive and dominant models involving rs36071027 also revealed that T allele carriers had a significantly higher risk for CAD than C allele carriers (additive model: OR 1.56, 95% CI 1.10-2.22, P = 0.013; dominant model: OR 1.60, 95% CI 1.07-2.41, P = 0.023). Furthermore, both diabetes and the CT + TT rs36071027 genotype were significantly associated with three-vessel stenosis. Our results in a Chinese population suggest that the TT genotype and T alleles in rs36071027 in the EBF1 gene are associated with an increased risk of CAD and its severity.

  1. Cell surface acid-base properties of Escherichia coli and Bacillus brevis and variation as a function of growth phase, nitrogen source and C:N ratio.

    Science.gov (United States)

    Hong, Yongsuk; Brown, Derick G

    2006-07-01

    Potentiometric titration has been conducted to systematically examine the acid-base properties of the cell surfaces of Escherichia coli K-12 and Bacillus brevis as a function of growth phase, nitrogen source (ammonium or nitrate), and carbon to nitrogen (C:N) ratio of the growth substrate. The two bacterial species revealed four distinct proton binding sites, with pK(a) values in the range of 3.08-4.05 (pK(1)), 4.62-5.57 (pK(2)), 6.47-7.30 (pK(3)), and 9.68-10.89 (pK(4)) corresponding to phosphoric/carboxylic, carboxylic, phosphoric, and hydroxyl/amine groups, respectively. Two general observations in the data are that for B. brevis the first site concentration (N(1)), corresponding to phosphoric/carboxylic groups (pK(1)), varied as a function of nitrogen source, while for E. coli the fourth site concentration (N(4)), corresponding to hydroxyl/amine groups (pK(4)), varied as a function of C:N ratio. Correspondingly, it was found that N(1) was the highest of the four site concentrations for B. brevis and N(4) was the highest for E. coli. The concentrations of the remaining sites showed little variation. Finally, comparison between the titration data and a number of cell surface compositional studies in the literature indicates one distinct difference between the two bacteria is that pK(4) of the Gram-negative E. coli can be attributed to hydroxyl groups while that of the Gram-positive B. brevis can be attributed to amine groups.

  2. Genetic variations in the regulator of G-protein signaling genes are associated with survival in late-stage non-small cell lung cancer.

    Directory of Open Access Journals (Sweden)

    Jingyao Dai

    Full Text Available The regulator of G-protein signaling (RGS pathway plays an important role in signaling transduction, cellular activities, and carcinogenesis. We hypothesized that genetic variations in RGS gene family may be associated with the response of late-stage non-small cell lung cancer (NSCLC patients to chemotherapy or chemoradiotherapy. We selected 95 tagging single nucleotide polymorphisms (SNPs in 17 RGS genes and genotyped them in 598 late-stage NSCLC patients. Thirteen SNPs were significantly associated with overall survival. Among them, rs2749786 of RGS12 was most significant. Stratified analysis by chemotherapy or chemoradiation further identified SNPs that were associated with overall survival in subgroups. Rs2816312 of RGS1 and rs6689169 of RGS7 were most significant in chemotherapy group and chemoradiotherapy group, respectively. A significant cumulative effect was observed when these SNPs were combined. Survival tree analyses identified potential interactions between rs944343, rs2816312, and rs1122794 in affecting survival time in patients treated with chemotherapy, while the genotype of rs6429264 affected survival in chemoradiation-treated patients. To our knowledge, this is the first study to reveal the importance of RGS gene family in the survival of late-stage NSCLC patients.

  3. MR-imaging of the breast at 0.5 Tesla: menstrual-cycle dependency of parenchymal contrast enhancement in healthy volunteers with oral contraceptive use?; MR-Mammographie bei 0,5 Tesla: Menstruationszyklusabhaengigkeit der Kontrastmittelanreicherung unter hormoneller Kontrazeption?

    Energy Technology Data Exchange (ETDEWEB)

    Lorenzen, J.; Welger, J.; Krupski, G.; Adam, G. [Klinik und Poliklinik fuer Diagnostische und Interventionelle Radiologie, Universitaetsklinikum Hamburg-Eppendorf (Germany); Lisboa, B.W. [Klinik und Poliklinik fuer Frauenheilkunde und Geburtshilfe, Universitaetsklinikum Hamburg-Eppendorf (Germany)

    2003-04-01

    Introduction: To evaluate changes of contrast medium enhancement of the breast parenchyma due to menstrual cycle in healthy volunteers with oral contraceptive use in MR-imaging of the breast. Material and Methods: 15 healthy volunteers (age: 22 - 36, mean 28,2) without breast disease were examined two times during one menstrual cycle (days 7 - 14 and days 21 - 2). Two volunteers were examined only in the second part of the cycle (days 21 - 2). All volunteers used oral contraceptives for more than 6 month continuously. Examinations were performed with a 0,5 T magnet (dynamic 3D-gradient echo protocol with subtraction postprocessing). We evaluated the number of enhancing foci and the parenchymal contrast medium enhancement during the different phases of the cycle by region of interest. Results: Only a total of two enhancing foci were found in 2 of 17 volunteers. Time/signal intensity diagrams in these both cases were not suspicious (< 80% initial signal increase after of contrast medium injection, no wash-out phenomenon) and sonography of the breast in these two cases was inconspicuous. Contrast medium enhancement of breast parenchyma in cycle days 7 - 14 (mean enhancement: 0.12 - 0.26, minutes 1 - 9 p.i.) was not significantly different (p = 0.2209; Wilcoxon signed rank test) from cycle days 21 - 2 (mean: 0.13 - 0.32). Conclusion: Menstrual cycle dependency of parenchymal contrast medium enhancement seems to be of minor relevance for premenopausal women with use of oral contraceptives. (orig.) [German] Fragestellung: Untersuchung der Kontrastmittelaufnahme des Brustparenchyms in Abhaengigkeit vom Menstruationszyklus bei gesunden Probandinnen unter oraler Kontrazeption. Material und Methode: Bei 15 gesunden Probandinnen ohne Brusterkrankung in der Anamnese wurde eine MR-Mammographie zweimal waehrend eines Menstruationszyklus durchgefuehrt (Zyklustag: 7 - 14 und 21 - 2). Bei zwei weiteren Probandinnen erfolgte die MR-Mammographie nur in der zweiten Zyklushaelfte

  4. Synchronized mammalian cell culture: part II--population ensemble modeling and analysis for development of reproducible processes.

    Science.gov (United States)

    Jandt, Uwe; Barradas, Oscar Platas; Pörtner, Ralf; Zeng, An-Ping

    2015-01-01

    The consideration of inherent population inhomogeneities of mammalian cell cultures becomes increasingly important for systems biology study and for developing more stable and efficient processes. However, variations of cellular properties belonging to different sub-populations and their potential effects on cellular physiology and kinetics of culture productivity under bioproduction conditions have not yet been much in the focus of research. Culture heterogeneity is strongly determined by the advance of the cell cycle. The assignment of cell-cycle specific cellular variations to large-scale process conditions can be optimally determined based on the combination of (partially) synchronized cultivation under otherwise physiological conditions and subsequent population-resolved model adaptation. The first step has been achieved using the physical selection method of countercurrent flow centrifugal elutriation, recently established in our group for different mammalian cell lines which is presented in Part I of this paper series. In this second part, we demonstrate the successful adaptation and application of a cell-cycle dependent population balance ensemble model to describe and understand synchronized bioreactor cultivations performed with two model mammalian cell lines, AGE1.HNAAT and CHO-K1. Numerical adaptation of the model to experimental data allows for detection of phase-specific parameters and for determination of significant variations between different phases and different cell lines. It shows that special care must be taken with regard to the sampling frequency in such oscillation cultures to minimize phase shift (jitter) artifacts. Based on predictions of long-term oscillation behavior of a culture depending on its start conditions, optimal elutriation setup trade-offs between high cell yields and high synchronization efficiency are proposed. © 2014 American Institute of Chemical Engineers.

  5. Factors influencing the development of lung fibrosis after chemoradiation for small cell carcinoma of the lung: Evidence for inherent interindividual variation

    International Nuclear Information System (INIS)

    Geara, Fady B.; Komaki, Ritsuko; Tucker, Susan L.; Travis, Elizabeth L.; Cox, James D.

    1998-01-01

    Purpose: Clinical observations often reveal individual differences in the severity of lung fibrosis after definitive radiation therapy for lung cancer. Recent experimental studies suggest that the risk of developing lung fibrosis may be genetically controlled. The present study was undertaken to examine the magnitude of individual variation in the incidence and severity of lung fibrosis in a well-defined patient population treated by concurrent chemoradiation for limited small-cell lung carcinomas (LSCLC). Materials and Methods: Between 1989 and 1994, 56 patients with LSCLC were enrolled in one of two controlled prospective studies of concurrent chemotherapy and concomitant conventional (45 Gy in 25 fractions q.d. over 5 weeks) or accelerated (45 Gy in 30 fractions b.i.d. over 3 weeks) radiotherapy. Chemotherapy consisted of cisplatin and etoposide (PE) or PE plus ifosfamide and mesna (PIE). Of the 56, a group of 25 patients who had serial computerized tomography (CT) examinations of the chest and were deemed to have unequivocal radiographic complete responses were selected for this study. The severity of lung fibrosis was recorded for each patient from the CT images using an arbitrary scale (0 to 3) at 1 year after treatment. Radiographic fibrosis scores were recorded on 1-3 CT slices in 3 different dose-areas (20-30 Gy; 30-40 Gy; and >40 Gy) that were defined using the corresponding CT slices from the patient's CT treatment plan. Of these patients, 23 (92%) had at least 2 slices scored; 11 patients had all 3 slices scored. Results: Among the clinical and treatment parameters investigated (including type of chemotherapy), only total dose and fractionation schedule were identified as significant and independent determinants of lung fibrosis. Radiographic fibrosis scores were higher in high-dose areas and among patients treated with the accelerated schedule. Using a fit of the proportional odds (PO) model based on the total dose and fractionation schedule, fibrosis

  6. Ethnic variation in medical and lifestyle risk factors for B cell non-Hodgkin lymphoma: A case-control study among Israelis and Palestinians.

    Directory of Open Access Journals (Sweden)

    Geffen Kleinstern

    Full Text Available Risk factors for B-cell non-Hodgkin lymphoma (B-NHL have not been assessed among Palestinian Arabs (PA and Israeli Jews (IJ.In a case-control study we investigated self-reported medical and lifestyle exposures, reporting odds ratios (ORs and 95% confidence intervals [CIs], by ethnicity, for overall B-NHL and subtypes.We recruited 823 cases and 808 healthy controls. Among 307 PA/516 IJ B-NHL cases (mean age at diagnosis = 51 [±17] versus 60 [±15] years, respectively subtype distributions differed, with diffuse large B-cell lymphoma (DLBCL being prominent among PA (71% compared to IJ (41%; follicular lymphoma (FL, was observed in 14% versus 28%, and marginal zone lymphoma, in 2% versus 14%, respectively. Overall B-NHL in both populations was associated with recreational sun exposure OR = 1.43 [CI:1.07-1.91], black hair-dye use OR = 1.70 [CI:1.00-2.87], hospitalization for infection OR = 1.68 [CI:1.34-2.11], and first-degree relative with hematopoietic cancer, OR = 1.69 [CI:1.16-2.48]. An inverse association was noted with alcohol use, OR = 0.46 [CI:0.34-0.62]. Subtype-specific exposures included smoking (FL, OR = 1.46 [CI:1.01-2.11] and >monthly indoor pesticide use (DLBCL, OR = 2.01 [CI:1.35-3.00]. Associations observed for overall B-NHL in PA only included: gardening OR = 1.93 [CI:1.39-2.70]; history of herpes, mononucleosis, rubella, blood transfusion (OR>2.5, P<0.01 for all; while for IJ risk factors included growing fruits and vegetables, OR = 1.87 [CI:1.11-3.15]; and self-reported autoimmune diseases, OR = 1.99 [CI:1.34-2.95].In these geographically proximate populations we found some unique risk factors for B-NHL. Heterogeneity in the observed associations by ethnicity could reflect differences in lifestyle, medical systems, and reporting patterns, while variations by histology infer specific etiologic factors for lymphoma subtypes.

  7. Circadian variation in biochemical markers of bone cell activity and insulin-like growth factor-I in two-year-old horses.

    Science.gov (United States)

    Jackson, B F; Blumsohn, A; Goodship, A E; Wilson, A M; Price, J S

    2003-11-01

    Studies in humans have found circadian changes to be one of the most important sources of controllable preanalytical variability when evaluating bone cell activity using biochemical markers. It remains unclear whether similar circadian changes influence bone marker concentrations in the horse. The aim of this study was to characterize changes in serum concentrations of three biochemical markers of bone cell activity over a 24-h period in six 2-yr-old Thoroughbred mares, and to determine circadian variability in IGF-I, which regulates bone turnover. Three bone markers were measured in serum: osteocalcin, a marker of bone formation, the carboxy-terminal propeptide of type-I collagen (a marker of bone formation), and the carboxy-terminal telopeptide of type-I collagen (a marker of bone resorption). Data were analyzed using the cosinor technique, which fits a 24-h cycle to each dataset. A significant circadian rhythm was observed for osteocalcin (P = 0.028), with an estimated amplitude of 7.6% of the mean (95% confidence interval 1.3% to 16.3%), and an estimated peak time of 0900. However, the observed rhythm for the carboxy-terminal telopeptide of type-I collagen (amplitude = 7.4%) was not significant (P = 0.067), and there were no significant changes in concentrations of the carboxy-terminal propeptide of type-I collagen over the 24-h study period (P = 0.44). There was a small but significant circadian rhythm for IGF-I (P = 0.04), with an estimated amplitude of 3.4% (95% confidence interval 0.2 to 7.1%) and peak at 1730. Further studies are now required to determine the potential association between circadian changes in IGF-I and osteocalcin in the horse. Although no significant circadian variation was found in concentrations of the car-boxy-terminal propeptide of type-I collagen and the carboxy-terminal telopeptide of type-I collagen, this may in part be a result of the age of the animals that were still skeletally immature. Future studies should aim to determine

  8. Effects of Integrating and Non-Integrating Reprogramming Methods on Copy Number Variation and Genomic Stability of Human Induced Pluripotent Stem Cells

    OpenAIRE

    Kang, Xiangjin; Yu, Qian; Huang, Yuling; Song, Bing; Chen, Yaoyong; Gao, Xingcheng; He, Wenyin; Sun, Xiaofang; Fan, Yong

    2015-01-01

    Human-induced pluripotent stem cells (iPSCs) are derived from differentiated somatic cells using defined factors and provide a renewable source of autologous cells for cell therapy. Many reprogramming methods have been employed to generate human iPSCs, including the use of integrating vectors and non-integrating vectors. Maintenance of the genomic integrity of iPSCs is highly desirable if the cells are to be used in clinical applications. Here, using the Affymetrix Cytoscan HD array, we inves...

  9. Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ

    Directory of Open Access Journals (Sweden)

    Norbert O.E. Vischer

    2015-06-01

    Full Text Available The rod-shaped Gram-negative bacterium Escherichia coli multiplies by elongation followed by binary fission. Longitudinal growth of the cell envelope and synthesis of the new poles are organized by two protein complexes called elongasome and divisome, respectively. We have analyzed the spatio-temporal localization patterns of many of these morphogenetic proteins by immunolabeling the wild type strain MC4100 grown to steady state in minimal glucose medium at 28°C. This allowed the direct comparison of morphogenetic protein localization patterns as a function of cell age as imaged by phase contrast and fluorescence wide field microscopy. Under steady state conditions the age distribution of the cells is constant and is directly correlated to cell length. To quantify cell size and protein localization parameters in thousands of labeled cells, we developed 'Coli-Inspector', which is a project running under ImageJ with the plugin 'ObjectJ'. ObjectJ organizes image-analysis tasks using an integrated approach with the flexibility to produce different output formats from existing markers such as intensity data and geometrical parameters. ObjectJ supports the combination of automatic and interactive methods giving the user complete control over the method of image analysis and data collection, with visual inspection tools for quick elimination of artifacts. Coli-inspector was used to sort the cells according to division cycle cell age and to analyze the spatio-temporal localization pattern of each protein. A unique dataset has been created on the concentration and position of the proteins during the cell cycle. We show for the first time that a subset of morphogenetic proteins have a constant cellular concentration during the cell division cycle whereas another set exhibits a cell division cycle dependent concentration variation. Using the number of proteins present at midcell, the stoichiometry of the divisome is discussed.

  10. Effect of variation of I{sub 01}/I{sub 02} on short-circuit current and fill factor of a real solar cell having resistive and current leakage losses

    Energy Technology Data Exchange (ETDEWEB)

    Dadu, M.; Kapoor, A.; Tripathi, K.N. [Department of Electronic Sciences, University of Delhi, South Campus, Benito Juarez Road, -110021 New Delhi (India)

    2001-11-01

    We analyze the effect of variation of I{sub 01}/I{sub 02} on short-circuit current and the fill factor of a solar cell having resistive and current leakage losses. This analysis is particularly important for the polycrystalline solar cells, where higher values of I{sub 02} and hence lower values of I{sub 01}/I{sub 02} can be expected due to the space charge regions associated with the grain boundaries. Also in polycrystalline solar cells, we cannot ignore the effect of series and shunt resistances. It is observed that the value of fill factor depends on R{sub s}, R{sub sh} and I{sub 01}/I{sub 02}, while the value of I{sub sc} depends only on R{sub s} and I{sub 01}/I{sub 02}.

  11. The existence of Th22, pure Th17 and Th1 cells in CIN and Cervical Cancer along with their frequency variation in different stages of cervical cancer

    International Nuclear Information System (INIS)

    Zhang, Wenjing; Tian, Xinli; Mumtahana, Fidia; Jiao, Jun; Zhang, Teng; Croce, Kimiko Della; Ma, Daoxin; Kong, Beihua; Cui, Baoxia

    2015-01-01

    Recently, it is found that T-helper (Th) 22 cells are involved in different types of autoimmune and tumor diseases. But, till now, no study has been carried out to understand the involvement of these cells in cervical cancer (CC). Flow cytometry was used to determine the expression of interferon gamma (IFN-γ), Interleukin-22 (IL-22), IL-17 in the peripheral blood of healthy controls (HC), CIN and cervical cancer patients. From peripheral blood mononuclear cells (PBMCs), mRNA expression levels of Aryl hydrocarbon receptor (AHR), RAR-related orphan receptor C (RORC), TNF-α and IL-6 were respectively determined. Using the method of ELISA, plasma concentrations of IL-22, IL-17 and TNF-α were examined. Th22 and Th17 cells were elevated in CC and CIN patients. Th1 cells and the plasma concentrations of IL-22 in CC patients were significantly increased compared with HC. In CC patients, an increased prevalence of Th22 cells was associated with lymph node metastases. There was a positive correlation between Th22 and Th17 cells, but an approximately negative correlation between Th22 and Th1 cells in CC patients. The mRNA expression of RORC, TNF-α and IL-6 was significantly high in CC patients. Our results indicate that there is a higher circulatory frequency of Th22, Th17 and Th1 cells in CC which may conjointly participate in the pathogenesis and growth of CC

  12. Variation in drug sensitivity of malignant mesothelioma cell lines with substantial effects of selenite and bortezomib, highlights need for individualized therapy.

    Directory of Open Access Journals (Sweden)

    Adam Szulkin

    Full Text Available Malignant mesothelioma cells have an epithelioid or sarcomatoid morphology, both of which may be present in the same tumor. The sarcomatoid phenotype is associated with worse prognosis and heterogeneity of mesothelioma cells may contribute to therapy resistance, which is often seen in mesothelioma. This study aimed to investigate differences in sensitivity between mesothelioma cell lines to anti-cancer drugs. We studied two novel drugs, selenite and bortezomib and compared their effect to four conventional drugs. We also investigated the immunoreactivity of potential predictive markers for drug sensitivity; Pgp, MRP-1, ERCC1, RRM1, TS, xCT and proteasome 20S subunit.We treated six mesothelioma cell lines with selenite, bortezomib, carboplatin, pemetrexed, doxorubicin or gemcitabine as single agents and in combinations. Viability was measured after 24 and 48 hours. Immunocytochemistry was used to detect predictive markers.As a single agent, selenite was effective on four out of six cell lines, and in combination with bortezomib yielded the greatest response in the studied mesothelioma cell lines. Cells with an epithelioid phenotype were generally more sensitive to the different drugs than the sarcomatoid cells. Extensive S-phase arrest was seen in pemetrexed-sensitive cell lines. MRP-1 predicted sensitivity of cell lines to treatment with carboplatin and xCT predicted pemetrexed effect.The observed heterogeneity in sensitivity of mesothelioma cell lines with different morphology highlights the need for more individualized therapy, requiring development of methods to predict drug sensitivity of individual tumors. Selenite and bortezomib showed a superior effect compared to conventional drugs, motivating clinical testing of these agents as future treatment regime components for patients with malignant mesothelioma.

  13. Variations in Mre11/Rad50/Nbs1 status and DNA damage-induced S-phase arrest in the cell lines of the NCI60 panel

    Directory of Open Access Journals (Sweden)

    Eastman Alan

    2011-05-01

    Full Text Available Abstract Background The Mre11/Rad50/Nbs1 (MRN complex is a regulator of cell cycle checkpoints and DNA repair. Defects in MRN can lead to defective S-phase arrest when cells are damaged. Such defects may elicit sensitivity to selected drugs providing a chemical synthetic lethal interaction that could be used to target therapy to tumors with these defects. The goal of this study was to identify these defects in the NCI60 panel of cell lines and identify compounds that might elicit selective cytotoxicity. Methods We screened the NCI60 panel in search of cell lines that express low levels of MRN proteins, or that fail to arrest in S-phase in response to the topisomerase I inhibitor SN38. The NCI COMPARE program was used to discover compounds that preferentially target cells with these phenotypes. Results HCT116 cells were initially identified as defective in MRN and S phase arrest. Transfection with Mre11 also elevated Rad50 and Nbs1, and rescued the defective S-phase arrest. Cells of the NCI60 panel exhibited a large range of protein expression but a strong correlation existed between Mre11, Rad50 and Nbs1 consistent with complex formation determining protein stability. Mre11 mRNA correlated best with protein level suggesting it was the primary determinant of the overall level of the complex. Three other cell lines failed to arrest in response to SN38, two of which also had low MRN. However, other cell lines with low MRN still arrested suggesting low MRN does not predict an inability to arrest. Many compounds, including a family of benzothiazoles, correlated with the failure to arrest in S phase. The activity of benzothiazoles has been attributed to metabolic activation and DNA alkylation, but we note several cell lines in which sensitivity does not correlate with metabolism. We propose that the checkpoint defect imposes an additional mechanism of sensitivity on cells. Conclusions We have identified cells with possible defects in the MRN complex

  14. The importance of investigation of anatomic variations in the ethmoid cells by computerized tomography in the planning of endoscopic nasal surgery; A importancia da investigacao de variacoes anatomicas das celulas etmoidais atraves da tomografia computadorizada no planejamento da cirurgia endoscopica nasal

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz, Cristiane Regina; Wafae, Nader; Nascimento, Sergio Ricardo Rios; Camelo, Julio Cesar; Maciel, Luana Teixeira; Consolari, Mario Agostinho Severo [Centro Universitario Sao Camilo, Sao Paulo, SP (Brazil)], e-mail: crisruiz@saocamilo-sp.br, e-mail: riosnascimento@uol.com.br

    2009-01-15

    The ethmoidal cells comprise many cavities that show many anatomical variations. Some of these variations deserve special attention when associated with sinusitis and the need of surgery. Computed tomography, considered a gold standard on the pathological investigation of the nasal cavity and the anatomic description of paranasal sinus, offers information about these cells, essential to minimize the surgical risks. The authors present a bibliographic revision of the importance of computed tomography on the investigation of anatomic variations of ethmoid cells. Not recurrent cells in all individuals, like Haller's cells, Onodi's cells and pneumatization of agger nasi, will do the endoscopic approach with precaution. The ethmoidal roof evaluation will result in more safety on the upper limits of the nasal cavity. The size and pneumatization level of ethmoidal bulla, ethmoidal crest, and middle nasal concha are important on the evaluation of the endoscopic accesses and the gravity of the stroked pathology and even diagnose your origin. (author)

  15. Do variations in mast cell hyperplasia account for differences in radiation-induced lung injury among different mouse strains, rats and nonhuman primates?

    Science.gov (United States)

    Down, Julian D; Medhora, Meetha; Jackson, Isabel L; Cline, J Mark; Vujaskovic, Zeljko

    2013-08-01

    The role of mast cell infiltrates in the pathology of radiation damage to the lung has been a subject of continuing investigation over the past four decades. This has been accompanied by a number of proposals as to how mast cells and the secretory products thereof participate in the generation of acute inflammation (pneumonitis) and the chronic process of collagen deposition (fibrosis). An additional pathophysiology examines the possible connection between mast cell hyperplasia and pulmonary hypertension through the release of vasoactive mediators. The timing and magnitude of pneumonitis and fibrosis are known to vary tremendously among different genetic mouse strains and animal species. Therefore, we have systematically compared mast cell numbers in lung sections from nine mouse strains, two rat strains and nonhuman primates (NHP) after whole thorax irradiation (WTI) at doses ranging from 10-15 Gy and at the time of entering respiratory distress. Mice of the BALB/c strain had a dramatic increase in interstitial mast cell numbers, similar to WAG/Rij and August rats, while relatively low levels of mast cell infiltrate were observed in other mouse strains (CBA, C3H, B6, C57L, WHT and TO mice). Enumeration of mast cell number in five NHPs (rhesus macaque), exhibiting severe pneumonitis at 17 weeks after 10 Gy WTI, also indicated a low response shared by the majority of mouse strains. There appeared to be no relationship between the mast cell response and the strain-dependent susceptibility towards pneumonitis or fibrosis. Further investigations are required to explore the possible participation of mast cells in mediating specific vascular responses and whether a genetically diverse mast cell response occurs in humans.

  16. Solar Cycle dependence of 5-55 keV Cassini/INCA energetic neutral atom (ENA) images of the Heliosheath and in situ Voyager/LECP ion measurements

    Science.gov (United States)

    Krimigis, S. M.; Dialynas, K.; Mitchell, D. G.; Decker, R. B.; Roelof, E. C.

    2015-12-01

    The heliosheath has been identified as the most probable source of ENAs that INCA detects but its variability due to solar activity throughout the solar cycle (SC) has not been resolved to date. We show all-sky, 5-55 keV ENA H maps from the year 2003 to 2014 and compare the solar cycle variation of the ENAs in both the heliospheric nose (upstream) and anti-nose (downstream) directions with the > 30 keV ions measured within the heliosheath by the Low Energy Charged Particle (LECP) detector on Voyagers 1, 2 (V1, V2) where we measure protons in overlapping energy bands ~30-55 keV. We find that a) Toward the anti-nose direction the ENA-H intensities decline during SC23, i.e. after 2003 ENA intensities decreased by ~ x2 at all energies by the end of year 2011, ~1 year after the observed minimum in solar activity; b) This ENA decrease (5.2-55 keV) during 2009-2011 is consistent with the concurrent intensity decrease of the > 30 keV ions (by a factor of 2-3) observed in situ by V1 and V2 in the heliosheath; c) Toward the nose direction, minimum intensities in both INCA ENAs and the V2 ions at E > 28 keV occur during the year 2013, with a subsequent recovery from 2014 to date (by a factor of ~2 in the > 35 keV ENA data). These quantitative correlations between the decreases of INCA ENAs (in both the heliospheric nose and anti-nose directions) and the in situ V1 and V2 ion measurements (separated by > 130 AU) during the declining phase of SC23, along with their concurrent jointly shared recoveries at the onset of SC24, imply that: 1) the 5-55 keV ENAs are produced in the heliosheath (because their transit times over 100 AU are less than a few months at energies > 40 keV), thus proving that our ENA observations can provide the ground truth for constructing comprehensive global heliosphere models; 2) the global heliosheath responds promptly (within ~1-1.5 yrs) to outward-propagating solar wind changes throughout the solar cycle.

  17. Co-ordinate variations in methylmalonyl-CoA mutase and methionine synthase, and the cobalamin cofactors in human glioma cells during nitrous oxide exposure and the subsequent recovery phase.

    Science.gov (United States)

    Riedel, B; Fiskerstrand, T; Refsum, H; Ueland, P M

    1999-07-01

    We investigated the co-ordinate variations of the two cobalamin (Cbl)-dependent enzymes, methionine synthase (MS) and methylmalonyl-CoA mutase (MCM), and measured the levels of their respective cofactors, methylcobalamin (CH3Cbl) and adenosylcobalamin (AdoCbl) in cultured human glioma cells during nitrous oxide exposure and during a subsequent recovery period of culture in a nitrous oxide-free atmosphere (air). In agreement with published data, MS as the primary target of nitrous oxide was inactivated rapidly (initial rate of 0.06 h(-1)), followed by reduction of CH3Cbl (to ordinate distribution of Cbl cofactors during depletion and repletion.

  18. Age and CD161 expression contribute to inter-individual variation in interleukin-23 response in CD8+ memory human T cells.

    Directory of Open Access Journals (Sweden)

    Hui Shen

    Full Text Available The interleukin-23 (IL-23 pathway plays a critical role in the pathogenesis of multiple chronic inflammatory disorders, however, inter-individual variability in IL-23-induced signal transduction in circulating human lymphocytes has not been well-defined. In this study, we observed marked, reproducible inter-individual differences in IL-23 responsiveness (measured by STAT3 phosphorylation in peripheral blood CD8+CD45RO+ memory T and CD3+CD56+ NKT cells. Age, but not gender, was a significant (Pearson's correlation coefficient, r = -0.37, p = 0.001 source of variability observed in CD8+CD45RO+ memory T cells, with IL-23 responsiveness gradually decreasing with increasing age. Relative to cells from individuals demonstrating low responsiveness to IL-23 stimulation, CD8+CD45RO+ memory T cells from individuals demonstrating high responsiveness to IL-23 stimulation showed increased gene expression for IL-23 receptor (IL-23R, RORC (RORγt and CD161 (KLRB1, whereas RORA (RORα and STAT3 expression were equivalent. Similar to CD4+ memory T cells, IL-23 responsiveness is confined to the CD161+ subset in CD8+CD45RO+ memory T cells, suggesting a similar CD161+ precursor as has been reported for CD4+ Th17 cells. We observed a very strong positive correlation between IL-23 responsiveness and the fraction of CD161+, CD8+CD45RO+ memory T cells (r = 0.80, p<0.001. Moreover, the fraction of CD161+, CD8+CD45RO+ memory T cells gradually decreases with aging (r = -0.34, p = 0.05. Our data define the inter-individual differences in IL-23 responsiveness in peripheral blood lymphocytes from the general population. Variable expression of CD161, IL-23R and RORC affects IL-23 responsiveness and contributes to the inter-individual susceptibility to IL-23-mediated defenses and inflammatory processes.

  19. Association of a single nucleotide polymorphic variation in the human chromosome 19q13.3 with drug responses in the NCI60 cell lines

    DEFF Research Database (Denmark)

    Nissen, K.K.; Vogel, Ulla Birgitte; Nexo, B.A.

    2009-01-01

    We studied the importance of certain polymorphisms on human chromosome 19q13.3 for drug sensitivity in human tumor cell cultures. NCI60 is a panel of 60 established tumor-derived cell lines, which have been tested for their sensitivity to tens of thousands of different drugs. Here we investigate...... the correlations between the responses of the NCI60 cells to different anticancer drugs and their respective alleles of five DNA polymorphisms located in a cancer-related chromosomal area. One polymorphism, located in the 5' noncoding region of the gene ASE-1, alias CD3EAP, proved to be associated with drug...... sensitivity (P=0.025). The same polymorphism has previously been associated with treatment response of multiple myeloma after bone marrow ablation. The polymorphism ASE-1-e1 was of importance for the drug response in the human cancer cell lines investigated and could eventually become important...

  20. Phenotypic variations of cartilage hair hypoplasia: granulomatous skin inflammation and severe T cell immunodeficiency as initial clinical presentation in otherwise well child with short stature.

    Science.gov (United States)

    McCann, Liza J; McPartland, Jo; Barge, Dawn; Strain, Lisa; Bourn, David; Calonje, Eduardo; Verbov, Julian; Riordan, Andrew; Kokai, George; Bacon, Chris M; Wright, Michael; Abinun, Mario

    2014-01-01

    We report a child with short stature since birth who was otherwise well, presenting at 2.8 years with progressive granulomatous skin lesions when diagnosed with severe T cell immunodeficiency. When previously investigated for short stature, and at the time of current investigations, she had no radiological skeletal features characteristics for cartilage hair hypoplasia, but we found a disease causing RMRP (RNase mitochondrial RNA processing endoribonuclease) gene mutation. Whilst search for HLA matched unrelated donor for haematopoietic stem cell transplantation (HSCT) was underway, she developed rapidly progressive EBV-related lymphoproliferative disorder requiring laparotomy and small bowel resection, and was treated with anti-B cell monoclonal antibody and eventually curative allogeneic HSCT. Screening for RMRP gene mutations should be part of immunological evaluation of patients with 'severe and/or combined' T cell immunodeficiency of unknown origin, especially when associated with short stature and regardless of presence or absence of radiological skeletal features.

  1. Variational principles for locally variational forms

    International Nuclear Information System (INIS)

    Brajercik, J.; Krupka, D.

    2005-01-01

    We present the theory of higher order local variational principles in fibered manifolds, in which the fundamental global concept is a locally variational dynamical form. Any two Lepage forms, defining a local variational principle for this form, differ on intersection of their domains, by a variationally trivial form. In this sense, but in a different geometric setting, the local variational principles satisfy analogous properties as the variational functionals of the Chern-Simons type. The resulting theory of extremals and symmetries extends the first order theories of the Lagrange-Souriau form, presented by Grigore and Popp, and closed equivalents of the first order Euler-Lagrange forms of Hakova and Krupkova. Conceptually, our approach differs from Prieto, who uses the Poincare-Cartan forms, which do not have higher order global analogues

  2. Estrogen receptor β regulates the tumoral suppressor PTEN to modulate pituitary cell growth.

    Science.gov (United States)

    Perez, Pablo A; Petiti, Juan P; Picech, Florencia; Guido, Carolina B; dV Sosa, Liliana; Grondona, Ezequiel; Mukdsi, Jorge H; De Paul, Ana L; Torres, Alicia I; Gutierrez, Silvina

    2018-02-01

    In this study, we focused on ERβ regulation in the adenohypophysis under different estrogenic milieu, by analyzing whether ER modulates the phosphatase and tensin homolog deleted on chromosome 10 (PTEN) expression and its subcellular localization on anterior pituitary glands from Wistar rats and GH3 lactosomatotroph cells that over-expressed ERβ. ERβ was regulated in a cyclic manner, and underwent dynamic changes throughout the estrous cycle, with decreased ERβ+ cells in estrus and under E2 treatment, but increased in ovariectomized rats. In addition, the ERα/β ratio increased in estrus and under E2 stimulation, but decreased in ovariectomized rats. Double immunofluorescence revealed that lactotroph and somatotroph ERβ+ were significantly decreased in estrus. Also, variations in the PTEN expression was observed, which was diminished with high E2 conditions but augmented with low E2 milieu. The subcellular localization of this phosphatase was cell cycle-dependent, with remarkable changes in the immunostaining pattern: nuclear in arrested pituitary cells but cytoplasmic in stimulated cells, and responding differently to ER agonists, with only DPN being able to increase PTEN expression and retaining it in the nucleus. Finally, ERβ over-expression increased PTEN with a noticeable subcellular redistribution, and with a significant nuclear signal increase in correlation with an increase of cells in G0/G1 phase. These results showed that E2 is able to inhibit ERβ expression and suggests that the tumoral suppressor PTEN might be one of the signaling proteins by which E2, through ERβ, acts to modulate pituitary cell proliferation, thereby adapting endocrine populations in relation with hormonal necessities. © 2017 Wiley Periodicals, Inc.

  3. Variations in T-helper 17 and Regulatory T Cells during The Menstrual Cycle in Peripheral Blood of Women with Recurrent Spontaneous Abortion

    Directory of Open Access Journals (Sweden)

    Nasrin Sereshki

    2014-03-01

    Full Text Available Background: Disorders in immune system regulation may result in pregnancy abnormalities such as recurrent spontaneous abortion (RSA. This study aims to determine the ratio of regulatory T (Treg and T helper (Th 17 cells in unexplained RSA (URSA women during proliferative and secretory phases of their menstrual cycles compared to healthy non-pregnant women. Materials and Methods: In this case control study, 25 women with URSA and 35 healthy, non-pregnant women were enrolled. The percentage of Th17 and Treg cells in participants peripheral blood were determined by flow cytometry. Results: The percentage of Th17 cells and their related cytokines in serum (IL-17A were higher in the proliferative and secretory phases of the menstrual cycles of URSA women compared to the control women. However, a lower percentage of Treg cells and their related cytokines in serum, transforming growth factor (TGF β1 and interleukin (IL-10 were detected in the proliferative but not the secretory phase of the URSA group. The ratio of Th17/CD4+ Treg was higher in the URSA group than the control group. We observed an increased ratio of Th17/CD4+ Treg during the proliferative and secretory phases in URSA women. Conclusion: The imbalance between Th17 and Treg cells during the proliferative phase of menstrual cycles in the URSA group may be considered a cause for spontaneous abortion.

  4. Gene variation in IL-7 receptor (IL-7R)α affects IL-7R response in CD4+ T cells in HIV-infected individuals

    DEFF Research Database (Denmark)

    Hartling, Hans Jakob; Ryder, Lars P.; Ullum, Henrik

    2017-01-01

    Optimal CD4+ T cell recovery after initiating combination antiretroviral treatment (cART) in HIV infection reduces risk of morbidity and mortality. T-allele homozygosity (‘TT’) in the single nucleotide polymorphism, rs6897932(C/T), in the IL-7 receptor α (IL-7RA) is associated with faster CD4+ T...... cell recovery after cART initiation compared to C-allele homozygosity in rs6897932 (‘CC’). However, underlying mechanisms are unknown. We aimed to examine potential mechanisms explaining the association between rs6897932 and CD4+ T cell recovery. Ten ‘TT’ and 10 ‘CC’ HIV-infected individuals matched...... on gender, age, and nadir and current CD4+ T cell counts were included in a cross-sectional study. ‘TT’ individuals had higher proportion of CD4+ T cells expressing pSTAT5 compared to ‘CC’ individuals after stimulating with IL-7, especially when co-stimulated with soluble IL7-RA (sIL-7RA). Furthermore, ‘TT...

  5. SU-D-207A-07: The Effects of Inter-Cycle Respiratory Motion Variation On Dose Accumulation in Single Fraction MR-Guided SBRT Treatment of Renal Cell Carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Stemkens, B; Glitzner, M; Kontaxis, C; Prins, F; Crijns, SPM; Kerkmeijer, L; Lagendijk, J; Berg, CAT van den; Tijssen, RHN [Department of Radiotherapy, University Medical Center Utrecht, Utrecht (Netherlands); Denis de Senneville, B [Imaging Division, University Medical Center Utrecht, Utrecht (Netherlands); IMB, UMR 5251 CNRS/University of Bordeaux (France)

    2016-06-15

    Purpose: To assess the dose deposition in simulated single-fraction MR-Linac treatments of renal cell carcinoma, when inter-cycle respiratory motion variation is taken into account using online MRI. Methods: Three motion characterization methods, with increasing complexity, were compared to evaluate the effect of inter-cycle motion variation and drifts on the accumulated dose for an SBRT kidney MR-Linac treatment: 1) STATIC, in which static anatomy was assumed, 2) AVG-RESP, in which 4D-MRI phase-volumes were time-weighted, based on the respiratory phase and 3) PCA, in which 3D volumes were generated using a PCA-model, enabling the detection of inter-cycle variations and drifts. An experimental ITV-based kidney treatment was simulated in a 1.5T magnetic field on three volunteer datasets. For each volunteer a retrospectively sorted 4D-MRI (ten respiratory phases) and fast 2D cine-MR images (temporal resolution = 476ms) were acquired to simulate MR-imaging during radiation. For each method, the high spatio-temporal resolution 3D volumes were non-rigidly registered to obtain deformation vector fields (DVFs). Using the DVFs, pseudo-CTs (generated from the 4D-MRI) were deformed and the dose was accumulated for the entire treatment. The accuracies of all methods were independently determined using an additional, orthogonal 2D-MRI slice. Results: Motion was most accurately estimated using the PCA method, which correctly estimated drifts and inter-cycle variations (RMSE=3.2, 2.2, 1.1mm on average for STATIC, AVG-RESP and PCA, compared to the 2DMRI slice). Dose-volume parameters on the ITV showed moderate changes (D99=35.2, 32.5, 33.8Gy for STATIC, AVG-RESP and PCA). AVG-RESP showed distinct hot/cold spots outside the ITV margin, which were more distributed for the PCA scenario, since inter-cycle variations were not modeled by the AVG-RESP method. Conclusion: Dose differences were observed when inter-cycle variations were taken into account. The increased inter

  6. Use of a novel cell adhesion method and digital measurement to show stimulus-dependent variation in somatic and oral ciliary beat frequency in Paramecium.

    Science.gov (United States)

    Bell, Wade E; Hallworth, Richard; Wyatt, Todd A; Sisson, Joseph H

    2015-01-01

    When Paramecium encounters positive stimuli, the membrane hyperpolarizes and ciliary beat frequency increases. We adapted an established immobilization protocol using a biological adhesive and a novel digital analysis system to quantify beat frequency in immobilized Paramecium. Cells showed low mortality and demonstrated beat frequencies consistent with previous studies. Chemoattractant molecules, reduction in external potassium, and posterior stimulation all increased somatic beat frequency. In all cases, the oral groove cilia maintained a higher beat frequency than mid-body cilia, but only oral cilia from cells stimulated with chemoattactants showed an increase from basal levels. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

  7. Genetic Variations in the Human G Protein-coupled Receptor Class C, Group 6, Member A (GPRC6A) Control Cell Surface Expression and Function

    DEFF Research Database (Denmark)

    Jorgensen, Stine; Have, Christian Theil; Underwood, Christina Rye

    2017-01-01

    GPRC6A is a G protein-coupled receptor activated by l-amino acids, which, based on analyses of knock-out mice, has been suggested to have physiological functions in metabolism and testicular function. The human ortholog is, however, mostly retained intracellularly in contrast to the cell surface...... of the human ortholog. Genetic analyses of the 1000 genome database and the Inter99 cohort of 6,000 Danes establish the distribution of genotypes among ethnic groups, showing that the cell surface-expressed and functional variant is much more prevalent in the African population than in European and Asian...

  8. Solar Cycle Spectral Irradiance Variation and Stratospheric Ozone

    Science.gov (United States)

    Stolarski, R. S.; Swartz, W. H.; Jackman, C. H.; Fleming, E. L.

    2011-12-01

    Recent measurements from the SIM instrument on the SORCE satellite have been interpreted by Harder et al (Geophys. Res. Lett., 36, L07801, doi:10.1029/2008GL036797, 2009) as implying a different spectral irradiance variation over the solar cycle than that put forward by Lean (Geophys. Res. Lett., 27, 2425-2428, 2000). When we inserted this new wavelength dependent solar cycle variation into our 3D CCM we found a different solar cycle dependence of the ozone concentration as a function of altitude from that we derived using the traditional Lean wavelength dependence. Examination of these results led us to realize that the main issue is the solar cycle variation of radiation at wavelengths less than 240 nm versus the solar cycle variation of radiation at wavelengths between 240 nm and 300 nm. The impact of wavelengths less than 240 nm occurs through photodissociation of O2 leading to the production of ozone. The impact of wavelengths between 240 nm and 300 nm occurs through photodissociation of O3 leading to an increase in O atoms and enhanced ozone destruction. Thus one wavelength region gives an in-phase relationship of ozone with the solar cycle while the other wavelength region gives an out-of-phase relationship of ozone with the solar cycle. We have used the Goddard two-dimensional (2D) photochemistry transport model to examine this relationship in more detail. We calculate the altitude and latitude sensitivity of ozone to changes in the solar UV irradiance as a function of wavelength. These results can be used to construct the ozone response to arbitrary wavelength dependencies of solar UV variation.

  9. AGONIST ANTAGONIST INTERACTIONS WITH CLONED HUMAN 5-HT1A RECEPTORS - VARIATIONS IN INTRINSIC ACTIVITY STUDIED IN TRANSFECTED HELA-CELLS

    NARCIS (Netherlands)

    BODDEKE, HWGM; FARGIN, A; RAYMOND, J.; SCHOEFFTER, P; HOYER, D

    The characteristics of 5-HT1A-recognition sites and receptor-mediated release of intracellular calcium were established in two transfected HeLa cell lines (HA 6 and HA 7) expressing different levels of human 5-HT1A receptors (about 3000 and 500 fmol/mg protein, Fargin et al. 1989; 1991; Raymond et

  10. Agonist/antagonist interactions with cloned human 5-HT(1A) receptors: Variations in intrinsic activity studied in transfected HeLa cells

    NARCIS (Netherlands)

    Boddeke, H.W.G.M.; Fargin, A.; Raymond, J.R.; Schoeffter, P.; Hoyer, D.

    1992-01-01

    The characteristics of 5-HT(1A)-recognition sites and receptor-mediated release of intracellular calcium were established in two transfected HeLa cell lines (HA 6 and HA 7) expressing different levels of human 5-HT(1A) receptors (about 3000 and 500 fmol/mg protein, Fargin et al. 1989; 1991; Raymond

  11. MiRNA-Related Genetic Variations Associated with Radiotherapy-Induced Toxicities in Patients with Locally Advanced Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Li, Rong; Pu, Xia; Chang, Joe Y; Ye, Yuanqing; Komaki, Ritsuko; Minna, John D; Roth, Jack A; Han, Baohui; Wu, Xifeng

    2016-01-01

    Severe radiation-induced toxicities limit treatment efficacy and compromise outcomes of lung cancer. We aimed to identify microRNA-related genetic variations as biomarkers for the prediction of radiotherapy-induced acute toxicities. We genotyped 233 SNPs (161 in microRNA binding site and 72 in processing gene) and analyzed their associations with pneumonitis and esophagitis in 167 stage III NSCLC patients received definitive radiation therapy. Sixteen and 11 SNPs were associated with esophagitis and pneumonitis, respectively. After multiple comparison correction, RPS6KB2:rs10274, SMO:rs1061280, SMO:rs1061285 remained significantly associated with esophagitis, while processing gene DGCR8:rs720014, DGCR8:rs3757, DGCR8:rs1633445 remained significantly associated with pneumonitis. Patients with the AA genotype of RPS6KB2:rs10274 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07-0.51, p = 0.001, q = 0.06). Patients with the AG+GG genotype of SMO:rs1061280 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07-0.53, p = 0.001, q = 0.06). Patients with the GG+GA genotype of DGCR8:rs720014 had a 3.54-fold increased risk of pneumonitis (OR: 3.54, 95% CI: 1.65-7.61, p pneumonitis. Our results provide strong evidence that microRNA-related genetic variations contribute to the development of radiotherapy-induced acute esophagitis and pneumonitis and could thus serve as biomarkers to help accurately predict radiotherapy-induced toxicity in NSCLC patients.

  12. MiRNA-Related Genetic Variations Associated with Radiotherapy-Induced Toxicities in Patients with Locally Advanced Non–Small Cell Lung Cancer

    Science.gov (United States)

    Li, Rong; Pu, Xia; Chang, Joe Y.; Ye, Yuanqing; Komaki, Ritsuko; Minna, John D.; Roth, Jack A.

    2016-01-01

    Severe radiation-induced toxicities limit treatment efficacy and compromise outcomes of lung cancer. We aimed to identify microRNA-related genetic variations as biomarkers for the prediction of radiotherapy-induced acute toxicities. We genotyped 233 SNPs (161 in microRNA binding site and 72 in processing gene) and analyzed their associations with pneumonitis and esophagitis in 167 stage III NSCLC patients received definitive radiation therapy. Sixteen and 11 SNPs were associated with esophagitis and pneumonitis, respectively. After multiple comparison correction, RPS6KB2:rs10274, SMO:rs1061280, SMO:rs1061285 remained significantly associated with esophagitis, while processing gene DGCR8:rs720014, DGCR8:rs3757, DGCR8:rs1633445 remained significantly associated with pneumonitis. Patients with the AA genotype of RPS6KB2:rs10274 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07–0.51, p = 0.001, q = 0.06). Patients with the AG+GG genotype of SMO:rs1061280 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07–0.53, p = 0.001, q = 0.06). Patients with the GG+GA genotype of DGCR8:rs720014 had a 3.54-fold increased risk of pneumonitis (OR: 3.54, 95% CI: 1.65–7.61, p pneumonitis. Our results provide strong evidence that microRNA-related genetic variations contribute to the development of radiotherapy-induced acute esophagitis and pneumonitis and could thus serve as biomarkers to help accurately predict radiotherapy-induced toxicity in NSCLC patients. PMID:26991123

  13. Elderly Men Have Low Levels of Anti-Müllerian Hormone and Inhibin B, but with High Interpersonal Variation: A Cross-Sectional Study of the Sertoli Cell Hormones in 615 Community-Dwelling Men

    Science.gov (United States)

    Chong, Yih Harng; Dennis, Nicola A.; Connolly, Martin J.; Teh, Ruth; Jones, Gregory T.; van Rij, Andre M.; Farrand, Stephanie; Campbell, A. John; MLennan, Ian S.

    2013-01-01

    The Sertoli cells of the testes secrete anti-Müllerian hormone (Müllerian inhibiting Substance, AMH) and inhibin B (InhB). AMH triggers the degeneration of the uterine precursor in male embryos, whereas InhB is part of the gonadal-pituitary axis for the regulation of sperm production in adults. However, both hormones are also putative regulators of homeostasis, and age-related changes in these hormones may therefore be important to the health status of elderly men. The levels of AMH in elderly men are unknown, with limited information being available about age-related changes in InhB. We have therefore used ELISAs to measure Sertoli cell hormone levels in 3 cohorts of community-dwelling men in New Zealand. In total, 615 men were examined, 493 of which were aged 65 or older. Serum AMH and InhB levels inversely correlated with age in men older than 50 years (p<0.001) but not in the younger men. A minority of elderly men had undetectable levels of AMH and InhB. The variation in hormone levels between similarly aged men increased with the age of men. AMH and InhB partially correlated with each other as expected (r = 0.48, p<0.001). However, the ratio of the two Sertoli hormones varied significantly between men, with this variation increasing with age. Elderly men selected for the absence of cardiovascular disease had AMH levels similar to those of young men whereas their InhB levels did not differ from aged-matched controls. These data suggests that Sertoli cell number and function changes with age, but with the extent and nature of the changes varying between men. PMID:23940675

  14. Infection of a Single Cell Line with Distinct Strains of Human Cytomegalovirus Can Result in Large Variations in Virion Production and Facilitate Efficient Screening of Virus Protein Function.

    Science.gov (United States)

    Zavala, Anamaria G; O'Dowd, John M; Fortunato, Elizabeth A

    2015-12-16

    Previously, we reported that the absence of the ataxia telangiectasia mutated (ATM) kinase, a critical DNA damage response (DDR) signaling component for double-strand breaks, caused no change in HCMV Towne virion production. Later, others reported decreased AD169 viral titers in the absence of ATM. To address this discrepancy, human foreskin fibroblasts (HFF) and three ATM(-) lines (GM02530, GM05823, and GM03395) were infected with both Towne and AD169. Two additional ATM(-) lines (GM02052 and GM03487) were infected with Towne. Remarkably, both previous studies' results were confirmed. However, the increased number of cell lines and infections with both lab-adapted strains confirmed that ATM was not necessary to produce wild-type-level titers in fibroblasts. Instead, interactions between individual virus strains and the cellular microenvironment of the individual ATM(-) line determined efficiency of virion production. Surprisingly, these two commonly used lab-adapted strains produced drastically different titers in one ATM(-) cell line, GM05823. The differences in titer suggested a rapid method for identifying genes involved in differential virion production. In silico comparison of the Towne and AD169 genomes determined a list of 28 probable candidates responsible for the difference. Using serial iterations of an experiment involving virion entry and input genome nuclear trafficking with a panel of related strains, we reduced this list to four (UL129, UL145, UL147, and UL148). As a proof of principle, reintroduction of UL148 largely rescued genome trafficking. Therefore, use of a battery of related strains offers an efficient method to narrow lists of candidate genes affecting various virus life cycle checkpoints. Human cytomegalovirus (HCMV) infection of multiple cell lines lacking ataxia telangiectasia mutated (ATM) protein produced wild-type levels of infectious virus. Interactions between virus strains and the microenvironment of individual ATM(-) lines

  15. Mutagenesis in mammalian cells

    International Nuclear Information System (INIS)

    Burki, H.J.

    1981-01-01

    Mutagenic processes in synchronous cultures of Chinese hamster ovary cells have been studied. There is a difference in the induction of mutants by ultraviolet light during the cell cycle. There appears to be a sensitive period in the middle of the G1 stage of the cell cycle suggesting some mutagenic mechanism is present at that time. Studies indicate that mutation induction during the cell cycle is also mutagen specific since exposure to ethyl nitrosourea in the same system produces different results. Two clones have been isolated which are ultrasensitive to ultraviolet light. These cells are being used to determine if this hypermutability is cell-cycle dependent, related to cell cycle biochemistry, or to repair processes independent of cell cycle. Tritium and bromodeoxyuridine induced damage to synchronously dividing cell cultures are also being studied in relation to DNA replication. Cell killing by ionizing radiation is also related to the cell cycle. Sensitive times in the cell cycle for mutation induction by ionization radiation are identified

  16. Clonal variation of DNA repair in a human glioma cell line This study was supported by the Cancer Research Campaign and the Bob Champion Cancer Trust

    International Nuclear Information System (INIS)

    Powell, Simon; McMillan, T.J.

    1991-01-01

    Clonal heterogeneity in response to ionizing radiation was found for a human glioma cell line, IN859. The authors have investigated the most sensitive clone, the most resistant clone and the parent line for differences in DNA repair fidelity using the method of plasmid reconstitution. Significant differences in repair fidelity were found between the two clones, and between the sensitive clone and the parent line. The resistant clone and the parent lines showed the greater repair fidelity. A comparison of two different restriction enzymes, which cleave the plasmid with blunt or cohesive-ended double-strand breaks, did not reveal differences in repair fidelity. Equal numbers of plasmids were integrated in each cell line, but the sensitive clone showed a higher frequency of misrepair of cleaved plasmid. Misrepair was characterized by partial or complete loss of sequence at the site of plasmid cleavage. It is concluded that the radiosensitive clone exhibits increased misrepair. (author). 15 refs.; 5 figs.; 2 tabs

  17. Cell reproductive patterns in the green alga Pseudokirchneriella subcapitata (=Selenastrum capricornutum and their variations under exposure to the typical toxicants potassium dichromate and 3,5-DCP.

    Directory of Open Access Journals (Sweden)

    Takahiro Yamagishi

    Full Text Available Pseudokirchneriella subcapitata is a sickle-shaped freshwater green microalga that is normally found in unicellular form. Currently, it is the best known and most frequently used species of ecotoxicological bioindicator because of its high growth rate and sensitivity to toxicants. However, despite this organism's, our knowledge of its cell biology-for example, the patterns of nuclear and cytoplasmic division in the mitotic stage-is limited. Although it has been reported that P. subcapitata proliferates by popularity forming four daughter cells (autospores through multiple fission after two nuclear divisions, here, we report two additional reproductive patterns by which two autospores are formed by binary fission ("two-autospore type" and eight autospores are formed by multiple fission ("eight-autospore type". Moreover, we found that cell reproductive patterns differed markedly with the culture conditions or with exposure to either of two typical toxicants, potassium dichromate (K2Cr2O7 and 3,5-dichlorophenol (3,5-DCP. The eight-autospore type occurred at the highest frequency in the early phase of culture, but it disappeared under 3,5-DCP at 2.0 mg/L. Under 0.3 mg/L K2CrO7 (Cr(VI the eight-autospore type took substantially longer to appear than in control culture. The two-autospore type occurred only in the late phase of culture. To our knowledge, this is the first detailed evaluation of the reproductive patterns of P. subcapitata, which changed dramatically in the presence of toxicants. These findings suggest that observation of the reproductive patterns of P. subcapitata will help to elucidate different cell reactions to toxicants.

  18. Non-invasive in-cell determination of free cytosolic [NAD+]/[NADH] ratios using hyperpolarized glucose show large variations in metabolic phenotypes

    DEFF Research Database (Denmark)

    Christensen, Caspar Elo; Karlsson, Magnus; Winther, Jakob R.

    2014-01-01

    Accumulating evidence suggest that the pyridine nucleotide NAD has far wider biological functions than its classical role in energy metabolism. NAD is used by hundreds of enzymes that catalyse substrate oxidation and as such it plays a key role in various biological processes such as aging, cell ......+]/[NADH] ratio, the bioprobe will enable better understanding of the origin of diverse pathological states of the cell as well as monitor cellular consequences of diseases and/or treatments.......Accumulating evidence suggest that the pyridine nucleotide NAD has far wider biological functions than its classical role in energy metabolism. NAD is used by hundreds of enzymes that catalyse substrate oxidation and as such it plays a key role in various biological processes such as aging, cell...... death and oxidative stress. It has been suggested that changes in the ratio of free cytosolic [NAD+]/[NADH] reflects metabolic alterations leading to, or correlating with, pathological states. We have designed an isotopically labelled metabolic bioprobe of free cytosolic [NAD+]/[NADH] by combining...

  19. Variation in the Optical Properties of the SiC-SiO2 Composite Antireflection Layer in Crystalline Silicon Solar Cells by Annealing

    Science.gov (United States)

    Jannat, Azmira; Li, Zhen Yu; Akhter, M. Shaheer; Yang, O.-Bong

    2017-11-01

    This study showed the effects of annealing on a sol-gel-derived SiC-SiO2 composite antireflection (AR) layer and investigated the optical and photovoltaic properties of crystalline silicon (Si) solar cells. The SiC-SiO2 composite AR coating showed a considerable decrease in reflectance from 7.18% to 3.23% at varying annealing temperatures of 450-800°C. The refractive indices of the SiC-SiO2 composite AR layer were tuned from 2.06 to 2.45 with the increase in annealing temperature. The analysis of the current density-voltage characteristics indicated that the energy conversion efficiencies of the fabricated Si solar cells gradually increased from 16.99% to 17.73% with increasing annealing temperatures of 450-800°C. The annealing of the SiC-SiO2 composite AR layer in Si solar cells was crucial to improving the optical, morphological, and photovoltaic properties.

  20. Variations in the structure of neutral sugar chains in the pectic polysaccharides of morphologically different carrot calli and correlations with the size of cell clusters.

    Science.gov (United States)

    Kikuchi, A; Edashige, Y; Ishii, T; Fujii, T; Satoh, S

    1996-01-01

    Carrot (Daucus carota L.) embryogenic callus (EC) loses its embryogenic competence and becomes non-embryogenic callus (NC) during long-term culture. With the loss of embryogenic competence, the cell clusters become smaller and the extent of intercellular attachments is reduced. Pectic fractions prepared from EC and NC were separated into two subfractions by gel filtration. A difference in sugar composition between EC and NC was found only in the high-molecular-mass (ca. 1300 kDa) subfraction, and the ratio of the amount of arabinose to that of galactose (Ara/Gal) was strongly and positively correlated with the size of cell clusters in several different cultures. From the results of sugar-composition and methylation analyses, and the results of treatment with exo-arabinanase, models of the neutral sugar chains of pectins from Ec and NC are proposed. Both neutral sugar chains are composed of three regions. The basal region is composed of linearly linked arabinan 5-Araf) moieties in both types of callus. The middle galactan region is composed of 6-linked galactose, some of which branches at the 3 and 4 positions, and this region is larger and more frequently branched in NC than in EC. Finally, the terminal arabinan region is composed of 5-linked arabinose, branched at the 3 position, and the size of the terminal arabinan is larger in EC than in NC. The significance of the neutral sugar chains of pectins in the interaction of cell wall components and intercellular attachment is discussed.

  1. Interannual Variations of MLS Carbon Monoxide Induced by Solar Cycle

    Science.gov (United States)

    Lee, Jae N.; Wu, Dong L.; Ruzmaikin, Alexander

    2013-01-01

    More than eight years (2004-2012) of carbon monoxide (CO) measurements from the Aura Microwave Limb Sounder (MLS) are analyzed. The mesospheric CO, largely produced by the carbon dioxide (CO2) photolysis in the lower thermosphere, is sensitive to the solar irradiance variability. The long-term variation of observed mesospheric MLS CO concentrations at high latitudes is likely driven by the solar-cycle modulated UV forcing. Despite of different CO abundances in the southern and northern hemispheric winter, the solar-cycle dependence appears to be similar. This solar signal is further carried down to the lower altitudes by the dynamical descent in the winter polar vortex. Aura MLS CO is compared with the Solar Radiation and Climate Experiment (SORCE) total solar irradiance (TSI) and also with the spectral irradiance in the far ultraviolet (FUV) region from the SORCE Solar-Stellar Irradiance Comparison Experiment (SOLSTICE). Significant positive correlation (up to 0.6) is found between CO and FUVTSI in a large part of the upper atmosphere. The distribution of this positive correlation in the mesosphere is consistent with the expectation of CO changes induced by the solar irradiance variations.

  2. MiRNA-Related Genetic Variations Associated with Radiotherapy-Induced Toxicities in Patients with Locally Advanced Non-Small Cell Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Rong Li

    Full Text Available Severe radiation-induced toxicities limit treatment efficacy and compromise outcomes of lung cancer. We aimed to identify microRNA-related genetic variations as biomarkers for the prediction of radiotherapy-induced acute toxicities. We genotyped 233 SNPs (161 in microRNA binding site and 72 in processing gene and analyzed their associations with pneumonitis and esophagitis in 167 stage III NSCLC patients received definitive radiation therapy. Sixteen and 11 SNPs were associated with esophagitis and pneumonitis, respectively. After multiple comparison correction, RPS6KB2:rs10274, SMO:rs1061280, SMO:rs1061285 remained significantly associated with esophagitis, while processing gene DGCR8:rs720014, DGCR8:rs3757, DGCR8:rs1633445 remained significantly associated with pneumonitis. Patients with the AA genotype of RPS6KB2:rs10274 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07-0.51, p = 0.001, q = 0.06. Patients with the AG+GG genotype of SMO:rs1061280 had an 81% reduced risk of developing esophagitis (OR: 0.19, 95% CI: 0.07-0.53, p = 0.001, q = 0.06. Patients with the GG+GA genotype of DGCR8:rs720014 had a 3.54-fold increased risk of pneumonitis (OR: 3.54, 95% CI: 1.65-7.61, p <0.05, q <0.1. Significantly cumulative effects of the top SNPs were observed for both toxicities (P-trend <0.001. Using bioinformatics tools, we found that the genotype of rs10274 was associated with altered expression of the RPS6KB2 gene. Gene-based analysis showed DGCR8 (p = 0.010 and GEMIN4 (p = 0.039 were the top genes associated with the risk of developing pneumonitis. Our results provide strong evidence that microRNA-related genetic variations contribute to the development of radiotherapy-induced acute esophagitis and pneumonitis and could thus serve as biomarkers to help accurately predict radiotherapy-induced toxicity in NSCLC patients.

  3. Improvement of Cycle Dependent Core Model for NPP Simulator

    International Nuclear Information System (INIS)

    Song, J. S.; Koo, B. S.; Kim, H. Y. and others

    2003-11-01

    The purpose of this study is to establish automatic core model generation system and to develop 4 cycle real time core analysis methodology with 5% power distribution and 500 pcm reactivity difference criteria for nuclear power plant simulator. The standardized procedure to generate database from ROCS and ANC, which are used for domestic PWR core design, was established for the cycle specific simulator core model generation. An automatic data interface system to generate core model also established. The system includes ARCADIS which edits group constant and DHCGEN which generates interface coupling coefficient correction database. The interface coupling coefficient correction method developed in this study has 4 cycle real time capability and accuracies of which the maximum differences between core design results are within 103 pcm reactivity, 1% relative power distribution and 6% control rod worth. A nuclear power plant core simulation program R-MASTER was developed using the methodology and applied by the concept of distributed client system in simulator. The performance was verified by site acceptance test in Simulator no. 2 in Kori Training Center for 30 initial condition generation and 27 steady state, transient and postulated accident situations

  4. Improvement of Cycle Dependent Core Model for NPP Simulator

    Energy Technology Data Exchange (ETDEWEB)

    Song, J. S.; Koo, B. S.; Kim, H. Y. and others

    2003-11-15

    The purpose of this study is to establish automatic core model generation system and to develop 4 cycle real time core analysis methodology with 5% power distribution and 500 pcm reactivity difference criteria for nuclear power plant simulator. The standardized procedure to generate database from ROCS and ANC, which are used for domestic PWR core design, was established for the cycle specific simulator core model generation. An automatic data interface system to generate core model also established. The system includes ARCADIS which edits group constant and DHCGEN which generates interface coupling coefficient correction database. The interface coupling coefficient correction method developed in this study has 4 cycle real time capability and accuracies of which the maximum differences between core design results are within 103 pcm reactivity, 1% relative power distribution and 6% control rod worth. A nuclear power plant core simulation program R-MASTER was developed using the methodology and applied by the concept of distributed client system in simulator. The performance was verified by site acceptance test in Simulator no. 2 in Kori Training Center for 30 initial condition generation and 27 steady state, transient and postulated accident situations.

  5. Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors.

    Science.gov (United States)

    Jiang, Wei; Johnson, Chris; Jayaraman, Jyothi; Simecek, Nikol; Noble, Janelle; Moffatt, Miriam F; Cookson, William O; Trowsdale, John; Traherne, James A

    2012-10-01

    The KIR complex appears to be evolving rapidly in humans, and more than 50 different haplotypes have been described, ranging from four to 14 KIR loci. Previously it has been suggested that most KIR haplotypes consist of framework genes, present in all individuals, which bracket a variable number of other genes. We used a new technique to type 793 families from the United Kingdom and United States for both the presence/absence of all individual KIR genes as well as copy number and found that KIR haplotypes are even more complex. It is striking that all KIR loci are subject to copy number variation (CNV), including the so-called framework genes, but CNV is much more frequent in KIR B haplotypes than KIR A haplotypes. These two basic KIR haplotype groups, A and B, appear to be following different evolutionary trajectories. Despite the great diversity, there are 11 common haplotypes, derived by reciprocal recombination near KIR2DL4, which collectively account for 94% of KIR haplotypes determined in Caucasian samples. These haplotypes could be derived from combinations of just three centromeic and two telomeric motifs, simplifying disease analysis for these haplotypes. The remaining 6% of haplotypes displayed novel examples of expansion and contraction of numbers of loci. Conventional KIR typing misses much of this additional complexity, with important implications for studying the genetics of disease association with KIR that can now be explored by CNV analysis.

  6. Variational Monte Carlo Technique

    Indian Academy of Sciences (India)

    ias

    RESONANCE ⎜ August 2014. GENERAL ⎜ ARTICLE. Variational Monte Carlo Technique. Ground State Energies of Quantum Mechanical Systems. Sukanta Deb. Keywords. Variational methods, Monte. Carlo techniques, harmonic os- cillators, quantum mechanical systems. Sukanta Deb is an. Assistant Professor in the.

  7. Elderly men have low levels of anti-Müllerian hormone and inhibin B, but with high interpersonal variation: a cross-sectional study of the sertoli cell hormones in 615 community-dwelling men.

    Science.gov (United States)

    Chong, Yih Harng; Dennis, Nicola A; Connolly, Martin J; Teh, Ruth; Jones, Gregory T; van Rij, Andre M; Farrand, Stephanie; Campbell, A John; McLennan, Ian S; Mlennan, Ian S

    2013-01-01

    The Sertoli cells of the testes secrete anti-Müllerian hormone (Müllerian inhibiting Substance, AMH) and inhibin B (InhB). AMH triggers the degeneration of the uterine precursor in male embryos, whereas InhB is part of the gonadal-pituitary axis for the regulation of sperm production in adults. However, both hormones are also putative regulators of homeostasis, and age-related changes in these hormones may therefore be important to the health status of elderly men. The levels of AMH in elderly men are unknown, with limited information being available about age-related changes in InhB. We have therefore used ELISAs to measure Sertoli cell hormone levels in 3 cohorts of community-dwelling men in New Zealand. In total, 615 men were examined, 493 of which were aged 65 or older. Serum AMH and InhB levels inversely correlated with age in men older than 50 years (phormone levels between similarly aged men increased with the age of men. AMH and InhB partially correlated with each other as expected (r = 0.48, phormones varied significantly between men, with this variation increasing with age. Elderly men selected for the absence of cardiovascular disease had AMH levels similar to those of young men whereas their InhB levels did not differ from aged-matched controls. These data suggests that Sertoli cell number and function changes with age, but with the extent and nature of the changes varying between men.

  8. Genome-Wide Uniparental Disomy and Copy Number Variations in Renal Cell Carcinomas Associated with Birt-Hogg-Dubé Syndrome.

    Science.gov (United States)

    Iribe, Yasuhiro; Yao, Masahiro; Tanaka, Reiko; Kuroda, Naoto; Nagashima, Yoji; Nakatani, Yukio; Furuya, Mitsuko

    2016-02-01

    Birt-Hogg-Dubé syndrome is an inherited disorder caused by germline mutations of the folliculin gene (FLCN). The affected patients are prone to developing renal cell carcinomas (RCCs). Most mutant FLCN-associated RCCs (mFLCN-RCCs) are histologically chromophobe RCCs and hybrid oncocytic/chromophobe tumors. It is incompletely understood whether mFLCN-RCCs have different chromosomal abnormalities compared with their sporadic histological counterparts. Herein, we describe somatic mutations of FLCN and DNA-copy number abnormalities using a high-density, whole-genome, single-nucleotide polymorphism array. The histological types included chromophobe RCC (n = 12), hybrid oncocytic/chromophobe tumor (n = 5), and clear-cell RCC (n = 2). Of 19 tumors, 8 had pathological somatic mutations of FLCN. Among 11 mFLCN-RCCs investigated by single-nucleotide polymorphism array, 8 showed balanced genomic profiles, 2 had gains in chromosome 3q, and 1 had gains in chromosomes 1q and 7. All had copious numbers of loss of heterozygosity in a wide range of chromosomes. The common loss-of-heterozygosity regions were chromosomes 3p24, 8q11, 16q11, Xp22-21, Xp11, Xq11, Xq13, and Xq23. Most of the loss of heterozygosity was because of uniparental disomy. Common uniparental disomy patterns in chromophobe RCCs and hybrid oncocytic/chromophobe tumors indicated that these types were relatively similar in cytogenetic events. Two clear-cell RCCs also shared several uniparental disomy regions with chromophobe RCCs and hybrid oncocytic/chromophobe tumors. mFLCN-RCCs may have common therapeutic targets among different histological types. Copyright © 2016 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  9. Variations in daily intakes of myristic and alpha-linolenic acids in sn-2 position modify lipid profile and red blood cell membrane fluidity.

    Science.gov (United States)

    Dabadie, Henry; Motta, Claude; Peuchant, Evelyne; LeRuyet, Pascale; Mendy, François

    2006-08-01

    The present study evaluated the effects of moderate intakes of myristic acid (MA), at 1.2% and 1.8% of total energy (TE), associated with a 0.9% TE intake of alpha-linolenic acid (ALA) on lipid and fatty acid profiles and red blood cell membrane fluidity. Twenty-nine monks without dyslipidaemia were enrolled in a 1-year nutritional study in which two experimental diets were tested for 3 months each: diet 1, MA 1.2 % and ALA 0.9%; diet 2, MA 1.8% and ALA 0.9%. A control diet (MA 1.2%, ALA 0.4%) was given 3 months before diets 1 and 2. Thus, two different levels of MA (1.2%, 1.8%) and ALA (0.4%, 0.9%) were tested. Intakes of other fatty acids were at recommended levels. Samples were obtained on completion of all three diets. For fluidity analysis, the red blood cells were labelled with 16-doxylstearate and the probe incorporated the membrane where relaxation-correlation time was calculated. Diet 1 was associated with a decrease in total cholesterol, in LDL-cholesterol, in triacylglycerols and in the ratio of total to HDL-cholesterol; ALA and EPA levels were increased in both phospholipids and cholesterol esters. Diet 2 was associated with a decrease in triacylglycerols and in the ratios of total to HDL-cholesterol and of triacylglycerols to HDL-cholesterol, and with an increase in HDL-cholesterol; EPA levels were decreased in phospholipids and cholesterol esters. Red blood cell membrane fluidity was increased in both diets (Pdiet 1, mainly in the oldest subjects. Intakes of myristic acid (1.2%TE) and ALA (0.9%TE), both mainly in the sn-2 position, were associated with favourable lipid and n-3 long-chain fatty acid profiles. These beneficial effects coexisted with particularly high membrane fluidity, especially among the oldest subjects.

  10. Interclonal variations in the molecular karyotype of Trypanosoma cruzi: chromosome rearrangements in a single cell-derived clone of the G strain.

    Science.gov (United States)

    Lima, Fabio Mitsuo; Souza, Renata Torres; Santori, Fábio Rinaldo; Santos, Michele Fernandes; Cortez, Danielle Rodrigues; Barros, Roberto Moraes; Cano, Maria Isabel; Valadares, Helder Magno Silva; Macedo, Andréa Mara; Mortara, Renato Arruda; da Silveira, José Franco

    2013-01-01

    Trypanosoma cruzi comprises a pool of populations which are genetically diverse in terms of DNA content, growth and infectivity. Inter- and intra-strain karyotype heterogeneities have been reported, suggesting that chromosomal rearrangements occurred during the evolution of this parasite. Clone D11 is a single-cell-derived clone of the T. cruzi G strain selected by the minimal dilution method and by infecting Vero cells with metacyclic trypomastigotes. Here we report that the karyotype of clone D11 differs from that of the G strain in both number and size of chromosomal bands. Large chromosomal rearrangement was observed in the chromosomes carrying the tubulin loci. However, most of the chromosome length polymorphisms were of small amplitude, and the absence of one band in clone D11 in relation to its reference position in the G strain could be correlated to the presence of a novel band migrating above or below this position. Despite the presence of chromosomal polymorphism, large syntenic groups were conserved between the isolates. The appearance of new chromosomal bands in clone D11 could be explained by chromosome fusion followed by a chromosome break or interchromosomal exchange of large DNA segments. Our results also suggest that telomeric regions are involved in this process. The variant represented by clone D11 could have been induced by the stress of the cloning procedure or could, as has been suggested for Leishmania infantum, have emerged from a multiclonal, mosaic parasite population submitted to frequent DNA amplification/deletion events, leading to a 'mosaic' structure with different individuals having differently sized versions of the same chromosomes. If this is the case, the variant represented by clone D11 would be better adapted to survive the stress induced by cloning, which includes intracellular development in the mammalian cell. Karyotype polymorphism could be part of the T. cruzi arsenal for responding to environmental pressure.

  11. Dengue virus genomic variation associated with mosquito adaptation defines the pattern of viral non-coding RNAs and fitness in human cells.

    Directory of Open Access Journals (Sweden)

    Claudia V Filomatori

    2017-03-01

    Full Text Available The Flavivirus genus includes a large number of medically relevant pathogens that cycle between humans and arthropods. This host alternation imposes a selective pressure on the viral population. Here, we found that dengue virus, the most important viral human pathogen transmitted by insects, evolved a mechanism to differentially regulate the production of viral non-coding RNAs in mosquitos and humans, with a significant impact on viral fitness in each host. Flavivirus infections accumulate non-coding RNAs derived from the viral 3'UTRs (known as sfRNAs, relevant in viral pathogenesis and immune evasion. We found that dengue virus host adaptation leads to the accumulation of different species of sfRNAs in vertebrate and invertebrate cells. This process does not depend on differences in the host machinery; but it was found to be dependent on the selection of specific mutations in the viral 3'UTR. Dissecting the viral population and studying phenotypes of cloned variants, the molecular determinants for the switch in the sfRNA pattern during host change were mapped to a single RNA structure. Point mutations selected in mosquito cells were sufficient to change the pattern of sfRNAs, induce higher type I interferon responses and reduce viral fitness in human cells, explaining the rapid clearance of certain viral variants after host change. In addition, using epidemic and pre-epidemic Zika viruses, similar patterns of sfRNAs were observed in mosquito and human infected cells, but they were different from those observed during dengue virus infections, indicating that distinct selective pressures act on the 3'UTR of these closely related viruses. In summary, we present a novel mechanism by which dengue virus evolved an RNA structure that is under strong selective pressure in the two hosts, as regulator of non-coding RNA accumulation and viral fitness. This work provides new ideas about the impact of host adaptation on the variability and evolution of

  12. Studying Variation in Tunes

    NARCIS (Netherlands)

    Janssen, B.; van Kranenburg, P.

    2014-01-01

    Variation in music can be caused by different phenomena: conscious, creative manipulation of musical ideas; but also unconscious variation during music recall. It is the latter phenomenon that we wish to study: variation which occurs in oral transmission, in which a melody is taught without the help

  13. A holistic high-throughput screening framework for biofuel feedstock assessment that characterises variations in soluble sugars and cell wall composition in Sorghum bicolor.

    Science.gov (United States)

    Martin, Antony P; Palmer, William M; Byrt, Caitlin S; Furbank, Robert T; Grof, Christopher Pl

    2013-12-23

    A major hindrance to the development of high yielding biofuel feedstocks is the ability to rapidly assess large populations for fermentable sugar yields. Whilst recent advances have outlined methods for the rapid assessment of biomass saccharification efficiency, none take into account the total biomass, or the soluble sugar fraction of the plant. Here we present a holistic high-throughput methodology for assessing sweet Sorghum bicolor feedstocks at 10 days post-anthesis for total fermentable sugar yields including stalk biomass, soluble sugar concentrations, and cell wall saccharification efficiency. A mathematical method for assessing whole S. bicolor stalks using the fourth internode from the base of the plant proved to be an effective high-throughput strategy for assessing stalk biomass, soluble sugar concentrations, and cell wall composition and allowed calculation of total stalk fermentable sugars. A high-throughput method for measuring soluble sucrose, glucose, and fructose using partial least squares (PLS) modelling of juice Fourier transform infrared (FTIR) spectra was developed. The PLS prediction was shown to be highly accurate with each sugar attaining a coefficient of determination (R2) of 0.99 with a root mean squared error of prediction (RMSEP) of 11.93, 5.52, and 3.23 mM for sucrose, glucose, and fructose, respectively, which constitutes an error of total fermentable yield calculation. It unifies and simplifies previous screening methodologies to produce a holistic assessment of biofuel feedstock potential.

  14. Variations of retinal nerve fiber layer thickness and ganglion cell-inner plexiform layer thickness according to the torsion direction of optic disc.

    Science.gov (United States)

    Lee, Kang Hoon; Kim, Chan Yun; Kim, Na Rae

    2014-02-20

    To examine the relationship between the optic disc torsion and peripapillary retinal nerve fiber layer (RNFL) thickness through a comparison with the macular ganglion cell inner plexiform layer complex (GCIPL) thickness measured by Cirrus optical coherence tomography (OCT). Ninety-four eyes of 94 subjects with optic disc torsion and 114 eyes of 114 subjects without optic disc torsion were enrolled prospectively. The participants underwent fundus photography and OCT imaging in peripapillary RNFL mode and macular GCIPL mode. The participants were divided into groups according to the presence or absence of optic disc torsion. The eyes with optic disc torsion were further divided into supranasal torsion and inferotemporal torsion groups according to the direction of optic disc torsion. The mean RNFL and GCIPL thicknesses for the quadrants and subsectors were compared. The superior and inferior peak locations of the RNFL were also measured according to the torsion direction. The temporal RNFL thickness was significantly thicker in inferotemporal torsion, whereas the GCIPL thickness at all segments was unaffected. The inferotemporal optic torsion had more temporally positioned superior peak locations of the RNFL than the nontorsion and supranasal-torted optic disc. Thickening of the temporal RNFL with a temporal shift in the superior peak within the eyes with inferotemporal optic disc torsion can lead to interpretation errors. The ganglion cell analysis algorithm can assist in differentiating eyes with optic disc torsion.

  15. A cell cycle-regulated histone H3 gene of alfalfa with an atypical promoter structure.

    Science.gov (United States)

    Robertson, A J; Kapros, T; Waterborg, J H

    1997-01-01

    The control of cell cycle expression of histone genes in plants is incompletely understood. A new histone H3 gene was cloned from alfalfa (Medicago sativa) that codes for the replication-dependent histone H3.1 variant protein. Despite lacking all promoter sequence motifs that have been associated with cell cycle-dependent histone gene expression in plants, northern analysis of synchronized cells clearly linked gene expression to DNA replication. TTAATNA was recognized as a new sequence element in the 3' untranslated regions of this and all other cell cycle-dependent histone H3 genes of dicotyledonous plants. It is not found in the replication-independent histone H3 genes.

  16. Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information

    DEFF Research Database (Denmark)

    Edsgärd, D; Scheel, M; Hansen, N T

    2011-01-01

    -associated genes among loci targeted by CNVs. The top-ranked candidate, RLN1, encoding a Relaxin-H1 peptide, although only detected in one of the families, was selected for further investigations. Validation of the CNV at the RLN1 locus was performed as an association study using qPCR with 106 sporadic testicular...... GCT patients and 200 healthy controls. Observed CNV frequencies of 1.9% among cases and 1.5% amongst controls were not significantly different and this was further confirmed by CNV data extracted from a genome-wide analysis of 189 cases and 380 controls, where similar frequencies of 2.2% were observed....... Collectively, the findings show that a heterozygous loss at the RLN1 locus is not a genetic factor mediating high population-wide risk for testicular germ cell tumour, but do not exclude a contribution of this aberration in some cases of cancer. The preliminary expression data suggest a possible role...

  17. Safe-by-Design CuO Nanoparticles via Fe-Doping, Cu-O Bond Length Variation, and Biological Assessment in Cells and Zebrafish Embryos.

    Science.gov (United States)

    Naatz, Hendrik; Lin, Sijie; Li, Ruibin; Jiang, Wen; Ji, Zhaoxia; Chang, Chong Hyun; Köser, Jan; Thöming, Jorg; Xia, Tian; Nel, Andre E; Mädler, Lutz; Pokhrel, Suman

    2017-01-24

    The safe implementation of nanotechnology requires nanomaterial hazard assessment in accordance with the material physicochemical properties that trigger the injury response at the nano/bio interface. Since CuO nanoparticles (NPs) are widely used industrially and their dissolution properties play a major role in hazard potential, we hypothesized that tighter bonding of Cu to Fe by particle doping could constitute a safer-by-design approach through decreased dissolution. Accordingly, we designed a combinatorial library in which CuO was doped with 1-10% Fe in a flame spray pyrolysis reactor. The morphology and structural properties were determined by XRD, BET, Raman spectroscopy, HRTEM, EFTEM, and EELS, which demonstrated a significant reduction in the apical Cu-O bond length while simultaneously increasing the planar bond length (Jahn-Teller distortion). Hazard screening was performed in tissue culture cell lines and zebrafish embryos to discern the change in the hazardous effects of doped vs nondoped particles. This demonstrated that with increased levels of doping there was a progressive decrease in cytotoxicity in BEAS-2B and THP-1 cells, as well as an incremental decrease in the rate of hatching interference in zebrafish embryos. The dissolution profiles were determined and the surface reactions taking place in Holtfreter's solution were validated using cyclic voltammetry measurements to demonstrate that the Cu + /Cu 2+ and Fe 2+ /Fe 3+ redox species play a major role in the dissolution process of pure and Fe-doped CuO. Altogether, a safe-by-design strategy was implemented for the toxic CuO particles via Fe doping and has been demonstrated for their safe use in the environment.

  18. Variação da contagem de células somáticas em vacas leiteiras de acordo com patógenos da mastite Somatic cell counts variation in dairy cows according to mastitis pathogens

    Directory of Open Access Journals (Sweden)

    G.N. Souza

    2009-10-01

    Full Text Available Avaliou-se o efeito de patógenos da mastite sobre a contagem de células somáticas (CCS em leite. Foram coletadas 3.987 amostras de leite de 2.657 animais oriundos de 24 rebanhos leiteiros localizados nos estados do Rio de Janeiro e Minas Gerais. As amostras de leite foram usadas para CCS e identificação de patógenos da mastite. Estatísticas descritivas, teste T para amostras independentes e modelo linear generalizado foram usados para análise dos dados. O modelo linear generalizado identificou os efeitos de rebanho, animal dentro de rebanho, ordem de parto, estação do ano e infecção intramamária causada por Streptococcus agalactiae e Streptococcus spp. que não S. agalactiae como significativos na variação da CCS. O efeito de animal dentro de rebanho foi maior que o efeito de rebanho. S. agalactiae foi o patógeno responsável pelo maior aumento da CCS em vacas e apresentou em média 1.520.000 células/mL. Foi observado efeito específico dos patógenos na variação da CCS.The influence of mastitis pathogens on variation of milk somatic cell count (SCC was evaluated. Three thousand nine hundred eighty-seven milk samples were colected from 2,657 dairy cows in 24 herds located in the states of Minas Gerais and Rio de Janeiro. The milk samples were used to SCC and identification of mastitis pathogens. Descriptive statistics, T test for independent samples, and generalized linear model were used to data analysis. The generalized linear model identified the effects of herd, animal within herd, parity, year season, intramammary infection, and infection caused by Streptococcus agalactiae and Streptococcus spp. except S. agalactiae as significant on SCC variation. The effect of animal within herd was higher than the effect of herd. S. agalactiae was the pathogen responsible for higher SCC increasing and presented the average of 1,520,000 cells/mL. The specific effect on SCC variation was observed in the study.

  19. Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information

    DEFF Research Database (Denmark)

    Edsgard, Stefan Daniel; Scheel, M.; Hansen, Niclas Tue

    2011-01-01

    ‐associated genes among loci targeted by CNVs. The top‐ranked candidate, RLN1, encoding a Relaxin‐H1 peptide, although only detected in one of the families, was selected for further investigations. Validation of the CNV at the RLN1 locus was performed as an association study using qPCR with 106 sporadic testicular...... GCT patients and 200 healthy controls. Observed CNV frequencies of 1.9% among cases and 1.5% amongst controls were not significantly different and this was further confirmed by CNV data extracted from a genome‐wide analysis of 189 cases and 380 controls, where similar frequencies of 2.2% were observed...... and spermatids. Collectively, the findings show that a heterozygous loss at the RLN1 locus is not a genetic factor mediating high population‐wide risk for testicular germ cell tumour, but do not exclude a contribution of this aberration in some cases of cancer. The preliminary expression data suggest a possible...

  20. Single nucleotide variation in the TP53 3' untranslated region in diffuse large B-cell lymphoma treated with rituximab-CHOP

    DEFF Research Database (Denmark)

    Li, Yong; Gordon, Michael W; Xu-Monette, Zijun Y

    2013-01-01

    We identified multiple single nucleotide variants (SNVs) in the TP53 3' untranslated region (3'UTR) in tumor specimens from 244 patients with diffuse large B-cell lymphoma (DLBCL). Patients carrying a wild-type TP53 coding sequence (CDS) and 1 or more 3'UTR SNVs had a better 5-year survival rate...... as a validation set. Altogether, we identified 187 novel SNVs; 36 occurred at least twice. Most of the newly identified 3'UTR SNVs were located at sites that are complementary to seed sequences of microRNAs (miRNAs) that are predicted or experimentally known to target TP53. Three SNVs disrupt the seed match...... between miR-125b and the TP53 3'UTR, thereby impeding suppression of p53 by this miRNA. In addition, a germline SNV (rs78378222) located in the TP53 polyadenylation signal resulted in downregulation of both p53 messenger RNA and protein levels and reduction of cellular apoptosis. This study is the first...

  1. Variation in external representations as part of the classroom lecture:An investigation of virtual cell animations in introductory photosynthesis instruction.

    Science.gov (United States)

    Goff, Eric E; Reindl, Katie M; Johnson, Christina; McClean, Phillip; Offerdahl, Erika G; Schroeder, Noah L; White, Alan R

    2017-05-01

    The use of external representations (ERs) to introduce concepts in undergraduate biology has become increasingly common. Two of the most prevalent are static images and dynamic animations. While previous studies comparing static images and dynamic animations have resulted in somewhat conflicting findings in regards to learning outcomes, the benefits of each have been shown individually. Using ERs developed by the Virtual Cell Animation project, we aim to further investigate student learning using different ERs as part of an introductory biology lecture. We focus our study on the topic of photosynthesis as reports have noted that students struggle with a number of basic photosynthesis concepts. Students (n = 167) in ten sections of introductory biology laboratory were introduced to photosynthesis concepts by instructional lectures differing only in the format of the embedded ERs. Normalized gain scores were calculated, showing that students who learned with dynamic animations outperformed students who learned from static images on the posttest. The results of this study provide possible instructional guidelines for those delivering photosynthesis instruction in the introductory biology classroom. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):226-234, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

  2. Variation in Chst8 gene expression level affects PrPC to PrPSc conversion efficiency in prion-infected Mov cells.

    Science.gov (United States)

    Martin, Renaud; Chantepie, Sandrine; Chapuis, Jérôme; Le-Duc, Aurélien; Maftah, Abderrahman; Papy-Garcia, Dulcé; Laude, Hubert; Petit, Jean-Michel; Gallet, Paul-François

    2011-10-28

    The conversion of the endogenous cellular prion protein to an abnormally folded isoform is a hallmark of transmissible spongiform encephalopathies. It occurs when a misfolded prion protein contacts the cellular PrP. Among the molecular partners suggested to be involved in the misfolding process, the glycosaminoglycans seem to be good candidates. The present study was aimed to examine a possible link between PrP conversion efficiency and transcript level of Chst8 gene that encodes the carbohydrate N-acetylgalactosamine 4-O-sulfotransferase 8. Mov cells expressing ovine PrP were transfected with shRNA directed against Chst8 transcripts. Resulting clones were characterized for their Chst8 and Prnp transcript levels, and for their content in sulfated glycosaminoglycans, more particularly sulfated chondroitins. Unexpectedly, the decreased amount of Chst8 transcript induced an increase of the chondroitin sulfate percentage among total GAGs, with an increased amount of 4-O-sulfation of GalNAc residues. Upon to infection by a sheep prion, a slight amount of PrP(Sc) was observed, which rapidly disappeared upon subpassaging. Together, these findings indicate that the Chst8 transcript level affects the glycosaminoglycan environment of the cellular prion protein, and as a consequence its ability for conversion into PrP(Sc). Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Androgen receptor functional analyses by high throughput imaging: determination of ligand, cell cycle, and mutation-specific effects.

    Directory of Open Access Journals (Sweden)

    Adam T Szafran

    Full Text Available Understanding how androgen receptor (AR function is modulated by exposure to steroids, growth factors or small molecules can have important mechanistic implications for AR-related disease therapies (e.g., prostate cancer, androgen insensitivity syndrome, AIS, and in the analysis of environmental endocrine disruptors.We report the development of a high throughput (HT image-based assay that quantifies AR subcellular and subnuclear distribution, and transcriptional reporter gene activity on a cell-by-cell basis. Furthermore, simultaneous analysis of DNA content allowed determination of cell cycle position and permitted the analysis of cell cycle dependent changes in AR function in unsynchronized cell populations. Assay quality for EC50 coefficients of variation were 5-24%, with Z' values reaching 0.91. This was achieved by the selective analysis of cells expressing physiological levels of AR, important because minor over-expression resulted in elevated nuclear speckling and decreased transcriptional reporter gene activity. A small screen of AR-binding ligands, including known agonists, antagonists, and endocrine disruptors, demonstrated that nuclear translocation and nuclear "speckling" were linked with transcriptional output, and specific ligands were noted to differentially affect measurements for wild type versus mutant AR, suggesting differing mechanisms of action. HT imaging of patient-derived AIS mutations demonstrated a proof-of-principle personalized medicine approach to rapidly identify ligands capable of restoring multiple AR functions.HT imaging-based multiplex screening will provide a rapid, systems-level analysis of compounds/RNAi that may differentially affect wild type AR or clinically relevant AR mutations.

  4. A combinatorial variation in surface chemistry and pore size of three-dimensional porous poly(ε-caprolactone) scaffolds modulates the behaviors of mesenchymal stem cells

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Yingdi; Tan, Ke; Zhou, Yan; Ye, Zhaoyang, E-mail: zhaoyangye@ecust.edu.cn; Tan, Wen-Song

    2016-02-01

    Biomaterial properties play significant roles in controlling cellular behaviors. The objective of the present study was to investigate how pore size and surface chemistry of three-dimensional (3D) porous scaffolds regulate the fate of mesenchymal stem cells (MSCs) in vitro in combination. First, on poly(ε-caprolactone) (PCL) films, the hydrolytic treatment was found to stimulate the adhesion, spreading and proliferation of human MSCs (hMSCs) in comparison with pristine films, while the aminolysis showed mixed effects. Then, 3D porous PCL scaffolds with varying pore sizes (100–200 μm, 200–300 μm and 300–450 μm) were fabricated and subjected to either hydrolysis or aminolysis. It was found that a pore size of 200–300 μm with hydrolysis in 3D scaffolds was the most favorable condition for growth of hMSCs. Importantly, while a pore size of 200–300 μm with hydrolysis for 1 h supported the best osteogenic differentiation of hMSCs, the chondrogenic differentiation was greatest in scaffolds with a pore size of 300–450 μm and treated with aminolysis for 1 h. Taken together, these results suggest that surface chemistry and pore size of 3D porous scaffolds may potentially have a synergistic impact on the behaviors of MSCs. - Highlights: • Surface chemistry of poly(ε-caprolactone) films actively modulates MSC behaviors. • Varying surface chemistry and pore size in combination is enabled in 3D scaffolds. • Surface chemistry and pore size potentially dictate MSC fates in synergy.

  5. Variations in the MHC Region Confer Risk to Esophageal Squamous Cell Carcinoma on the Subjects from High-Incidence Area in Northern China

    Science.gov (United States)

    Pan, Ying; Zhao, Xue-Ke; Jin, Yan; Song, Xin; Li, Bei; Han, Xue-Na; Tang, Sa; Li, Yan; Yuan, Guo; Chen, Li-Sha; Liu, Ya-Li; Hu, Yan-Long; Li, Xiu-Min; Ren, Jing-Li; Wang, Li-Dong

    2014-01-01

    Background The human major histocompatibility complex (MHC) is the most important region in vertebrate genome, and is crucial in innate immunity. Recent studies have demonstrated the possible role of polymorphisms in the MHC region to high risk for esophageal squamous cell carcinoma (ESCC). Our previous genome-wide association study (GWAS) has indicated that the MHC region may confer important risk loci for ESCC, but without further fine mapping. The aim of this study is to further identify the risk loci in the MHC region for ESCC in Chinese population. Methods Conditional logistic regression analysis (CLRA) was performed on 24 single nucleotide polymorphisms (SNPs) within the MHC region, which were obtained from the genetically matched 937 cases and 692 controls of Chinese Han population. The identified promising SNPs were further correlated with clinical and clinicopathology characteristics. Immunohistochemistry was performed to explore the protein expression pattern of the related genes in ESCC and neighboring normal tissues. Results Of the 24 promising SNPs analyzed, we identified three independent SNPs in the MHC region associated with ESCC: rs35399661 (P = 6.07E-06, OR = 1.71, 95%CI = 1.36–2.17), rs3763338 (P = 1.62E-05, OR = 0.63, 95%CI = 0.50–0.78) and rs2844695 (P = 7.60E-05, OR = 0.74, 95%CI = 0.64–0.86). These three SNPs were located at the genes of HLA-DQA1, TRIM27, and DPCR1, respectively. Further analyses showed that rs2844695 was preferentially associated with younger ESCC cases (P = 0.009). The positive immunostaining rates both for HLA-DQA1 and TRIM27 were much higher in ESCC tissues than in neighboring normal tissues (69.4% vs. 26.8% for HLA-DQA1 and 77.6% vs. 47.8% for TRIM27, PHLA-DQA1 is correlated significantly with age (P = 0.001) and family history (P<0.001). Conclusion This study for the first time provides evidence that multiple genetic factors within the MHC region confer risk to ESCC on

  6. Variations in the MHC region confer risk to esophageal squamous cell carcinoma on the subjects from high-incidence area in northern China.

    Directory of Open Access Journals (Sweden)

    Fang-Fang Shen

    Full Text Available BACKGROUND: The human major histocompatibility complex (MHC is the most important region in vertebrate genome, and is crucial in innate immunity. Recent studies have demonstrated the possible role of polymorphisms in the MHC region to high risk for esophageal squamous cell carcinoma (ESCC. Our previous genome-wide association study (GWAS has indicated that the MHC region may confer important risk loci for ESCC, but without further fine mapping. The aim of this study is to further identify the risk loci in the MHC region for ESCC in Chinese population. METHODS: Conditional logistic regression analysis (CLRA was performed on 24 single nucleotide polymorphisms (SNPs within the MHC region, which were obtained from the genetically matched 937 cases and 692 controls of Chinese Han population. The identified promising SNPs were further correlated with clinical and clinicopathology characteristics. Immunohistochemistry was performed to explore the protein expression pattern of the related genes in ESCC and neighboring normal tissues. RESULTS: Of the 24 promising SNPs analyzed, we identified three independent SNPs in the MHC region associated with ESCC: rs35399661 (P = 6.07E-06, OR = 1.71, 95%CI = 1.36-2.17, rs3763338 (P = 1.62E-05, OR = 0.63, 95%CI = 0.50-0.78 and rs2844695 (P = 7.60E-05, OR = 0.74, 95%CI = 0.64-0.86. These three SNPs were located at the genes of HLA-DQA1, TRIM27, and DPCR1, respectively. Further analyses showed that rs2844695 was preferentially associated with younger ESCC cases (P = 0.009. The positive immunostaining rates both for HLA-DQA1 and TRIM27 were much higher in ESCC tissues than in neighboring normal tissues (69.4% vs. 26.8% for HLA-DQA1 and 77.6% vs. 47.8% for TRIM27, P<0.001. Furthermore, the overexpression of HLA-DQA1 is correlated significantly with age (P = 0.001 and family history (P<0.001. CONCLUSION: This study for the first time provides evidence that multiple genetic

  7. Calculus of variations

    CERN Document Server

    Gelfand, I M

    2000-01-01

    Based on a series of lectures given by I. M. Gelfand at Moscow State University, this book actually goes considerably beyond the material presented in the lectures. The aim is to give a treatment of the elements of the calculus of variations in a form both easily understandable and sufficiently modern. Considerable attention is devoted to physical applications of variational methods, e.g., canonical equations, variational principles of mechanics, and conservation laws.The reader who merely wishes to become familiar with the most basic concepts and methods of the calculus of variations need on

  8. Longitudinal, seasonal and solar cycle variation in lunar tide influence on the equatorial electrojet

    Energy Technology Data Exchange (ETDEWEB)

    Yizengaw, Endawoke [Boston College, Chestnut Hill, MA (United States). Inst. for Scientific Research; Carter, Brett A. [RMIT Univ., Melbourne, VIC (Australia). SPACE Research Centre

    2017-07-01

    It has been well documented that the lunar tidal waves can modulate the ionospheric electrodynamics and create a visible influence on the equatorial electrojet (EEJ). The lunar tide influence gets intensified around noon, primarily during new and full Moon periods. However, the longitudinal, seasonal and solar cycle variability in the lunar tide influence on ionospheric current systems is not well understood yet. In order to investigate this, 17 years (1998-2014) of extensive magnetometer observations at four longitudinal sectors (western American, western and eastern African, and Asian) have been analyzed. All observations performed during magnetically active periods (K{sub p}>3) have been excluded for this study to eliminate storm contributions to the geomagnetic field variation at the geomagnetic equator. This study's quantitative analysis revealed significant longitudinal, seasonal and solar cycle dependence of the lunar tide influence on the equatorial electrojet.

  9. Longitudinal, seasonal and solar cycle variation in lunar tide influence on the equatorial electrojet

    International Nuclear Information System (INIS)

    Yizengaw, Endawoke; Carter, Brett A.

    2017-01-01

    It has been well documented that the lunar tidal waves can modulate the ionospheric electrodynamics and create a visible influence on the equatorial electrojet (EEJ). The lunar tide influence gets intensified around noon, primarily during new and full Moon periods. However, the longitudinal, seasonal and solar cycle variability in the lunar tide influence on ionospheric current systems is not well understood yet. In order to investigate this, 17 years (1998-2014) of extensive magnetometer observations at four longitudinal sectors (western American, western and eastern African, and Asian) have been analyzed. All observations performed during magnetically active periods (K p >3) have been excluded for this study to eliminate storm contributions to the geomagnetic field variation at the geomagnetic equator. This study's quantitative analysis revealed significant longitudinal, seasonal and solar cycle dependence of the lunar tide influence on the equatorial electrojet.

  10. Longitudinal, seasonal and solar cycle variation in lunar tide influence on the equatorial electrojet

    Directory of Open Access Journals (Sweden)

    E. Yizengaw

    2017-04-01

    Full Text Available It has been well documented that the lunar tidal waves can modulate the ionospheric electrodynamics and create a visible influence on the equatorial electrojet (EEJ. The lunar tide influence gets intensified around noon, primarily during new and full Moon periods. However, the longitudinal, seasonal and solar cycle variability in the lunar tide influence on ionospheric current systems is not well understood yet. In order to investigate this, 17 years (1998–2014 of extensive magnetometer observations at four longitudinal sectors (western American, western and eastern African, and Asian have been analyzed. All observations performed during magnetically active periods (Kp>3 have been excluded for this study to eliminate storm contributions to the geomagnetic field variation at the geomagnetic equator. This study's quantitative analysis revealed significant longitudinal, seasonal and solar cycle dependence of the lunar tide influence on the equatorial electrojet.

  11. The Variational Fair Autoencoder

    NARCIS (Netherlands)

    Louizos, C.; Swersky, K.; Li, Y.; Welling, M.; Zemel, R.

    2016-01-01

    We investigate the problem of learning representations that are invariant to certain nuisance or sensitive factors of variation in the data while retaining as much of the remaining information as possible. Our model is based on a variational autoencoding architecture with priors that encourage

  12. The Effects of Predator Evolution and Genetic Variation on Predator-Prey Population-Level Dynamics.

    Science.gov (United States)

    Cortez, Michael H; Patel, Swati

    2017-07-01

    This paper explores how predator evolution and the magnitude of predator genetic variation alter the population-level dynamics of predator-prey systems. We do this by analyzing a general eco-evolutionary predator-prey model using four methods: Method 1 identifies how eco-evolutionary feedbacks alter system stability in the fast and slow evolution limits; Method 2 identifies how the amount of standing predator genetic variation alters system stability; Method 3 identifies how the phase lags in predator-prey cycles depend on the amount of genetic variation; and Method 4 determines conditions for different cycle shapes in the fast and slow evolution limits using geometric singular perturbation theory. With these four methods, we identify the conditions under which predator evolution alters system stability and shapes of predator-prey cycles, and how those effect depend on the amount of genetic variation in the predator population. We discuss the advantages and disadvantages of each method and the relations between the four methods. This work shows how the four methods can be used in tandem to make general predictions about eco-evolutionary dynamics and feedbacks.

  13. Ensembl variation resources

    Directory of Open Access Journals (Sweden)

    Marin-Garcia Pablo

    2010-05-01

    Full Text Available Abstract Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.

  14. Variational Transition State Theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, Donald G. [Univ. of Minnesota, Minneapolis, MN (United States)

    2016-09-29

    This is the final report on a project involving the development and applications of variational transition state theory. This project involved the development of variational transition state theory for gas-phase reactions, including optimized multidimensional tunneling contributions and the application of this theory to gas-phase reactions with a special emphasis on developing reaction rate theory in directions that are important for applications to combustion. The development of variational transition state theory with optimized multidimensional tunneling as a useful computational tool for combustion kinetics involved eight objectives.

  15. Variational principles in physics

    CERN Document Server

    Basdevant, Jean-Louis

    2007-01-01

    Optimization under constraints is an essential part of everyday life. Indeed, we routinely solve problems by striking a balance between contradictory interests, individual desires and material contingencies. This notion of equilibrium was dear to thinkers of the enlightenment, as illustrated by Montesquieu’s famous formulation: "In all magistracies, the greatness of the power must be compensated by the brevity of the duration." Astonishingly, natural laws are guided by a similar principle. Variational principles have proven to be surprisingly fertile. For example, Fermat used variational methods to demonstrate that light follows the fastest route from one point to another, an idea which came to be known as Fermat’s principle, a cornerstone of geometrical optics. Variational Principles in Physics explains variational principles and charts their use throughout modern physics. The heart of the book is devoted to the analytical mechanics of Lagrange and Hamilton, the basic tools of any physicist. Prof. Basdev...

  16. Variational Monte Carlo Technique

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 8. Variational Monte Carlo Technique: Ground State Energies of Quantum Mechanical Systems. Sukanta Deb. General Article Volume 19 Issue 8 August 2014 pp 713-739 ...

  17. Generalized quasi variational inequalities

    Energy Technology Data Exchange (ETDEWEB)

    Noor, M.A. [King Saud Univ., Riyadh (Saudi Arabia)

    1996-12-31

    In this paper, we establish the equivalence between the generalized quasi variational inequalities and the generalized implicit Wiener-Hopf equations using essentially the projection technique. This equivalence is used to suggest and analyze a number of new iterative algorithms for solving generalized quasi variational inequalities and the related complementarity problems. The convergence criteria is also considered. The results proved in this paper represent a significant improvement and refinement of the previously known results.

  18. Germanic Verb Particle Variation

    DEFF Research Database (Denmark)

    Vikner, Sten

    2017-01-01

    This paper has two closely related goals. The more "global" one is to present an overview of the variation conceming verb particles across the Germanic languages (see e.g. den Dikken 1995; Haiden 2005; Mclntyre 2007 and many others), and the more "local" one is to use some of this variation data...... to argue for Yiddish being an SOV-language like German and Dutch rather than an SVO-language like English and the Scandinavian languages....

  19. Variational Bayesian Filtering

    Czech Academy of Sciences Publication Activity Database

    Šmídl, Václav; Quinn, A.

    2008-01-01

    Roč. 56, č. 10 (2008), s. 5020-5030 ISSN 1053-587X R&D Projects: GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : Bayesian filtering * particle filtering * Variational Bayes Subject RIV: BC - Control Systems Theory Impact factor: 2.335, year: 2008 http://library.utia.cas.cz/separaty/2008/AS/smidl-variational bayesian filtering.pdf

  20. Variational Neural Machine Translation

    OpenAIRE

    Zhang, Biao; Xiong, Deyi; Su, Jinsong; Duan, Hong; Zhang, Min

    2016-01-01

    Models of neural machine translation are often from a discriminative family of encoderdecoders that learn a conditional distribution of a target sentence given a source sentence. In this paper, we propose a variational model to learn this conditional distribution for neural machine translation: a variational encoderdecoder model that can be trained end-to-end. Different from the vanilla encoder-decoder model that generates target translations from hidden representations of source sentences al...

  1. Induction of cell death by chemotherapeutic methylating agents

    International Nuclear Information System (INIS)

    Quiros Barrantes, Steve

    2012-01-01

    The mechanism of cell death induced by O 6 MeG has been investigated and inhibition of homologous recombination as a strategy for sensitization of tumor cells against methylating agents S N 1. Dependence of the cell cycle was determined toxic responses triggered by O''6 MeG and evaluated by proliferation assays if apoptotic cells have originated exclusively from the second post-treatment cycle. Dependence of O''6 MeG was found at DSB formation. The activation of the control points of the cell cycle and induction of apoptosis is generated during the second cell cycle. Additionally, a portion of the cells has been determined that triggers apoptosis in subsequent generations in the second cell cycle. Inhibition of homologous recombination has been a reasonable strategy to increase S N 1 alkylating agent effectiveness. Evidence has been provided in NHEJ dependent inhibition of DNA-PK that not significantly sensitizes the glioblastoma cells against temozolomide [es

  2. Ladder Variational Autoencoder

    DEFF Research Database (Denmark)

    Sønderby, Casper Kaae; Raiko, Tapani; Maaløe, Lars

    2016-01-01

    Variational autoencoders are powerful models for unsupervised learning. However deep models with several layers of dependent stochastic variables are difficult to train which limits the improvements obtained using these highly expressive models. We propose a new inference model, the Ladder...... Variational Autoencoder, that recursively corrects the generative distribution by a data dependent approximate likelihood in a process resembling the recently proposed Ladder Network. We show that this model provides state of the art predictive log-likelihood and tighter log-likelihood lower bound compared...... to the purely bottom-up inference in layered Variational Autoencoders and other generative models. We provide a detailed analysis of the learned hierarchical latent representation and show that our new inference model is qualitatively different and utilizes a deeper more distributed hierarchy of latent...

  3. Ladder variational autoencoders

    DEFF Research Database (Denmark)

    Sønderby, Casper Kaae; Raiko, Tapani; Maaløe, Lars

    2016-01-01

    Variational autoencoders are powerful models for unsupervised learning. However deep models with several layers of dependent stochastic variables are difficult to train which limits the improvements obtained using these highly expressive models. We propose a new inference model, the Ladder...... Variational Autoencoder, that recursively corrects the generative distribution by a data dependent approximate likelihood in a process resembling the recently proposed Ladder Network. We show that this model provides state of the art predictive log-likelihood and tighter log-likelihood lower bound compared...... to the purely bottom-up inference in layered Variational Autoencoders and other generative models. We provide a detailed analysis of the learned hierarchical latent representation and show that our new inference model is qualitatively different and utilizes a deeper more distributed hierarchy of latent...

  4. Simulation of Cycle-to-Cycle Variation in Dual-Fuel Engines

    KAUST Repository

    Jaasim, Mohammed

    2017-03-13

    Standard practices of internal combustion (IC) engine experiments are to conduct the measurements of quantities averaged over a large number of cycles. Depending on the operating conditions, the cycle-to-cycle variation (CCV) of quantities, such as the indicated mean effective pressure (IMEP) are observed at different levels. Accurate prediction of CCV in IC engines is an important but challenging task. Computational fluid dynamics (CFD) simulations using high performance computing (HPC) can be used effectively to visualize such 3D spatial distributions. In the present study, a dual fuel large engine is considered, with natural gas injected into the manifold accompanied with direct injection of diesel pilot fuel to trigger ignition. Multiple engine cycles in 3D are simulated in series as in the experiments to investigate the potential of HPC based high fidelity simulations to accurately capture the cycle to cycle variation in dual fuel engines. Open cycle simulations are conducted to predict the combined effect of the stratification of fuel-air mixture, temperature and turbulence on the CCV of pressure. The predicted coefficient of variation (COV) of pressure compared to the results from closed cycle simulations and the experiments.

  5. Long-term variations and trends in the polar E-region

    Science.gov (United States)

    Bjoland, L. M.; Ogawa, Y.; Hall, C.; Rietveld, M.; Løvhaug, U. P.; La Hoz, C.; Miyaoka, H.

    2017-10-01

    As the EISCAT UHF radar system in Northern Scandinavia started its operations in the early 1980s, the collected data cover about three solar cycles. These long time-series provide us the opportunity to study long-term variations and trends of ionospheric parameters in the high latitude region. In the present study we have used the EISCAT Tromsø UHF data to investigate variations of the Hall conductivity and ion temperatures in the E-region around noon. Both the ion temperature and the peak altitude of the Hall conductivity are confirmed to depend strongly on solar zenith angle. However, the dependence on solar activity seems to be weak. In order to search for trends in these parameters, the ion temperature and peak altitude of the Hall conductivity data were adjusted for their seasonal and solar cycle dependence. A very weak descent (∼0.2 km/ decade) was seen in the peak altitude of the Hall conductivity. The ion temperature at 110 km shows a cooling trend (∼10 K/ decade). However, other parameters than solar zenith angle and solar activity seem to affect the ion temperature at this altitude, and a better understanding of these parameters is necessary to derive a conclusive trend. In this paper, we discuss what may cause the characteristics of the variations in the electric conductivities and ion temperatures in the high latitude region.

  6. Splines and variational methods

    CERN Document Server

    Prenter, P M

    2008-01-01

    One of the clearest available introductions to variational methods, this text requires only a minimal background in calculus and linear algebra. Its self-contained treatment explains the application of theoretic notions to the kinds of physical problems that engineers regularly encounter. The text's first half concerns approximation theoretic notions, exploring the theory and computation of one- and two-dimensional polynomial and other spline functions. Later chapters examine variational methods in the solution of operator equations, focusing on boundary value problems in one and two dimension

  7. Fluency Variation in Adolescents

    Science.gov (United States)

    De Andrade, Claudia Regina Furquim; Martins, Vanessa De Oliveira

    2007-01-01

    The Speech Fluency Profile of fluent adolescent speakers of Brazilian Portuguese, were examined with respect to gender and neurolinguistic variations. Speech samples of 130 male and female adolescents, aged between 12;0 and 17;11 years were gathered. They were analysed according to type of speech disruption; speech rate; and frequency of speech…

  8. Generalized Variational Inequalities

    Czech Academy of Sciences Publication Activity Database

    Krejčí, Pavel; Laurencot, P.

    2002-01-01

    Roč. 9, č. 1 (2002), s. 159-183 ISSN 0944-6532 Institutional research plan: CEZ:AV0Z1019905 Keywords : hysteresis%evolution variational inequality%Young integral Subject RIV: BA - General Mathematics Impact factor: 0.145, year: 2002

  9. The variational spiked oscillator

    International Nuclear Information System (INIS)

    Aguilera-Navarro, V.C.; Ullah, N.

    1992-08-01

    A variational analysis of the spiked harmonic oscillator Hamiltonian -d 2 / d x 2 + x 2 + δ/ x 5/2 , δ > 0, is reported in this work. A trial function satisfying Dirichlet boundary conditions is suggested. The results are excellent for a large range of values of the coupling parameter. (author)

  10. A variational approach

    Indian Academy of Sciences (India)

    We study the optical switching of the two-dimensional nonlinear coupler in a doped photopolymer. The coupled ... Optical switching; variational approach; Jacobi's elliptic function; surface plasmon resonance ..... [4] G P Agrawal, Applications of nonlinear fiber optics (Academic Press, New York,. 2006). [5] R G Hunsperger ...

  11. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José

    2013-01-01

    This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.

  12. Variation in decision making

    NARCIS (Netherlands)

    Dall, Sasha R. X.; Gosling, Samuel; Gordon D.A., Brown,; Dingemanse, Niels; Ido, Erev,; Martin, Kocher,; Laura, Schulz,; Todd, Peter M; Weissing, Franz; Wolf, Max; Hammerstein, Peter; Stevens, Jeffrey R.

    2012-01-01

    Variation in how organisms allocate their behavior over their lifetimes is key to determining Darwinian fitness., and thus the evolution of human and nonhuman decision making. This chapter explores how decision making varies across biologically and societally significant scales and what role such

  13. On exterior variational calculus

    International Nuclear Information System (INIS)

    Aldrovandi, R.; Kraenkel, R.A.

    1987-01-01

    Exterior variational calculus is introduced through examples in field theory. It provides a very simple technique to decide on the existence of Lagrangians for given equations of motions and, in the case, to find them. Only local aspects are discussed but the analogy to exterior calculus on finite dimensional manifolds is complete, strongly suggesting its suitability to the study of topological aspects. (Author) [pt

  14. Intronic variation at the

    NARCIS (Netherlands)

    Trimbos, K.B.; Kentie, R.; van der Velde, M.; Hooijmeijer, J.C.E.W.; Poley, C.; Musters, C.J.M.; de Snoo, G.R.; Piersma, T.

    2013-01-01

    Recently, Schroeder etal. (2010, Ibis 152: 368-377) suggested that intronic variation in the CHD1-Z gene of Black-tailed Godwits breeding in southwest Friesland, The Netherlands, correlated with fitness components. Here we re-examine this surprising result using an expanded dataset (2088 birds

  15. Seasonal Variation in Epidemiology

    Science.gov (United States)

    Marrero, Osvaldo

    2013-01-01

    Seasonality analyses are important in medical research. If the incidence of a disease shows a seasonal pattern, then an environmental factor must be considered in its etiology. We discuss a method for the simultaneous analysis of seasonal variation in multiple groups. The nuts and bolts are explained using simple trigonometry, an elementary…

  16. Variational transition state theory

    International Nuclear Information System (INIS)

    Truhlar, D.G.

    1986-01-01

    This project is concerned with the development and applications of generalized transition state theory and multidimensional tunneling approximations to chemical reaction rates. They have developed and implemented several practical versions of variational transition state theory (VTST), namely canonical variational theory (CVT), improved canonical variational theory (ICVT), and microcanonical variational theory (μVT). They have also developed and implemented several accurate multidimensional semiclassical tunneling approximations, the most accurate of which are the small-curvature semiclassical adiabatic (SCSA), large-curvature version-3 (LC3), and least-action (LA) approximations. They have applied the methods to thermal rate constants, using transmission coefficients based on ground-state tunneling, and they have also presented and applied adiabatic and diabatic extensions to calculated rate constants for vibrationally excited reactants. Their general goal is to develop accurate methods for calculating chemical reaction rate constants that remain practical even for reasonably complicated molecules. The approximations mentioned above yield rate constants for systems whose potential energy surface is known or assumed. Thus a second, equally important aspect of their work is the determination or modeling, semi-empirically and/or from electronic structure calculations, of potential energy surfaces

  17. Measuring Linguistic Variation Commensurably

    NARCIS (Netherlands)

    Wieling, M.; Nerbonne, J.

    2011-01-01

    The primary data on pronunciation variation — e.g., dialect atlas data — is often recorded incommensurably, i.e. in different ways in different atlases, and even in different ways within the same atlas when teams of fieldworkers and transcribers are involved. In particular these data collections

  18. Variational transition state theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, D.G. [Univ. of Minnesota, Minneapolis (United States)

    1993-12-01

    This research program involves the development of variational transition state theory (VTST) and semiclassical tunneling methods for the calculation of gas-phase reaction rates and selected applications. The applications are selected for their fundamental interest and/or their relevance to combustion.

  19. Diurnal variations of Titan

    Science.gov (United States)

    Cui, J.; Galand, M.; Yelle, R. V.; Vuitton, V.; Wahlund, J.-E.; Lavvas, P. P.; Mueller-Wodarg, I. C. F.; Kasprzak, W. T.; Waite, J. H.

    2009-04-01

    We present our analysis of the diurnal variations of Titan's ionosphere (between 1,000 and 1,400 km) based on a sample of Ion Neutral Mass Spectrometer (INMS) measurements in the Open Source Ion (OSI) mode obtained from 8 close encounters of the Cassini spacecraft with Titan. Though there is an overall ion depletion well beyond the terminator, the ion content on Titan's nightside is still appreciable, with a density plateau of ~700 cm-3 below ~1,300 km. Such a plateau is associated with the combination of distinct diurnal variations of light and heavy ions. Light ions (e.g. CH5+, HCNH+, C2H5+) show strong diurnal variation, with clear bite-outs in their nightside distributions. In contrast, heavy ions (e.g. c-C3H3+, C2H3CNH+, C6H7+) present modest diurnal variation, with significant densities observed on the nightside. We propose that the distinctions between light and heavy ions are associated with their different chemical loss pathways, with the former primarily through "fast" ion-neutral chemistry and the latter through "slow" electron dissociative recombination. The INMS data suggest day-to-night transport as an important source of ions on Titan's nightside, to be distinguished from the conventional scenario of auroral ionization by magnetospheric particles as the only ionizing source on the nightside. This is supported by the strong correlation between the observed night-to-day ion density ratios and the associated ion lifetimes. We construct a time-dependent ion chemistry model to investigate the effects of day-to-night transport on the ionospheric structures of Titan. The predicted diurnal variation has similar general characteristics to those observed, with some apparent discrepancies which could be reconciled by imposing fast horizontal thermal winds in Titan's upper atmosphere.

  20. Phonological Variation in Short Message Service (SMS) in Kenya ...

    African Journals Online (AJOL)

    Phonological Variation in Short Message Service (SMS) in Kenya. NA Ong'onda, O Oketch, PM Matu. Abstract. In this paper, we analyze the sociolinguistic aspect of Short Message Service (SMS) with a view to identifying phonological variations in Kenyan text messages. The widespread use of cell phones has led to the ...

  1. Advanced Microscopy of Microbial Cells

    DEFF Research Database (Denmark)

    Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

    2011-01-01

    Growing awareness of heterogeneity in cells of microbial populations has emphasized the importance of advanced microscopy for visualization and understanding of the molecular mechanisms underlying cell-to-cell variation. In this review, we highlight some of the recent advances in confocal...... for visualization of variation between cells in phenotypic traits such as gene expression....

  2. Conformable variational iteration method

    Directory of Open Access Journals (Sweden)

    Omer Acan

    2017-02-01

    Full Text Available In this study, we introduce the conformable variational iteration method based on new defined fractional derivative called conformable fractional derivative. This new method is applied two fractional order ordinary differential equations. To see how the solutions of this method, linear homogeneous and non-linear non-homogeneous fractional ordinary differential equations are selected. Obtained results are compared the exact solutions and their graphics are plotted to demonstrate efficiency and accuracy of the method.

  3. Canonical variate regression.

    Science.gov (United States)

    Luo, Chongliang; Liu, Jin; Dey, Dipak K; Chen, Kun

    2016-07-01

    In many fields, multi-view datasets, measuring multiple distinct but interrelated sets of characteristics on the same set of subjects, together with data on certain outcomes or phenotypes, are routinely collected. The objective in such a problem is often two-fold: both to explore the association structures of multiple sets of measurements and to develop a parsimonious model for predicting the future outcomes. We study a unified canonical variate regression framework to tackle the two problems simultaneously. The proposed criterion integrates multiple canonical correlation analysis with predictive modeling, balancing between the association strength of the canonical variates and their joint predictive power on the outcomes. Moreover, the proposed criterion seeks multiple sets of canonical variates simultaneously to enable the examination of their joint effects on the outcomes, and is able to handle multivariate and non-Gaussian outcomes. An efficient algorithm based on variable splitting and Lagrangian multipliers is proposed. Simulation studies show the superior performance of the proposed approach. We demonstrate the effectiveness of the proposed approach in an [Formula: see text] intercross mice study and an alcohol dependence study. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Somaclonal variation in rice

    International Nuclear Information System (INIS)

    Kucherenko, L.

    1990-01-01

    Full text: 32 varieties of Oryza sativa L. ssp. japonica were used as donors for callus induction from somatic tissues. In some cases, the callus was treated before regeneration with the chemical mutagen MNU. Some of the regenerated plants demonstrated heritable alterations, among them chlorophyll deficiencies, variation in plant height, awness, glume colouring and fertility. Along with these, a number of lines with agronomically valuable alterations concerning maturity time, panicle structure, plant productivity and grain quality were found. The spectrum of variability was very wide. Vivipary was noticed. Superdwarfs with plant height of about 15 cm were found. Plants with no visible distinctions could be variants too, for example, with increased protein content or disease resistance. The rate and the spectrum of the somaclonal variation were not influenced by the culture media but depended on the donor's genotype. On the basis of somaclonal variation a variety 'Bioryza' was developed. It is an early maturing (about 95-100 days), long grain variety, with grain yield up to 8 t/ha. (author)

  5. Time variations of geomagnetic activity indices Kp and Ap: an update

    Directory of Open Access Journals (Sweden)

    G. K. Rangarajan

    Full Text Available Kp and Ap indices covering the period 1932 to 1995 are analysed in a fashion similar to that attempted by Bartels for the 1932–1961 epoch to examine the time variations in their characteristics. Modern analysis techniques on the extended data base are used for further insight. The relative frequencies of occurrence of Kp with different magnitudes and the seasonal and solar cycle dependences are seen to be remarkably consistent despite the addition of 35 years of observations. Many of the earlier features seen in the indices and special intervals are shown to be replicated in the present analysis. Time variations in the occurrence of prolonged periods of geomagnetic calm or of enhanced activity are presented and their relation to solar activity highlighted. It is shown that in the declining phase the occurrence frequencies of Kp = 4–5 (consecutively over 4 intervals can be used as a precursor for the maximum sunspot number to be expected in the next cycle. The semi-annual variation in geomagnetic activity is re-examined utilising not only the Ap index but also the occurrence frequencies of Kp index with different magnitudes. Lack of dependence of the amplitude of semi-annual variation on sunspot number is emphasised. Singular spectrum analysis of the mean monthly Ap index shows some distinct periodic components. The temporal evolution of ~44 month, ~21 month and ~16 month oscillations are examined and it is postulated that while QBO and the 16 month oscillations could be attributed to solar wind and IMF oscillations with analogous periodicity, the 44 month variation is associated with a similar periodicity in recurrent high speed stream caused by sector boundary passage. It is reconfirmed that there could have been only one epoch around 1940 when solar wind speed could have exhibited a 1.3-year periodicity comparable to that seen during the post-1986 period.

  6. Transcriptional control of the cell cycle.

    Science.gov (United States)

    Sánchez, I; Dynlacht, B D

    1996-06-01

    Although a significant amount of evidence has demonstrated that there are intimate connections between transcriptional controls and cell cycle regulation, the precise mechanisms underlying these connections remain largely obscure. A number of recent advances have helped to define how critical cell cycle regulators, such as the retinoblastoma family of tumor suppressor proteins and the cyclin-dependent kinases, might function on a biochemical level and how such mechanisms of action have been conserved not only in the regulation of transcription by all three RNA polymerases but also across species lines. In addition, the use of in vivo techniques has begun to explain how the activity of the E2F transcription factor family is tied to the cell cycle dependent expression of target genes.

  7. Variation, structure and norms

    DEFF Research Database (Denmark)

    Harder, Peter

    2014-01-01

    After a period when the focus was essentially on mental architecture, the cognitive sciences are increasingly integrating the social dimension. The rise of a cognitive sociolinguistics is part of this trend. The article argues that this process requires a re-evaluation of some entrenched positions...... in linguistics: those that see linguistic norms as antithetical to a descriptive and variational linguistics. Once such a re-evaluation has taken place, however, the social recontextualization of cognition will enable linguistics (including sociolinguistics as an integral part), to eliminate the cracks...

  8. Introduction to global variational geometry

    CERN Document Server

    Krupka, Demeter

    2015-01-01

    The book is devoted to recent research in the global variational theory on smooth manifolds. Its main objective is an extension of the classical variational calculus on Euclidean spaces to (topologically nontrivial) finite-dimensional smooth manifolds; to this purpose the methods of global analysis of differential forms are used. Emphasis is placed on the foundations of the theory of variational functionals on fibered manifolds - relevant geometric structures for variational principles in geometry, physical field theory and higher-order fibered mechanics. The book chapters include: - foundations of jet bundles and analysis of differential forms and vector fields on jet bundles, - the theory of higher-order integral variational functionals for sections of a fibred space, the (global) first variational formula in infinitesimal and integral forms- extremal conditions and the discussion of Noether symmetries and generalizations,- the inverse problems of the calculus of variations of Helmholtz type- variational se...

  9. Gauging Variational Inference

    Energy Technology Data Exchange (ETDEWEB)

    Chertkov, Michael [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ahn, Sungsoo [Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea, Republic of); Shin, Jinwoo [Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea, Republic of)

    2017-05-25

    Computing partition function is the most important statistical inference task arising in applications of Graphical Models (GM). Since it is computationally intractable, approximate methods have been used to resolve the issue in practice, where meanfield (MF) and belief propagation (BP) are arguably the most popular and successful approaches of a variational type. In this paper, we propose two new variational schemes, coined Gauged-MF (G-MF) and Gauged-BP (G-BP), improving MF and BP, respectively. Both provide lower bounds for the partition function by utilizing the so-called gauge transformation which modifies factors of GM while keeping the partition function invariant. Moreover, we prove that both G-MF and G-BP are exact for GMs with a single loop of a special structure, even though the bare MF and BP perform badly in this case. Our extensive experiments, on complete GMs of relatively small size and on large GM (up-to 300 variables) confirm that the newly proposed algorithms outperform and generalize MF and BP.

  10. Harmonically excited orbital variations

    International Nuclear Information System (INIS)

    Morgan, T.

    1985-01-01

    Rephrasing the equations of motion for orbital maneuvers in terms of Lagrangian generalized coordinates instead of Newtonian rectangular cartesian coordinates can make certain harmonic terms in the orbital angular momentum vector more readily apparent. In this formulation the equations of motion adopt the form of a damped harmonic oscillator when torques are applied to the orbit in a variationally prescribed manner. The frequencies of the oscillator equation are in some ways unexpected but can nonetheless be exploited through resonant forcing functions to achieve large secular variations in the orbital elements. Two cases are discussed using a circular orbit as the control case: (1) large changes in orbital inclination achieved by harmonic excitation rather than one impulsive velocity change, and (2) periodic and secular changes to the longitude of the ascending node using both stable and unstable excitation strategies. The implications of these equations are also discussed for both artificial satellites and natural satellites. For the former, two utilitarian orbits are suggested, each exploiting a form of harmonic excitation. 5 refs

  11. Cell surface expression level variation between two common Human Leukocyte Antigen alleles, HLA-A2 and HLA-B8, is dependent on the structure of the C terminal part of the alpha 2 and the alpha 3 domains

    DEFF Research Database (Denmark)

    Dellgren, Christoffer; Nehlin, Jan O; Barington, Torben

    2015-01-01

    Constitutive cell surface expression of Human Leukocyte Antigen (HLA) class I antigens vary extremely from tissue to tissue and individual antigens may differ widely in expression levels. Down-regulation of class I expression is a known immune evasive mechanism used by cancer cells and viruses....... Moreover, recent observations suggest that even minor differences in expression levels may influence the course of viral infections and the frequency of complications to stem cell transplantation. We have shown that some human multipotent stem cells have high expression of HLA-A while HLA-B is only weakly...... expressed, and demonstrate here that this is also the case for the human embryonic kidney cell line HEK293T. Using quantitative flow cytometry and quantitative polymerase chain reaction we found expression levels of endogenous HLA-A3 (median 71,204 molecules per cell) 9.2-fold higher than the expression of...

  12. Evaluation of variational approximations

    International Nuclear Information System (INIS)

    Trevisan, L.A.

    1991-01-01

    In Feynman's approach to quantum statistical mechanics, the partition function can e represented as a path integral. A recently proposed variation method of Feynman-Kleinert is able to transform the path integral into an integral in phase space, in which the quantum fluctuations have been taken care of by introducing the effective classical potential. This method has been testes with succeed for the smooth potentials and for the singular potential of delta. The method to the strong singular potentials is applied: a quadratic potential and a linear potential both with a rigid wall at the origin. By satisfying the condition that the density of the particle be vanish at the origin, and adapted method of Feynman-Kleinert in order to improve the method is introduced. (author)

  13. Dynamics of nonholonomic systems from variational principles embedded variation identity

    International Nuclear Information System (INIS)

    Guo Yongxin; Liu Shixing; Liu Chang; Chang Peng

    2009-01-01

    Nondeterminacy of dynamics, i.e., the nonholonomic or the vakonomic, fundamental variational principles, e.g., the Lagrange-d'Alembert or Hamiltonian, and variational operators, etc., of nonholonomic mechanical systems can be attributed to the non-uniqueness of ways how to realize nonholonomic constraints. Making use of a variation identity of nonholonomic constraints embedded into the Hamilton's principle with the method of Lagrange undetermined multipliers, three kinds of dynamics for the nonholonomic systems including the vakonomic and nonholonomic ones and a new one are obtained if the variation is respectively reduced to three conditional variations: vakonomic variation, Hoelder's variation and Suslov's variation, defined by the identity. Therefore, different dynamics of nonholonomic systems can be derived from an integral variational principle, utilizing one way of embedding constraints into the principle, with different variations. It is verified that the similar embedding of the identity into the Lagrange-d'Alembert principle gives rise to the nonholonomic dynamics but fails to give the vakonomic one unless the constraints are integrable.

  14. Solar Cycle Variations as Observed by MLS Carbon Monoxide

    Science.gov (United States)

    Lee, J. N.; Wu, D. L.; Ruzmaikin, A.; Fontenla, J. M.

    2017-12-01

    More than thirteen years (2004-2017) of carbon monoxide (CO) measurements from the Aura Microwave Limb Sounder (MLS) are analyzed to better understand impacts of solar cycle 24. The upper mesospheric CO, produced primarily by the carbon dioxide (CO2) photolysis in the lower thermosphere, is sensitive to solar irradiance variability. We find that interannual variations of the mesospheric CO concentration are largely driven by the solar-cycle modulated ultraviolet (UV) variation in most of the UV wavelengths (120 to 280 nm) in high latitude regions. Despite different mean CO abundances in the SH and NH winters, their solar-cycle dependence appears to be symmetric with respect to the winter pole. This solar signal extends down to the lower altitudes by the dynamical descent in the polar vortex, showing a time lag that is consistent with the average descent velocity. To characterize a global distribution of the solar influence, Aura MLS CO is correlated with the Solar Radiation and Climate Experiment (SORCE) Total Irradiance Monitor (TIM) measured total solar irradiance (TSI) and with the SORCE Solar-Stellar Irradiance Comparison Experiment (SOLSTICE) measured UV. As high as 0.8 in most of the polar mesosphere, the linear correlation coefficients between CO and UV/TSI are more robust than those found in the previous work, with the extended analysis period. Different from the result shown in Lee et al. (2013), the downward propagation of the solar signals is similar in both NH and SH high latitudes. Effects of solar forcing on mesospheric CO extend far beyond the polar region. CO is a good tracer to show that the solar induced CO anomaly seems to follow the global meridional residual circulation and hemispheric transition from pole to pole in every six months. WACCM simulation experiment with two different solar spectral irradiance models, SRPM (Solar Radiation Physical Modeling) 2012 and NRLSSI (Naval Research Laboratory Spectral Solar Irradiance), shows that the

  15. A survey of variational principles

    International Nuclear Information System (INIS)

    Lewins, J.D.

    1993-01-01

    In this article survey of variational principles has been given. Variational principles play a significant role in mathematical theory with emphasis on the physical aspects. There are two principals used i.e. to represent the equation of the system in a succinct way and to enable a particular computation in the system to be carried out with greater accuracy. The survey of variational principles has ranged widely from its starting point in the Lagrange multiplier to optimisation principles. In an age of digital computation, these classic methods can be adapted to improve such calculations. We emphasize particularly the advantage of basic finite element methods on variational principles. (A.B.)

  16. How Polycomb-Mediated Cell Memory Deals With a Changing Environment: Variations in PcG complexes and proteins assortment convey plasticity to epigenetic regulation as a response to environment.

    Science.gov (United States)

    Marasca, Federica; Bodega, Beatrice; Orlando, Valerio

    2018-04-01

    Cells and tissues are continuously exposed to a changing microenvironment, hence the necessity of a flexible modulation of gene expression that in complex organism have been achieved through specialized chromatin mechanisms. Chromatin-based cell memory enables cells to maintain their identity by fixing lineage specific transcriptional programs, ensuring their faithful transmission through cell division; in particular PcG-based memory system evolved to maintain the silenced state of developmental and cell cycle genes. In evolution the complexity of this system have increased, particularly in vertebrates, indicating combinatorial and dynamic properties of Polycomb proteins, in some cases even overflowing outside the cell nucleus. Therefore, their function may not be limited to the imposition of rigid states of genetic programs, but on the ability to recognize signals and allow plastic transcriptional changes in response to different stimuli. Here, we discuss the most novel PcG mediated memory functions in facing and responding to the challenges posed by a fluctuating environment. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  17. Radiobiological properties of radiosensitive XR-1 Chinese hamster cells and hybrids from these and human A-T cells

    International Nuclear Information System (INIS)

    Bahari, I.B.

    1989-01-01

    Results indicate that XR-1 cells were very radiosensitive to gamma-irradiation compared to its parental type, and that this radiosensitivity is cell cycle dependent. Irradiating the cells the G 1 or plateau phase did not induce any delay entering S-phase but mitotic delays were observed in both XR-1 and the wild-type cells. The delays per unit dose were much longer for XR-1. A delay in subculture from plateau phase reduced the mitotic delay in both cell lines. Unlike the wild-type cells which expressed virtually all chromosome-type aberrations after irradiation of G 1 cells, the XR-1 cells expressed both chromatid- as well as chromosome-type aberrations. There was a one-to-one correlation between total aberrations induced and lethality for both cells. Many of these radiobiological properties of XR-1 cells relative to the wild-type cells, mimic the response of A-T cells relative to the normal human cells. However, the restoration of radioresistance and cytogenetic response in the XR1/AT5BI(4) hybrid cells suggest that the XR-1 and A-T cells have different defects because of the complementation in the hybrids. It also appears that this genetic defect is recessive in nature

  18. Temporal Variations of the Magnetic Flux in the Solar Photosphere

    Science.gov (United States)

    Merzlyakov, V. L.; Starkova, L. I.

    2017-12-01

    The problem of the transport and transformation of magnetic fields from the generation zone to the photosphere is studied in this paper. For this purpose, the temporal variations of parameters of bipolar magnetic regions are analyzed based on the magnetic synoptic maps of the Wilcox Solar Observatory (WSO) for the declining phase of cycle 22. A 150-day modulation of the magnetic flux value in bipolar regions and a variation in their rotation velocity with a duration of 80-100 days have been found. Such variations in the parameters are interpreted as a result of action of supergiant and giant convection cells. The magnetic flux from the generation zone emerges through the local channels formed by the supergiant convection cells. From the level of 0.95 R Sun, the flux is redistributed by giant cells, which form bipolar magnetic regions on the photosphere.

  19. Controlling variation in the comet assay

    Directory of Open Access Journals (Sweden)

    Andrew Richard Collins

    2014-10-01

    Full Text Available Variability of the comet assay is a serious issue, whether it occurs from experiment to experiment in the same laboratory, or between different laboratories analysing identical samples. Do we have to live with high variability, just because the comet assay is a biological assay rather than analytical chemistry? Numerous attempts have been made to limit variability by standardising the assay protocol, and the critical steps in the assay have been identified; agarose concentration, duration of alkaline incubation, and electrophoresis conditions (time, temperature and voltage gradient are particularly important. Even when these are controlled, variation seems to be inevitable. It is helpful to include in experiments reference standards, i.e. cells with a known amount of specific damage to the DNA. They can be aliquots frozen from a single large batch of cells, either untreated (negative controls or treated with, for example, H2O2 or X-rays to induce strand breaks (positive control for the basic assay, or photosensitiser plus light to oxidise guanine (positive control for Fpg- or OGG1-sensitive sites. Reference standards are especially valuable when performing a series of experiments over a long period - for example, analysing samples of white blood cells from a large human biomonitoring trial - to check that the assay is performing consistently, and to identify anomalous results necessitating a repeat experiment. The reference values of tail intensity can also be used to iron out small variations occurring from day to day. We present examples of the use of reference standards in human trials, both within one laboratory and between different laboratories, and describe procedures that can be used to control variation.

  20. General strongly nonlinear variational inequalities

    International Nuclear Information System (INIS)

    Siddiqi, A.H.; Ansari, Q.H.

    1990-07-01

    In this paper we develop iterative algorithms for finding approximate solutions for new classes of variational and quasi-variational inequalities which include, as special case, some known results in this field. It is shown that the solutions of the iterative schemes converge to the exact solutions. (author). 15 refs

  1. Exploiting natural variation in Arabidopsis

    NARCIS (Netherlands)

    Molenaar, J.A.; Keurentjes, J.J.B.; Sanchez-Serrano, J.J.; Salinas, J.

    2014-01-01

    Natural variation for many traits is present within the species Arabidopsis thaliana. This chapter describes the use of natural variation to elucidate genes underlying the regulation of quantitative traits. It deals with the development and use of mapping populations, the detection and handling of

  2. Quantitative characterization of cell behaviors through cell cycle progression via automated cell tracking.

    Directory of Open Access Journals (Sweden)

    Yuliang Wang

    Full Text Available Cell behaviors are reflections of intracellular tension dynamics and play important roles in many cellular processes. In this study, temporal variations in cell geometry and cell motion through cell cycle progression were quantitatively characterized via automated cell tracking for MCF-10A non-transformed breast cells, MCF-7 non-invasive breast cancer cells, and MDA-MB-231 highly metastatic breast cancer cells. A new cell segmentation method, which combines the threshold method and our modified edge based active contour method, was applied to optimize cell boundary detection for all cells in the field-of-view. An automated cell-tracking program was implemented to conduct live cell tracking over 40 hours for the three cell lines. The cell boundary and location information was measured and aligned with cell cycle progression with constructed cell lineage trees. Cell behaviors were studied in terms of cell geometry and cell motion. For cell geometry, cell area and cell axis ratio were investigated. For cell motion, instantaneous migration speed, cell motion type, as well as cell motion range were analyzed. We applied a cell-based approach that allows us to examine and compare temporal variations of cell behavior along with cell cycle progression at a single cell level. Cell body geometry along with distribution of peripheral protrusion structures appears to be associated with cell motion features. Migration speed together with motion type and motion ranges are required to distinguish the three cell-lines examined. We found that cells dividing or overlapping vertically are unique features of cell malignancy for both MCF-7 and MDA-MB-231 cells, whereas abrupt changes in cell body geometry and cell motion during mitosis are unique to highly metastatic MDA-MB-231 cells. Taken together, our live cell tracking system serves as an invaluable tool to identify cell behaviors that are unique to malignant and/or highly metastatic breast cancer cells.

  3. Variational and quasi-variational inequalities in mechanics

    CERN Document Server

    Kravchuk, Alexander S

    2007-01-01

    The essential aim of the present book is to consider a wide set of problems arising in the mathematical modelling of mechanical systems under unilateral constraints. In these investigations elastic and non-elastic deformations, friction and adhesion phenomena are taken into account. All the necessary mathematical tools are given: local boundary value problem formulations, construction of variational equations and inequalities, and the transition to minimization problems, existence and uniqueness theorems, and variational transformations (Friedrichs and Young-Fenchel-Moreau) to dual and saddle-point search problems. Important new results concern contact problems with friction. The Coulomb friction law and some others are considered, in which relative sliding velocities appear. The corresponding quasi-variational inequality is constructed, as well as the appropriate iterative method for its solution. Outlines of the variational approach to non-stationary and dissipative systems and to the construction of the go...

  4. HGVA: the Human Genome Variation Archive.

    Science.gov (United States)

    Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gräf, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

    2017-07-03

    High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. A study on parameter variation effects on battery packs for electric vehicles

    Science.gov (United States)

    Zhou, Long; Zheng, Yuejiu; Ouyang, Minggao; Lu, Languang

    2017-10-01

    As one single cell cannot meet power and driving range requirement in an electric vehicle, the battery packs with hundreds of single cells connected in parallel and series should be constructed. The most significant difference between a single cell and a battery pack is cell variation. Not only does cell variation affect pack energy density and power density, but also it causes early degradation of battery and potential safety issues. The cell variation effects on battery packs are studied, which are of great significant to battery pack screening and management scheme. In this study, the description for the consistency characteristics of battery packs was first proposed and a pack model with 96 cells connected in series was established. A set of parameters are introduced to study the cell variation and their impacts on battery packs are analyzed through the battery pack capacity loss simulation and experiments. Meanwhile, the capacity loss composition of the battery pack is obtained and verified by the temperature variation experiment. The results from this research can demonstrate that the temperature, self-discharge rate and coulombic efficiency are the major affecting parameters of cell variation and indicate the dissipative cell equalization is sufficient for the battery pack.

  6. Observer variation in skeletal radiology

    Energy Technology Data Exchange (ETDEWEB)

    Cockshott, W.P.; Park, W.M.

    1983-08-01

    The factors that affect observer variation in bone radiology are analysed from data in the literature and on the basis of studies carried out at McMaster University on the hands and sacroiliac joints. A plea is made for presenting results in terms of Kappa statistics so that agreement due purely to chance is eliminated. In the conclusions the main variables that affect concordance are listed so that strategies can be developed to reduce observer variation. This is important in serial studies to ensure that the observer variations are smaller than the effect one wishes to measure.

  7. Statistics, Uncertainty, and Transmitted Variation

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, Joanne Roth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-11-05

    The field of Statistics provides methods for modeling and understanding data and making decisions in the presence of uncertainty. When examining response functions, variation present in the input variables will be transmitted via the response function to the output variables. This phenomenon can potentially have significant impacts on the uncertainty associated with results from subsequent analysis. This presentation will examine the concept of transmitted variation, its impact on designed experiments, and a method for identifying and estimating sources of transmitted variation in certain settings.

  8. Variation within the PPARG gene is associated with residual beta-cell function and glycemic control in children and adolescents during the first year of clinical type 1 diabetes

    DEFF Research Database (Denmark)

    Porksen, S.; Nielsen, L.B.; Mortensen, H.B.

    2008-01-01

    Context: Conflicting evidence exists as to whether the Pro12Ala single nucleotide polymorphism of the type 2 diabetes susceptibility gene peroxisome proliferator-activated receptor gamma (PPARG) also confers risk for type 1 diabetes (T1D). Objective: The objective of this study was to investigate...... the PPARG gene in relation to residual beta-cell function and glycemic control in newly diagnosed T1D. Design: Prospective, non-interventional, 12-month follow-up study, conducted in 18 centers in 15 countries. Patients: Two hundred and fifty-seven children and adolescents (aged ... diagnosed T1D. Main outcome measures: Beta-cell function was determined as 90-min meal-stimulated C-peptide (Boost test) 1, 6, and 12 months after diagnosis. Hemoglobin A1c (HbA1c) and daily insulin dose (IU/kg/d) were recorded at 1, 3, 6, 9, and 12 months after diagnosis. Haplotypes within PPARG were...

  9. Skin dose variation: influence of energy

    International Nuclear Information System (INIS)

    Cheung, T.; Yu, P.K.N.; Butson, M.J.; Cancer Services, Wollongong, NSW

    2004-01-01

    Full text: This research aimed to quantitatively evaluate the differences in percentage dose of maximum for 6MV and 18MV x-ray beams within the first lcm of interactions. Thus provide quantitative information regarding the basal, dermal and subcutaneous dose differences achievable with these two types of high-energy x-ray beams. Percentage dose of maximum build up curves are measured for most clinical field sizes using 6MV and 18MV x-ray beams. Calculations are performed to produce quantitative results highlighting the percentage dose of maximum differences delivered to various depths within the skin and subcutaneous tissue region by these two beams Results have shown that basal cell layer doses are not significantly different for 6MV and 18Mv x-ray beams At depths beyond the surface and basal cell layer there is a measurable and significant difference in delivered dose. This variation increases to 20% of maximum and 22% of maximum at Imm and 1cm depths respectively. The percentage variations are larger for smaller field sizes where the photon in phantom component of the delivered dose is the most significant contributor to dose By producing graphs or tables of % dose differences in the build up region we can provide quantitative information to the oncologist for consideration (if skin and subcutaneous tissue doses are of importance) during the beam energy selection process for treatment. Copyright (2004) Australasian College of Physical Scientists and Engineers in Medicine

  10. Avaliação cronológica da variação no volume globular sanguíneo de bovinos leiteiros Cronological evaluation of variation in packed cell volume on dairy cattle

    Directory of Open Access Journals (Sweden)

    Wilmar Sachetin Marçal

    1995-01-01

    Full Text Available Os autores avaliaram a variação no volume globular sangüíneo de 321 bovinos da raça Holandês preta e branca, sadios e criados em granjas leiteiras no Estado de São Paulo. Todos os animais trabalhados na presente pesquisa eram sadios, não reagentes ao vírus da Leucose Bovina, livres de hemoparasitas, brucelose e tuberculose. O volume globular sangüíneo foi efetuado através do método do hematócrito com tubos capilares. Os resultados mostram haver influência da idade sobre o volume globular sangüíneo, com valores médios encontrados de 30,12 ± 2,72%.The packet cell volume was evaluated by the authors in 321 healthy female Holstein cattle raised at Campinas dairy region. São Paulo State. All the animais used in this assay were healthy and free of Leucosis, Tuberculosis, Brucellosis and blood parasites. The packed cell volume has been studied by method of hematocrit with capilary tubos. The results showed an influence of age on packed cell volume with average reference values of 30.12 ± 2.72%.

  11. Quick-low-density parity check and dynamic threshold voltage optimization in 1X nm triple-level cell NAND flash memory with comprehensive analysis of endurance, retention-time, and temperature variation

    Science.gov (United States)

    Doi, Masafumi; Tokutomi, Tsukasa; Hachiya, Shogo; Kobayashi, Atsuro; Tanakamaru, Shuhei; Ning, Sheyang; Ogura Iwasaki, Tomoko; Takeuchi, Ken

    2016-08-01

    NAND flash memory’s reliability degrades with increasing endurance, retention-time and/or temperature. After a comprehensive evaluation of 1X nm triple-level cell (TLC) NAND flash, two highly reliable techniques are proposed. The first proposal, quick low-density parity check (Quick-LDPC), requires only one cell read in order to accurately estimate a bit-error rate (BER) that includes the effects of temperature, write and erase (W/E) cycles and retention-time. As a result, 83% read latency reduction is achieved compared to conventional AEP-LDPC. Also, W/E cycling is extended by 100% compared with conventional Bose-Chaudhuri-Hocquenghem (BCH) error-correcting code (ECC). The second proposal, dynamic threshold voltage optimization (DVO) has two parts, adaptive V Ref shift (AVS) and V TH space control (VSC). AVS reduces read error and latency by adaptively optimizing the reference voltage (V Ref) based on temperature, W/E cycles and retention-time. AVS stores the optimal V Ref’s in a table in order to enable one cell read. VSC further improves AVS by optimizing the voltage margins between V TH states. DVO reduces BER by 80%.

  12. Diurnal variation of radon progeny

    International Nuclear Information System (INIS)

    Seftelis, I.; Nicolaou, G.; Trassanidis, S.; Tsagas, F.N.

    2007-01-01

    The diurnal variation of the gross alpha (α) radioactivity in the air near the ground and the gamma (γ) radioactivity emitted from the ground have been monitored in North-eastern Greece. Meteorological information comprising air temperature and humidity has been simultaneously recorded. Over a period of the 24 h of a typical day, the variation of α-radioactivity reaches a peak in the morning followed by a remarkable decrease, rising to a second peak in the afternoon. Furthermore, its significant dependence on the air temperature and humidity is confirmed, rising with an increase in humidity and decrease in temperature. The variation of the ground γ-radioactivity follows that of the air α-radioactivity. A mathematical model has been developed to describe the diurnal variation of the α-radioactivity in the air near the ground in terms of the above meteorological variables and ground level γ-radioactivity

  13. Fractional variational principles with delay

    International Nuclear Information System (INIS)

    Baleanu, Dumitru; Abdeljawad, Thabet Maaraba; Jarad, Fahd

    2008-01-01

    The fractional variational principles within Riemann-Liouville fractional derivatives in the presence of delay are analyzed. The corresponding Euler-Lagrange equations are obtained and one example is analyzed in detail

  14. Exploring language variation across Europe

    DEFF Research Database (Denmark)

    Hovy, Dirk; Johannsen, Anders Trærup

    2016-01-01

    Language varies not only between countries, but also along regional and sociodemographic lines. This variation is one of the driving factors behind language change. However, investigating language variation is a complex undertaking: the more factors we want to consider, the more data we need....... Traditional qualitative methods are not well-suited to do this, an thus restricted to isolated factors. This reduction limits the potential insights, and risks attributing undue importance to easily observed factors. While there is a large interest in linguistics to improve upon such studies, it requires...... training in both variational linguistics and computational methods, a combination that is still not common. We take a first step here to alleviate the problem by providing an interface to explore large-scale language variation along several socio-demographic factors without programming knowledge. It makes...

  15. Explaining variation in nascent entrepreneurship

    NARCIS (Netherlands)

    A.J. van Stel (André); A.R.M. Wennekers (Sander); P. Reynolds (Paul); A.R. Thurik (Roy)

    2004-01-01

    textabstractThis paper aims at explaining cross-country variation in nascent entrepreneurship. Regression analysis is applied using various explanatory variables derived from three different approaches. We make use of the Global Entrepreneurship Monitor database, including nascent entrepreneurship

  16. Study of band gap reduction of TiO{sub 2} thin films with variation in GO contents and use of TiO{sub 2}/Graphene composite in hybrid solar cell

    Energy Technology Data Exchange (ETDEWEB)

    Saleem, Hareema, E-mail: hareemasaleem@gmail.com; Habib, Amir

    2016-09-15

    We have successfully designed a hybrid solar cell for improved performance of the P3HT based photovoltaic devices by using TiO{sub 2}/Graphene composites. There has been significant improvement in IV characteristics of organic solar cells prepared by this method. The TiO{sub 2}/Graphene composites act as electron collectors in active layer along with P3HT: PCBM in inverted organic photovoltaic devices. The energy bandgap was prominently reduced from 3.00 eV to 2.71 eV as confirmed by cyclic voltametery (CV) and UV–Vis spectroscopy. We have separately synthesized the TiO{sub 2} nanoparticles of size range (15 nm–22 nm) through condensed refluxed sol gel method in which titanium isopropoxide was taken as precursor. Modified Hummer's Method was used for the oxidation of graphite flakes into graphene oxide (GO) using KMnO{sub 4} as an oxidizing agent. TiO{sub 2}/Graphene composites were prepared by the subsequent sonication and heating processes. We have rigorously characterized the sample through various characterization tools. Scanning electron microscopy (SEM) results of TiO{sub 2}/Graphene films reveal the homogenous distribution of graphene nanosheets among the homogenously distributed titanium nanoparticles. X-ray diffraction (XRD) has shown the pure anatase phase peaks of TiO{sub 2} nanoparticles and oxidation of graphite at 11.8°. Fourier transform infrared spectroscopy (FTIR) has been used to study the vibrating modes. The chemical bonding Ti−O−C resulted to enhance the electron transport in obtained TiO{sub 2}/Graphene composite films. UV–Vis spectroscopy has expressed the oxidation peaks of graphite around 216 nm and all composite films were observed in visible region. The significant reduction in band gap and improved performance of hybrid solar cell using TiO{sub 2}/Graphene composite as electron collector in active layer, is attributed to getting better economical power conversion efficiency solar cell. - Highlights: • Reduction of

  17. Variational aspects of Faddeev calculations

    International Nuclear Information System (INIS)

    Payne, G.L.; Gibson, B.F.

    1993-01-01

    Variational bounds generated from Faddeev solutions for various realistic potential models are presented as a function of the number of partial waves retained in the potential expansion. The authors demonstrate that the Faddeev wave function yields an optimal variational bound for the partial-wave truncated potential from which it was generated, but it does not yield an optimal bound for the full Hamiltonian or when the potential is partial-wave truncated at a different level

  18. Variational calculus on Banach spaces

    International Nuclear Information System (INIS)

    Uglanov, A V

    2000-01-01

    The problem of variational calculus is considered in a (variable) subdomain of a Banach space. Analogues of the basic principles of the finite-dimensional theory are derived: the main formula for variations of a functional, necessary conditions of an extremum, Noether's theorem. All the results obtained are dimension-invariant and become the classical ones in the finite-dimensional setting. The main tool of the analysis is the theory of surface integration in Banach spaces

  19. Nonlinear Analysis and Variational Problems

    CERN Document Server

    Pardalos, Panos M

    2010-01-01

    The chapters in this volume, written by international experts from different fields of mathematics, are devoted to honoring George Isac, a renowned mathematician. These contributions focus on recent developments in complementarity theory, variational principles, stability theory of functional equations, nonsmooth optimization, and several other important topics at the forefront of nonlinear analysis and optimization. "Nonlinear Analysis and Variational Problems" is organized into two parts. Part I, Nonlinear Analysis, centers on stability issues for functional equations, fixed point

  20. Etude quantitative des variations structurelles des chromosomes chez Saccharomyces cerevisiae

    OpenAIRE

    Gillet-Markowska , Alexandre

    2015-01-01

    The accumulation of chromosomal rearrangements also called Structural Variations (SV) is a major contributor to the transformation of tumoral cells and to the constitution of intratumoral heterogeneity. We have developed a bio-informatic tool that can now provide a sharp image of SV that occur in the human genome. We have demonstrated the existence of SV present in low proportions in different supposedly clonal cell populations showing that the rates of SV formation could be greatly underesti...

  1. Global variations of zonal mean ozone during stratospheric warming events

    Science.gov (United States)

    Randel, William J.

    1993-01-01

    Eight years of Solar Backscatter Ultraviolet (SBUV) ozone data are examined to study zonal mean variations associated with stratospheric planetary wave (warming) events. These fluctuations are found to be nearly global in extent, with relatively large variations in the tropics, and coherent signatures reaching up to 50 deg in the opposite (summer) hemisphere. These ozone variations are a manifestation of the global circulation cells associated with stratospheric warming events; the ozone responds dynamically in the lower stratosphere to transport, and photochemically in the upper stratosphere to the circulation-induced temperature changes. The observed ozone variations in the tropics are of particular interest because transport is dominated by zonal-mean vertical motions (eddy flux divergences and mean meridional transports are negligible), and hence, substantial simplifications to the governing equations occur. The response of the atmosphere to these impulsive circulation changes provides a situation for robust estimates of the ozone-temperature sensitivity in the upper stratosphere.

  2. Variations in Cellular Responses of Mouse T Cells to Adenosine-5′-Triphosphate Stimulation Do Not Depend on P2X7 Receptor Expression Levels but on Their Activation and Differentiation Stage

    Directory of Open Access Journals (Sweden)

    Hanaa Safya

    2018-02-01

    Full Text Available A previous report has shown that regulatory T cells (Treg were markedly more sensitive to adenosine-5′-triphosphate (ATP than conventional T cells (Tconv. Another one has shown that Tregs and CD45RBlow Tconvs, but not CD45RBhigh Tconvs, displayed similar high sensitivity to ATP. We have previously reported that CD45RBlow Tconvs expressing B220/CD45RABC molecules in a pre-apoptotic stage are resistant to ATP stimulation due to the loss of P2X7 receptor (P2X7R membrane expression. To gain a clearer picture on T-cell sensitivity to ATP, we have quantified four different cellular activities triggered by ATP in mouse T cells at different stages of activation/differentiation, in correlation with levels of P2X7R membrane expression. P2X7R expression significantly increases on Tconvs during differentiation from naive CD45RBhighCD44low to effector/memory CD45RBlowCD44high stage. Maximum levels of upregulation are reached on recently activated CD69+ naive and memory Tconvs. Ectonucleotidases CD39 and CD73 expression levels increase in parallel with those of P2X7R. Recently activated CD69+ CD45RBhighCD44low Tconvs, although expressing high levels of P2X7R, fail to cleave homing receptor CD62L after ATP treatment, but efficiently form pores and externalize phosphatidylserine (PS. In contrast, naive CD45RBhighCD44low Tconvs cleave CD62L with high efficiency although they express a lower level of P2X7, thus suggesting that P2X7R levels are not a limiting factor for signaling ATP-induced cellular responses. Contrary to common assumption, P2X7R-mediated cellular activities in mouse Tconvs are not triggered in an all-or-none manner, but depend on their stage of activation/differentiation. Compared to CD45RBlow Tconvs, CD45RBlowFoxp3+ Tregs show significantly higher levels of P2X7R membrane expression and of sensitivity to ATP as evidenced by their high levels of CD62L shedding, pore formation and PS externalization observed after ATP treatment. In summary, the

  3. Variations in Cellular Responses of Mouse T Cells to Adenosine-5′-Triphosphate Stimulation Do Not Depend on P2X7 Receptor Expression Levels but on Their Activation and Differentiation Stage

    Science.gov (United States)

    Safya, Hanaa; Mellouk, Amine; Legrand, Julie; Le Gall, Sylvain M.; Benbijja, Mohcine; Kanellopoulos-Langevin, Colette; Kanellopoulos, Jean M.; Bobé, Pierre

    2018-01-01

    A previous report has shown that regulatory T cells (Treg) were markedly more sensitive to adenosine-5′-triphosphate (ATP) than conventional T cells (Tconv). Another one has shown that Tregs and CD45RBlow Tconvs, but not CD45RBhigh Tconvs, displayed similar high sensitivity to ATP. We have previously reported that CD45RBlow Tconvs expressing B220/CD45RABC molecules in a pre-apoptotic stage are resistant to ATP stimulation due to the loss of P2X7 receptor (P2X7R) membrane expression. To gain a clearer picture on T-cell sensitivity to ATP, we have quantified four different cellular activities triggered by ATP in mouse T cells at different stages of activation/differentiation, in correlation with levels of P2X7R membrane expression. P2X7R expression significantly increases on Tconvs during differentiation from naive CD45RBhighCD44low to effector/memory CD45RBlowCD44high stage. Maximum levels of upregulation are reached on recently activated CD69+ naive and memory Tconvs. Ectonucleotidases CD39 and CD73 expression levels increase in parallel with those of P2X7R. Recently activated CD69+ CD45RBhighCD44low Tconvs, although expressing high levels of P2X7R, fail to cleave homing receptor CD62L after ATP treatment, but efficiently form pores and externalize phosphatidylserine (PS). In contrast, naive CD45RBhighCD44low Tconvs cleave CD62L with high efficiency although they express a lower level of P2X7, thus suggesting that P2X7R levels are not a limiting factor for signaling ATP-induced cellular responses. Contrary to common assumption, P2X7R-mediated cellular activities in mouse Tconvs are not triggered in an all-or-none manner, but depend on their stage of activation/differentiation. Compared to CD45RBlow Tconvs, CD45RBlowFoxp3+ Tregs show significantly higher levels of P2X7R membrane expression and of sensitivity to ATP as evidenced by their high levels of CD62L shedding, pore formation and PS externalization observed after ATP treatment. In summary, the different

  4. Variations in Cellular Responses of Mouse T Cells to Adenosine-5'-Triphosphate Stimulation Do Not Depend on P2X7 Receptor Expression Levels but on Their Activation and Differentiation Stage.

    Science.gov (United States)

    Safya, Hanaa; Mellouk, Amine; Legrand, Julie; Le Gall, Sylvain M; Benbijja, Mohcine; Kanellopoulos-Langevin, Colette; Kanellopoulos, Jean M; Bobé, Pierre

    2018-01-01

    A previous report has shown that regulatory T cells (Treg) were markedly more sensitive to adenosine-5'-triphosphate (ATP) than conventional T cells (Tconv). Another one has shown that Tregs and CD45RB low Tconvs, but not CD45RB high Tconvs, displayed similar high sensitivity to ATP. We have previously reported that CD45RB low Tconvs expressing B220/CD45RABC molecules in a pre-apoptotic stage are resistant to ATP stimulation due to the loss of P2X7 receptor (P2X7R) membrane expression. To gain a clearer picture on T-cell sensitivity to ATP, we have quantified four different cellular activities triggered by ATP in mouse T cells at different stages of activation/differentiation, in correlation with levels of P2X7R membrane expression. P2X7R expression significantly increases on Tconvs during differentiation from naive CD45RB high CD44 low to effector/memory CD45RB low CD44 high stage. Maximum levels of upregulation are reached on recently activated CD69 + naive and memory Tconvs. Ectonucleotidases CD39 and CD73 expression levels increase in parallel with those of P2X7R. Recently activated CD69 + CD45RB high CD44 low Tconvs, although expressing high levels of P2X7R, fail to cleave homing receptor CD62L after ATP treatment, but efficiently form pores and externalize phosphatidylserine (PS). In contrast, naive CD45RB high CD44 low Tconvs cleave CD62L with high efficiency although they express a lower level of P2X7, thus suggesting that P2X7R levels are not a limiting factor for signaling ATP-induced cellular responses. Contrary to common assumption, P2X7R-mediated cellular activities in mouse Tconvs are not triggered in an all-or-none manner, but depend on their stage of activation/differentiation. Compared to CD45RB low Tconvs, CD45RB low Foxp3 + Tregs show significantly higher levels of P2X7R membrane expression and of sensitivity to ATP as evidenced by their high levels of CD62L shedding, pore formation and PS externalization observed after ATP treatment. In summary

  5. Forced Expression of ZNF143 Restrains Cancer Cell Growth

    Directory of Open Access Journals (Sweden)

    Kimitoshi Kohno

    2011-10-01

    Full Text Available We previously reported that the transcription factor Zinc Finger Protein 143 (ZNF143 regulates the expression of genes associated with cell cycle and cell division, and that downregulation of ZNF143 induces cell cycle arrest at G2/M. To assess the function of ZNF143 expression in the cell cycle, we established two cells with forced expression of ZNF143 derived from PC3 prostate cancer cell lines. These cell lines overexpress genes associated with cell cycle and cell division, such as polo-like kinase 1 (PLK1, aurora kinase B (AURKB and some minichromosome maintenance complex components (MCM. However, the doubling time of cells with forced expression of ZNF143 was approximately twice as long as its control counterpart cell line. Analysis following serum starvation and re-seeding showed that PC3 cells were synchronized at G1 in the cell cycle. Also, ZNF143 expression fluctuated, and was at its lowest level in G2/M. However, PC3 cells with forced expression of ZNF143 synchronized at G2/M, and showed lack of cell cycle-dependent fluctuation of nuclear expression of MCM proteins. Furthermore, G2/M population of both cisplatin-resistant PCDP6 cells over-expressing ZNF143 (derived from PC3 cells and cells with forced expression of ZNF143 was significantly higher than that of each counterpart, and the doubling time of PCDP6 cells is about 2.5 times longer than that of PC3 cells. These data suggested that fluctuations in ZNF143 expression are required both for gene expression associated with cell cycle and for cell division.

  6. Forced Expression of ZNF143 Restrains Cancer Cell Growth

    International Nuclear Information System (INIS)

    Izumi, Hiroto; Yasuniwa, Yoshihiro; Akiyama, Masaki; Yamaguchi, Takahiro; Kuma, Akihiro; Kitamura, Noriaki; Kohno, Kimitoshi

    2011-01-01

    We previously reported that the transcription factor Zinc Finger Protein 143 (ZNF143) regulates the expression of genes associated with cell cycle and cell division, and that downregulation of ZNF143 induces cell cycle arrest at G2/M. To assess the function of ZNF143 expression in the cell cycle, we established two cells with forced expression of ZNF143 derived from PC3 prostate cancer cell lines. These cell lines overexpress genes associated with cell cycle and cell division, such as polo-like kinase 1 (PLK1), aurora kinase B (AURKB) and some minichromosome maintenance complex components (MCM). However, the doubling time of cells with forced expression of ZNF143 was approximately twice as long as its control counterpart cell line. Analysis following serum starvation and re-seeding showed that PC3 cells were synchronized at G1 in the cell cycle. Also, ZNF143 expression fluctuated, and was at its lowest level in G2/M. However, PC3 cells with forced expression of ZNF143 synchronized at G2/M, and showed lack of cell cycle-dependent fluctuation of nuclear expression of MCM proteins. Furthermore, G2/M population of both cisplatin-resistant PCDP6 cells over-expressing ZNF143 (derived from PC3 cells) and cells with forced expression of ZNF143 was significantly higher than that of each counterpart, and the doubling time of PCDP6 cells is about 2.5 times longer than that of PC3 cells. These data suggested that fluctuations in ZNF143 expression are required both for gene expression associated with cell cycle and for cell division

  7. Forced Expression of ZNF143 Restrains Cancer Cell Growth

    Energy Technology Data Exchange (ETDEWEB)

    Izumi, Hiroto, E-mail: h-izumi@med.uoeh-u.ac.jp; Yasuniwa, Yoshihiro; Akiyama, Masaki; Yamaguchi, Takahiro; Kuma, Akihiro; Kitamura, Noriaki; Kohno, Kimitoshi [Department of Molecular Biology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555 (Japan)

    2011-10-19

    We previously reported that the transcription factor Zinc Finger Protein 143 (ZNF143) regulates the expression of genes associated with cell cycle and cell division, and that downregulation of ZNF143 induces cell cycle arrest at G2/M. To assess the function of ZNF143 expression in the cell cycle, we established two cells with forced expression of ZNF143 derived from PC3 prostate cancer cell lines. These cell lines overexpress genes associated with cell cycle and cell division, such as polo-like kinase 1 (PLK1), aurora kinase B (AURKB) and some minichromosome maintenance complex components (MCM). However, the doubling time of cells with forced expression of ZNF143 was approximately twice as long as its control counterpart cell line. Analysis following serum starvation and re-seeding showed that PC3 cells were synchronized at G1 in the cell cycle. Also, ZNF143 expression fluctuated, and was at its lowest level in G2/M. However, PC3 cells with forced expression of ZNF143 synchronized at G2/M, and showed lack of cell cycle-dependent fluctuation of nuclear expression of MCM proteins. Furthermore, G2/M population of both cisplatin-resistant PCDP6 cells over-expressing ZNF143 (derived from PC3 cells) and cells with forced expression of ZNF143 was significantly higher than that of each counterpart, and the doubling time of PCDP6 cells is about 2.5 times longer than that of PC3 cells. These data suggested that fluctuations in ZNF143 expression are required both for gene expression associated with cell cycle and for cell division.

  8. Is there much variation in variation? Revisiting statistics of small area variation in health services research

    Directory of Open Access Journals (Sweden)

    Ibáñez Berta

    2009-04-01

    Full Text Available Abstract Background The importance of Small Area Variation Analysis for policy-making contrasts with the scarcity of work on the validity of the statistics used in these studies. Our study aims at 1 determining whether variation in utilization rates between health areas is higher than would be expected by chance, 2 estimating the statistical power of the variation statistics; and 3 evaluating the ability of different statistics to compare the variability among different procedures regardless of their rates. Methods Parametric bootstrap techniques were used to derive the empirical distribution for each statistic under the hypothesis of homogeneity across areas. Non-parametric procedures were used to analyze the empirical distribution for the observed statistics and compare the results in six situations (low/medium/high utilization rates and low/high variability. A small scale simulation study was conducted to assess the capacity of each statistic to discriminate between different scenarios with different degrees of variation. Results Bootstrap techniques proved to be good at quantifying the difference between the null hypothesis and the variation observed in each situation, and to construct reliable tests and confidence intervals for each of the variation statistics analyzed. Although the good performance of Systematic Component of Variation (SCV, Empirical Bayes (EB statistic shows better behaviour under the null hypothesis, it is able to detect variability if present, it is not influenced by the procedure rate and it is best able to discriminate between different degrees of heterogeneity. Conclusion The EB statistics seems to be a good alternative to more conventional statistics used in small-area variation analysis in health service research because of its robustness.

  9. [Geographic variations in freshwater molluscs].

    Science.gov (United States)

    Vinarskiĭ, M V

    2012-01-01

    The phenomenon of geographic variation is known in practically all taxa of living beings. However, the reality of this phenomenon in freshwater molluscs (snails and bivalves) has many times been questioned in the past. It was accepted that these animals do not demonstrate spatially-oriented variation, where specific "local race" is arisen in each specific habitat. Till the beginning of 1970s, there was no statistical evidence that geographic clines in freshwater molluscs really exist. However, a few species of freshwater molluscs has been studied in this respect so far, therefore it is almost impossible to draw any general patterns of geographical variation in this group of animals. Most species of freshwater molluscs studied to the date exhibit statistically significant decrease of their body size in the south-north direction. Perhaps, it may be explained by decrease of the duration of the growth season in high latitudes. Some species of freshwater snails demonstrate clinal changes in shell proportions. This allows to reject subspecies separation within these species since diagnostic characters of such "subspecies" may blur when geographic variation is taken into consideration. The data on geographic variation in anatomical traits in freshwater molluscs is much more scarce. At least one species of pond snails (Lymnaea terebra) demonstrates clinal variation in proportions of the copulative apparatus in the south-north direction. Further studies of geographic variation in freshwater molluscs should reveal whether it is truly adaptive, i.e. whether geographical clines have underlying genetic basis. Otherwise, the clines may arise as a result of direct modifying effect of a habitat.

  10. Variation in N-linked carbohydrate chains in different batches of two chimeric monoclonal IgG1 antibodies produced by different murine SP2/0 transfectoma cell subclones.

    Science.gov (United States)

    Bergwerff, A A; Stroop, C J; Murray, B; Holtorf, A P; Pluschke, G; Van Oostrum, J; Kamerling, J P; Vliegenthart, J F

    1995-06-01

    Two chimeric human/murine monoclonal antibodies were constructed by substitution of the murine constant regions with human gamma 1 and kappa constant regions for heavy and light chains, respectively. The chimeric human/murine molecules are anti-idiotypic antibodies, meaning that they were directed against the antigen binding site in the variable region of another antibody. Antibody batches were produced under identical production conditions, using two selected SP2/0 myeloma cell subclones, which produce chimeric antibodies with different variable regions, but identical constant regions. Several samples were collected during the production of the antibodies in hollow-fibre reactors. The heavy chain, but not the light chain, of the two different chimeric IgG1 antibodies is glycosylated. Structural analysis of the enzymically released N-linked carbohydrate chains by 1H-NMR spectroscopy, as well as by chromatographic profiling, demonstrated that the collection of N-glycans comprises a small amount of monoantennary, and for the greater part diantennary structures. The N-glycans are completely (alpha 1-->6)-fucosylated at the innermost GlcNAc residue. The antennae of the neutral diantennary N-glycans are built up from GlcNAc beta 1-->2, Gal beta 1-->4GlcNAc beta 1-->2 or Gal alpha 1-->3G alpha 1 beta 1-->4GlcNAc beta 1-->2 elements, whereas the antennae of the neutral monoantennary carbohydrate chains have only (beta 1-->2)-linked GlcNAc residues. Galactosylation of the GlcNAc beta 1-->2Man alpha 1-->6 branch occurs four times more frequently than that of the GlcNAc beta 1-->2Man alpha 1-->3 branch, independently of the production batch. A small amount of the diantennary N-glycans are mono- or disialylated, carrying N-acetylneuraminic acid (Neu5Ac) or N-glycolylneuraminic acid (Neu5Gc), exclusively (alpha 2-->6)-linked to beta Gal. Analysis of the different production batches demonstrates that the structures of the N-linked carbohydrate chains are identical in the two

  11. Seasonal variation in sports participation.

    Science.gov (United States)

    Schüttoff, Ute; Pawlowski, Tim

    2018-02-01

    This study explores indicators describing socio-demographics, sports participation characteristics and motives which are associated with variation in sports participation across seasons. Data were drawn from the German Socio-Economic Panel which contains detailed information on the sports behaviour of adults in Germany. Overall, two different measures of seasonal variation are developed and used as dependent variables in our regression models. The first variable measures the coefficient of (seasonal) variation in sport-related energy expenditure per week. The second variable measures whether activity drops below the threshold as defined by the World Health Organization (WHO). Results suggest that the organisational setting, the intensity and number of sports practised, and the motive for participation are strongly correlated with the variation measures used. For example, both, participation in a sports club and a commercial facility, are associated with reduced seasonal variation and a significantly higher probability of participating at a volume above the WHO threshold across all seasons. These findings give some impetus for policymaking and the planning of sports programmes as well as future research directions.

  12. Variational methods in molecular modeling

    CERN Document Server

    2017-01-01

    This book presents tutorial overviews for many applications of variational methods to molecular modeling. Topics discussed include the Gibbs-Bogoliubov-Feynman variational principle, square-gradient models, classical density functional theories, self-consistent-field theories, phase-field methods, Ginzburg-Landau and Helfrich-type phenomenological models, dynamical density functional theory, and variational Monte Carlo methods. Illustrative examples are given to facilitate understanding of the basic concepts and quantitative prediction of the properties and rich behavior of diverse many-body systems ranging from inhomogeneous fluids, electrolytes and ionic liquids in micropores, colloidal dispersions, liquid crystals, polymer blends, lipid membranes, microemulsions, magnetic materials and high-temperature superconductors. All chapters are written by leading experts in the field and illustrated with tutorial examples for their practical applications to specific subjects. With emphasis placed on physical unders...

  13. Solid mechanics a variational approach

    CERN Document Server

    Dym, Clive L

    2013-01-01

    Solid Mechanics: A Variational Approach, Augmented Edition presents a lucid and thoroughly developed approach to solid mechanics for students engaged in the study of elastic structures not seen in other texts currently on the market. This work offers a clear and carefully prepared exposition of variational techniques as they are applied to solid mechanics. Unlike other books in this field, Dym and Shames treat all the necessary theory needed for the study of solid mechanics and include extensive applications. Of particular note is the variational approach used in developing consistent structural theories and in obtaining exact and approximate solutions for many problems.  Based on both semester and year-long courses taught to undergraduate seniors and graduate students, this text is geared for programs in aeronautical, civil, and mechanical engineering, and in engineering science. The authors’ objective is two-fold: first, to introduce the student to the theory of structures (one- and two-dimensional) as ...

  14. Characterization and functional analysis of a slow-cycling subpopulation in colorectal cancer enriched by cell cycle inducer combined chemotherapy.

    Science.gov (United States)

    Wu, Feng-Hua; Mu, Lei; Li, Xiao-Lan; Hu, Yi-Bing; Liu, Hui; Han, Lin-Tao; Gong, Jian-Ping

    2017-10-03

    The concept of cancer stem cells has been proposed in various malignancies including colorectal cancer. Recent studies show direct evidence for quiescence slow-cycling cells playing a role in cancer stem cells. There exists an urgent need to isolate and better characterize these slow-cycling cells. In this study, we developed a new model to enrich slow-cycling tumor cells using cell-cycle inducer combined with cell cycle-dependent chemotherapy in vitro and in vivo . Our results show that Short-term exposure of colorectal cancer cells to chemotherapy combined with cell-cycle inducer enriches for a cell-cycle quiescent tumor cell population. Specifically, these slow-cycling tumor cells exhibit increased chemotherapy resistance in vitro and tumorigenicity in vivo . Notably, these cells are stem-cell like and participate in metastatic dormancy. Further exploration indicates that slow-cycling colorectal cancer cells in our model are less sensitive to cytokine-induced-killer cell mediated cytotoxic killing in vivo and in vitro . Collectively, our cell cycle inducer combined chemotherapy exposure model enriches for a slow-cycling, dormant, chemo-resistant tumor cell sub-population that are resistant to cytokine induced killer cell based immunotherapy. Studying unique signaling pathways in dormant tumor cells enriched by cell cycle inducer combined chemotherapy treatment is expected to identify novel therapeutic targets for preventing tumor recurrence.

  15. Decadal variations in groundwater quality

    DEFF Research Database (Denmark)

    Jessen, Søren; Postma, Dieke; Thorling, Lærke

    2017-01-01

    Twenty-five years of groundwater quality monitoring in a sandy aquifer beneath agricultural fields showed large temporal and spatial variations in major ion groundwater chemistry, which were linked closely to the nitrate (NO3) content of agricultural recharge. Between 1988 and 2013, the NO3 content...... loading. Agriculture thus is an important determinant of major ion groundwater chemistry. Temporal and spatial variations in the groundwater quality were simulated using a 2D reactive transport model, which combined effects of the historical NO3 leaching and denitrification, with dispersive mixing...

  16. Structure variations of carbonizing lignin

    International Nuclear Information System (INIS)

    Otani, C.; Polidoro, H.A.; Otani, S.; Craievich, A.F.

    1984-01-01

    The studied lignin is a by-product of the process of ethanol production from eucaliptus. It was heat-treated under inert atmosphere conditions at increasing temperatures from 300C up to 2400C. The structural variations were studied by wide-angle X-ray diffraction, small-angle X-ray scattering and infrared absorption spectroscopy. The bulk and 'real' density of the compacted materials have also been determined as functions of the final temperature. These experimental results enabled us to establish a mechanism of structure variation based on the formation of a turbostratic graphite-like and porous structure within the initially amorphous lignin matrix. (Author) [pt

  17. Protein dynamics in individual human cells: experiment and theory.

    Directory of Open Access Journals (Sweden)

    Ariel Aharon Cohen

    Full Text Available A current challenge in biology is to understand the dynamics of protein circuits in living human cells. Can one define and test equations for the dynamics and variability of a protein over time? Here, we address this experimentally and theoretically, by means of accurate time-resolved measurements of endogenously tagged proteins in individual human cells. As a model system, we choose three stable proteins displaying cell-cycle-dependant dynamics. We find that protein accumulation with time per cell is quadratic for proteins with long mRNA life times and approximately linear for a protein with short mRNA lifetime. Both behaviors correspond to a classical model of transcription and translation. A stochastic model, in which genes slowly switch between ON and OFF states, captures measured cell-cell variability. The data suggests, in accordance with the model, that switching to the gene ON state is exponentially distributed and that the cell-cell distribution of protein levels can be approximated by a Gamma distribution throughout the cell cycle. These results suggest that relatively simple models may describe protein dynamics in individual human cells.

  18. Derivation of Schwinger variational principles

    International Nuclear Information System (INIS)

    Szmytkowski, R.

    2003-01-01

    We present systematic derivations of bilinear and fractional Schwinger variational principles for matrix elements of a generalized transition operator in the context of quantum mechanical potential scattering. The employed method is based on a generalization of the method of Lagrange multipliers

  19. Variation of elements in nature

    International Nuclear Information System (INIS)

    Venkatavaradan, V.S.

    1977-01-01

    A review is made of nuclear reactions and other physical processes during the formations of planets, leading to the existing elemental and isotope variation. Thermonuclear fusion, radioactive decay, nuclear reactions caused by cosmic rays, man-made isotopes as some of the causes are discussed in details

  20. Symmetries and variation of spectra

    OpenAIRE

    Bhatia, Rajendra; Elsner, Ludwig

    1992-01-01

    An interesting class of matrices is shown to have the property that the spectrum of each of its elements is invariant under multiplication by p-th roots of unity. For this class and tor a class of Hamiltonian matrices improved spectral variation bounds are obtained.

  1. Linking numbers and variational method

    International Nuclear Information System (INIS)

    Oda, I.; Yahikozawa, S.

    1989-09-01

    The ordinary and generalized linking numbers for two surfaces of dimension p and n-p-1 in an n dimensional manifold are derived. We use a variational method based on the properties of topological quantum field theory in order to derive them. (author). 13 refs, 2 figs

  2. Morphological variation of Stromatella monostromatica

    Science.gov (United States)

    Nielsen, Ruth

    1988-09-01

    Thirty two isolates of Stromatella monostromatica (Dangeard) Kornmann were studied in unialgal culture; extensive morphological variation was documented. The shape of bicellular germlings and development of young plants were similar for all isolates which had globular sporangia. These features are, therefore, the most important diagnostic characteristics of the species. The widespread distribution of S. monostromatica suggests that this is a cosmopolitan species.

  3. On quadratic variation of martingales

    Indian Academy of Sciences (India)

    starting point for the development of stochastic calculus for continuous semimartingales without bringing in any results from general theory of processes (see [5]). The almost sure convergence of Qn t to 〈M,M〉t also gives a pathwise formula for the quadratic variation of a continuous local martingale. It also directly shows that ...

  4. On quadratic variation of martingales

    Indian Academy of Sciences (India)

    On quadratic variation of martingales. 459. The proof relied on the theory of stochastic integration. Subsequently, in Karandikar. [4], the formula was derived using only Doob's maximal inequality. Thus this could be the starting point for the development of stochastic calculus for continuous semimartingales without bringing in ...

  5. Evolutionary significance of epigenetic variation

    NARCIS (Netherlands)

    Richards, C.L.; Verhoeven, K.J.F.; Bossdorf, O.; Wendel, J.F.; Greilhuber, J.; Dolezel, J.; Leitch, I.J.

    2012-01-01

    Several chapters in this volume demonstrate how epigenetic work at the molecular level over the last few decades has revolutionized our understanding of genome function and developmental biology. However, epigenetic processes not only further our understanding of variation and regulation at the

  6. PHOTOSPHERIC VARIATIONS OF THE SUPERGIANT γ Cyg

    International Nuclear Information System (INIS)

    Gray, David F.

    2010-01-01

    New high-resolution spectroscopic observations of the supergiant γ Cyg (F8 Iab) taken between 2000 and 2008 consistently show strongly reversed-C-shaped bisectors for all unblended spectral lines. Small-amplitude variations in radial velocity and line shapes occur in an irregular manner with time scales ∼100 days and longer. The radial velocities occasionally show changes as large as 2 km s -1 , but much smaller changes are going on continuously. Differential line bisectors show shape changes and Doppler displacement characteristic of radial expansion and contraction. These might arise from non-periodic radial pulsation-like motions or from the appearance of giant convection cells that occupy most of the visible hemisphere of the star. Line-depth ratios are correlated with the line shifts on a seasonal basis and indicate temperature changes ranging up to ∼15 K, with larger temperature occurring during times of most rapid contraction.

  7. Deep sequence analysis of non-small cell lung cancer: Integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations

    Directory of Open Access Journals (Sweden)

    Krishna R Kalari

    2012-02-01

    Full Text Available KRAS mutations are highly prevalent in non-small cell lung cancer (NSCLC, and tumors harboring these mutations tend to be aggressive and resistant to chemotherapy. We used next-generation sequencing technology to identify pathways that are specifically altered in lung tumors harboring a KRAS mutation. Paired-end RNA-sequencing of 15 primary lung adenocarcinoma tumors (8 harboring mutant KRAS and 7 with wild-type KRAS were performed. Sequences were mapped to the human genome, and genomic features, including differentially expressed genes, alternate splicing isoforms and single nucleotide variants, were determined for tumors with and without KRAS mutation using a variety of computational methods. Network analysis was carried out on genes showing differential expression (374 genes, alternate splicing (259 genes and SNV-related changes (65 genes in NSCLC tumors harboring a KRAS mutation. Genes exhibiting two or more connections from the lung adenocarcinoma network were used to carry out integrated pathway analysis. The most significant signaling pathways identified through this analysis were the NFkB, ERK1/2 and AKT pathways. A 27 gene mutant KRAS-specific sub network was extracted based on gene-gene connections within the integrated network, and interrogated for druggable targets. Our results confirm previous evidence that mutant KRAS tumors exhibit activated NFkB, ERK1/2 and AKT pathways and may be preferentially sensitive to target therapeutics toward these pathways. In addition, our analysis indicates novel, previously unappreciated links between mutant KRAS and the TNFR and PPARγ signaling pathways, suggesting that targeted PPARγ antagonists and TNFR inhibitors may be useful therapeutic strategies for treatment of mutant KRAS lung tumors. Our study is the first to integrate genomic features from RNA-Seq data from NSCLC and to define a first draft genomic landscape model that is unique to tumors with oncogenic KRAS mutations.

  8. Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations

    International Nuclear Information System (INIS)

    Kalari, Krishna R.; Rossell, David; Necela, Brian M.; Asmann, Yan W.; Nair, Asha

    2012-01-01

    KRAS mutations are highly prevalent in non-small cell lung cancer (NSCLC), and tumors harboring these mutations tend to be aggressive and resistant to chemotherapy. We used next-generation sequencing technology to identify pathways that are specifically altered in lung tumors harboring a KRAS mutation. Paired-end RNA-sequencing of 15 primary lung adenocarcinoma tumors (8 harboring mutant KRAS and 7 with wild-type KRAS) were performed. Sequences were mapped to the human genome, and genomic features, including differentially expressed genes, alternate splicing isoforms and single nucleotide variants, were determined for tumors with and without KRAS mutation using a variety of computational methods. Network analysis was carried out on genes showing differential expression (374 genes), alternate splicing (259 genes), and SNV-related changes (65 genes) in NSCLC tumors harboring a KRAS mutation. Genes exhibiting two or more connections from the lung adenocarcinoma network were used to carry out integrated pathway analysis. The most significant signaling pathways identified through this analysis were the NFκB, ERK1/2, and AKT pathways. A 27 gene mutant KRAS-specific sub network was extracted based on gene–gene connections from the integrated network, and interrogated for druggable targets. Our results confirm previous evidence that mutant KRAS tumors exhibit activated NFκB, ERK1/2, and AKT pathways and may be preferentially sensitive to target therapeutics toward these pathways. In addition, our analysis indicates novel, previously unappreciated links between mutant KRAS and the TNFR and PPARγ signaling pathways, suggesting that targeted PPARγ antagonists and TNFR inhibitors may be useful therapeutic strategies for treatment of mutant KRAS lung tumors. Our study is the first to integrate genomic features from RNA-Seq data from NSCLC and to define a first draft genomic landscape model that is unique to tumors with oncogenic KRAS mutations.

  9. An ecophysiological and developmental perspective on variation in vessel diameter.

    Science.gov (United States)

    Hacke, Uwe G; Spicer, Rachel; Schreiber, Stefan G; Plavcová, Lenka

    2017-06-01

    Variation in xylem vessel diameter is one of the most important parameters when evaluating plant water relations. This review provides a synthesis of the ecophysiological implications of variation in lumen diameter together with a summary of our current understanding of vessel development and its endogenous regulation. We analyzed inter-specific variation of the mean hydraulic vessel diameter (D v ) across biomes, intra-specific variation of D v under natural and controlled conditions, and intra-plant variation. We found that the D v measured in young branches tends to stay below 30 µm in regions experiencing winter frost, whereas it is highly variable in the tropical rainforest. Within a plant, the widest vessels are often found in the trunk and in large roots; smaller diameters have been reported for leaves and small lateral roots. D v varies in response to environmental factors and is not only a function of plant size. Despite the wealth of data on vessel diameter variation, the regulation of diameter is poorly understood. Polar auxin transport through the vascular cambium is a key regulator linking foliar and xylem development. Limited evidence suggests that auxin transport is also a determinant of vessel diameter. The role of auxin in cell expansion and in establishing longitudinal continuity during secondary growth deserve further study. © 2016 John Wiley & Sons Ltd.

  10. Height dependence of secondary cosmic ray variations

    International Nuclear Information System (INIS)

    Belov, A.V.; Dorman, L.I.; Sirotina, I.V.

    1986-01-01

    Altitude dependences of coupling coefficients and secondary cosmic ray variations are investigated. The partial and variational barometric coefficients are calculated according to data on coupling coefficients of a neutron component. Application of data on altitude dependence of variations for calculation of barometric coefficient changes and for determination of a rigidity primary variation spectrum is discussed

  11. High frequency genetic variation of purine biosynthesis genes is a mechanism of success in Campylobacter jejuni

    Science.gov (United States)

    Phenotypic variation is prevalent among progeny of the zoonotic pathogen Campylobacter jejuni, the leading agent of enterocolitis in the developed world. Heterogeneity bestows increased survival to bacterial populations because variable phenotypes ensure some cells will be protected against future s...

  12. Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation

    DEFF Research Database (Denmark)

    Csikász-Nagy, Attila; Kapuy, Orsolya; Tóth, Attila

    2009-01-01

    The eukaryotic cell cycle requires precise temporal coordination of the activities of hundreds of 'executor' proteins (EPs) involved in cell growth and division. Cyclin-dependent protein kinases (Cdks) play central roles in regulating the production, activation, inactivation and destruction......) from Cdk1. By mathematical modelling, we show that such FFLs can activate EPs at different phases of the cell cycle depending of the effective signs (+ or -) of the regulatory steps of the FFL. We provide several case studies of EPs that are controlled by FFLs exactly as our models predict. The signal......-transduction properties of FFLs allow one (or a few) Cdk signal(s) to drive a host of cell cycle responses in correct temporal sequence....

  13. Outdoor radon variation in Romania

    International Nuclear Information System (INIS)

    Simion, Elena; Simion, Florin

    2008-01-01

    Full text: The results of a long-term survey (1992 - 2006) of the variations of outdoor radon concentrations in semi-natural location from Romania are reported in the present paper. Measurements, covering between two and four sessions of the day (morning, afternoon, evening and night), were performed on a daily bases by 37 Environmental Radioactivity Monitoring Stations from National Environmental Radioactivity Survey Network. The method used was based on indirect determination of outdoor radon from aerosol samples collected on glass micro-fibre filters by drawing the air through the filters. The sampling was performed in a fixed place at a height of 2 m above the ground surface. Total beta counting of aerosol samples collected was performed immediately and after 20 hours. Values recorded during the years of continuous measurement indicated the presence of several patterns in the long-term variation of outdoor radon concentration: diurnal, seasonal and annual variation. For diurnal variation, outdoor radon concentration shows a maximum values in the night (early hours) and minimum values by day (in the afternoon). On average, this maximum is a factor of 2 higher than the minimum. Late autumn - beginning of winter maximum and an early spring minimum are characteristic for seasonal patterns. In the long term a seasonal pattern was observed for diurnal variation, with an average diurnal maximum to minimum ratio of 1.33 in winter compared with 3.0 in the summer months. The variations of outdoor radon levels showed little correlation with the uranium concentration of the ground and were attributed to changes in soil moisture content. In dry seasons, because of the low precipitation, the soil was drying out in the summer allowing fractures to develop and radon to migrate easily through the ground. Depending on micro-climatic and geological conditions, outdoor radon average concentrations in different regions of Romania are from 1200 mBq/mc to 13065 mBq/mc. The smallest

  14. Cellular Allometry of Mitochondrial Functionality Establishes the Optimal Cell Size.

    Science.gov (United States)

    Miettinen, Teemu P; Björklund, Mikael

    2016-11-07

    Eukaryotic cells attempt to maintain an optimal size, resulting in size homeostasis. While cellular content scales isometrically with cell size, allometric laws indicate that metabolism per mass unit should decline with increasing size. Here we use elutriation and single-cell flow cytometry to analyze mitochondrial scaling with cell size. While mitochondrial content increases linearly, mitochondrial membrane potential and oxidative phosphorylation are highest at intermediate cell sizes. Thus, mitochondrial content and functional scaling are uncoupled. The nonlinearity of mitochondrial functionality is cell size, not cell cycle, dependent, and it results in an optimal cell size whereby cellular fitness and proliferative capacity are maximized. While optimal cell size is controlled by growth factor signaling, its establishment and maintenance requires mitochondrial dynamics, which can be controlled by the mevalonate pathway. Thus, optimization of cellular fitness and functionality through mitochondria can explain the requirement for size control, as well as provide means for its maintenance. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Bernoulli Variational Problem and Beyond

    KAUST Repository

    Lorz, Alexander

    2013-12-17

    The question of \\'cutting the tail\\' of the solution of an elliptic equation arises naturally in several contexts and leads to a singular perturbation problem under the form of a strong cut-off. We consider both the PDE with a drift and the symmetric case where a variational problem can be stated. It is known that, in both cases, the same critical scale arises for the size of the singular perturbation. More interesting is that in both cases another critical parameter (of order one) arises that decides when the limiting behaviour is non-degenerate. We study both theoretically and numerically the values of this critical parameter and, in the symmetric case, ask if the variational solution leads to the same value as for the maximal solution of the PDE. Finally we propose a weak formulation of the limiting Bernoulli problem which incorporates both Dirichlet and Neumann boundary condition. © 2013 Springer-Verlag Berlin Heidelberg.

  16. VARIATIONAL PRINCIPLE FOR PLANETARY INTERIORS

    International Nuclear Information System (INIS)

    Zeng, Li; Jacobsen, Stein B.

    2016-01-01

    In the past few years, the number of confirmed planets has grown above 2000. It is clear that they represent a diversity of structures not seen in our own solar system. In addition to very detailed interior modeling, it is valuable to have a simple analytical framework for describing planetary structures. The variational principle is a fundamental principle in physics, entailing that a physical system follows the trajectory, which minimizes its action. It is alternative to the differential equation formulation of a physical system. Applying the variational principle to the planetary interior can beautifully summarize the set of differential equations into one, which provides us some insight into the problem. From this principle, a universal mass–radius relation, an estimate of the error propagation from the equation of state to the mass–radius relation, and a form of the virial theorem applicable to planetary interiors are derived.

  17. Tidal variations of earth rotation

    Science.gov (United States)

    Yoder, C. F.; Williams, J. G.; Parke, M. E.

    1981-01-01

    The periodic variations of the earths' rotation resulting from the tidal deformation of the earth by the sun and moon were rederived including terms with amplitudes of 0.002 millisec and greater. The series applies to the mantle, crust, and oceans which rotate together for characteristic tidal periods; the scaling parameter is the ratio of the fraction of the Love number producing tidal variations in the moment of inertia of the coupled mantle and oceans (k) to the dimensionless polar moment of inertia of the coupled moments (C). The lunar laser ranging data shows that k/C at monthly and fortnightly frequencies equals 0.99 + or - 0.15 and 0.99 + or - 0.20 as compared to the theoretical value of 0.94 + or - 0.04.

  18. Numerical integration of variational equations.

    Science.gov (United States)

    Skokos, Ch; Gerlach, E

    2010-09-01

    We present and compare different numerical schemes for the integration of the variational equations of autonomous Hamiltonian systems whose kinetic energy is quadratic in the generalized momenta and whose potential is a function of the generalized positions. We apply these techniques to Hamiltonian systems of various degrees of freedom and investigate their efficiency in accurately reproducing well-known properties of chaos indicators such as the Lyapunov characteristic exponents and the generalized alignment indices. We find that the best numerical performance is exhibited by the "tangent map method," a scheme based on symplectic integration techniques which proves to be optimal in speed and accuracy. According to this method, a symplectic integrator is used to approximate the solution of the Hamilton equations of motion by the repeated action of a symplectic map S , while the corresponding tangent map TS is used for the integration of the variational equations. A simple and systematic technique to construct TS is also presented.

  19. Variational approach in transport theory

    Energy Technology Data Exchange (ETDEWEB)

    Panta Pazos, R. [Nucler Engineering Department, UFRGS, Porto-Alegre (Brazil); Tullio de Vilhena, M. [Institute of Mathematics, UFRGS, Porto-Alegre (Brazil)

    2004-07-01

    In this work we present a variational approach to some methods to solve transport problems of neutral particles. We consider a convex domain X (for example the geometry of a slab, or a convex set in the plane, or a convex bounded set in the space) and we use discrete ordinates quadrature to get a system of differential equations derived from the neutron transport equation. The boundary conditions are vacuum for a subset of the boundary, and of specular reflection for the complementary subset of the boundary. Recently some different approximation methods have been presented to solve these transport problems. We introduce in this work the adjoint equations and the conjugate functions obtained by means of the variational approach. First we consider the general formulation, and then some numerical methods such as spherical harmonics and spectral collocation method. (authors)

  20. Quantitative variation in natural populations

    International Nuclear Information System (INIS)

    Parsons, P.A.

    1975-01-01

    Quantitative variation is considered in natural populations using Drosophila as the example. A knowledge of such variation enables its rapid exploitation in directional selection experiments as shown for scutellar chaeta number. Where evidence has been obtained, genetic architectures are in qualitative agreement with Mather's concept of balance for traits under stabilizing selection. Additive genetic control is found for acute environmental stresses, but not for less acute stresses as shown by exposure to 60 Co-γ rays. D. simulans probably has a narrower ecological niche than its sibling species D. melanogaster associated with lower genetic heterogeneity. One specific environmental stress to which D. simulans is sensitive in nature is ethyl alcohol as shown by winery data. (U.S.)

  1. Coarse Grained Exponential Variational Autoencoders

    KAUST Repository

    Sun, Ke

    2017-02-25

    Variational autoencoders (VAE) often use Gaussian or category distribution to model the inference process. This puts a limit on variational learning because this simplified assumption does not match the true posterior distribution, which is usually much more sophisticated. To break this limitation and apply arbitrary parametric distribution during inference, this paper derives a \\\\emph{semi-continuous} latent representation, which approximates a continuous density up to a prescribed precision, and is much easier to analyze than its continuous counterpart because it is fundamentally discrete. We showcase the proposition by applying polynomial exponential family distributions as the posterior, which are universal probability density function generators. Our experimental results show consistent improvements over commonly used VAE models.

  2. Secular variations of tropospheric ozone

    Energy Technology Data Exchange (ETDEWEB)

    Khrgian, A.KH.

    1988-02-01

    The dependence of secular variations of tropospheric ozone on decreases of temperature and cloud growth in Central Europe is assessed on the basis of Vienna, Paris, and Athens data for 1853-1920. Decreases in ozone content occurring with a certain time lag after major volcanic eruptions (e.g., Krakatoa) are examined. The effect of the Tungusk-meteorite fall on ozone content is also discussed. 13 references.

  3. Secular variations of tropospheric ozone

    Science.gov (United States)

    Khrgian, A. Kh.

    1988-02-01

    The dependence of secular variations of tropospheric ozone on decreases of temperature and cloud growth in Central Europe is assessed on the basis of Vienna, Paris, and Athens data for 1853-1920. Decreases in ozone content occurring with a certain time lag after major volcanic eruptions (e.g., Krakatoa) are examined. The effect of the Tungusk-meteorite fall on ozone content is also discussed.

  4. On Quadratic Variation of Martingales

    Indian Academy of Sciences (India)

    where D ( [ 0 , ∞ ) , R ) denotes the class of real valued r.c.l.l. functions on [ 0 , ∞ ) such that for a locally square integrable martingale ( M t ) with r.c.l.l. paths,. Ψ ( M . ( ) ) = A . ( ). gives the quadratic variation process (written usually as [ M , M ] t ) of ( M t ) . We also show that this process ( A t ) is the unique increasing ...

  5. Variations of posterior vitreous detachment

    OpenAIRE

    Kakehashi, A.; Kado, M.; Akiba, J.; Hirokawa, H.

    1997-01-01

    AIMS—To identify variations in posterior vitreous detachment (PVD) and establish a clinical classification system for PVD.
METHODS—400 consecutive eyes were examined using biomicroscopy and vitreous photography and classified the PVD variations—complete PVD with collapse, complete PVD without collapse, partial PVD with thickened posterior vitreous cortex (TPVC), or partial PVD without TPVC.
RESULTS—In each PVD type, the most frequently seen ocular pathologies were as follows: in complete PVD ...

  6. Deep Feature Consistent Variational Autoencoder

    OpenAIRE

    Hou, Xianxu; Shen, Linlin; Sun, Ke; Qiu, Guoping

    2016-01-01

    We present a novel method for constructing Variational Autoencoder (VAE). Instead of using pixel-by-pixel loss, we enforce deep feature consistency between the input and the output of a VAE, which ensures the VAE's output to preserve the spatial correlation characteristics of the input, thus leading the output to have a more natural visual appearance and better perceptual quality. Based on recent deep learning works such as style transfer, we employ a pre-trained deep convolutional neural net...

  7. Variational nodal transport perturbation theory

    International Nuclear Information System (INIS)

    Laurin-Kovitz, K.F.; Lewis, E.E.

    1996-01-01

    A perturbation method based on the variational nodal method for solving the neutron transport equation is developed for multidimensional geometries. The method utilizes the solution of the corresponding adjoint transport equation to calculate changes in the critical eigenvalue due to cross-section changes. Both first-order and exact perturbation theory expressions are derived. The adjoint solution algorithm has been formulated and incorporated into the variational nodal option of the Argonne National Laboratory DIF3D production code. To demonstrate the efficacy of the methods, perturbation calculations are performed on the three-dimensional Takeda benchmark problems in both Cartesian and hexagonal geometries. The resulting changes in eigenvalue are also obtained by direct calculation with the variational nodal method and compared with the change approximated by the first-order and exact theory expressions from the perturbation method. Exact perturbation results are in excellent agreement with the actual eigenvalue differences calculated in VARIANT. First-order theory holds well for sufficiently small perturbations. The times required for the perturbation calculations are small compared with those expended for the base-forward and adjoint calculations

  8. Longitudinal Variations in Jupiter's Winds

    Science.gov (United States)

    Simon-Miller, Amy A.; Gierasch, P. J.; Tierney, G.

    2010-01-01

    Long-term studies of Jupiter's zonal wind field revealed temporal variations on the order of 20 to 40 m/s at many latitudes, greater than the typical data uncertainties of 1 to 10 m/s. No definitive periodicities were evident, however, though some latitudinally-confined signals did appear at periods relevant to the Quasi- Quadrennial Oscillation (Simon-Miller & Gierasch, Icarus, in press). As the QQO appears, from vertical temperature profiles, to propagate downward, it is unclear why a signal is not more obvious, unless other processes dominate over possibly weaker forcing from the QQO. An additional complication is that zonal wind profiles represent an average over some particular set of longitudes for an image pair and most data sets do not offer global wind coverage. Lien avoiding known features, such as the large anticyclonic vortices especially prevalent in the south, there can be distinct variations in longitude. We present results on the full wind field from Voyager and Cassini data, showing apparent longitudinal variations of up to 60 m/s or more. These are particularly obvious near disruptions such as the South Equatorial Disturbance, even when the feature itself is not clearly visible. These two dates represent very different states of the planet for comparison: Voyagers 1 & 2 flew by Jupiter shortly after a global upheaval, while many regions were in a disturbed state, while the Cassini view is typical of a more quiescent period present during much of the 1990s and early 2000s.

  9. Genetic basis of metabolome variation in yeast.

    Directory of Open Access Journals (Sweden)

    Jeffrey S Breunig

    2014-03-01

    Full Text Available Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across ~ 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.

  10. Action of caffeine on x-irradiated HeLa cells. II. Synergistic lethality

    International Nuclear Information System (INIS)

    Busse, P.M.; Bose, S.K.; Jones, R.W.; Tolmach, L.J.

    1977-01-01

    Postirradiation treatment of HeLa S3 cells with 1 mM caffeine results in a marked diminution of the surviving fraction as scored by colony formation. The decrease is dose dependent; the effect of a 24-hour postirradiation treatment of a nonsynchronous population with caffeine is to change the terminal slope of the survival curve and its intercept. D 0 is reduced from 130 to 60 rad; the extrapolation number is increased about twofold. The amount of postirradiation killing is maximal if cells are exposed to caffeine at a concentration of at least 1 mM for 8 hours; less than 10% of unirradiated cells are killed under these conditions. Dose-response curves were also obtained for synchronous cells at various phases of the cell cycle. Similar results were obtained at all cell ages, but the magnitude of the effect is age dependent. This age dependence was further explored in experiments in which mitotically collected cells were exposed to 300 or 500 rad doses at 2-hour intervals throughout the cell cycle. Treatment with caffeine for 24 hours after irradiation enchances the killing of cells late in the cycle more than cells in G1. The sensitivities of two other cell lines, CHO and EMT6, also were examined; both are substantially less sensitive to caffeine. The smaller cell-cycle dependence of CHO cells is qualitatively the same as that of HeLa cells

  11. Anatomic Variations of the Paranasal Sinuses on CT Scan Images

    Directory of Open Access Journals (Sweden)

    AR. Talaiepour

    2005-12-01

    Full Text Available Statement of Problem: Variation in paranasal sinus anatomy as shown on computed tomographic scans is of potential significance for it may pose risks during surgery or predispose to certain pathologic conditions.Purpose: The aim of this study was to assess the relative frequency and concurrence of variations in paranasal sinus anatomy in a given population and to compare the results with previous investigations conducted on different populations.Materials and Methods: All patients over 16 years of age referred to Valiasr hospital,Tehran, Iran, with paranasal sinus tomographic scans and a clinical diagnosis of chronic sinusitis were considered for this study. After excluding those with altered anatomy(iatrogenic or pathologic, scans of unaltered patients were meticulously analyzed for variations in sinus anatomy. Findings were recorded on the patient’s data sheet. The distance between the maxillary sinus floor and the alveolar ridge at the level of the 1stmolar was recorded. All findings were analyzed, and tested with Chi square, where applicable.Results: Overall 143 patients were analyzed (48.3% male and 51.7% female. The frequency of major sinus variations was: Agger nasi cell in 56.7%, Haller cell in 3.5%,Onodi cell in 7%, nasal septal deviation in 63%, Concha bullosa in 35%, and dental anomalies in 4.9% of the studied cases. The distance between the upper alveolar ridge and maxillary sinus floor was 0-30mm (mean 12.16 on the right, and 0-52mm (mean 12.20 on the left.Conclusion: The frequency of anatomic variations in sinus anatomy may be related to race and heredity. A lower number of cases in addition to the use of low yield imaging may explain the discrepancies observed between our results and other investigations.The findings of the present study were based on computed tomography.

  12. Ethmomaxillary sinus: a particular anatomic variation of the paranasal sinuses

    Energy Technology Data Exchange (ETDEWEB)

    Sirikci, Akif; Bayram, Metin [Department of Radiology, Faculty of Medicine, Gaziantep University, Kolejtepe, 27310, Gaziantep (Turkey); Bayazit, Y.A.; Kanlikama, Muzaffer [Department of Otorhinolaryngology and Head and Neck Surgery, Faculty of Medicine, Gaziantep University, Kolejtepe, 27310, Gaziantep (Turkey)

    2004-02-01

    We assessed the morphological and radiological characteristics of ethmomaxillary sinus (EMS), which is an enlarged posterior ethmoidal air cell occupying the superior portion of the maxillary sinus while draining into superior meatus. This study is based on 1450 patients submitted to CT examination of the paranasal sinuses between 1998 and 2002. Sequential CT scans were obtained in the coronal plane in all the patients with 2.5- to 5-mm section thickness and were evaluated for EMS. The diagnosis of EMS was made when there was a posterior ethmoidal cell occupying the superior part of the maxillary sinus while draining to the superior meatus. When EMS was diagnosed, the morphology of the septum between the and maxillary sinus, and width of the superior meatus, were noted. The EMS was found in 10 of 1450 (0.7%) patients. The coexisting anatomic variations were concha bullosa (50%), upper concha pneumatization (20%), maxillary sinus hypoplasia (20%), uncinate bulla (10%), hypertrophied inferior concha (10%), paradoxic middle concha (10%), and septate maxillary sinus (10%). There was no relation between EMS and sinus disease. The EMS is a rare anatomic variation and does not appear to be associated with sinusitis. The EMS is not a well-studied anatomic variation, and the literature is lacking adequate information about this anatomic variation. This study performed in a large series of patients will possibly contribute to better understanding of this particular anomaly. (orig.)

  13. Gender-specific and menstrual cycle dependent differences in circulating microparticles

    NARCIS (Netherlands)

    Toth, Bettina; Nikolajek, Katharina; Rank, Andreas; Nieuwland, Rienk; Lohse, Peter; Pihusch, Verena; Friese, Klaus; Thaler, Christian J.

    2007-01-01

    In comparison to age-matched men, young women are at increased risk to suffer from venous thromboembolism (VTE). Some risk factors of inherited and acquired thrombophilia are known, but approximately 30% of the overall risk remains unexplained. Recently, a role for microparticles (MP) in coagulation

  14. Solar cycle dependence of the radial gradient of cosmic ray intensity

    International Nuclear Information System (INIS)

    Allen, J.A.V.

    1988-01-01

    Observation of the interplanetary intensity of cosmic rays (E/sub p/>80 MeV) by Pioneers 10 and 11 now spans a sixteen-year time period 1972--1988 and heliocentric radial distances, r/sub 10/ and r/sub 11/, out to 43.7 AU for Pioneer 10 and 25.8 AU for Pioneer 11. Solar modulation continues to be present at the current distances of both spacecraft. The radial gradient of intensity is measured continuously over the slowly varying, outward moving radial segment Δr = r/sub 10/--r/sub 11/. The 50-day mean values of the gradient G vary systematically and cyclically in phase with solar activity as measured by sunspot number, with a maximum value of about 2.1 percent (AU)/sup -1/ at sunspot maximum and a miminum value of about 1.2 percent (AU)/sup -1/ at sunspot minimum. Thus, the apparent scale size of the heliospheric modulation region as measured by 1/G is about 48 AU at solar max and about 83 AU at solar min: a result that is the inverse of the conjectural inference of Randall and Van Allen [1986] using most of the same body of data but a different analytical point of view. There is persuasive evidence that G is independent of radial distance over the range 2.5 to 34 AU in the mid-point of the segment Δr. No dependence of G on heliographic latitude is evident, but this result does not lend itself to a quantitative statement. copyright American Geophysical Union 1988

  15. Diurnal variations of Titan's ionosphere

    Science.gov (United States)

    Cui, J.; Galand, M.; Yelle, R. V.; Vuitton, V.; Wahlund, J.-E.; Lavvas, P. P.; Müller-Wodarg, I. C. F.; Cravens, T. E.; Kasprzak, W. T.; Waite, J. H.

    2009-06-01

    We present our analysis of the diurnal variations of Titan's ionosphere (between 1000 and 1300 km) based on a sample of Ion Neutral Mass Spectrometer (INMS) measurements in the Open Source Ion (OSI) mode obtained from eight close encounters of the Cassini spacecraft with Titan. Although there is an overall ion depletion well beyond the terminator, the ion content on Titan's nightside is still appreciable, with a density plateau of ˜700 cm-3 below ˜1300 km. Such a plateau is a combined result of significant depletion of light ions and modest depletion of heavy ones on Titan's nightside. We propose that the distinctions between the diurnal variations of light and heavy ions are associated with their different chemical loss pathways, with the former primarily through “fast” ion-neutral chemistry and the latter through “slow” electron dissociative recombination. The strong correlation between the observed night-to-day ion density ratios and the associated ion lifetimes suggests a scenario in which the ions created on Titan's dayside may survive well to the nightside. The observed asymmetry between the dawn and dusk ion density profiles also supports such an interpretation. We construct a time-dependent ion chemistry model to investigate the effect of ion survival associated with solid body rotation alone as well as superrotating horizontal winds. For long-lived ions, the predicted diurnal variations have similar general characteristics to those observed. However, for short-lived ions, the model densities on the nightside are significantly lower than the observed values. This implies that electron precipitation from Saturn's magnetosphere may be an additional and important contributor to the densities of the short-lived ions observed on Titan's nightside.

  16. Single cell enzyme diagnosis on the chip

    DEFF Research Database (Denmark)

    Jensen, Sissel Juul; Harmsen, Charlotte; Nielsen, Mette Juul

    2013-01-01

    Conventional diagnosis based on ensemble measurements often overlooks the variation among cells. Here, we present a droplet-microfluidics based platform to investigate single cell activities. Adopting a previously developed isothermal rolling circle amplification-based assay, we demonstrate detec...

  17. Variational collocation on finite intervals

    International Nuclear Information System (INIS)

    Amore, Paolo; Cervantes, Mayra; Fernandez, Francisco M

    2007-01-01

    In this paper, we study a set of functions, defined on an interval of finite width, which are orthogonal and which reduce to the sinc functions when the appropriate limit is taken. We show that these functions can be used within a variational approach to obtain accurate results for a variety of problems. We have applied them to the interpolation of functions on finite domains and to the solution of the Schroedinger equation, and we have compared the performance of the present approach with others

  18. Quadratic Variation by Markov Chains

    DEFF Research Database (Denmark)

    Hansen, Peter Reinhard; Horel, Guillaume

    We introduce a novel estimator of the quadratic variation that is based on the the- ory of Markov chains. The estimator is motivated by some general results concerning filtering contaminated semimartingales. Specifically, we show that filtering can in prin- ciple remove the effects of market...... microstructure noise in a general framework where little is assumed about the noise. For the practical implementation, we adopt the dis- crete Markov chain model that is well suited for the analysis of financial high-frequency prices. The Markov chain framework facilitates simple expressions and elegant analyti...

  19. Neodymium isotopic variations in seawater

    Science.gov (United States)

    Piepgras, D. J.; Wasserburg, G. J.

    1980-01-01

    Direct measurement of the isotopic composition of Nd in the Atlantic agree with the Nd content in ferromanganese sediments and differ from the observed amounts in the Pacific samples. These data indicate the existence of distinctive differences in the isotopic composition of Nd in the waters of major oceans; the average values determined from seawater and ferromanganese sediments are considerably lower than in sources with oceanic mantle affinities showing that the REE in the oceans is dominated by continental sources. The Nd isotopic variations in seawater are applied to relate the residence time of Nd and mixing rates between the oceans.

  20. Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins.

    Science.gov (United States)

    Mitchison, A

    1997-01-01

    In considering genetic variation in eukaryotes, a fundamental distinction can be made between variation in regulatory (software) and coding (hardware) gene segments. For quantitative traits the bulk of variation, particularly that near the population mean, appears to reside in regulatory segments. The main exceptions to this rule concern proteins which handle extrinsic substances, here termed extrovert proteins. The immune system includes an unusually large proportion of this exceptional category, but even so its chief source of variation may well be polymorphism in regulatory gene segments. The main evidence for this view emerges from genome scanning for quantitative trait loci (QTL), which in the case of the immune system points to a major contribution of pro-inflammatory cytokine genes. Further support comes from sequencing of major histocompatibility complex (Mhc) class II promoters, where a high level of polymorphism has been detected. These Mhc promoters appear to act, in part at least, by gating the back-signal from T cells into antigen-presenting cells. Both these forms of polymorphism are likely to be sustained by the need for flexibility in the immune response. Future work on promoter polymorphism is likely to benefit from the input from genome informatics.

  1. DNA fork displacement rates in human cells

    International Nuclear Information System (INIS)

    Kapp, L.N.; Painter, R.B.

    1981-01-01

    DNA fork displacement rates were measured in 20 human cell lines by a bromodeoxyuridine-313 nm photolysis technique. Cell lines included representatives of normal diploid, Fanconi's anemia, ataxia telangiectasia, xeroderma pigmentosum, trisomy-21 and several transformed lines. The average value for all the cell lines was 0.53 +- 0.08 μm/min. The average value for individual cell lines, however, displayed a 30% variation. Less than 10% of variation in the fork displacement rate appears to be due to the experimental technique; the remainder is probably due to true variation among the cell types and to culture conditions. (Auth.)

  2. Exogenous lactate interferes with cell-cycle control in BALB/3T3 mouse fibroblasts

    International Nuclear Information System (INIS)

    Rutz, H. Peter; Little, John B.

    1995-01-01

    Purpose: Previous studies have shown that exogenous lactate may influence proliferation rates, radiation sensitivity, and postirradiation repair capacity of mammalian cells. In the present study, we addressed the question of potential underlying mechanisms and, therefore, examined effects of exogenous lactate on proliferation rates and cell-cycle distribution in immortal but nontumorigenic mammalian cells. Methods and Materials: Cells were grown at 37 deg. C in an incubator with 5% CO 2 and 95% air, in a culture medium supplemented or not with lactate at a 10 mM concentration. Daily, we changed the culture medium and counted cells per dish. On selected days, cell-cycle distribution was determined by flow cytometry. Balb/3T3 mouse fibroblasts were used. Results: During the exponential phase of cell proliferation, mean population doubling time was significantly increased from 17.7 to 19.9 h, due to selective prolongation of G 2 /M. However, in density-inhibited cultures, exogenous lactate stimulated entry into S and proliferation to a significantly higher saturation density. Conclusions: These findings indicate that exogenous lactate interferes with mechanisms of cell-cycle control at two different points in the cell-cycle, depending on cell density and the resulting absence or presence of inhibition of cell proliferation. Interference with cell-cycle control may underlay the modification by exogenous lactate of radiosensitivity and postirradiation repair capacity in mammalian cells

  3. Single-cell sequencing in stem cell biology.

    Science.gov (United States)

    Wen, Lu; Tang, Fuchou

    2016-04-15

    Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for omic analysis. Single-cell sequencing technologies serve as powerful tools to dissect cellular heterogeneity comprehensively and to identify distinct phenotypic cell types, even within a 'homogeneous' stem cell population. These technologies, including single-cell genome, epigenome, and transcriptome sequencing technologies, have been developing rapidly in recent years. The application of these methods to different types of stem cells, including pluripotent stem cells and tissue-specific stem cells, has led to exciting new findings in the stem cell field. In this review, we discuss the recent progress as well as future perspectives in the methodologies and applications of single-cell omic sequencing technologies.

  4. Control, optimisation and calculus of variations

    OpenAIRE

    Colonius, Fritz (Prof.)

    2002-01-01

    Control, optimisation and calculus of variations : COCV = Contrôle, optimisation et calcul des variations / Editorial Board: F. Colonius ... - Vol. 1-7. - Paris : EDP Sciences, SMAI, 1995/96-2002. - (ESAIM) [http://www.emath.fr/cocv/

  5. Amazing variational approach to chemical reactions

    OpenAIRE

    Fernández, Francisco M.

    2009-01-01

    In this letter we analyse an amazing variational approach to chemical reactions. Our results clearly show that the variational expressions are unsuitable for the analysis of empirical data obtained from chemical reactions.

  6. Variational inference & deep learning : A new synthesis

    NARCIS (Netherlands)

    Kingma, D.P.

    2017-01-01

    In this thesis, Variational Inference and Deep Learning: A New Synthesis, we propose novel solutions to the problems of variational (Bayesian) inference, generative modeling, representation learning, semi-supervised learning, and stochastic optimization.

  7. Genetic variation in radiation-induced cell death

    OpenAIRE

    Smirnov, Denis A.; Brady, Lauren; Halasa, Krzysztof; Morley, Michael; Solomon, Sonia; Cheung, Vivian G.

    2012-01-01

    Radi