Sample records for chain variable region

  1. Anti-Staphylococcus aureus single-chain variable region fragments provide protection against mastitis in mice. (United States)

    Wang, Man; Zhang, Yan; Zhu, Jianguo


    Staphylococcus aureus is a leading causative agent of bovine mastitis, which can result in significant economic losses to the dairy industry. However, available vaccines against bovine mastitis do not confer adequate protection, although passive immunization with antibodies may be useful to prevent disease. Hence, we constructed a bovine single-chain variable region fragment (scFv) phage display library using cDNAs from peripheral blood lymphocytes of cows with S. aureus-induced mastitis. After four rounds of selection, eight scFvs that bound S. aureus antigens with high affinity were obtained. The framework regions of the variable domains (VH and VL) of the eight scFvs were highly conserved, and the complementarity-determining regions (CDRs) displayed significant diversity, especially CDR3 of the VH domain. All eight scFvs inhibited S. aureus growth in culture medium. Lactating mice were challenged by injecting S. aureus into the fourth mammary gland. Histopathological analysis showed that treatment with these scFvs prior to bacterial challenge maintained the structure of the mammary acini, decreased infiltration of polymorphonuclear neutrophils, increased levels of interferon-gamma and interleukin-4, and reduced tumor necrosis factor-alpha levels in mammary tissues, as compared with mice treatment with physiological saline (P < 0.05). These novel bovine scFvs may be suitable candidates for therapeutic agents for the prevention of S. aureus-induced bovine mastitis.

  2. Possible deletion of a developmentally regulated heavy-chain variable region gene in autoimmune diseases

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Pei-Ming; Olee, Tsaiwei; Kozin, F.; Carson, D.A.; Chen, P.P. (Research Institute of Scripps Clinic, La Jolla, CA (USA)); Olsen, N.J. (Vanderbilt Univ., Nashville, TN (USA)); Siminovitch, K.A. (Univ. of Toronto (Canada))


    Several autoantibody-associated variable region (V) genes are preferentially expressed during early ontogenic development, suggesting strongly that they are of developmental and physiological importance. As such, it is possible that polymorphisms in one or more of these genes may alter susceptibility to autoimmune disease. The authors have searched extensively for a probe related to a developmentally regulated V gene that has the power to differentiate among highly homologous V genes in human populations. Using such a probe (i.e., Humhv3005/P1) related to both anti-DNA and anti-IgG autoantibodies, they studied restriction fragment length polymorphisms in patients with rheumatoid arthritis and systemic lupus erythematosus and found an apparent heavy-chain V (V{sub H}) gene deletion that was nearly restricted to the autoimmune patients. These data suggest that deletions of physiologically important V{sub H} genes may increase the risk of autoimmunity through indirect effects on the development and homeostasis of the B-cell repertoire.

  3. Suppression of Aggrus/podoplanin-induced platelet aggregation and pulmonary metastasis by a single-chain antibody variable region fragment. (United States)

    Miyata, Kenichi; Takagi, Satoshi; Sato, Shigeo; Morioka, Hiroshi; Shiba, Kiyotaka; Minamisawa, Tamiko; Takami, Miho; Fujita, Naoya


    Almost all highly metastatic tumor cells possess high platelet aggregating abilities, thereby form large tumor cell-platelet aggregates in the microvasculature. Embolization of tumor cells in the microvasculature is considered to be the first step in metastasis to distant organs. We previously identified the platelet aggregation-inducing factor expressed on the surfaces of highly metastatic tumor cells and named as Aggrus. Aggrus was observed to be identical to the marker protein podoplanin (alternative names, T1α, OTS-8, and others). Aggrus is frequently overexpressed in several types of tumors and enhances platelet aggregation by interacting with the platelet receptor C-type lectin-like receptor 2 (CLEC-2). Here, we generated a novel single-chain antibody variable region fragment (scFv) by linking the variable regions of heavy and light chains of the neutralizing anti-human Aggrus monoclonal antibody MS-1 with a flexible peptide linker. Unfortunately, the generated KM10 scFv failed to suppress Aggrus-induced platelet aggregation in vitro. Therefore, we performed phage display screening and finally obtained a high-affinity scFv, K-11. K-11 scFv was able to suppress Aggrus-induced platelet aggregation in vitro. Moreover, K-11 scFv prevented the formation of pulmonary metastasis in vivo. These results suggest that K-11 scFv may be useful as metastasis inhibitory scFv and is expected to aid in the development of preclinical and clinical examinations of Aggrus-targeted cancer therapies.

  4. Evidence for gene conversion among immunoglobulin heavy chain variable region genes. (United States)

    Clarke, S H; Rudikoff, S


    We have previously reported that the VH region amino acid sequence of a phosphocholine (PC)-binding hybridoma antibody of CBA/J origin, HP101 6G6 (6G6), differs extensively from the VH regions of other PC-binding antibodies. The sequence of 6G6 VH appears to be derived from a gene homologous to the BALB/c V11 gene, a member of the PC VH (T15 VH) gene family not normally used to encode PC-binding antibodies. The 6G6 VH sequence differs from the translated sequence of V11 by six amino acids, four of which occur at the same position in other members of this gene family. This coincidence led to the proposal that the 6G6 VH gene was derived by gene conversion involving three genes of the PC VH gene family. We report here the nucleic acid sequence of the rearranged VH gene of hybridoma 6G6. This sequence supports our previous suggestion of gene conversion by confirming those differences, relative to the BALB/c V11 gene sequence, that are encoded by other members of this gene family, and extends this correlation to include three silent base pair substitutions as well. In addition, 5' noncoding region sequence and Southern blot analysis using probes derived from the coding and 5' noncoding regions confirm that the 6G6 VH gene is likely to be derived from the V11 homologue in CBA/J mice, and suggest that all three genes believed to be involved in the generation of the 6G6 VH gene are present in the CBA/J genome, a prerequisite for their involvement in gene conversion.


    Directory of Open Access Journals (Sweden)

    Ashish Agarwal


    Full Text Available In order to understand the dynamic behavior of the variables that can play a major role in the performance improvement in a supply chain, a System Dynamics-based model is proposed. The model provides an effective framework for analyzing different variables affecting supply chain performance. Among different variables, a causal relationship among different variables has been identified. Variables emanating from performance measures such as gaps in customer satisfaction, cost minimization, lead-time reduction, service level improvement and quality improvement have been identified as goal-seeking loops. The proposed System Dynamics-based model analyzes the affect of dynamic behavior of variables for a period of 10 years on performance of case supply chain in auto business.

  6. Recombination events near the immunoglobulin Cmu gene join variable and constant region genes, switch heavy-chain expression, or inactivate the locus. (United States)

    Cory, S; Webb, E; Gough, J; Adams, J M


    Immunoglobulin heavy-chain expression is initiated by recombination between a variable region (VH) gene and one of several joining region (JH) genes located near the mu constant region (Cmu) gene, and the active VH gene can subsequently switch to another CH gene. That the general mechanism for CH switching involves recombination between sites within the JH-Cmu intervening sequence and the 5' flanking region of another CH gene is supported here by Southern blot hybridization analysis of eight IgG- and IgA-secreting plasmacytomas. An alternative model requiring successive VH linkage to similar JH clusters near each CH gene is shown to be very unlikely since the mouse genome appears to contain only one complement of the JH locus and no JH gene was detectable within large cloned sequences flanking germline C gamma 3 and C gamma 1 genes. Thus, VH-JH joining and CH switching are mediated by separate regions of "the joining-switch" or J-S element. In each plasmacytoma examined, the J-S element had undergone recombination within both the JH locus and the switch region and was shown to be linked to the functional CH gene in an IgG3, and IgG1, and three IgA secretors. Both JH joining and CH switching occurred by deletion of DNA. Switch recombination occurred at more than one site within the J-S element in different lines, even for recombination with the same CH gene. Significantly, although heavy-chain expression is restricted to one allele ("allelic exclusion"), all rearranged in each plasmacytoma. Some rearrangements were aberrant, involving, for example, deletion of all JH genes from the allele. Hence, an error-prone recombination machinery may account for allelic exclusion in many plasmacytomas.

  7. Somatic diversification in the heavy chain variable region genes expressed by human autoantibodies bearing a lupus-associated nephritogenic anti-DNA idiotype

    Energy Technology Data Exchange (ETDEWEB)

    Demaison, C.; Chastagner, P.; Theze, J.; Zouali, M. (Institut Pasteur, Paris (France))


    Monoclonal anti-DNA antibodies bearing a lupus nephritis-associated idiotype were derived from five patients with systemic lupus erythematosus (SLE). Genes encoding their heavy (H)-chain variable (V[sub H]) regions were cloned and sequenced. When compared with their closest V[sub h] germ-line gene relatives, these sequences exhibit a number of silent (S) and replacement (R) substitutions. The ratios of R/S mutations were much higher in the complementarity-determining regions (CDRs) of the antibodies than in the framework regions. Molecular amplification of genomic V[sub H] genes and Southern hybridization with somatic CDR2-specific oligonucleotide probes showed that the configuration of the V[sub H] genes corresponding to V[sub H] sequences in the nephritogenic antibodies is not present in the patient's own germ-line DNA, implying that the B-cell clones underwent somatic mutation in vivo. These findings, together with the characteristics of the diversity and junctional gene elements utilized to form the antibody, indicate that these autoantibodies have been driven through somatic selection processes reminiscent of those that govern antibody responses triggered by exogenous stimuli.

  8. Dominant and shared T cell receptor beta chain variable regions of T cells inducing synovial hyperplasia in rheumatoid arthritis. (United States)

    Mima, T; Ohshima, S; Sasai, M; Nishioka, K; Shimizu, M; Murata, N; Yasunami, R; Matsuno, H; Suemura, M; Kishimoto, T; Saeki, Y


    Previously, we demonstrated the presence of at least two distinct subpopulations of patients with rheumatoid arthritis (RA) employing a cell-transfer experiment using severe combined immunodeficient (SCID) mice. One group of patients, whose T cells derived from the rheumatoid joints, induced synovial hyperplasia (SH) in the SCID mice (the positive group). The other group did not display the induction of SH (the negative group). TCR/Vbeta gene usage analysis indicated that some dominant T cell subpopulations were oligoclonally expanding only in the rheumatoid joints, and not in the periphery of the patients of the positive group. Moreover, these T cell subpopulations were not seen in the joints of patients in the negative group or in non-RA patients. In addition, the preferential uses of certain TCR/Vbetas (Vbeta8, Vbeta12, Vbeta13, and Vbeta14) genes were demonstrated in these T cells. In this study, to investigate whether these T cells are driven by a certain antigen(s), the third complementarity determining regions (CDR3s) of TCR/Vbeta, especially Vbeta8 and Vbeta14 PCR products, were cloned and sequenced. As a result, a dominant CDR3 sequence, CASS-PRERAT-YEQ, was found in Vbeta14+ T cells from the rheumatoid joint of a patient (Patient 1) of the positive group with a Vbeta14 skew. The identical CDR3 sequence also predominated in Vbeta14+ T cells from the rheumatoid joint of another patient (Patient 7) of the positive group with a Vbeta14 skew. In addition, in the patients (Patients 4, 7, 8) of the positive group with a Vbeta8 skew, other dominant CDR3 sequences, CASS-ENS-YEQ and CASS-LTEP-DTQ, were found as in the case of Vbeta14. However, no identical CDR3 sequences were detected dominantly in the joints of the patients in the negative group or in non-RA patients. A Vbeta14+ T cell clone (TCL), named G3, with the identical CDR3 sequence, CASS-PRERAT-YEQ, was isolated successfully from Patient 1, and cell transfer of G3 with autologous irradiated peripheral

  9. Variable length Markov chains and dynamical sources

    CERN Document Server

    Cénac, Peggy; Paccaut, Frédéric; Pouyanne, Nicolas


    Infinite random sequences of letters can be viewed as stochastic chains or as strings produced by a source, in the sense of information theory. The relationship between Variable Length Markov Chains (VLMC) and probabilistic dynamical sources is studied. We establish a probabilistic frame for context trees and VLMC and we prove that any VLMC is a dynamical source for which we explicitly build the mapping. On two examples, the ``comb'' and the ``bamboo blossom'', we find a necessary and sufficient condition for the existence and the unicity of a stationary probability measure for the VLMC. These two examples are detailed in order to provide the associated Dirichlet series as well as the generating functions of word occurrences.

  10. Design Method Amelioration of Human Immunoglobulin Gene Primer in Heavy Chain Variable Region%人免疫球蛋白重链可变区基因引物设计方法的改良

    Institute of Scientific and Technical Information of China (English)

    姜晶; 孙颖; 刘红艳; 牟玲; 罗恩杰


    针对抗体胚系基因数据库的数据不断更新和完善,为获得人全部免疫球蛋白(Ig)重链可变区基因,改进引物设计方法,自主设计针对可变区基因高度保守的框架区1(FR1)和框架区4(FR4)的引物,提取未经免疫的健康人外周血单个核细胞,通过RT-PCR扩增重链可变区基因.其DNA序列与GenBank数据库和IMGT/V-QUEST软件比对,序列分析符合人免疫球蛋白重链基本框架结构,为胚系基因重排产生的序列.多个克隆的测序结果对比分析显示了良好的多样性.获得的重链序列为研制基因工程抗体及构建噬菌体抗体库奠定了物质基础,也为扩增其他物种Ig可变区基因的引物提供新的设计思路.%Aiming at the continuous renovation and consummation of dala of databank on antibody germ line gene, in order to obtain full gene of heavy chain variable region of human immunoglobin (Ig) , to ameliorate primer design method, a primer was independently designed aiming at variable gene highly conservative region framework 1 ( FR1) and framework 4 ( FR4) , and extracted peripheral blood mononuclear cells (PBMCs) from healthy volunteer, and amplified its heavy chain variable region gene through RT-PCR. After comparison with databank in CenBank and IMGT/V-QUEST software and sequence analysis, the DNA sequence accorded with basic framework structure of human Ig heavy chain, and was the sequence produced by the rearrangement of germ line gene. Comparative analysis of multiple clones sequencing showed a good diversity. The obtained data of heavy chain sequence had provided the material foundation for research and development of gene engineering antibodies and phage libraries, and new design ideas for amplifying Ig variable region gene primers of other species.

  11. Evidence indicating independent assortment of framework and complementarity-determining segments of the variable regions of rabbit light chains. Delineation of a possible J minigene. (United States)

    Kabat, E A; Wu, T T; Bilofsky, H


    Amino acid sequences of rabbit light chains show considerable evidence of independent assortment of framework (FR) and complementarity-determining (CDR) segments. This suggests that they are coded for by independent genetic units (minigaenes) and that individual light chains are assembled somatically by recombining these units. Identical FR sets with multiple members generally comprise chains with different specificities, whereas identical CDR sets tend to have chains of a single specificity. A J segment, which, by analogy with mouse light chains, is made up of the last two residues of CDR3 plus all of FR4, contained 18 different sets and could contribute to diversity generated by CDR3. The longest segment, FR3, had a very large number of sets. Evidence is presented showing that the number of sets could be substantially reduced by permitting FR3 to be formed by two independently assorting segments comprising residues 57-68 and 69-88.

  12. Regional fuzzy chain model for evapotranspiration estimation (United States)

    Güçlü, Yavuz Selim; Subyani, Ali M.; Şen, Zekai


    Evapotranspiration (ET) is one of the main hydrological cycle components that has extreme importance for water resources management and agriculture especially in arid and semi-arid regions. In this study, regional ET estimation models based on the fuzzy logic (FL) principles are suggested, where the first stage includes the ET calculation via Penman-Monteith equation, which produces reliable results. In the second phase, ET estimations are produced according to the conventional FL inference system model. In this paper, regional fuzzy model (RFM) and regional fuzzy chain model (RFCM) are proposed through the use of adjacent stations' data in order to fill the missing ones. The application of the two models produces reliable and satisfactory results for mountainous and sea region locations in the Kingdom of Saudi Arabia, but comparatively RFCM estimations have more accuracy. In general, the mean absolute percentage error is less than 10%, which is acceptable in practical applications.

  13. Supply chain performance: the role of regional markets

    Directory of Open Access Journals (Sweden)

    Ali Ghasemi


    Full Text Available This paper investigates the role of exports in the regional markets on the performance of supply chain. The study first determines critical variables affecting exports for entering into the regional markets and then measures the effects of these variables on the effectiveness of supply chain performance. The study uses two questionnaires, one for measuring the effects of various factors on export development and the other for measuring supply chain performance in Likert scale. Cronbach alpha for the mentioned questionnaires were calculated as 0.84 and 0.78, respectively. The population of the survey includes all small and medium enterprises active in city of Tehran, Iran and the study selects a sample of 250 people as a sample size. Using factor analysis, the study has determined seven factors including product development, government support, strategic orientation, customer satisfaction, competitive pressures, organizational capability and distribution strategies for entry into regional markets. In addition, the implementation of structural equation modeling has disclosed that product development and distribution strategies maintained the highest impact on export activities.

  14. Cloning of IgG heavy chain variable region genes directly from rabbit peripheral blood%从兔外周血直接克隆IgG重链可变区

    Institute of Scientific and Technical Information of China (English)

    周世权; 廖智; 杨林; 周吉航; 刘晓光


    Objective To amplify IgG heavy chain variable region genes directly from rabbit peripheral blood. Methods Two pairs of PCR primers were designed according to the cDNA sequence of rabbit germline Immunoglobulin (Ig)heavy chain variable region( VH) and constant-region( CH) genes, which were obtained from IMGT/GENE-DB. With the total RNA that was extracted from rabbit peripheral blood as a template, an one-step RT-PCR reaction was done and followed by a nested-PCR. By cloning the PCR products to T vector, DNA sequencing and blasting in Bioedit software and IMGT/V-QUEST network database, the genotype of CH and three VH gene segments, V_H(IGHV), D(IGHD)and J-H (IGHJ) , were confirmed, and the specificity and compatibility of the primers were evaluated. Results A total of 25 clones were analyzed. Their DNA sequences were different from each other, and all belonged to rabbit IgG heavy chain coding genes. Their constant regions were encoded by the same allele gene, IGHG * 02. Of these 25 clones, there were 2 of 37 IGHV, 8 of 11 IGHD, and 4 of 11 IGHJ functional genes; and they assembled to 18 kinds of V_H -D-J_H combinations. [IGHV1S40 * 01 ]-[IGHD8-l * 01 ]-[IGHJ4 * 01 ] was the topmost V_H-D-J_H combinations, which appeared in 4 clones, but some differences existed some differences in sequence. Conclusion We have succeeded in amplifying IgG heavy chain variable region genes rapidly and specifically from rabbit peripheral blood, and the primers, which designed by ourselves, have displayed a relatively good compatibility, but the V_H-D-J_H combinations with IGHV1S40 * 01 or IGHV1S45 * 01 seem to be amplified preferentially.%目的 从兔外周血总RNA中直接扩增出IgG重链可变区基因.方法 先从IMGT/GENE-DB数据库中获取编码大耳白兔免疫球蛋白(Ig)重链可变区(VH)的3个胚系基因片段VH(IGHV)、D(IGHD)和JH(IGHJ),以及编码γ重链恒定区(CH)基因Cγ(IGHG)的cDNA序列,然后设计嵌套引物,以兔外周血总RNA为模板,进行RT

  15. Analysis of Chaotic Behaviour in Supply Chain Variables


    Ramírez, Sergio A.; Peña, Gloria E.


    In this article we develop a supply chain model of four levels through the utilization of system dynamics with Ithink® and Mathlab® softwares to analyze data. The supply chain is studied from the chaos theory perspective, which helps identifying the sensitive variables that can lead to a state of chaos. A generic structure model that comprehends factory links, distribution, wholesale, retail and the client is constructed. The difficulty of operations and logistics managers to decide how much ...

  16. The association of heavy and light chain variable domains in antibodies: implications for antigen specificity.

    KAUST Repository

    Chailyan, Anna


    The antigen-binding site of immunoglobulins is formed by six regions, three from the light and three from the heavy chain variable domains, which, on association of the two chains, form the conventional antigen-binding site of the antibody. The mode of interaction between the heavy and light chain variable domains affects the relative position of the antigen-binding loops and therefore has an effect on the overall conformation of the binding site. In this article, we analyze the structure of the interface between the heavy and light chain variable domains and show that there are essentially two different modes for their interaction that can be identified by the presence of key amino acids in specific positions of the antibody sequences. We also show that the different packing modes are related to the type of recognized antigen.

  17. Variable context Markov chains for HIV protease cleavage site prediction. (United States)

    Oğul, Hasan


    Deciphering the knowledge of HIV protease specificity and developing computational tools for detecting its cleavage sites in protein polypeptide chain are very desirable for designing efficient and specific chemical inhibitors to prevent acquired immunodeficiency syndrome. In this study, we developed a generative model based on a generalization of variable order Markov chains (VOMC) for peptide sequences and adapted the model for prediction of their cleavability by certain proteases. The new method, called variable context Markov chains (VCMC), attempts to identify the context equivalence based on the evolutionary similarities between individual amino acids. It was applied for HIV-1 protease cleavage site prediction problem and shown to outperform existing methods in terms of prediction accuracy on a common dataset. In general, the method is a promising tool for prediction of cleavage sites of all proteases and encouraged to be used for any kind of peptide classification problem as well.

  18. Somatic mutations in the Ig variable region genes and expression of novel Cmu-germline transcripts in a B-lymphoma cell line ("Farage") not producing Ig polypeptide chains. (United States)

    Hochberg, M; Gabay, C; Laskov, R


    Non-Hodgkin's B-lymphomas (B-NHL) are a very heterogeneous group of B-cell neoplasias originating from the germinal centers of lymphatic follicles. Thus, they represent a suitable experimental model to study the molecular basis of certain key events which take place in the lymphatic follicles, including somatic hypermutation and heavy chain isotypic switch. An unusual B-NHL cell line ("Farage") not producing Ig polypeptide chains was previously shown to rearrange its IgH and Igkappa genes and transcribe seemingly normal size mu and kappa mRNAs. In an attempt to characterize the phenotype of Farage cells better and to elucidate the molecular basis of the failure of Farage cells to synthesize Ig chains, we sequenced its VH and Vkappa rearranged gene segments by PCR and RT-PCR. It was found that both V genes are somatically, heavily mutated compared to their germline counterparts. In addition, this rearranged VDJ gene of the heavy chain is not transcribed. Instead, the Farage cells express a low level of a new family of germline transcripts starting with a VH like sequence, continuing with a small segment of the 3'VH germline flanking region, and ending within the Cmu region. These transcripts lack D and J segments and do not contain the open reading frame of the full-length Cmu protein. Thus, Farage cells fail to produce mu heavy chains due to silencing of the expression of the conventional VDJCmu transcript and expression of unusual Cmu-germline transcripts. In contrast to the IgH genes, the rearranged VJ gene of Farage is transcribed and gives rise to a full-size kappa-mRNA. This transcript, however, is not translated to a full-length kappa-chain, as it contains a stop codon in its coding region. All the above show that Farage cells are unable to produce Ig polypeptide chains, due to somatic mutations altering the kappa-chain gene, and mutations and/or regulatory events that shutoff the transcription of the IgH gene. The heavily mutated Vkappa and Vkappa genes

  19. Separation of variables in the open XXX chain

    Energy Technology Data Exchange (ETDEWEB)

    Frahm, Holger [Institut fuer Theoretische Physik, Leibniz Universitaet Hannover, Appelstr. 2, 30167 Hannover (Germany)], E-mail:; Seel, Alexander [Institut fuer Theoretische Physik, Leibniz Universitaet Hannover, Appelstr. 2, 30167 Hannover (Germany)], E-mail:; Wirth, Tobias [Institut fuer Theoretische Physik, Leibniz Universitaet Hannover, Appelstr. 2, 30167 Hannover (Germany)], E-mail:


    We apply the Sklyanin method of separation of variables to the reflection algebra underlying the open spin-1/2 XXX chain with non-diagonal boundary fields. The spectral problem can be formulated in terms of a TQ-equation which leads to the known Bethe equations for boundary parameters satisfying a constraint. For generic boundary parameters we study the asymptotic behaviour of the solutions of the TQ-equation.

  20. Separation of Variables in the open XXX chain

    CERN Document Server

    Frahm, H; Wirth, T


    We apply the Sklyanin method of separation of variables to the reflection algebra underlying the open spin-1/2 XXX chain with non-diagonal boundary fields. The spectral problem can be formulated in terms of a TQ-equation which leads to the known Bethe equations for boundary parameters satisfying a constraint. For generic boundary parameters we study the asymptotic behaviour of the solutions of the TQ-equation.

  1. Engineered single-chain variable fragment antibody for immunodiagnosis of groundnut bud necrosis virus infection. (United States)

    Maheshwari, Yogita; Vijayanandraj, S; Jain, R K; Mandal, Bikash


    Few studies have been done on engineered antibodies for diagnosis of tospovirus infections. The present study was undertaken to develop a single-chain variable fragment (scFv) for specific diagnosis of infection by groundnut bud necrosis virus (GBNV), the most prevalent serogroup IV tospovirus in India. Heavy chain (372 nucleotide [nt]) and light chain (363 nt) variable region clones obtained from a hybridoma were used to make an scFv construct that expressed a ~29-kDa protein in E. coli. The scFv specifically detected GBNV in field samples of cowpea, groundnut, mung bean, and tomato, and it did not recognize watermelon bud necrosis virus, a close relative of GBNV belonging to tospovirus serogroup IV. This study for the first time demonstrated the application of a functional scFv against a serogroup-IV tospovirus.

  2. Construction of single-chain variable fragment antibodies against MCF-7 breast cancer cells. (United States)

    Zuhaida, A A; Ali, A M; Tamilselvan, S; Alitheen, N B; Hamid, M; Noor, A M; Yeap, S K


    A phage display library of single chain variable fragment (scFv) against MCF-7 breast cancer cells was constructed from C3A8 hybridoma cells. RNA from the C3A8 was isolated, cDNA was constructed, and variable heavy and light immunoglobulin chain gene region were amplified using PCR. The variable heavy and light chain gene regions were combined with flexible linker, linked to a pCANTAB 5E phagemid vector and electrophoresed into supE strain of Escherichia coli TG1 cells. Forty-eight clones demonstrated positive binding activity to MCF-7 breast cancer cell membrane fragments and the strongest of 48 clones was selected for analysis. The anti-MCF-7 library evaluated by SfiI and NotI digests demonstrated that anti-MCF-7 scFv antibodies possess individual patterns that should be able to recognize distinct human breast cancer cells. The C3A8 scFv, with an apparent molecular weight of 32 kDa, showed high homology (99%) with single chain antibody against rice stripe virus protein P20. In summary, the anti MCF-7 scFv antibody can be used for pretargeting breast cancer for clinical diagnosis of patients; it also has potential for therapeutic applications.

  3. Genomic variation in the porcine immunoglobulin lambda variable region. (United States)

    Guo, Xi; Schwartz, John C; Murtaugh, Michael P


    Production of a vast antibody repertoire is essential for the protection against pathogens. Variable region germline complexity contributes to repertoire diversity and is a standard feature of mammalian immunoglobulin loci, but functional V region genes are limited in swine. For example, the porcine lambda light chain locus is composed of 23 variable (V) genes and 4 joining (J) genes, but only 10 or 11 V and 2 J genes are functional. Allelic variation in V and J may increase overall diversity within a population, yet lead to repertoire holes in individuals lacking key alleles. Previous studies focused on heavy chain genetic variation, thus light chain allelic diversity is not known. We characterized allelic variation of the porcine immunoglobulin lambda variable (IGLV) region genes. All intact IGLV genes in 81 pigs were amplified, sequenced, and analyzed to determine their allelic variation and functionality. We observed mutational variation across the entire length of the IGLV genes, in both framework and complementarity determining regions (CDRs). Three recombination hotspot motifs were also identified suggesting that non-allelic homologous recombination is an evolutionarily alternative mechanism for generating germline antibody diversity. Functional alleles were greatest in the most highly expressed families, IGLV3 and IGLV8. At the population level, allelic variation appears to help maintain the potential for broad antibody repertoire diversity in spite of reduced gene segment choices and limited germline sequence modification. The trade-off may be a reduction in repertoire diversity within individuals that could result in an increased variation in immunity to infectious disease and response to vaccination.

  4. Value chain dynamics, settlement trajectories and regional development

    DEFF Research Database (Denmark)

    Fold, Niels


    Global value chain (GVC) analysis has little to say about the interaction between regions and global chain dynamics. However, recent calls to address broader development issues have resulted in efforts to incorporate a spatial dimension in GVC analysis. Addressing this issue, the paper argues tha...... by value chain dynamics will improve by adding elements from global production network (GPN) theory to the combined methodology, namely by an examination of territorial embeddedness and value (creation, enhancement, capture, distribution) at settlement level.......Global value chain (GVC) analysis has little to say about the interaction between regions and global chain dynamics. However, recent calls to address broader development issues have resulted in efforts to incorporate a spatial dimension in GVC analysis. Addressing this issue, the paper argues...

  5. The C-terminal region of laminin beta chains modulates the integrin binding affinities of laminins. (United States)

    Taniguchi, Yukimasa; Ido, Hiroyuki; Sanzen, Noriko; Hayashi, Maria; Sato-Nishiuchi, Ryoko; Futaki, Sugiko; Sekiguchi, Kiyotoshi


    Laminins are major cell-adhesive proteins in basement membranes that are capable of binding to integrins. Laminins consist of three chains (alpha, beta, and gamma), in which three laminin globular modules in the alpha chain and the Glu residue in the C-terminal tail of the gamma chain have been shown to be prerequisites for binding to integrins. However, it remains unknown whether any part of the beta chain is involved in laminin-integrin interactions. We compared the binding affinities of pairs of laminin isoforms containing the beta1 or beta2 chain toward a panel of laminin-binding integrins, and we found that beta2 chain-containing laminins (beta2-laminins) bound more avidly to alpha3beta1 and alpha7X2beta1 integrins than beta1 chain-containing laminins (beta1-laminins), whereas alpha6beta1, alpha6beta4, and alpha7X1beta1 integrins did not show any preference toward beta2-laminins. Because alpha3beta1 contains the "X2-type" variable region in the alpha3 subunit and alpha6beta1 and alpha6beta4 contain the "X1-type" region in the alpha6 subunit, we hypothesized that only integrins containing the X2-type region were capable of discriminating between beta1-laminins and beta2-laminins. In support of this possibility, a putative X2-type variant of alpha6beta1 was produced and found to bind preferentially to beta2-laminins. Production of a series of swap mutants between the beta1 and beta2 chains revealed that the C-terminal 20 amino acids in the coiled-coil domain were responsible for the enhanced integrin binding by beta2-laminins. Taken together, the results provide evidence that the C-terminal region of beta chains is involved in laminin recognition by integrins and modulates the binding affinities of laminins toward X2-type integrins.

  6. Cloning,sequencing and analyzing of the heavy chain V region genes of human polyreactive antibodies

    Institute of Scientific and Technical Information of China (English)



    The heavy chain variable region genes of 5 human polyreactive mAbs generated in our laboratory have been cloned and sequenced using polymerase chain reaction(PCR) technique.We found that 2 and 3 mAbs utilized genes of the VHIV and VHⅢ families,respectively.The former 2 VH segments were in germline configuration.A common VH segment,with the best similarity of 90.1% to the published VHⅢ germline genes,was utilized by 2 different rearranged genes encoding the V regions of other 3 mAbs.This strongly suggests that the common VH segment is a unmutated copy of an unidentified germline VHⅢ gene.All these polyreactive mAbs displayed a large NDN region(VH-D-JH junction).The entire H chain V regions of these polyreactive mAbs are unusually basic.The analysis of the charge properties of these mAbs as well as those of other poly-and mono-reactive mAbs from literatures prompts us to propose that the charged amino acids with a particular distribution along the H chain V region,especially the binding sites(CDRs),may be an important structural feature involved in antibody polyreactivity.

  7. Cloning and Sequence Analysis of Light Variable Region Gene of Anti-human Retinoblastoma Monoclonal Antibody

    Institute of Scientific and Technical Information of China (English)

    Xiufeng Zhong; Yongping Li; Shuqi Huang; Bo Ning; Chunyan Zhang; Jianliang Zheng; Guanguang Feng


    Purpose: To clone the variable region gene of light chain of monoclonal antibody against human retinoblastoma and to analyze the characterization of its nucleotide sequence as well as amino acid sequence.Methods: Total RNA was extracted from 3C6 hybridoma cells secreting specific monoclonal antibody(McAb)against human retinoblastoma(RB), then transcripted reversely into cDNA with olig-dT primers.The variable region of the light chain (VL) gene fragments was amplified using polymeerase chain reaction(PCR) and further cloned into pGEM(R) -T Easy vector. Then, 3C6 VL cDNA was sequenced by Sanger's method.Homologous analysis was done by NCBI BLAST.Results: The complete nucleotide sequence of 3C6 VL cDNA consisted of 321 bp encoding 107 amino acid residues, containing four workframe regions(FRs)and three complementarity-determining regions (CDRs) as well as the typical structure of two cys residues. The sequence is most homological to a member of the Vk9 gene family, and its chain utilizes the Jkl gene segment.Conclusion: The light chain variable region gene of the McAb against human RB was amplified successfully , which belongs to the Vk9 gene family and utilizes Vk-Jk1 gene rearrangement. This study lays a good basis for constructing a recombinant antibody and for making a new targeted therapeutic agents against retinoblastoma.

  8. Mutations in specific structural regions of immunoglobulin light chains are associated with free light chain levels in patients with AL amyloidosis.

    Directory of Open Access Journals (Sweden)

    Tanya L Poshusta

    Full Text Available BACKGROUND: The amyloidoses are protein misfolding diseases characterized by the deposition of amyloid that leads to cell death and tissue degeneration. In immunoglobulin light chain amyloidosis (AL, each patient has a unique monoclonal immunoglobulin light chain (LC that forms amyloid deposits. Somatic mutations in AL LCs make these proteins less thermodynamically stable than their non-amyloidogenic counterparts, leading to misfolding and ultimately the formation of amyloid fibrils. We hypothesize that location rather than number of non-conservative mutations determines the amyloidogenicity of light chains. METHODOLOGY/PRINCIPAL FINDINGS: We performed sequence alignments on the variable domain of 50 kappa and 91 lambda AL light chains and calculated the number of non-conservative mutations over total number of patients for each secondary structure element in order to identify regions that accumulate non-conservative mutations. Among patients with AL, the levels of circulating immunoglobulin free light chain varies greatly, but even patients with very low levels can have very advanced amyloid deposition. CONCLUSIONS: Our results show that in specific secondary structure elements, there are significant differences in the number of non-conservative mutations between normal and AL sequences. AL sequences from patients with different levels of secreted light chain have distinct differences in the location of non-conservative mutations, suggesting that for patients with very low levels of light chains and advanced amyloid deposition, the location of non-conservative mutations rather than the amount of free light chain in circulation may determine the amyloidogenic propensity of light chains.


    Directory of Open Access Journals (Sweden)

    Bianca Cristina Aléssio


    Full Text Available The last decades witnessed a transformation of the concept of development and of the analysis of its explanatory variables. Regional/local specificities became important aspects of development processes since each territory reacts differently to different strategies and creates specific solutions for its development. This article analyzes the path of a regional development process from the perspective of the institutional, schumpeterian and territorial approach theories. They provide important references to analyze development processes at the local level, as they consider history, culture, behavior codes, values and techniques as determinants of development. The study builds on Santa Catarina's Western region case and shows that regional development processes can be analyzed with the support of these theories as a chain of organizational dynamics and local technological trajectories that influence each other and determine the possible courses of territorial development.

  10. Conditional probability Markov chain simulation based reliability analysis method for nonnormal variables

    Institute of Scientific and Technical Information of China (English)


    Based on fast Markov chain simulation for generating the samples distributed in failure region and saddlepoint approximation(SA) technique,an efficient reliability analysis method is presented to evaluate the small failure probability of non-linear limit state function(LSF) with non-normal variables.In the presented method,the failure probability of the non-linear LSF is transformed into a product of the failure probability of the introduced linear LSF and a feature ratio factor.The introduced linear LSF which approximately has the same maximum likelihood points as the non-linear LSF is constructed and its failure probability can be calculated by SA technique.The feature ratio factor,which can be evaluated on the basis of multiplicative rule of probability,exhibits the relation between the failure probability of the non-linear LSF and that of the linear LSF,and it can be fast computed by utilizing the Markov chain algorithm to directly simulate the samples distributed in the failure regions of the non-linear LSF and those of the linear LSF.Moreover,the expectation and variance of the failure probability estimate are derived.The results of several examples demonstrate that the presented method has wide applicability,can be easily implemented,and possesses high precision and high efficiency.

  11. Laminin alpha2 chain-deficient congenital muscular dystrophy: variable epitope expression in severe and mild cases

    DEFF Research Database (Denmark)

    Cohn, R D; Herrmann, R; Sorokin, L;


    To characterize the expression of distinct fragments of laminin alpha2 chain in patients with partial laminin alpha2 chain deficiency and variable clinical severity.......To characterize the expression of distinct fragments of laminin alpha2 chain in patients with partial laminin alpha2 chain deficiency and variable clinical severity....

  12. Gladiolus plants transformed with single-chain variable fragment antibodies to Cucumber mosaic virus (United States)

    Transgenic plants of Gladiolus ‘Peter Pears’ or ‘Jenny Lee’ were developed that contain single-chain variable fragments (scFv) to Cucumber mosaic virus (CMV) subgroup I or II. The CMV subgroup I heavy and light chain scFv fragments were placed under control of either the duplicated CaMV 35S or suga...

  13. Equivalence of chain conformations in the surface region of a polymer melt and a single Gaussian chain nder critical conditions

    NARCIS (Netherlands)

    Skvortsov, A.M.; Leermakers, F.A.M.; Fleer, G.J.


    In the melt polymer conformations are nearly ideal according to Flory's ideality hypothesis. Silberberg generalized this statement for chains in the interfacial region. We check the Silberberg argument by analyzing the conformations of a probe chain end-grafted at a solid surface in a sea of floatin

  14. Water Column Variability in Coastal Regions (United States)


    transported into the Bay beneath the Bay’s less dense surface layer. Tang, Ni, Kester, and Müller-Karger have conducted a study of a winter...water inputs and urban nutrient inputs. The second buoy is located in the mid-region of the Bay between Quonset Point and Newport. Both buoys are...additional time-series measurements systems near the head of Narragansett Bay in the urban area of Providence, RI. REFERENCES Czitrom, S.P.R. and Simpson

  15. 甲型H1N1流感病毒血凝素单克隆抗体轻链和重链可变区基因的巢式PCR扩增及序列分析%Nested PCR Amplifying and DNA Sequence Analysis of Light and Heavy Chain Variable Region Gene of Monoclonal Antibody Against H1N1 Influenza Virus Hemagglutinin

    Institute of Scientific and Technical Information of China (English)

    李慧瑾; 胡军; 李研; 孙晶莹; 高锦伟; 赵向绒; 封青; 谭天天; 胡巧侠; 李元


    Objective: To clone and analysis light and heavy chain genes of monoclonal antibody against H1N1 influenza virus hemagglutinin by Nested PCR, then construct a common method for cloning light and heavy chain variable region genes of mouse anti-human H1N1 influenza virus hemagglutinin monoclonal antibody. Methods:We designed 22 pairs of primers for amplifying Igκ light and heavy chain variable region gene, and cloned light and heavy chain variable region genes of 6 mouse anti-human H1N1 influenza virus hemagglutinin monoclonal anti⁃bodies. Cloning and subsequent sequences analysis of immunoglobulin gene were performed, sequence alignment with mouse immunoglobulin in NCBI. Results: The nucleotide and corresponding amino acid sequences were in line with characteristics of mouse immunoglobulin variable region. Conclusion: In this study, we cloned 6 mouse antibody variable region genes, and found a common method for cloning immunoglobulin light and heavy chain variable region genes. It provides a basis for late amplifying monoclonal antibody variable region, and experimental data for analysis of H1N1 influenza virus hemagglutinin and antibody binding sites.%  目的:采用巢式PCR对甲型H1N1流感病毒血凝素单克隆抗体的轻链和重链基因进行扩增,对获得的基因进行序列分析,并找出克隆鼠Igκ轻链和重链可变区基因的通用方法。方法:设计22对扩增鼠Igκ轻链可变区和重链可变区基因的引物,对6株鼠抗人甲型H1N1流感病毒血凝素单克隆抗体的轻链和重链可变区基因进行克隆并测序,与NCBI公布的鼠免疫球蛋白序列比对分析。结果:巢式PCR方法可以有效避免单克隆抗体克隆过程的假基因,并且得到的单克隆抗体的氨基酸序列均符合鼠免疫球蛋白可变区特征。结论:建立了克隆鼠免疫球蛋白轻链和重链可变区基因的通用方法,为后期克隆鼠源性单克隆抗体的可变区基因提供了

  16. Chimeric antibody with human constant regions and mouse variable regions directed against carcinoma-associated antigen 17-1A

    Energy Technology Data Exchange (ETDEWEB)

    Sun, L.K.; Curtis, P.; Rakowicz-Szulczynska, E.; Ghrayeb, J.; Chang, N.; Morrison, S.L.; Koprowski, H.


    The authors have cloned the genomic DNA fragments encoding the heavy and light chain variable regions of monoclonal antibody 17-1A, and they have inserted them into mammalian expression vectors containing genomic DNA segments encoding human ..gamma..3 and kappa constant regions. The transfer of these expression vectors containing mouse-human chimeric immunoglobulin genes into Sp2/0 mouse myeloma cells resulted in the production of functional IgG that retained the specific binding to the surface antigen 17-1A expressed on colorectal carcinoma cells.

  17. Conserved termini and adjacent variable region of Twortlikevirus Staphylococcus phages

    Institute of Scientific and Technical Information of China (English)

    Xianglilan Zhang; Huaixing Kang; Yuyuan Li; Xiaodong Liu; Yu Yang; Shasha Li; Guangqian Pei; Qiang Sun; Peng Shu; Zhiqiang Mi; Yong Huang; Zhiyi Zhang; Yannan Liu; Xiaoping An; Xiaolu Xu; Yigang Tong


    Methicillin-resistant Staphylococcus aureus(MRSA) is an increasing cause of serious infection,both in the community and hospital settings. Despite sophisticated strategies and efforts, the antibiotic options for treating MRSA infection are narrowing because of the limited number of newly developed antimicrobials. Here, four newly-isolated MRSA-virulent phages, IME-SA1, IMESA2, IME-SA118 and IME-SA119, were sequenced and analyzed. Their genome termini were identified using our previously proposed "termini analysis theory". We provide evidence that remarkable conserved terminus sequences are found in IME-SA1/2/118/119, and, moreover, are widespread throughout Twortlikevirus Staphylococcus phage G1 and K species. Results also suggested that each phage of the two species has conserved 5′ terminus while the 3′ terminus is variable. More importantly, a variable region with a specific pattern was found to be present near the conserved terminus of Twortlikevirus S. phage G1 species. The clone with the longest variable region had variable terminus lengths in successive generations, while the clones with the shortest variable region and with the average length variable region maintained the same terminal length as themselves during successive generations. IME-SA1 bacterial infection experiments showed that the variation is not derived from adaptation of the phage to different host strains. This is the first study of the conserved terminus and variable region of Twortlikevirus S. phages.

  18. Climate variability in the Carpathian Mountains Region over 1961-2010 (United States)

    Cheval, Sorin; Birsan, Marius-Victor; Dumitrescu, Alexandru


    The Carpathian Mountains Region (CMR) lies over parts of the territories of seven Central and Southeastern European countries, and the mountain chain induces major changes in the temperate climate specific to the latitudes between 43° and 49°N. Different administrations govern the long-term meteorological networks; the infrastructure, collection protocols, and storage capacities are specific to each country, so that a comprehensive study on the climate of the area has met considerable difficulties along time. Climate of the Carpathian Region (CARPATCLIM) is a regional initiative developed between 2010 and 2013 aiming to enhance the climatic information in the area by providing comprehensive, temporally and spatially homogenous data sets of the main meteorological variables. Based on daily data aggregated to a monthly scale at 10-km resolution, this study exploits and promotes the results of the CARPATCLIM project, documenting the variability of the main climatic variables over 1961-2010. For each month, the significant increasing or decreasing trends were identified, mapped and placed in the context of previous studies and climate change perspectives. The study has revealed several patterns in the climatic variability, i.e., positive or negative trends prevailing over the entire area, very distinct delineation between various trends induced by the Carpathian Mountain chain, and pledges for further scientific approaches, i.e., causes of the variability and applications in other domains.

  19. Expression and production of llama variable heavy-chain antibody fragments (VHHs) by Aspergillus awamori

    NARCIS (Netherlands)

    Joosten, V.; Gouka, R.J.; Hondel, C.A.M.J.J. van den; Verrips, C.T.; Lokman, B.C.


    We report the expression and production of llama variable heavy-chain antibody fragments (VHHs) by Aspergillus awamori. Fragments encoding VHHs were cloned in a suitable Aspergillus expression vector and transformants secreting VHH fragments were analysed for integrated gene copy-numbers, mRNA level

  20. Affinity improvement by fine tuning of single-chain variable fragment against aflatoxin B1. (United States)

    Min, Won-Ki; Na, Kang-In; Yoon, Jung-Hyun; Heo, Yoon-Jee; Lee, Daesang; Kim, Sung-Gun; Seo, Jin-Ho


    Aflatoxin B1 (AFB1) produced in Aspergillus flavus is a major hepatocarcinogen found in foods and feed. For effective immunological detection of AFB1 at low concentrations, the development of high affinity antibody for AFB1 is required. Previously, an affinity-maturated single-chain variable fragment containing 6 mutations (scFv-M37) was isolated from an artificial mutagenic library, which showed a 9-fold higher affinity than its wild type scFv. In this study, the effect of the 6 mutated residues on the affinity improvement was characterized using surface plasmon resonance analysis, which identified a deleterious mutation (VH-A110T) located on a framework region of the scFv-M37. The back mutation of VH-A110T resulted in a 3.2-fold affinity improvement, which was attributed to decrease of dissociation rate constant (kd) in interaction between AFB1 and the back mutant scFv. The biophysical analyses using circular dichroism and gel filtration revealed that the back mutation of VH-A110T caused a subtle conformational change of the scFv toward tighter binding to AFB1.

  1. The role of CTCF binding sites in the 3' immunoglobulin heavy chain regulatory region. (United States)

    Birshtein, Barbara K


    The immunoglobulin heavy chain locus undergoes a series of DNA rearrangements and modifications to achieve the construction and expression of individual antibody heavy chain genes in B cells. These events affect variable regions, through VDJ joining and subsequent somatic hypermutation, and constant regions through class switch recombination (CSR). Levels of IgH expression are also regulated during B cell development, resulting in high levels of secreted antibodies from fully differentiated plasma cells. Regulation of these events has been attributed primarily to two cis-elements that work from long distances on their target sequences, i.e., an ∼1 kb intronic enhancer, Eμ, located between the V region segments and the most 5' constant region gene, Cμ; and an ∼40 kb 3' regulatory region (3' RR) that is located downstream of the most 3' C(H) gene, Cα. The 3' RR is a candidate for an "end" of B cell-specific regulation of the Igh locus. The 3' RR contains several B cell-specific enhancers associated with DNase I hypersensitive sites (hs1-4), which are essential for CSR and for high levels of IgH expression in plasma cells. Downstream of this enhancer-containing region is a region of high-density CTCF binding sites, which extends through hs5, 6, and 7 and further downstream. CTCF, with its enhancer-blocking activities, has been associated with all mammalian insulators and implicated in multiple chromosomal interactions. Here we address the 3' RR CTCF-binding region as a potential insulator of the Igh locus, an independent regulatory element and a predicted modulator of the activity of 3' RR enhancers. Using chromosome conformation capture technology, chromatin immunoprecipitation, and genetic approaches, we have found that the 3' RR with its CTCF-binding region interacts with target sequences in the V(H), Eμ, and C(H) regions through DNA looping as regulated by protein binding. This region impacts on B cell-specific Igh processes at different stages of B cell

  2. Variability of QSOs with variable regions in broad absorption troughs from the Sloan Digital Sky Survey

    CERN Document Server

    He, Zhi-Cheng; Jiang, Xiao-Lei; Ge, Xue


    The variability of broad absorption lines is investigated for a sample of 188 broad-absorption-line (BAL) quasars (QSOs) ($z > 1.7$) with at least two-epoch observations from the Sloan Digital Sky Survey Data Release 7 (SDSS DR7), covering a time-scale of about 0.001 -- 3 years in the rest frame. Considering only the longest time-scale between epochs for each QSO, 73 variable regions in the \\civ BAL troughs are detected for 43 BAL QSOs. The proportion of BAL QSOs showing variable regions increases with longer time-interval than about 1 year in the rest frame. The velocity width of variable regions is narrow compared to the BAL-trough outflow velocity. For 43 BAL QSOs with variable regions, it is found that there is a medium strong correlation between the variation of the continuum luminosity at 1500 \\AA\\ and the variation of the spectral index. With respect to the total 188 QSOs, larger proportion of BAL QSOs with variable regions appears bluer during their brighter phases, which implies that the origin of BA...

  3. Development of an Immunoassay for Chloramphenicol Based on the Preparation of a Specific Single-Chain Variable Fragment Antibody. (United States)

    Du, Xin-jun; Zhou, Xiao-nan; Li, Ping; Sheng, Wei; Ducancel, Frédéric; Wang, Shuo


    Specific antibodies are essential for the immune detection of small molecule contaminants. In the present study, the heavy and light variable regions (V(H )and V(L)) of the immunoglobulin genes from a hybridoma secreting a chloramphenicol (CAP)-specific monoclonal antibody (mAb) were cloned and sequenced. In addition, the light and heavy chains obtained from the monoclonal antibody were separated using SDS-PAGE and analyzed using Orbitrap mass spectrometry. The results of DNA sequencing and mass spectrometry analysis were compared, and the V(H) and V(L) chains specific for CAP were determined and used to construct a single-chain variable fragment (scFv). This fragment was recombinantly expressed as a soluble scFv-alkaline phosphatase fusion protein and used to develop a direct competitive ELISA. Compared with the parent mAb, scFv exhibits lower sensitivity but better food matrix resistance. This work highlights the application of engineered antibodies for CAP detection.

  4. Amplifying variable region gene of light chain(VL)of monoclonal antibody against human papillomavirus 16 L1(HPV16 L1)protein by 5'-RACE and sequence analysis%5'-RACE法扩增抗人乳头瘤病毒16型L1蛋白单克隆抗体轻链可变区基因及序列分析

    Institute of Scientific and Technical Information of China (English)

    王燕; 商庆龙; 陈思佳; 邵迪; 韩聪; 李茉; 谷鸿喜


    Objective To acquire the variable region gene of light chain(VL)of monoclonal antibody a-gainst human papillomavirus 16 LI(HPV16 LI)protein.Methods Total RNA waft extract from hybridoma cells secreting specific monoclonal antibody against HPV16L1,transcripted reversely into cDNA with random primers.The variable region of the light chain gene fragments was ampliflied using 5'-RACE.Sequencing was confirmed by agarose gel electrophoresis and sequencing analysis.Results Full letIsth of VL gene Was 336bp that encoding 112 amino acids.The VL gene was homologous with the published gene sequences of mouse antibody variable region.Conclusion The light chain sequence of monoclonal antibody against HPV16L1 protein Was obtained by 5'-RACE,which provides a good basis for construction of a recombinant antibody against HPV16 L1.%目的 获得抗人乳头瘤病毒16型(HPV16)L1蛋白单克隆抗体的轻链可变区(VL)基因并分析序列.方法 从分泌抗HPV16L1蛋白单克隆抗体的杂交瘤细胞中提取总RNA,逆转录形成cDNA,用5'-RACE策略扩增抗体轻链可变区基因,经琼脂糖凝胶电泳鉴定,并测序及进行序列分析.结果 VL基因全长336bp,编码112个氨基酸,基因测序结果符合小鼠抗体轻链可变区特征.结论 5'-RACE法成功获得了抗HPV16L1蛋白的单克隆抗体轻链可变区基因的真实序列,为基因工程抗体研究奠定了良好基础.

  5. Selection of single chain variable fragments specific for the human-inducible costimulator using ribosome display. (United States)

    Pan, Yangbin; Mao, Weiping; Liu, Xuanxuan; Xu, Chong; He, Zhijuan; Wang, Wenqian; Yan, Hao


    We applied a ribosome display technique to a mouse single chain variable fragment (scFv) library to select scFvs specific for the inducible costimulator (ICOS). mRNA was isolated from the spleens of BALB/c mice immunized with ICOS protein. Heavy and κ chain genes (VH and κ) were amplified separately by reverse transcriptase polymerase chain reaction, and the anti-ICOS VH/κ chain ribosome display library was constructed with a special flexible linker by overlap extension PCR. The VH/κ chain library was transcribed and translated in vitro using a rabbit reticulocyte lysate system. Then, antibody-ribosome-mRNA complexes were produced and panned against ICOS protein under appropriate conditions. However, in order to isolate specific scFvs for ICOS, negative selection using CD28 was carried out before three rounds of positive selection on ICOS. After three rounds of panning, the selected scFv DNAs were cloned into pET43.1a and detected by SDS-PAGE. Then, enzyme-linked immunosorbent assay showed that we successfully constructed a native ribosome display library, and among seven clones, clone 5 had the highest affinity for the ICOS and low for the CD28. Anti-ICOS scFvs are assessed for binding specificity and affinity and may provide the potential for development of the humanized and acute and chronic allograft rejection.

  6. Applying Markov Chains for NDVI Time Series Forecasting of Latvian Regions

    Directory of Open Access Journals (Sweden)

    Stepchenko Arthur


    Full Text Available Time series of earth observation based estimates of vegetation inform about variations in vegetation at the scale of Latvia. A vegetation index is an indicator that describes the amount of chlorophyll (the green mass and shows the relative density and health of vegetation. NDVI index is an important variable for vegetation forecasting and management of various problems, such as climate change monitoring, energy usage monitoring, managing the consumption of natural resources, agricultural productivity monitoring, drought monitoring and forest fire detection. In this paper, we make a one-step-ahead prediction of 7-daily time series of NDVI index using Markov chains. The choice of a Markov chain is due to the fact that a Markov chain is a sequence of random variables where each variable is located in some state. And a Markov chain contains probabilities of moving from one state to other.

  7. Test of a dynamical downscaling chain for assessing climate at regional scale. (United States)

    Vargiu, A.; Peneva, E.; Marrocu, M.


    During last years reanalysis datasets (ECMWF ERA40 or NCEP Reanalysis Project) have been widely used to investigate climate and detect some signals of global climate changes. Heavy limitations of those datasets are found when investigating the variables with intrinsic small coherence: precipitation, local winds, fogs, etc. Our aim was to perform a dynamical downscaling of ERA40 dataset using a local model (BOLAM, developed at the ISAC-CNR, Bologna, Italy). We focused our study mainly on precipitation verification. More specifically we verified the downscaling chain with CRU daily precipitation over Europe at 0.25 degrees. A test period, covering about a year, was studied adding up runs of 36 hours forecast. Some common verification indexes for precipitation, (ETS, POD, FAR, HK, etc.) were computed at different thresholds. The verification results have shown the benefits of the downscaling chain particularly for events of deep convective precipitation and precipitation forced by orography. Comparison of the results obtained using the BOLAM model and a specific regional climate model (REGCM3, developed at the ICTP, Trieste, Italy) will be also discussed.

  8. SDI and Markov Chains for Regional Drought Characteristics

    Directory of Open Access Journals (Sweden)

    Chen-Feng Yeh


    Full Text Available In recent years, global climate change has altered precipitation patterns, causing uneven spatial and temporal distribution of precipitation that gradually induces precipitation polarization phenomena. Taiwan is located in the subtropical climate zone, with distinct wet and dry seasons, which makes the polarization phenomenon more obvious; this has also led to a large difference between river flows during the wet and dry seasons, which is significantly influenced by precipitation, resulting in hydrological drought. Therefore, to effectively address the growing issue of water shortages, it is necessary to explore and assess the drought characteristics of river systems. In this study, the drought characteristics of northern Taiwan were studied using the streamflow drought index (SDI and Markov chains. Analysis results showed that the year 2002 was a turning point for drought severity in both the Lanyang River and Yilan River basins; the severity of rain events in the Lanyang River basin increased after 2002, and the severity of drought events in the Yilan River basin exhibited a gradual upward trend. In the study of drought severity, analysis results from periods of three months (November to January and six months (November to April have shown significant drought characteristics. In addition, analysis of drought occurrence probabilities using the method of Markov chains has shown that the occurrence probabilities of drought events are higher in the Lanyang River basin than in the Yilan River basin; particularly for extreme events, the occurrence probability of an extreme drought event is 20.6% during the dry season (November to April in the Lanyang River basin, and 3.4% in the Yilan River basin. This study shows that for analysis of drought/wet occurrence probabilities, the results obtained for the drought frequency and occurrence probability using short-term data with the method of Markov chains can be used to predict the long-term occurrence

  9. Business systems, value chains and inclusive regional development in South-East Asia

    NARCIS (Netherlands)

    E. Andriesse; N. Beerepoot; B. van Helvoirt; G. van Westen


    Regional economic development is played out in a network of relations along value chains and within a territorial setting. Chain insertion favours growth but also exclusion or inclusion on adverse terms. This may happen at different levels of scale, especially when a nation-state has not produced a

  10. Mid-Holocene regional reorganization of climate variability

    Directory of Open Access Journals (Sweden)

    K. W. Wirtz


    Full Text Available We integrate 130 globally distributed proxy time series to refine the understanding of climate variability during the Holocene. Cyclic anomalies and temporal trends in periodicity from the Lower to the Upper Holocene are extracted by combining Lomb-Scargle Fourier-transformed spectra with bootstrapping. Results were cross-checked by counting events in the time series. Main outcomes are: First, the propensity of the climate system to fluctuations is a region specific property. Many records of adjacent sites reveal a similar change in variability although they belong to different proxy types (e.g., δ18O, lithic composition. Secondly, at most sites, irreversible change occured in the Mid-Holocene. We suggest that altered ocean circulation together with slightly modified coupling intensity between regional climate subsystems around the 5.5 kyr BP event (termination of the African Humid Period were responsible for the shift. Fluctuations especially intensified along a pan-American corridor. This may have led to an unequal crisis probability for early human civilizations in the Old and New World. Our study did not produce evidence for millennial scale cyclicity in some solar activity proxies for the Upper Holocene, nor for a privileged role of the prominent 250, 550, 900 and 1450 yr cycles. This lack of global periodicities corroborates the regional character of climate variability.

  11. Attributing Sources of Variability in Regional Climate Model Experiments (United States)

    Kaufman, C. G.; Sain, S. R.


    Variability in regional climate model (RCM) projections may be due to a number of factors, including the choice of RCM itself, the boundary conditions provided by a driving general circulation model (GCM), and the choice of emission scenario. We describe a new statistical methodology, Gaussian Process ANOVA, which allows us to decompose these sources of variability while also taking account of correlations in the output across space. Our hierarchical Bayesian framework easily allows joint inference about high probability envelopes for the functions, as well as decompositions of total variance that vary over the domain of the functions. These may be used to create maps illustrating the magnitude of each source of variability across the domain of the regional model. We use this method to analyze temperature and precipitation data from the Prudence Project, an RCM intercomparison project in which RCMs were crossed with GCM forcings and scenarios in a designed experiment. This work was funded by the North American Regional Climate Change Assessment Program (NARCCAP).

  12. Decadal climate variability in the Mediterranean region: roles of large-scale forcings and regional processes

    Energy Technology Data Exchange (ETDEWEB)

    Mariotti, Annarita [University of Maryland, Earth System Science Interdisciplinary Center, College Park, MD (United States); Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome (Italy); Dell' Aquila, Alessandro [Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome (Italy)


    We analyze decadal climate variability in the Mediterranean region using observational datasets over the period 1850-2009 and a regional climate model simulation for the period 1960-2000, focusing in particular on the winter (DJF) and summer (JJA) seasons. Our results show that decadal variability associated with the winter and summer manifestations of the North Atlantic Oscillation (NAO and SNAO respectively) and the Atlantic Multidecadal Oscillation (AMO) significantly contribute to decadal climate anomalies over the Mediterranean region during these seasons. Over 30% of decadal variance in DJF and JJA precipitation in parts of the Mediterranean region can be explained by NAO and SNAO variability respectively. During JJA, the AMO explains over 30% of regional surface air temperature anomalies and Mediterranean Sea surface temperature anomalies, with significant influence also in the transition seasons. In DJF, only Mediterranean SST still significantly correlates with the AMO while regional surface air temperature does not. Also, there is no significant NAO influence on decadal Mediterranean surface air temperature anomalies during this season. A simulation with the PROTHEUS regional ocean-atmosphere coupled model is utilized to investigate processes determining regional decadal changes during the 1960-2000 period, specifically the wetter and cooler 1971-1985 conditions versus the drier and warmer 1986-2000 conditions. The simulation successfully captures the essence of observed decadal changes. Model set-up suggests that AMO variability is transmitted to the Mediterranean/European region and the Mediterranean Sea via atmospheric processes. Regional feedbacks involving cloud cover and soil moisture changes also appear to contribute to observed changes. If confirmed, the linkage between Mediterranean temperatures and the AMO may imply a certain degree of regional decadal climate predictability. The AMO and other decadal influences outlined here should be

  13. New Construction of Eigenstates and Separation of Variables for SU(N) Quantum Spin Chains

    CERN Document Server

    Gromov, Nikolay; Sizov, Grigory


    We conjecture a new way to construct eigenstates of integrable XXX quantum spin chains with SU(N) symmetry. The states are built by repeatedly acting on the vacuum with a single operator B^{good}(u) evaluated at the Bethe roots. Our proposal serves as a compact alternative to the usual nested algebraic Bethe ansatz. Furthermore, the roots of the operator B^{good}(u) give the separated variables of the model, explicitly generalizing Sklyanin's approach to the SU(N) case. We present many tests of the conjecture and prove it in several special cases. We focus on rational spin chains with fundamental representation at each site, but expect many of the results to be valid more generally.

  14. Porous silicon biosensor for detection of variable domain of heavy-chain of HCAb antibody

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hong-yan; Lü Xiao-yi; JIA Zhen-hong; LI Jiang-wei; ZHANG Fu-chun


    In this paper,we produce porous silicon (PSi) by electrochemical etching,and it is the first time to evaluate the performance of label-free porous silicon biosensor for detection of variable domain of heavy chain of heavy-chain antibody (VHH).The binding of hen egg white lysozyme (HEWL) and VHH causes a red shift in the reflection spectrum of the biosensor.The red shift is proportional to the VHH concentration in the range from 14 μg · ml-1 to 30μg·ml-1 with a detection limit of 0.648 ng ·ml-1.The research is useful for the development of label-free biosensor applied in the rapid and sensitive determination of small molecules.

  15. Trends and variability of droughts over the Indian monsoon region

    Directory of Open Access Journals (Sweden)

    Ganeshchandra Mallya


    Full Text Available Drought characteristics for the Indian monsoon region are analyzed using two different datasets and standard precipitation index (SPI, standardized precipitation-evapotranspiration index (SPEI, Gaussian mixture model-based drought index (GMM-DI, and hidden Markov model-based drought index (HMM-DI for the period 1901–2004. Drought trends and variability were analyzed for three epochs: 1901–1935, 1936–1971 and 1972–2004. Irrespective of the dataset and methodology used, the results indicate an increasing trend in drought severity and frequency during the recent decades (1972–2004. Droughts are becoming more regional and are showing a general shift to the agriculturally important coastal south-India, central Maharashtra, and Indo-Gangetic plains indicating higher food security and socioeconomic vulnerability in the region.

  16. A Strategy for Generating a Broad-Spectrum Monoclonal Antibody and Soluble Single-Chain Variable Fragments against Plant Potyviruses. (United States)

    Liu, Han-Lin; Lin, Wei-Fang; Hu, Wen-Chi; Lee, Yung-An; Chang, Ya-Chun


    Potyviruses are major pathogens that often cause mixed infection in calla lilies. To reduce the time and cost of virus indexing, a detection method for the simultaneous targeting of multiple potyviruses was developed by generating a broad-spectrum monoclonal antibody (MAb) for detecting the greatest possible number of potyviruses. The conserved 121-amino-acid core regions of the capsid proteins of Dasheen mosaic potyvirus (DsMV), Konjak mosaic potyvirus (KoMV), and Zantedeschia mild mosaic potyvirus (ZaMMV) were sequentially concatenated and expressed as a recombinant protein for immunization. After hybridoma cell fusion and selection, one stable cell line that secreted a group-specific antibody, named C4 MAb, was selected. In the reaction spectrum test, the C4 MAb detected at least 14 potyviruses by indirect enzyme-linked immunosorbent assay (I-ELISA) and Western blot analysis. Furthermore, the variable regions of the heavy (VH) and light (VL) chains of the C4 MAb were separately cloned and constructed as single-chain variable fragments (scFvs) for expression in Escherichia coli. Moreover, the pectate lyase E (PelE) signal peptide of Erwinia chrysanthemi S3-1 was added to promote the secretion of C4 scFvs into the medium. According to Western blot analysis and I-ELISA, the soluble C4 scFv (VL-VH) fragment showed a binding specificity similar to that of the C4 MAb. Our results demonstrate that a recombinant protein derived from fusion of the conserved regions of viral proteins has the potential to produce a broad-spectrum MAb against a large group of viruses and that the PelE signal peptide can improve the secretion of scFvs in E. coli.

  17. Development of single-chain variable fragments (scFv) against influenza virus targeting hemagglutinin subunit 2 (HA2). (United States)

    Li, Tai-Wei; Cheng, Shu-Fang; Tseng, Yen-Tzu; Yang, Yu-Chih; Liu, Wen-Chun; Wang, Sheng-Cyuan; Chou, Mei-Ju; Lin, Yu-Jen; Wang, Yueh; Hsiao, Pei-Wen; Wu, Suh-Chin; Chang, Ding-Kwo


    Influenza A viruses (IAV) are widespread in birds and domestic poultry, occasionally causing severe epidemics in humans and posing health threats. Hence, the need to develop a strategy for prophylaxis or therapy, such as a broadly neutralizing antibody against IAV, is urgent. In this study, single-chain variable fragment (scFv) phage display technology was used to select scFv fragments recognizing influenza envelope proteins. The Tomlinson I and J scFv phage display libraries were screened against the recombinant HA2 protein (rHA2) for three rounds. Only the third-round elution sample of the Tomlinson J library showed high binding affinity to rHA2, from which three clones (3JA18, 3JA62, and 3JA78) were chosen for preparative-scale production as soluble antibody by E. coli. The clone 3JA18 was selected for further tests due to its broad affinity for influenza H1N1, H3N2 and H5N1. Simulations of the scFv 3JA18-HA trimer complex revealed that the complementarity-determining region of the variable heavy chain (VH-CDR2) bound the stem region of HA. Neutralization assays using a peptide derived from VH-CDR2 also supported the simulation model. Both the selected antibody and its derived peptide were shown to suppress infection with H5N1 and H1N1 viruses, but not H3N2 viruses. The results also suggested that the scFvs selected from rHA2 could have neutralizing activity by interfering with the function of the HA stem region during virus entry into target cells.

  18. ZnO hybrid photovoltaics with variable side-chain lengths of thienothiophene polymer

    Energy Technology Data Exchange (ETDEWEB)

    Han, SeungJin [Advanced Technology Institute, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH (United Kingdom); Fei, Zhuping [Department of Chemistry and Centre for Plastic Electronics, Imperial College London, South Kensington SW7 2AZ (United Kingdom); Jayawardena, K.D.G.I.; Beliatis, Michail J. [Advanced Technology Institute, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH (United Kingdom); Hahn, Yoon-Bong [School of Chemical Engineering, Chonbuk National University, Jeon-ju, Jeonbuk 561-756 (Korea, Republic of); Adikaari, A.A.D.T. [Advanced Technology Institute, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH (United Kingdom); Heeney, Martin J. [Department of Chemistry and Centre for Plastic Electronics, Imperial College London, South Kensington SW7 2AZ (United Kingdom); Silva, S. Ravi P., E-mail: [Advanced Technology Institute, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH (United Kingdom)


    The effect of the side-chain length of poly(3,6-dialkylthieno[3,2-b]thiophene-co-bithiophene) (pATBT) on the performance of hybrid polymer-metal oxide photovoltaics (PVs) utilizing zinc oxide (ZnO) acceptor is investigated. The pATBT attached with a dodecyl side chain (pATBT-C{sub 12}) in hybrid photovoltaics with ZnO was compared to pATBT with a hexadecyl side chain (pATBT-C{sub 16}). Atomic force microscopic analysis reveals a smoother surface for the pATBT-C{sub 16} photoactive layer compared to the pATBT-C{sub 12}. For hybrid PVs using pATBT-C{sub 16}, the relative intensity of the external quantum efficiency (EQE) increased particularly in wavelength region associated with the ZnO. Furthermore, the EQE spectrum shows a red shift for pATBT-C{sub 16} indicating better structural ordering compared to hybrid PVs with pATBT-C{sub 12}. As a result, the hybrid PV utilizing pATBT-C{sub 16}:ZnO blend layer is observed to display a better performance with a power conversion efficiency of 1.02% compared to 0.672% of pATBT-C{sub 12}:ZnO PV. - Highlights: • The effect of polymer side-chain length on hybrid photovoltaics is investigated. • Longer side chains positively influence structural and optical properties of hybrid films. • Longer side-chain length leads to better photovoltaic performance.

  19. Climatic variability between SST and river discharge at Amazon region (United States)

    Silva, M. E.; Silva, E. R. L.


    Climatic variability, related both to precipitation and river discharge, has been associated to ocean variability. Authors commonly relate Pacific sea surface temperature (SST) variation to South America (SA) precipitation. Zonal displacement of Walker cell, with intensified subsidence over northern portion of SA, Subtropical Jet strengthening/weakening over extratropical latitudes of SA are, respectively, dynamical reasons scientifically accepted for increasing and depletion of precipitation at the respective areas. Many studies point out the influence of tropical Atlantic SST anomalies in relation to precipitation/river discharge variability over northeast of Brazil. Aliseos variability at tropical Atlantic is also a physic process that contributes to explain precipitation and river flow variability over SA, mainly over the north portion. In this study, we aim to investigate the temporal correlation between SST, mainly from Pacific and Atlantic oceans, and rivers discharge at the Amazon region. Ji-Parana, Madeira and Tapajós river discharge in monthly and annual scale, between 1968 and 2008, were the time series selected to reach the purpose. Time series for river discharge were obtained from Agência Nacional de Águas (ANA, in Portuguese) and, SST data were obtained from CDC/NOAA. Before linear correlation computations between river discharge and SST have been made, seasonal cycle and linear tendency were removed from all original time series. Areas better correlated to river discharge at Amazon region show oceanic patterns apparently associated to PDO (Pacific Decadal Oscillation) and ENSO (El Niño-South Oscillation) variability, with absolute values greater than 0.3 and reaching 0.5 or 0.6. The spatial pattern observed at Pacific basin is similar to that showed by the first mode of PCA (Principal Component Analysis), such seen in many studies (the "horse shoe" pattern). In general, negative correlation values appear far more to the west of Pacific basin

  20. Generation of a recombinant single-chain variable fragment (scFv) targeting 5-methyl-2'-deoxycytidine. (United States)

    Ohshima, Motohiro; Tadakuma, Tomomi; Hayashi, Hideki; Inoue, Kazuyuki; Itoh, Kunihiko


    We generated a single-chain variable fragment (scFv) against 5-methyl-2'-deoxycytidine (m(5)dCyd) using phage display technology. The heavy and light chain variable region genes were amplified by the polymerase chain reaction (PCR) from hybridoma cell line FMC9 and assembled as an scFv fragment with a flexible linker (Gly(4)-Ser)(3). The scFv DNA fragment was then cloned into pCANTAB-5E, and a phage displaying the scFv was produced. Antigen-positive phage clones were successfully selected by enzyme-linked immunosorbent assay (ELISA). The scFv was modified with FLAG and His tags for detection and purification. The scFv reacted strongly with m(5)dCyd and weakly with 5-methylcytidine (m(5)Cyd) but not with cytidine (Cyd) and 1-methyladenosine in a manner similar to the monoclonal antibody (MoAb). Although the specificities of scFv and MoAb were almost identical, the sensitivity of the scFv (IC(50) 0.054 microg/ml) was approximately 80 times higher than that of the parent MoAb (IC(50) 4.27 microg/ml), determined by inhibition ELISA. As a biochemical application of this scFv, we quantified the m(5)dCyd content of genomic DNA by enzymatic hydrolysis using inhibition ELISA. The cancer cell lines HeLa, HeLa S3 and MDA-MB-453 contained approximately 1% of the methylated DNA in total genomic DNA, as did peripheral blood cell genomic DNA from healthy volunteers, but HT29 and T-47D showed hypomethylation compared with the HeLa, HeLa S3 and MDA-MB-453 cell lines. The scFv generated here may be applicable to the assessment of cellular DNA methylation levels and is more sensitive than the MoAb.

  1. Expression, purification, and characterization of anti-plumbagin single-chain variable fragment antibody in Sf9 insect cell. (United States)

    Sakamoto, Seiichi; Taura, Futoshi; Tsuchihashi, Ryota; Putalun, Waraporn; Kinjo, Junei; Tanaka, Hiroyuki; Morimoto, Satoshi


    Plumbagin (PL; 5-hydroxy-2-methyl-1, 4-naphthoquinone) is an important secondary metabolite, mainly produced in the Plumbago zeylanica L. (Plumbaginaceae). A single-chain variable fragment (scFv) antibody, fusion of the variable regions of the heavy chain and light chain of immunoglobulin against PL (PL-scFv) was expressed by Bac-to-Bac Baculovirus Expression System using Spodoptera frugiperda (Sf9) insect cells and characterized to investigate potential use of PL-scFv as a tool for plant immunomodulation. Functional PL-scFv expressed in the Sf9 insect cells were purified using cation exchange chromatography followed by immobilized metal ion affinity chromatography (IMAC). The yields of the purified PL-scFv in the culture supernatant and Sf9 insect cells were 2.0 mg and 5.2 mg per 1 liter of Sf9 culture medium, respectively. Recombinant purified PL-scFv was then characterized by the indirect competitive enzyme-linked immunosorbent assay (ELISA). The cross-reactivity and sensitivity of PL-scFv expressed in Sf9 insect cells were compared with PL-scFv expressed in Escherichia coli and its parental anti-plumbagin monoclonal antibody (MAb 3A3) secreted from hybridoma cells. Intriguingly, the specificity of the PL-scFv expressed in Sf9 insect cells was found to be different from that expressed in E. coli and parental MAb 3A3, although the detectable level (0.2-25 μg/mL) was the same in ELISA using each antibody. Even more interestingly, the characteristics of PL-scFv, which have wide cross-reactivity against 1,4-napththoquinone, suggest its potential use as a tool for plant immunomodulation not only for breeding Plumbaginacea family containing PL but also for breeding other medicinal plants containing bioactive naphthoquinones.

  2. IgG variable region and VH CDR3 diversity in unimmunized mice analyzed by massively parallel sequencing. (United States)

    Lu, Jin; Panavas, Tadas; Thys, Kim; Aerssens, Jeroen; Naso, Michael; Fisher, Jamie; Rycyzyn, Michael; Sweet, Raymond W


    Most antigen-specific mouse antibodies have been derived by hybridoma technology, predominantly through use of the Balb/c strain. Much of the Balb/c germline repertoire of variable genes (V regions) is known. However, there is little information about the background expressed repertoire of IgG antibodies in mice, which reflects the baseline against which antigen-specific antibodies are generated through immunization. To assess this baseline repertoire, RNA was isolated from splenic B-cells enriched for expression of IgG from three mice. The RNA was individually amplified with three distinct PCR primer sets for comprehensive recovery of the heavy and light chain variable regions. Each PCR product was independently subjected to deep sequencing using 454 pyro-sequencing technology and analysed for redundancy, open reading frame, germline representation, and CDR3 sequence of the heavy chain variable region (VH CDR3) within and across the primer sets and mice. A highly skewed abundance of heavy and light chain variable gene usage was observed for all three primers in all three mice. While showing considerable overlap, there were differences among these profiles indicative of primer bias and animal-to-animal variation. VH CDR3 sequences were likewise highly skewed indicating that the heavy chain genes profiles substantially reflected individual antibodies. This observation was confirmed through analysis of randomly selected complete heavy chain variable sequences. However, there was very little redundancy in VH CDR3 sequences across the different mice. We conclude that the background IgG repertoire in young, unimmunized mice is highly skewed within individual mice and is diverse among them, a pattern similar to that observed in highly immunized mice.

  3. Cloning approach and functional analysis of anti-intimin single-chain variable fragment (scFv

    Directory of Open Access Journals (Sweden)

    Elias Waldir P


    Full Text Available Abstract Background Intimin is an important virulence factor involved in the pathogenesis of enteropathogenic Escherichia coli (EPEC and enterohemorrhagic Escherichia coli (EHEC. Both pathogens are still important causes of diarrhea in children and adults in many developing and industrialized countries. Considering the fact that antibodies are important tools in the detection of various pathogens, an anti-intimin IgG2b monoclonal antibody was previously raised in immunized mice with the conserved sequence of the intimin molecule (int388-667. In immunoblotting assays, this monoclonal antibody showed excellent specificity. Despite good performance, the monoclonal antibody failed to detect some EPEC and EHEC isolates harboring variant amino acids within the 338-667 regions of intimin molecules. Consequently, motivated by its use for diagnosis purposes, in this study we aimed to the cloning and expression of the single-chain variable fragment from this monoclonal antibody (scFv. Findings Anti-intimin hybridoma mRNA was extracted and reversely transcripted to cDNA, and the light and heavy chains of the variable fragment of the antibody were amplified using commercial primers. The amplified chains were cloned into pGEM-T Easy vector. Specific primers were designed and used in an amplification and chain linkage strategy, obtaining the scFv, which in turn was cloned into pAE vector. E. coli BL21(DE3pLys strain was transformed with pAE scFv-intimin plasmid and subjected to induction of protein expression. Anti-intimin scFv, expressed as inclusion bodies (insoluble fraction, was denatured, purified and submitted to refolding. The protein yield was 1 mg protein per 100 mL of bacterial culture. To test the functionality of the scFv, ELISA and immunofluorescence assays were performed, showing that 275 ng of scFv reacted with 2 mg of purified intimin, resulting in an absorbance of 0.75 at 492 nm. The immunofluorescence assay showed a strong reactivity with

  4. Using Intensive Variables to Constrain Magma Source Regions (United States)

    Edwards, B. R.; Russell, J. K.


    In the modern world of petrology, magma source region characterization is commonly the realm of trace element and isotopic geochemistry. However, major element analyses of rocks representing magmatic compositions can also be used to constrain source region charactertistics, which enhance the results of isotopic and trace element studies. We show examples from the northern Cordilleran volcanic province (NCVP), in the Canadian Cordillera, where estimations of thermodynamic intensive variables are used to resolve different source regions for mafic alkaline magmas. We have taken a non-traditional approach to using the compositions of three groups of mafic, alkaline rocks to characterize the source regions of magmas erupted in the NCVP. Based on measured Fe2O3 and FeO in rocks from different locations, the Atlin volcanic district (AVD), the Fort Selkirk volcanic complex (FSVC), the West Tuya volcanic field, (WTVF), we have estimated oxygen fugacities (fO2) for the source regions of magmas based on the model of Kress and Carmichael (1991) and the computational package MELTS/pMelts (Ghiorso and Sack, 1995; Ghiorso et al., 2002). We also have used Melts/pMelts to estimate liquidus conditions for the compositions represented by the samples as well as activities of major element components. The results of our calculations are useful for distinguishing between three presumably different magma series: alkaline basalts, basanites, and nephelinites (Francis and Ludden, 1990; 1995). Calculated intensive variables (fO2, activities SiO2, KAlSiO4, Na2SiO3) show clear separation of the samples into two groups: i) nephelinites and ii) basanites/alkaline basalts. The separation is especially evident on plots of log fO2 versus activity SiO2. The source region for nephelinitic magmas in the AVD is up to 2 log units more oxidized than that for the basanites/basalts as well as having a distinctly lower range of activities of SiO2. Accepting that our assumptions about the magmas

  5. Stoichiometry and heterogeneity of the pro-region chain in tetrameric human cathepsin C. (United States)

    Cigić, B; Krizaj, I; Kralj, B; Turk, V; Pain, R H


    The subunit structure and composition of mature human cathepsin C, an oligomeric cysteine proteinase, has been characterised in detail. The heavy chain, light chain and pro-region peptides are shown to be held together solely by non-covalent interactions, and to be present in equimolar ratio, suggesting an important structural role for the residual pro-region chain which is strongly bound to the enzyme. The mass of the light chain, as determined by mass spectrometry, combined with its N-terminal sequence, determines the position of cleavage from the heavy chain. Amino-acid sequencing has led to definition of the 13.5 kDa N-terminal part of the pro-region which remains in the mature enzyme, the C-terminal moiety of 10 kDa being cleaved out and lost from the pro-peptide on activation. The residual pro-region is heterogeneous, a proportion being intact and the remainder being cleaved at alternative positions 58 or 61, yielding two smaller peptides joined by disulphide bond. The proportion of cleaved form was found to vary with tissue and enzyme preparation but did not affect enzyme activity. The molecular masses of the constituent chains after deglycosylation lead to a protein mass of 158 kDa. All four potential glycosylation sites are glycosylated.

  6. Development of single chain variable fragment (scFv) antibodies against Xylella fastidiosa subsp. pauca by phage display. (United States)

    Yuan, Qing; Jordan, Ramon; Brlansky, Ronald H; Istomina, Olga; Hartung, John


    Xylella fastidiosa is a member of the gamma proteobacteria. It is fastidious, insect-vectored and xylem-limited and causes a variety of diseases, some severe, on a wide range of economically important perennial crops, including grape and citrus. Antibody based detection assays are commercially available for X. fastidiosa, and are effective at the species, but not at the subspecies level. We have made a library of scFv antibody fragments directed against X. fastidiosa subsp. pauca strain 9a5c (citrus) by using phage display technology. Antibody gene repertoires were PCR-amplified using 23 primers for the heavy chain variable region (V(H)) and 21 primers for the light chain variable region (V(L)). The V(H) and V(L) were joined by overlap extension PCR, and then the genes of the scFv library were ligated into the phage vector pKM19. The library contained 1.2×10(7) independent clones with full-length scFv inserts. In each of 3cycles of affinity-selection with 9a5c, about 1.0×10(12) phage were used for panning with 4.1×10(6), 7.1×10(6), 2.1×10(7) phage recovered after the first, second and third cycles, respectively. Sixty-six percent of clones from the final library bound X. fastidiosa 9a5c in an ELISA. Some of these scFv antibodies recognized strain 9a5c and did not recognize X. fastidiosa strains that cause Pierce's disease of grapevine.

  7. Comprehensive optimization of a single-chain variable domain antibody fragment as a targeting ligand for a cytotoxic nanoparticle. (United States)

    Zhang, Kathy; Geddie, Melissa L; Kohli, Neeraj; Kornaga, Tad; Kirpotin, Dmitri B; Jiao, Yang; Rennard, Rachel; Drummond, Daryl C; Nielsen, Ulrik B; Xu, Lihui; Lugovskoy, Alexey A


    Antibody-targeted nanoparticles have the potential to significantly increase the therapeutic index of cytotoxic anti-cancer therapies by directing them to tumor cells. Using antibodies or their fragments requires careful engineering because multiple parameters, including affinity, internalization rate and stability, all need to be optimized. Here, we present a case study of the iterative engineering of a single chain variable fragment (scFv) for use as a targeting arm of a liposomal cytotoxic nanoparticle. We describe the effect of the orientation of variable domains, the length and composition of the interdomain protein linker that connects VH and VL, and stabilizing mutations in both the framework and complementarity-determining regions (CDRs) on the molecular properties of the scFv. We show that variable domain orientation can alter cross-reactivity to murine antigen while maintaining affinity to the human antigen. We demonstrate that tyrosine residues in the CDRs make diverse contributions to the binding affinity and biophysical properties, and that replacement of non-essential tyrosines can improve the stability and bioactivity of the scFv. Our studies demonstrate that a comprehensive engineering strategy may be required to identify a scFv with optimal characteristics for nanoparticle targeting.

  8. North Karelia regional chain of care: Finnish experiences. (United States)

    Itkonen, Pentti


    Information--and communication technology is one of the most important cornerstones in more and more data and knowledge intensive health care sector. However these factors don't create financial gains and productivity benefits spontaneously. They need organisational and social innovations and new business models. The growth of productivity is connected to the process and organisational innovations and not to the number of computers and the growth of using ICT. One of the problems prohibiting health care profession to move to real e-work environment is the lack of the reliable measures and on these measures based performance measurement and strategic management. Health care can be improved by utilizing ICT and tools like performance measuring are key weapons in the arsenal of new e-work environment and measuring based new strategic management. Neither public sector nor not-for-profit hospitals look for financial rewards as their ultimate proof of success. Instead, they seek to achieve ambitious missions aimed at improving the health standards and wellbeing of the citizens. ICT- based new way of managing in the public sector is just beginning to gain a critical level of digitalization and will most likely come to its own in the coming years. Therefore, it is essential to research on how the health care sector can be moved towards new regional models and clinical workflow using intelligent standard based strategic management and performance measurement. If the breakthrough of the eight-hour working day and shortening of working time are evaluated afterwards, it can be stated that they have made the society more anthropocentric and humane. During one century the annual working time has shortened from 3000 hours to 1700 hours in the European Union countries. These foundations of a more humane society--eight-hour working day and shortening of regular working time--are however disappearing in the post-industrialized information society. There are various grounds for the

  9. Multiplex genotype determination at a DNA sequence polymorphism cluster in the human immunoglobulin heavy-chain region

    Energy Technology Data Exchange (ETDEWEB)

    Li, H.; Hood, L. [California Institute of Technology, Pasadena, CA (United States)


    We have developed a method for multilocus genotype determination. The method involves using restriction fragment length polymorphisms (RFLPs) for allele discrimination. If a polymorphism is not an RFLP, it is converted into an RFLP during the polymerase chain reaction (PCR). After amplification and restriction enzyme digestion, samples are analyzed by sequential gel loading during electrophoresis. The efficiency of this method was demonstrated by determining the genotypes of 108 semen samples at seven DNA sequence polymorphic sites identified in the human immunoglobulin heavy-chain variable region. It was shown that more than 1000 PCR products could be easily analyzed per day per investigator. To show the reliability of this method, some of the typing results were confirmed by DNA sequence analysis. By computer simulation, most (98%) polymorphisms were shown to be natural or convertible (by changing 1 bp close to or next to each polymorphic site) RFLPs for the commercially available 4-base cutters. 47 refs., 4 figs., 3 tabs.

  10. Effect of linker length between variable domains of single chain variable fragment antibody against daidzin on its reactivity. (United States)

    Yusakul, Gorawit; Sakamoto, Seiichi; Pongkitwitoon, Benyakan; Tanaka, Hiroyuki; Morimoto, Satoshi


    The peptide linker between variable domains of heavy (VH) and light (VL) chains is one of important factors that influence the characteristics of scFv, including binding activity and specificity against target antigen. The scFvs against daidzin (DZ-scFvs) with different linker lengths were constructed in the format of VH-(GGGGS)n-VL (n = 1, 3, 5, and 7). They were expressed in the hemolymph of silkworm larvae using the Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system, and their reactivity against daidzin and related compounds were evaluated using an indirect competitive enzyme-linked immunosorbent assay (icELISA), which is applicable for quantitative analysis of daidzin. The results showed that the reactivity of scFvs against daidzin was increased, whereas specificity slightly decreased when their peptide linker was lengthened. These results suggested that the linker length of DZ-scFvs contributes to its reactivity. In addition, the results emphasize that the linker length could control the reactivity of DZ-scFvs.

  11. Neutralization Analysis of a Chicken Single-Chain Variable Fragment Derived from an Immune Antibody Library Against Infectious Bronchitis Virus. (United States)

    Lin, Yuan; Li, Benqiang; Ye, Jiaxin; Wang, Man; Wang, Jianhua; Zhang, Ying; Zhu, Jianguo


    Avian infectious bronchitis virus (IBV), which is prevalent in many countries causing severe economic loss to the poultry industry, causes infectious bronchitis (IB) in birds. Recombinant single-chain variable fragments (scFvs) have been proven to effectively inhibit many viruses, both in vitro and in vivo, and they could be a potential diagnostic and therapeutic reagent to control IB. In this study, six anti-IBV chicken scFvs, ZL.10, ZL.64, ZL.78, ZL.80, ZL.138, and ZL.256, were obtained by screening random clones from an immune antibody library. An analysis of nucleotide sequences revealed that they represented distinctive genetic sequences and greatly varied in complementarity-determining region three of the heavy chain. Neutralization tests showed that ZL.10, which bound the S1 protein in western blots, inhibited the formation of syncytia in Vero cells 48 h post IBV infection and decreased the transcriptional level of nucleoprotein mRNA to 17.2%, while the other five scFvs, including ZL.78 and ZL.256, that bound the N protein did not. In conclusion, the results suggested that specific and neutralizing chicken scFvs against IBV, which can be safe and economical antibody reagents, can be produced in vitro through prokaryotic expression.

  12. Immunoglobulin variable region structure and B-cell malignancies. (United States)

    Kiyoi, H; Naoe, T


    The enormous diversity of immunoglobulin (Ig) variable (V) gene sequences encoding the antibody repertoire are formed by the somatic recombination of relatively few genetic elements. In B-lineage malignancies, Ig gene rearrangements have been widely used for determining clonality and cell origin. The recent development of rapid cloning and sequencing techniques has resulted in a substantial accumulation of IgV region sequences at various stages of B-cell development and has revealed stage-specific trends in the use of V, diversity, joining genes, the degree of noncoding nucleotide addition, and the rate of somatic mutations. Furthermore, sequences from B-lineage malignant cells nearly reflect the characteristics of the normal counterpart at each respective stage of development. Alternatively, from the IgV region structure of the malignant cells, it is possible to speculate at which stage of B-cell development the cells were transformed. As the complete nucleotide sequences of the human Ig heavy and Ig light V region loci have now been determined, the study of Ig genetics has entered into the super-information era.

  13. Automotive Lithium-ion Cell Manufacturing: Regional Cost Structures and Supply Chain Considerations

    Energy Technology Data Exchange (ETDEWEB)

    Donald Chung, Emma Elgqvist, and Shriram Santhanagopalan


    Manufacturing capacity for lithium-ion batteries (LIBs) — which power many consumer electronics and are increasingly used to power electric vehicles — is heavily concentrated in East Asia. To illuminate the factors that drive regional competitiveness in automotive LIB cell production, this study models cell manufacturing cost and minimum sustainable price, and examines development of LIB supply chains and current LIB market conditions. The study shows that factors driving the cost competitiveness of LIB manufacturing locations are mostly built—supply chain developments and competition, access to materials, and production expertise. Some regional costs — including cost of capital, labor, and materials — are significant and should be considered.

  14. Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter. (United States)

    Kim, Dong-Sik; Song, Hyung-Nam; Nam, Hyo Jung; Kim, Sung-Geun; Park, Young-Seoub; Park, Jae-Chan; Woo, Eui-Jeon; Lim, Hyung-Kwon


    Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.

  15. Regional Patterns of Baseflow Variability in Mexican Subwatersheds

    Directory of Open Access Journals (Sweden)

    Víctor Salas-Aguilar


    Full Text Available One of the challenges faced by subwatershed hydrology is the discovery of patterns associated with climate and landscape variability with the available data. This study has three objectives: (1 to evaluate the annual recession curves; (2 to relate the recession parameter (RP with physiographic characteristics of 21 Mexican subwatersheds in different climate regions; and (3 to formulate a Baseflow (BF model based on a top-down approach. The RP was calibrated utilizing the largest magnitude curves. The RP was related to topographical, climate and soil variables. A non-linear model was employed to separate the baseflow which considers RP as a recharge rate. Our results show that RP increases with longitude and decreases with latitude. RP displayed a sustained non-linear behavior determined by precipitation rate and evapotranspiration replace the P/E parts with \\(\\frac{P}{E}\\ over years and subwatersheds. The model was fit to a parameter concurrent with invariance and space-time symmetry conditions. The dispersion of our model was associated with the product of replace the P/E parts with \\(\\frac{P}{E}\\ by the aquifer’s transmissivity. We put forward a generalized baseflow model, which made the discrimination of baseflow from direct flow in subwatersheds possible. The proposed model involves the recharge-storage-discharge relation and could be implemented in basins where there are no suitable ground-based data.

  16. Regional and interannual variability of sea ice mass balance (United States)

    Richter-Menge, J. A.; Perovich, D. K.; Nghiem, S. V.; Overland, J. E.


    The Arctic sea ice cover is undergoing significant climate-induced changes, affecting both its extent and thickness. The ice mass balance provides key insights into the nature of these changes by attributing them to variations in growth, surface melt, and bottom ablation. Ice mass balance buoys (IMB) autonomously monitor snow accumulation and ablation, ice growth and melt, and internal ice temperature. These buoys have been deployed in many locations, with an emphasis on the Beaufort Sea and the North Pole Environmental Observatory (NPEO). At the NPEO, the IMB sites are complemented by web cams which provide photographs showing changing surface conditions and the evolution of melt ponds in summer. IMB results indicate that there is significant regional and interannual variability in the mass balance. North Pole buoys, in particular, have recorded significant interannual variability in surface ablation, with values ranging from 0 to 35 cm from 2000 to 2005. There is good agreement determining the onset of melt and freezeup dates at the sites from both IMB results and from QuikScat satellite data. Results suggest that the total amount of surface melting is most significantly influenced by the date of the onset of summer melt. Quikscat results indicated that melt onset occurs concurrently over hundreds of kilometers providing a thermodynamic length scale, which may then be used to extrapolate the point measurements from the IMBs to larger scales.

  17. Separation of variables for the quantum SL(2,R) spin chain

    CERN Document Server

    Derkachov, S E; Manashov, A N


    We construct representation of the Separated Variables (SoV) for the quantum SL(2,R) Heisenberg closed spin chain and obtain the integral representation for the eigenfunctions of the model. We calculate explicitly the Sklyanin measure defining the scalar product in the SoV representation and demonstrate that the language of Feynman diagrams is extremely useful in establishing various properties of the model. The kernel of the unitary transformation to the SoV representation is described by the same "pyramid diagram" as appeared before in the SoV representation for the SL(2,C) spin magnet. We argue that this kernel is given by the product of the Baxter Q-operators projected onto a special reference state.

  18. Ancestry inference in complex admixtures via variable-length Markov chain linkage models. (United States)

    Rodriguez, Jesse M; Bercovici, Sivan; Elmore, Megan; Batzoglou, Serafim


    Inferring the ancestral origin of chromosomal segments in admixed individuals is key for genetic applications, ranging from analyzing population demographics and history, to mapping disease genes. Previous methods addressed ancestry inference by using either weak models of linkage disequilibrium, or large models that make explicit use of ancestral haplotypes. In this paper we introduce ALLOY, an efficient method that incorporates generalized, but highly expressive, linkage disequilibrium models. ALLOY applies a factorial hidden Markov model to capture the parallel process producing the maternal and paternal admixed haplotypes, and models the background linkage disequilibrium in the ancestral populations via an inhomogeneous variable-length Markov chain. We test ALLOY in a broad range of scenarios ranging from recent to ancient admixtures with up to four ancestral populations. We show that ALLOY outperforms the previous state of the art, and is robust to uncertainties in model parameters.

  19. Fusion protein of single-chain variable domain fragments for treatment of myasthenia gravis

    Institute of Scientific and Technical Information of China (English)

    Fangfang Li; Fanping Meng; Quanxin Jin; Changyuan Sun; Yingxin Li; Honghua Li; Songzhu Jin


    Single-chain variable domain fragment (scFv) 637 is an antigen-specific scFv of myasthenia gravis. In this study, scFv and human serum albumin genes were conjugated and the fusion pro-tein was expressed in Pichia pastoris. The afifnity of scFv-human serum albumin fusion protein to bind to acetylcholine receptor at the neuromuscular junction of human intercostal muscles was detected by immunolfuorescence staining. The ability of the fusion protein to block myas-thenia gravis patient sera binding to acetylcholine receptors and its stability in healthy serum were measured by competitive ELISA. The results showed that the inhibition rate was 2.0-77.4%, and the stability of fusion protein in static healthy sera was about 3 days. This approach suggests the scFv-human serum albumin is a potential candidate for speciifc immunosuppressive therapy of myasthenia gravis.

  20. Construction and characterization of single-chain variable fragment antibody library derived from germline rearranged immunoglobulin variable genes.

    Directory of Open Access Journals (Sweden)

    Man Cheng

    Full Text Available Antibody repertoires for library construction are conventionally harvested from mRNAs of immune cells. To examine whether germline rearranged immunoglobulin (Ig variable region genes could be used as source of antibody repertoire, an immunized phage-displayed scFv library was prepared using splenocytic genomic DNA as template. In addition, a novel frame-shifting PCR (fsPCR step was introduced to rescue stop codon and to enhance diversity of the complementarity-determining region 3 (CDR3. The germline scFv library was initially characterized against the hapten antigen phenyloxazolone (phOx. Sequence analysis of the phOx-selective scFvs indicated that the CDRs consisted of novel as well as conserved motifs. In order to illustrate that the diversity of CDR3 was increased by the fsPCR step, a second scFv library was constructed using a single scFv clone L3G7C as a template. Despite showing similar binding characteristics towards phOx, the scFv clones that were obtained from the L3G7C-derived antibody library gave a lower non-specific binding than that of the parental L3G7C clone. To determine whether germline library represented the endogenous immune status, specific scFv clones for nucleocapsid (N protein of SARS-associated coronavirus (SCoV were obtained both from naïve and immunized germline scFv libraries. Both libraries yielded specific anti-N scFvs that exhibited similar binding characteristics towards recombinant N protein, except the immunized library gave a larger number of specific anti-N scFv, and clones with identical nucleotide sequences were found. In conclusion, highly diversified antibody library can be efficiently constructed using germline rearranged immunoglobulin variable genes as source of antibody repertoires and fsPCR to diversify the CDR3.

  1. Human lambda light-chain constant region gene CMor lambda: the primary structure of lambda VI Bence Jones protein Mor.


    Frangione, B.; Moloshok, T; Prelli, F; Solomon, A


    Serologic, structural, and genetic analyses have shown that the constant (C) region of human kappa light chains is encoded by a single gene, whereas that of lambda chains is encoded by multiple genes. We have determined the complete C region amino acid sequence of two monoclonal lambda VI light chains, Bence Jones proteins Sut and Mor. The C region of lambda chains Sut and Mor consists of 105 residues, as is characteristic for human lambda light chains, of which 102 are identical in sequence....

  2. Climate variability and wine quality over Portuguese regions (United States)

    Gouveia, Célia M.; Gani, Érico A.; Liberato, Margarida L. R.


    characterized in each region by high/low quality wines. Finally, we also investigated how climate variability is related to DOC wine quality for different regions using North Atlantic Oscillation (NAO) index. Results reveal a strong dependence of wine quality for all regions on maximum temperature and precipitation during spring and summer (the growing season) as expected. However the role of temperature on wine quality seems to be distinct among the diverse regions probably due to their different climate zoning. Moreover, it is shown that the differences associated with high/low quality wine are in agreement with different synoptic fields patterns. Our results suggest that this type of analysis may be used in developing a tool that may help anticipating a vintage/high quality year, based on already available seasonal climate outlooks. Santo F.E., de Lima M.I.P., Ramos A.M., Trigo R.M., Trends in seasonal surface air temperature in mainland Portugal, since 1941, International Journal Climatolology, 34: 1814-1837, doi: 10.1002/joc.3803 (2014) de Lima M.I.P., Santo F.E., Ramos A.M. , Trigo, R.M., Trends and correlations in annual extreme precipitation indices for mainland Portugal, 1941-2007, Theoretical and Applied Climatology, DOI:10.1007/s00704-013-1079-6 (2014) Acknowledgements: This work was partially supported by national funds through FCT (Fundação para a Ciência e a Tecnologia, Portugal) under project QSECA (PTDC/AAGGLO/4155/2012).

  3. An Analysis of Some Moderating Variables on the Value, Brand Trust and Brand Loyalty Chain

    Directory of Open Access Journals (Sweden)

    Kambiz Heidarzadeh Hanzaee


    Full Text Available The objective in this study was to investigate the moderating effect of some variables on the value, brand trust, and brand loyalty chain. These moderating variables are customer characteristics (Age, Gender, Involvement, Price consciousness, Brand consciousness. More specifically, we investigate both the link between hedonic and utilitarian values of a product and brand trust and the link between brand trust and attitudinal and purchase loyalty and the impact of selected customer characteristics on these relationships in the context of four product groups (mobile phones, sunglasses, running shoes, and notebooks that can be characterized as consumer durables with high brand relevance. In a basic research model after reviewing the literature on brand trust, hedonic and utilitarian value as selected contributors to brand trust and brand loyalty as an important outcome of trust, we measured the effects of product value-brand loyalty on brand trust. Then in the second phase we analyzed the moderator effects. The proposed relationships have been tested using Structural Equation Modeling (SEM via lisrel. We first report the main effect model and then present the impact of moderators.

  4. Averaging over fast variables in the fluid limit for Markov chains: Application to the supermarket model with memory



    We set out a general procedure which allows the approximation of certain Markov chains by the solutions of differential equations. The chains considered have some components which oscillate rapidly and randomly, while others are close to deterministic. The limiting dynamics are obtained by averaging the drift of the latter with respect to a local equilibrium distribution of the former. Some general estimates are proved under a uniform mixing condition on the fast variable which give explicit ...


    Directory of Open Access Journals (Sweden)

    Kavita Tariyal


    Full Text Available The Himalayan region represents enormous variability of climates, hydrological and ecological systems, plus a diversity of cultures and communities. It is an essentiality to the ecological security of the Indian landmass, through providing forest cover, feeding recurrent rivers that are the source of potable water, irrigation, and hydropower, conserving biodiversity, providing a rich foundation for high value agriculture, and spectacular landscapes for sustainable tourism. Increasing concentration of greenhouse gases in the troposphere and the consequential global warming is posing a great environmental threat to water and food security at universal level. Change in climate may affect exposures to air pollutants by affecting weather, anthropogenic emissions, and by changing the distribution and types of airborne allergens. This potential variability in climate will have a serious impact on several ecosystem services, such as cleaning water and removing carbon from the atmosphere. Various services of ecosystems viz. land and water resources, agriculture, biodiversity will experience a wide range of stresses together with pests and pathogens, invasive species, atmospheric pollution, acute events, wildfires and floods. Direct stresses posed due to climate change may get intensified through high temperatures, reduced water availability, and altered frequency of extreme events and severe storms. Climate change will potentially make a threat on the availability of, and access to, water resources. The Himalayan ecosystem is vulnerable to the impacts and consequences of a changes on account of natural causes, b climate change resulting from human-induced emissions and c developmental paradigms of the modern society. Adaptation factors in the element of ‘sustainability’ into development initiatives and provides for additional measures and resources to safeguard environmental gains against climate impacts.

  6. Production of a human single-chain variable fragment antibody against esophageal carcinoma

    Institute of Scientific and Technical Information of China (English)

    Ming-Yan Xu; Xiao-Hu Xu; Geng-Zhen Chen; Xiao-Ling Deng; Jonathan Li; Xiao-Jun Yu; Mei-Zhen Chen


    AIM: To construct a phage display library of human singlechain variable fragment (scFv) antibodies associated with esophageal cancer and to preliminarily screen a scFv antibody against esophageal cancer.METHODS: Total RNA extracted from metastatic lymph nodes of esophageal cancer patients was used to construct a scFv gene library. Rescued by M13K07 helper phage, the scFv phage display library was constructed. esophageal cancer cell line Eca 109 and normal human esophageal epithelial cell line (NHEEC) were used for panning and subtractive panning of the scFv phage display library to obtain positive phage clones. Soluble scFv was expressed in E.coli HB2151 which was transfected with the positive phage clone, then purified by affinity chromatography.Relative molecular mass of soluble scFv was estimated by Western blotting, its bioactivity was detected by cell ELISA assay. Sequence of scFv was determined using the method of dideoxynucleotide sequencing.RESULTS: The size of scFv gene library was approximately 9×106 clones. After four rounds of panning with Eca109 and three rounds of subtractive panning with NHEEC cells, 25 positive phage clones were obtained. Soluble scFv was found to have a molecular mass of 31 ku and was able to bind to Eca109 cells, but not to HeLa and NHEEC cells. Variable heavy (VH) gene from one of the positive clones was shown to be derived from the γ chain subgroup Ⅳ of immunoglobulin, and variable light (VL) gene from the κchain subgroup I of immunoglobulin.CONCLUSION: A human scFv phage display library can be constructed from the metastatic lymph nodes of esophageal cancer patients. A whole human scFv against esophageal cancer shows some bioactivity.

  7. Solar wind influences on atmospheric electricity variables in polar regions (United States)

    Michnowski, Stanisław

    The measurement techniques applied in magnetospheric and ionospheric research enable detection of strong, intrinsic effects of solar wind on ionospheric electrical potential distribution and conductivity of the atmosphere. These manifestations of the solar wind interaction with the magnetosphere and ionosphere are especially evident at high latitudes. The possibility of observing there the response of the atmospheric electricity variables to solar wind has been questioned for a long time despite the fact that the atmospheric electric field and current variations at the ground are physically linked with electric potential of the ionosphere and conductivity of the lower atmosphere. The serious doubts were mainly due to the generally accepted opinion that the highly conducting ionosphere is an almost ideal equipotential electric screen that separates the weakly conductive lower atmosphere of the influence from space. This assumption could not be further upheld in view of the new findings. They have been provided for some time by ground-based atmospheric electric field and current measurements (AEMs) with simultaneous upper atmosphere observations and by corresponding balloon measurements. Recent ground-based AEMs in polar regions, i.e., in the near-subauroral, auroral, and polar cap high-latitude regions, have detected considerable influence of solar wind on the lower-atmosphere electric variables. However, the use of atmospheric electric observations in studying solar-terrestrial relations is still limited. The main reason is difficulty in separating various local meteorological effects, anthropogenic effects, and the effects of the global electric current circuit which affect simultaneously the measured quantities. Transmission of the electric signals through the lower atmosphere can also introduce troublesome disturbances. The paper outlines these problems and hints how the difficulties involved might be partly overcome in a feasible way. The needs and possible

  8. Temperature dependence of amino acid side chain IR absorptions in the amide I' region. (United States)

    Anderson, Benjamin A; Literati, Alex; Ball, Borden; Kubelka, Jan


    Amide I' IR spectra are widely used for studies of structural changes in peptides and proteins as a function of temperature. Temperature dependent absorptions of amino acid side-chains that overlap the amide I' may significantly complicate the structural analyses. While the side-chain IR spectra have been investigated previously, thus far their dependence on temperature has not been reported. Here we present the study of the changes in the IR spectra with temperature for side-chain groups of aspartate, glutamate, asparagine, glutamine, arginine, and tyrosine in the amide I' region (in D2O). Band fitting analysis was employed to extract the temperature dependence of the individual spectral parameters, such as peak frequency, integrated intensity, band width, and shape. As expected, the side-chain IR bands exhibit significant changes with temperature. The majority of the spectral parameters, particularly the frequency and intensity, show linear dependence on temperature, but the direction and magnitude vary depending on the particular side-chain group. The exception is arginine, which exhibits a distinctly nonlinear frequency shift with temperature for its asymmetric CN3H5(+) bending signal, although a linear fit can account for this change to within ~1/3 cm(-1). The applicability of the determined spectral parameters for estimations of temperature-dependent side-chain absorptions in peptides and proteins are discussed.

  9. Regional variability in sea ice melt in a changing Arctic. (United States)

    Perovich, Donald K; Richter-Menge, Jacqueline A


    In recent years, the Arctic sea ice cover has undergone a precipitous decline in summer extent. The sea ice mass balance integrates heat and provides insight on atmospheric and oceanic forcing. The amount of surface melt and bottom melt that occurs during the summer melt season was measured at 41 sites over the time period 1957 to 2014. There are large regional and temporal variations in both surface and bottom melting. Combined surface and bottom melt ranged from 16 to 294 cm, with a mean of 101 cm. The mean ice equivalent surface melt was 48 cm and the mean bottom melt was 53 cm. On average, surface melting decreases moving northward from the Beaufort Sea towards the North Pole; however interannual differences in atmospheric forcing can overwhelm the influence of latitude. Substantial increases in bottom melting are a major contributor to ice losses in the Beaufort Sea, due to decreases in ice concentration. In the central Arctic, surface and bottom melting demonstrate interannual variability, but show no strong temporal trends from 2000 to 2014. This suggests that under current conditions, summer melting in the central Arctic is not large enough to completely remove the sea ice cover.

  10. Preparation of single chain variable fragment of MG7 mAb by phage display technology

    Institute of Scientific and Technical Information of China (English)

    Zhao-Cai Yu; Jie Ding; Yong-Zhan Nie; Dai-Ming Fan; Xue-Yong Zhang


    AIM To develop the single chain variable fragment of MG7 murine anti-human gastric cancer monoclonal antibody using the phage display technology for obtaining a tumor-targeting mediator. METHODS mRNA was isolated from MG7-producing murine hybridoma cell line and converted into cDNA. The variable fragments of heavy and light chain were amplified separately and assembled into ScFv with a specially constructed DNA linker by PCR. The ScFvs DNA was ligated into the phagmid vector pCANTAB5E and the ligated sample was transformed into competent E. Coli TG1. The transformed cells were infected with M13K07 helper phage to form MG7 recombinant phage antibody library. The volume and recombinant rate of the library were evaluated by means of bacterial colony count and restriction analysis. After two rounds of panning with gastric cancer cell line KATOⅢ of highly expressing MG7binding antigen, the phage clones displaying ScFv of the antibody were selected by ELISA from the enriched phage clones. The antigen-binding affinity of the positive clone was detected by competition ELISA. HB2151 E. Coli was transfected with the positive phage clone demonstrated by competition ELISA for production of a soluble form of the MG7 ScFv. ELISA assay was used to detect the antigenbinding affinity of the soluble MG7 ScFv. Finally, the relative molecular mass of soluble MG7 ScFv was measured by SDS-PAGE. RESULTS The VH, VL and ScFv DNAs were about 340bp,320bp and 750bp, respectively. The volume of the library was up to 2 × 106 and 8 of 11 random clones were recombinants. Two phage clones could strongly compete with the original MG7 antibody for binding to the antigen expressed on KATO Ⅲ cells. Within 2 strong positive phage clones, the soluble MG7 ScFv from one clone was found to have the binding activity with KATO Ⅲ cells.SDS-PAGE showed that the relative molecular weight of soluble MG7 ScFv was 32. CONCLUSION The MG7 ScFv was successfully produced by phage antibody technology, which may

  11. Isolation and characterization of anti ROR1 single chain fragment variable antibodies using phage display technique. (United States)

    Aghebati-Maleki, Leili; Younesi, Vahid; Jadidi-Niaragh, Farhad; Baradaran, Behzad; Majidi, Jafar; Yousefi, Mehdi


    Receptor tyrosine kinase-like orphan receptor (ROR1) belongs to one of the families of receptor tyrosine kinases (RTKs). RTKs are involved in the various physiologic cellular functions including proliferation, migration, survival, signaling and differentiation. Several RTKs are deregulated in various cancers implying the targeting potential of these molecules in cancer therapy. ROR1 has recently been shown to be expressed in various types of cancer cells but not in normal adult cells. Hence a molecular inhibitor of extracellular domain of ROR1 that inhibits ROR1-cell surface interaction is of great therapeutic importance. In an attempt to develop molecular inhibitors of ROR1, we screened single chain variable fragment (scFv) phage display libraries, Tomlinson I + J, against one specific synthetic oligopeptide from extracellular domain of ROR1 and selected scFvs were characterized using various immunological techniques. Several ROR1 specific scFvs were selected following five rounds of panning procedure. The scFvs showed specific binding to ROR1 using immunological techniques. Our results demonstrate successful isolation and characterization of specific ROR1 scFvs that may have great therapeutic potential in cancer immunotherapy.

  12. Duplex microfluidic SERS detection of pathogen antigens with nanoyeast single-chain variable fragments. (United States)

    Wang, Yuling; Rauf, Sakandar; Grewal, Yadveer S; Spadafora, Lauren J; Shiddiky, Muhammad J A; Cangelosi, Gerard A; Schlücker, Sebastian; Trau, Matt


    Quantitative and accurate detection of multiple biomarkers would allow for the rapid diagnosis and treatment of diseases induced by pathogens. Monoclonal antibodies are standard affinity reagents applied for biomarkers detection; however, their production is expensive and labor-intensive. Herein, we report on newly developed nanoyeast single-chain variable fragments (NYscFv) as an attractive alternative to monoclonal antibodies, which offers the unique advantage of a cost-effective production, stability in solution, and target-specificity. By combination of surface-enhanced Raman scattering (SERS) microspectroscopy using glass-coated, highly purified SERS nanoparticle clusters as labels, with a microfluidic device comprising multiple channels, a robust platform for the sensitive duplex detection of pathogen antigens has been developed. Highly sensitive detection for individual Entamoeba histolytica antigen EHI_115350 (limit of detection = 1 pg/mL, corresponding to 58.8 fM) and EHI_182030 (10 pg/mL, corresponding 453 fM) with high specificity has been achieved, employing the newly developed corresponding NYscFv as probe in combination with SERS microspectroscopy at a single laser excitation wavelength. Our first report on SERS-based immunoassays using the novel NYscFv affinity reagent demonstrates the flexibility of NYscFv fragments as viable alternatives to monoclonal antibodies in a range of bioassay platforms and paves the way for further applications.

  13. Construction of an antimyoglobin single-chain variable fragment with rapid reaction kinetics. (United States)

    Jang, Jun-Hyuck; Kim, Dong-Hyung; Paek, Se-Hwan; Woo, Eui-Jeon; Kim, Young-Wan


    Antibodies with rapid reaction kinetics (high association and dissociation rates), named reversible antibodies, are used to perform continuous monitoring of sensitive disease biomarkers. In cases of acute myocardial infarction (AMI), continuous monitoring and early diagnosis are important. Human myoglobin (Myo) is a useful biomarker for AMI during the early stage after the onset of symptoms. In this study, a single-chain variable fragment (scFv) specific to Myo was derived from an IgG antibody that has rapid reaction kinetics. Enzyme-linked immunosorbent assay revealed that recombinant scFv exhibited 3.8-fold reduced affinity compared with the parent IgG antibody based on the antibody concentration necessary for 50% of the maximum signal. The scFv retained the rapid reaction kinetic mode with average kon and koff of 2.63 × 10(5) M(-1) Sec(-1) and 3.25 × 10(-3) Sec(-1) , respectively, which were reduced to 10- and 2.3-fold compared with those of the parent antibody. The equilibrium constant for the association of the scFv (KA = 8.09 × 10(7) M(-1) ) was 4.6-fold lower than that of its parent IgG antibody. This scFv may be a starting point for further mutagenesis/kinetic and structural analyses providing valuable insight into the mechanism of reversible antibodies.

  14. Antiperiodic XXZ chains with arbitrary spins: Complete eigenstate construction by functional equations in separation of variables

    CERN Document Server

    Niccoli, G


    Generic inhomogeneous integrable XXZ chains with arbitrary spins are studied by means of the quantum separation of variables (SOV) method. Within this framework, a complete description of the spectrum (eigenvalues and eigenstates) of the antiperiodic transfer matrix is derived in terms of discrete systems of equations involving the inhomogeneity parameters of the model. We show here that one can reformulate this discrete SOV characterization of the spectrum in terms of functional T-Q equations of Baxter's type, hence proving the completeness of the solutions to the associated systems of Bethe-type equations. More precisely, we consider here two such reformulations. The first one is given in terms of Q-solutions, in the form of trigonometric polynomials of a given degree $N_s$, of a one-parameter family of T-Q functional equations with an extra inhomogeneous term. The second one is given in terms of Q-solutions, again in the form of trigonometric polynomials of degree $N_s$ but with double period, of Baxter's ...

  15. Expression of secreted human single-chain fragment variable antibody against human amyloid beta peptide in Pichia pastoris

    Institute of Scientific and Technical Information of China (English)

    Jiong Cai; Fang Li; Shizhen Wang


    BACKGROUND: Studies have shown that monoclonal or polyclonal antibody injections ofamyloid β peptide arc effective in removing amyloid β peptide overload in the brain.OBJECTIVE: Based on successful screening of a human single-chain fragment variable antibody specific to amyloid β peptide, this paper aimed to express recombinant human single-chain variable antibody against amyloid β peptide.DESIGN, TIME AND SETTING: A single sample experiment was performed at the Department of Nuclear Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Hospital (Beijing, China) from January to July 2006.MATERIALS: Human single-chain fragment variable antibody gene against amyloid β peptide was screened from a human phage-display antibody library.METHODS: Human single-chain fragment variable antibody gene was mutated to eliminate a BamHI restriction site and cloned into a Teasy plasmid for pT-seFvAβ construction, which was identified by PCR amplification and endonuclease digestion. Plasmid pT-scFvA β was cut by EcoRl and Notl endonucleases, and the antibody gene was cloned into pPIC9K plasmid to construct pPIC9K-scFvA β expression vector, which was confirmed by gene sequencing. Linearized pPICgK-scFvA β was used to transform a Pichia pastoris GS115 cell line, and the recombinant was induced by 0.5 % methanol to express human single-chain fragment variable antibody specific to amyloid β peptide.MAIN OUTCOME MEASURES: Protein electrophoresis was used to identify PCR products, gene sequencing was uscd to verify the pPIC9K-scFvA sequence, and SDS-PAGE was used to detect recombinant expression of human single-chain fragment variable antibody specific to amyloid β peptide in Pichia pastoris.RESULTS: Gene sequencing confirmed pPICgK-scFvA β orientation. Rccomhinants were obtained by lineadzed pPIC9K-scFvA β transformation. After induction with 0.5% methanol, the recombinant yeast cells secreted proteins of 33-ku size

  16. Design and construction of a new human naïve single-chain fragment variable antibody library, IORISS1. (United States)

    Pasello, Michela; Zamboni, Silvia; Mallano, Alessandra; Flego, Michela; Picci, Piero; Cianfriglia, Maurizio; Scotlandi, Katia


    Human monoclonal antibodies are a powerful tool with increasingly successful exploitations and the single chain fragment variable format can be considered the building block for the implementation of more complex and effective antibody-based constructs. Phage display is one of the best and most efficient methods to isolate human antibodies selected from an efficient and variable phage display library. We report a method for the construction of a human naïve single-chain variable fragment library, termed IORISS1. Many different sets of oligonucleotide primers as well as optimized electroporation and ligation reactions were used to generate this library of 1.2×10(9) individual clones. The key difference is the diversity of variable gene templates, which was derived from only 15 non-immunized human donors. The method described here, was used to make a new human naïve single-chain fragment variable phage display library that represents a valuable source of diverse antibodies that can be used as research reagents or as a starting point for the development of therapeutics. Using biopanning, we determined the ability of IORISS1 to yield antibodies. The results we obtained suggest that, by using an optimized protocol, an efficient phage antibody library can be generated.

  17. Viability assessment of regional biomass pre-processing center based bioethanol value chains (United States)

    Carolan, Joseph E.

    Petroleum accounts for 94% of all liquid fuels and 36% of the total of all energy consumed in the United States. Petroleum dependence is problematic because global petroleum reserves are estimated to last only for 40 to 60 years at current consumption rates; global supplies are often located in politically unstable or unfriendly regions; and fossil fuels have negative environmental footprints. Domestic policies have aimed at promoting alternative, renewable liquid fuels, specifically bio-fuels derived from organic matter. Cellulosic bio-ethanol is one promising alternative fuel that has featured prominently in federal bio-fuel mandates under the Energy Independence and Security Act, 2007. However, the cellulosic bio-ethanol industry faces several technical, physical and industrial organization challenges. This dissertation examines the concept of a network of regional biomass pre-treatment centers (RBPC) that form an extended biomass supply chain feeding into a simplified biorefinery as a way to overcome these challenges. The analyses conducted address the structural and transactional issues facing bio-ethanol value chain establishment; the technical and financial feasibility of a stand alone pre-treatment center (RBPC); the impact of distributed pre-treatment on biomass transport costs; a comparative systems cost evaluation of the performance of the RBPC chain versus a fully integrated biorefinery (gIBRh), followed by application of the analytical framework to three case study regions.

  18. Inhibiting angiogenesis with human single-chain variable fragment antibody targeting VEGF. (United States)

    Hosseini, Hossien; Rajabibazl, Masoumeh; Ebrahimizadeh, Walead; Dehbidi, Gholamreza Rafiei


    Vascular endothelial growth factor (VEGF) is a highly specific angiogenesis factor which has crucial roles in the angiogenesis of tumors. Anti-angiogenesis agents can inhibit growth and metastasis of tumor cells. Single-chain variable fragments (scFv) have the same affinity as whole antibodies and smaller size, thus result in more tissue permeability and higher production yield. In this research we aim to isolate a human scFv antibody against VEGF that inhibits angiogenesis. For that, we have used human scFv phage library to isolate a specific scFv antibody against binding site of VEGF. The human scFv phage library was amplified according to the manufacture protocol and panned against recombinant VEGF. ScFv antibody was isolated after five rounds of panning. Phage ELISA was used for detection of the highest affinity binder (HR6). Soluble HR6 scFv was expressed in non-suppressor strain of Escherichia coli HB2151 and purified using Ni-NTA chromatography. In vivo and in vitro function of the HR6 scFv was analyzed by chorioallantoic membrane assay and endothelial cell proliferation assay on VEGF stimulated HUVECs. Result of the cross reactivity showed that HR6 scFv specifically bounds to VEGF. The affinity was calculated to be 1.8×10(-7)M. HR6 could stop HUVEC proliferation in a dose dependent manner and anti-angiogenesis activity was observed using 10μg of HR6 in chorioallantoic membrane assay. In this work, we demonstrate that a HR6 scFv selected from human library phage display specifically blocks VEGF signaling, furthermore, this scFv has an anti-angiogenesis effect and because of its small size has more tissue diffusion. The HR6 antibody was isolated form a human library thus, it is not immunogenic for humans and could serve as a potential therapeutic agent in cancer.

  19. Isolation and characterization of anti c-met single chain fragment variable (scFv) antibodies. (United States)

    Qamsari, Elmira Safaie; Sharifzadeh, Zahra; Bagheri, Salman; Riazi-Rad, Farhad; Younesi, Vahid; Abolhassani, Mohsen; Ghaderi, Sepideh Safaei; Baradaran, Behzad; Somi, Mohammad Hossein; Yousefi, Mehdi


    The receptor tyrosine kinase (RTK) Met is the cell surface receptor for hepatocyte growth factor (HGF) involved in invasive growth programs during embryogenesis and tumorgenesis. There is compelling evidence suggesting important roles for c-Met in colorectal cancer proliferation, migration, invasion, angiogenesis, and survival. Hence, a molecular inhibitor of an extracellular domain of c-Met receptor that blocks c-Met-cell surface interactions could be of great thera-peutic importance. In an attempt to develop molecular inhibitors of c-Met, single chain variable fragment (scFv) phage display libraries Tomlinson I + J against a specific synthetic oligopeptide from the extracellular domain of c-Met receptor were screened; selected scFv were then characterized using various immune techniques. Three c-Met specific scFv (ES1, ES2, and ES3) were selected following five rounds of panning procedures. The scFv showed specific binding to c-Met receptor, and significantly inhibited proliferation responses of a human colorectal carcinoma cell line (HCT-116). Moreover, anti- apoptotic effects of selected scFv antibodies on the HCT-116 cell line were also evaluated using Annexin V/PI assays. The results demonstrated rates of apoptotic cell death of 46.0, 25.5, and 37.8% among these cells were induced by use of ES1, ES2, and ES3, respectively. The results demonstrated ability to successfully isolate/char-acterize specific c-Met scFv that could ultimately have a great therapeutic potential in immuno-therapies against (colorectal) cancers.

  20. Construction of humanized carcinoembryonic antigen specific single chain variable fragment and mitomycin conjugate

    Institute of Scientific and Technical Information of China (English)


    AIM: To construct a new target-oriented conjugate of humanized carcinoembryonic antigen (CEA) specific single chain variable fragment (scFv) and mitomycin (MMC) against colorectal cancer, and to investigate its influence on the growth and apoptosis of colorectal cancer cells.METHODS: The primer was designed according to the gene sequence described in reference 16, which respectively contains restriction enzyme cleavage sites BamH Ⅰ and EcoR Ⅰ in its upstream and downstream.PCR was performed with the plasmid as template containing genes of humanized anti-CEA scFv. The product was digested by BamH Ⅰ and EcoR Ⅰ, and connected to an expression vector which also has the restriction enzyme cleavage sites BamH Ⅰ and EcoR.Expression of the reaction was induced by isopropy-β-D-thiogalactoside (IPTG). Then the expression product was covalently coupled with MMC by dextran T-40. The immunoreactivity of the conjugate against colorectal cancer cells as well as CEA was measured by enzyme linked immunosorbent assay (ELISA). The inhibiting ratio of conjugate on the growth of colorectal cancer cells was also measured by ELISA. The effect of conjugate on the apoptosis of colorectal cancer cells was determined by flow cytometry (FCM).RESULTS: Restriction endonuclease cleavage and gene sequencing confirmed that the expression vector was successfully constructed. Sodium dodecyl sulfate polyacrylamide gel electropheresis (SDS-VAGE) confirmed that this vector correctly expressed the fusion protein.ELISA confirmed that the conjugate had quite a strong immunoreactivity against colorectal cancer cells and CEA. The conjugate had inhibitory effects on colorectal cancer cells in a concentration-dependent manner and could induce apoptosis of colorectal cancer cells in a concentration-dependent manner.CONCLUSION: The CEA-scFv-MMC conjugate can be successfully constructed and is able to inhibit the growth and induce apoptosis of colorectal cancer cells.

  1. Altered development and function of the placental regions in preeclampsia and its association with long-chain polyunsaturated fatty acids. (United States)

    Rani, Alka; Wadhwani, Nisha; Chavan-Gautam, Preeti; Joshi, Sadhana


    The placenta is an essential organ formed during pregnancy that mainly transfers nutrients from the mother to the fetus. Nutrients taken up by the placenta are required for its own growth and development and to optimize fetal growth. Hence, placental function is an important determinant of pregnancy outcome. Among various nutrients, fatty acids, especially long-chain polyunsaturated fatty acids (LCPUFAs), including omega 3 and omega 6 fatty acids, are essential for placental development from the time of implantation. Studies have associated these LCPUFAs with placental development through their roles in regulating oxidative stress, angiogenesis, and inflammation, which may in turn influence their transfer to the fetus. The placenta has a heterogeneous morphology with variable regional vasculature, oxidative stress, and LCPUFA levels in healthy pregnancies depending upon the location within the placenta. However, these regional structural and functional parameters are found to be disturbed in pathological conditions, such as preeclampsia (PE), thereby affecting pregnancy outcome. Hence, the alterations in LCPUFA metabolism and transport in different regions of the PE placenta as compared with normal placenta could potentially be contributing to the pathological features of PE. The regional variations in development and function of the placenta and its possible association with placental LCPUFA metabolism and transport in normal and PE pregnancies are discussed in this review. WIREs Dev Biol 2016, 5:582-597. doi: 10.1002/wdev.238 For further resources related to this article, please visit the WIREs website.

  2. Epigenetic Regulation of Individual Modules of the immunoglobulin heavy chain locus 3' Regulatory Region. (United States)

    Birshtein, Barbara K


    The Igh locus undergoes an amazing array of DNA rearrangements and modifications during B cell development. During early stages, the variable region gene is constructed from constituent variable (V), diversity (D), and joining (J) segments (VDJ joining). B cells that successfully express an antibody can be activated, leading to somatic hypermutation (SHM) focused on the variable region, and class switch recombination (CSR), which substitutes downstream constant region genes for the originally used Cμ constant region gene. Many investigators, ourselves included, have sought to understand how these processes specifically target the Igh locus and avoid other loci and potential deleterious consequences of malignant transformation. Our laboratory has concentrated on a complex regulatory region (RR) that is located downstream of Cα, the most 3' of the Igh constant region genes. The ~40 kb 3' RR, which is predicted to serve as a downstream major regulator of the Igh locus, contains two distinct segments: an ~28 kb region comprising four enhancers, and an adjacent ~12 kb region containing multiple CTCF and Pax5 binding sites. Analysis of targeted mutations in mice by a number of investigators has concluded that the entire 3' RR enhancer region is essential for SHM and CSR (but not for VDJ joining) and for high levels of expression of multiple isotypes. The CTCF/Pax5 binding region is a candidate for influencing VDJ joining early in B cell development and serving as a potential insulator of the Igh locus. Components of the 3' RR are subject to a variety of epigenetic changes during B cell development, i.e., DNAse I hypersensitivity, histone modifications, and DNA methylation, in association with transcription factor binding. I propose that these changes provide a foundation by which regulatory elements in modules of the 3' RR function by interacting with each other and with target sequences of the Igh locus.

  3. Retargeted oncolytic adenovirus displaying a single variable domain of camelid heavy-chain-only antibody in a fiber protein. (United States)

    van Erp, Elisabeth A; Kaliberova, Lyudmila N; Kaliberov, Sergey A; Curiel, David T


    Conditionally replicative adenoviruses are promising agents for oncolytic virotherapy. Various approaches have been attempted to retarget adenoviruses to tumor-specific antigens to circumvent deficiency of receptor for adenoviral binding and to provide an additional level of tumor specificity. Functional incorporation of highly specific targeting molecules into the viral capsid can potentially retarget adenoviral infection. However, conventional antibodies are not compatible with the cytoplasmic adenovirus capsid synthesis. The goal of this study was to evaluate the utility of single variable domains derived from heavy chain camelid antibodies for retargeting of adenovirus infection. We have combined transcriptional targeting using a tumor-specific promoter with transductional targeting through viral capsid incorporation of antihuman carcinoembryonic antigen single variable domains. Obtained data demonstrated that employment of a single variable domain genetically incorporated into an adenovirus fiber increased specificity of infection and efficacy of replication of single variable domain-targeted oncolytic adenovirus. The double targeting, both transcriptional through the C-X-C chemokine receptor type 4 promoter and transductional using the single variable domain, is a promising means to improve the therapeutic index for these advanced generation conditionally replicative adenoviruses. A successful strategy to transductional retargeting of oncolytic adenovirus infection has not been shown before and therefore we believe this is the first employment of transductional targeting using single variable domains derived from heavy chain camelid antibodies to enhance specificity of conditionally replicative adenoviruses.

  4. An efficient method for variable region assembly in the construction of scFv phage display libraries using independent strand amplification. (United States)

    Sotelo, Pablo; Collazo, Noberto; Zuñiga, Roberto; Gutiérrez-González, Matías; Catalán, Diego; Ribeiro, Carolina Hager; Aguillón, Juan Carlos; Molina, María Carmen


    Phage display library technology is a common method to produce human antibodies. In this technique, the immunoglobulin variable regions are displayed in a bacteriophage in a way that each filamentous virus displays the product of a single antibody gene on its surface. From the collection of different phages, it is possible to isolate the virus that recognizes specific targets. The most common form in which to display antibody variable regions in the phage is the single chain variable fragment format (scFv), which requires assembly of the heavy and light immunoglobulin variable regions in a single gene. In this work, we describe a simple and efficient method for the assembly of immunoglobulin heavy and light chain variable regions in a scFv format. This procedure involves a two-step reaction: (1) DNA amplification to produce the single strand form of the heavy or light chain gene required for the fusion; and (2) mixture of both single strand products followed by an assembly reaction to construct a complete scFv gene. Using this method, we produced 6-fold more scFv encoding DNA than the commonly used splicing by overlap extension PCR (SOE-PCR) approach. The scFv gene produced by this method also proved to be efficient in generating a diverse scFv phage display library. From this scFv library, we obtained phages that bound several non-related antigens, including recombinant proteins and rotavirus particles.

  5. Structural re-alignment in an immunologic surface region of ricin A chain

    Energy Technology Data Exchange (ETDEWEB)

    Zemla, A T; Zhou, C E


    We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.

  6. Robust Optimization on Regional WCO-for-Biodiesel Supply Chain under Supply and Demand Uncertainties

    Directory of Open Access Journals (Sweden)

    Yong Zhang


    Full Text Available This paper aims to design a robust waste cooking oil- (WCO- for-biodiesel supply chain under WCO supply and price as well as biodiesel demand and price uncertainties, so as to improve biorefineries’ ability to cope with the poor environment. A regional supply chain is firstly introduced based on the biggest WCO-for-biodiesel company in Changzhou, Jiangsu province, and it comprises three components: WCO supplier, biorefinery, and demand zone. And then a robust mixed integer linear model with multiple objectives (economic, environmental, and social objectives is proposed for both biorefinery location and transportation plans. After that, a heuristic algorithm based on genetic algorithm is proposed to solve this model. Finally, the 27 cities in Yangtze River delta are adopted to verify the proposed models and methods, and the sustainability and robustness of biodiesel supply are discussed.

  7. The spread amongst ENSEMBLES regional scenarios: regional climate models, driving general circulation models and interannual variability

    Energy Technology Data Exchange (ETDEWEB)

    Deque, M.; Somot, S. [Meteo-France, Centre National de Recherches Meteorologiques, CNRS/GAME, Toulouse Cedex 01 (France); Sanchez-Gomez, E. [Cerfacs/CNRS, SUC URA1875, Toulouse Cedex 01 (France); Goodess, C.M. [University of East Anglia, Climatic Research Unit, Norwich (United Kingdom); Jacob, D. [Max Planck Institute for Meteorology, Hamburg (Germany); Lenderink, G. [KNMI, Postbus 201, De Bilt (Netherlands); Christensen, O.B. [Danish Meteorological Institute, Copenhagen Oe (Denmark)


    Various combinations of thirteen regional climate models (RCM) and six general circulation models (GCM) were used in FP6-ENSEMBLES. The response to the SRES-A1B greenhouse gas concentration scenario over Europe, calculated as the difference between the 2021-2050 and the 1961-1990 means can be viewed as an expected value about which various uncertainties exist. Uncertainties are measured here by variance explained for temperature and precipitation changes over eight European sub-areas. Three sources of uncertainty can be evaluated from the ENSEMBLES database. Sampling uncertainty is due to the fact that the model climate is estimated as an average over a finite number of years (30) despite a non-negligible interannual variability. Regional model uncertainty is due to the fact that the RCMs use different techniques to discretize the equations and to represent sub-grid effects. Global model uncertainty is due to the fact that the RCMs have been driven by different GCMs. Two methods are presented to fill the many empty cells of the ENSEMBLES RCM x GCM matrix. The first one is based on the same approach as in FP5-PRUDENCE. The second one uses the concept of weather regimes to attempt to separate the contribution of the GCM and the RCM. The variance of the climate response is analyzed with respect to the contribution of the GCM and the RCM. The two filling methods agree that the main contributor to the spread is the choice of the GCM, except for summer precipitation where the choice of the RCM dominates the uncertainty. Of course the implication of the GCM to the spread varies with the region, being maximum in the South-western part of Europe, whereas the continental parts are more sensitive to the choice of the RCM. The third cause of spread is systematically the interannual variability. The total uncertainty about temperature is not large enough to mask the 2021-2050 response which shows a similar pattern to the one obtained for 2071-2100 in PRUDENCE. The uncertainty

  8. Biological activities of the homologous loop regions in the laminin α chain LG modules. (United States)

    Katagiri, Fumihiko; Hara, Toshihiro; Yamada, Yuji; Urushibata, Shunsuke; Hozumi, Kentaro; Kikkawa, Yamato; Nomizu, Motoyoshi


    Each laminin α chain (α1-α5 chains) has chain-specific diverse biological functions. The C-terminal globular domain of the α chain consists of five laminin-like globular (LG1-5) modules and plays a critical role in biological activities. The LG modules consist of a 14-stranded β-sheet (A-N) sandwich structure. Previously, we described the chain-specific biological activities of the loop regions between the E and F strands in the LG4 modules using five homologous peptides (G4EF1-G4EF5). Here, we further analyze the biological activities of the E-F strands loop regions in the rest of LG modules. We designed 20 homologous peptides (approximately 20 amino acid length), and 17 soluble peptides were used for the cell attachment assay. Thirteen peptides promoted cell attachment activity with different cell morphologies. Cell attachment to peptides G1EF1, G1EF2, G2EF1, G3EF4, and G5EF4 was inhibited by heparin, and peptides G1EF1, G1EF2, and G2EF1 specifically bound to syndecan-overexpressing cells. Cell attachment to peptides G2EF3, G3EF1, G3EF3, G5EF1, G5EF3, and G5EF5 was inhibited EDTA. Further, cell attachment to peptides G3EF3, G5EF1, and G5EF5 was inhibited by both anti-integrin α2 and β1 antibodies, whereas cell attachment to peptide G5EF3 was inhibited by only anti-integrin β1 antibody. Cell attachment to peptides G1EF4, G3EF4, and G5EF4 was inhibited by both heparin and EDTA and was not inhibited by anti-integrin antibodies. The active peptide sequence alignments suggest that the syndecan-binding peptides contain a "basic amino acid (BAA)-Gly-BAA" motif in the middle of the molecule and that the integrin-binding peptides contain an "acidic amino acid (AAA)"-Gly-BAA motif. Core-switched peptide analyses suggested that the "BAA-Gly-BAA" motif is critical for binding to syndecans and that the "AAA-Gly-BAA" motif has potential to recognize integrins. These findings are useful for understanding chain-specific biological activities of laminins and to evaluate

  9. Regional variability among nonlinear chlorophyll-phosphorus relationships in lakes (United States)

    Filstrup, Christopher T.; Wagner, Tyler; Soranno, Patricia A.; Stanley, Emily H.; Stow, Craig A.; Webster, Katherine E.; Downing, John A.


    The relationship between chlorophyll a (Chl a) and total phosphorus (TP) is a fundamental relationship in lakes that reflects multiple aspects of ecosystem function and is also used in the regulation and management of inland waters. The exact form of this relationship has substantial implications on its meaning and its use. We assembled a spatially extensive data set to examine whether nonlinear models are a better fit for Chl a—TP relationships than traditional log-linear models, whether there were regional differences in the form of the relationships, and, if so, which regional factors were related to these differences. We analyzed a data set from 2105 temperate lakes across 35 ecoregions by fitting and comparing two different nonlinear models and one log-linear model. The two nonlinear models fit the data better than the log-linear model. In addition, the parameters for the best-fitting model varied among regions: the maximum and lower Chl aasymptotes were positively and negatively related to percent regional pasture land use, respectively, and the rate at which chlorophyll increased with TP was negatively related to percent regional wetland cover. Lakes in regions with more pasture fields had higher maximum chlorophyll concentrations at high TP concentrations but lower minimum chlorophyll concentrations at low TP concentrations. Lakes in regions with less wetland cover showed a steeper Chl a—TP relationship than wetland-rich regions. Interpretation of Chl a—TP relationships depends on regional differences, and theory and management based on a monolithic relationship may be inaccurate.

  10. Regional variability in the permeability of human dentine. (United States)

    Pashley, D H; Andringa, H J; Derkson, G D; Derkson, M E; Kalathoor, S R


    This was measured qualitatively by using dyes and quantitatively by hydraulic conductance in dentine discs and crown segments in vitro. Both types of preparation demonstrated large regional differences in permeability, with the highest values at the periphery and the lowest in the centre of the disc or crown. As dentine permeability may vary 3-10-fold across a few millimetres, investigators should use as large a surface area as possible to compensate for these regional differences.

  11. Potential, spatial distribution and economic performance of regional biomass chains: The North of the Netherlands as example

    NARCIS (Netherlands)

    Hilst, van der F.; Dornburg, V.; Sanders, J.P.M.; Elbersen, B.S.; Graves, A.; Turkenburg, W.C.; Elbersen, H.W.; Dam, van J.M.C.; Faaij, A.


    This work assesses the viability of regional biomass chains by comparing the economic performance of potential bioenergy crops with the performance of current agricultural land uses. The biomass chains assessed are ethanol production from Miscanthus and from sugar beet in the North of the Netherland

  12. [Cloning and expression of a single human immunoglobulin heavy-chain variable domain with vascular endothelial growth factor binding activity]. (United States)

    Liu, Heng; Liu, Siguo; Wu, Yi; Zili, M; Liu, Yu; Zhang, Aimin; Chen, Jianquan; Cheng, Guoxiang


    In the application of therapeutic antibodies, large molecular weight of antibodies is always a problem that prevents them from penetrating into tissues or binding to antigenic determinants. To overcome this problem, we investigated the function of the heavy chain variable domain of a monoclonal anti-VEGF human IgM antibody derived from the Five-Feature Translocus Mice. We cloned the cDNA of the heavy chain variable domain, which was then inserted into pET28a vector and expressed in Escherichia coli. After purification and renaturation of the denatured recombinant protein, we obtained a 16 kDa antibody fragment, which is named as rhVVH. By immunoassaying its VEGF-binding capability in vitro, we proved that rhVVH retains this activity as the complete IgM. Importantly, rhVVH is shown to inhibit the HUVEC cell proliferation in a concentration-dependent manner. Our results indicate that the single heavy chain variable domain might inherit part of the biological function of the complete IgM antibody, which provided a valuable potential in further research on antibody miniaturisation.

  13. Nonlinear dynamics of a friction-limited drive: Application to a chain continuously variable transmission (CVT) system (United States)

    Srivastava, Nilabh; Haque, Imtiaz


    Over the past two decades, extensive research has been conducted on developing vehicle transmissions that meet the goals of reduced exhaust emissions and increased vehicle efficiency. A continuously variable transmission is an emerging automotive transmission technology that offers a continuum of gear ratios between desired limits. A chain CVT is a friction-limited drive whose dynamic performance and torque capacity rely significantly on the friction characteristic of the contact patch between the chain and the pulley. Although a CVT helps to maximize the vehicle fuel economy, its complete potential has not been accomplished in a mass-production vehicle. The present research focuses on developing models to analyze friction-induced nonlinear dynamics of a chain CVT drive and identify possible mechanisms that cause degradation of the overall dynamic performance by inducing chaos and self-sustained vibrations in the system. Two different mathematical models of friction, which characterize different operating or loading conditions, are embedded into a detailed planar multibody model of chain CVT in order to capture the various friction-induced effects in the system. Tools such as stick-slip oscillator dynamics, Lyapunov exponents, phase-space reconstruction, and recurrence plotting are incorporated to characterize the nonlinear dynamics of such a friction-limited system. The mathematical models, the computational scheme, and the results corresponding to different loading scenarios are discussed. The results discuss the influence of friction characteristics on the nonlinear dynamics and torque transmitting capacity of a chain CVT drive.

  14. A Single Mutation at the Sheet Switch Region Results in Conformational Changes Favoring 6 Light-Chain Fibrillogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Hernández-Santoyo, A.; Del Pozo Yauner, L; Fuentes-Silva, D; Ortiz, E; Rudiño-Piñera, E; Sánchez-López, R; Horjales, E; Becerril, B; Rodríguez-Romero, A


    Systemic amyloid light-chain (LC) amyloidosis is a disease process characterized by the pathological deposition of monoclonal LCs in tissue. All LC subtypes are capable of fibril formation although {lambda} chains, particularly those belonging to the {lambda}6 type, are overrepresented. Here, we report the thermodynamic and in vitro fibrillogenic properties of several mutants of the {lambda}6 protein 6aJL2 in which Pro7 and/or His8 was substituted by Ser or Pro. The H8P and H8S mutants were almost as stable as the wild-type protein and were poorly fibrillogenic. In contrast, the P7S mutation decreased the thermodynamic stability of 6aJL2 and greatly enhanced its capacity to form amyloid-like fibrils in vitro. The crystal structure of the P7S mutant showed that the substitution induced both local and long-distance effects, such as the rearrangement of the VL (variable region of the light chain)-VL interface. This mutant crystallized in two orthorhombic polymorphs, P2{sub 1}2{sub 1}2{sub 1} and C222{sub 1}. In the latter, a monomer that was not arranged in the typical Bence-Jones dimer was observed for the first time. Crystal-packing analysis of the C222{sub 1} lattice showed the establishment of intermolecular {beta}-{beta} interactions that involved the N-terminus and {beta}-strand B and that these could be relevant in the mechanism of LC fibril formation. Our results strongly suggest that Pro7 is a key residue in the conformation of the N-terminal sheet switch motif and, through long-distance interactions, is also critically involved in the contacts that stabilized the VL interface in {lambda}6 LCs.

  15. Regional variability of imaging biomarkers in autosomal dominant Alzheimer's disease. (United States)

    Benzinger, Tammie L S; Blazey, Tyler; Jack, Clifford R; Koeppe, Robert A; Su, Yi; Xiong, Chengjie; Raichle, Marcus E; Snyder, Abraham Z; Ances, Beau M; Bateman, Randall J; Cairns, Nigel J; Fagan, Anne M; Goate, Alison; Marcus, Daniel S; Aisen, Paul S; Christensen, Jon J; Ercole, Lindsay; Hornbeck, Russ C; Farrar, Angela M; Aldea, Patricia; Jasielec, Mateusz S; Owen, Christopher J; Xie, Xianyun; Mayeux, Richard; Brickman, Adam; McDade, Eric; Klunk, William; Mathis, Chester A; Ringman, John; Thompson, Paul M; Ghetti, Bernardino; Saykin, Andrew J; Sperling, Reisa A; Johnson, Keith A; Salloway, Stephen; Correia, Stephen; Schofield, Peter R; Masters, Colin L; Rowe, Christopher; Villemagne, Victor L; Martins, Ralph; Ourselin, Sebastien; Rossor, Martin N; Fox, Nick C; Cash, David M; Weiner, Michael W; Holtzman, David M; Buckles, Virginia D; Moulder, Krista; Morris, John C


    Major imaging biomarkers of Alzheimer's disease include amyloid deposition [imaged with [(11)C]Pittsburgh compound B (PiB) PET], altered glucose metabolism (imaged with [(18)F]fluro-deoxyglucose PET), and structural atrophy (imaged by MRI). Recently we published the initial subset of imaging findings for specific regions in a cohort of individuals with autosomal dominant Alzheimer's disease. We now extend this work to include a larger cohort, whole-brain analyses integrating all three imaging modalities, and longitudinal data to examine regional differences in imaging biomarker dynamics. The anatomical distribution of imaging biomarkers is described in relation to estimated years from symptom onset. Autosomal dominant Alzheimer's disease mutation carrier individuals have elevated PiB levels in nearly every cortical region 15 y before the estimated age of onset. Reduced cortical glucose metabolism and cortical thinning in the medial and lateral parietal lobe appeared 10 and 5 y, respectively, before estimated age of onset. Importantly, however, a divergent pattern was observed subcortically. All subcortical gray-matter regions exhibited elevated PiB uptake, but despite this, only the hippocampus showed reduced glucose metabolism. Similarly, atrophy was not observed in the caudate and pallidum despite marked amyloid accumulation. Finally, before hypometabolism, a hypermetabolic phase was identified for some cortical regions, including the precuneus and posterior cingulate. Additional analyses of individuals in which longitudinal data were available suggested that an accelerated appearance of volumetric declines approximately coincides with the onset of the symptomatic phase of the disease.

  16. Indian monsoon variability in relation to Regional Pressure Index

    Indian Academy of Sciences (India)

    S S Dugam; S B Kakade


    In this paper Regional Pressure Index (RPI) over the Indian region (20°N-40°N and 70°E-85°E) has been constructed for 101 years (1899-1999) on a monthly scale. The relationship of these indices was carried out with the Indian Summer Monsoon Rainfall (June-September) (ISMR) over the various homogeneous regions, for all the time scales. From the analysis it has been seen that RPI in the month of May is significantly associated with ISMR over various regions on all the scales. The relationship is statistically significant at 1% level. The study reveals that RPI in the month of May and January will be a new precursor for the long range forecasting of ISMR on the smaller spatial scale. On the decadal and climatological scale, winter and spring time RPI show a significant inverse relationship with the rainfall over the regions Peninsular India (PI) and North West India (NWI), while the association is direct with Central North East India (CNEI) and North East India (NEI). The relationship is significant at 0.1 and 1% level respectively.

  17. Screening, expression, and characterization of an anti-human oxidized low-density lipoprotein single-chain variable fragment. (United States)

    Kumano-Kuramochi, Miyuki; Fujimura, Takashi; Komba, Shiro; Maeda-Yamamoto, Mari; Machida, Sachiko


    Increased levels of oxidized low-density lipoprotein (OxLDL) in the blood circulation are correlated with atherosclerosis. Monoclonal antibody-based detection systems have been reported for OxLDL. We identified novel single-chain variable fragments (scFvs) having affinity for human OxLDL and related ligands. We constructed an scFv library from nonimmunized human spleen mRNA. Two types (γ+κ and μ+λ) of scFv phage libraries were enriched by biopanning, and five scFv clones with affinity for OxLDL were identified. The γκ5 scFv, which showed the highest affinity for OxLDL, was cloned into pET-22b(+) and expressed in Escherichia coli BL21(DE3). γκ5, expressed as an inclusion body in BL21(DE3), was refolded and purified. The specificity and sensitivity of γκ5 were analyzed using enzyme-linked immunosorbent assays (ELISAs). The γκ5 scFv showed affinity for OxLDL and acetylated LDL. The sensitivity of γκ5 to low concentrations (1-2 μg/mL) of OxLDL was higher than that to AcLDL and LDL. Finally, we developed a sandwich ELISA using γκ5 and CTLD14 (a lectin-like OxLDL receptor-1 ligand recognition region), which allowed specific detection of OxLDL at a level below 0.1 μg/mL. Our results indicated that the γκ5 scFv was a promising molecule for the detection of modified LDL at very low concentrations.

  18. The protective effects and underlying mechanism of an anti-oligomeric Aβ42 single-chain variable fragment antibody. (United States)

    Zhang, Yuan; Chen, Xu; Liu, Jinyu; Zhang, Yingjiu


    Oligomeric Aβ42 aggregates have been identified as one of the major neurotoxic components of Alzheimer's disease (AD). Immunotherapy targeted against these Aβ42 aggregates has been proposed as an appropriate therapeutic approach for the treatment of AD. Here, we report an anti-oligomeric Aβ42 single-chain variable fragment (scFv) antibody, named MO6, obtained from the human antibody library of a healthy donor. ScFv MO6 specifically recognized and bound to the oligomeric Aβ42 (Aβ42 oligomers and immature protofibrils; 18-37 kDa), and reduced their levels mainly by blocking their formation, although scFv MO6 also induced disaggregation of Aβ42 aggregates. More importantly, scFv MO6 ameliorated or attenuated Aβ42-induced cytotoxicity and increased cell viability by up to 33%. Furthermore, scFv MO6 efficiently passed through an in vitro blood-brain barrier (BBB) model with a delivery efficiency of 66% after 60 min post-administration. ScFv MO6 is a monovalent antibody with an affinity constant (KD) of 5.2×10(-6) M for Aβ42 oligomers. Molecular docking simulations of Aβ42 to scFv MO6 revealed that the approach and specific binding of scFv MO6 to oligomeric Aβ42 aggregates was achieved by conformational recognition and directed induction, which resulted in a more dynamic adaptation of Aβ42 to scFv MO6, occurring mainly in the N-terminal (3-4), middle (12-19) and C-terminal (34-42) regions of Aβ42. This binding mode of scFv MO6 to Aβ42 explains its protective effects against oligomeric Aβ42. Our findings may be applied for the design of a smaller antibody specific for Aβ42 oligermers.

  19. A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity. (United States)

    Ordóñez, Adriana; Pérez, Juan; Tan, Lu; Dickens, Jennifer A; Motamedi-Shad, Neda; Irving, James A; Haq, Imran; Ekeowa, Ugo; Marciniak, Stefan J; Miranda, Elena; Lomas, David A


    Mutant Z α1-antitrypsin (E342K) accumulates as polymers within the endoplasmic reticulum (ER) of hepatocytes predisposing to liver disease, whereas low levels of circulating Z α1-antitrypsin lead to emphysema by loss of inhibition of neutrophil elastase. The ideal therapy should prevent polymer formation while preserving inhibitory activity. Here we used mAb technology to identify interactors with Z α1-antitrypsin that comply with both requirements. We report the generation of an mAb (4B12) that blocked α1-antitrypsin polymerization in vitro at a 1:1 molar ratio, causing a small increase of the stoichiometry of inhibition for neutrophil elastase. A single-chain variable fragment (scFv) intrabody was generated based on the sequence of mAb4B12. The expression of scFv4B12 within the ER (scFv4B12KDEL) and along the secretory pathway (scFv4B12) reduced the intracellular polymerization of Z α1-antitrypsin by 60%. The scFv4B12 intrabody also increased the secretion of Z α1-antitrypsin that retained inhibitory activity against neutrophil elastase. MAb4B12 recognized a discontinuous epitope probably located in the region of helices A/C/G/H/I and seems to act by altering protein dynamics rather than binding preferentially to the native state. This novel approach could reveal new target sites for small-molecule intervention that may block the transition to aberrant polymers without compromising the inhibitory activity of Z α1-antitrypsin.

  20. Intraregional and inter-regional variability of herbicide sensitivity in common arable weed populations

    DEFF Research Database (Denmark)

    de Mol, Friederike; Gerowitt, Bärbel; Kaczmarek, Sylwia


    The question on intraregional versus inter-regional variability in herbicide sensitivity for weed populations is of major importance, both in extrapolation of model parameters and in herbicide zonal approval procedures. We hypothesised that inter-regional variability in herbicide sensitivity for ...

  1. SST Diurnal Variability: Regional Extent & Implications in Atmospheric Modelling

    DEFF Research Database (Denmark)

    Karagali, Ioanna; Høyer, Jacob L.


    and quantify regional diurnal warming from the experimental MSG/SEVIRI hourly SST fields, for the period 2006-2012. ii) To investigate the impact of the increased SST temporal resolution in the atmospheric model WRF, in terms of modeled 10-m winds and surface heat fluxes. Withing this context, 3 main tasks...... regional diurnal warming over the SEVIRI disk, a SEVIRI derived reference field representative of the well mixed night-time conditions is required. Different methodologies are tested and the results are validated against SEVIRI pre-dawn SSTs and in situ data from moored and drifting buoys....

  2. Maps of mesoscale wind variability over the North Sea region

    DEFF Research Database (Denmark)

    Vincent, Claire Louise; Hahmann, Andrea N.; Badger, Jake

    Mesoscale wind fluctuations affect the operation of wind farms, particularly as the number of geographically concentrated wind farms in the North Sea increases (Akhmatov et al. 2007). The frequency and intensity of wind fluctuations could be considered as a new siting criterion, together with exi......Mesoscale wind fluctuations affect the operation of wind farms, particularly as the number of geographically concentrated wind farms in the North Sea increases (Akhmatov et al. 2007). The frequency and intensity of wind fluctuations could be considered as a new siting criterion, together...... with existing criteria such as the wind resource and proximity to grid connection points. We used the Weather Research and Forecasting (WRF) model to calculate the average wind variability over the North Sea for wind fluctuations with periods of 30 minutes to 8 hours. Modelled winds are saved every 10 minutes...... for a 1 year period. The model was run with a horizontal grid spacing of 2 km. The variability maps are created by integrating the average 24 hour spectra at every grid point over different time-scales....

  3. A novel variable antibody fragment dimerized by leucine zippers with enhanced neutralizing potency against rabies virus G protein compared to its corresponding single-chain variable antibody fragment. (United States)

    Li, Zhuang; Cheng, Yue; Xi, Hualong; Gu, Tiejun; Yuan, Ruosen; Chen, Xiaoxu; Jiang, Chunlai; Kong, Wei; Wu, Yongge


    Fatal rabies can be prevented effectively by post-exposure prophylactic (PEP) with rabies immunoglobulin (RIG). Single-chain variable fragments (scFv), which are composed of a variable heavy chain (VH) and a variable light chain (VL) connected by a peptide linker, can potentially be used to replace RIG. However, in our previous study, a scFv (scFV57S) specific for the rabies virus (RV) G protein showed a lower neutralizing potency than that of its parent IgG due to lower stability and altered peptide assembly pattern. In monoclonal antibodies, the VH and VL interact non-covalently, while in scFvs the VH is connected covalently with the VL by the artificial linker. In this study, we constructed and expressed two peptides 57VL-JUN-HIS and 57VH-FOS-HA in Escherichia coli. The well-known Fos and Jun leucine zippers were utilized to dimerize VH and VL similarly to the IgG counterpart. The two peptides assembled to form zipFv57S in vitro. Due to the greater similarity in structure with IgG, the zipFv57S protein showed a higher binding ability and affinity resulting in notable improvement of in vitro neutralizing activity over its corresponding scFv. The zipFv57S protein was also found to be more stable and showed similar protective rate as RIG in mice challenged with a lethal dose of RV. Our results not only indicated zipFv57S as an ideal alternative for RIG in PEP but also offered a novel and efficient hetero-dimerization pattern of VH and VL leading to enhanced neutralizing potency.

  4. A green supply chain network design model for enhancing competitiveness and sustainability of companies in high north arctic regions

    Directory of Open Access Journals (Sweden)

    Hao Yu, Wei Deng Solvang, Chen Chen


    Full Text Available To survive in today’s competitive and ever-changing marketplace, companies need not only to engage in their products and/or services, but also to focus on the management of the whole supply chain. Effectively managing and balancing the profitability and interconnection of each player in the supply chain will improve the overall supply chain surplus as well as individual profit. However, it is extremely difficult to simultaneously optimize several objectives in design and planning of a supply chain, i.e., cost-minimization, risk-minimization, responsiveness-maximization, etc., which are somehow conflict with one another. Furthermore, the natural and infrastructural challenges in high north arctic regions make it become much more difficult and complicated to design and develop cost-efficient, highly responsive, environmentally friendly, and sustainable supply chain network. In order to provide companies in high north arctic regions with decision support tool for the design and planning of theirs supply chain networks, a green supply chain network design (GrSCND model is formulated in this study based on multi-objective mixed integer programming (MIP. The optimal trade-off among several conflicting objectives is the focus of this GrSCND model aiming to enhance both competitive competence and sustainability of companies and supply chains operated in high north regions. In addition, a numerical experiment is also given to present a deep insight of the GrSCND model.

  5. Automotive Lithium-ion Cell Manufacturing: Regional Cost Structures and Supply Chain Considerations

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Donald [Clean Energy Manufacturing Analysis Center, Godlen, CO (United States); Elgqvist, Emma [Clean Energy Manufacturing Analysis Center, Godlen, CO (United States); Santhanagopalan, Shriram [Clean Energy Manufacturing Analysis Center, Godlen, CO (United States)


    Manufacturing capacity for lithium-ion batteries (LIBs)--which power many consumer electronics and are increasingly used to power electric vehicles--is heavily concentrated in east Asia. Currently, China, Japan, and Korea collectively host 88% of all LIB cell and 79% of automotive LIB cell manufacturing capacity. Mature supply chains and strong cumulative production experience suggest that most LIB cell production will remain concentrated in Asia. However, other regions--including North America--could be competitive in the growing automotive LIB cell market under certain conditions. To illuminate the factors that drive regional competitiveness in automotive LIB cell production, this study models cell manufacturing cost and minimum sustainable price, and examines development of LIB supply chains and current LIB market conditions. Modeled costs are for large format, 20-Ah stacked pouch cells with lithium-nickel-manganese-cobalt-oxide (NMC) cathodes and graphite anodes suitable for automotive application. Production volume is assumed to be at commercial scale, 600 MWh per year.

  6. Biodegradation of Variable-Chain-Length Alkanes at Low Temperatures by a Psychrotrophic Rhodococcus sp.


    Whyte, Lyle G; Hawari, Jalal; Zhou, Edward; Bourbonnière, Luc; Inniss, William E.; Charles W Greer


    The psychrotroph Rhodococcus sp. strain Q15 was examined for its ability to degrade individual n-alkanes and diesel fuel at low temperatures, and its alkane catabolic pathway was investigated by biochemical and genetic techniques. At 0 and 5°C, Q15 mineralized the short-chain alkanes dodecane and hexadecane to a greater extent than that observed for the long-chain alkanes octacosane and dotriacontane. Q15 utilized a broad range of aliphatics (C10 to C21 alkanes, branched alkanes, and a substi...

  7. A Four-Type Decision-Variable MINLP Model for a Supply Chain Network Design

    Directory of Open Access Journals (Sweden)

    M. M. Monteiro


    Full Text Available We propose a mixed integer nonlinear programming model for the design of a one-period planning horizon supply chain with integrated and flexible decisions on location of plants and of warehouses, on levels of production and of inventory, and on transportation models, considering stochastic demand and the ABC classification for finished goods, which is an NP-hard industrial engineering optimization problem. Furthermore, computational implementation of the proposed model is presented through the direct application of the outer approximation algorithm on some randomly generated supply chain data.

  8. Yeast artificial chromosome contigs reveal that distal variable-region genes reside at least 3 megabases from the joining regions in the murine immunoglobulin kappa locus. (United States)

    George, J B; Li, S; Garrard, W T


    The immunoglobulin kappa gene locus encodes 95% of the light chains of murine antibody molecules and is thought to contain up to 300 variable (V kappa)-region genes generally considered to comprise 20 families. To delineate the locus we have isolated 29 yeast artificial chromosome genomic clones that form two contigs, span > 3.5 megabases, and contain two known non-immunoglobulin kappa markers. Using PCR primers specific for 19 V kappa gene families and Southern analysis, we have refined the genetically defined order of these V kappa gene families. Of these, V kappa 2 maps at least 3.0 Mb from the joining (J kappa) region and appears to be the most distal V kappa gene segment. Images Fig. 3 Fig. 4 PMID:8618913

  9. Regional variability in sea ice melt in a changing Arctic


    Perovich, Donald K.; Richter-Menge, Jacqueline A.


    In recent years, the Arctic sea ice cover has undergone a precipitous decline in summer extent. The sea ice mass balance integrates heat and provides insight on atmospheric and oceanic forcing. The amount of surface melt and bottom melt that occurs during the summer melt season was measured at 41 sites over the time period 1957 to 2014. There are large regional and temporal variations in both surface and bottom melting. Combined surface and bottom melt ranged from 16 to 294 cm, with a mean of...

  10. Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains. (United States)

    Singer, Meromit; Engström, Alexander; Schönhuth, Alexander; Pachter, Lior


    Recent experimental and computational work confirms that CpGs can be unmethylated inside coding exons, thereby showing that codons may be subjected to both genomic and epigenomic constraint. It is therefore of interest to identify coding CpG islands (CCGIs) that are regions inside exons enriched for CpGs. The difficulty in identifying such islands is that coding exons exhibit sequence biases determined by codon usage and constraints that must be taken into account. We present a method for finding CCGIs that showcases a novel approach we have developed for identifying regions of interest that are significant (with respect to a Markov chain) for the counts of any pattern. Our method begins with the exact computation of tail probabilities for the number of CpGs in all regions contained in coding exons, and then applies a greedy algorithm for selecting islands from among the regions. We show that the greedy algorithm provably optimizes a biologically motivated criterion for selecting islands while controlling the false discovery rate. We applied this approach to the human genome (hg18) and annotated CpG islands in coding exons. The statistical criterion we apply to evaluating islands reduces the number of false positives in existing annotations, while our approach to defining islands reveals significant numbers of undiscovered CCGIs in coding exons. Many of these appear to be examples of functional epigenetic specialization in coding exons.

  11. Quarterly Regional GDP Flash Estimates by Means of Benchmarking and Chain Linking

    Directory of Open Access Journals (Sweden)

    Cuevas Ángel


    Full Text Available In this article we propose a methodology for estimating the GDP of a country’s different regions, providing quarterly profiles for the annual official observed data. Thus the article offers a new instrument for short-term monitoring that allows the analysts to quantify the degree of synchronicity among regional business cycles. Technically, we combine time-series models with benchmarking methods to process short-term quarterly indicators and to estimate quarterly regional GDPs ensuring their temporal and transversal consistency with the National Accounts data. The methodology addresses the issue of nonadditivity, explicitly taking into account the transversal constraints imposed by the chain-linked volume indexes used by the National Accounts, and provides an efficient combination of structural as well as short-term information. The methodology is illustrated by an application to the Spanish economy, providing real-time quarterly GDP estimates, that is, with a minimum compilation delay with respect to the national quarterly GDP. The estimated quarterly data are used to assess the existence of cycles shared among the Spanish regions.

  12. Climate Change and Climate Variability in the Latin American Region (United States)

    Magrin, G. O.; Gay Garcia, C.; Cruz Choque, D.; Gimenez-Sal, J. C.; Moreno, A. R.; Nagy, G. J.; Nobre, C.; Villamizar, A.


    Over the past three decades LA was subjected to several climate-related impacts due to increased El Niño occurrences. Two extremely intense episodes of El Niño and other increased climate extremes happened during this period contributing greatly to augment the vulnerability of human systems to natural disasters. In addition to weather and climate, the main drivers of the increased vulnerability are demographic pressure, unregulated urban growth, poverty and rural migration, low investment in infrastructure and services, and problems in inter-sector coordination. As well, increases in temperature and increases/decreases in precipitation observed during the last part of 20th century have yet led to intensification of glaciers melting, increases in floods/droughts and forest fires frequency, increases in morbidity and mortality, increases in plant diseases incidence; lost of biodiversity, reduction in dairy cattle production, and problems with hydropower generation, highly affecting LA human system. For the end of the 21st century, the projected mean warming for LA ranges from 1 to 7.5ºC and the frequency of weather and climate extremes could increase. Additionally, deforestation is projected to continue leading to a reduction of 25 percent in Amazonia forest in 2020 and 40 percent in 2050. Soybeans planted area in South America could increase by 55 percent by 2020 enhancing aridity/desertification in many of the already water- stressed regions. By 2050 LA population is likely to be 50 percent larger than in 2000, and migration from the country sides to the cities will continue. In the near future, these predicted changes are very likely to severely affect a number of ecosystems and sectors distribution; b) Disappearing most tropical glaciers; c) Reducing water availability and hydropower generation; d) Increasing desertification and aridity; e) Severely affecting people, resources and economic activities in coastal areas; f) Increasing crop's pests and diseases


    Directory of Open Access Journals (Sweden)



    Full Text Available Theoretical evidence is presented in this review that architectural aspects can play an important role, not only in the bulk but also in confined geometries by using our recursive lattice theory, which is equally applicable to fixed architectures (regularly branched polymers, stars, dendrimers, brushes, linear chains, etc. and variable architectures, i.e. randomly branched structures. Linear chains possess an inversion symmetry (IS of a magnetic system (see text, whose presence or absence determines the bulk phase diagram. Fixed architectures possess the IS and yield a standard bulk phase diagram in which there exists a theta point at which two critical lines C and C' meet and the second virial coefficient A2 vanishes. The critical line C appears only for infinitely large polymers, and an order parameter is identified for this criticality. The critical line C' exists for polymers of all sizes and represents phase separation criticality. Variable architectures, which do not possess the IS, give rise to a topologically different phase diagram with no theta point in general. In confined regions next to surfaces, it is not the IS but branching and monodispersity, which becomes important in the surface regions. We show that branching plays no important role for polydisperse systems, but become important for monodisperse systems. Stars and linear chains behave differently near a surface.

  14. Averaging over fast variables in the fluid limit for Markov chains: application to the supermarket model with memory

    CERN Document Server

    Luczak, M J


    We set out a general procedure which allows the approximation of certain Markov chains by the solutions of differential equations. The chains considered have some components which oscillate rapidly and randomly, while others are close to deterministic. The limiting dynamics are obtained by averaging the drift of the latter with respect to a local equilibrium distribution of the former. Some general estimates are proved under a uniform mixing condition on the fast variable which give explicit error probabilities for the fluid approximation. Mitzenmacher, Prabhakar and Shah \\cite{MPS} introduced a variant with memory of the `join the shortest queue' or `supermarket' model, and obtained a limit picture for the case of a stable system in which the number of queues and the total arrival rate are large. In this limit, the empirical distribution of queue sizes satisfies a differential equation, while the memory of the system oscillates rapidly and randomly. We illustrate our general fluid limit estimate in giving a ...

  15. Regional variability in food availability for Arctic marine mammals. (United States)

    Bluhm, Bodil A; Gradinger, Rolf


    This review provides an overview of prey preferences of seven core Arctic marine mammal species (AMM) and four non-core species on a pan-Arctic scale with regional examples. Arctic marine mammal species exploit prey resources close to the sea ice, in the water column, and at the sea floor, including lipid-rich pelagic and benthic crustaceans and pelagic and ice-associated schooling fishes such as capelin and Arctic cod. Prey preferred by individual species range from cephalopods and benthic bivalves to Greenland halibut. A few AMM are very prey-, habitat-, and/or depth-specific (e.g., walrus, polar bear), while others are rather opportunistic and, therefore, likely less vulnerable to change (e.g., beluga, bearded seal). In the second section, we review prey distribution patterns and current biomass hotspots in the three major physical realms (sea ice, water column, and seafloor), highlighting relations to environmental parameters such as advection patterns and the sea ice regime. The third part of the contribution presents examples of documented changes in AMM prey distribution and biomass and, subsequently, suggests three potential scenarios of large-scale biotic change, based on published observations and predictions of environmental change. These scenarios discuss (1) increased pelagic primary and, hence, secondary production, particularly in the central Arctic, during open-water conditions in the summer (based on surplus nutrients currently unutilized); (2) reduced benthic and pelagic biomass in coastal/shelf areas (due to increased river runoff and, hence, changed salinity and turbidity conditions); and (3) increased pelagic grazing and recycling in open-water conditions at the expense of the current tight benthic-pelagic coupling in part of the ice-covered shelf regions (due to increased pelagic consumption vs. vertical flux). Should those scenarios hold true, pelagic-feeding and generalist AMM might be advantaged, while the range for benthic shelf

  16. Role of regional wetland emissions in atmospheric methane variability (United States)

    McNorton, J.; Gloor, E.; Wilson, C.; Hayman, G. D.; Gedney, N.; Comyn-Platt, E.; Marthews, T.; Parker, R. J.; Boesch, H.; Chipperfield, M. P.


    Atmospheric methane (CH4) accounts for 20% of the total direct anthropogenic radiative forcing by long-lived greenhouse gases. Surface observations show a pause (1999-2006) followed by a resumption in CH4 growth, which remain largely unexplained. Using a land surface model, we estimate wetland CH4 emissions from 1993 to 2014 and study the regional contributions to changes in atmospheric CH4. Atmospheric model simulations using these emissions, together with other sources, compare well with surface and satellite CH4 data. Modeled global wetland emissions vary by ±3%/yr (σ = 4.8 Tg), mainly due to precipitation-induced changes in wetland area, but the integrated effect makes only a small contribution to the pause in CH4 growth from 1999 to 2006. Increasing temperature, which increases wetland area, drives a long-term trend in wetland CH4 emissions of +0.2%/yr (1999 to 2014). The increased growth post-2006 was partly caused by increased wetland emissions (+3%), mainly from Tropical Asia, Southern Africa, and Australia.

  17. Is Regional Root Reinforcement Controlled by Soil Moisture Variability? (United States)

    Hales, T.; Ford, C. R.


    of "bound water" (water present in the cell wall), which in turn affected the strength of the cellulose fibrils that provide tensile strength. This phenomenon, which is the reason any wet wood is weaker than dry wood, results in a 50% difference in root tensile strength within the range of soil moisture measured in the field. We used a one-dimensional finite difference model to explore the effects of soil moisture on root cohesion. Our model shows that changes in the distribution of root biomass represent the primary control on root cohesion (representing up to 50% of intra-specific variability in root cohesion). Local changes in soil moisture result in ~20% change in the overall root cohesion. Our work suggest a feed-forward process in precipitation (and thus soil moisture), root strength changes, and debris flow hazard.

  18. ADM-CLE approach for detecting slow variables in continuous time Markov chains and dynamic data

    CERN Document Server

    Cucuringu, Mihai


    A method for detecting intrinsic slow variables in high-dimensional stochastic chemical reaction networks is developed and analyzed. It combines anisotropic diffusion maps (ADM) with approximations based on the chemical Langevin equation (CLE). The resulting approach, called ADM-CLE, has the potential of being more efficient than the ADM method for a large class of chemical reaction systems, because it replaces the computationally most expensive step of ADM (running local short bursts of simulations) by using an approximation based on the CLE. The ADM-CLE approach can be used to estimate the stationary distribution of the detected slow variable, without any a-priori knowledge of it. If the conditional distribution of the fast variables can be obtained analytically, then the resulting ADM-CLE approach does not make any use of Monte Carlo simulations to estimate the distributions of both slow and fast variables.

  19. Construction of a human functional single-chain variable fragment (scFv) antibody recognizing the malaria parasite Plasmodium falciparum. (United States)

    Wajanarogana, Sumet; Prasomrothanakul, Teerawat; Udomsangpetch, Rachanee; Tungpradabkul, Sumalee


    Falciparum malaria is one of the most deadly and profound human health problems around the tropical world. Antimalarial drugs are now considered to be a powerful treatment; however, there are drugs currently being used that are resistant to Plasmodium falciparum parasites spreading in different parts of the world. Although the protective immune response against intraerythrocytic stages of the falciparum malaria parasite is still not fully understood, immune antibodies have been shown to be associated with reduced parasite prevalence. Therefore antibodies of the right specificity present in adequate concentrations and affinity are reasonably effective in providing protection. In the present study, VH (variable domain of heavy chain) and VL (variable domain of light chain) were isolated from human blood lymphocytes of P. falciparum in one person who had high serum titre to RESA (ring-infected erythrocyte surface antigen). Equal amounts of VH and VL were assembled together with universal linker (G4S)3 to generate scFvs (single-chain variable fragments). The scFv antibodies were expressed with a phage system for the selection process. Exclusively, an expressed scFv against asynchronous culture of P. falciparum-infected erythrocytes was selected and characterized. Sequence analysis of selected scFv revealed that this clone could be classified into a VH family-derived germline gene (VH1) and Vkappa family segment (Vkappa1). Using an indirect immunofluorescence assay, we could show that soluble expressed scFv reacted with falciparum-infected erythrocytes. The results encourage the further study of scFvs for development as a potential immunotherapeutic agent.



    Oliinyk O. S.; Kaberniuk A. A.; Kolibo D. V.; Komisarenko S. V.


    Diphtheria toxin is an exoantigen of Corynebacterium diphtheriae that inhibits protein synthesis and kills sensitive cells. The aim of this study was to obtain human recombinant single-chain variable fragment (scFv) antibodies against receptor-binding B subunit of diphtheria toxin. 12 specific clones were selected after three rounds of a phage display naїve (unimmunized) human antibody library against recombinant B-subunit. scFv DNA inserts from these 12 clones were digested with MvaI, an...

  1. Regional variability of environmental effects of energy crop rotations (United States)

    Prescher, Anne-Katrin; Peter, Christiane; Specka, Xenia; Willms, Matthias; Glemnitz, Michael


    The use of energy crops for bioenergy production is increasingly promoted by different frameworks and policies (ECCP, UNFCCC). Energy cropping decreases greenhouse gas emissions by replacing the use of fossil fuel. However, despite this, growing in monocultures energy crop rotations has low environmental benefit. It is broadly accepted consensus that sustainable energy cropping is only realizable by crop rotations which include several energy crop species. Four crop rotations consisting of species mixtures of C3, C4 and leguminous plants and their crop positions were tested to identify the environmental effect of energy cropping systems. The experimental design included four replicates per crop rotation each covering four cultivation years. The study took place at five sites across Germany covering a considerable range of soil types (loamy sand to silt loam), temperatures (7.5 ° C - 10.0 ° C) and precipitation (559 mm - 807 mm) which allow a regional comparison of crop rotation performance. Four indicators were used to characterize the environmental conditions: (1) greenhouse gas (GHG) emissions from the management actions; (2) change in humus carbon (Chum); (3) groundwater recharge (RGW) and (4) nitrogen dynamics. The indicators were derived by balance, by an empirical model and by a dynamic model, respectively, all based and calibrated on measured values. The results show that the crop rotation impact on environmental indicators varied between plant species mixtures and the crop positions, between sites and climate. Crop rotations with 100 % energy crops (including C4 plants) had negative influence on Chum, GHG emissions per area and RGW in comparison to the rotation of 50 % energy crops and 50 % cash crops, which were mainly due to the remaining straw on the field. However, the biogas yield of the latter rotation was smaller, thus GHG emissions per product were higher, pointing out the importance to distinguish between GHG emissions per product and per area

  2. Variability in regional background aerosols within the Mediterranean

    Directory of Open Access Journals (Sweden)

    X. Querol


    Full Text Available The main objective of this study is the identification of major factors controlling levels and chemical composition of aerosols in the regional background (RB along the Mediterranean Basin (MB. To this end, data on PM levels and speciation from Montseny (MSY, Northeastern Spain, Finokalia (FKL, Southern Greece and Erdemli (ERL, Southern Turkey for the period 2001 to 2008 are evaluated. Important differences on PM levels and composition are evident when comparing the Western and Eastern MBs. The results manifest W-E and N-S PM10 and PM2.5 gradients along the MB, attributed to the higher frequency and intensity of African dust outbreaks in the EMB, while for PM1 very similar levels are encountered.

    PM in the EMB is characterized by higher levels of crustal material and sulphate as compared to WMB (and central European sites, however, RB nitrate and OC+EC levels are relatively constant across the Mediterranean and lower than other European sites. Marked seasonal trends are evidenced for PM levels, nitrate (WMB, ammonium and sulphate. Also relatively higher levels of V and Ni (WMB are measured in the Mediterranean basin, probably as a consequence of high emissions from fuel-oil combustion (power generation, industrial and shipping emissions.

    Enhanced sulphate levels in EMB compared to WMB were measured. The high levels of sulphate in the EMB may deplete the available gas-phase NH3 so that little ammonium nitrate can form due to the low NH3 levels.

    This study illustrates the existence of three very important features within the Mediterranean that need to be accounted for when modeling climate effects of aerosols in the area, namely: (a the increasing gradient of dust from WMB to EMB; (b the change of hygroscopic behavior of mineral aerosols (dust via nitration and sulphation; and (c the abundance of highly hygroscopic aerosols during high insolation (low cloud formation

  3. Variability in regional background aerosols within the Mediterranean

    Directory of Open Access Journals (Sweden)

    M. Koçak


    Full Text Available The main objective of this study is the identification of major factors controlling levels and chemical composition of aerosols in the regional background (RB along the Mediterranean Basin (MB. To this end, data on PM levels and speciation from Montseny (MSY, NE Spain, Finokalia (FKL, Southern Greece and Erdemli (ERL, Southern Turkey for the period 2001 to 2008 are evaluated. Important differences on PM levels and composition are evident when comparing the Western and Eastern MBs. The results manifest W-E and N-S PM10 and PM2.5 gradients along the MB, attributed to the higher frequency and intensity of African dust outbreaks in the EMB, while for PM1 very similar levels are encountered.

    PM in the EMB is characterized by higher levels of crustal material and sulphate as compared to WMB (and central European sites, however, RB nitrate and OC + EC levels are relatively constant across the Mediterranean and lower than other European sites. Marked seasonal trends are evidenced for PM levels, nitrate (WMB, ammonium and sulphate. Also relatively higher levels of V and Ni (WMB are measured in the Mediterranean basin, probably as a consequence of high emissions from fuel-oil combustion (power generation, industrial and shipping emissions.

    Enhanced sulphate levels in EMB compared to WMB were measured. The high levels of sulphate in the EMB may deplete the available gas-phase NH3 so that little ammonium nitrate can form due to the low NH3 levels.

    This study illustrates the existence of three very important features within the Mediterranean that need to be accounted for when modeling climate effects of aerosols in the area, namely: a the increasing gradient of dust from WMB to EMB; b the change of hygroscopic behavior of mineral aerosols (dust via nitration and sulfation; and c the abundance of highly hygroscopic aerosols during high insolation (low cloud formation periods.

  4. Explosive Nuclear Burning in the pp-Chain Region and the Breakout Processes

    Directory of Open Access Journals (Sweden)

    Kubono S.


    Full Text Available The nuclear reactions in the pp-chain region and on the breakout process from the pp-chain region under very high temperature conditions are reviewed, and some possibilities for experimental investigation are discussed. The reactions discussed could play an important role typically for the primordial nucleosynthesis and supernova nucleosynthesis. Specifically, I discuss here the reactions starting from the two key nuclei, 7Be and 7Li. The 7Be(n,α reaction, which destroys 7Be, is considered to have a large impact to the primordial 7Li problem. Our recent estimate of the reaction rate indicates that the reaction rate can be about one order of magnitude smaller than the rate currently adopted, suggesting this channel has a minor effect for the 7Li problem. Under a proton-rich environment at high temperature like the νp-process, the 7Be(α,γ11C(α,p14N pathway is expected to play a majpr role for heavy element synthesis, comparable to the triple alpha process. These two reactions on the pathway were investigated by using low-energy, high-intensity RI beams of 7Be and 11C. The results support the theoretical prediction of heavy nucleus production at around mass 90-100 by the νp-process, where the anomalously abundant p-nuclei exist. The reactions on the breakout sequence of 7Li(n,γ8Li(α,n11B are also discussed which could paly a crucial role in nuetron-rich envirnments, like in the primirdial universe as well as the early stage of the r-process. The cross sections of the first step reaction 7Li(n,γ8Li seems well confirmed, but the second step reaction 8Li(α,n11B still is not well known yet, whose status of the study is discussed.

  5. Dairy Supply Chain Risk Management in Bangladesh: Field studies of Factors and Variables

    Directory of Open Access Journals (Sweden)

    Tasnuba Nasir


    Full Text Available Supply chain risk management (SCRM has gained wide attention among the academia and the business community in the present competitive business world. This paper aims to investigate the main risk factors associated with the dairy industry along with focuses on possible mitigation strategy to mitigate those risks. Qualitative field study has been undertaken in this research. The results of the interviews identify the different risk issues along with the possible mitigation strategies, embedded at storage, processing and distribution level in dairy industry of Bangladesh. The practical implication will contribute significantly to the dairy sector in terms of mitigating risks.

  6. ADM-CLE Approach for Detecting Slow Variables in Continuous Time Markov Chains and Dynamic Data (United States)


    Max Plank ...v a ri a b le s (d) 0 50 100 150 200 0 0.2 0.4 0.6 0.8 1 Our recovered slow variables (1:201) J a c c a rd S im ila ri ty I n d e x Max matching in...250 300 0 0.2 0.4 0.6 0.8 1 Our recovered slow variables (1:314) J a c c a rd S im ila ri ty I n d e x Max matching in the Jaccard index matrix

  7. Short arm region of laminin-5 gamma2 chain: structure, mechanism of processing and binding to heparin and proteins

    DEFF Research Database (Denmark)

    Sasaki, T; Göhring, W; Mann, K;


    Laminin-5 is a typical component of several epithelial tissues and contains a unique gamma2 chain which can be proteolytically processed by BMP-1. This occurs in the N-terminal half of the gamma2 chain (606 residues), which consists of two rod-like tandem arrays of LE modules, LE1-3 and LE4...... in processed laminin-5 showed only a strong binding to fibulin-2. Immunological studies showed a similar partial processing in cell culture and tissues and the persistence of the released fragment in tissues. This indicated that both N-terminal regions of the gamma2 chain may have a function in vivo....

  8. Efficient heterologous expression and secretion in Aspergillus oryzae of a llama variable heavy-chain antibody fragment V(HH) against EGFR. (United States)

    Okazaki, Fumiyoshi; Aoki, Jun-ichi; Tabuchi, Soichiro; Tanaka, Tsutomu; Ogino, Chiaki; Kondo, Akihiko


    We have constructed a filamentous fungus Aspergillus oryzae that secretes a llama variable heavy-chain antibody fragment (V(HH)) that binds specifically to epidermal growth factor receptor (EGFR) in a culture medium. A major improvement in yield was achieved by fusing the V(HH) with a Taka-amylase A signal sequence (sTAA) and a segment of 28 amino acids from the N-terminal region of Rhizopus oryzae lipase (N28). The yields of secreted, immunologically active anti-EGFR V(HH) reached 73.8 mg/1 in a Sakaguchi flask. The V(HH) fragments were released from the sTAA or N28 proteins by an indigenous A. oryzae protease during cultivation. The purified recombinant V(HH) fragment was specifically recognized and could bind to the EGFR with a high affinity.


    Directory of Open Access Journals (Sweden)

    Oliinyk O. S.


    Full Text Available Diphtheria toxin is an exoantigen of Corynebacterium diphtheriae that inhibits protein synthesis and kills sensitive cells. The aim of this study was to obtain human recombinant single-chain variable fragment (scFv antibodies against receptor-binding B subunit of diphtheria toxin. 12 specific clones were selected after three rounds of a phage display naїve (unimmunized human antibody library against recombinant B-subunit. scFv DNA inserts from these 12 clones were digested with MvaI, and 6 unique restriction patterns were found. Single-chain antibodies were expressed in Escherichia coli XL1-blue. The recombinant proteins were characterized by immunoblotting of bacterial extracts and detection with an anti-E-tag antibody. The toxin B-subunit-binding function of the single-chain antibody was shown by ELISA. The affinity constants for different clones were found to be from 106 to 108 М–1. Due to the fact, that these antibody fragments recognized epitopes in the receptor-binding Bsubunit of diphtheria toxin, further studies are interesting to evaluate their toxin neutralization properties and potential for therapeutic applications. Obtained scFv-antibodies can also be used for detection and investigation of biological properties of diphtheria toxin.

  10. Supplemental dietary inulin of variable chain lengths alters intestinal bacterial populations in young pigs. (United States)

    Patterson, Jannine K; Yasuda, Koji; Welch, Ross M; Miller, Dennis D; Lei, Xin Gen


    Previously, we showed that supplementation of diets with short-chain inulin (P95), long-chain inulin (HP), and a 50:50 mixture of both (Synergy 1) improved body iron status and altered expression of the genes involved in iron homeostasis and inflammation in young pigs. However, the effects of these 3 types of inulin on intestinal bacteria remain unknown. Applying terminal restriction fragment length polymorphism analysis, we determined the abundances of luminal and adherent bacterial populations from 6 segments of the small and large intestines of pigs (n = 4 for each group) fed an iron-deficient basal diet (BD) or the BD supplemented with 4% of P95, Synergy 1, or HP for 5 wk. Compared with BD, all 3 types of inulin enhanced (P inulin on bacterial populations in the lumen contents were found. Meanwhile, all 3 types of inulin suppressed the less desirable bacteria Clostridium spp. and members of the Enterobacteriaceae in the lumen and mucosa of various gut segments. Our findings suggest that the ability of dietary inulin to alter intestinal bacterial populations may partially account for its iron bioavailability-promoting effect and possibly other health benefits.

  11. Modelling the Consequences of Variability in Food Production Chains on Human Health

    NARCIS (Netherlands)

    Dekker, M.; Verkerk, R.


    Epidemiological studies on the relation between fruit and vegetable intake and chronic diseases show variable results. In many studies a small protective effect is found for fruit and vegetable intake and the risk for cardiovascular diseases and cancers. In other studies these effects could not be f

  12. Capturing subregional variability in regional-scale climate change vulnerability assessments of natural resources. (United States)

    Buotte, Polly C; Peterson, David L; McKelvey, Kevin S; Hicke, Jeffrey A


    Natural resource vulnerability to climate change can depend on the climatology and ecological conditions at a particular site. Here we present a conceptual framework for incorporating spatial variability in natural resource vulnerability to climate change in a regional-scale assessment. The framework was implemented in the first regional-scale vulnerability assessment conducted by the US Forest Service. During this assessment, five subregional workshops were held to capture variability in vulnerability and to develop adaptation tactics. At each workshop, participants answered a questionnaire to: 1) identify species, resources, or other information missing from the regional assessment, and 2) describe subregional vulnerability to climate change. Workshop participants divided into six resource groups; here we focus on wildlife resources. Participants identified information missing from the regional assessment and multiple instances of subregional variability in climate change vulnerability. We provide recommendations for improving the process of capturing subregional variability in a regional vulnerability assessment. We propose a revised conceptual framework structured around pathways of climate influence, each with separate rankings for exposure, sensitivity, and adaptive capacity. These revisions allow for a quantitative ranking of species, pathways, exposure, sensitivity, and adaptive capacity across subregions. Rankings can be used to direct the development and implementation of future regional research and monitoring programs. The revised conceptual framework is equally applicable as a stand-alone model for assessing climate change vulnerability and as a nested model within a regional assessment for capturing subregional variability in vulnerability.

  13. Variable fragment of heavy chain antibody against the terminal protein region of hepatitis B virus polymerase introduced by Tat protein transduction domain inhibits the replication of hepatitis B virus in vitro%蛋白转导结构域介导乙型肝炎病毒聚合酶末端蛋白重链可变区抗体体外抑制病毒的复制

    Institute of Scientific and Technical Information of China (English)

    于俊岩; 兰林; 李俊刚; 张长江; 王宇明


    目的 蛋白转导结构域(TAT)介导HBV聚合酶末端蛋白(TP)重链可变区(VH)抗体,研究特异性TAT-VH抗体体外对HBV复制的影响.方法 将TAT-VH基因克隆入原核表达载体pET28a(+),在大肠埃希菌BL21(DE3)LysS内诱导融合蛋白表达并进行纯化.纯化的TAT-VH加入培养的HepG2.2.15细胞,间接免疫荧光法检测其导入HepG2.2.15细胞的效率,四甲基偶氮唑盐(MTT)法检测其对细胞生长代谢的影响,将TAT-VH加入培养的HepG2.2.15细胞,定量PCR法检测HBV DNA水平.数据行单因素方差分析和t检验.结果 成功制备了TAT-VH融合蛋白,间接免疫荧光及MTT证实TAT-VH可以跨膜导入HepG2.2.15细胞,且对细胞生长无影响;加入5 000 nmol/L TAT-VH的HepG2.2.15细胞培养上清液内HBV DNA为(1.211±0.132)lg拷贝/mL,对照组为(5.325±0.041)lg拷贝/mL(t=72.91,P<0.05);细胞内分别为(3.521±0.411)和(8.532±0.132)Ig拷贝/mL(t=28.41,P<0.05).结论 HBV聚合酶TP区特异性TAT-VH抗体在体外可抑制HBV复制,为应用细胞内抗体治疗HBV感染提供了良好的实验基础.%Objective To study a functional variable fragment of heavy chain(VH)antibody against the terminal protein(TP)region of hepatitis B virus(HBV)polymerase introduced by human immunodeficiency virus Tat protein transduction domain(TAT)and the inhibitive activity of TAT-VH on the replication of HBV in vitro.Methods The gene encoding TAT-VH was cloned into prokaryotic expression vector pET28a(+).Recombinant plasmid was transduced into E coli BL21(DE3)LysS,then the protein was expressed and purified.The purified TAT-VH fusion protein was added into HepG2.2.15 cell culture.The transduction efficiency was evaluated by indirect fluorescence assay(IFA).The cytotoxicity of TAT-VH was detected by Methabenzthiazuron(MTT)assay.HBV DNA level in HepG2.2.15 cell culture was measured using quantitative polymerase chain reaction(PCR).The data were analyzed by one-factor analysis of variance and t test.Results TAT

  14. Synthesis and antimicrobial studies of hydroxylated chalcone derivatives with variable chain length. (United States)

    Ngaini, Zainab; Fadzillah, Siti M Haris; Hussain, Hasnain


    A series of (E)-1-(4-alkyloxyphenyl)-3-(hydroxyphenyl)-prop-2-en-1-one have been successfully synthesised via Claisen-Schmidt condensation. The synthesised chalcone derivatives consisted of hydroxyl groups at either ortho, meta or para position and differed in the length of the alkyl groups, C (n) H(2) (n) (+1,) where n = 6, 10, 12 and 14. The structures of all compounds were defined by elemental analysis, IR, (1)H- and (13)C-NMR. The antimicrobial studies were carried out against wild-type Escherichia coli American Type Culture Collection 8739 to evaluate the effect of the hydroxyl and the alkyl groups of the synthesised chalcones. All the synthesised compounds have shown significant antimicrobial activities. The optimum inhibition was dependent on the position of the hydroxyl group as well as the length of the alkyl chains.

  15. Biodegradation of variable-chain-length alkanes at low temperatures by a psychrotrophic Rhodococcus sp.

    Energy Technology Data Exchange (ETDEWEB)

    Whyte, L.G.; Hawari, J.; Zhou, E.; Bourbonniere, L.; Greer, C.W. [NRC-Biotechnology Research Inst., Montreal, Quebec (Canada); Inniss, W.E. [Univ. of Waterloo, Ontario (Canada). Dept. of Biology


    The psychrotroph Rhodococcus sp. strain Q15 was examined for its ability to degrade individual n-alkanes and diesel fuel at low temperatures, and its alkane catabolic pathway was investigated by biochemical and genetic techniques. At 0 and 5 C, Q15 mineralized the short-chain alkanes dodecane and hexadecane to a greater extent than that observed for the long-chain alkanes octacosane and dotriacontane. Q15 utilized a broad range of aliphatics (C{sub 10} to C{sub 21} alkanes, branched alkanes, and a substituted cyclohexane) present in diesel fuel at 5 C. Mineralization of hexadecane at 5 C was significantly greater in both hydrocarbon-contaminated and pristine soil microcosms seeded with Q15 cells than in uninoculated control soil microcosms. The detection of hexadecane and dodecane metabolic intermediates (1-hexadecanol and 2-hexadecanol and 1-do-decanol and 2-dodecanone, respectively) by solid-phase microextraction-gas chromatography-mass spectrometry and the utilization of potential metabolic intermediates indicated that Q15 oxidizes alkanes by both the terminal oxidation pathway and the subterminal oxidation pathway. Genetic characterization by PCR and nucleotide sequence analysis indicated that Q15 possesses an aliphatic aldehyde dehydrogenase gene highly homologous to the Rhodococcus erythropolis thcA gene. Rhodococcus sp. strain Q15 possessed two large plasmids of approximately 90 and 115 kb (shown to mediate Cd resistance) which were not required for alkane mineralization, although the 90-kb plasmid enhanced mineralization of some alkanes and growth on diesel oil at both 5 and 25 C.

  16. 5DFRXXL region of long myosin light chain kinase causes F-actin bundle formation

    Institute of Scientific and Technical Information of China (English)

    YANG Chunxiang; WEI Dongmei; CHEN Chen; YU Weiping; ZHU Minsheng


    Long myosin light chain kinase (L-MLCK) contains five DFRXXL motifs with ability to bind F-actin. Binding stoichiometry data indicated that each DFRXXL motif might bind each G-actin, but its biological significance remained unknown. We hypothesized that L-MLCK might act as an F-actin bundle peptides by its multiple binding sites of 5DFRXXL motifs to actin. In order to characterize F-actin-bundle formation properties of 5DFRXXL region of long myosin light chain kinase, we expressed and purified 5DFRXXL peptides tagged with HA in vitro. The properties of 5DFRXXL peptides binding to myofilaments or F-actin were analyzed by binding stoichiometries assays. The results indicated that 5DFRXXL peptides bound to myofilaments or F-actin with high affinity. KD values of 5DFRXXL binding to myofilaments and F-actin were 0.45 and 0.41 μmol/L, re- spectively. Cross-linking assay demonstrated that 5DFRXXL peptides could bundle F-actin efficiently. Typical F-actin bundles were observed morphologically through determina- tion of confocal and electron microscopy after adding 5DFRXXL peptides. After transfection of pEGFP-5DFRXXL plasmid into eukaryocyte, spike structure was observed around cell membrane edge. We guess that such structure formation may be attributable to F-actin over-bundle forma- tion caused by 5DFRXXL peptides. Therefore, we suppose that L-MLCK may be a new bundling protein and somehow play a certain role in organization of cell skeleton besides mediating cell contraction by it kinase activity.

  17. Linking the uncertainty of low frequency variability in tropical forcing in regional climate change

    Energy Technology Data Exchange (ETDEWEB)

    Forest, Chris E. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Meteorology; Barsugli, Joseph J. [Univ. of Colorado, Boulder, CO (United States). CIRES; Li, Wei [Pennsylvania State Univ., University Park, PA (United States). Dept. of Meteorology


    The project utilizes multiple atmospheric general circulation models (AGCMs) to examine the regional climate sensitivity to tropical sea surface temperature forcing through a series of ensemble experiments. The overall goal for this work is to use the global teleconnection operator (GTO) as a metric to assess the impact of model structural differences on the uncertainties in regional climate variability.

  18. Airborne black carbon concentrations over an urban region in western India-temporal variability, effects of meteorology, and source regions. (United States)

    Bapna, Mukund; Sunder Raman, Ramya; Ramachandran, S; Rajesh, T A


    This study characterizes over 5 years of high time resolution (5 min), airborne black carbon (BC) concentrations (July 2003 to December 2008) measured over Ahmedabad, an urban region in western India. The data were used to obtain different time averages of BC concentrations, and these averages were then used to assess the diurnal, seasonal, and annual variability of BC over the study region. Assessment of diurnal variations revealed a strong association between BC concentrations and vehicular traffic. Peaks in BC concentration were co-incident with the morning (0730 to 0830, LST) and late evening (1930 to 2030, LST) rush hour traffic. Additionally, diurnal variability in BC concentrations during major festivals (Diwali and Dushera during the months of October/November) revealed an increase in BC concentrations due to fireworks displays. Maximum half hourly BC concentrations during the festival days were as high as 79.8 μg m(-3). However, the high concentrations rapidly decayed suggesting that local meteorology during the festive season was favorable for aerosol dispersion. A multiple linear regression (MLR) model with BC as the dependent variable and meteorological parameters as independent variables was fitted. The variability in temperature, humidity, wind speed, and wind direction accounted for about 49% of the variability in measured BC concentrations. Conditional probability function (CPF) analysis was used to identify the geographical location of local source regions contributing to the effective BC measured (at 880 nm) at the receptor site. The east north-east (ENE) direction to the receptor was identified as a major source region. National highway (NH8) and two coal-fired thermal power stations (at Gandhinagar and Sabarmati) were located in the identified direction, suggesting that local traffic and power plant emissions were likely contributors to the measured BC.

  19. Capturing field-scale variability in crop performance across a regional-scale climosequence (United States)

    Brooks, E. S.; Poggio, M.; Anderson, T. R.; Gasch, C.; Yourek, M. A.; Ward, N. K.; Magney, T. S.; Brown, D. J.; Huggins, D. R.


    With the increasing availability of variable rate technology for applying fertilizers and other agrichemicals in dryland agricultural production systems there is a growing need to better capture and understand the processes driving field scale variability in crop yield and soil water. This need for a better understanding of field scale variability has led to the recent designation of the R. J. Cook Agronomy Farm (CAF) (Pullman, WA, USA) as a United States Department of Agriculture Long-Term Agro-Ecosystem Research (LTAR) site. Field scale variability at the CAF is closely monitored using extensive environmental sensor networks and intensive hand sampling. As investigating land-soil-water dynamics at CAF is essential for improving precision agriculture, transferring this knowledge across the regional-scale climosequence is challenging. In this study we describe the hydropedologic functioning of the CAF in relation to five extensively instrumented field sites located within 50 km in the same climatic region. The formation of restrictive argillic soil horizons in the wetter, cooler eastern edge of the region results in the development of extensive perched water tables, surface saturation, and surface runoff, whereas excess water is not an issue in the warmer, drier, western edge of the region. Similarly, crop and tillage management varies across the region as well. We discuss the implications of these regional differences on field scale management decisions and demonstrate how we are using proximal soil sensing and remote sensing imagery to better understand and capture field scale variability at a particular field site.

  20. Modelling the regional variability of the probability of high trihalomethane occurrence in municipal drinking water. (United States)

    Cool, Geneviève; Lebel, Alexandre; Sadiq, Rehan; Rodriguez, Manuel J


    The regional variability of the probability of occurrence of high total trihalomethane (TTHM) levels was assessed using multilevel logistic regression models that incorporate environmental and infrastructure characteristics. The models were structured in a three-level hierarchical configuration: samples (first level), drinking water utilities (DWUs, second level) and natural regions, an ecological hierarchical division from the Quebec ecological framework of reference (third level). They considered six independent variables: precipitation, temperature, source type, seasons, treatment type and pH. The average probability of TTHM concentrations exceeding the targeted threshold was 18.1%. The probability was influenced by seasons, treatment type, precipitations and temperature. The variance at all levels was significant, showing that the probability of TTHM concentrations exceeding the threshold is most likely to be similar if located within the same DWU and within the same natural region. However, most of the variance initially attributed to natural regions was explained by treatment types and clarified by spatial aggregation on treatment types. Nevertheless, even after controlling for treatment type, there was still significant regional variability of the probability of TTHM concentrations exceeding the threshold. Regional variability was particularly important for DWUs using chlorination alone since they lack the appropriate treatment required to reduce the amount of natural organic matter (NOM) in source water prior to disinfection. Results presented herein could be of interest to authorities in identifying regions with specific needs regarding drinking water quality and for epidemiological studies identifying geographical variations in population exposure to disinfection by-products (DBPs).

  1. Molecular characterization of a single-chain antibody variable fragment (scFv) specific for PspA from Streptococcus pneumoniae. (United States)

    Jang, ShinA; Kim, Gyuhee; Oh, Jihye; Lee, Seungyeop; Kim, Dongho; Kim, Kook-Han; Kim, Yong Ho; Rhee, Dong-Kwon; Lee, Sangho


    Streptococcus pneumoniae is a major infectious agent responsible for pneumonia, otitis media, sepsis and meningitis. Pneumococcal surface protein A (PspA) is a well-characterized virulence factor localized on the surface and a target for vaccine development. In this study, we screened a single-chain antibody variable fragment (scFv) using phage display from a human synthetic library to select a clone 2B11. Affinity (Kd) of 2B11 was measured to be 5 nM using biolayer interferometry. 2B11 exhibited a dose-dependent recognition of recombinant PspA with no cross-reactivity towards pneumococcal antigens. The epitope on PspA was defined to residues 231-242 by mutational analysis. Molecular docking analysis supported the experimentally determined epitope, suggesting that the helix spanning residues 231-242 can bind to 2B11 with residues in the CDR-H3 (complementarity determining region 3 in the heavy chain) actively participating in the molecular contacts. Comparison of 2B11 with a commercial PspA antibody revealed that 2B11 exhibited a better specificity towards recombinant PspA antigen. 2B11 was capable of detecting endogenous PspA from pneumococcal lysates with affinity similar to that of the commercial antibody. Our study provides a molecular tool for biosensors detecting pneumococcal diseases.

  2. Cloning and expression in Escherichia coli of a human gelatinase B-inhibitory single-chain immunoglobulin variable fragment (scFv). (United States)

    Zhou, N; Paemen, L; Opdenakker, G; Froyen, G


    The murine monoclonal antibody REGA-3G12 selectively and specifically inhibits the activity of human gelatinase B. The cDNA fragments which encode the variable regions of the light and heavy chains were isolated by PCR-mediated cloning and sequenced. Single-chain Fv expression constructs for Escherichia coli were generated in which c-myc tag sequences were encoded. Inducible expression of the scFv and secretion to the periplasm were obtained with higher yields when the c-myc tag sequence was positioned at the amino-terminal side. The inhibitory activity of purified scFv on neutrophil gelatinase B was tested in a gelatin degradation assay and it was found to possess a similar specific activity as that of the intact monoclonal antibody and of the pepsin-clipped F(ab')2 derivative. This shows for the first time that inhibition of soluble enzymes with scFv is possible and opens new perspectives for the treatment of diseases with excessive and detrimental enzyme production in the host.

  3. Natural and forced air temperature variability in the Labrador region of Canada during the past century (United States)

    Way, Robert G.; Viau, Andre E.


    Evaluation of Labrador air temperatures over the past century (1881-2011) shows multi-scale climate variability and strong linkages with ocean-atmospheric modes of variability and external forcings. The Arctic Oscillation, Atlantic Multidecadal Oscillation, and El Nino Southern Oscillation are shown to be the dominant seasonal and interannual drivers of regional air temperature variability for most of the past century. Several global climate models show disagreement with observations on the rate of recent warming which suggests that models are currently unable to reproduce regional climate variability in Labrador air temperature. Using a combination of empirical statistical modeling and global climate models, we show that 33 % of the variability in annual Labrador air temperatures over the period 1881-2011 can be explained by natural factors alone; however, the inclusion of anthropogenic forcing increases the explained variance to 65 %. Rapid warming over the past 17 years is shown to be linked to both natural and anthropogenic factors with several anomalously warm years being primarily linked to recent anomalies in the Arctic Oscillation and North Atlantic sea surface temperatures. Evidence is also presented that both empirical statistical models and global climate models underestimate the regional air temperature response to ocean salinity anomalies and volcanic eruptions. These results provide important insight into the predictability of future regional climate impacts for the Labrador region.

  4. Variation trends of meteorological variables and their impacts on potential evaporation in Hailar region

    Directory of Open Access Journals (Sweden)

    Jin-liang REN


    Full Text Available Evaporation, which is an important factor in the water balance at the basin scale, is a critical variable in the determination of local available water resources. Since the potential evaporation is mainly influenced by meteorological variables, it is necessary to investigate the extent to which different meteorological variables affect the potential evaporation. The aim of this study was to explore the variation trends of different meteorological variables, and their impacts on the potential evaporation. This study selected the Hailar Meteorological Station of the Hailar region, which is situated in a cold, semi-arid, and sub-humid region, as a case study site. Based on observed daily meteorological data from 1951 to 2009, the potential evaporation was calculated with the Penman formula, and the variations of meteorological variables were investigated with the nonparametric Mann-Kendall test. The correlation between the potential evaporation and each meteorological variable at annual and seasonal scales was also analyzed. The results show that the annual and seasonal potential evaporation and air temperature present increasing trends, whereas the wind speed, sunshine duration, and relative humidity present decreasing trends. Among the meteorological variables, the air temperature and relative humidity are the key factors that affect potential evaporation at different time scales, and the impacts of other meteorological variables on the potential evaporation are not significant and vary with time scales.

  5. Production of a soluble single-chain variable fragment antibody against okadaic acid and exploration of its specific binding. (United States)

    He, Kuo; Zhang, Xiuyuan; Wang, Lixia; Du, Xinjun; Wei, Dong


    Okadaic acid is a lipophilic marine algal toxin commonly responsible for diarrhetic shellfish poisoning (DSP). Outbreaks of DSP have been increasing and are of worldwide public health concern; therefore, there is a growing demand for more rapid, reliable, and economical analytical methods for the detection of this toxin. In this study, anti-okadaic acid single-chain variable fragment (scFv) genes were prepared by cloning heavy and light chain genes from hybridoma cells, followed by fusion of the chains via a linker peptide. An scFv-pLIP6/GN recombinant plasmid was constructed and transformed into Escherichia coli for expression, and the target scFv was identified with IC-CLEIA (chemiluminescent enzyme immunoassay). The IC15 was 0.012 ± 0.02 μg/L, and the IC50 was 0.25 ± 0.03 μg/L. The three-dimensional structure of the scFv was simulated with computer modeling, and okadaic acid was docked to the scFv model to obtain a putative structure of the binding complex. Two predicted critical amino acids, Ser32 and Thr187, were then mutated to verify this theoretical model. Both mutants exhibited significant loss of binding activity. These results help us to understand this specific scFv-antigen binding mechanism and provide guidance for affinity maturation of the antibody in vitro. The high-affinity scFv developed here also has potential for okadaic acid toxin detection.

  6. Development of competitive ELISA for the detection of bovine serum albumin using single-chain variable fragments. (United States)

    Liu, Yuan; Lin, Manman; Zhang, Xifeng; Hu, Xiaodan; Lin, Jieru; Hao, Jia; He, Dan; Zhang, Xiao; Xu, Chongxin; Zhong, Jianfeng; Xie, Yajing; Zhang, Cunzheng; Liu, Xianjin


    Soluble anti-bovine serum albumin (BSA) single-chain variable fragments (scFvs) were expressed in E. Coli. HB2151. The antigen-binding equilibrium dissociation constant of the scFvs was determined to be 2.9 × 10(-8) M by surface plasmon resonance analysis. A competitive ELISA for the detection of BSA was developed using the antibody fragment above. The limits of detection (I10) and I50 were 0.002 and 0.74 μg/ml respectively, with a recovery between 87.8 and 119.2% in spiked milk samples. The assay has the potential to be used to detect concentration of BSA in milk or other matrix instead of the ELISA based on traditional antibodies.

  7. [Differential geometry expression and analysis of regionalized variables of typical pollutants concentration in terrestrial environment]. (United States)

    Ye, Han-Feng; Guo, Shu-Hai; Wu, Bo; Wang, Yan-Hu


    Based on the basic concepts of differential geometry in analyzing environmental data and establishing related models, the methodology for differential geometry expression and analysis of pollutants concentration in terrestrial environment was presented. As a kind of regionalized variables, the spatial distribution pattern of the pollutants concentration was transformed into 3-dimension form, and fitted with conicoid. This approach made it possible to analyze the quantitative relationships between the regionalized variables and their spatial structural attributes. For illustration purpose, several sorts of typical space fabrics, such as convexity, concavity, ridge, ravine, saddle, and slope, were calculated and characterized. It was suggested that this approach was feasible for analyzing the regionalized variables of pollutants concentration in terrestrial environment.


    Energy Technology Data Exchange (ETDEWEB)

    Wolk, Scott J.; Rice, Thomas S. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Aspin, Colin [Institute for Astronomy, University of Hawaii at Manoa, 640 North Aohoku Place, Hilo, HI 96720 (United States)


    We present an analysis of near-infrared time-series photometry in J, H, and K bands for about 100 epochs of a 1 Degree-Sign Multiplication-Sign 1 Degree-Sign region of the Lynds 1003/1004 dark cloud in the Cygnus OB7 region. Augmented by data from the Wide-field Infrared Survey Explorer, we identify 96 candidate disk bearing young stellar objects (YSOs) in the region. Of these, 30 are clearly Class I or earlier. Using the Wide-Field Imaging Camera on the United Kingdom Infrared Telescope, we were able to obtain photometry over three observing seasons, with photometric uncertainty better than 0.05 mag down to J Almost-Equal-To 17. We study detailed light curves and color trajectories of {approx}50 of the YSOs in the monitored field. We investigate the variability and periodicity of the YSOs and find the data are consistent with all YSOs being variable in these wavelengths on timescales of a few years. We divide the variability into four observational classes: (1) stars with periodic variability stable over long timescales, (2) variables which exhibit short-lived cyclic behavior, (3) long-duration variables, and (4) stochastic variables. Some YSO variability defies simple classification. We can explain much of the observed variability as being due to dynamic and rotational changes in the disk, including an asymmetric or changing blocking fraction, changes to the inner disk hole size, as well as changes to the accretion rate. Overall, we find that the Class I:Class II ratio of the cluster is consistent with an age of <1 Myr, with at least one individual, wildly varying source {approx}100, 000 yr old. We have also discovered a Class II eclipsing binary system with a period of 17.87 days.

  9. Regional Variability of the Effects of Land Use Systems on Soil Properties

    Institute of Scientific and Technical Information of China (English)


    In order to explore the regional variability of the effects of land use systems on soil properties, Shouyang County in Shanxi Province and Danling County in Sichuan Province of China were selected as the study areas. Field soil samples of the four land use systems (natural forest, forest plantation, shrubland, and cropland) were collected, respectively, from the two areas. The general statistical tools were used to analyze soil data. The results showed that the influence of land use systems on soil properties was significant. In general, soils in slightly human-disturbed land use systems presented a higher fertility level than those in strongly human-disturbed land use systems in both areas. Furthermore, the impacts of the same land use systems on soil properties showed a distinct regional variability, and even in the same land use system,different farming systems and site management measures (such as irrigation, fertilization, and pesticides) could also lead to the regional heterogeneity in soil properties. The regional variability of land use effects on soil properties reveals the regional variability of the effects of human activities on environmental changes, and could explain the complex relationship between humans and the natural environment in certain ways.

  10. Integrated Variable Speed Limits Control and Ramp Metering for Bottleneck Regions on Freeway

    Directory of Open Access Journals (Sweden)

    Ming-hui Ma


    Full Text Available To enhance the efficiency of the existing freeway system and therefore to mitigate traffic congestion and related problems on the freeway mainline lane-drop bottleneck region, the advanced strategy for bottleneck control is essential. This paper proposes a method that integrates variable speed limits and ramp metering for freeway bottleneck region control to relieve the chaos in bottleneck region. To this end, based on the analyses of spatial-temporal patterns of traffic flow, a macroscopic traffic flow model is extended to describe the traffic flow operating characteristic by considering the impacts of variable speed limits in mainstream bottleneck region. In addition, to achieve the goal of balancing the priority of the vehicles on mainline and on-ramp, increasing capacity, and reducing travel delay on bottleneck region, an improved control model, as well as an advanced control strategy that integrates variable speed limits and ramp metering, is developed. The proposed method is tested in simulation for a real freeway infrastructure feed and calibrates real traffic variables. The results demonstrate that the proposed method can substantially improve the traffic flow efficiency of mainline and on-ramp and enhance the quality of traffic flow at the investigated freeway mainline bottleneck.

  11. An Exploration into the Effects of Fiscal Variables on Regional Growth



    This paper explores the effects of several fiscal variables on regional economic growth in Spain over period 1965-1997. Panel estimates are provided for this sample. The results show that public consumption affects negatively growth, public investment exerts a positive (but non significant) effect on growth rate and public deficit reduces private investment and hence economic growth. The effects of taxes and social benefits seem not to be beneficial for regional growth. Alternative estimates ...

  12. Development of a single-chain variable fragment-alkaline phosphatase fusion protein and a sensitive direct competitive chemiluminescent enzyme immunoassay for detection of ractopamine in pork

    Energy Technology Data Exchange (ETDEWEB)

    Dong Jiexian; Li Zhenfeng; Lei Hongtao; Sun Yuanming [Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642 (China); Ducancel, Frederic [CEA, iBiTec-S, Service de Pharmacologie et d' Immnoanalyse (SPI), CEA Saclay, F-91191 Gif sur Yvette (France); Xu Zhenlin [Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642 (China); Boulain, Jean-Claude [CEA, iBiTec-S, Service de Pharmacologie et d' Immnoanalyse (SPI), CEA Saclay, F-91191 Gif sur Yvette (France); Yang Jinyi; Shen Yudong [Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642 (China); Wang Hong, E-mail: [Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642 (China)


    Graphical abstract: Detection model of dc-CLEIA based on anti-RAC scFv-AP fusion protein. Highlights: Black-Right-Pointing-Pointer The scFv-AP fusion protein against ractopamine (RAC) was produced. Black-Right-Pointing-Pointer A dc-CLEIA for RAC was developed based on the purified scFv-AP fusion protein. Black-Right-Pointing-Pointer The sensitivity of dc-CLEIA was 10 times as sensitive as dc-ELISA for RAC. Black-Right-Pointing-Pointer Recovery tests from pork samples were studied. Black-Right-Pointing-Pointer Good accuracy was obtained. - Abstract: A rapid, sensitive chemiluminescent enzyme immunoassay (CLEIA) for ractopamine (RAC) based on a single-chain variable fragment (scFv)-alkaline phosphatase (AP) fusion protein was developed. The scFv gene was prepared by cloning the heavy- and light-chain variable region genes (V{sub H} and V{sub L}) from hybridoma cell line AC2, which secretes antibodies against RAC, and assembling V{sub H} and V{sub L} genes with a linker by means of splicing overlap extension polymerase chain reaction. The resulting scFv gene was inserted into the expression vector pLIP6/GN containing AP to produce the fusion protein in Escherichia coli strain BL21. The purified scFv-AP fusion protein was used to develop a direct competitive CLEIA (dcCLEIA) protocol for detection of RAC. The average concentration required for 50% inhibition of binding and the limit of detection of the assay were 0.25 {+-} 0.03 and 0.02 {+-} 0.004 ng mL{sup -1}, respectively, and the linear response range extended from 0.05 to 1.45 ng mL{sup -1}. The assay was 10 times as sensitive as the corresponding enzyme-linked immunosorbent assay based on the same fusion protein. Cross-reactivity studies showed that the fusion protein did not cross react with RAC analogs. DcCLEIA was used to analyze RAC spiked pork samples, and the validation was confirmed by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS). The results showed a good correlation between

  13. Regional Climate and Variability of the Summertime Continental United States in Reanalyses (United States)

    Bosilovich, M G.; Robertson, F. R.; Roberts, B.


    Understanding climate variability at regional scales is an important for research and societal needs. Atmospheric retrospective-analyses (or reanalyses) integrate multitudes of observing systems with numerical models to produce continuous data that include variables not easily observed, if at all. The breadth of variables as well as observational influence included in reanalyses make them ideal for investigating climate variability. In this paper, we assess NASA s Modern Era Retrospective-analysis for Research and Application (MERRA) regional variability in North America, specifically the United States, in conjunction with current satellite data reanalyses. Emphasis is placed on summertime precipitation because 1) it is a difficult parameter to capture in the most difficult season, 2) significant observational resources exist to benchmark comparisons, and 3) accurate assessment of precipitation variability is crucial to a multitude of sectors and applications. Likewise, we have also begun to evaluate surface air temperature. While precipitation biases are identified, year to year variability of the precipitation variations, in many cases, are quite reasonable. However, some spurious long term trends and sudden shifts in the time series are also identified. In surface air temperature, analysis of station observations provides ERA Interim a clear overall advantage. However, in a number of regions, all the reanalyses are quite comparable in variability and trend. In other regions, significant precipitation biases may occur, which has implications for the ancillary process data in a reanalysis, such as surface fluxes. We also characterize the reanalyses ability to capture variability related to ENSO. In general, the summertime variations of precipitation in the reanalyses are more highly correlated (positively) to ENSO (using ENSO34) than are the observations. The Northwestern US shows the largest positive correlations to ENSO34, and reanalyses agree with that, and

  14. 服务供应链及其区域经济影响研究%Research on Service Supply Chain and Its Impacts on Regional Economics.

    Institute of Scientific and Technical Information of China (English)



    It shows in the tendency of the global economic development in recent years that Services Science would no doubt become the next hot topic in economic study. And service supply chain is a new study aspect in supply chain management of services science. This article begins with study on the definition and characters of service supply chain, compares this with traditional supply chain, establishes the structure of its form and puts it into our regional economics to examine its impacts.

  15. Internal and external variability in regional simulations of the Iberian Peninsula climate over the last millennium

    Directory of Open Access Journals (Sweden)

    J. J. Gómez-Navarro


    Full Text Available In this study we analyse the role of internal variability in regional climate simulations through a comparison of two regional paleoclimate simulations for the last millennium. They share the same external forcings and model configuration, differing only in the initial condition used to run the driving global model simulation. A comparison of these simulations allows us to study the role of internal variability in climate models at regional scales, and how it affects the long-term evolution of climate variables such as temperature and precipitation. The results indicate that, although temperature is homogeneously sensitive to the effect of external forcings, the evolution of precipitation is more strongly governed by random and unpredictable internal dynamics. There are, however, some areas where the role of internal variability is lower than expected, allowing precipitation to respond to the external forcings, and we explore the underlying physical mechanisms responsible. We find that special attention should be paid when comparing the evolution of simulated precipitation with proxy reconstructions at regional scales. In particular, this study identifies areas, depending on the season, in which this comparison would be meaningful, but also other areas where good agreement between model simulations and reconstructions should not be expected even if both are perfect.

  16. YSOVAR: Mid-infrared variability in the star-forming region Lynds 1688

    Energy Technology Data Exchange (ETDEWEB)

    Günther, H. M.; Poppenhaeger, K.; Wolk, S. J.; Hora, J. L. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Cody, A. M. [Spitzer Science Center, California Institute of Technology, Pasadena, CA 91125 (United States); Covey, K. R. [Lowell Observatory, 1400 West Mars Hill Road, Flagstaff, AZ 86001 (United States); Hillenbrand, L. A. [Department of Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Plavchan, P. [NASA Exoplanet Science Institute, California Institute of Technology, 770 South Wilson Avenue, Pasadena, CA 91125 (United States); Rebull, L. M.; Stauffer, J. R. [Spitzer Science Center/Caltech, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Allen, L. [National Optical Astronomy Observatories, Tucson, AZ 85719 (United States); Bayo, A. [Max Planck Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg (Germany); Gutermuth, R. A. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Meng, H. Y. A. [Infrared Processing and Analysis Center, California Institute of Technology, MC 100-22, 770 South Wilson Avenue, Pasadena, CA 91125 (United States); Morales-Calderón, M. [Centro de Astrobiología (INTA-CSIC), ESAC Campus, P.O. Box 78, E-28691 Villanueva de la Canada (Spain); Parks, J. R. [Department of Physics and Astronomy, Georgia State University, 25 Park Place South, Atlanta, GA 30303 (United States); Song, Inseok, E-mail: [Physics and Astronomy Department, University of Georgia, Athens, GA 30602-2451 (United States)


    The emission from young stellar objects (YSOs) in the mid-infrared (mid-IR) is dominated by the inner rim of their circumstellar disks. We present IR data from the Young Stellar Object VARiability (YSOVAR) survey of ∼800 objects in the direction of the Lynds 1688 (L1688) star-forming region over four visibility windows spanning 1.6 yr using the Spitzer Space Telescope in its warm mission phase. Among all light curves, 57 sources are cluster members identified based on their spectral energy distribution and X-ray emission. Almost all cluster members show significant variability. The amplitude of the variability is larger in more embedded YSOs. Ten out of 57 cluster members have periodic variations in the light curves with periods typically between three and seven days, but even for those sources, significant variability in addition to the periodic signal can be seen. No period is stable over 1.6 yr. Nonperiodic light curves often still show a preferred timescale of variability that is longer for more embedded sources. About half of all sources exhibit redder colors in a fainter state. This is compatible with time-variable absorption toward the YSO. The other half becomes bluer when fainter. These colors can only be explained with significant changes in the structure of the inner disk. No relation between mid-IR variability and stellar effective temperature or X-ray spectrum is found.

  17. High variability of the gvpA-gvpC region in Microcystis

    Institute of Scientific and Technical Information of China (English)


    Gas vesicles provide buoyancy to Microcystis and other common cyanobacterial bloom-forming species. gvpA and gvpC are structural genes encoding gas vesicle proteins. Phylogenetic analyses of 10 Microcystis strains/uncultured samples showed that gvpC and each intergenic segment of the gvpA-gvpC region can be divided into two types. The combination of different types of gvpC and intergenic segments is an important factor that diversifies this genomic region. Some Microcystis strains isolated in China possess a 172 to 176 bp sequence tag in the intergenic segment between gvpA and gvpC. The gvpA-gvpC region in Microcystis can be divided into at least 4 classes and more numbers of subclasses. Compared to rbcLX and other regions, the high variability of the gvpA-gvpC region should be more useful in identifying geographical isolates or ecotypes of Microcystis.

  18. Nitrogen and phosphorus use efficiencies and losses in the food chain in China at regional scales in 1980 and 2005. (United States)

    Ma, L; Velthof, G L; Wang, F H; Qin, W; Zhang, W F; Liu, Z; Zhang, Y; Wei, J; Lesschen, J P; Ma, W Q; Oenema, O; Zhang, F S


    Crop and animal production in China has increased significantly during the last decades, but at the cost of large increases in nitrogen (N) and phosphorus (P) losses, which contribute to ecosystem degradation and human health effects. This information is largely based on scattered field experiments, surveys and national statistics. As a consequence, there is as yet no comprehensive understanding of the changes in N and P cycling and losses at regional and national scales. Here, we present the results of an integrated assessment of the N and P use efficiencies (NUE and PUE) and N and P losses in the chain of crop and animal production, food processing and retail, and food consumption at regional scale in 1980 and 2005, using a uniform approach and databases. Our results show that the N and P costs of food production-consumption almost doubled between 1980 and 2005, but with large regional variation. The NUE and PUE of crop production decreased dramatically, while NUE and PUE in animal production increased. Interestingly, NUE and PUE of the food processing sector decreased from about 75% to 50%. Intake of N and P per capita increased, but again with large regional variation. Losses of N and P from agriculture to atmosphere and water bodies increased in most regions, especially in the east and south of the country. Highest losses were estimated for the Beijing and Tianjin metropolitan regions (North China), Pearl River Delta (South China) and Yangzi River Delta (East China). In conclusion, the changes and regional variations in NUE and PUE in the food chain of China are large and complex. Changes occurred in the whole crop and animal production, food processing and consumption chain, and were largest in the most populous areas between 1980 and 2005.

  19. Modeling Urban Expansion in Bangkok Metropolitan Region Using Demographic–Economic Data through Cellular Automata-Markov Chain and Multi-Layer Perceptron-Markov Chain Models

    Directory of Open Access Journals (Sweden)

    Chudech Losiri


    Full Text Available Urban expansion is considered as one of the most important problems in several developing countries. Bangkok Metropolitan Region (BMR is the urbanized and agglomerated area of Bangkok Metropolis (BM and its vicinity, which confronts the expansion problem from the center of the city. Landsat images of 1988, 1993, 1998, 2003, 2008, and 2011 were used to detect the land use and land cover (LULC changes. The demographic and economic data together with corresponding maps were used to determine the driving factors for land conversions. This study applied Cellular Automata-Markov Chain (CA-MC and Multi-Layer Perceptron-Markov Chain (MLP-MC to model LULC and urban expansions. The performance of the CA-MC and MLP-MC yielded more than 90% overall accuracy to predict the LULC, especially the MLP-MC method. Further, the annual population and economic growth rates were considered to produce the land demand for the LULC in 2014 and 2035 using the statistical extrapolation and system dynamics (SD. It was evident that the simulated map in 2014 resulting from the SD yielded the highest accuracy. Therefore, this study applied the SD method to generate the land demand for simulating LULC in 2035. The outcome showed that urban occupied the land around a half of the BMR.

  20. The rules governing hydrogen combustion close to the lower ignition limit in the kinetic region of chain termination (United States)

    Rubtsov, N. M.; Tsvetkov, G. I.; Chernysh, V. I.


    The kinetic scheme of hydrogen combustion near the lower self-ignition limit in the kinetic region can be augmented by the reactions of bimolecular nonlinear termination O + OH → H + O2 and heterogeneous propagation of chains with the participation of adsorbed hydrogen atoms Hs. The literature data on the experimental determination of the probability of hydrogen atom trapping by the surface of quartz were analyzed.

  1. Impact of region contouring variability on image-based focal therapy evaluation (United States)

    Gibson, Eli; Donaldson, Ian A.; Shah, Taimur T.; Hu, Yipeng; Ahmed, Hashim U.; Barratt, Dean C.


    Motivation: Focal therapy is an emerging low-morbidity treatment option for low-intermediate risk prostate cancer; however, challenges remain in accurately delivering treatment to specified targets and determining treatment success. Registered multi-parametric magnetic resonance imaging (MPMRI) acquired before and after treatment can support focal therapy evaluation and optimization; however, contouring variability, when defining the prostate, the clinical target volume (CTV) and the ablation region in images, reduces the precision of quantitative image-based focal therapy evaluation metrics. To inform the interpretation and clarify the limitations of such metrics, we investigated inter-observer contouring variability and its impact on four metrics. Methods: Pre-therapy and 2-week-post-therapy standard-of-care MPMRI were acquired from 5 focal cryotherapy patients. Two clinicians independently contoured, on each slice, the prostate (pre- and post-treatment) and the dominant index lesion CTV (pre-treatment) in the T2-weighted MRI, and the ablated region (post-treatment) in the dynamic-contrast- enhanced MRI. For each combination of clinician contours, post-treatment images were registered to pre-treatment images using a 3D biomechanical-model-based registration of prostate surfaces, and four metrics were computed: the proportion of the target tissue region that was ablated and the target:ablated region volume ratio for each of two targets (the CTV and an expanded planning target volume). Variance components analysis was used to measure the contribution of each type of contour to the variance in the therapy evaluation metrics. Conclusions: 14-23% of evaluation metric variance was attributable to contouring variability (including 6-12% from ablation region contouring); reducing this variability could improve the precision of focal therapy evaluation metrics.

  2. Genetic fusion of single-chain variable fragments to partial spider silk improves target detection in micro- and nanoarrays. (United States)

    Thatikonda, Naresh; Delfani, Payam; Jansson, Ronnie; Petersson, Linn; Lindberg, Diana; Wingren, Christer; Hedhammar, My


    Immobilizing biomolecules with retained functionality and stability on solid supports is crucial for generation of sensitive immunoassays. However, upon use of conventional immobilization strategies, a major portion of the biomolecules (e.g. antibodies) frequently tends to lose their bioactivity. In this study, we describe a procedure to immobilize human single-chain variable fragment (scFv) via genetic fusion to partial spider silk, which have a high tendency to adhere to solid supports. Two scFvs, directed towards serum proteins, were genetically fused to partial spider silk proteins and expressed as silk fusion proteins in E. coli. Antigen binding ability of scFvs attached to a partial silk protein denoted RC was investigated using microarray analysis, whereas scFvs fused to the NC silk variant were examined using nanoarrays. Results from micro- and nanoarrays confirmed the functionality of scFvs attached to both RC and NC silk, and also for binding of targets in crude serum. Furthermore, the same amount of added scFv gives higher signal intensity when immobilized via partial spider silk compared to when immobilized alone. Together, the results suggest that usage of scFv-silk fusion proteins in immunoassays could improve target detection, in the long run enabling novel biomarkers to be detected in crude serum proteomes.

  3. Phase analysis in single-chain variable fragment production by recombinant Pichia pastoris based on proteomics combined with multivariate statistics. (United States)

    Fujiki, Yuya; Kumada, Yoichi; Kishimoto, Michimasa


    The proteomics technique, which consists of two-dimensional gel electrophoresis (2-DE), peptide mass fingerprinting (PMF), gel image analysis, and multivariate statistics, was applied to the phase analysis of a fed-batch culture for the production of a single-chain variable fragment (scFv) of an anti-C-reactive protein (CRP) antibody by Pichia pastoris. The time courses of the fed-batch culture were separated into three distinct phases: the growth phase of the batch process, the growth phase of the fed-batch process, and the production phase of the fed-batch process. Multivariate statistical analysis using 2-DE gel image analysis data clearly showed the change in the culture phase and provided information concerning the protein expression, which suggested a metabolic change related to cell growth and production during the fed-batch culture. Furthermore, specific proteins, such as alcohol oxidase, which is strongly related to scFv expression, and proteinase A, which could biodegrade scFv in the latter phases of production, were identified via the PMF method. The proteomics technique provided valuable information about the effect of the methanol concentration on scFv production.

  4. Affinity maturation of single-chain variable fragment specific for aflatoxin B(1) using yeast surface display. (United States)

    Min, Won-Ki; Kim, Sung-Gun; Seo, Jin-Ho


    As aflatoxin B1 is one of the most toxic mycotoxins, it is important to detect and to quantify aflatoxin B1 accurately by immunological methods. To enhance aflatoxin B1-binding affinity of the single-chain variable fragment, yeast surface display technique combined with fluorescence-activated cell sorting was applied. A randomly mutated scFv library was subjected to 4 rounds of fluorescence-activated cell sorting, resulting in isolation of 5 scFv variants showing an affinity improvement compared to the parental wild type scFv. The best scFv with a 9-fold improvement in affinity for aflatoxin B1 exhibited similar specificity to the monoclonal antibody. Most of the mutations in scFv-M37 were located outside of the canonical antigen-contact loops, suggesting that its affinity improvement might be driven by an allosteric effect inducing scFv-M37 to form a more favorable binding pocket for aflatoxin B1 than the wild type scFv.

  5. Expression and characterization of single-chain variable fragment antibody against staphylococcal enterotoxin A in Escherichia coli. (United States)

    Chen, Weifeng; Hu, Li; Liu, Aiping; Li, Jinquan; Chen, Fusheng; Wang, Xiaohong


    The staphylococcal enterotoxins (SEs) are potent gastrointestinal exotoxins synthesized by Staphylococcus aureus, which is responsible for various diseases including septicemia, food poisoning, and toxic shock syndrome, as well as bovine mastitis. Among them, staphylococcal enterotoxin A (SEA) is one of the most commonly present serotypes in staphylococcal food poisoning cases. In this study, the stable hybridoma 3C12 producing anti-SEA monoclonal antibody was established with an equilibrium dissociation constant (KD) of 1.48 × 10(-8) mol·L(-1), its ScFv-coding genes were obtained and then the anti-SEA single chain variable fragment (ScFv) protein was expressed in Escherichia coli. Characterization of the expressed target ScFv protein was analyzed by sodium dodecyl sulfate - polyacrylamide gel electrophoresis, Western blot, and enzyme-linked immunosorbent assay. The results demonstrated that the recombinant anti-SEA ScFv protein retained a specific binding activity for SEA, and the KD value of the soluble ScFv was about 3.75 × 10(-7) mol·L(-1). The overall yield of bioactive anti-SEA ScFv in E. coli flask culture was more than 10 mg·L(-1).

  6. Expression, production, and renaturation of a functional single-chain variable antibody fragment (scFv against human ICAM-1

    Directory of Open Access Journals (Sweden)

    H. Sun


    Full Text Available Intercellular adhesion molecule-1 (ICAM-1 is an important factor in the progression of inflammatory responses in vivo. To develop a new anti-inflammatory drug to block the biological activity of ICAM-1, we produced a monoclonal antibody (Ka=4.19×10−8 M against human ICAM-1. The anti-ICAM-1 single-chain variable antibody fragment (scFv was expressed at a high level as inclusion bodies in Escherichia coli. We refolded the scFv (Ka=2.35×10−7 M by ion-exchange chromatography, dialysis, and dilution. The results showed that column chromatography refolding by high-performance Q Sepharose had remarkable advantages over conventional dilution and dialysis methods. Furthermore, the anti-ICAM-1 scFv yield of about 60 mg/L was higher with this method. The purity of the final product was greater than 90%, as shown by denaturing gel electrophoresis. Enzyme-linked immunosorbent assay, cell culture, and animal experiments were used to assess the immunological properties and biological activities of the renatured scFv.

  7. Novel Selenium-containing Human Single-chain Variable Fragment with Glutathione Peroxidase Activity from Computer-aided Molecular Design

    Institute of Scientific and Technical Information of China (English)

    WANG Cheng; MU Ying; L(U) Shao-wu; LUO Gui-min; WAN Pei; GONG Ping-sheng; L(U) Li-min; XU Ya-wei; ZHAO Yang; HE Bo; ZHAO Gang; YAN Gang-lin


    In order to enhance the glutathione peroxidase(GPX) catalytic activity of the selenium-containing single-chain variable fragments(Se-scFv),a novel human scFv was designed on the basis of the structure of human antibody and optimized via bioinformatics methods such as homologous sequence analysis,three-dimensional(3D)model building,binding-site analysis and docking.The DNA sequence of the new human scFv was synthesized and cloned into the expression vector pET22b(+),then the scFv protein was expressed in soluble form in Escherichia coli BL21(DE3) and purified by Ni2+-immobilized metal affinity chromatography(IMAC).The serine residue of scFv in the active site was converted into selenocysteine(Sec) with the chemical modification method,thus,the human Se-scFv with GPX activity was obtained.The GPX activity of the Se-scFv protein was characterized.Compared with other Se-scFv,the new human Se-scFv showed similar efficiency for catalyzing the reduction of hydrogen peroxide by glutathione.It exhibited pH and temperature dependent catalytic activity and a typical ping-pong kinetic mechanism.

  8. High production of llama variable heavy-chain antibody fragment (VHH) fused to various reader proteins by Aspergillus oryzae. (United States)

    Hisada, Hiromoto; Tsutsumi, Hiroko; Ishida, Hiroki; Hata, Yoji


    Llama variable heavy-chain antibody fragment (VHH) fused to four different reader proteins was produced and secreted in culture medium by Aspergillus oryzae. These fusion proteins consisted of N-terminal reader proteins, VHH, and a C-terminal his-tag sequence which facilitated purification using one-step his-tag affinity chromatography. SDS-PAGE analysis of the deglycosylated purified fusion proteins confirmed that the molecular weight of each corresponded to the expected sum of VHH and the respective reader proteins. The apparent high molecular weight reader protein glucoamylase (GlaB) was found to be suitable for efficient VHH production. The GlaB-VHH-His protein bound its antigen, human chorionic gonadotropin, and was detectable by a new ELISA-based method using a coupled assay with glucoamylase, glucose oxidase, peroxidase, maltose, and 3,3',5,5'-tetramethylbenzidine as substrates. Addition of potassium phosphate to the culture medium induced secretion of 0.61 mg GlaB-VHH-His protein/ml culture medium in 5 days.

  9. Two centuries of observed atmospheric variability and change over the North Sea region (United States)

    Stendel, Martin; van den Besselaar, Else; Hannachi, Abdel; Kent, Elizabeth; Lefebvre, Christiana; Rosenhagen, Gudrun; Schenk, Frederik; van der Schrier, Gerard; Woollings, Tim


    In the upcoming North Sea Region Climate Change Assessment (NOSCCA), we present a synthesis of current knowledge about past, present and possible future climate change in the North Sea region. A climate change assessment from published scientific work has been conducted as a kind of regional IPCC report, and a book has been produced that will be published by Springer in 2016. In the framework of the NOSCCA project, we examine past and present studies of variability and changes in atmospheric variables within the North Sea region over the instrumental period, roughly the past 200 years, based on observations and reanalyses. The variables addressed in this presentation are large-scale circulation, pressure and wind, surface air temperature, precipitation and radiative properties (clouds, solar radiation, and sunshine duration). While air temperature over land, not unexpectedly, has increased everywhere in the North Sea region, with strongest trends in spring and in the north of the region, a precipitation increase has been observed in the north and a decrease in the south of the region. This pattern goes along with a north-eastward shift of storm tracks and is in agreement with climate model projections under enhanced greenhouse gas concentrations. For other variables, it is not obvious which part of the observed changes may be due to anthropogenic activities and which is internally forced. It remains also unclear to what extent atmospheric circulation over the North Sea region is influenced by distant factors, in particular Arctic sea-ice decline in recent decades. There are indications of an increase in the number of deep cyclones (but not in the total number of cyclones), while storminess since the late 19th century shows no robust trends. The persistence of circulation types appears to have increased over the last century, and consequently, there is an indication for 'more extreme' extreme events. However, changes in extreme weather events are difficult to assess

  10. Characterization of the interaction between human complement protein C4 and a single-chain variable fragment antibody by capillary electrophoresis and surface plasmon resonance

    NARCIS (Netherlands)

    Seifar, R.M.; Cool, Robbert; Quax, Wim; Bischoff, Rainer


    Immunoaffinity capillary electrophoresis and surface plasmon resonance have been used for the characterization of the interaction between two large-sized proteins, the human complement protein C4 and the single-chain variable fragment C43. The rather high kinetic rate constants as determined by surf

  11. Production of bifunctional proteins by Aspergillus awamori: Llama variable heavy chain antibody fragment (V-HH) R9 coupled to Arthromyces ramosus peroxidase (ARP)

    NARCIS (Netherlands)

    Joosten, V.; Roelofs, M.S.; Dries, van den N.; Goosen, T.; Verrips, C.T.; Hondel, van den C.A.M.J.J.; Lokman, B.C.


    The Arthromyces ramosus peroxidase gene (arp) was genetically fused to either the 5'- or 3'-terminal ends of the gene encoding llama variable heavy chain antibody fragment V-HH R9, resulting in the fusion expression cassettes ARP-R9 or R9-ARP. Aspergillus awamori transformants were obtained which pr

  12. Production of bifunctional proteins by Aspergillus awamori: Llama variable heavy chain antibody fragment (VHH) R9 coupled to Arthromyces ramosus peroxidase (ARP)

    NARCIS (Netherlands)

    Joosten, V.; Roelofs, M.S.; Dries, N. van den; Goosen, T.; Verrips, C.T.; Hondel, C.A.M.J.J. van den; Lokman, B.C.


    The Arthromyces ramosus peroxidase gene (arp) was genetically fused to either the 5′- or 3′-terminal ends of the gene encoding llama variable heavy chain antibody fragment VHH R9, resulting in the fusion expression cassettes ARP-R9 or R9-ARP. Aspergillus awamori transformants were obtained which pro

  13. Climatic variability of river outflow in the Pantanal region and the influence of sea surface temperature (United States)

    Silva, Carlos Batista; Silva, Maria Elisa Siqueira; Ambrizzi, Tércio


    This paper investigates possible linear relationships between climate, hydrology, and oceanic surface variability in the Pantanal region (in South America's central area), over interannual and interdecadal time ranges. In order to verify the mentioned relations, lagged correlation analysis and linear adjustment between river discharge at the Pantanal region and sea surface temperature were used. Composite analysis for atmospheric fields, air humidity flux divergence, and atmospheric circulation at low and high levels, for the period between 1970 and 2003, was analyzed. Results suggest that the river discharge in the Pantanal region is linearly associated with interdecadal and interannual oscillations in the Pacific and Atlantic oceans, making them good predictors to continental hydrological variables. Considering oceanic areas, 51 % of the annual discharge in the Pantanal region can be linearly explained by mean sea surface temperature (SST) in the Subtropical North Pacific, Tropical North Pacific, Extratropical South Pacific, and Extratropical North Atlantic over the period. Considering a forecast approach in seasonal scale, 66 % of the monthly discharge variance in Pantanal, 3 months ahead of SST, is explained by the oceanic variables, providing accuracy around 65 %. Annual discharge values in the Pantanal region are strongly related to the Pacific Decadal Oscillation (PDO) variability (with 52 % of linear correlation), making it possible to consider an interdecadal variability and a consequent subdivision of the whole period in three parts: 1st (1970-1977), 2nd (1978-1996), and 3rd (1997-2003) subperiods. The three subperiods coincide with distinct PDO phases: negative, positive, and negative, respectively. Convergence of humidity flux at low levels and the circulation pattern at high levels help to explain the drier and wetter subperiods. During the wetter 2nd subperiod, the air humidity convergence at low levels is much more evident than during the other two

  14. Identification of mammalian species using the short and highly variable regions of mitochondrial DNA. (United States)

    Xie, Jianhui; Zhu, Wei; Zhou, Yueqin; Liu, Zhiping; Chen, Yang; Zhao, Ziqin


    The mitochondrial DNA (mtDNA) typing is useful for the species determination of degraded samples and the nucleotide diversity of target fragments across species is crucial for the discrimination. In this study, the short and highly polymorphic regions flanked by two conserved termini were sought by the sequence alignment of mtDNA across species and two target regions located at 12S rRNA gene were characterized. Two universal primer sets were developed that appear to be effective for a wide variety of mammalian species, even for domestic birds. The two target regions could be efficiently amplified using their universal primer sets on degraded samples and provide sufficient information for species determination. Therefore, the two short and highly variable target regions might provide a high discriminative capacity and should be suitable for the species determination of degraded samples.

  15. Constant region of a kappa III immunoglobulin light chain as a major AL-amyloid protein

    DEFF Research Database (Denmark)

    Engvig, J P; Olsen, K E; Gislefoss, R E


    and the corresponding AL protein as a kappa III immunoglobulin light chain from material of a patient with systemic AL-amyloidosis presenting as a local inguinal tumour. The two proteins showed some unique features. The major part of the AL amyloid fibril protein consisted of C-terminal fragments of the Bence...

  16. Coupled decadal variability of the North Atlantic Oscillation, regional rainfall and karst spring discharges in the Campania region (southern Italy

    Directory of Open Access Journals (Sweden)

    P. De Vita


    Full Text Available Thus far, studies on climate change have focused mainly on the variability of the atmospheric and surface components of the hydrologic cycle, investigating the impact of this variability on the environment, especially with respect to the risks of desertification, droughts and floods. Conversely, the impacts of climate change on the recharge of aquifers and on the variability of groundwater flow have been less investigated, especially in Mediterranean karst areas whose water supply systems depend heavily upon groundwater exploitation.

    In this paper, long-term climatic variability and its influence on groundwater recharge were analysed by examining decadal patterns of precipitation, air temperature and spring discharges in the Campania region (southern Italy, coupled with the North Atlantic Oscillation (NAO.

    The time series of precipitation and air temperature were gathered over 90 yr, from 1921 to 2010, using 18 rain gauges and 9 air temperature stations with the most continuous functioning. The time series of the winter NAO index and of the discharges of 3 karst springs, selected from those feeding the major aqueducts systems, were collected for the same period.

    Regional normalised indexes of the precipitation, air temperature and karst spring discharges were calculated, and different methods were applied to analyse the related time series, including long-term trend analysis using smoothing numerical techniques, cross-correlation and Fourier analysis.

    The investigation of the normalised indexes highlighted the existence of long-term complex periodicities, from 2 to more than 30 yr, with differences in average values of up to approximately ±30% for precipitation and karst spring discharges, which were both strongly correlated with the winter NAO index.

    Although the effects of the North Atlantic Oscillation (NAO had already been demonstrated in the long-term precipitation and streamflow patterns of

  17. Negative effects of a disulfide bond mismatch in anti-rabies G protein single-chain antibody variable fragment FV57. (United States)

    Duan, Ye; Gu, Tiejun; Zhang, Xizhen; Jiang, Chunlai; Yuan, Ruosen; Li, Zhuang; Wang, Dandan; Chen, Xiaoxu; Wu, Chunlai; Chen, Yan; Wu, Yongge; Kong, Wei


    Rabies virus (RV) causes a fatal infectious disease requiring efficient post-exposure prophylaxis (PEP), which includes a rabies vaccine and rabies immunoglobulin (RIG). The single-chain antibody variable fragment (scFv), a small engineered antibody fragment derived from an antibody variable heavy chain and light chain, has the potential to replace the current application of RIG. In previous studies, we constructed and evaluated an anti-rabies virus G protein scFv (FV57) based on the monoclonal antibody CR57. Of the five cysteines in FV57, four are linked in intra-chain disulfide bonds (Cys-VH28/Cys-VH98 and Cys-VL16/Cys-VL84), and one is free (Cys-VL85). However, the thiol in Cys-VL85 neighboring Cys-VL84 in the CDR3 of the light chain is likely to mismatch with the thiol in Cys-VL16 during the renaturing process. In order to study effects of the mismatched disulfide bond, Cys-VL85 and Cys-VL84 of FV57 were mutated to serine to construct mutants FV57(VL85S) and FV57(VL84S). Furthermore, the disulfide bonds in the light chain of FV57, FV57(VL85S) and FV57(VL84S) were deleted by mutating Cys-VL16 to serine. All mutants were prepared and evaluated along with the original FV57. The results indicated that the mismatched disulfide bond of FV57 linking the light chain FR1 and CDR3 would confer deleterious negative effects on its activity against RV, likely due to spatial hindrance in the light chain CDR3. Moreover, avoidance of the disulfide bond mismatch provided an additional 30% protective efficacy against RV infection in the mouse RV challenge model. Thus, modifications of FV57 to eliminate the disulfide bond mismatch may provide a candidate therapeutic agent for effective PEP against rabies.

  18. The variable rotation period of the inner region of Saturn's plasma disk. (United States)

    Gurnett, D A; Persoon, A M; Kurth, W S; Groene, J B; Averkamp, T F; Dougherty, M K; Southwood, D J


    We show that the plasma and magnetic fields in the inner region of Saturn's plasma disk rotate in synchronism with the time-variable modulation period of Saturn's kilometric radio emission. This relation suggests that the radio modulation has its origins in the inner region of the plasma disk, most likely from a centrifugally driven convective instability and an associated plasma outflow that slowly slips in phase relative to Saturn's internal rotation. The slippage rate is determined by the electrodynamic coupling of the plasma disk to Saturn and by the drag force exerted by its interaction with the Enceladus neutral gas torus.

  19. [Morphological variability of Microtus oeconomus pallas (Rodentia, Rrvicolidae) from Baikal region]. (United States)

    Pozdniakov, A A; Litvinov, Iu N; Demidovich, P A


    The analysis of morphological variability of the ten samples of Microtus oeconomus from islands of Baikal and adjacent regions gas shown, that island samples differ from continental ones by complex of parameters, defining proportions of a skuul, mainly, proportions of an auditory region. Island samples also differ higher indexes of complexity and asymmetry of morphotypes of the third upper molar. An environment of the Baikal islands differ absence of the damp habitats preferred Microtus oeconomus, and also colder microclimate that has caused forming original morphological character of island micropopulations.

  20. Drain current local variability from linear to saturation region in 28 nm bulk NMOSFETs (United States)

    Karatsori, T. A.; Theodorou, C. G.; Haendler, S.; Dimitriadis, C. A.; Ghibaudo, G.


    In this work, we investigate the impact of the source - drain series resistance mismatch on the drain current variability in 28 nm bulk MOSFETs. For the first time, a mismatch model including the local fluctuations of the threshold voltage (Vt), the drain current gain factor (β) and the source - drain series resistance (RSD) in both linear and saturation regions is presented. Furthermore, it is demonstrated that the influence of the source - drain series resistance mismatch is attenuated in the saturation region, due to the weaker sensitivity of the drain current variability on the series resistance variation. The experimental results were further verified by numerical simulations of the drain current characteristics with sensitivity analysis of the MOSFET parameters Vt, β and RSD.

  1. Characterization of a single-chain variable fragment recognizing a linear epitope of aβ: a biotechnical tool for studies on Alzheimer's disease?

    Directory of Open Access Journals (Sweden)

    Silke Dornieden

    Full Text Available Alzheimer's disease (AD is a progressive neurodegenerative disorder with devastating effects. Currently, therapeutic options are limited to symptomatic treatment. For more than a decade, research focused on immunotherapy for the causal treatment of AD. However, clinical trials with active immunization using Aβ encountered severe complications, for example meningoencephalitis. Consequently, attention focused on passive immunization using antibodies. As an alternative to large immunoglobulins (IgGs, Aβ binding single-chain variable fragments (scFvs were used for diagnostic and therapeutic research approaches. scFvs can be expressed in E. coli and may provide improved pharmacokinetic properties like increased blood-brain barrier permeability or reduced side-effects in vivo. In this study, we constructed an scFv from an Aβ binding IgG, designated IC16, which binds the N-terminal region of Aβ (Aβ(1-8. scFv-IC16 was expressed in E. coli, purified and characterized with respect to its interaction with different Aβ species and its influence on Aβ fibril formation. We were able to show that scFv-IC16 strongly influenced the aggregation behavior of Aβ and could be applied as an Aβ detection probe for plaque staining in the brains of transgenic AD model mice. The results indicate potential for therapy and diagnosis of AD.

  2. Hydrological Impacts of Land Use Change and Climate Variability in the Headwater Region of the Heihe River Basin, Northwest China. (United States)

    Zhang, Ling; Nan, Zhuotong; Xu, Yi; Li, Shuo


    Land use change and climate variability are two key factors impacting watershed hydrology, which is strongly related to the availability of water resources and the sustainability of local ecosystems. This study assessed separate and combined hydrological impacts of land use change and climate variability in the headwater region of a typical arid inland river basin, known as the Heihe River Basin, northwest China, in the recent past (1995-2014) and near future (2015-2024), by combining two land use models (i.e., Markov chain model and Dyna-CLUE) with a hydrological model (i.e., SWAT). The potential impacts in the near future were explored using projected land use patterns and hypothetical climate scenarios established on the basis of analyzing long-term climatic observations. Land use changes in the recent past are dominated by the expansion of grassland and a decrease in farmland; meanwhile the climate develops with a wetting and warming trend. Land use changes in this period induce slight reductions in surface runoff, groundwater discharge and streamflow whereas climate changes produce pronounced increases in them. The joint hydrological impacts are similar to those solely induced by climate changes. Spatially, both the effects of land use change and climate variability vary with the sub-basin. The influences of land use changes are more identifiable in some sub-basins, compared with the basin-wide impacts. In the near future, climate changes tend to affect the hydrological regimes much more prominently than land use changes, leading to significant increases in all hydrological components. Nevertheless, the role of land use change should not be overlooked, especially if the climate becomes drier in the future, as in this case it may magnify the hydrological responses.

  3. Hydrological Impacts of Land Use Change and Climate Variability in the Headwater Region of the Heihe River Basin, Northwest China.

    Directory of Open Access Journals (Sweden)

    Ling Zhang

    Full Text Available Land use change and climate variability are two key factors impacting watershed hydrology, which is strongly related to the availability of water resources and the sustainability of local ecosystems. This study assessed separate and combined hydrological impacts of land use change and climate variability in the headwater region of a typical arid inland river basin, known as the Heihe River Basin, northwest China, in the recent past (1995-2014 and near future (2015-2024, by combining two land use models (i.e., Markov chain model and Dyna-CLUE with a hydrological model (i.e., SWAT. The potential impacts in the near future were explored using projected land use patterns and hypothetical climate scenarios established on the basis of analyzing long-term climatic observations. Land use changes in the recent past are dominated by the expansion of grassland and a decrease in farmland; meanwhile the climate develops with a wetting and warming trend. Land use changes in this period induce slight reductions in surface runoff, groundwater discharge and streamflow whereas climate changes produce pronounced increases in them. The joint hydrological impacts are similar to those solely induced by climate changes. Spatially, both the effects of land use change and climate variability vary with the sub-basin. The influences of land use changes are more identifiable in some sub-basins, compared with the basin-wide impacts. In the near future, climate changes tend to affect the hydrological regimes much more prominently than land use changes, leading to significant increases in all hydrological components. Nevertheless, the role of land use change should not be overlooked, especially if the climate becomes drier in the future, as in this case it may magnify the hydrological responses.

  4. Measuring structural-functional correspondence: spatial variability of specialised brain regions after macro-anatomical alignment. (United States)

    Frost, Martin A; Goebel, Rainer


    The central question of the relationship between structure and function in the human brain is still not well understood. In order to investigate this fundamental relationship we create functional probabilistic maps from a large set of mapping experiments and compare the location of functionally localised regions across subjects using different whole-brain alignment schemes. To avoid the major problems associated with meta-analysis approaches, all subjects are scanned using the same paradigms, the same scanner and the same analysis pipeline. We show that an advanced, curvature driven cortex based alignment (CBA) scheme largely removes macro-anatomical variability across subjects. Remaining variability in the observed spatial location of functional regions, thus, reflects the "true" functional variability, i.e. the quantified variability is a good estimator of the underlying structural-functional correspondence. After localising 13 widely studied functional areas, we found a large variability in the degree to which functional areas respect macro-anatomical boundaries across the cortex. Some areas, such as the frontal eye fields (FEF) are strongly bound to a macro-anatomical location. Fusiform face area (FFA) on the other hand, varies in its location along the length of the fusiform gyrus even though the gyri themselves are well aligned across subjects. Language areas were found to vary greatly across subjects whilst a high degree of overlap was observed in sensory and motor areas. The observed differences in functional variability for different specialised areas suggest that a more complete estimation of the structure-function relationship across the whole cortex requires further empirical studies with an expanded test battery.

  5. Regional Fat Distribution and Blood Pressure Level and Variability: The Dallas Heart Study. (United States)

    Yano, Yuichiro; Vongpatanasin, Wanpen; Ayers, Colby; Turer, Aslan; Chandra, Alvin; Carnethon, Mercedes R; Greenland, Philip; de Lemos, James A; Neeland, Ian J


    Our aim was to investigate the associations of regional fat distribution with home and office blood pressure (BP) levels and variability. Participants in the Dallas Heart Study, a multiethnic cohort, underwent 5 BP measurements on 3 occasions during 5 months (2 in home and 1 in office) and quantification of visceral adipose tissue, abdominal subcutaneous adipose tissue, and liver fat by magnetic resonance imaging, and lower body subcutaneous fat by dual x-ray absorptiometry. The relation of regional adiposity with short-term (within-visit) and long-term (overall visits) mean BP and average real variability was assessed with multivariable linear regression. We have included 2595 participants with a mean age of 44 years (54% women; 48% black), and mean body mass index was 29 kg/m(2) Mean systolic BP/diastolic BP was 127/79 mm Hg and average real variability systolic BP was 9.8 mm Hg during 3 visits. In multivariable-adjusted models, higher amount of visceral adipose tissue was associated with higher short-term (both home and office) and long-term mean systolic BP (β[SE]: 1.9[0.5], 2.7[0.5], and 2.1[0.5], respectively; all Pfat was associated with lower short-term home and long-term mean BP (β[SE]: -0.30[0.13] and -0.24[0.1], respectively; both Pfat was associated with BP levels or variability. In conclusion, excess visceral fat was associated with persistently higher short- and long-term mean BP levels and with lower long-term BP variability, whereas lower body fat was associated with lower short- and long-term mean BP. Persistently elevated BP, coupled with lower variability, may partially explain increased risk for cardiac hypertrophy and failure related to visceral adiposity.

  6. Coupled decadal variability of the North Atlantic Oscillation, regional rainfall and spring discharges in the Campania region (Southern Italy

    Directory of Open Access Journals (Sweden)

    P. De Vita


    Full Text Available Climate change is one of the issues most debated by the scientific community with a special focus to the combined effects of anthropogenic modifications of the atmosphere and the natural climatic cycles. Various scenarios have been formulated in order to forecast the global atmospheric circulation and consequently the variability of the global distribution of air temperature and rainfall. The effects of climate change have been analysed with respect to the risks of desertification, droughts and floods, remaining mainly limited to the atmospheric and surface components of the hydrologic cycle. Consequently the impact of the climate change on the recharge of regional aquifers and on the groundwater circulation is still a challenging topic especially in those areas whose aqueduct systems depend basically on springs or wells, such as the Campania region (Southern Italy.

    In order to analyse the long-term climatic variability and its influence on groundwater circulation, we analysed decadal patterns of precipitation, air temperature and spring discharges in the Campania region (Southern Italy, coupled with the North Atlantic Oscillation (NAO.

    The time series of precipitation and air temperature were gathered over 90 yr, in the period from 1921 to 2010, choosing 18 rain gauges and 9 air temperature stations among those with the most continuous functioning as well as arranged in a homogeneous spatial distribution. Moreover, for the same period, we gathered the time series of the winter NAO index (December to March mean and of the discharges of the Sanità spring, belonging to an extended carbonate aquifer (Cervialto Mount located in the central-eastern area of the Campania region, as well as of two other shorter time series of spring discharges. The hydrogeological features of this aquifer, its relevance due to the feeding of an important regional aqueduct system, as well as the unique availability of a long-lasting time series of

  7. Regional-scale climate-variability synchrony of cholera epidemics in West Africa

    Directory of Open Access Journals (Sweden)

    Petit Michel


    Full Text Available Abstract Background The relationship between cholera and climate was explored in Africa, the continent with the most reported cases, by analyzing monthly 20-year cholera time series for five coastal adjoining West African countries: Côte d'Ivoire, Ghana, Togo, Benin and Nigeria. Methods We used wavelet analyses and derived methods because these are useful mathematical tools to provide information on the evolution of the periodic component over time and allow quantification of non-stationary associations between time series. Results The temporal variability of cholera incidence exhibits an interannual component, and a significant synchrony in cholera epidemics is highlighted at the end of the 1980's. This observed synchrony across countries, even if transient through time, is also coherent with both the local variability of rainfall and the global climate variability quantified by the Indian Oscillation Index. Conclusion Results of this study suggest that large and regional scale climate variability influence both the temporal dynamics and the spatial synchrony of cholera epidemics in human populations in the Gulf of Guinea, as has been described for two other tropical regions of the world, western South America and Bangladesh.

  8. Characterization of CagA variable region of Helicobacter pylori isolates from Chinese patients

    Institute of Scientific and Technical Information of China (English)

    Yong-Liang Zhu; Shu Zheng; Qin Du; Ke-Da Qian; Ping-Chu Fang


    AIM: To characterize the CagA variable region of Helicobacter pylori isolates from Chinese patients.METHODS: DNA fragments in CagA variable region were amplified and sequenced respectively from genomic DNA of 19 isolates from patients with gastric cancer and 20isolates from patients with chronic gastritis. The tendency of phosphorylation in tyrosine(s) of CagA proteins was evaluated subsequently by phosphorylation assay in vivo and in vitro respectively.RESULTS: About 97.44% (38/39) H pylori isolates possessed CagA gene. CagA+ strains contained 2-4tandem five-amino-acid motifs EPIYA but only one EPIYA had repeated sequence in CagA variable region in different isolates. There was no significant difference between the number of EPIYA motifs in H pylori from patients with different diseases. However, only tyrosine site in EPIYA within repeated sequence could be phosphorylated by AGS cells in vivo although all tyrosine sites in EPIYA could be phosphorylated in vitro.CONCLUSION: CagA in Chinese has no functional difference in perturbing cellular signal pathway among different H pylori isolates.

  9. Epigenetic regulation of individual modules of the immunoglobulin heavy chain locus 3’ regulatory region (3’ RR

    Directory of Open Access Journals (Sweden)

    Barbara K Birshtein


    Full Text Available The Igh locus undergoes an amazing array of DNA rearrangements and modifications during B cell development. During early stages, the variable region gene is constructed from constituent variable (V, diversity (D and joining (J segments (VDJ joining. B cells that successfully express an antibody can be activated, leading to somatic hypermutation (SHM focused on the variable region, and class switch recombination (CSR, which substitutes downstream constant region genes for the originally used Cμ constant region gene. Many investigators, ourselves included, have sought to understand how these processes specifically target the Igh locus and avoid other loci and potential deleterious consequences of malignant transformation. Our laboratory has concentrated on a complex regulatory region (RR that is located downstream of Cα, the most 3’ of the Igh constant region genes. The ~40 kb 3’ RR, which is predicted to serve as a downstream major regulator of the Igh locus, contains two distinct segments: an ~28 kb region of four enhancers and an adjacent ~12 kb region containing multiple CTCF and Pax5 binding sites. Analysis of targeted mutations in mice by a number of investigators has concluded that the entire 3’ RR enhancer region is essential for SHM and CSR (but not for VDJ joining and for high levels of expression of multiple isotypes. The CTCF/Pax5 binding region is a candidate for influencing VDJ joining early in B cell development and serving as a potential insulator of the Igh locus. Components of the 3’ RR are subject to a variety of epigenetic changes during B cell development, i.e., DNAse I hypersensitivity, histone modifications and DNA methylation, in association with transcription factor binding. We propose that these changes provide a foundation by which regulatory elements in modules of the 3’ RR function by interacting with each other and with target sequences of the Igh locus.

  10. CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data

    Directory of Open Access Journals (Sweden)

    Rajashekara Gireesh


    Full Text Available Abstract Background Comparative genomic hybridization can rapidly identify chromosomal regions that vary between organisms and tissues. This technique has been applied to detecting differences between normal and cancerous tissues in eukaryotes as well as genomic variability in microbial strains and species. The density of oligonucleotide probes available on current microarray platforms is particularly well-suited for comparisons of organisms with smaller genomes like bacteria and yeast where an entire genome can be assayed on a single microarray with high resolution. Available methods for analyzing these experiments typically confine analyses to data from pre-defined annotated genome features, such as entire genes. Many of these methods are ill suited for datasets with the number of measurements typical of high-density microarrays. Results We present an algorithm for analyzing microarray hybridization data to aid identification of regions that vary between an unsequenced genome and a sequenced reference genome. The program, CGHScan, uses an iterative random walk approach integrating multi-layered significance testing to detect these regions from comparative genomic hybridization data. The algorithm tolerates a high level of noise in measurements of individual probe intensities and is relatively insensitive to the choice of method for normalizing probe intensity values and identifying probes that differ between samples. When applied to comparative genomic hybridization data from a published experiment, CGHScan identified eight of nine known deletions in a Brucella ovis strain as compared to Brucella melitensis. The same result was obtained using two different normalization methods and two different scores to classify data for individual probes as representing conserved or variable genomic regions. The undetected region is a small (58 base pair deletion that is below the resolution of CGHScan given the array design employed in the study

  11. Quantification of β region IgA paraproteins - should we include immunochemical "heavy/light chain" measurements? Counterpoint. (United States)

    Paolini, Lucia


    Serum protein electrophoresis (SPE), serum immunofixation (s-IFE), free light chain measurement (FLC) and nephelometric measurements of total immunoglobulin in serum (IgTot) are some of the laboratory tests required for the management of plasma cell proliferative disorders. The monoclonal protein is usually visible on SPE as a spike (M-spike) in the γ region and the derived densitogram is used to quantify it relative to serum total protein concentration. IgA M-protein, however, often migrates in the β region on SPE and its quantification can be masked by other serum proteins that migrate in this region. The immunoassay Hevylite™ (heavy/light chain, HLC) seems to solve this problem: it quantifies the involved/uninvolved isotype, calculating the ratio IgAκ/IgAλ, considered indicative of clonal proliferation. However, this test seems redundant in the case of artifacts on SPE such as obvious hemolysis or lipemia, or if the IgA M-spike is clearly visible in the β region. In conclusion whereas the IgA HLC assay does not represent an alternative to SPE and s-IFE in the diagnostic patient workup, it may prove to be an alternative to SPE, s-IFE and total IgA quantification in risk stratification and evaluation of response to therapy in patients affected by MM and other monoclonal plasma proliferative disorders.

  12. Secretion of an immunoreactive single-chain variable fragment antibody against mouse interleukin 6 by Lactococcus lactis. (United States)

    Shigemori, Suguru; Ihara, Masaki; Sato, Takashi; Yamamoto, Yoshinari; Nigar, Shireen; Ogita, Tasuku; Shimosato, Takeshi


    Interleukin 6 (IL-6) is an important pathogenic factor in development of various inflammatory and autoimmune diseases and cancer. Blocking antibodies against molecules associated with IL-6/IL-6 receptor signaling are an attractive candidate for the prevention or therapy of these diseases. In this study, we developed a genetically modified strain of Lactococcus lactis secreting a single-chain variable fragment antibody against mouse IL-6 (IL6scFv). An IL6scFv-secretion vector was constructed by cloning an IL6scFv gene fragment into a lactococcal secretion plasmid and was electroporated into L. lactis NZ9000 (NZ-IL6scFv). Secretion of recombinant IL6scFv (rIL6scFv) by nisin-induced NZ-IL6scFv was confirmed by western blotting and was optimized by tuning culture conditions. We found that rIL6scFv could bind to commercial recombinant mouse IL-6. This result clearly demonstrated the immunoreactivity of rIL6scFv. This is the first study to engineer a genetically modified strain of lactic acid bacteria (gmLAB) that produces a functional anti-cytokine scFv. Numerous previous studies suggested that mucosal delivery of biomedical proteins using gmLAB is an effective and low-cost way to treat various disorders. Therefore, NZ-IL6scFv may be an attractive tool for the research and development of new IL-6 targeting agents for various inflammatory and autoimmune diseases as well as for cancer.

  13. Expression, characterization, and evaluation of a RANK-binding single chain fraction variable: an osteoclast targeting drug delivery strategy. (United States)

    Newa, Madhuri; Lam, Michael; Bhandari, Krishna Hari; Xu, Biwen; Doschak, Michael R


    A single chain Fraction variable (scFv) employs antibody-like target recognition specificity. Osteoclasts, responsible for bone resorption, express Receptor Activator of Nuclear factor Kappa B (RANK) receptors. This study aimed to express, characterize, and evaluate scFv against RANK receptors that may serve as a platform to target osteoclasts. Using phage display technology, scFv against RANK receptor was expressed and characterized by DNA sequencing, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), matrix-assisted laser desorption-ionization time-of-flight (MALDI TOF), enzyme-linked immunosorbent assay (ELISA), Western blot, and immunocytochemistry. The potential for cytotoxicity was evaluated using an MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide) assay, and its cross reactivity was evaluated using ELISA. Osteoclast-like cells were generated from RAW 264.7 cells, and the osteoclast targeting ability of scFv was evaluated using immunocytochemistry. ScFv's antiresorptive efficacy was studied using a tartrate-resistant acid phosphatase (TRAP) assay and resorption assay. Anti-RANK scFv was successfully expressed and characterized. No cross reactivity with other tumor necrosis factor receptor (TNFR) members and no cytotoxic effect on a non-RANK bearing cell line were observed. It showed specificity toward a RANK receptor and an inhibitory effect on osteoclast activity. With the increase in development trends for biologics as therapeutics and growing knowledge on the importance of osteoclast targeted therapy, this study may provide a drug delivery strategy to target osteoclasts, thereby leading to a promising therapy for resorptive bone diseases.

  14. Development of single chain variable fragment (scFv) antibodies against surface proteins of 'Ca. Liberibacter asiaticus'. (United States)

    Yuan, Qing; Jordan, Ramon; Brlansky, Ronald H; Minenkova, Olga; Hartung, John


    'Candidatus Liberibacter asiaticus' is the causal agent of citrus huanglongbing, the most serious disease of citrus worldwide. We have developed and applied immunization and affinity screening methods to develop a primary library of recombinant single chain variable fragment (scFv) antibodies in an M13 vector, pKM19. The antibody population is enriched for antibodies that bind antigens of 'Ca. Liberibacter asiaticus'. The primary library has more than 10(7) unique antibodies and the genes that encode them. We have screened this library for antibodies that bind to specifically-chosen proteins that are present on the surface of 'Ca. Liberibacter asiaticus'. These proteins were used as targets for affinity-based selection of scFvs that bind to the major outer membrane protein, OmpA; the polysaccharide capsule protein KpsF; a protein component of the type IV pilus (CapF); and, two flagellar proteins FlhA and FlgI. These scFvs have been used in ELISA and dot blot assays against purified protein antigens and 'Ca. Liberibacter asiaticus' infected plant extracts. We have also recloned many of these scFvs into a plasmid expression vector designed for the production of scFvs. Screening of these scFvs was more efficient when phage-bound, rather than soluble scFvs, were used. We have demonstrated a technology to produce antibodies at will and against any protein target encoded by 'Ca. Liberibacter asiaticus'. Applications could include advanced diagnostic methods for huanglongbing and the development of immune labeling reagents for in planta applications.

  15. Expression and characterization of a single-chain variable fragment against human LOX-1 in Escherichia coli and Brevibacillus choshinensis. (United States)

    Hu, Wei; Xiang, Jun-Yan; Kong, Ping; Liu, Ling; Xie, Qiuhong; Xiang, Hongyu


    The single-chain variable fragment (scFv) against lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a promising molecule for its potential use in the diagnosis and immunotherapy of atherosclerosis. Producing this scFv in several milligram amounts could be the starting point for further engineering and application of the scFv. In this study, the abundant expression of the anti-LOX-1 scFv was attempted using Escherichia coli (E. coli) and Brevibacillus choshinensis (B. choshinensis). The scFv had limited soluble yield in E. coli, but it was efficiently secreted by B. choshinensis. The optimized fermentation was determined using the Plackett-Burman screening design and the response surface methodology (RSM), under which the yield reached up to 1.5 g/L in a 5-L fermentor. Moreover, the properties of the scFvs obtained from the two expression systems were different. The antigen affinity, transition temperature and particle diameter size is 1.01E-07 M, 55.2 ± 0.3°C and 9.388 nm for the scFv expressed by B. choshinensis and 4.53E-07 M, 52.5 ± 0.3°C and 13.54 nm for the scFv expressed by E. coli. This study established an efficient scale-up production methodology for the anti-LOX-1 scFv, which will boost its use in LOX-1-based therapy.

  16. Cloning and expression of an anti-LDL(-) single-chain variable fragment, and its inhibitory effect on experimental atherosclerosis. (United States)

    Kazuma, Soraya M; Cavalcante, Marcela F; Telles, Andréia E R; Maranhão, Andrea Queiroz; Abdalla, Dulcineia S P


    The in vivo modified forms of low-density lipoprotein (LDL) are important for the formation of foam cells and as mediators of the immuno-inflammatory process involved in the progression of atherosclerosis. Electronegative LDL, LDL(-), is a LDL subfraction with pro-inflammatory properties that is present in human blood. To investigate possible atheroprotective effects, an anti-LDL(-) single-chain variable fragment (scFv) was expressed in the methylotrophic yeast Pichia pastoris and its activity was evaluated in vitro against macrophages and in experimental atherosclerosis in Ldlr(-/-) mice. The recombinant 2C7 scFv was produced in a yield of 9.5 mg of protein/L. The specificity and affinity of purified 2C7 scFv against LDL(-) was confirmed by ELISA. To assess the activity of 2C7 scFv on foam cell formation, RAW 264.7 macrophages were exposed to LDL(-) in the presence or absence of 2C7 scFv. The 2C7 scFv inhibited the uptake of LDL(-) by macrophages in a dose-dependent manner, and internalization of LDL(-) by these cells was found to be mediated by the CD36 and CD14 receptor. In addition, compared with untreated cells, lipid accumulation in macrophages was decreased, and the expression of Cd36, Tlr-4 and Cox-2 was downregulated in macrophages treated with 2C7 scFv. Importantly, compared with untreated mice, the treatment of Ldlr(-/-) mice with 2C7 scFv decreased the atherosclerotic lesion area at the aortic sinus. In conclusion, our data show that 2C7 scFv inhibits foam cell formation and atherosclerotic plaque development by modulating the expression of genes relevant to atherogenesis. These results encourage further use of this antibody fragment in the development of new therapeutic strategies that neutralize the pro-atherogenic effects of LDL(-).

  17. A conjugate of an anti-midkine single-chain variable fragment to doxorubicin inhibits tumor growth

    Directory of Open Access Journals (Sweden)

    Shuli Zhao


    Full Text Available Doxorubicin (DOX was conjugated to a single-chain variable fragment (scFv against human midkine (MK, and the conjugate (scFv-DOX was used to target the chemotherapeutic agent to a mouse solid tumor model in which the tumor cells expressed high levels of human MK. The His-tagged recombinant scFv was expressed in bacteria, purified by metal affinity chromatography, and then conjugated to DOX using oxidative dextran (Dex as a linker. The molecular formula of this immunoconjugate was scFv(Dex1.3(DOX20. In vitro apoptosis assays showed that the scFv-DOX conjugate was more cytotoxic against MK-transfected human adenocarcinoma cells (BGC823-MK than untransfected cells (55.3 ± 2.4 vs 22.4 ± 3.8% for three independent experiments. Nude mice bearing BGC823-MK solid tumors received scFv-DOX or equivalent doses of scFv + DOX for 2 weeks and tumor growth was more effectively inhibited by the scFv-DOX conjugate than by scFv + DOX (51.83% inhibition vs 40.81%. Histological analysis of the tumor tissues revealed that the highest levels of DOX accumulated in tumors from mice treated with scFv-DOX and this resulted in more extensive tumor cell death than in animals treated with the equivalent dose of scFv + DOX. These results show that the scFv-DOX conjugate effectively inhibited tumor growth in vivo and suggest that antigen-specific scFv may be competent drug-carriers.

  18. Generation and transfer of internal variability in a regional climate model

    Directory of Open Access Journals (Sweden)

    Thorsten Simon


    Full Text Available There is a strong need for tools allowing the comparison between the performance of a regional climate model (RCM and the corresponding model providing lateral boundary conditions (LBC for the RCM, which is a global general circulation model (GCM in most cases. A method is presented to investigate the temporal scales on which a RCM is able to generate internal variability on its own and on which variability is copied from the driving model. This is implemented by a cross-spectral analysis between the RCM output and a bi-linearly interpolated version of the driving model, leading to an estimate of the coherence spectrum. Applying the aforementioned technique to surface temperature and temperature and specific humidity at 850 hPa from the RCM COSMO-CLM East Asia with a horizontal resolution of 50 km and its driving model ECHAM5, it was found that features in the spatial distribution of coherence are related to atmospheric dynamics in East Asia, e.g. monsoons and inter-tropical convergence zone (ITCZ. A further application to a double-nesting approach, where COSMO-CLM East Asia is the driving model for two domains – namely the Haihe catchment and the Poyang catchment – each with a horizontal resolution of 7 km, shows that the frequencies on which internal variability is generated by the driven model are much higher compared to the first nesting step. Concluding RCMs can produce a considerable variability on the respective temporal scales. This implies that a dynamical downscaling with a re-analysis as LBC is conceptually different to a regional re-analysis, i.e. data assimilation on the regional scale.

  19. Basal respiration - a proxy to understand spatial variability of soil CO2 emissions in urban regions (United States)

    Vasenev, Viacheslav; Stoorvogel, Jetse; Ananyeva, Nadezhda; Ivashchenko, Kristina; Vizirskaya, Marya; Valentini, Riccardo


    Soil respiration (Rs) is an important terrestrial CO2 efflux and received significant attention at different scale levels. However, the sampling density is limited and global Rs databases are biased towards natural ecosystems and towards north America and Europe. This limits our understanding of the spatial variability of Rs. The methodological constraints of direct Rs measurements in the field limit the number of observations. As an alternative approach to approximate the spatial variability of Rs, we used basal respiration (BR) as an indirect measurement. First, the direct Rs and indirect BR measurements were compared at a 10 km2 test area in Moscow city, which included adjacent forests, croplands and urban lawn plots. Rs was monitored by in situ chamber approach with an IR Li-820 gas analyzer at 50 points during the growing season (June-October 2013, 9 time repetitions per point). In the same area, 32 locations were sampled and BR was measured under controlled conditions. Rs was affected by anthropogenic disturbance with the highest values in urban lawns. BR was mainly controlled by soil organic carbon (SOC) with maximum rates in the forested area. Total variability reported by direct observations was 10% higher, than one for BR, although the spatial variability captured by both approaches was similar confirmed by significant correlation between variance coefficients (CV) of the values. This shows that BR is a relevant proxy to analyze the spatial variability of Rs. Subsequently, the sampling area was expanded to the Moscow region for which respiration was mapped using digital soil mapping techniques and BR as a proxy for Rs. Although the absolute levels of respiration remained uncertain, the spatial patterns of BR are likely to correspond well with Rs patterns. Land use largely determined the spatial heterogeneity of soil respiration. Most variation occurred in the urban areas. BR is a relevant and straightforward proxy to understand patterns of Rs especially


    Energy Technology Data Exchange (ETDEWEB)

    Wolk, Scott J.; Günther, H. Moritz; Poppenhaeger, Katja; Forbrich, J. [Harvard–Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Cody, A. M. [NASA Ames Research Center, M/S 244-5 Moffett Field, CA 94035 (United States); Rebull, L. M.; Stauffer, J. R. [Spitzer Science Center/Caltech, 1200 E. California Blvd., Pasadena, CA 91125 (United States); Gutermuth, R. A. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Hillenbrand, L. A. [Department of Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Plavchan, P. [Department of Physics Astronomy and Materials Science, Missouri State University, Springfield, MO 65897 (United States); Covey, K. R. [Department of Physics and Astronomy, Western Washington Univ., Bellingham, WA 98225-9164 (United States); Song, Inseok, E-mail: [Physics and Astronomy Department, University of Georgia, Athens, GA 30602-2451 (United States)


    We present an IR-monitoring survey with the Spitzer Space Telescope of the star-forming region GGD 12-15. More than 1000 objects were monitored, including about 350 objects within the central 5′, which is found to be especially dense in cluster members. The monitoring took place over 38 days and is part of the Young Stellar Object VARiability project. The region was also the subject of a contemporaneous 67 ks Chandra observation. The field includes 119 previously identified pre-main sequence star candidates. X-rays are detected from 164 objects, 90 of which are identified with cluster members. Overall, we find that about half the objects in the central 5′ are young stellar objects (YSOs) based on a combination of their spectral energy distribution, IR variability, and X-ray emission. Most of the stars with IR excess relative to a photosphere show large amplitude (>0.1 mag) mid-infrared (mid-IR) variability. There are 39 periodic sources, and all but one is found to be a cluster member. Almost half of the periodic sources do not show IR excesses. Overall, more than 85% of the Class I, flat spectrum, and Class II sources are found to vary. The amplitude of the variability is larger in more embedded YSOs. Most of the Class I/II objects exhibit redder colors in a fainter state, which is compatible with time-variable extinction. A few become bluer when fainter, which can be explained with significant changes in the structure of the inner disk. A search for changes in the IR due to X-ray events is carried out, but the low number of flares prevented an analysis of the direct impact of X-ray flares on the IR light curves. However, we find that X-ray detected Class II sources have longer timescales for change in the MIR than a similar set of non-X-ray detected Class IIs.

  1. Specific amplification by PCR of rearranged genomic variable regions of immunoglobulin genes from mouse hybridoma cells. (United States)

    Berdoz, J; Monath, T P; Kraehenbuhl, J P


    We have designed a novel strategy for the isolation of the rearranged genomic fragments encoding the L-VH-D-JH and L-V kappa/lambda-J kappa/lambda regions of mouse immunoglobulin genes. This strategy is based on the PCR amplification of genomic DNA from mouse hybridomas using multiple specific primers chosen in the 5'-untranslated region and in the intron downstream of the rearranged JH/J kappa/lambda sequences. Variable regions with intact coding sequences, including full-length leader peptides (L) can be obtained without previous DNA sequencing. Our strategy is based on a genomic template that produces fragments that do not need to be adapted for recombinant antibody expression, thus facilitating the generation of chimeric and isotype-switched immunoglobulins.

  2. Circulation and its seasonal variability in region around the Kerguelen Plateau

    Institute of Scientific and Technical Information of China (English)

    Shi Jiuxin(史久新); Le Kentang(乐肯堂); Byung Ho Choi


    A coupled ice-ocean isopycnal numerical model of the Southern Ocean is established to study the circulation and its seasonal variability in the region around the Kerguelen Plateau. An analysis of the simulated results shows significant stripe-like structure and non-zonal feature of the Antarctic Circumpolar Current (ACC) in this region. ACC begins to bifurcate and to turn its direction before meeting the plateau. The southernmost branch of ACC is near to the Antarctic coast and displays its strong interaction with the westward Antarctic Slope Current. The northern branch of ACC has a tendency of annual variations while the southern one varies in a semiannual cycle. The variation phases of both branches are coincident with that of the wind stress in this region.

  3. Site-directed Mutagenesis Reveals Regions Implicated in the Stability and Fiber Formation of Human λ3r Light Chains* (United States)

    Villalba, Miryam I.; Canul-Tec, Juan C.; Luna-Martínez, Oscar D.; Sánchez-Alcalá, Rosalba; Olamendi-Portugal, Timoteo; Rudiño-Piñera, Enrique; Rojas, Sonia; Sánchez-López, Rosana; Fernández-Velasco, Daniel A.; Becerril, Baltazar


    Light chain amyloidosis (AL) is a disease that affects vital organs by the fibrillar aggregation of monoclonal light chains. λ3r germ line is significantly implicated in this disease. In this work, we contrasted the thermodynamic stability and aggregation propensity of 3mJL2 (nonamyloidogenic) and 3rJL2 (amyloidogenic) λ3 germ lines. Because of an inherent limitation (extremely low expression), Cys at position 34 of the 3r germ line was replaced by Tyr reaching a good expression yield. A second substitution (W91A) was introduced in 3r to obtain a better template to incorporate additional mutations. Although the single mutant (C34Y) was not fibrillogenic, the second mutation located at CDR3 (W91A) induced fibrillogenesis. We propose, for the first time, that CDR3 (position 91) affects the stability and fiber formation of human λ3r light chains. Using the double mutant (3rJL2/YA) as template, other variants were constructed to evaluate the importance of those substitutions into the stability and aggregation propensity of λ3 light chains. A change in position 7 (P7D) boosted 3rJL2/YA fibrillogenic properties. Modification of position 48 (I48M) partially reverted 3rJL2/YA fibril aggregation. Finally, changes at positions 8 (P8S) or 40 (P40S) completely reverted fibril formation. These results confirm the influential roles of N-terminal region (positions 7 and 8) and the loop 40–60 (positions 40 and 48) on AL. X-ray crystallography revealed that the three-dimensional topology of the single and double λ3r mutants was not significantly altered. This mutagenic approach helped to identify key regions implicated in λ3 AL. PMID:25505244

  4. Temporal Structures of the North Atlantic Oscillation and Its Impact on the Regional Climate Variability

    Institute of Scientific and Technical Information of China (English)


    In this study, the temporal structure of the variation of North Atlantic Oscillation (NAO) and its impact on regional climate variability are analyzed using various datasets. The results show that blocking formations in the Atlantic region are sensitive to the phase of the NAO. Sixty-seven percent more winter blocking days are observed during the negative phase compared to the positive phase of the NAO. The average length of blocking during the negative phase is about 11 days, which is nearly twice as long as the 6-day length observed during the positive phase of the NAO. The NAO-related differences in blocking frequency and persistence are associated with changes in the distribution of the surface air temperature anomaly, which, to a large extent, is determined by the phase of the NAO. The distribution of regional cloud amount is also sensitive to the phase of the NAO. For the negative phase, the cloud amounts are significant, positive anomalies in the convective zone in the Tropics and much less cloudiness in the mid latitudes. But for the positive phase of the NAO, the cloud amount is much higher in the mid-latitude storm track region. In the whole Atlantic region, the cloud amount shows a decrease with the increase of surface air temperature. These results suggest that there may be a negative feedback between the cloud amount and the surface air temperature in the Atlantic region.

  5. Impacts of seasonal and regional variability in biogenic VOC emissions on surface ozone in the Pearl River Delta region, China

    Energy Technology Data Exchange (ETDEWEB)

    Situ, S.; Guenther, Alex B.; Wang, X. J.; Jiang, X.; Turnipseed, A.; Wu, Z.; Bai, J.; Wang, X.


    In this study, the BVOC emissions in November 2010 over the Pearl River Delta (PRD) region in southern China have been estimated by the latest version of a Biogenic Volatile Organic Compound (BVOC) emission model (MEGAN v2.1). The evaluation of MEGAN performance at a representative forest site within this region indicates MEGAN can estimate BVOC emissions reasonably well in this region except overestimating isoprene emission in autumn for reasons that are discussed in this manuscript. Along with the output from MEGAN, the Weather Research and Forecasting model with chemistry (WRF-Chem) is used to estimate the impacts of BVOC emissions on surface ozone in the PRD region. The results show BVOC emissions increase the daytime ozone peak by *3 ppb on average, and the max hourly impacts of BVOC emissions on the daytime ozone peak is 24.8 ppb. Surface ozone mixing ratios in the central area of Guangzhou- Foshan and the western Jiangmen are most sensitive to BVOC emissions BVOCs from outside and central PRD influence the central area of Guangzhou-Foshan and the western Jiangmen significantly while BVOCs from rural PRD mainly influence the western Jiangmen. The impacts of BVOC emissions on surface ozone differ in different PRD cities, and the impact varies in different seasons. Foshan and Jiangmen being most affected in autumn, result in 6.0 ppb and 5.5 ppb increases in surface ozone concentrations, while Guangzhou and Huizhou become more affected in summer. Three additional experiments concerning the sensitivity of surface ozone to MEGAN input variables show that surface ozone is more sensitive to landcover change, followed by emission factors and meteorology.

  6. Impacts of seasonal and regional variability in biogenic VOC emissions on surface ozone in the Pearl River Delta region, China

    Directory of Open Access Journals (Sweden)

    S. Situ


    Full Text Available In this study, the BVOC emissions in November 2010 over the Pearl River Delta (PRD region in southern China have been estimated by the latest version of a Biogenic Volatile Organic Compound (BVOC emission model (MEGAN v2.1. The evaluation of MEGAN performance at a representative forest site within this region indicates MEGAN can estimate BVOC emissions reasonably well in this region except overestimating isoprene emission in autumn for reasons that are discussed in this manuscript. Along with the output from MEGAN, the Weather Research and Forecasting model with chemistry (WRF-Chem is used to estimate the impacts of BVOC emissions on surface ozone in the PRD region. The results show BVOC emissions increase the daytime ozone peak by ~3 ppb on average, and the max hourly impacts of BVOC emissions on the daytime ozone peak is 24.8 ppb. Surface ozone mixing ratios in the central area of Guangzhou-Foshan and the western Jiangmen are most sensitive to BVOC emissions BVOCs from outside and central PRD influence the central area of Guangzhou-Foshan and the western Jiangmen significantly while BVOCs from rural PRD mainly influence the western Jiangmen. The impacts of BVOC emissions on surface ozone differ in different PRD cities, and the impact varies in different seasons. Foshan and Jiangmen being most affected in autumn, result in 6.0 ppb and 5.5 ppb increases in surface ozone concentrations, while Guangzhou and Huizhou become more affected in summer. Three additional experiments concerning the sensitivity of surface ozone to MEGAN input variables show that surface ozone is more sensitive to landcover change, followed by emission factors and meteorology.

  7. Streamflow estimation using WRF-Hydro with dynamically downscaled climate variables over southern tropical Indian region (United States)

    Davis, S.; Sudheer, K. P.; Gunthe, S. S.


    Indian summer monsoon rainfall (ISMR; June to September), which constitutes around 80% of India's annual rainfall, has shown an increasing trend in intensity and frequency of extreme events (Goswami et al., 2006). It is a widely recognized fact that the increasing temperature in association with anthropogenic activities can affect the hydrological cycle, which leads to extreme events. In addition a shift in extremes of the spatial pattern of ISMR has recently been observed (Ghosh et al., 2011). Such changes in rainfall on temporal and spatial scale can further affect the stream flow over a given region subsequently making water resource management a difficult task (Mondal and Mujumdar, 2015). The hydrological models used for the stream flow estimation are dependent on various climate variables as input data. These climate variables could be obtained through either observational networks or climate model outputs. Due to the scarcity of the observational data over the Indian region and the coarse resolution of global climate model output, which is used as input to hydrologic models, large uncertainties are introduced in stream flow output (Overgaard et al., 2007). In the present study we have used the Weather Research and Forecasting (WRF) model (Skamarock et al. 2008) to downscale the essential climate variables (surface temperature, precipitation, relative humidity, etc.) as an input for its coupled hydrological extension, WRF Hydro (NCAR user's guide). We will present the results obtained from the WRF-hydro simulation to estimate the stream flow over the Thamirabarani river basin in Southern Tropical Indian region. Preliminary simulations using WRF to estimate the precipitation showed the reasonable quantitative agreement with observed values. An attempt will be made to demonstrate how these results can further be used for developing flood-forecasting techniques and for local regional water resource management.

  8. Use of variability modes to evaluate AR4 climate models over the Euro-Atlantic region

    Energy Technology Data Exchange (ETDEWEB)

    Casado, M.J.; Pastor, M.A. [Agencia Estatal de Meteorologia (AEMET), Madrid (Spain)


    This paper analyzes the ability of the multi-model simulations from the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC) to simulate the main leading modes of variability over the Euro-Atlantic region in winter: the North-Atlantic Oscillation (NAO), the Scandinavian mode (SCAND), the East/Atlantic Oscillation (EA) and the East Atlantic/Western Russia mode (EA/WR). These modes of variability have been evaluated both spatially, by analyzing the intensity and location of their anomaly centres, as well as temporally, by focusing on the probability density functions and e-folding time scales. The choice of variability modes as a tool for climate model assessment can be justified by the fact that modes of variability determine local climatic conditions and their likely change may have important implications for future climate changes. It is found that all the models considered are able to simulate reasonably well these four variability modes, the SCAND being the mode which is best spatially simulated. From a temporal point of view the NAO and SCAND modes are the best simulated. UKMO-HadGEM1 and CGCM3.1(T63) are the models best at reproducing spatial characteristics, whereas CCSM3 and CGCM3.1(T63) are the best ones with regard to the temporal features. GISS-AOM is the model showing the worst performance, in terms of both spatial and temporal features. These results may bring new insight into the selection and use of specific models to simulate Euro-Atlantic climate, with some models being clearly more successful in simulating patterns of temporal and spatial variability than others. (orig.)

  9. YSOVAR: Mid-infrared Variability Among YSOs in the Star Formation Region GGD 12-15

    CERN Document Server

    Wolk, Scott J; Poppenhaeger, Katja; Cody, A M; Rebull, L M; Forbrich, J; Gutermuth, R A; Hillenbrand, L A; Plavchan, P; Stauffer, J R; Covey, K R; Song, Inseok


    We present an IR-monitoring survey with the $Spitzer$ Space Telescope of the star forming region GGD 12-15. Over 1000 objects were monitored including about 350 objects within the central 5 arcminutes which is found to be especially dense in cluster members. The monitoring took place over 38 days and is part of the Young Stellar Object VARiability (YSOVAR) project. The region was also the subject of a contemporaneous 67ks $Chandra$ observation. The field includes 119 previously identified pre-main sequence star candidates. X-rays are detected from 164 objects, 90 of which are identified with cluster members. Overall, we find that about half the objects in the central 5 arcminutes are young stellar objects based on a combination of their spectral energy distribution, IR variability and X-ray emission. Most of the stars with IR excess relative to a photosphere show large amplitude (>0.1 mag) mid-IR variability. There are 39 periodic sources, all but one of these is found to be a cluster member. Almost half of t...

  10. Interannual variability of tropical cyclone activity and regional Hadley circulation over the Northeastern Pacific (United States)

    Zhang, Gan; Wang, Zhuo


    The interannual variability of the regional Hadley circulation (HC) and tropical cyclone (TC) activity over the Northeastern Pacific (NEP) was investigated. The interannual variability of the HC in the NEP hurricane season is found dominated by a mode (M1EP) regulating the strength and meridional extent of the Intertropical Convergence Zone. M1EP has a more robust correlation with NEP TC activity than the El Niño-Southern Oscillation sea surface temperature indices. The strong correlation is attributed to the impacts of M1EP on environmental conditions. In addition, the leading mode of the Atlantic HC, which has an anticorrelation with M1EP, also strongly impacts NEP TC activity. The findings, together with Zhang and Wang (2013), highlight the role of the HC in controlling the variability of TC activity as well as the interbasin connection between the NEP and the Atlantic. The regional HC is thus recommended as a useful metric to benchmark models in simulating TC activity.

  11. YSOVAR: Mid-IR variability in the star forming region Lynds 1688

    CERN Document Server

    Günther, H M; Covey, K R; Hillenbrand, L A; Plavchan, P; Poppenhaeger, K; Rebull, L M; Stauffer, J R; Wolk, S J; Allen, L; Bayo, A; Gutermuth, R A; Hora, J L; Meng, H Y A; Morales-Calderon, M; Parks, J R; Song, Inseok


    The emission from young stellar objects (YSOs) in the mid-IR is dominated by the inner rim of their circumstellar disks. We present an IR-monitoring survey of about 800 objects in the direction of the Lynds 1688 (L1688) star forming region over four visibility windows spanning 1.6 years using the \\emph{Spitzer} space telescope in its warm mission phase. Among all lightcurves, 57 sources are cluster members identified based on their spectral-energy distribution and X-ray emission. Almost all cluster members show significant variability. The amplitude of the variability is larger in more embedded YSOs. Ten out of 57 cluster members have periodic variations in the lightcurves with periods typically between three and seven days, but even for those sources, significant variability in addition to the periodic signal can be seen. No period is stable over 1.6 years. Non-periodic lightcurves often still show a preferred timescale of variability which is longer for more embedded sources. About half of all sources exhib...

  12. Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index

    Directory of Open Access Journals (Sweden)

    Makarenkov Vladimir


    Full Text Available Abstract Background The identification of functional regions contained in a given multiple sequence alignment constitutes one of the major challenges of comparative genomics. Several studies have focused on the identification of conserved regions and motifs. However, most of existing methods ignore the relationship between the functional genomic regions and the external evidence associated with the considered group of species (e.g., carcinogenicity of Human Papilloma Virus. In the past, we have proposed a method that takes into account the prior knowledge on an external evidence (e.g., carcinogenicity or invasivity of the considered organisms and identifies genomic regions related to a specific disease. Results and conclusion We present a new algorithm for detecting genomic regions that may be associated with a disease. Two new variability functions and a bipartition optimization procedure are described. We validate and weigh our results using the Adjusted Rand Index (ARI, and thus assess to what extent the selected regions are related to carcinogenicity, invasivity, or any other species classification, given as input. The predictive power of different hit region detection functions was assessed on synthetic and real data. Our simulation results suggest that there is no a single function that provides the best results in all practical situations (e.g., monophyletic or polyphyletic evolution, and positive or negative selection, and that at least three different functions might be useful. The proposed hit region identification functions that do not benefit from the prior knowledge (i.e., carcinogenicity or invasivity of the involved organisms can provide equivalent results than the existing functions that take advantage of such a prior knowledge. Using the new algorithm, we examined the Neisseria meningitidis FrpB gene product for invasivity and immunologic activity, and human papilloma virus (HPV E6 oncoprotein for carcinogenicity, and confirmed

  13. Analysis of meteorological variables in the Australasian region using ground- and space-based GPS techniques (United States)

    Kuleshov, Yuriy; Choy, Suelynn; Fu, Erjiang Frank; Chane-Ming, Fabrice; Liou, Yuei-An; Pavelyev, Alexander G.


    Results of analysis of meteorological variables (temperature and moisture) in the Australasian region using the global positioning system (GPS) radio occultation (RO) and GPS ground-based observations verified with in situ radiosonde (RS) data are presented. The potential of using ground-based GPS observations for retrieving column integrated precipitable water vapour (PWV) over the Australian continent has been demonstrated using the Australian ground-based GPS reference stations network. Using data from the 15 ground-based GPS stations, the state of the atmosphere over Victoria during a significant weather event, the March 2010 Melbourne storm, has been investigated, and it has been shown that the GPS observations has potential for monitoring the movement of a weather front that has sharp moisture contrast. Temperature and moisture variability in the atmosphere over various climatic regions (the Indian and the Pacific Oceans, the Antarctic and Australia) has been examined using satellite-based GPS RO and in situ RS observations. Investigating recent atmospheric temperature trends over Antarctica, the time series of the collocated GPS RO and RS data were examined, and strong cooling in the lower stratosphere and warming through the troposphere over Antarctica has been identified, in agreement with outputs of climate models. With further expansion of the Global Navigation Satellite Systems (GNSS) system, it is expected that GNSS satellite- and ground-based measurements would be able to provide an order of magnitude larger amount of data which in turn could significantly advance weather forecasting services, climate monitoring and analysis in the Australasian region.

  14. Simulated impacts of afforestation in East China monsoon region as modulated by ocean variability (United States)

    Ma, Di; Notaro, Michael; Liu, Zhengyu; Chen, Guangshan; Liu, Yongqiang


    Using the National Center for Atmospheric Research Community Climate System Model Version 3.5, this paper examines the climatic effects of afforestation in the East China monsoon region with a focus on land-atmosphere interactions and the modulating influence of ocean variability. In response to afforestation, the local surface air temperature significantly decreases in summer and increases in winter. The summer cooling is attributed to enhanced evapotranspiration from increased tree cover. During winter, afforestation induces greater roughness and weaker winds over the adjacent coastal ocean, leading to diminished latent heat flux and increased sea-surface temperature (SST). The enhanced SST supports greater atmospheric water vapor, which is accompanied by anomalous wind, and transported into the East China monsoon region. The increase in atmospheric water vapor favors more cloud cover and precipitation, especially in the eastern afforestation region. Furthermore, the increase in atmospheric water vapor and cloud cover produce a greenhouse effect, raising the wintertime surface air temperature. By comparing simulations in which ocean temperature are either fixed or variable, we demonstrate that a significant hydrologic response in East China to afforestation only occurs if ocean temperatures are allowed to vary and the oceanic source of moisture to the continent is enhanced.

  15. Shannon information entropy for assessing space-time variability of rainfall and streamflow in semiarid region. (United States)

    Rodrigues da Silva, Vicente de P; Belo Filho, Adelgcio F; Rodrigues Almeida, Rafaela S; de Holanda, Romildo Morant; da Cunha Campos, João Hugo Baracuy


    The principle of maximum entropy can provide consistent basis to analyze water resources and geophysical processes in general. In this paper, we propose to assess the space-time variability of rainfall and streamflow in northeastern region of Brazil using the Shannon entropy. Mean values of marginal and relative entropies were computed for a 10-year period from 189 stations in the study area and entropy maps were then constructed for delineating annual and seasonal characteristics of rainfall and streamflow. The Mann-Kendall test was used to evaluate the long-term trend in marginal entropy as well as relative entropy for two sample stations. High degree of similarity was found between rainfall and streamflow, particularly during dry season. Both rainfall and streamflow variability can satisfactorily be obtained in terms of marginal entropy as a comprehensive measure of the regional uncertainty of these hydrological events. The Shannon entropy produced spatial patterns which led to a better understanding of rainfall and streamflow characteristics throughout the northeastern region of Brazil. The total relative entropy indicated that rainfall and streamflow carried the same information content at annual and rainy season time scales.

  16. Analysis of information on food chain in Europe and Piedmont region, Italy

    Directory of Open Access Journals (Sweden)

    Daniele Pattono


    Full Text Available Food chain information (FCI is an innovation of the new European regulation. Its purpose is to enhance the concept of food security. FCI includes specifications such as: health status, information on treatments and diseases, analytical reports on control plans, zoonoses or environmental contaminants, production performance, etc. The aim of this article is to compare the different European guidelines and analyse the situation in Piedmont in order to assess potential problems and propose solutions. European guidelines are similar one another, but they have been tailored to the epidemiological situations of each state. Except for Spain and Germany, FCI models are different for each species and the poultry sector is the most detailed. Unfortunately, Italy has not provided guidelines yet, and this has generated considerable differences. Overall, the number of FCI models with incomplete information is the largest group compared to the models not completed for each entry. The main deficiencies are related to pharmacological treatments. The health status of the farm is listed consistently regarding the compulsory eradication plans, but other national voluntary or accreditation plans are rarely mentioned. The situation is similar in other European countries. In conclusion, FCI is an effective tool if applied with consistency and reason. Only in this way the collection of data will be effective and representative of the food chain.

  17. Role of climate variability in the heatstroke death rates of Kanto region in Japan. (United States)

    Akihiko, Takaya; Morioka, Yushi; Behera, Swadhin K


    The death toll by heatstroke in Japan, especially in Kanto region, has sharply increased since 1994 together with large interannual variability. The surface air temperature and humidity observed during boreal summers of 1980-2010 were examined to understand the role of climate in the death toll. The extremely hot days, when the daily maximum temperature exceeds 35 °C, are more strongly associated with the death toll than the conventional Wet Bulb Globe Temperature index. The extremely hot days tend to be associated with El Niño/Southern Oscillation or the Indian Ocean Dipole, suggesting a potential link with tropical climate variability to the heatstroke related deaths. Also, the influence of these climate modes on the death toll has strengthened since 1994 probably related to global warming. It is possible to develop early warning systems based on seasonal climate predictions since recent climate models show excellent predictability skills for those climate modes.

  18. Detection of Natural Toxoplasma gondii Infection in Chicken in Thika Region of Kenya Using Nested Polymerase Chain Reaction



    The detection of Toxoplasma gondii in free-range chickens is a good indicator of possible risk to human beings. The aim of this study was to investigate the occurrence of T. gondii in free-range chicken using polymerase chain reaction (PCR). Brain samples from 105 free-range chickens from three administrative areas in Thika region, Kenya, were collected, DNA-extracted, and analyzed using PCR to detect presence of T. gondii. The overall prevalence of T. gondii in all the three areas was 79.0% ...

  19. Ocean Current Energy Conversion System in Wallacea Region Using Variable Speed Control Approach

    Directory of Open Access Journals (Sweden)

    Aditya Sukma Nugraha


    Full Text Available Ocean Current Energy Conversion System (OCECS is a promising green energy resource in this globe. The Thermohaline circulation data indicates that the Wallacea region has the potential of ocean current energy resources. This paper is aimed to propose research and development of OCECSs to be implemented in the Wallacea region. Firstly, four types of green energy conversion systems extracted from ocean are reviewed. Their advantages and disadvantages are discussed. Secondly, the potential of OCECS in the Wallacea region is described. Third, many types of turbines used for OCECS are reviewed and the turbine type for OCECS is selected to be implemented in the Wallacea region. Fourth, control strategy is proposed.From the work reported in this paper it is concluded that it is appropriate to implement OCECSs using axial flow water turbines in the Wallacea region, and that to maximize energy conversion variable speed control approach is selected together with control of mechanism to move the turbine vertically as well as to rotate the turbine in yaw direction. 

  20. [Spatial variability and management zone of soil major nutrients in tobacco fields in Qiannan mountainous region]. (United States)

    Wu, De-Chuan; Luo, Hong-Xiang; Song, Ze-Min; Guo, Guang-Dong; Chen, Yong-An; Li, Yu-Xiang; Jiang, Yu-Ping; Li, Zhang-Hai


    Spatial variability and management zone of soil major nutrients in tobacco fields in Qian-nan mountainous region were analyzed using geostatistics and fuzzy c-mean algorithm. Results indicated that the level of soil organic matter (OM) was moderate, and alkalytic nitrogen (AN), available phosphorus (AP) and available potassium (AK) were rich according to tobacco soil nutrient classification standards. Coefficients of variation (CV) of OM, AN, AP and AK were moderate. Contents of OM, AN, AP and AK fitted log-normal distributions. Correlation analysis showed moderate correlations between OM and AN, AP and AK. OM and AN were best described by Gaussian semivariogram models, while AP and AK were described by exponential models. The four nutrients displayed moderate spatial autocorrelation. There were significant differences among lag distances of four soil nutrients. OM, AN, AP and AK in the majority of studied regions varied at moderate to very rich levels, and deficiencies of OM, AN, AP and AK only accounted for 0.93%, 0.53%, 0.24% and 7.91% of the total studied region, respectively. Based on the results, the studied region was divided into two management zones (MZ), namely MZ1 and MZ2, accounting for 69. 8% and 30. 2% of the studied region respectively. The soil levels of OM, AN, AP and AK in MZ1 were significantly lower than those in MZ2 (P < 0.01).

  1. Spatial and Temporal Variability of Remotely Sensed Ocean Color Parameters in Coral Reef Regions (United States)

    Otis, Daniel Brooks

    The variability of water-column absorption due to colored dissolved organic matter (CDOM) and phytoplankton in coral reef regions is the focus of this study. Hydrographic and CDOM absorption measurements made on the Bahamas Banks and in Exuma Sound during the spring of 1999 and 2000 showed that values of salinity and CDOM absorption at 440nm were higher on the banks (37.18 psu, 0.06 m. -1), compared to Exuma Sound (37.04 psu, 0.03 m. -1). Spatial patternsof CDOM absorption in Exuma Sound revealed that plumes of CDOM-rich water flow into Exuma Sound from the surrounding banks. To examine absorption variability in reef regions throughout the world, a thirteen-year time series of satellite-derived estimates of water-column absorption due to CDOM and phytoplankton were created from Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate Resolution Imaging Spectroradiometer (MODIS) data. Time series data extracted adjacent to coral reef regions showed that variability in absorption depends on oceanographic conditions such as circulation patterns and winds as well as proximity to sources of light-absorbing materials that enter the water column, such as from terrestrial runoff. Waters near reef regions are generally clear, exhibiting a lower "baseline" level of CDOM absorption of approximately 0.01 m. -1 at 443nm. The main differences between regions lie in the periodsduring the year when increased levels of absorption are observed, which can be triggered by inputs of terrestrially-derived material, as in the Great Barrier Reef lagoon, or wind-driven upwelling as in the Andaman Sea and eastern Pacific Ocean near Panama. The lowest CDOM absorption levels found were approximately 0.003 m. -1 at 443nm near the islands of Palau and Yap, which are removed fromsources of colored materials. The highest absorption levels near reefs were associated with wind-driven upwelling during the northeast monsoon on the Andaman coast of Thailand where values of CDOM absorption at 443nm

  2. Intraseasonal Variability of the Indian Summer Monsoon in the Regional Climate Model COSMO-CLM (United States)

    Befort, Daniel J.; Leckebusch, Gregor C.; Cubasch, Ulrich


    The regional climate model COSMO-CLM driven by ERA-Interim reanalysis data with a spatial resolution of 55km is used to simulate observed features of the intraseasonal variability of the Indian summer monsoon (ISM) during the period 1979 until 2011. One of these features is the northward propagation of the monsoon intraseasonal oscillations. We find, that the temporal evolution of this oscillation between model and observation is in good agreement, but the strength is less well simulated. Additionally, the models capability to simulate observed dry and wet events on a weekly time scale is investigated using the standardized precipitation index. In general, the model is capable to simulate these events with a similar magnitude at the same time, but we find a higher ability for dry compared to wet events. We hypothesize this is related to differences in the atmospheric circulation during dry and wet events. Analyses show, that dry events are characterized by a cyclonic vortex over India as well as an anti-cyclonic vortex over Pakistan region in 500hPa, whereas wet events are characterized by an anti-cyclonic vortex over India, only. It is found that COSMO-CLM has a higher ability to simulate the observed anomalous circulation over Pakistan region compared to observed anomalous circulation patterns over India. Overall, this study shows that the current configuration of COSMO-CLM is able to simulate key features of the intraseasonal variability of the Indian summer monsoon. Thus, under consideration of its limitations, COSMO-CLM is suitable to investigate possible changes of the intraseasonal variability of ISM under changed climate conditions.

  3. Source, variability, and transformation of nitrate in a regional karst aquifer: Edwards aquifer, central Texas. (United States)

    Musgrove, M; Opsahl, S P; Mahler, B J; Herrington, C; Sample, T L; Banta, J R


    Many karst regions are undergoing rapid population growth and expansion of urban land accompanied by increases in wastewater generation and changing patterns of nitrate (NO3(-)) loading to surface and groundwater. We investigate variability and sources of NO3(-) in a regional karst aquifer system, the Edwards aquifer of central Texas. Samples from streams recharging the aquifer, groundwater wells, and springs were collected during 2008-12 from the Barton Springs and San Antonio segments of the Edwards aquifer and analyzed for nitrogen (N) species concentrations and NO3(-) stable isotopes (δ(15)N and δ(18)O). These data were augmented by historical data collected from 1937 to 2007. NO3(-) concentrations and discharge data indicate that short-term variability (days to months) in groundwater NO3(-) concentrations in the Barton Springs segment is controlled by occurrence of individual storms and multi-annual wet-dry cycles, whereas the lack of short-term variability in groundwater in the San Antonio segment indicates the dominance of transport along regional flow paths. In both segments, longer-term increases (years to decades) in NO3(-) concentrations cannot be attributed to hydrologic conditions; rather, isotopic ratios and land-use change indicate that septic systems and land application of treated wastewater might be the source of increased loading of NO3(-). These results highlight the vulnerability of karst aquifers to NO3(-) contamination from urban wastewater. An analysis of N-species loading in recharge and discharge for the Barton Springs segment during 2008-10 indicates an overall mass balance in total N, but recharge contains higher concentrations of organic N and lower concentrations of NO3(-) than does discharge, consistent with nitrification of organic N within the aquifer and consumption of dissolved oxygen. This study demonstrates that subaqueous nitrification of organic N in the aquifer, as opposed to in soils, might be a previously unrecognized

  4. The influence of daily meteorology on boreal fire emissions and regional trace gas variability (United States)

    Wiggins, E. B.; Veraverbeke, S.; Henderson, J. M.; Karion, A.; Miller, J. B.; Lindaas, J.; Commane, R.; Sweeney, C.; Luus, K. A.; Tosca, M. G.; Dinardo, S. J.; Wofsy, S.; Miller, C. E.; Randerson, J. T.


    Relationships between boreal wildfire emissions and day-to-day variations in meteorological variables are complex and have important implications for the sensitivity of high-latitude ecosystems to climate change. We examined the influence of environmental conditions on boreal fire emissions and fire contributions to regional trace gas variability in interior Alaska during the summer of 2013 using two types of analysis. First, we quantified the degree to which meteorological and fire weather indices explained regional variability in fire activity using four different products, including active fires, fire radiative power, burned area, and carbon emissions. Second, we combined daily emissions from the Alaskan Fire Emissions Database (AKFED) with the coupled Polar Weather Research and Forecasting/Stochastic Time-Inverted Lagrangian Transport model to estimate fire contributions to trace gas concentration measurements at the Carbon in Arctic Reservoirs Vulnerability Experiment-NOAA Global Monitoring Division (CRV) tower in interior Alaska. Tower observations during two high fire periods were used to estimate CO and CH4 emission factors. We found that vapor pressure deficit and temperature had a level of performance similar to more complex fire weather indices. Emission factors derived from CRV tower measurements were 134 ± 25 g CO per kg of combusted biomass and 7.74 ± 1.06 g CH4 per kg of combusted biomass. Predicted daily CO mole fractions from AKFED emissions were moderately correlated with CRV observations (r = 0.68) and had a high bias. The modeling system developed here allows for attribution of emission factors to individual fires and has the potential to improve our understanding of regional CO, CH4, and CO2 budgets.

  5. Long-term Radiation Budget Variability in the Northern Eurasian Region: Assessing the Interaction with Fire (United States)

    Stackhouse, P. W.; Soja, A. J.; Zhang, T.; Mikovitz, J. C.


    In terms of global change, boreal regions are particularly important, because significant warming and change are already evident and significant future warming is predicted. Mean global air temperature has increased by 0.74°C in the last century, and temperatures are predicted to increase by 1.8°C to 4°C by 2090, depending on the Inter-governmental Panel on Climate Change (IPCC) scenario. Some of the greatest temperature increases are currently found in the Northern Eurasian winter and spring, which has led to longer growing seasons, increased potential evapotranspiration and extreme fire weather [Groisman et al., 2007]. In the Siberian Sayan, winter temperatures have already exceeded a 2090 Hadley Centre scenario (HadCM3GGa1) [Soja et al., 2007]. There is evidence of climate-induced change across the circumboreal in terms of increased infestations, alterations in vegetation and increased fire regimes (area burned, fire frequency, severity and number of extreme fire seasons). In this paper, we analyzed long-term surface radiation data sets from the NASA/GEWEX (Global Energy and Water Exchanges) Surface Radiation Budget data products, CERES Surface EBAF and SYN data products and also the available surface radiation measurements in the region. First, we show that during overlap years SRB and CERES data products agree very well in terms of anomalies and we'll use this fact to evaluate 30 years of satellite based estimates of the variability of downwelling SW parameters first corresponding to locations of surface measurements and then for the region as a whole. We also show the observed variability of other SW components such as the net SW and the albedo. Next we assess the variability of the downward and LW fluxes over time and compare these to variability observed in the surface temperature and other meteorological measurements. We assess anomalies on various spatial scales. Finally, we assess the correlation of this variability in specific locations to known fire

  6. Hydrological response to changing climate conditions: Spatial streamflow variability in the boreal region (United States)

    Teutschbein, Claudia; Grabs, Thomas; Karlsen, Reinert H.; Laudon, Hjalmar; Bishop, Kevin


    It has long been recognized that streamflow-generating processes are not only dependent on climatic conditions, but also affected by physical catchment properties such as topography, geology, soils and land cover. We hypothesize that these landscape characteristics do not only lead to highly variable hydrologic behavior of rather similar catchments under the same stationary climate conditions (Karlsen et al., 2014), but that they also play a fundamental role for the sensitivity of a catchment to a changing climate (Teutschbein et al., 2015). A multi-model ensemble based on 15 regional climate models was combined with a multi-catchment approach to explore the hydrologic sensitivity of 14 partially nested and rather similar catchments in Northern Sweden to changing climate conditions and the importance of small-scale spatial variability. Current (1981-2010) and future (2061-2090) streamflow was simulated with the HBV model. As expected, projected increases in temperature and precipitation resulted in increased total available streamflow, with lower spring and summer flows, but substantially higher winter streamflow. Furthermore, significant changes in flow durations with lower chances of both high and low flows can be expected in boreal Sweden in the future. This overall trend in projected streamflow pattern changes was comparable among the analyzed catchments while the magnitude of change differed considerably. This suggests that catchments belonging to the same region can show distinctly different degrees of hydrological responses to the same external climate change signal. We reason that differences in spatially distributed physical catchment properties at smaller scales are not only of great importance for current streamflow behavior, but also play a major role as first-order control for the sensitivity of catchments to changing climate conditions. References Karlsen, R.H., T. Grabs, K. Bishop, H. Laudon, and J. Seibert (2014). Landscape controls on

  7. Observations of regional and local variability in the optical properties of maritime clouds

    Energy Technology Data Exchange (ETDEWEB)

    White, A.B. [Univ. of Colorado at Boulder/National Oceanic and Atmospheric Administration, Boulder, CO (United States); Fairall, C.W. [Environmental Technology Lab., Boulder, CO (United States)


    White and Fairall (1995) calculated the optical properties of the marine boundary layer (MBL) clouds observed during the Atlantic Stratocumulus Transition Experiment (ASTEX) and compared their results with the results obtained by Fairall et al. for the MBL clouds observed during the First International Satellite Climatology Program (ISSCP) Regional Experiment (FIRE). They found a factor of two difference in the optical depth versus liquid water relationship that applies to the clouds observed in each case. In the present study, we present evidence to support this difference. We also investigate the local variability exhibited in the ASTEX optical properties using measurements of the boundary layer aerosol concentration.

  8. Effects of initial conditions uncertainty on regional climate variability: An analysis using a low-resolution CESM ensemble (United States)

    Sriver, Ryan L.; Forest, Chris E.; Keller, Klaus


    The uncertainties surrounding the initial conditions in Earth system models can considerably influence interpretations about climate trends and variability. Here we present results from a new climate change ensemble experiment using the Community Earth System Model (CESM) to analyze the effect of internal variability on regional climate variables that are relevant for decision making. Each simulation is initialized from a unique and dynamically consistent model state sampled from a ~10,000 year fully coupled equilibrium simulation, which captures the internal unforced variability of the coupled Earth system. We find that internal variability has a sizeable contribution to the modeled ranges of temperature and precipitation. The effects increase for more localized regions. The ensemble exhibits skill in simulating key regional climate processes relevant to decision makers, such as seasonal temperature variability and extremes. The presented ensemble framework and results can provide useful resources for uncertainty quantification, integrated assessment, and climate risk management.

  9. Variability in the Water Footprint of Arable Crop Production across European Regions

    Directory of Open Access Journals (Sweden)

    Anne Gobin


    Full Text Available Crop growth and yield are affected by water use during the season: the green water footprint (WF accounts for rain water, the blue WF for irrigation and the grey WF for diluting agri-chemicals. We calibrated crop yield for FAO’s water balance model “Aquacrop” at field level. We collected weather, soil and crop inputs for 45 locations for the period 1992–2012. Calibrated model runs were conducted for wheat, barley, grain maize, oilseed rape, potato and sugar beet. The WF of cereals could be up to 20 times larger than the WF of tuber and root crops; the largest share was attributed to the green WF. The green and blue WF compared favourably with global benchmark values (R2 = 0.64–0.80; d = 0.91–0.95. The variability in the WF of arable crops across different regions in Europe is mainly due to variability in crop yield ( c v ¯ = 45% and to a lesser extent to variability in crop water use ( c v ¯ = 21%. The WF variability between countries ( c v ¯ = 14% is lower than the variability between seasons ( c v ¯ = 22% and between crops ( c v ¯ = 46%. Though modelled yields increased up to 50% under sprinkler irrigation, the water footprint still increased between 1% and 25%. Confronted with drainage and runoff, the grey WF tended to overestimate the contribution of nitrogen to the surface and groundwater. The results showed that the water footprint provides a measurable indicator that may support European water governance.

  10. Regional precipitation variability in East Asia related to climate and environmental factors during 1979-2012. (United States)

    Deng, Yinyin; Gao, Tao; Gao, Huiwang; Yao, Xiaohong; Xie, Lian


    This paper studies the inter-annual precipitation variations in different regions of East Asia from oceans to interior areas in China during 1979 - 2012. The results computed by Empirical Orthogonal Functions (EOF) demonstrate that the annual precipitation changes are mainly related to the El Niño-Southern Oscillation, East Asian summer monsoon and aerosols. We also found that the increased Sea surface temperature (SST) could explain the precipitation changes over the Northwest Pacific in the dry season (Oct. - May) and the East China Sea and the South China Sea in the rainy season (Jun. - Sep.). The precipitation changes over the ocean unexplained by SST were likely due to the water vapor transport dominated by dynamic factors. With the increased SST, the moisture transported from oceans to interior land was likely redistributed and caused the complicated regional variability of precipitation. Moreover, the impacts of aerosols on cloud and precipitation varied with different pollution levels and different seasons.

  11. Confidence Region Approach for Assessing Bioequivalence and Biosimilarity Accounting for Heterogeneity of Variability

    Directory of Open Access Journals (Sweden)

    Jianghao Li


    Full Text Available For approval of generic drugs, the FDA requires that evidence of bioequivalence in average bioequivalence in terms of drug absorption be provided through the conduct of a bioequivalence study. A test product is said to be average bioequivalent to a reference (innovative product if the 90% confidence interval of the ratio of means (after log-transformation is totally within (80%, 125%. This approach is considered a one-parameter approach, which does not account for possible heterogeneity of variability between drug products. In this paper, we study a two-parameter approach (i.e., confidence region approach for assessing bioequivalence, which can also be applied to assessing biosimilarity of biosimilar products. The proposed confidence region approach is compared with the traditional one-parameter approach both theoretically and numerically (i.e., simulation study for finite sample performance.

  12. Regional precipitation variability in East Asia related to climate and environmental factors during 1979-2012 (United States)

    Deng, Yinyin; Gao, Tao; Gao, Huiwang; Yao, Xiaohong; Xie, Lian


    This paper studies the inter-annual precipitation variations in different regions of East Asia from oceans to interior areas in China during 1979 - 2012. The results computed by Empirical Orthogonal Functions (EOF) demonstrate that the annual precipitation changes are mainly related to the El Niño-Southern Oscillation, East Asian summer monsoon and aerosols. We also found that the increased Sea surface temperature (SST) could explain the precipitation changes over the Northwest Pacific in the dry season (Oct. - May) and the East China Sea and the South China Sea in the rainy season (Jun. - Sep.). The precipitation changes over the ocean unexplained by SST were likely due to the water vapor transport dominated by dynamic factors. With the increased SST, the moisture transported from oceans to interior land was likely redistributed and caused the complicated regional variability of precipitation. Moreover, the impacts of aerosols on cloud and precipitation varied with different pollution levels and different seasons.

  13. Aerosol composition and variability in the Baltimore-Washington, DC region (United States)

    Beyersdorf, A. J.; Ziemba, L. D.; Chen, G.; Corr, C. A.; Crawford, J. H.; Diskin, G. S.; Moore, R. H.; Thornhill, K. L.; Winstead, E. L.; Anderson, B. E.


    In order to utilize satellite-based aerosol measurements for the determination of air quality, the relationship between aerosol optical properties (wavelength-dependent, column-integrated extinction measured by satellites) and mass measurements of aerosol loading (PM2.5 used for air quality monitoring) must be understood. This connection varies with many factors including those specific to the aerosol type, such as composition, size and hygroscopicity, and to the surrounding atmosphere, such as temperature, relative humidity (RH) and altitude, all of which can vary spatially and temporally. During the DISCOVER-AQ (Deriving Information on Surface conditions from Column and Vertically Resolved Observations Relevant to Air Quality) project, extensive in-situ atmospheric profiling in the Baltimore, MD-Washington, DC region was performed during fourteen flights in July 2011. Identical flight plans and profile locations throughout the project provide meaningful statistics for determining the variability in and correlations between aerosol loading, composition, optical properties and meteorological conditions. Measured water-soluble aerosol mass was composed primarily of ammonium sulfate (campaign average of 32 %) and organics (57 %). A distinct difference in composition was observed with high-loading days having a proportionally larger percentage of ammonium sulfate (up to 49 %) due to transport from the Ohio River Valley. This composition shift caused a change in the aerosol water-uptake potential (hygroscopicity) such that higher relative contributions of ammonium sulfate increased the bulk aerosol hygroscopicity. These days also tended to have higher relative humidity causing an increase in the water content of the aerosol. Conversely, low aerosol loading days had lower ammonium sulfate and higher black carbon contributions causing lower single scattering albedos (SSAs). The average black carbon concentrations were 240 ng m-3 in the lowest 1 km decreasing to 35 ng m-3

  14. Using mi impute chained to fit ANCOVA models in randomized trials with censored dependent and independent variables

    DEFF Research Database (Denmark)

    Andersen, Andreas; Rieckmann, Andreas


    In this article, we illustrate how to use mi impute chained with intreg to fit an analysis of covariance analysis of censored and nondetectable immunological concentrations measured in a randomized pretest–posttest design....

  15. Stalk region of beta-chain enhances the coreceptor function of CD8. (United States)

    Wong, Jenny S; Wang, Xiaosong; Witte, Torsten; Nie, Linghu; Carvou, Nicolas; Kern, Petra; Chang, Hsiu-Ching


    CD8 glycoproteins are expressed as either alphaalpha homodimers or alphabeta heterodimers on the surface of T cells. CD8alphabeta is a more efficient coreceptor than the CD8alphaalpha for peptide Ag recognition by TCR. Each CD8 subunit is composed of four structural domains, namely, Ig-like domain, stalk region, transmembrane region, and cytoplasmic domain. In an attempt to understand why CD8alphabeta is a better coreceptor than CD8alphaalpha, we engineered, expressed, and functionally tested a chimeric CD8alpha protein whose stalk region is replaced with that of CD8beta. We found that the beta stalk region enhances the coreceptor function of chimeric CD8alphaalpha to a level similar to that of CD8alphabeta. Surprisingly, the beta stalk region also restored functional activity to an inactive CD8alpha variant, carrying an Ala mutation at Arg(8) (R8A), to a level similar to that of wild-type CD8alphabeta. Using the R8A variant of CD8alpha, a panel of anti-CD8alpha Abs, and three MHC class I (MHCI) variants differing in key residues known to be involved in CD8alpha interaction, we show that the introduction of the CD8beta stalk leads to a different topology of the CD8alpha-MHCI complex without altering the overall structure of the Ig-like domain of CD8alpha or causing the MHCI to employ different residues to interact with the CD8alpha Ig domain. Our results show that the stalk region of CD8beta is capable of fine-tuning the coreceptor function of CD8 proteins as a coreceptor, possibly due to its distinct protein structure, smaller physical size and the unique glycan adducts associated with this region.

  16. Precipitation variability, extremes and uncertainties over southeastern Brazil projected by the Eta regional model (United States)

    Cavalcanti, Iracema; Silveira, Virginia; Chan, Chou; Marengo, Jose Antonio


    Southeastern Brazil is an area affected by extreme precipitation, mainly in the austral summer, associated with frontal systems or the South Atlantic Convergence Zone (SACZ). Flooding and landslides have occurred in the region with serious impact on society and economy. The region has many vulnerable areas, therefore, projections of precipitation and extremes in the future for the region are important to provide information that can be used in adaptations and management decisions. Results of regional models in South America have been analyzed to assess the future climate changes with higher resolution than global models. In this study the Regional Eta model is used with resolution of 40 and 20 Km to analyze the projections of precipitation changes and extremes over Brazil and mainly over the southeastern region. Simulations and projections obtained from four integrations of the Regional Eta model are analyzed to investigate the model behavior during the period of 1961-1990 and the projections in the near (2011 to 2040) and more distant future (2041 to 2100). Results from four integrations with resolution of 40 km with different lateral boundary conditions from the HadCM3 Global Model and one integration with resolution of 20 km are used to give a confidence interval and the related uncertainty. The first analysis was to verify changes in the main mode of precipitation variability in the future projections, compared to the base period. There is a change in the main centers of extremes variability over South America, which was comparable to changes projected in CMIP5 models. The second analysis was related to changes in the position and intensity of the SACZ. Specific locations in southeastern Brazil were analyzed regarding indices of extremes, such as SDII (mean precipitation of rainy days), SDII_10 (mean precipitation of rainy days >=10 mm/day), R10mm (number of days with precipitation >= 10 mm/day), CDD (maximum number of consecutive dry days), CWD (maximum number

  17. Aerosol variability and atmospheric transport in the Himalayan region from CALIOP 2007-2010 observations (United States)

    Bucci, S.; Cagnazzo, C.; Cairo, F.; Di Liberto, L.; Fierli, F.


    Himalayan Plateau is surrounded by regions with high natural and anthropogenic aerosol emissions that have a strong impact on regional climate. This is particularly critical for the Himalayan glaciers whose equilibrium is also largely influenced by radiative direct and indirect effects induced by aerosol burden. This work focuses on the spatial and vertical distribution of different aerosol types, their seasonal variability and sources. The analysis of the 2007-2010 yr of CALIPSO vertically resolved satellite data allows the identification of spatial patterns of desert dust and carbonaceous particles in different atmospheric layers. Clusters of Lagrangian back-trajectories highlight the transport pathways from source regions during the dusty spring season. The analysis shows a prevalence of dust; at low heights they are distributed mainly north (with a main contribution from the Gobi and Taklamakan deserts) and west of the Tibetan Plateau (originating from the deserts of South-West Asia and advected by the westerlies). Above the Himalayas the dust amount is minor but still not negligible (detectable in around 20% of the measurements), and transport from more distant deserts (Sahara and Arabian Peninsula) is important. Smoke aerosol, produced mainly in North India and East China, is subject to shorter range transport and is indeed observed closer to the sources while there is a limited amount reaching the top of the plateau. Data analysis reveals a clear seasonal variability in the frequencies of occurrence for the main aerosol types; dust is regulated principally by the monsoon dynamics, with maxima of occurrence in spring. The study also highlights relevant interannual differences, showing a larger presence of aerosol in the region during 2007 and 2008 yr.

  18. Generation of cytotoxic T lymphocytes specific for B-cell acute lymphoblastic leukemia family-shared peptides derived from immunoglobulin heavy chain framework region

    Institute of Scientific and Technical Information of China (English)

    LIU Ying; ZHU Ping; HU Ya-mei


    Background Immunoglobulin heavy chain variable region (IgHV) is a well-characterized tumor antigen for B-cell malignancies. It can function as a target for T cell-mediated immune response. Clinical trials of IgHV protein vaccines against lymphoma have demonstrated induction of tumor-specific cytotoxic T lymphocyte (CTL) responses. However,complementary determining regions-based individual vaccines have disadvantages for wide clinical application. Although a recent study demonstrated that immunogenic peptides are derived from framework regions (FR) shared among patients with B-cell lymphoma, how to choose the appropriate peptides for each patient is still unsolved. The aim of this study was to investigate whether immunoglobulin heavy chain FR-derived peptides shared in each IgHV family are potential CTL epitopes presented by B-cell acute lymphoblastic leukemia (B-ALL). Such CTL epitopes might be beneficial to shifting vaccination strategies against B-ALL from individual specificity to family specificity.Methods Seven IgHV gene families were amplified respectively by PCR and sequenced directly from 71 childhood B-ALL cases. Bioinformatics was applied in analyzing characteristics of sequences available and predicting HLA-A*0201-restricted CTL epitopes for each IgHV family. An antigen-specific T cell expansion system was used to generate peptide-specific CTLs. The cytotoxicity of CTLs against B-ALL cells was assessed in the lactate dehydrogenase release assay.Results Complete IgHV rearrangements were identified in all of the 71 B-ALL cases. All of 40 sequences available showed ≥98% homology with the nearest germline IgHV genes, indicating IgHV genes in B-ALL of germline nature.Twelve nonapeptides of high HLA-A*0201-binding scores were obtained from 26 productive IgHV protein sequences. Ten (83%) of the peptides were located in FR1 and FR3 shared among the corresponding IgHV family. CTLs specific for the peptide QLVQSGAEV located in FR1 (3-11) shared among the IgHV1

  19. Protein loops, solitons, and side-chain visualization with applications to the left-handed helix region. (United States)

    Lundgren, Martin; Niemi, Antti J; Sha, Fan


    Folded proteins have a modular assembly. They are constructed from regular secondary structures like α helices and β strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C_{α} atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-handed helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C_{β} carbons on the two-sphere. We show that the residue independent localization extends to C_{γ} and C_{δ} carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that left-handed β turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.

  20. A VL-linker-VH Orientation Dependent Single Chain Variable Antibody Fragment Against Rabies Virus G Protein with Enhanced Neutralizing Potency in vivo. (United States)

    Cheng, Yue; Li, Zhuang; Xi, Hualong; Gu, Tiejun; Yuan, Ruosen; Chen, Xiaoxu; Jiang, Chunlai; Kong, Wei; Wu, Yongge


    Lethal rabies can be prevented effectively by post-exposure prophylactic (PEP) with rabies immunoglobulin (RIG). Single-chain variable fragment (scFv), which is composed of a variable heavy chain (VH) and variable light chain (VL) connected by a peptide linker, may be developed as alternative to RIG for neutralizing rabies virus (RV). However, our previously constructed scFv (FV57S) with the (NH2) VH-linker-VL (COOH) orientation showed a lower neutralizing potency than its parent RIG. This orientation may inhibit FV57S from refolding into an intact and correct conformation. Therefore, the RFV57S protein with a VL-linker-VH orientation was constructed based on FV57S. A HIS tag was incorporated to aid in purification and detection of RFV57S and FV57S. However, abilities of RFV57S and FV57S to bind with the anti-HIS tag mAb were different. Therefore, a novel direct ELISA was established by utilizing a biotin-labeled truncated glycoprotein of RV. Although with similar stability and in vitro neutralizing potency as FV57S, RFV57S showed enhanced binding ability, affinity and in vivo protective efficacy against lethal dose of RV. Our studies support the feasibility of developing a scFv with reversed orientation and provide a novel method for evaluating the binding ability, stability and affinity of engineered antibodies recognizing linear epitope.

  1. Regional sea level variability from ice sheets, glaciers and land hydrology (United States)

    Velicogna, I.; Hsu, C. W.


    Closing the sea level budget is a most important scientific and societal issue of climate change. Here, we report on the status of ice sheets and glaciers mass balance throughout the world and their contribution to sea level rise using time series of time-variable gravity from the NASA/DLR GRACE satellite mission for the time period 2003-2014. We also evaluate static regional sea level variations (or sea level fingerprints, SLF) from these observations of ice sheet and glacier loss, combined with observations of changes in global land hydrology also from GRACE, and water input from the atmosphere from re-analysis data. We evaluate the relative contribution of each component to regional sea level. We compare the cumulative SLF signal at global scale and at the scale of large ocean basins with satellite altimetry data corrected for the steric component from Argo floats. We find an excellent agreement between the two datasets. Although the regional SLF do not include sea level variations from ocean dynamics that re-distributes water mass around the world's oceans at the analyzed scales, we find that the SLF represent a large fraction of the trend and annual amplitude of the sea level signal. We also show an analysis of the contributions of regional sea level from mass changes in Greenland and Antarctica going back to the 1970s. This work was conducted at the University of California Irvine and at Caltech's Jet Propulsion Laboratory under a contract with the National Aeronautics and Space Administration.

  2. Interannual variability in rainy season characteristics over the Limpopo region of southern Africa (United States)

    Reason, C. J. C.; Hachigonta, S.; Phaladi, R. F.


    This study focuses on the interannual variability of dry spell frequencies, dry and wet spell characteristics and onset dates of the austral summer rainy season over the Limpopo region (22-25 °S, 27-32 °E) of northern South Africa. These characteristics of the rainy season are of considerable interest to farmers, water resource managers and other user groups. The Limpopo region supports a large rural population dependent on rain-fed agriculture as well as significant biodiversity, particularly in the Kruger National/Limpopo Transfrontier Park. It is also a region prone to devastating floods and droughts. Evidence is presented that summer dry spell frequency and onset date are related to ENSO via changes in regional circulation. Niño 3.4 sea surface temperature (SST) anomalies appear to show a robust relationship with dry spell frequency during the 1979-2002 period analysed. Anomalies in onset date of the rainy season during 1979-2002 appear to be inversely related to Niño 3.4 SST, with the relationship strengthening after 1986. These results suggest that there may be some predictability in these parameters, particularly in dry spell frequency during austral summer, based on existing skill in predicting tropical Pacific SST. Copyright

  3. Pathogenic variability of Moniliophthora perniciosa in three agroecological zones of the cacao region of Bahia, Brazil

    Directory of Open Access Journals (Sweden)

    Karina Peres Gramacho


    Full Text Available Resistant cacao genotypes are the best measure to control the Witches’ broom disease of cacao. To ensure efficiency, the pathogen variability in the cacao region of Bahia must be investigated. The pathogenic variability of Moniliophthora perniciosa inocula from nine municipalities was analyzed: Ilhéus, Floresta Azul and Jussari (agroecological zone Almada; Ipiaú, Itagibá and Jitaúna (agroecological zone Ipiaú, Camacan, Santa Luzia and Pau Brasil (agroecological zone Camacan, by inoculating progenies of Sca 6, ICS 1 and SIC 23 seedlings with 2 x 105 basidiospore.mL-1 of inocula and inoculum mixtures per agroecological zone, in a factorial 3 x 13 design, with 4 replications of 28 plants, in two seasons. Symptoms were assessed 60 days after inoculation. Pathogenic variability of inoculum in relation to the progeny performance was found; Ipiaú was the most aggressive and progeny ICS 1 the most susceptible. The mixtures of the agroecological zones Almada and Ipiaú were contrasting.

  4. Climate Variability, Andean Livelihood Strategies, Development and Adaptation in the Andean Region (United States)

    Valdivia, C.; Quiroz, R.; Zorogastua, P.; Baigorrea, G.


    Development programs in the Andes have failed to recognize climate variability as an element that is crucial to the adoption of new alternatives. Dairy, potatoes, improved sheep, forages are all part of the history of development in this region. A combination of climate variability, changes in the economy, the political environment, and land tenure reform shape rural livelihoods and welfare. Diversification, linking to markets, and networking are some elements that contribute to the resilience of families in the Andes. Strategies change, are flexible, and may incorporate non-agricultural activities. While some farmers are able to improve their welfare through the life cycle, others become poorer. Climate variability increases the vulnerability of some groups; in other cases, because of diversification and assets, households build economic portfolios that are more resilient to the elements. The many projects provide insights into how in the long run households improve their environment, hinting at mechanisms to adapt to climate change. In order to understand changing composition of portfolios in future scenarios of spatial heterogeneous areas such as mountains (Andes), estimates of models predicting climate change at a global scale are not useful because their resolution. Therefore, downscaling tools are useful. Spatial heterogeneity is assessed through agroecozoning. Both production and the impact on some environmental indicators are simulated through process-based models, for the Ilave-Huenque watershed in Peru that help in discussing scenarios of adaptation.

  5. An X-ray variable absorber within the Broad Line Region in Fairall 51

    CERN Document Server

    Svoboda, Jiri; Guainazzi, Matteo; Longinotti, Anna Lia; Piconcelli, Enrico; Wilms, Joern


    Fairall 51 is a polar-scattered Seyfert 1 galaxy, a type of active galaxies believed to represent a bridge between unobscured type-1 and obscured type-2 objects. Fairall 51 has shown complex and variable X-ray absorption but only little is known about its origin. In our research, we observed Fairall 51 with the X-ray satellite Suzaku in order to constrain a characteristic time-scale of its variability. We performed timing and spectral analysis of four observations separated by 1.5, 2 and 5.5 day intervals. We found that the 0.5-50 keV broadband X-ray spectra are dominated by a primary power-law emission (with the photon index ~ 2). This emission is affected by at least three absorbers with different ionisations (log(xi) ~ 1-4). The spectrum is further shaped by a reprocessed emission, possibly coming from two regions -- the accretion disc and a more distant scattering region. The accretion disc emission is smeared by the relativistic effects, from which we measured the spin of the black hole as a ~ 0.8 (+-0.2...

  6. Assessment of Impacts of Climate Variability on Crop Yield over the Terai Region of Nepal (United States)

    Subedi, S.; Acharya, A.


    Agricultural sector in Nepal which alone contributes about 42 % of the total GDP have a huge influence on national economy. This sector is very much susceptible to climate change. This study is emphasized on Terai region (situated at an altitude of 60m to 300m) of Nepal which investigates the impacts of climate variability on various stages of cropping (paddy) periods such as transplant, maturity and harvest. The climate variables namely temperature and rainfall are used to explore the relationship between climate and paddy yields based on 30 years of historical observed data. Observed monthly rainfall and temperature data are collected from the department of hydrology and meteorology, and paddy yield data are collected from the Ministry of Agricultural Development. A correlation analysis will be carried out between the backward difference filtered climate parameters and the backward difference filtered rice yield. This study will also analyze average monthly and annual rainfall, and, min, max and mean temperature during the period of 1981-2010 based on 15 synoptic stations of Nepal. This study will visualize rainfall and temperature distribution over Nepal, and also evaluate the effect of change in rainfall and temperature in the paddy yield. While evaluating the impacts of climate on crop yield, this study will not consider the impact of irrigation in crop yield. The major results, climate distribution and its local/regional impacts on agriculture, could be utilized by planners, decision makers, and climate and agricultural scientists as a basis in formulating/implementing future plans, policies and projects.

  7. Late Holocene climate variability in the southwestern Mediterranean region: an integrated marine and terrestrial geochemical approach

    Directory of Open Access Journals (Sweden)

    C. Martín-Puertas


    Full Text Available A combination of marine (Alboran Sea cores, ODP 976 and TTR 300 G and terrestrial (Zoñar Lake, Andalucia, Spain geochemical proxies provides a high-resolution reconstruction of climate variability and human influence in the southwestern Mediterranean region for the last 4000 years at inter-centennial resolution. Proxies respond to changes in precipitation rather than temperature alone. Our combined terrestrial and marine archive documents a succession of dry and wet periods coherent with the North Atlantic climate signal. A dry period occurred prior to 2.7 cal ka BP – synchronously to the global aridity crisis of the third-millennium BC – and during the Medieval Climate Anomaly (1.4–0.7 cal ka BP. Wetter conditions prevailed from 2.7 to 1.4 cal ka BP. Hydrological signatures during the Little Ice Age are highly variable but consistent with more humidity than the Medieval Climate Anomaly. Additionally, Pb anomalies in sediments at the end of the Bronze Age suggest anthropogenic pollution earlier than the Roman Empire development in the Iberian Peninsula. The Late Holocene climate evolution of the in the study area confirms the see-saw pattern between the eastern and western Mediterranean regions and the higher influence of the North Atlantic dynamics in the western Mediterranean.

  8. Improving plot- and regional-scale crop models for simulating impacts of climate variability and extremes (United States)

    Tao, F.; Rötter, R.


    Many studies on global climate report that climate variability is increasing with more frequent and intense extreme events1. There are quite large uncertainties from both the plot- and regional-scale models in simulating impacts of climate variability and extremes on crop development, growth and productivity2,3. One key to reducing the uncertainties is better exploitation of experimental data to eliminate crop model deficiencies and develop better algorithms that more adequately capture the impacts of extreme events, such as high temperature and drought, on crop performance4,5. In the present study, in a first step, the inter-annual variability in wheat yield and climate from 1971 to 2012 in Finland was investigated. Using statistical approaches the impacts of climate variability and extremes on wheat growth and productivity were quantified. In a second step, a plot-scale model, WOFOST6, and a regional-scale crop model, MCWLA7, were calibrated and validated, and applied to simulate wheat growth and yield variability from 1971-2012. Next, the estimated impacts of high temperature stress, cold damage, and drought stress on crop growth and productivity based on the statistical approaches, and on crop simulation models WOFOST and MCWLA were compared. Then, the impact mechanisms of climate extremes on crop growth and productivity in the WOFOST model and MCWLA model were identified, and subsequently, the various algorithm and impact functions were fitted against the long-term crop trial data. Finally, the impact mechanisms, algorithms and functions in WOFOST model and MCWLA model were improved to better simulate the impacts of climate variability and extremes, particularly high temperature stress, cold damage and drought stress for location-specific and large area climate impact assessments. Our studies provide a good example of how to improve, in parallel, the plot- and regional-scale models for simulating impacts of climate variability and extremes, as needed for

  9. Demolition waste generation for development of a regional management chain model. (United States)

    Bernardo, Miguel; Gomes, Marta Castilho; de Brito, Jorge


    Even though construction and demolition waste (CDW) is the bulkiest waste stream, its estimation and composition in specific regions still faces major difficulties. Therefore new methods are required especially when it comes to make predictions limited to small areas, such as counties. This paper proposes one such method, which makes use of data collected from real demolition works and statistical information on the geographical area under study. Based on a correlation analysis between the demolition waste estimates and indicators such as population density, buildings ageing index, buildings density and land occupation type, relationships are established that can be used to determine demolition waste outputs in a given area. The derived models are presented and explained. This methodology is independent from the specific region with which it is exemplified (the Lisbon Metropolitan Area) and can therefore be applied to any region of the world, from the country to the county level. Generation of demolition waste data at the county level is the basis of the design of a systemic model for CDW management in a region. Future developments proposed include a mixed-integer linear programming formulation of such recycling network.

  10. The National Biofuels Strategy - Importance of sustainable feedstock production systems in regional-based supply chains (United States)

    Region-based production systems are needed to produce the feedstocks that will be turned into the biofuels required to meet Federal mandated targets. Executive and Legislative actions have put into motion significant government responses designed to advance the development and production of domestic...

  11. Regional variability of acidification in the Arctic: a sea of contrasts

    Directory of Open Access Journals (Sweden)

    E. E. Popova


    Full Text Available The Arctic Ocean is a region that is particularly vulnerable to the impact of ocean acidification driven by rising atmospheric CO2, negatively impacting calcifying organisms such as coccolithophorids and foraminiferans. In this study, we use an ocean general circulation model, with embedded biogeochemistry and a full description of the carbon cycle, to study the response of pH and saturation states of calcite and aragonite to changing climate in the Arctic Ocean. Particular attention is paid to the strong regional variability within the Arctic and, for comparison, simulation results are contrasted with those for the global ocean. Simulations were run to year 2099 using the RCP 8.5 (the highest IPCC AR5 CO2 emission scenario. The separate impacts of the direct increase in atmospheric CO2 and indirect effects via climate feedbacks (changing temperature, stratification, primary production and fresh water fluxes were examined by undertaking two simulations, one with the full system and the other in which ocean-atmosphera exchange of CO2 was prevented from increasing beyond the flux calculated for year 2000. Results indicate that climate feedbacks, and spatial heterogeneity thereof, play a strong role in the declines in pH and carbonate saturation (Ω seen in the Arctic. The central Arctic, Canadian Arctic Archipelago and Baffin Bay show greatest rates of acidification and Ω decline as a result of melting sea ice. In contrast, areas affected by Atlantic inflow including the Greenland Sea and outer shelves of the Barents, Kara and Laptev seas, had minimal decreases in pH and Ω because weakening stratification associated with diminishing ice cover led to greater mixing and primary production. As a consequence, the predicted onset of undersaturation is highly variable regionally within the Arctic, occurring during the decade of 2000–2010 in the Siberian shelves and Canadian Arctic Archipelago, but as late

  12. Regional variability of acidification in the Arctic: a sea of contrasts

    Directory of Open Access Journals (Sweden)

    E. E. Popova


    Full Text Available The Arctic Ocean is a region that is particularly vulnerable to the impact of ocean acidification driven by rising atmospheric CO2, with potentially negative consequences for calcifying organisms such as coccolithophorids and foraminiferans. In this study, we use an ocean-only general circulation model, with embedded biogeochemistry and a comprehensive description of the ocean carbon cycle, to study the response of pH and saturation states of calcite and aragonite to rising atmospheric pCO2 and changing climate in the Arctic Ocean. Particular attention is paid to the strong regional variability within the Arctic, and, for comparison, simulation results are contrasted with those for the global ocean. Simulations were run to year 2099 using the RCP8.5 (an Intergovernmental Panel on Climate Change (IPCC Fifth Assessment Report (AR5 scenario with the highest concentrations of atmospheric CO2. The separate impacts of the direct increase in atmospheric CO2 and indirect effects via impact of climate change (changing temperature, stratification, primary production and freshwater fluxes were examined by undertaking two simulations, one with the full system and the other in which atmospheric CO2 was prevented from increasing beyond its preindustrial level (year 1860. Results indicate that the impact of climate change, and spatial heterogeneity thereof, plays a strong role in the declines in pH and carbonate saturation (Ω seen in the Arctic. The central Arctic, Canadian Arctic Archipelago and Baffin Bay show greatest rates of acidification and Ω decline as a result of melting sea ice. In contrast, areas affected by Atlantic inflow including the Greenland Sea and outer shelves of the Barents, Kara and Laptev seas, had minimal decreases in pH and Ω because diminishing ice cover led to greater vertical mixing and primary production. As a consequence, the projected onset of undersaturation in respect to aragonite is highly variable regionally within the

  13. Intensification of the regional scale variability of extreme precipitation derived from RCM simulations and observations (United States)

    Feldmann, H.; Schädler, G.; Panitz, H.-J.


    Future climate change patterns are usually derived from ensembles of coarse global climate model simulations (GCMs), for instance within the Coupled Model Intercomparison Project (CMIP) or from regional climate projections at resolutions of some tens of km, for instance for Europe from the ENSEMBLES or PRUDENCE projects. For regions with complex topography like Central Europe the horizontal resolution of these climate projections is still too coarse to resolve the typical topographical length scales, and therefore the impact of the large scale changes with the regional geography cannot be captured adequately. For this task high resolution ensemble simulations with regional climate models (RCMs) are needed. The generation of an ensemble of such high resolution simulations requires great computational efforts. With the RCM COSMO-CLM several simulations with resolutions down to 7 km have been performed, using different driving GCMs and GCM realisations. This ensemble approach is needed to estimate the robustness of the change signals and to account for the uncertainties introduced by differences in the large scale forcing due to the variability of the climate change signals caused by the different GCMs or the natural variability. The focus of the study is on the changes of extreme precipitation for the near future until the middle of the 21st century. An increase of the temporal and spatial variability is found for the precipitation extremes, especially for summer. The change patterns seem to be statistically robust. Based on long-term observation climatologies for the second half of the 20th century, similar structures where found with areas of decrease and increase only a few tens of kilometres apart from each other. The combination of the findings from the RCM projections and observations suggests a continuation of the trends from the recent past into the near future. Possible causes for the horizontally heterogeneous change patterns are related to weather pattern

  14. Polymerase chain reaction based epidemiological investigation of canine parvoviral disease in dogs at Bareilly region

    Directory of Open Access Journals (Sweden)

    Jobin Thomas


    Full Text Available Aim: The aim of this study was to screen the suspected samples by polymerase chain reaction (PCR and epidemiological analysis of positive cases of canine parvovirus type2. Materials and Methods: Fecal samples were collected from dogs suspected for canine parvovirus type 2 (CPV-2 and viral DNA was extracted. Primers were designed, and PCR was done with all extracted DNA samples. Age, sex and breed wise distribution of positive cases were analyzed. Results: Out of a total 44 collected fecal samples, 23 were found to be positive for CPV-2 by developed PCR. The disease was found to be more common in Labrador male pups of 3-6 months of age. The percentage of positive cases in vaccinated dogs was found to be around 17.4%. Conclusion: Almost half (52.3% of total collected samples were found to be positive by PCR. However, number of field samples are needed to further validate this test and additionally sequence analysis needs to be done to ensure the prevalent field strain of CPV-2.

  15. The preferential codon usages in variable and constant regions of immunoglobulin genes are quite distinct from each other. (United States)

    Miyata, T; Hayashida, H; Yasunaga, T; Hasegawa, M


    The pattern of codon utilization in the variable and constant regions of immunoglobulin genes are compared. It is shown that, in these regions, codon utilizations are quite distinct from one another: For most degenerate codons, there is a selective bias that prefers C and/or G ending codons to U and/or A ending codons in the constant region compared with the bias in the variable region. This would strongly suggest that, in immunoglobulin genes, the bias in code word usage is determined by other factors than those concerning with the translational mechanism such as tRNA availability and codon-anticodon interaction. A possibility is also suggested that this differance of code word usage between them is due to the existence of secondary structure in the constant region but not in the variable region.

  16. Characterization of the regional variability of flood regimes within the Omo-Gibe River Basin, Ethiopia (United States)

    Yared, Adanech; Demissie, Solomon S.; Sivapalan, Murugesu; Viglione, Alberto; MacAlister, Charlotte


    Hydrological variability and seasonality is one of the Ethiopia's primary water resource management challenges. Variability is most obviously manifest in endemic, devastating droughts and floods. While the level of flooding is quite often extremely high and destroys human beings and property, in many cases flooding is of vital importance because the community benefits from flood recession agriculture. This is the case of the lower Omo plain whose agriculture is based on the regularity of the inundations due to flooding of the Omo Gibe River. The big flood in 2006, which caused death for more than 300 people and 2000 cattle, poses a dilemma. Flooding must be controlled and regulated in a way that the damages are reduced as much as possible but the flooding-related benefits are not lost. To this aim, characterization and understanding of hydrological variability of the Omo Gibe River basin is fundamental. The goal of this work is to extract the maximal amount of information on the hydrological variability and specially on the flooding regime from the few data available in the region. Because most of the basin is ungauged, hydrological information is reconstructed using the data from 9 gauged catchments. A daily water balance model has been developed, calibrated and validated for 9 gauged catchments and, subsequently, the parameters have been correlated to catchment characteristics in order to establish a functional relationship that allows to apply the model to ungauged catchments. Daily streamflow has been predicted for 15 ungauged catchments, which are assumed to comprehensively represent the hydrological variability of the Omo-Gibe River Basin. Even though both northern and southern catchments are affected by a strong seasonality of precipitation, with most of the rain falling in less than 3 months, most of the northern catchments are humid, while in the southern part of the Omo-Gibe River basin, the catchments are either humid, dry sub humid, semiarid or arid. As

  17. Rapid amplification of cDNA ends (RACE) improves the PCR-based isolation of immunoglobulin variable region genes from murine and human lymphoma cells and cell lines. (United States)

    Doenecke, A; Winnacker, E L; Hallek, M


    The isolation of rearranged immunoglobulin (Ig) variable region (V) genes is usually performed by PCR with consensus primers binding to conserved regions within the V sequences. However, the isolation of Ig genes by this method is hampered in 15-35% by technical difficulties, mostly mismatches of oligonucleotide primers to V sequences. In order to obtain DNA sequences from V heavy chain (VH) genes which could not be amplified with consensus primers, we used a modified PCR technique, the rapid amplification of cDNA ends (RACE) PCR in combination with new heavy chain constant region primers for the isolation of human and murine VH genes. In comparison, consensus primer PCR with different sets of previously published oligonucleotide primers was used. Both methods were applied to isolate VH genes from murine B cell lymphoma (A20 and BCL1), myeloma (NS1) and hybridoma (SP6) cell lines and from freshly isolated human chronic lymphocytic leukemia and lymphoma cells. RACE PCR allowed the amplification and subsequent cloning of the complete VH gene in all cases. In contrast, consensus primer PCR failed to isolate the VH sequence of the murine A20 cell line; this was explained by a mismatch of consensus primers with VH sequences. When both PCR methods amplified VH sequences, the DNA sequences obtained were identical. Taken together, RACE PCR represents a reliable and versatile method for the isolation of VH genes from human and murine lymphoma cells, in particular if consensus primer PCR fails.

  18. Climate Variability is Influencing Agricultural Expansion and Output in a Key Agricultural Region of Brazil (United States)

    Spera, S. A.; Cohn, A.; VanWey, L.; Mustard, J. F.


    Over the last decade, the Brazilian state of Mato Grosso has both expanded and intensified its agricultural production to become the country's leading producer of soy, corn, and cotton. Yet this increase in agricultural production may be threatened due to changes in the region's climate stemming from deforestation caused by the agricultural expansion itself. The sensitivity of Mato Grosso's agriculture to climate variability has important implications for both climate change mitigation and climate adaptation. The vast bulk of research on the drivers of land use change in the region has examined economic and institutional drivers. Leveraging a novel remote sensing-derived dataset classifying shifts between single (cultivating one commercial crop per growing season) and double cropping (cultivating two commercial crops per growing season), we investigated the influence of climate variability on land use change during the period 2000 to 2011. Over the past decade, over half of Mato Grosso's farm area transitioned from single cropping to double cropping. We used regression analysis (controlling for space and time fixed effects) to show monthly rainfall, monthly temperature, agricultural commodity prices, and agricultural revenue to be the main drivers of adoption of double cropping and reversion to single cropping in the region. The influence of climate varies as much as five orders of magnitude across these outcomes, with both temperature and precipitation exhibiting the largest climatic influence on the transition from single to double cropping. Temperature consistently proves to be more important, explaining three times more of the variance than precipitation for each outcome. Months at the beginning of a given first crop season, the end of that first crop season, and middle of the subsequent second crop season are particularly important for planting decisions in the subsequent growing year. Fitting our land transition models using remote-sensing derived

  19. Aerosol and rainfall variability over the Indian monsoon region. Distributions, trends and coupling

    Energy Technology Data Exchange (ETDEWEB)

    Gautam, R. [Maryland Univ., Baltimore County, MD (United States). Goddard Earth Science and Technology Center; NASA Goddard Space Flight Center, Greenbelt, MD (United States). Lab. for Atmospheres; Hsu, N.C.; Lau, K.M. [NASA Goddard Space Flight Center, Greenbelt, MD (United States). Lab. for Atmospheres; Kafatos, M. [Chapman Univ., Orange, CA (United States). Center of Excellence in Earth Observing


    Aerosol solar absorption over the Indian monsoon region has a potential role of modulating the monsoon circulation and rainfall distribution as suggested by recent studies based on model simulations. Prior to the onset of the monsoon, northern India is influenced by significant dust transport that constitutes the bulk of the regional aerosol loading over the Gangetic-Himalayan region. In this paper, a multi-sensor characterization of the increasing pre-monsoon aerosol loading over northern India, in terms of their spatial, temporal and vertical distribution is presented. Aerosol transport from the northwestern arid regions into the Indo-Gangetic Plains and over the foothills of the Himalayas is found to be vertically extended to elevated altitudes (up to 5 km) as observed from the space-borne lidar measurements (CALIPSO). In relation with the enhanced pre-monsoon aerosol loading and the associated solar absorption effects on tropospheric temperature anomalies, this paper investigates the monsoon rainfall variability over India in recent past decades from an observational viewpoint. It is found that the early summer monsoon rainfall over India is on the rise since 1950s, as indicated by historical rainfall data, with over 20% increase for the period 1950-2004. This large sustained increase in the early summer rainfall is led by the observed strengthening of the pre-monsoon tropospheric land-sea thermal gradient over the Indian monsoon region as indicated by microwave satellite measurements (MSU) of tropospheric temperatures from 1979-2007. Combined analysis of changes in tropospheric temperatures and summer monsoon rainfall in the past three decades, suggest a future possibility of an emerging rainfall pattern of a wetter monsoon over South Asia in early summer followed by a drier period. (orig.)

  20. Food Supply Chains in Lagging Rural Regions of Finland: an SME Perspective


    Viitaharju, Leena; LÀhdesmÀki, Merja; Kurki, Sami; Valkosalo, Pauli


    An essential component of the food production sector in lagging regions consists of small-scale enterprises located in rural areas. A high proportion utilise traditional production methods, emphasising local identity and distinctiveness, thereby differentiating products and servicing niche or segmented markets. Such enterprises frequently integrate with other sectors of the local economy, such as raw material suppliers, distributors, tourism and catering, thereby enhancing local activity. Thu...

  1. Analysis of the 3' Cmu region of the rabbit Ig heavy chain locus. (United States)

    Lanning, Dennis K; Zhai, Shi-Kang; Knight, Katherine L


    The immunoglobulin D (IgD) antibody class was, for many years, identified only in primates, rodents and teleost fish. The limited distribution of IgD among vertebrates suggested that IgD is a functionally redundant antibody class that has been lost by many vertebrate species during evolution. The recent identification of IgD in artiodactyls, however, suggests that IgD might be more widely expressed among vertebrates than previously thought, possibly serving a unique role in immunity. IgD expression has been searched for but not detected in rabbits. In order to search directly for a rabbit Cdelta locus encoding the constant region of IgD, we determined the nucleotide sequence of 13.5 kb of genomic DNA downstream of the rabbit Cmu locus. We did not find a rabbit Cdelta locus in this region, but found instead that this region is densely populated by repetitive elements, including a long interspersed DNA element repeat, six C repeats, and two processed pseudogenes. We conclude that the rabbit probably does not express IgD because there is no Cdelta locus immediately downstream of the rabbit Cmu locus.

  2. Effects of regional infrastructure and offered services in the supply chains performance: Case Ciudad Juarez

    Directory of Open Access Journals (Sweden)

    Liliana Avelar-Sosa


    Full Text Available Este trabajo presenta un análisis de los efectos que tienen la infraestructura regional y los servicios en el desempeño de la cadena de suministro en empresas manufactureras de Ciudad Juárez, Chihuahua, México. Para colectar la información se aplicaron cuestionarios a 120 empresas, y para obtener un modelo de ecuaciones estructurales explicativo de los efectos se utilizó la metodología de mínimos cuadrados parciales usando WarpPLS 3.0. Los resultados obtenidos muestran que cuando existe buen nivel en la infraestructura regional se tienen impactos positivos sobre los servicios logísticos; y éstos a su vez impactan en los costos. Asimismo, la infraestructura regional tiene impactos positivos sobre el tiempo de entrega de los productos. Con relación al nivel de infraestructura (transporte, telecomunicaciones, internet y de servicios (aéreos, terrestres, financieros, legales en Ciudad Juárez, los encuestados lo consideran bueno por lo que las entregas de producto han sido completas y a tiempo en los últimos 3 años.

  3. A Study of Precipitation Climatology and Its Variability over Europe Using an Advanced Regional Model (WRF)

    KAUST Repository

    Dasari, Hari Prasad


    In recent years long-term precipitation trends on a regional scale have been given emphasis due to the impacts of global warming on regional hydrology. In this study, regional precipitation trends are simulated over the Europe continent for a 60-year period in 1950-2010 using an advanced regional model, WRF, to study extreme precipitation events over Europe. The model runs continuously for each year during the period at a horizontal resolution of 25 km with initial/ boundary conditions derived from the National Center for Environmental Prediction (NCEP) 2.5 degree reanalysis data sets. The E-OBS 0.25 degree rainfall observation analysis is used for model validation. Results indicate that the model could reproduce the spatial annual rainfall pattern over Europe with low amounts (250 - 750 mm) in Iberian Peninsula, moderate to large amounts (750 - 1500 mm) in central, eastern and northeastern parts of Europe and extremely heavy falls (1500 - 2000 mm) in hilly areas of Alps with a slight overestimation in Alps and underestimation in other parts of Europe. The regional model integrations showed increasing errors (mean absolute errors) and decreasing correlations with increasing time scale (daily to seasonal). Rainfall is simulated relatively better in Iberian Peninsula, northwest and central parts of Europe. A large spatial variability with the highest number of wet days over eastern, central Europe and Alps (~200 days/year) and less number of wet days over Iberian Peninsula (≤150 days/year) is also found in agreement with observations. The model could simulate the spatial rainfall climate variability reasonably well with low rainfall days (1 - 10 mm/days) in almost all zones, heavy rainfall events in western, northern, southeastern hilly and coastal zones and extremely heavy rainfall events in northern coastal zones. An increasing trend of heavy rainfall in central, southern and southeastern parts, a decreasing trend in Iberian Peninsula and a steady trend in other

  4. Temporal variability in emission category influence on organic matter aerosols in the Indian region (United States)

    Cherian, R.; Venkataraman, C.; Ramachandran, S.


    The dependence of carbonaceous aerosol properties, like radiation absorption and hygroscopicity, on the emission source of origin motivate this work. The influence of emission categories, including crop residue and forest burning, biofuel combustion, brick kilns, thermal power plants, diesel transport and ``other industry'', is estimated on organic matter (OM) surface concentrations in the Indian ocean region. The approach uses general circulation model predicted OM surface concentrations during a ship cruise, identifies probable source regions for high concentration episodes using the potential source contribution function, and estimates collocated OM emissions resolved by category. Distinct source regions identified, are the Indo-Gangetic Plain during 20-30th January, 1999, and central/south India during 1-11th March, 1999. Contributing emission categories are primarily biofuel combustion (18 Gg) during 20-30th January, but a combination of forest burning (8 Gg), biofuel combustion (7 Gg) and crop residue (5 Gg) during 1-11th March. The magnitude of emission flux rather than spatial extent of an emission category, was seen to increase its influence on the receptor. This approach can be used to investigate seasonal and inter-annual variability in emission category influence on atmospheric pollutants.

  5. Drought variability at the northern fringe of the Asian summer monsoon region over the past millennia (United States)

    Yang, Bao; Kang, Shuyuan; Ljungqvist, Fredrik Charpentier; He, Minhui; Zhao, Yan; Qin, Chun


    The northern fringe of the Asian summer monsoon region (NASM) in China refers to the most northwestern extent of the Asian summer monsoon. Understanding the characteristics and underlying mechanisms of drought variability at long and short time-scales in the NASM region is of great importance, because present and future water shortages are of great concern. Here, we used newly developed and existing tree-ring, historical documentary and instrumental data available for the region to identify spatial and temporal patterns, and possible mechanisms of drought variability, over the past two millennia. We found that drought variations were roughly consistent in the western (the Qilian Mountains and Hexi Corridor) and eastern (the Great Bend of the Yellow River, referred to as GBYR) parts of the NASM on decadal to centennial timescales. We also identified the spatial extent of typical multi-decadal GBYR drought events based on historical dryness/wetness data and the Monsoon Asia Drought Atlas. It was found that the two periods of drought, in AD 1625-1644 and 1975-1999, exhibited similar patterns: specifically, a wet west and a dry east in the NASM. Spatial characteristics of wetness and dryness were also broadly similar over these two periods, such that when drought occurred in the Karakoram Mountains, western Tianshan Mountains, the Pamirs, Mongolia, most of East Asia, the eastern Himalayas and Southeast Asia, a wet climate dominated in most parts of the Indian subcontinent. We suggest that the warm temperature anomalies in the tropical Pacific might have been mainly responsible for the recent 1975-1999 drought. Possible causes of the drought of 1625-1644 were the combined effects of the weakened Asian summer monsoon and an associated southward shift of the Pacific Intertropical Convergence Zone. These changes occurred due to a combination of Tibetan Plateau cooling together with more general Northern Hemisphere cooling, rather than being solely due to changes in the sea

  6. Satellite observations of seasonal and regional variability of particulate organic carbon concentration in the Barents Sea (United States)

    Stramska, Malgorzata; Białogrodzka, Jagoda


    The Nordic and Barents Seas are of special interest for research on climate change, since they are located on the main pathway of the heat transported from low to high latitudes. Barents Sea is known to be an important area for formation of deep water and significant uptake from the atmosphere and sequestration of carbon dioxide (CO2). This region is characterized by supreme phytoplankton blooms and large amount of carbon is sequestered here due to biological processes. It is important to monitor the biological variability in this region in order to derive in depth understanding whether the size of carbon reservoirs and fluxes may vary as a result of climate change. In this presentation we analyze the 17 years (1998-2014) of particulate organic carbon (POC) concentration derived from remotely sensed ocean color. POC concentrations in the Barents Sea are among the highest observed in the global ocean with monthly mean concentrations in May exceeding 300 mg m-3. The seasonal amplitude of POC concentration in this region is larger when compared to other regions in the global ocean. Our results indicate that the seasonal increase in POC concentration is observed earlier in the year and higher concentrations are reached in the southeastern part of the Barents Sea in comparison to the southwestern part. Satellite data indicate that POC concentrations in the southern part of the Barents Sea tend to decrease in recent years, but longer time series of data are needed to confirm this observation. This work was funded by the Norway Grants (NCBR contract No. 201985, project NORDFLUX). Partial support for MS comes from the Institute of Oceanology (IO PAN).

  7. Characterizing isotopic variability of primary production and consumers in Great Plains ecosystems during protracted regional drought (United States)

    Haveles, A. W.; Fox-Dobbs, K.; Talmadge, K. A.; Fetrow, A.; Fox, D. L.


    Over the last few years (2010-2012), the Great Plains of the central USA experienced protracted drought conditions, including historically severe drought during Summer, 2011. Drought severity in the region generally decreases with increasing latitude, but episodic drought is a fundamental trait of grassland ecosystems. Documenting above ground energy and nutrient flow with current drought is critical to understanding responses of grassland ecosystems in the region to predicted increased episodicity of rainfall and recurrence of drought due to anthropogenic climate change. Characterization of biogeochemical variability of modern ecosystems at the microhabitat, local landscape, and regional scales is also necessary to interpret biogeochemical records of ancient grasslands based on paleosols and fossil mammals. Here, we characterize three grassland ecosystems that span the drought gradient in the Great Plains (sites in the Texas panhandle, southwest Kansas, and northwest Nebraska). We measured δ13C and δ15N values of plants and consumers to characterize the biogeochemical variability within each ecosystem. Vegetation at each site is a mix of trees, shrubs, herbs, and cool- and warm-growing season grasses (C3 and C4, respectively). Thus, consumers have access to isotopically distinct sources of forage that vary in abundance with microhabitat (e.g., open grassland, shrub thicket, riparian woodland). Observations indicate herbivorous arthropod (grasshoppers and crickets) abundance follows drought severity, with high abundance of many species in Texas, and low abundance of few species in Nebraska. Small mammal (rodents) abundance follows the inverse pattern with 0.8%, 3.2% and 17.2% capture success in Texas, Kansas and Nebraska, respectively. The inverse abundance patterns of consumer groups may result from greater sensitivity of small mammal consumers with high metabolic needs to lower local net primary productivity and forage quality under drought conditions. As a

  8. Estimation of Variability Characteristics of Regional Drought during 1964–2013 in Horqin Sandy Land, China

    Directory of Open Access Journals (Sweden)

    Yongfang Wang


    Full Text Available Drought has an important influence on the hydrological cycle, ecological system, industrial and agricultural production, and social life. Based on the different time scales of characteristics of drought variability, the standardized precipitation evapotranspiration index (SPEI, a multi-timescale index with consideration of evaporation, was used in this study to estimate the spatial and temporal variability characteristics of drought. Climatic data from 15 meteorological stations across Horqin Sandy Land during 1964–2013 were used to calculate the SPEI of 1, 3, 6, and 12 months. In order to examine the relationship between droughts and other variables, 10 extreme climate indices were calculated based on the daily precipitation and maximum/mean/minimum temperature data of 15 meteorological stations, and linkages between SPEI-12 and atmosphere indices were established using by the cross wavelet transform method. The results indicated that the climate of Horqin Sandy Land had a tendency towards drought conditions, which is particularly apparent from the year 2000 onwards. During the study period, drought events were frequent in the region. Mild drought occurred in a quarter of the month, with that of moderate, severe, and extreme drought accounting for 0.11, 0.05, and 0.02 of the total months. The spatial trend of multi-timescale drought revealed that there was an increase in the severity of drought throughout Horqin Sandy Land, among which the magnitude in southern parts was larger than that of northern parts. The results also showed that the short time scale drought negatively correlated with precipitation extremes and positively correlated with temperature extremes. Furthermore, the long time scale drought (SPEI-12 was associated with atmosphere indices. Significant resonance periods were found between El Nino southern oscillation (ENSO, the East Asian summer monsoon index (EASMI, and SPEI-12.

  9. Epitope characterization and variable region sequence of f1-40, a high-affinity monoclonal antibody to botulinum neurotoxin type a (Hall strain.

    Directory of Open Access Journals (Sweden)

    Miles C Scotcher

    Full Text Available BACKGROUND: Botulism, an often fatal neuroparalytic disease, is caused by botulinum neurotoxins (BoNT which consist of a family of seven serotypes (A-H produced by the anaerobic bacterium Clostridium botulinum. BoNT, considered the most potent biological toxin known, is a 150 kDa protein consisting of a 100 kDa heavy-chain (Hc and a 50 kDa light-chain (Lc. F1-40 is a mouse-derived, IgG1 monoclonal antibody that binds the light chain of BoNT serotype A (BoNT/A and is used in a sensitive immunoassay for toxin detection. We report the fine epitope mapping of F1-40 and the deduced amino acid sequence of the variable regions of the heavy and light chains of the antibody. METHODS AND FINDINGS: To characterize the binding epitope of F1-40, three complementary experimental approaches were selected. Firstly, recombinant peptide fragments of BoNT/A light-chain were used in Western blots to identify the epitope domains. Secondly, a peptide phage-display library was used to identify the specific amino acid sequences. Thirdly, the three-dimensional structure of BoNT/A was examined in silico, and the amino acid sequences determined from the phage-display studies were mapped onto the three-dimensional structure in order to visualize the epitope. F1-40 was found to bind a peptide fragment of BoNT/A, designated L1-3, which spans from T125 to L200. The motif QPDRS was identified by phage-display, and was mapped to a region within L1-3. When the three amino acids Q138, P139 and D140 were all mutated to glycine, binding of F1-40 to the recombinant BoNT/A light chain peptide was abolished. Q-138, P-139 and D-140 form a loop on the external surface of BoNT/A, exposed to solvent and accessible to F1-40 binding. CONCLUSIONS: The epitope of F1-40 was localized to a single exposed loop (ss4, ss5 on the Lc of BoNT. Furthermore amino acids Q138, P139 and D140 forming the tip of the loop appear critical for binding.

  10. Genomic variability of Helicobacter pylori isolates of gastric regions from two Colombian populations (United States)

    Matta, Andrés Jenuer; Pazos, Alvaro Jairo; Bustamante-Rengifo, Javier Andrés; Bravo, Luis Eduardo


    AIM To compare the genomic variability and the multiple colonization of Helicobacter pylori (H. pylori) in patients with chronic gastritis from two Colombian populations with contrast in the risk of developing gastric cancer (GC): Túquerres-Nariño (High risk) and Tumaco-Nariño (Low risk). METHODS Four hundred and nine patients from both genders with dyspeptic symptoms were studied. Seventy-two patients were included in whom H. pylori was isolated from three anatomic regions of the gastric mucosa, (31/206) of the high risk population of GC (Túquerres) and (41/203) of the low risk population of GC (Tumaco). The isolates were genotyped by PCR-RAPD. Genetic diversity between the isolates was evaluated by conglomerates analysis and multiple correspondence analyses. RESULTS The proportion of virulent genotypes of H. pylori was 99% in Túquerres and 94% in Tumaco. The coefficient of similarity of Nei-Li showed greater genetic diversity among isolates of Túquerres (0.13) than those of Tumaco (0.07). After adjusting by age, gender and type of gastritis, the multiple colonization was 1.7 times more frequent in Túquerres than in Tumaco (P = 0.05). CONCLUSION In Túquerres, high risk of GC there was a greater probability of multiple colonization by H. pylori. From the analysis of the results of the PCR-RAPD, it was found higher genetic variability in the isolates of H. pylori in the population of high risk for the development of GC. PMID:28223724

  11. Extreme Infrared Variables from UKIDSS - I. A Concentration in Star Forming Regions

    CERN Document Server

    Peña, C Contreras; Froebrich, D; Kumar, M S N; Goldstein, J; Drew, J E; Adamson, A; Davis, C J; Barentsen, G; Wright, N J


    We present initial results of the first panoramic search for high-amplitude near-infrared variability in the Galactic Plane. We analyse the widely separated two-epoch K-band photometry in the 5th and 7th data releases of the UKIDSS Galactic Plane Survey. We find 45 stars with \\Delta K > 1 mag, including 2 previously known OH/IR stars and a Nova. Even though the mid-plane is not yet included in the dataset, we find the majority (66%) of our sample to be within known star forming regions (SFRs), with two large concentrations in the Serpens OB2 association (11 stars) and the Cygnus-X complex (12 stars). Sources in SFRs show spectral energy distributions (SEDs) that support classification as Young Stellar Objects (YSOs). This indicates that YSOs dominate the Galactic population of high amplitude infrared variable stars at low luminosities and therefore likely dominate the total high amplitude population. Spectroscopic follow up of the DR5 sample shows at least four stars with clear characteristics of eruptive pre...

  12. The properties of tests for spatial effects in discrete Markov chain models of regional income distribution dynamics (United States)

    Rey, Sergio J.; Kang, Wei; Wolf, Levi


    Discrete Markov chain models (DMCs) have been widely applied to the study of regional income distribution dynamics and convergence. This popularity reflects the rich body of DMC theory on the one hand and the ability of this framework to provide insights on the internal and external properties of regional income distribution dynamics on the other. In this paper we examine the properties of tests for spatial effects in DMC models of regional distribution dynamics. We do so through a series of Monte Carlo simulations designed to examine the size, power and robustness of tests for spatial heterogeneity and spatial dependence in transitional dynamics. This requires that we specify a data generating process for not only the null, but also alternatives when spatial heterogeneity or spatial dependence is present in the transitional dynamics. We are not aware of any work which has examined these types of data generating processes in the spatial distribution dynamics literature. Results indicate that tests for spatial heterogeneity and spatial dependence display good power for the presence of spatial effects. However, tests for spatial heterogeneity are not robust to the presence of strong spatial dependence, while tests for spatial dependence are sensitive to the spatial configuration of heterogeneity. When the spatial configuration can be considered random, dependence tests are robust to the dynamic spatial heterogeneity, but not so to the process mean heterogeneity when the difference in process means is large relative to the variance of the time series.

  13. Aligning, analyzing, and visualizing sequences for antibody engineering: Automated recognition of immunoglobulin variable region features. (United States)

    Jarasch, Alexander; Skerra, Arne


    The analysis and comparison of large numbers of immunoglobulin (Ig) sequences that arise during an antibody selection campaign can be time-consuming and tedious. Typically, the identification and annotation of framework as well as complementarity-determining regions (CDRs) is based on multiple sequence alignments using standardized numbering schemes, which allow identification of equivalent residues among different family members but often necessitate expert knowledge and manual intervention. Moreover, due to the enormous length variability of some CDRs the benefit of conventional Ig numbering schemes is limited and the calculation of correct sequence alignments can become challenging. Whereas, in principle, a well established set of rules permits the assignment of CDRs from the amino acid sequence alone, no currently available sequence alignment editor provides an algorithm to annotate new Ig sequences accordingly. Here we present a unique pattern matching method implemented into our recently developed ANTICALIgN editor that automatically identifies all hypervariable and framework regions in experimentally elucidated antibody sequences using so-called "regular expressions." By combination of this widely supported software syntax with the unique capabilities of real-time aligning, editing and analyzing extended sets of amino acid and/or nucleotide sequences simultaneously on a local workstation, ANTICALIgN provides a powerful utility for antibody engineering. Proteins 2016; 85:65-71. © 2016 Wiley Periodicals, Inc.

  14. Aquifer response to regional climate variability in a part of Kashmir Himalaya in India (United States)

    Jeelani, Gh


    Forty major perennial springs, under different lithological controls, in a part of Kashmir Himalaya in India were studied to understand the response of spring discharges to regional climate variability. The average monthly spring discharge is high in Triassic Limestone-controlled springs (karst springs) and low in alluvium- and Karewa-controlled springs. In general, the measured monthly spring discharges show an inverse relation with the monthly precipitation data. However, a direct correlation exists between the spring discharges and the degree of snow/ice melt. The results suggest that the creation of a low and continuous (but stable) recharge from the Triassic Limestone and Panjal Trap aquifers, due to blockage of groundwater flow between strata with contrasting hydraulic conductivity, attenuates the discharge and gives rise to small fluctuations in the alluvium- and Karewa-controlled springs. The average monthly discharge of the karst and alluvial springs showed an overall decreasing trend for two and a half decades, with the lowest discharge recorded in 2001. The study revealed that the regional/global warming and below-normal precipitation in the period of snow accumulation (PSA) has triggered the receding of glaciers and attenuation of spring discharges.

  15. An analysis of the variables that provide a supply chain with sustainable competitiveness An analysis of the variables that provide a supply chain with sustainable competitiveness Análisis de las variables que proporcionan una competitividad sostenible de la cadena de suministro

    Directory of Open Access Journals (Sweden)

    José A.D. Machuca


    Full Text Available Purpose: An agile, adaptable and aligned (Triple A supply chain (SC would seem to be key to obtaining sustainable competitive advantages. Little previous research has been done into the topic, however, and there are even discrepancies on the conceptual level. For this reason this study aims to propose a reference framework to determine the dimensions and factors that define agility, adaptability and alignment in the SC and to facilitate both the evaluation of its state by managers and researchers with respect to these variables and also the development of empirical research that determines its impact on performance.Design/methodology: A systematic literature review was carried out of specialist Operations Management, Logistics, Management and Supply Chain Management journals using the ProQuest (Abi/Inform Global database. The articles retrieved were examined and those that were relevant for this study were selected. Using these, a qualitative analysis was done that led to the proposed goal being achieved. Findings: This study sets out the definitions, dimensions and factors of the three variables and groups them together for the first time, thus providing a solid conceptual frame. Although the number of articles that analyse one or other of the variables is growing, it is still low. Agility is the variable on which most research has been done, while adaptability is the least analysed.Research limitations/implications: A theoretical reference framework is proposed for the Triple A in the SC based on earlier studies which do not discuss the joint effect of three variables, as a result of which there is no tested theoretical base. The model will be analysed empirically in future research.Originality/value: The lack of papers on agility, adaptability and alignment in the supply chain and the lack of a consensus regarding the dimensions and factors to define them reveal a need for studies such as this. Normal 0 21 false false false Microsoft

  16. Deciphering the importance of the palindromic architecture of the immunoglobulin heavy-chain 3' regulatory region. (United States)

    Saintamand, Alexis; Vincent-Fabert, Christelle; Garot, Armand; Rouaud, Pauline; Oruc, Zeliha; Magnone, Virginie; Cogné, Michel; Denizot, Yves


    The IgH 3' regulatory region (3'RR) controls class switch recombination (CSR) and somatic hypermutation (SHM) in B cells. The mouse 3'RR contains four enhancer elements with hs1,2 flanked by inverted repeated sequences and the centre of a 25-kb palindrome bounded by two hs3 enhancer inverted copies (hs3a and hs3b). hs4 lies downstream of the palindrome. In mammals, evolution maintained this unique palindromic arrangement, suggesting that it is functionally significant. Here we report that deconstructing the palindromic IgH 3'RR strongly affects its function even when enhancers are preserved. CSR and IgH transcription appear to be poorly dependent on the 3'RR architecture and it is more or less preserved, provided 3'RR enhancers are present. By contrast, a 'palindromic effect' significantly lowers VH germline transcription, AID recruitment and SHM. In conclusion, this work indicates that the IgH 3'RR does not simply pile up enhancer units but also optimally exposes them into a functional architecture of crucial importance.

  17. Impact of the Nature of the Side-Chains on the Polymer-Fullerene Packing in the Mixed Regions of Bulk Heterojunction Solar Cells

    KAUST Repository

    Wang, Tonghui


    Polymer-fullerene packing in mixed regions of a bulk heterojunction solar cell is expected to play a major role in exciton-dissociation, charge-separation, and charge-recombination processes. Here, molecular dynamics simulations are combined with density functional theory calculations to examine the impact of nature and location of polymer side-chains on the polymer-fullerene packing in mixed regions. The focus is on poly-benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione (PBDTTPD) as electron-donating material and [6,6]-phenyl-C61-butyric acid methyl ester (PC61BM) as electron-accepting material. Three polymer side-chain patterns are considered: i) linear side-chains on both benzodithiophene (BDT) and thienopyrroledione (TPD) moieties; ii) two linear side-chains on BDT and a branched side-chain on TPD; and iii) two branched side-chains on BDT and a linear side-chain on TPD. Increasing the number of branched side-chains is found to decrease the polymer packing density and thereby to enhance PBDTTPD–PC61 BM mixing. The nature and location of side-chains are found to play a determining role in the probability of finding PC61BM molecules close to either BDT or TPD. The electronic couplings relevant for the exciton-dissociation and charge-recombination processes are also evaluated. Overall, the findings are consistent with the experimental evolution of the PBDTTPD–PC61BM solar-cell performance as a function of side-chain patterns. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

  18. Immunological fine structure of the variable and constant regions of a polymorphic malarial surface antigen from Plasmodium falciparum. (United States)

    Jones, G L; Edmundson, H M; Lord, R; Spencer, L; Mollard, R; Saul, A J


    The 51-kDa merozoite surface antigen MSA2 of Plasmodium falciparum shows considerable strain-dependent polymorphism. Although marked sequence variation occurs in the central region of the molecule, the N and C-terminal sequences are highly conserved. A number of monoclonal antibodies directed against MSA2 have been described which inhibit parasite growth in vitro, but these are all directed against variable regions. In an attempt to raise strain independent antibodies we have prepared peptide-diphtheria toxoid (DT) constructs from 36 N-terminal octapeptides spanning the constant region and extending into the variable region of the FCQ/27 PNG variant staggered by one amino acid at either end. Similarly, we prepared 26 C-terminal octapeptides spanning the C-terminal constant region as well as 10 octapeptides from the variable region of the Indochina I variant MSA2. Most of the peptides elicited antipeptide titres in excess of 1/10(4) when administered to mice as peptide-DT adducts emulsified with Freund's complete adjuvant. Only 3 of the 43 N- and C-terminal constant region peptides elicited antibodies which reacted appropriately on immunofluorescence (IFA) or immunoblotting analysis with the intact MSA2 of both strains studied (FCQ/27 and Indochina I), whereas 3 other peptides from the variable region elicited antibodies reactive with the parent MSA2 only. Peptide constructs eliciting antibodies recognising the intact protein corresponded to elements in the cognate sequence of high antigenicity as predicted by the Jameson and Wolf algorithm.

  19. Assessing Regional Scale Variability in Extreme Value Statistics Under Altered Climate Scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Brunsell, Nathaniel [Univ. of Kansas, Lawrence, KS (United States); Mechem, David [Univ. of Kansas, Lawrence, KS (United States); Ma, Chunsheng [Wichita State Univ., KS (United States)


    Recent studies have suggested that low-frequency modes of climate variability can significantly influence regional climate. The climatology associated with extreme events has been shown to be particularly sensitive. This has profound implications for droughts, heat waves, and food production. We propose to examine regional climate simulations conducted over the continental United States by applying a recently developed technique which combines wavelet multi–resolution analysis with information theory metrics. This research is motivated by two fundamental questions concerning the spatial and temporal structure of extreme events. These questions are 1) what temporal scales of the extreme value distributions are most sensitive to alteration by low-frequency climate forcings and 2) what is the nature of the spatial structure of variation in these timescales? The primary objective is to assess to what extent information theory metrics can be useful in characterizing the nature of extreme weather phenomena. Specifically, we hypothesize that (1) changes in the nature of extreme events will impact the temporal probability density functions and that information theory metrics will be sensitive these changes and (2) via a wavelet multi–resolution analysis, we will be able to characterize the relative contribution of different timescales on the stochastic nature of extreme events. In order to address these hypotheses, we propose a unique combination of an established regional climate modeling approach and advanced statistical techniques to assess the effects of low-frequency modes on climate extremes over North America. The behavior of climate extremes in RCM simulations for the 20th century will be compared with statistics calculated from the United States Historical Climatology Network (USHCN) and simulations from the North American Regional Climate Change Assessment Program (NARCCAP). This effort will serve to establish the baseline behavior of climate extremes, the

  20. Dynamic changes in binding of immunoglobulin heavy chain 3' regulatory region to protein factors during class switching. (United States)

    Chatterjee, Sanjukta; Ju, Zhongliang; Hassan, Rabih; Volpi, Sabrina A; Emelyanov, Alexander V; Birshtein, Barbara K


    The 3' regulatory region (3' RR) of the Igh locus works at long distances on variable region (V(H)) and switch region (I) region promoters to initiate germ line (non-coding) transcription (GT) and promote class switch recombination (CSR). The 3' RR contains multiple elements, including enhancers (hs3a, hs1.2, hs3b, and hs4) and a proposed insulator region containing CTCF (CCCTC-binding factor) binding sites, i.e. hs5/6/7 and the downstream region ("38"). Notably, deletion of each individual enhancer (hs3a-hs4) has no significant phenotypic consequence, suggesting that the 3' RR has considerable structural flexibility in its function. To better understand how the 3' RR functions, we identified transcription factor binding sites and used chromatin immunoprecipitation (ChIP) assays to monitor their occupancy in splenic B cells that initiate GT and undergo CSR (LPS±IL4), are deficient in GT and CSR (p50(-/-)), or do not undergo CSR despite efficient GT (anti-IgM+IL4). Like 3' RR enhancers, hs5-7 and the 38 region were observed to contain multiple Pax5 binding sites (in addition to multiple CTCF sites). We found that the Pax5 binding profile to the 3' RR dynamically changed during CSR independent of the specific isotype to which switching was induced, and binding focused on hs1.2, hs4, and hs7. CTCF-associated and CTCF-independent cohesin interactions were also identified. Our observations are consistent with a scaffold model in which a platform of active protein complexes capable of facilitating GT and CSR can be formed by varying constellations of 3' RR elements.

  1. Interannual variability of Mediterranean evaporation and its relation to regional climate

    Energy Technology Data Exchange (ETDEWEB)

    Zveryaev, Igor I. [Moscow State University, P.P. Shirshov Institute of Oceanology, RAS and Faculty of Geography, Moscow (Russian Federation); Hannachi, Abdel A. [Stockholm University, Department of Meteorology, Stockholm (Sweden)


    Gridded monthly evaporation data for 1958-2006 from the Woods Hole Oceanographic Institution data set are used to investigate interannual variability of Mediterranean evaporation during cold and hot seasons and its relation to regional atmospheric dynamics, sea surface temperature and atmospheric elements of the hydrological cycle. The first EOF mode of Mediterranean evaporation, explaining more than 50% of its total variance, is characterized by the monopole pattern both in winter and summer. However, despite structural similarity, the EOF-1 of Mediterranean evaporation is affected by different climate signals in cold and hot seasons. During winter the EOF-1 is associated with the East Atlantic teleconnection pattern. In summer, there is indication of tropical influence on the EOF-1 of Mediterranean evaporation (presumably from Asian monsoon). Both in winter and summer, principal components of EOF-1 demonstrate clear interdecadal signals (with a stronger signature in summer) associated with large sea surface temperature anomalies. The results of a sensitivity analysis suggest that in winter both the meridional wind and the vertical gradient of saturation specific humidity (GSSH) near the sea surface contribute to the interdecadal evaporation signal. In summer, however, it is likely that the signal is more related to GSSH. Our analysis did not reveal significant links between the Mediterranean evaporation and the North Atlantic Oscillation in any season. The EOF-2 of evaporation accounts for 20% (11%) of its total variance in winter (in summer). Both in winter and summer the EOF-2 is characterized by a zonal dipole with opposite variations of evaporation in western and eastern parts of the Mediterranean Sea. This mode is associated presumably with smaller scale (i.e., local) effects of atmospheric dynamics. Seasonality of the leading modes of the Mediterranean evaporation is also clearly seen in the character of their links to atmospheric elements of the regional

  2. Variability of trace gas concentrations over Asian region: satellite observations vs model (United States)

    Sheel, Varun; Richter, Andreas; Srivastava, Shuchita; Lal, Shyam


    Nitrogen dioxide (NO_2) and Carbon Monoxide (CO) play a key role in the chemistry of the tropospheric ozone and are emitted mainly by anthropogenic processes. These emissions have been increasing over Asia over the past few years due to rapid economic growth and yet there are very few systematic ground based observations of these species over this region. We have analysed ten years of data from space borne instruments: Global Ozone Monitoring Experiment (GOME), SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY) and Measurements of Pollution in the Troposphere (MOPITT), which have been measuring the tropospheric abundance of these trace gases. We have examined trends over the period 1996-2008 in NO_2 and CO over a few Indian regions where high economic growth in the present decade is likely to see increased emissions for these species. However, even the highest growth rate of these species seen in the present study, is less when compared with similar polluted regions of China, where a much more rapid increase has been observed. In order to understand the trends and variability in atmospheric trace gas concentrations, one must take into account changes in emissions and transport. Only by assessing the relevance of each of these factors will it be possible to predict future changes with reasonable confidence. To this effect we have used a global chemical transport model, MOZART, to simulate concentrations of NO_2 and CO using the POET (European) and REAS (Asian) emission inventories. These are compared with satellite measurements to study seasonal variations and the discrepancies are discussed. The combined uncertainties of the emission inventory and retrieval of the satellite data could be contributing factors to the discrepancies. It may be thus worthwhile to develop emission inventories for India at a higher resolution to include local level activity data.

  3. Cost and time models for the evaluation of intermodal chains by using short sea shipping in the North Sea Region: the Rosyth-Zeebrugge route

    DEFF Research Database (Denmark)

    Lopez, Alba Martínez; Kronbak, Jacob; Jiang, Liping


    This paper is framed in the context of the EU Interreg IVB North Sea Region project Food Port. In line with this project, this paper aims to define mathematically cost and time models able to provide realistic information about the performances of road haulage and of intermodal chains using short...... for the success of intermodal chains using the Rosyth-Zeebrugge route. The results obtained validate the utility of the models and they suggest possible changes to the current operation of this SSS service in order to increase the marked potential possibilities for the intermodal chains through Rosyth-Zeebrugge....

  4. Detection of Natural Toxoplasma gondii Infection in Chicken in Thika Region of Kenya Using Nested Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    John Mokua Mose


    Full Text Available The detection of Toxoplasma gondii in free-range chickens is a good indicator of possible risk to human beings. The aim of this study was to investigate the occurrence of T. gondii in free-range chicken using polymerase chain reaction (PCR. Brain samples from 105 free-range chickens from three administrative areas in Thika region, Kenya, were collected, DNA-extracted, and analyzed using PCR to detect presence of T. gondii. The overall prevalence of T. gondii in all the three areas was 79.0% (95% CI: 70.0–86.4% and the prevalence across the three areas was not significantly different (P=0.5088; χ2=1.354. Female chickens had higher (79.4% prevalence than males (78.6%, although the difference was not significant (P=0.922, χ2 = 0.01. However, chickens that were more than 2 years old had significantly (P=0.003; χ2 = 11.87 higher prevalence compared to younger ones. The study indicates that there was a high occurrence of T. gondii infection in free-range chickens from Thika region and that the infection rate is age dependent. Further studies should be carried out to determine the possible role of roaming chickens in the epidemiology of the disease among humans in the area.

  5. The Effect of Regional Climate Variability on Outbreak of Bartonellosis Epidemics in Peru (United States)

    Zhou, Jia-Yu; Lau, K.-M.; Laughlin, Larry W.; Masuoka, Penny M.; Andre, Richard G.; Chamberlin, Judith; Lawyer, Phillip; Lau, William K. M. (Technical Monitor)


    Bartonellosis is a vector-borne, highly fatal, emerging infectious disease, which has been known in the Peruvian Andes since the early 1600s and has continued to be a problem in many mountain valleys in Peru and other Andean South American countries. The causative bacterium, Bartonella bacilliformis (Bb), is believed to be transmitted to humans by bites of the sand fly Lutzomyia verrucarum. According to available medical records, the transmission of infection often occurs in river valleys of the Andes Mountains at an altitude between 800 and 3500 meters above sea level. It shows a seasonal pattern, which usually begins to rise in December, peaks in February and March, and is at its lowest from July until November. The epidemics of bartonellosis also vary interannually, occurring every four to eight years, and appear to be associated with the El Nino cycle. In response to the National Oceanic and Atmospheric Administration (NOAA) announcement on climate variability and human health, which was constructed to stimulate integrated multidisciplinary research in the area of climate variability and health interactions, we have conducted a study to investigate the relationship between the El Nino induced regional climate variation and the outbreak of bartonellosis epidemics in Peru. Two test sites, Caraz and Cusco, were selected for this study. According to reports, Caraz has a long-standing history of endemic transmission and Cusco, which is located about five degrees poleward of Caraz, had no recorded epidemics until the most recent 1997/1998 El Nino event. The goal of this study is to clarify the relative importance of climatic risk factors for each area that could be predicted in advance, thus allowing implementation of cost-effective control measures, which would reduce disease morbidity and mortality.

  6. [Study on three-dimension spatial variability of regional soil salinity based on spectral indices]. (United States)

    Liu, Guang-Ming; Wu, Ya-Kun; Yang, Jin-Song; Yu, Shi-Peng


    In order to illustrate the three-dimension spatial variability of soil salinity in central China flood area of the Yellow river, integrated soil sampling data and remote sensing data, spectral indices and inverse distance weighting (IDW) method were applied to the estimation and simulation of three-dimension spatial distribution of soil salinity. The study was carried out in typical central China flood area of the Yellow river in Fengqiu County, Henan Province, China. The electrical conductivity of the saturation extract (EC1: 5) of 505 soil samples collected at 101 points was measured. The results indicated that the coefficient of variation of soil salinity at each soil layer is from 0.218 to 0.324 and exhibited the moderate spatial variability. The average of soil electrical conductivity is from 0.121 to 0.154 ds x m(-1). The 2 820 three-dimension spatial scattered data for soil electrical conductivity were taken at soil salinity mapping interpreted by spectral indices and soil electrical conductivity. Three-dimension IDW interpolation showed that a large area of high soil salinity mainly located in the region of Tianran canal and the along of the Yellow river. The shape of the soil salinity profile was downward flowed, revealing soil salinity increasing with depth in whole soil profile and soil salinity accumulated in the subsoil. The accuracy of the predictions was tested using 20 soil sampled points. The root mean square error (RMSE) of calibration for three-dimension distribution of soil salinity showed that the IDW method based on spectral indices was ideal. The research results can provide theoretical foundations to the management and utilization of salt-affected land in China flood area, especially in the Yellow river zone.

  7. Adaptation of rainfed agriculture to climatic variability in the Mixteca Alta Region of Oaxaca, Mexico (United States)

    Rogé, P.; Friedman, A. R.; Astier, M.; Altieri, M.


    The traditional management systems of the Mixteca Alta Region of Oaxaca, Mexico offer historical lessons about resilience to climatic variability. We interviewed small farmers to inquire about the dynamics of abandonment and persistence of a traditional management systems. We interpret farmers' narratives from a perspective of general agroecological resilience. In addition, we facilitated workshops in small farmers described their adaptation to past climate challenges and identified 14 indicators that they subsequently used to evaluate the condition of their agroecosystems. The most recent years presented increasingly extreme climatic and socioeconomic hardships: increased temperatures, delayed rainy seasons, reduced capacity of soils to retain soil moisture, changing cultural norms, and reduced rural labor. Farmers reported that their cropping systems were changing for multiple reasons: more drought, later rainfall onset, decreased rural labor, and introduced labor-saving technologies. Examination of climate data found that farmers' climate narratives were largely consistent with the observational record. There have been increases in temperature and rainfall intensity, and an increase in rainfall seasonality that may be perceived as later rainfall onset. Farmers ranked landscape-scale indicators as more marginal than farmer management or soil quality indicators. From this analysis, farmers proposed strategies to improve the ability of their agroecosystems to cope with climatic variability. Notably, they recognized that social organizing and education are required for landscape-level indicators to be improved. Transformative change is required to develop novel cropping systems and complementary activities to agriculture that will allow for farming to be sustained in the face of these challenges. Climate change adaptation by small farmers involves much more than just a set of farming practices, but also community action to tackle collective problems.

  8. Modeling South America regional smoke plume: aerosol optical depth variability and shortwave surface forcing (United States)

    Rosário, N. E.; Longo, K. M.; Freitas, S. R.; Yamasoe, M. A.; Fonseca, R. M.


    Intra-seasonal variability of smoke aerosol optical depth (AOD) and downwelling solar irradiance at the surface during the 2002 biomass burning season in South America was modeled using the Coupled Chemistry-Aerosol-Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CCATT-BRAMS). Measurements of AOD from the AErosol RObotic NETwork (AERONET) and solar irradiance at the surface from the Solar Radiation Network (SolRad-NET) were used to evaluate model results. In general, the major features associated with AOD evolution over the southern part of the Amazon Basin and cerrado ecosystem are captured by the model. The main discrepancies were found for high aerosol loading events. In the northeastern portion of the Amazon Basin the model systematically underestimated AOD. This is likely due to the cloudy nature of the region, preventing accurate detection of the fire spots used in the emission model. Moreover, measured AOD were very often close to background conditions and emissions other than smoke were not considered in the simulation. Therefore, under the background scenario, one would expect the model to underestimate AOD. The issue of high aerosol loading events in the southern part of the Amazon and cerrado is also discussed in the context of emission shortcomings. The Cuiabá cerrado site was the only one where the highest quality AERONET data were unavailable. Thus, lower quality data were used. Root-mean-square-error (RMSE) between the model and observations decreased from 0.48 to 0.17 when extreme AOD events (AOD550 nm ≥ 1.0) and Cuiabá were excluded from analysis. Downward surface solar irradiance comparisons also followed similar trends when extremes AOD were excluded. This highlights the need to improve the modelling of the regional smoke plume in order to enhance the accuracy of the radiative energy budget. Aerosol optical model based on the mean intensive properties of smoke from the southern part of the

  9. Singular vector decomposition of the internal variability of the Canadian Regional Climate Model

    Energy Technology Data Exchange (ETDEWEB)

    Diaconescu, Emilia Paula; Laprise, Rene [University of Quebec at Montreal (UQAM), Department of Earth and Atmospheric Sciences, Canadian Network for Regional Climate Modelling and Diagnostics, P.O. Box 8888, Montreal, QC (Canada); Centre ESCER (Etude et Simulation du Climat a l' Echelle Regionale), Montreal, QC (Canada); Zadra, Ayrton [University of Quebec at Montreal (UQAM), Department of Earth and Atmospheric Sciences, Canadian Network for Regional Climate Modelling and Diagnostics, P.O. Box 8888, Montreal, QC (Canada); Environment Canada, Meteorological Research Division, Montreal, QC (Canada); Centre ESCER (Etude et Simulation du Climat a l' Echelle Regionale), Montreal, QC (Canada)


    Previous studies have shown that Regional Climate Models (RCM) internal variability (IV) fluctuates in time depending on synoptic events. This study focuses on the physical understanding of episodes with rapid growth of IV. An ensemble of 21 simulations, differing only in their initial conditions, was run over North America using version 5 of the Canadian RCM (CRCM). The IV is quantified in terms of energy of CRCM perturbations with respect to a reference simulation. The working hypothesis is that IV is arising through rapidly growing perturbations developed in dynamically unstable regions. If indeed IV is triggered by the growth of unstable perturbations, a large proportion of the CRCM perturbations must project onto the most unstable singular vectors (SVs). A set of ten SVs was computed to identify the orthogonal set of perturbations that provide the maximum growth with respect to the dry total-energy norm during the course of the CRCM ensemble of simulations. CRCM perturbations were then projected onto the subspace of SVs. The analysis of one episode of rapid growth of IV is presented in detail. It is shown that a large part of the IV growth is explained by initially small-amplitude unstable perturbations represented by the ten leading SVs, the SV subspace accounting for over 70% of the CRCM IV growth in 36 h. The projection on the leading SV at final time is greater than the projection on the remaining SVs and there is a high similarity between the CRCM perturbations and the leading SV after 24-36 h tangent-linear model integration. The vertical structure of perturbations revealed that the baroclinic conversion is the dominant process in IV growth for this particular episode. (orig.)

  10. A Variable-resolution Surface Wave Dispersion Study of Eurasia, North Africa, and Surrounding Regions

    Energy Technology Data Exchange (ETDEWEB)

    Pasyanos, M E


    This paper presents the results of a large-scale study of surface wave dispersion performed across Eurasia and North Africa. Improvements were made to previous surface wave work by enlarging the study region, increasing path density, improving spatial resolution, and expanding the period range. This study expands the coverage area northwards and eastwards relative to a previous dispersion analysis, which covered only North Africa and the Middle East. We have significantly increased the number of seismograms examined and group velocity measurements made. We have now made good quality dispersion measurements for about 30,000 Rayleigh wave and 20,000 Love wave paths, and have incorporated measurements from several other researchers into the study. A conjugate gradient method was employed for the group velocity tomography, which improved the inversion from the previous study by adopting a variable smoothness. This technique allows us to go to higher resolution where the data allow without producing artifacts. The current results include both Love and Rayleigh wave inversions across the region for periods from 7 to 100 seconds at 1{sup o} resolution. Short period group velocities are sensitive to slow velocities associated with large sedimentary features such as the Caspian Sea, West Siberian Platform, Mediterranean Sea, Bay of Bengal, Tarim Basin, and Persian Gulf. Intermediate periods are sensitive to differences in crustal thickness, such as those between oceanic and continental crust or along orogenic zones and continental plateaus. At longer periods, fast velocities are consistently found beneath cratons while slow upper mantle velocities occur along rift systems, subduction zones, and collision zones such as the Tethys Belt. We have compared the group velocities at various periods with features such as sediment thickness, topographic height, crustal thickness, proximity to plate boundaries, lithospheric age and lithospheric thickness, and find significant

  11. Seasonal and Intraseasonal Variability of Mesoscale Convective Systems over the South Asian Monsoon Region

    Energy Technology Data Exchange (ETDEWEB)

    Virts, Katrina S.; Houze, Robert A.


    Seasonal and intraseasonal differences in mesoscale convective systems (MCSs) over South Asia are examined using A-Train satellites, a ground-based lightning network, and reanalysis fields. Pre-monsoon (April-May) MCSs occur primarily over Bangladesh and the eastern Bay of Bengal. During the monsoon (June-September), small MCSs occur over the Meghalaya Plateau and northeast Himalayan notch, while large and connected MCSs are most widespread over the Bay of Bengal. Monsoon MCSs produce less lightning and exhibit more extensive stratiform and anvil reflectivity structures in CloudSat observations than do pre-monsoon MCSs. During the monsoon season, Bay of Bengal and Meghalaya Plateau MCSs vary with the 30-60 day northward-propagating intraseasonal oscillation, while northeast Himalayan notch MCSs are associated with weak large-scale anomalies but locally enhanced CAPE. During intraseasonal active periods, a zone of enhanced large and connected MCSs, precipitation, and lightning extends from the northeastern Arabian Sea southeast over India and the Bay of Bengal, flanked by suppressed anomalies. Spatial variability is observed within this enhancement zone: lightning is most enhanced where MCSs are less enhanced, and vice versa. Reanalysis composites indicate that Bay of Bengal MCSs are associated with monsoon depressions, which are frequent during active monsoon periods, while Meghalaya Plateau MCSs are most frequent at the end of break periods, as anomalous southwesterly winds strengthen moist advection toward the terrain. Over both regions, MCSs exhibit more extensive stratiform and anvil regions and less lightning when the large-scale environment is moister, and vice versa.

  12. Airborne mineral components and trace metals in Paris region: spatial and temporal variability. (United States)

    Poulakis, E; Theodosi, C; Bressi, M; Sciare, J; Ghersi, V; Mihalopoulos, N


    A variety of mineral components (Al, Fe) and trace metals (V, Cr, Mn, Ni, Cu, Zn, Cd, Pb) were simultaneously measured in PM2.5 and PM10 fractions at three different locations (traffic, urban, and suburban) in the Greater Paris Area (GPA) on a daily basis throughout a year. Mineral species and trace metal levels measured in both fractions are in agreement with those reported in the literature and below the thresholds defined by the European guidelines for toxic metals (Cd, Ni, Pb). Size distribution between PM2.5 and PM10 fractions revealed that mineral components prevail in the coarse mode, while trace metals are mainly confined in the fine one. Enrichment factor analysis, statistical analysis, and seasonal variability suggest that elements such as Mn, Cr, Zn, Fe, and Cu are attributed to traffic, V and Ni to oil combustion while Cd and Pb to industrial activities with regional origin. Meteorological parameters such as rain, boundary layer height (BLH), and air mass origin were found to significantly influence element concentrations. Periods with high frequency of northern and eastern air masses (from high populated and industrialized areas) are characterized by high metal concentrations. Finally, inner city and traffic emissions were also evaluated in PM2.5 fraction. Significant contributions (>50 %) were measured in the traffic site for Mn, Fe, Cr, Zn, and Cu, confirming that vehicle emissions contribute significantly to their levels, while in the urban site, the lower contributions (18 to 33 %) for all measured metals highlight the influence of regional sources on their levels.

  13. Characterization of the native and denatured herceptin by enzyme linked immunosorbent assay and quartz crystal microbalance using a high-affinity single chain fragment variable recombinant antibody. (United States)

    Shang, Yuqin; Mernaugh, Ray; Zeng, Xiangqun


    Herceptin/Trastuzumab is a humanized IgG1κ light chain antibody used to treat some forms of breast cancer. A phage-displayed recombinant antibody library was used to obtain a single chain fragment variable (scFv, designated 2B4) to a linear synthetic peptide representing Herceptin's heavy chain CDR3. Enzyme linked immunosorbent assays (ELISAs) and piezoimmunosensor/quartz crystal microbalance (QCM) assays were used to characterize 2B4-binding activity to both native and heat denatured Herceptin. The 2B4 scFv specifically bound to heat denatured Herceptin in a concentration dependent manner over a wide (35-220.5 nM) dynamic range. Herceptin denatures and forms significant amounts of aggregates when heated. UV-vis characterization confirms that Herceptin forms aggregates as the temperature used to heat Herceptin increases. QCM affinity assay shows that binding stoichiometry between 2B4 scFv and Herceptin follows a 1:2 relationship proving that 2B4 scFv binds strongly to the dimers of heat denatured Herceptin aggregates and exhibits an affinity constant of 7.17 × 10(13) M(-2). The 2B4-based QCM assay was more sensitive than the corresponding ELISA. Combining QCM with ELISA can be used to more fully characterize nonspecific binding events in assays. The potential theoretical and clinical implications of these results and the advantages of the use of QCM to characterize human therapeutic antibodies in samples are also discussed.

  14. Modelling spatial, altitudinal and temporal variability of annual precipitation in mountainous regions: The case of the Middle Zagros, Iran (United States)

    Saeidabadi, Rashid; Najafi, Mohammed S.; Roshan, GholamReza; Fitchett, Jennifer M.; Abkharabat, Shoaieb


    Relationships between precipitation and elevation are difficult to model for mountainous regions, due to complexities in topography and moisture sources. Attempts to model these relationships need to be tested against long-term location specific meteorological data, and hence require a case-study approach. This study uses artificial neural networks to model these relationships for the Middle of Zagros region, in semi-arid western Iran. Precipitation data for the region were collected for 1995-2007. Annual precipitation was designated as the target variable for the network, which additionally included variables significantly related to precipitation for the region, including longitude, latitude, elevation, slope, distance from the ridge, and relative distance from moisture. Long-term changes in annual precipitation for the region are investigated for 1961-2010. The artificial neural network (ANN) model explains 76% of the spatial variability of precipitation in the Middle Zagros. Precipitation predominantly increases with elevation on the windward slope, to a maximum height of 2500 m.asl, and thereafter either remains constant or decreases slowly to the ridge. Precipitation in the region has decreased significantly over the study period, with fluctuations driven by AO, NAO, ENSO and variability in the strength of pressure centers. Spectral analysis reveals significant oscillations of 2-4 and 5 yr periods, which correspond temporally with cycles in macro-scale circulation, ENSO and the Mediterranean Low pressure.

  15. Global and regional methane budget and its inter-annual variability (United States)

    Bourakkadi, Zakia; Payan, Sébastien; Locatelli, Robin; Chevallier, Frederic; Saunois, Marielle; Bousquet, Philippe


    Methane global concentration has more than doubled since the pre-industrial times. This increase is generally caused by the anthropogenic activities like the massive use and extraction of fossil fuel, rice paddies agriculture and emissions from landfills. Space observations are very useful to monitor and quantify methane concentration in the atmosphere, in order to improve our knowledge of its sources, sinks, transport and trends. Since 2002 global methane total-columns mixing ratois from the SCanning Imaging Absorption spectroMeter for Atmospheric ChartographY (SCIAMACHY) on board ENVISAT was the first space-borne sensitive to methane in the boundary layer. However the communication with the instrument was lost in April 2012. Since January 2009 methane columns retrievals have been available also from the Thermal And Near Infrared Sensor for carbon Observations-Fourier Transform Spectrometer (TANSO-FTS), on-board the GOSAT satellite. In this study, we used measurements in the short wave infrared radiation (SWIR) from TANSO-FTS covering 5 years, from January 2010 to December 2014 to estimate global methane fluxes by inverse modeling, using the PYVAR-LMDZ model. We present here the results of global and regional methane budget, and its inter-annual variability during this period.

  16. Mitochondrial Control Region Variability in Mytilus galloprovincialis Populations from the Central-Eastern Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    Ioannis A. Giantsis


    Full Text Available The variable domain 1 (VD1 domain of the control region and a small segment of the rrnaL gene of the F mtDNA type were sequenced and analyzed in 174 specimens of Mytilus galloprovincialis. Samples were collected from eight locations in four Central-Eastern (CE Mediterranean countries (Italy, Croatia, Greece and Turkey. A new primer, specific for the F mtDNA type, was designed for the sequencing procedure. In total 40 different haplotypes were recorded, 24 of which were unique. Aside from the two populations situated in Thermaikos gulf (Northern Aegean, Greece, relatively high levels of haplotype and nucleotide diversity were estimated for both Central and Eastern Mediterranean populations. Eight out of the 40 haplotypes were shared by at least three populations while two of them were found in all populations. ΦST and cluster analysis revealed lack of structuring among CE Mediterranean populations with the exception of those located at the Sea of Marmara and Croatian coast which were highly differentiated. Apart from the species’ inherit dispersal ability, anthropogenic activities, such as the repeated translocations of mussel spat, seem to have played an important role in shaping the current genetic population structure of CE M. galloprovincialis mussels.

  17. Survey into the seafood consumption preferences and patterns in the portuguese population. Gender and regional variability. (United States)

    Cardoso, Carlos; Lourenço, Helena; Costa, Sara; Gonçalves, Susana; Nunes, Maria Leonor


    With the purpose of achieving a deeper knowledge of one of the most important seafood markets in Europe, a survey into the seafood consumption preferences and patterns in the Portuguese population was carried out. A thorough, comprehensive, and simple questionnaire was developed. Consumers were asked to state their preferences towards fish products, their consumption frequencies, the average meal portion, and the usual culinary treatments. Respondents provided personal data: gender, age, geographical location, education level, weight, height, and health condition. This paper presents the first part of the study's results, focusing mainly on the gender and regional variables. Portuguese consumers prefer wild to cultured fish as well as fat to lean fish. Chilled fish is preferred over frozen, salted/dried, canned, and smoked fish, being the latter the least preferred. Soaked cod, hake, and canned tuna are the most eaten seafood products. Men prefer to a greater extent wild and smoked fish. Men consume more cephalopods and sardine and women eat more frequently hake, pink cusk-eel, and redfish. Coastal populations prefer wild fish. Algarve (southern Portugal) consumers exhibit a stronger tendency to wild and whole fish and consume more sardine and sole. Madeira archipelago consumers are particularly fond of black scabbard fish.

  18. Structural characteristics of the variable regions of immunoglobulin genes encoding a pathogenic autoantibody in murine lupus. (United States)

    Tsao, B P; Ebling, F M; Roman, C; Panosian-Sahakian, N; Calame, K; Hahn, B H


    We have studied several monoclonal anti-double-stranded (ds) DNA antibodies for their ability to accelerate lupus nephritis in young NZB X NZW F1 female mice and to induce it in BALB/c mice. Two identified as pathogens in both strains have characteristics previously associated with nephritogenicity: expression of IgG2a isotype and IdGN2 idiotype. Both pathogenic antibodies used the combination of genes from the VHJ558 and VK9 subfamilies. Two weak pathogens failed to accelerate nephritis in young BW mice, but induced lupus nephritis in BALB/c mice. They both express IdGN2; one is cationic and an IgG3, the other is an IgG2a. Additional MAbs (some IgG2a, one IdGN2-positive) did not accelerate or induce nephritis. We have cloned and sequenced the variable regions of the immunoglobulin genes of one pathogenic autoantibody. No unique V, D, or J gene segments and no evidence of unusual mechanisms in generating diversity were used to construct this antibody. These data argue against use of unique abnormal Ig genes by systemic lupus erythematosus individuals to construct pathogenic autoantibody subsets. Instead, the major abnormality may be immunoregulatory.

  19. Spatial variability of 137Cs in the soil of Belgrade region (Serbia

    Directory of Open Access Journals (Sweden)

    Janković-Mandić Ljiljana J.


    Full Text Available Among radionuclides in the soil deposited after Chernobyl accident, 137Cs poses considerable environmental and radiological problems because of its relatively long half-life (30.17 y, its abundance in the fallout, high mobility and similarity to potassium as the major plant nutrient. In this study the samples of undisturbed surface soil (n=250 were taken from 70 regions in Belgrade, during 2006-2010. The specific activities of 137Cs were measured by gamma-ray spectrometry. Based on obtained results external effective dose rates were calculated according to the internationally accepted activity to dose rate conversion equations. The specific activities of 137Cs were geographically mapped. The presence of 137Cs has been detected in all soil samples, with high variability of its specific activity, ranging from 3 Bq kg-1 to 87 Bq kg-1. The mean specific activity of 137Cs was 23 Bq kg-1 and the corresponding absorbed dose was 1.5 nSv h-1. The observed range reflects the inhomogeneity of the deposition process following the Chernobyl accident. It could also be attributed to topographic differences and spatial differences in physicochemical and biological soil properties, soil type and vegetation cover. The results of the present study could be valuable database for future estimations of the impact of radioactive pollution.

  20. Assessment of sequence variability in a p23 gene region within and among three genotypes of the Theileria orientalis complex from south-eastern Australia. (United States)

    Perera, Piyumali K; Gasser, Robin B; Jabbar, Abdul


    Oriental theileriosis is a tick-borne, protozoan disease of cattle caused by one or more genotypes of Theileria orientalis complex. In this study, we assessed sequence variability in a region of the 23kDa piroplasm membrane protein (p23) gene within and among three T. orientalis genotypes (designated buffeli, chitose and ikeda) in south-eastern Australia. Genomic DNA (n=100) was extracted from blood of infected cattle from various locations endemic for oriental theileriosis and tested by polymerase chain reaction (PCR)-coupled mutation scanning (single-strand conformation polymorphism (SSCP)) and targeted sequencing analysis. Eight distinct sequences represented all DNA samples, and three genotypes were found: buffeli (n=3), chitose (3) and ikeda (2). Nucleotide pairwise comparisons among these eight sequences revealed considerably higher variability among the genotypes (6.6-11.7%) than within them (0-1.9%), indicating that the p23 gene region allows the accurate identification of T. orientalis genotypes. In the future, we will combine this gene with other molecular markers to study the genetic structure of T. orientalis populations in Australasia, which will pave the way to establish a highly sensitive and specific PCR-based assay for genotypic diagnosis of infection and for assessing levels of parasitaemia in cattle.

  1. An evolutionarily mobile antigen receptor variable region gene: doubly rearranging NAR-TcR genes in sharks. (United States)

    Criscitiello, Michael F; Saltis, Mark; Flajnik, Martin F


    Distinctive Ig and T cell receptor (TcR) chains define the two major lineages of vertebrate lymphocyte yet similarly recognize antigen with a single, membrane-distal variable (V) domain. Here we describe the first antigen receptor chain that employs two V domains, which are generated by separate VDJ gene rearrangement events. These molecules have specialized "supportive" TcRdeltaV domains membrane-proximal to domains with most similarity to IgNAR V. The ancestral NAR V gene encoding this domain is hypothesized to have recombined with the TRD locus in a cartilaginous fish ancestor >200 million years ago and encodes the first V domain shown to be used in both Igs and TcRs. Furthermore, these data support the view that gamma/delta TcRs have for long used structural conformations recognizing free antigen.

  2. Modulation of extremes in the Atlantic region by modes of climate variability/change: A mechanistic coupled regional model study

    Energy Technology Data Exchange (ETDEWEB)

    Saravanan, Ramalingam [Texas A & M Univ., College Station, TX (United States)


    During the course of this project, we have accomplished the following: 1) Explored the parameter space of component models to minimize regional model bias 2) Assessed the impact of air-sea interaction on hurricanes, focusing in particular on the role of the oceanic barrier layer 3) Contributed to the activities of the U.S. CLIVAR Hurricane Working Group 4) Assessed the impact of lateral and lower boundary conditions on extreme flooding events in the U.S. Midwest in regional model simulations 5) Analyzed the concurrent impact of El Niño-Southern Oscillation and Atlantic Meridional Mode on Atlantic Hurricane activity using observations and regional model simulations

  3. A two-in-one antibody engineered from a humanized interleukin 4 antibody through mutation in heavy chain complementarity-determining regions. (United States)

    Lee, Chingwei V; Koenig, Patrick; Fuh, Germaine


    A mono-specific antibody may recruit a second antigen binding specificity, thus converting to a dual-specific Two-in-One antibody through mutation at the light chain complementarity-determining regions (CDRs). It is, however, unknown whether mutation at the heavy chain CDRs may evolve such dual specificity. Herein, we examined the CDRs of a humanized interleukin 4 (IL4) antibody using alanine scanning and structural modeling, designed libraries of mutants in regions that tolerate mutation, and isolated dual specific antibodies harboring mutation at the heavy chain CDRs only. We then affinity improved an IL4/IL5 dual specific antibody to variants with dissociation constants in the low nanomolar range for both antigens. The results demonstrate the full capacity of antibodies to evolve dual binding specificity.

  4. The C-terminal Region of Laminin β Chains Modulates the Integrin Binding Affinities of Laminins*S⃞


    Taniguchi, Yukimasa; Ido, Hiroyuki; Sanzen, Noriko; Hayashi, Maria; Sato-Nishiuchi, Ryoko; Futaki, Sugiko; Sekiguchi, Kiyotoshi


    Laminins are major cell-adhesive proteins in basement membranes that are capable of binding to integrins. Laminins consist of three chains (α, β, and γ), in which three laminin globular modules in the α chain and the Glu residue in the C-terminal tail of the γ chain have been shown to be prerequisites for binding to integrins. However, it remains unknown whether any part of the β chain is involved in laminin-integrin interactions. We compared the binding affinities of ...

  5. Variability of adenoidectomy/tonsillectomy rates among children of the Veneto Region, Italy

    Directory of Open Access Journals (Sweden)

    Andretta Marilisa


    Full Text Available Abstract Background Despite national guidelines in 2003 aimed at limiting the recourse to tonsillectomy and/or adenoidectomy (A/T, the latter are among the most frequent pediatric surgeries performed in Italy. Aim of the study is to investigate variability of A/T rates among children of the Veneto Region, Italy. Methods All discharges of Veneto residents with Diagnosis-Related Groups 57–60 and ICD9-CM intervention codes 28.2 (tonsillectomy, 28.3 (adenotonsillectomy, 28.6 (adenoidectomy were selected in the period 2000–2006 for a descriptive analysis. A multilevel Poisson regression model was applied to estimate Incidence Rate Ratios (IRR with 95% Confidence Intervals (CI for A/T surgery among children aged 2–9 years in 2004–2006, while taking into account clustering of interventions within the 21 Local Health Units. Results Through 2000–2006, the overall number of A/T surgeries decreased (-8%; there was a decline of adenoidectomies (-20% and tonsillectomies (-8%, whereas adenotonsillectomies raised (+18%. Analyses on children aged 2–9 resulted in an overall rate of 14.4 surgeries per 1000 person-years (16.1 among males and 12.5 among females, with a wide heterogeneity across Local Health Units (range 8.1–27.6. At random intercept Poisson regression, while adjusting for sex and age, intervention rates were markedly lower among foreign than among Italian children (IRR = 0.57, CI 0.53–0.61. A/T rates in the 10–40 age group (mainly tonsillectomies computed for each Local Health Unit and introduced in the regression model accounted for 40% of the variance at Local Health Unit level of pediatric rates (mainly adenoidectomies and adenotonsillectomies. Conclusion A/T rates in the Veneto Region, especially adenoidectomies among children aged 2–9 years, remain high notwithstanding a decrease through 2000–2006. A wide heterogeneity according to nationality and Local Health Units is evident. The propensity to A/T surgery of each Local

  6. Evaluating climate variables, indexes and thresholds governing Arctic urban sustainability: case study of Russian permafrost regions (United States)

    Anisimov, O. A.; Kokorev, V.


    Addressing Arctic urban sustainability today forces planners to deal with the complex interplay of multiple factors, including governance and economic development, demography and migration, environmental changes and land use, changes in the ecosystems and their services, and climate change. While the latter can be seen as a factor that exacerbates the existing vulnerabilities to other stressors, changes in temperature, precipitation, snow, river and lake ice, and the hydrological regime also have direct implications for the cities in the North. Climate change leads to reduced demand for heating energy, on one hand, and heightened concerns about the fate of the infrastructure built upon thawing permafrost, on the other. Changes in snowfall are particularly important and have direct implications for the urban economy, as together with heating costs, expenses for snow removal from streets, airport runways, roofs and ventilation corridors underneath buildings erected on pile foundations on permafrost constitute the bulk of the city's maintenance budget. Many cities are located in river valleys and are prone to flooding that leads to enormous economic losses and casualties, including human deaths. The severity of the northern climate has direct implications for demographic changes governed by regional migration and labor flows. Climate could thus be viewed as an inexhaustible public resource that creates opportunities for sustainable urban development. Long-term trends show that climate as a resource is becoming more readily available in the Russian North, notwithstanding the general perception that globally climate change is one of the challenges facing humanity in the 21st century. In this study we explore the sustainability of the Arctic urban environment under changing climatic conditions. We identify key governing variables and indexes and study the thresholds beyond which changes in the governing climatic parameters have significant impact on the economy

  7. Preparation and characterization of anti-tissue factor single-chain variable fragment antibody for cancer diagnosis. (United States)

    Sato, Ryuta; Obonai, Toshifumi; Tsumura, Ryo; Tsumoto, Kouhei; Koga, Yoshikatsu; Yasunaga, Masahiro; Matsumura, Yasuhiro


    Tissue factor (TF), which serves as the initiator of the extrinsic blood coagulation cascade, has been found to be overexpressed in various solid tumors, especially brain tumors, pancreatic cancer, and gastric cancer. Overexpression of TF is considered to contribute to the high incidence of thrombotic complications and poor prognosis in patients with such cancers. Therefore, detection or targeting of TF may be a promising approach for the diagnosis and treatment of solid tumors that are known to overexpress the protein. Here, we used the recombinant DNA technology to develop an anti-TF single-chain Fv (scFv) of small size and high affinity for its target. The biochemical characteristics of the anti-TF scFv were evaluated using surface plasmon resonance (SPR) sensing and flow cytometry. The data obtained showed that the affinity of the anti-TF scFv was 2.04 × 10(-8) (KD), and that the protein showed significant binding to the cancer cells. Then, Alexa 647-labeled anti-TF scFv and anti-TF IgG were administered to mice bearing chemically induced spontaneous tumors. The maximum tumor to background ratios of anti-TF scFv and anti-TF IgG were obtained 3 and 24 h after the injections, respectively. This study indicates anti-TF scFv may be suitable as an imaging probe for the diagnosis of solid tumors.

  8. Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions

    Directory of Open Access Journals (Sweden)

    Alberto Muñoz


    Full Text Available Ecological Niche Models (ENMs are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models. Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species and taxonomy (amphibians and reptiles. Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural

  9. Interannual Arctic sea ice variability and associated winter weather patterns: A regional perspective for 1979-2014 (United States)

    Chen, Hans W.; Alley, Richard B.; Zhang, Fuqing


    Using Arctic sea ice concentration derived from passive microwave satellite observations in autumn and early winter over the 1979-2014 period, the Arctic region was objectively classified into several smaller regions based on the interannual sea ice variability through self-organizing map analyses. The trend in regional sea ice extent (RSIE) in each region was removed using an adaptive, nonlinear, and nonstationary method called Ensemble Empirical Mode Decomposition, which captures well the accelerating decline of Arctic RSIEs in recent decades. Although the linear trend in RSIE is negative in all regions in both seasons, there are marked differences in RSIE trends and variability between regions, with the largest negative trends found during autumn in the Beaufort Sea, the Barents-Kara Seas, and the Laptev-East Siberian Seas. Winter weather patterns associated with the nonlinearly detrended RSIEs show distinct features for different regions and tend to be better correlated with the autumn than early winter RSIE anomalies. Sea ice losses in the Beaufort Sea and the Barents-Kara Seas are both associated with a cooling of Eurasia, but in the former case the circulation anomaly is reminiscent of a Rossby wave train, whereas in the latter case the pattern projects onto the negative phase of the Arctic Oscillation. These results highlight the nonuniform changes in Arctic sea ice and suggest that regional sea ice variations may play a crucial role for the winter weather patterns.

  10. Relationship between Eurasian large-scale patterns and regional climate variability over the Black and Baltic Seas

    Energy Technology Data Exchange (ETDEWEB)

    Stankunavicius, G.; Pupienis, D. [Vilnius Univ. (Lithuania). Dept. of Hydrology and Climatology; Basharin, D. [National Academy of Science of Ukraine, Sevastopol (Ukraine). Sevastopol Marine Hydrophysical Inst.


    Using a NCEP/NCAR Reanalysis dataset and the empirical orthogonal function (EOF) analysis approach we studied interannual to decadal variabilities of the sea-level air pressure (SLP) and the surface air temperature (SAT) fields over Eurasia during the 2nd part of the 20th century. Our results agree with those of the previous studies, which conclude that Eurasian trends are the result of storm-path changes driven by the interdecadal behaviour of the NAO-like meridional dipole pattern in the Atlantic. On interannual and decadal time scales, significant synchronous correlations between correspondent modes of SAT and SLP EOF patterns were found. This fact suggests that there is a strong and stable Eurasian interrelationship between SAT and SLP large-scale fields which affects the local climate of two sub-regions: the Black and Baltic Seas. The climate variability in these sub-regions was studied in terms of Eurasian large-scale surface-temperature and air-pressure patterns responses. We concluded that the sub-regional climate variability substantially differs over the Black and Baltic Seas, and depends on different Eurasian large-scale patterns. We showed that the Baltic Sea region is influenced by the patterns arising primary from NAO-like meridional dipole, as well as Scandinavian patterns, while the Black Sea's SAT/SLP variability is influenced mainly by the second mode EOF (eastern Atlantic) and large scale tropospheric wave structures. (orig.)

  11. Generation and characterization of a human single-chain fragment variable (scFv antibody against cytosine deaminase from Yeast

    Directory of Open Access Journals (Sweden)

    Tombesi Marina


    Full Text Available Abstract Background The ability of cytosine deaminase (CD to convert the antifungal agent 5-fluorocytosine (5-FC into one of the most potent and largely used anticancer compound such as 5-fluorouracil (5-FU raised considerable interest in this enzyme to model gene or antibody – directed enzyme-prodrug therapy (GDEPT/ADEPT aiming to improve the therapeutic ratio (benefit versus toxic side-effects of cancer chemotherapy. The selection and characterization of a human monoclonal antibody in single chain fragment (scFv format represents a powerful reagent to allow in in vitro and in vivo detection of CD expression in GDEPT/ADEPT studies. Results An enzymatic active recombinant CD from yeast (yCD was expressed in E. coli system and used as antigen for biopanning approach of the large semi-synthetic ETH-2 antibody phage library. Several scFvs were isolated and specificity towards yCD was confirmed by Western blot and ELISA. Further, biochemical and functional investigations demonstrated that the binding of specific scFv with yCD did not interfere with the activity of the enzyme in converting 5-FC into 5-FU. Conclusion The construction of libraries of recombinant antibody fragments that are displayed on the surface of filamentous phage, and the selection of phage antibodies against target antigens, have become an important biotechnological tool in generating new monoclonal antibodies for research and clinical applications. The scFvH5 generated by this method is the first human antibody which is able to detect yCD in routinary laboratory techniques without interfering with its enzymatic function.

  12. Analysis of inter-variable relations in regional climate model output (United States)

    Wilcke, Renate; Chandler, Richard


    The topic of physical consistency and inter-variable relations of climate model output, in particular when applying statistical downscaling and bias correction to single variables, is widely discussed in the climate impact modelling and climate impact communities. Many situations require the consideration of several climate variables simultaneously, as a result of which it is also necessary to check that the inter-variable dependence structure is simulated realistically by the RCMs. Given that it is common practice to bias-adjust RCM outputs so as to improve their properties with respect to the distribution of variables taken individually, it is also of interest to determine whether inter-variable relationships are affected by empirical bias adjustment procedures such as quantile mapping, that are applied separately to each variable. A pragmatic reason to look at this is, if bias-adjusted outputs are to be used in impacts studies, it is necessary to check that the inter-variable relationships are realistic. A more fundamental reason is, that RCMs are physically based and, before bias correction, their outputs should therefore ideally be physically consistent. However, an empirical bias adjustment procedure has the potential to break the physical consistency, thereby removing one of the strongest justifications for using RCMs in the first place. Based on these considerations, the study aims to answer two questions. The first is to assess the inter-variable relationships in a suite of RCM outputs in more detail than has previously been attempted, by examining conditional probability densities instead of correlations. The second is to quantify the extent to which these conditional densities are distorted by an empirical bias adjustment procedure. The results can be used both to evaluate the ability of current RCMs (bias-adjusted or not) to provide useful information for climate change impact assessments; and also to determine the viability of quantile mapping as a

  13. Molecular characterization of the variable heavy and light chain regions of five HIV-1 specific human monoclonal antibodies.

    NARCIS (Netherlands)

    E.M.M. van der Donk; M. Schutten (Martin); A.D.M.E. Osterhaus (Albert); R.W.J. van der Heijden (Roger)


    textabstractWe have reported the generation and characterization of four HIV-1 neutralizing human monoclonal antibodies. Three antibodies recognize a conformational epitope within the CD4-binding site of HIV-1 gp120 and one recognizes a linear epitope located within the hypervariable V3 domain of gp

  14. A regional landslide warning system based on spatially variable rainfall thresholds (United States)

    Segoni, Samuele; Rossi, Guglielmo; Rosi, Ascanio; Catani, Filippo


    Rainfall is widely recognized as one of the major causes for landsliding. When studying the conditions of triggering of mass movements at regional scale, a process-based approach is seldom possible because of the complexity in the spatial organization of the involved independent variables (e.g. soil properties). Therefore, empirical methods based on the definition of triggering thresholds are usually employed for the definition of warning systems or for landslide hazard assessments. Such thresholds are defined by observing the characteristics of past rainfall events that have resulted in landslides and selecting the lower bound envelope curve in intensity-duration plots depicting such events. These curves, generally represented by power-law type functions linking, e.g., intensity and duration of the critical rainfall, define the lowest level above which landslides should be expected. In the present work, concerning the territory of Tuscany (ab. 23,000 km2), a similar approach is adopted and described which presents some improvements with respect to traditional methods. First of all, the strong variability of environmental, meteorological and geological factors within the study area, together with evidences from available data on triggering conditions, imply that a single general threshold would be affected by a too large degree of overestimation of hazard and suggest the adoption of locally defined thresholds. The studied area was then partitioned in 25 Alert Zones and each of them has been analyzed separately to provide distinct rainfall thresholds. Secondly, to handle the amount of available data (the analysis regards the period 2000-2007 and involves 408 rainfall events, which were registered by a network of 332 rain-gauges and that caused 2132 landslides), a software has been developed for automatically analyzing rainfall patterns and defining such thresholds. In particular, the automated analysis performs the following tasks: i) Defining, for every rain

  15. Generation and characterization of chicken-sourced single-chain variable fragments (scFvs) against porcine interferon-gamma (pIFN-γ). (United States)

    Chen, Hong-Xiu; He, Fan; Sun, Yuan; Luo, Yuzi; Qiu, Hua-Ji; Zhang, Xiao-Ying; Sutton, Brian J


    Development of chicken-sourced antibodies offers an alternative strategy for the development of highly specific antibodies against mammalian proteins with conserved epitopes due to the phylogenetic distance between avian and mammalian species. In this study, the single-chain variable fragments (scFvs) against porcine interferon-gamma was screened and characterized from a hyperimmunized chicken phage display library. The expressed soluble scFvs exhibited highly specific recognition of porcine interferon-gamma in ELISA, Western blot, and immunofluorescence staining assays. Results of the current study indicate that it is possible to develop scFv IgY antibodies to a mammalian interferon by using Biopanning technology. Furthermore, it also confirms that monoclonal avian IgY antibody technique could be applied as a promising tool to produce immunoglobulin molecules with high specificity and affinity towards conserved mammalian epitopes or antigens.

  16. Screening and identification of human ZnT8-specific single-chain variable fragment (scFv) from type 1 diabetes phage display library. (United States)

    Wu, Qian; Wang, Xiaodong; Gu, Yong; Zhang, Xiao; Qin, Yao; Chen, Heng; Xu, Xinyu; Yang, Tao; Zhang, Mei


    Zinc transporter 8 (ZnT8) is a major autoantigen and a predictive marker in type 1 diabetes (T1D). To investigate ZnT8-specific antibodies, a phage display library from T1D was constructed and single-chain antibodies against ZnT8 were screened and identified. Human T1D single-chain variable fragment (scFv) phage display library consists of approximately 1×10(8) clones. After four rounds of bio-panning, seven unique clones were positive by phage ELISA. Among them, C27 and C22, which demonstrated the highest affinity to ZnT8, were expressed in Escherichia coli Top10F' and then purified by affinity chromatography. C27 and C22 specifically bound ZnT8 N/C fusion protein and ZnT8 C terminal dimer with one Arg325Trp mutation. The specificity to human islet cells of these scFvs were further confirmed by immunohistochemistry. In conclusion, we have successfully constructed a T1D phage display antibody library and identified two ZnT8-specific scFv clones, C27 and C22. These ZnT8-specific scFvs are potential agents in immunodiagnostic and immunotherapy of T1D.

  17. Temporal and spatial variability of aerosol optical depth in the Sahel region in relation to vegetation remote sensing (United States)

    Holben, B. N.; Fraser, R. S.; Eck, T. F.


    In order to monitor the aerosol characteristics needed for atmospheric correction of remotely sensed data, a network of sun photometers was established in the Sahel region of Senegal, Mali, and Niger. Data analysis suggests that there is a high spatial variability of the aerosol optical thickness tau(a) in the western Sahel region. At a 67 percent confidence level the instantaneous values of tau(a) can be extrapolated approximately 270-400 km with an error tolerance of 50 percent. Spatial variability in the dry season is found to be of a similar magnitude. The ranges of variations in the NDVI in the Sahel region are shown to be approximately 0.02 and 0.01, respectively, due to commonly observed fluctuations in the aerosol optical thickness and aerosol size distribution.

  18. Regional variability in dust-on-snow processes and impacts in the Upper Colorado River Basin (United States)

    Skiles, S. McKenzie; Painter, Thomas H.; Belnap, Jayne; Holland, Lacey; Reynolds, Richard; Goldstein, Harland; Lin, J.


    Dust deposition onto mountain snow cover in the Upper Colorado River Basin frequently occurs in the spring when wind speeds and dust emission peaks on the nearby Colorado Plateau. Dust loading has increased since the intensive settlement in the western USA in the mid 1880s. The effects of dust-on-snow have been well studied at Senator Beck Basin Study Area (SBBSA) in the San Juan Mountains, CO, the first high-altitude area of contact for predominantly southwesterly winds transporting dust from the southern Colorado Plateau. To capture variability in dust transport from the broader Colorado Plateau and dust deposition across a larger area of the Colorado River water sources, an additional study plot was established in 2009 on Grand Mesa, 150 km to the north of SBBSA in west central, CO. Here, we compare the 4-year (2010–2013) dust source, deposition, and radiative forcing records at Grand Mesa Study Plot (GMSP) and Swamp Angel Study Plot (SASP), SBBSA's subalpine study plot. The study plots have similar site elevations/environments and differ mainly in the amount of dust deposited and ensuing impacts. At SASP, end of year dust concentrations ranged from 0.83 mg g−1 to 4.80 mg g−1, and daily mean spring dust radiative forcing ranged from 50–65 W m−2, advancing melt by 24–49 days. At GMSP, which received 1.0 mg g−1 less dust per season on average, spring radiative forcings of 32–50 W m−2 advanced melt by 15–30 days. Remote sensing imagery showed that observed dust events were frequently associated with dust emission from the southern Colorado Plateau. Dust from these sources generally passed south of GMSP, and back trajectory footprints modelled for observed dust events were commonly more westerly and northerly for GMSP relative to SASP. These factors suggest that although the southern Colorado Plateau contains important dust sources, dust contributions from other dust sources contribute to dust loading in this region

  19. Modelling spatial variability and uncertainty of cadmium leaching to groundwater in an urban region (United States)

    Beyer, Christof; Altfelder, Sven; Duijnisveld, Wilhelmus H. M.; Streck, Thilo


    SummaryOver the last century, soils in the region of Nordenham in northern Germany received high loads of heavy-metals by air-borne immissions from a close-by metal smelter. Based on measured soil properties and cadmium contamination data the leaching of Cd to groundwater was predicted for Nordenham using a numerical transport model based on the convection-dispersion equation. The main objective in this study was to account for the spatial variability and uncertainty of Cd sorption controlling soil properties ( pH, organic carbon content) and to analyze their propagation into the variance of area-related model outputs, i.e. Cd breakthrough concentrations at the groundwater surface. For this purpose a nested Monte-Carlo method was combined with deterministic numerical 1D simulations of Cd leaching. The transport model was parameterized without any parameter fitting involved. The validity of the model was verified by retrospective simulations from the initial operation of the smelter until the year of soil sampling. Forecast simulations were run for a period of 200 years. Predicted local scale Cd breakthrough concentrations at the groundwater surface were evaluated by spatial aggregation for single blocks at the field scale, yielding area-related concentrations with associated uncertainties from imprecise knowledge on local soil properties. Significant exceedance of the limit of the German drinking water ordinance of 5 μg L -1 is observed on approximately 90% of the study area with the average point in time of limit value exceedance being the year 2066 and a 90% prediction interval of 2049-2092. At the end of the simulation period, Cd concentrations at the groundwater surface still increase on large parts of the study area. The spatially averaged Cd concentration is 19.89 μg L -1 with a 90% prediction interval of 15.28-24.69 μg L -1. Locally, however, concentrations larger than 60 μg L -1 may be reached. Prediction uncertainty is only moderate and does not

  20. A single mutation in framework 2 of the heavy variable domain improves the properties of a diabody and a related single-chain antibody. (United States)

    Rodríguez-Rodríguez, Everardo Remi; Ledezma-Candanoza, Luis M; Contreras-Ferrat, Luis Gabriel; Olamendi-Portugal, Timoteo; Possani, Lourival D; Becerril, Baltazar; Riaño-Umbarila, Lidia


    Excellent results regarding improved therapeutic properties have been often obtained through the conversion of a single-chain variable fragment (scFv) into a noncovalent dimeric antibody (diabody) via peptide linker shortening. We utilized this approach to obtain a dimeric version of the human scFv 6009F, which was originally engineered to neutralize the Cn2 toxin of Centruroides noxius scorpion venom. However, some envenoming symptoms remained with diabody 6009F. Diabody 6009F was subjected to directed evolution to obtain a variant capable of eliminating envenoming symptoms. After two rounds of biopanning, diabody D4 was isolated. It exhibited a single mutation (E43G) in framework 2 of the heavy-chain variable domain. Diabody D4 displayed an increase in T(m) (thermal transition midpoint temperature) of 6.3°C compared with its dimeric precursor. The importance of the E43G mutation was tested in the context of the human scFv LR, a highly efficient antibody against Cn2, which was previously generated by our group [Riaño-Umbarila, L., Contreras-Ferrat, G., Olamendi-Portugal, T., Morelos-Juárez, C., Corzo, G., Possani, L. D. and Becerril, B. (2011). J. Biol. Chem.286, 6143-6151]. The new variant, scFv LER, displayed an increase in T(m) of 3.4°C and was capable of neutralizing 2 LD(50) of Cn2 toxin with no detectable symptoms when injected into mice at a 1:1 toxin-to-antibody molar ratio. These results showed that the E43G mutation might increase the therapeutic properties of these antibody fragments. Molecular modeling and dynamics results suggest that the rearrangement of the hydrogen-bonding network near the E43G mutation could explain the improved functional stability and neutralization properties of both the diabody D4 and scFv LER.

  1. The variability of radiative balance elements and air temperature over the Asian region of Russia

    Directory of Open Access Journals (Sweden)

    E. V. Kharyutkina


    Full Text Available The variability of spatial-temporal distribution of temperature and heat balance elements is investigated for the Asian territory of Russia (45–80° N, 60–180° E using JRA-25, NCEP/DOE AMIP-II reanalysis data and observational data for the period of global warming 1979–2008. It is shown that temperature trend over the territory is 1.4 °C for the period under study according to reanalysis data. Since the beginning of 90s of 20th century the increase of back earth-atmosphere shortwave radiation is observed. Such tendency is in conformity with the cloud cover distribution and downward shortwave radiation at the surface. Regression model describing temperature variability with variability of heat balance elements was presented. We conclude that possible applications for the model include the convenient estimate of temperature variability according to reanalysis data.

  2. Morphological variability of Carex dioica L. (Cyperaceae Juss.) in Polissya region


    Svetlana V. Izmestieva


    Morphological variability of Carex dioica L. generative individuals in 4 habitats on the territory of Polissya has analysed. It is established that antropogenic influence and biotope heterogenity determine the highest level of morphological changeability of individuals in one of the localities on the bog Koza. The length of leaves and stems are the most variable traits which depend on the environmental conditions. Stability of such characteristics, as a width of leaves and a length of spikes ...

  3. Searching for I band variability in stars in the M/L spectral transition region

    CERN Document Server

    Ramsay, Gavin; Doyle, J Gerry


    We report on I band photometric observations of 21 stars with spectral types between M8 and L4 made using the Isaac Newton Telescope. The total amount of time for observations which had a cadence of <2.3 mins was 58.5 hrs, with additional data with lower cadence. We test for photometric variability using the Kruskal-Wallis H-test and find that 4 sources (2MASS J10224821+5825453, 2MASS J07464256+2000321, 2MASS J16262034+3925190 and 2MASS J12464678+4027150) were found to be significantly variable at least on one epoch. Three of these sources are reported as photometrically variable for the first time. If we include sources which were deemed marginally variable, the number of variable sources is 6 (29 percent). No flares were detected from any source. The percentage of sources which we found were variable is similar to previous studies. We summarise the mechanisms which have been put forward to explain the light curves of brown dwarfs.

  4. Variability analyses, site characterization, and regional [OH] estimates using trace gas measurements from the NOAA Global Greenhouse Gas Reference Network

    Directory of Open Access Journals (Sweden)

    Jan Pollmann


    Full Text Available Abstract Trace gas measurements from whole air samples collected weekly into glass flasks at background monitoring sites within the NOAA Global Greenhouse Gas Reference Network program (with most of the sites also being World Meteorological Organization (WMO Global Atmospheric Watch (GAW stations were used to investigate the variability-lifetime relationship for site characterization and to estimate regional and seasonal OH concentrations. Chemical species considered include the atmospheric trace gases CO, H2, and CH4, as well as the non-methane hydrocarbons (NMHC ethane (C2H6, propane (C3H8, i-butane (i-C4H10, and n-butane (n-C4H10. The correlation between atmospheric variability and lifetime was applied on a global scale spanning 42 sites with observations covering a period of 5 years. More than 50,000 individual flask measurement results were included in this analysis, making this the most extensive study of the variability-lifetime relationship to date. Regression variables calculated from the variability-lifetime relationship were used to assess the “remoteness” of sampling sites and to estimate the effect of local pollution on the measured distribution of atmospheric trace gases. It was found that this relationship yields reasonable results for description of the site remoteness and local pollution influences. Comparisons of seasonal calculated OH concentrations ([OH] from the variability-lifetime relationships with six direct station measurements yielded variable agreement, with deviations ranging from ∼20% to a factor of ∼2–3 for locations where [OH] monitoring results had been reported. [OH] calculated from the variability-lifetime relationships was also compared to outputs from a global atmospheric model. Resutls were highly variable, with approximately half of the sites yielding agreement to within a factor of 2–3, while others showed deviations of up to an order of magnitude, especially during winter.

  5. Diverse Responses of Remotely Sensed Grassland Phenology to Interannual Climate Variability over Frozen Ground Regions in Mongolia

    Directory of Open Access Journals (Sweden)

    Zhigang Sun


    Full Text Available Frozen ground may regulate the phenological shifts of dry and cold grasslands at the southern edge of the Eurasian cryosphere. In this study, an investigation based on the MODIS Collection 5 phenology product and climatic data collected from 2001 to 2009 reveals the diverse responses of grassland phenology to interannual climate variability over various frozen ground regions in Mongolia. Compared with middle and southern typical steppe and desert steppe, the spring (start of season; SOS and autumn (end of season; EOS phenological events of northern forest steppe with lower air temperature tend to be earlier and later, respectively. Both the SOS and EOS are less sensitive to climate variability in permafrost regions than in other regions, whereas the SOS of typical steppe is more sensitive to both air temperature and precipitation over sporadic permafrost and seasonal frozen ground regions. Over various frozen ground regions in Mongolia; the SOS is mainly dominated by the prior autumn precipitation, and frozen ground plays a vital role in storing the precipitation of the previous autumn for the subsequent grass green-up. The EOS is mainly dominated by autumn air temperature. These findings could help to improve phenological models of grasslands in extremely dry and cold regions.

  6. Santa Ana Winds of Southern California: Their Climatology and Variability Spanning 6.5 Decades from Regional Dynamical Modelling (United States)

    Guzman-Morales, J.; Gershunov, A.


    Santa Ana Winds (SAWs) are an integral feature of the regional climate of Southern California/Northern Baja California region. In spite of their tremendous episodic impacts on the health, economy and mood of the region, climate-scale behavior of SAW is poorly understood. In the present work, we identify SAWs in mesoscale dynamical downscaling of a global reanalysis product and construct an hourly SAW catalogue spanning 65 years. We describe the long-term SAW climatology at relevant time-space resolutions, i.e, we developed local and regional SAW indices and analyse their variability on hourly, daily, annual, and multi-decadal timescales. Local and regional SAW indices are validated with available anemometer observations. Characteristic behaviors are revealed, e.g. the SAW intensity-duration relationship. At interdecadal time scales, we find that seasonal SAW activity is sensitive to prominent large-scale low-frequency modes of climate variability rooted in the tropical and north Pacific ocean-atmosphere system that are also known to affect the hydroclimate of this region. Lastly, we do not find any long-term trend in SAW frequency and intensity as previously reported. Instead, we identify a significant long-term trend in SAW behavior whereby contribution of extreme SAW events to total seasonal SAW activity has been increasing at the expense of moderate events. These findings motivate further investigation on SAW evolution in future climate and its impact on wildfires.

  7. Description, evaluation and clinical decision making according to various fetal heart rate patterns. Inter-observer and regional variability

    DEFF Research Database (Denmark)


    At 10 Danish obstetrical departments, 116 residents (42 senior and 74 junior) participated in a study to assess inter-observer and regional variability in the description and evaluation of and clinical decision regarding 11 fetal heart rate patterns. The 11 traces included normal as well...... and the presence of silent or sinusoidal pattern (87-94% on an arbitrary 0-100% scale), and low regarding the assessment of variability and type of deceleration (50-72%). The degree of agreement in interpreting heart rate patterns was 59% (on an arbitrary 0-100% scale). Senior residents generally interpreted...

  8. Novel Exons and Splice Variants in the Human Antibody Heavy Chain Identified by Single Cell and Single Molecule Sequencing (United States)

    Vollmers, Christopher; Penland, Lolita; Kanbar, Jad N.; Quake, Stephen R.


    Antibody heavy chains contain a variable and a constant region. The constant region of the antibody heavy chain is encoded by multiple groups of exons which define the isotype and therefore many functional characteristics of the antibody. We performed both single B cell RNAseq and long read single molecule sequencing of antibody heavy chain transcripts and were able to identify novel exons for IGHA1 and IGHA2 as well as novel isoforms for IGHM antibody heavy chain. PMID:25611855

  9. Novel exons and splice variants in the human antibody heavy chain identified by single cell and single molecule sequencing.

    Directory of Open Access Journals (Sweden)

    Christopher Vollmers

    Full Text Available Antibody heavy chains contain a variable and a constant region. The constant region of the antibody heavy chain is encoded by multiple groups of exons which define the isotype and therefore many functional characteristics of the antibody. We performed both single B cell RNAseq and long read single molecule sequencing of antibody heavy chain transcripts and were able to identify novel exons for IGHA1 and IGHA2 as well as novel isoforms for IGHM antibody heavy chain.

  10. Enhanced production of functional extracellular single chain variable fragment against HIV-1 matrix protein from Escherichia coli by sequential simplex optimization. (United States)

    Intachai, Kannaporn; Singboottra, Panthong; Leksawasdi, Noppol; Kasinrerk, Watchara; Tayapiwatana, Chatchai; Butr-Indr, Bordin


    The optimal culture condition for extracellular recombinant single chain variable fragment anti HIV-1 p17 protein (scFv anti-p17) production in Escherichia coli HB2151 was investigated by the sequential simplex optimization (SS) method. Five variable parameters were submitted in the fermentation process. The most favorable condition obtained from 19 independent experiments was as followed: 58 µM of IPTG induction to 1.7 OD600 nm at 25.5°C for 16 h with 202 rpm agitation rate. The amount of secreted scFv anti-p17 at the optimal condition was 38% higher than under the control condition. The binding activity of soluble extracellular scFv anti-p17 protein increased 95.5% and 73.2% in comparison with the control condition and non-optimized condition respectively. The soluble scFv anti-p17 from crude HB2151 lysated was subsequently purified by immobilized metal ion affinity chromatography (IMAC) with His-tag. The purified scFv anti-p17 was intact and retained its antigen-binding affinity against HIV-1 p17. We demonstrated that the sequential simplex optimization method was a key for exertion of high yield with fewer experimental requirements for acquiring of large scale secretory protein production.

  11. Biodegradation of variable-chain-length n-alkanes in Rhodococcus opacus R7 and the involvement of an alkane hydroxylase system in the metabolism. (United States)

    Zampolli, Jessica; Collina, Elena; Lasagni, Marina; Di Gennaro, Patrizia


    Rhodococcus opacus R7 is a Gram-positive bacterium isolated from a polycyclic aromatic hydrocarbon contaminated soil for its versatile metabolism; indeed the strain is able to grow on naphthalene, o-xylene, and several long- and medium-chain n-alkanes. In this work we determined the degradation of n-alkanes in Rhodococcus opacus R7 in presence of n-dodecane (C12), n-hexadecane (C16), n-eicosane (C20), n-tetracosane (C24) and the metabolic pathway in presence of C12. The consumption rate of C12 was 88%, of C16 was 69%, of C20 was 51% and of C24 it was 78%. The decrement of the degradation rate seems to be correlated to the length of the aliphatic chain of these hydrocarbons. On the basis of the metabolic intermediates determined by the R7 growth on C12, our data indicated that R. opacus R7 metabolizes medium-chain n-alkanes by the primary alcohol formation. This represents a difference in comparison with other Rhodococcus strains, in which a mixture of the two alcohols was observed. By GC-MSD analysis we also identified the monocarboxylic acid, confirming the terminal oxidation. Moreover, the alkB gene cluster from R. opacus R7 was isolated and its involvement in the n-alkane degradation system was investigated by the cloning of this genomic region into a shuttle-vector E. coli-Rhodococcus to evaluate the alkane hydroxylase activity. Our results showed an increased biodegradation of C12 in the recombinant strain R. erythropolis AP (pTipQT1-alkR7) in comparison with the wild type strain R. erythropolis AP. These data supported the involvement of the alkB gene cluster in the n-alkane degradation in the R7 strain.

  12. Regional Genetic Structure and Environmental Variables Influence our Conservation Approach for Feather Heads (Ptilotus macrocephalus). (United States)

    Ahrens, Collin W; James, Elizabeth A


    Continued alterations to the Australian environment compromise the long-term viability of many plant species. We investigate the population genetics of Ptilotus macrocephalus, a perennial herb that occurs in 2 nationally endangered communities on the Victorian Volcanic Plain Bioregion (VVP), Australia, to answer key questions regarding regional differentiation and to guide conservation strategies. We evaluate genetic structure and diversity within and among 17 P. macrocephalus populations from 3 regions of southeastern Australia using 17 microsatellite markers developed de novo. Genetic structure was present in P. macrocephalus between the 3 regions but not at the population level. Environmental factors, namely temperature and precipitation, significantly explained differentiation between the North region and the other 2 regions indicating isolation by environment. Within regions, genetic structure currently shows a high level of gene flow and genetic variation. Our results suggest that within-region gene flow does not reflect current habitat fragmentation in southeastern Australia whereas temperature and precipitation are likely to be responsible for the differentiation detected among regions. Climate change may severely impact P. macrocephalus on the VVP and test its evolutionary resilience. We suggest taking a proactive conservation approach to improve long-term viability by sourcing material for restoration to assist gene flow to the VVP region to promote an increased adaptive capacity.

  13. Screening of integrin-binding peptides in a laminin peptide library derived from the mouse laminin β chain short arm regions. (United States)

    Katagiri, Fumihiko; Takagi, Masaharu; Nakamura, Minako; Tanaka, Yoichiro; Hozumi, Kentaro; Kikkawa, Yamato; Nomizu, Motoyoshi


    Laminins, major components of basement membrane, consist of three different subunits, α, β, and γ chains, and so far, five α, three β, and three γ chains have been identified. We have constructed synthetic peptide libraries derived from the laminin sequences and identified various cell-adhesive peptides. Ten active peptides from the laminin α chain sequences (α1-α5) were found to promote integrin-mediated cell adhesion. Previously, we found fourteen cell-adhesive peptides from the β1 chain sequence but their receptors have not been analyzed. Here, we expanded the synthetic peptide library to add peptides from the short arm regions of the laminin β2 and β3 chains and screened for integrin-binding peptides. Twenty-seven peptides promoted human dermal fibroblast (HDF) attachment in a peptide-coated plate assay. The morphological appearance of HDFs on the peptide-coated plates differed depending on the peptides. B34 (REKYYYAVYDMV, mouse laminin β1 chain, 255-266), B67 (IPYSMEYEILIRY, mouse laminin β1 chain, 604-616), B2-105 (APNFWNFTSGRG, mouse laminin β2 chain, 1081-1092), and B3-19 (GHLTGGKVQLNL, mouse laminin β3 chain, 182-193) promoted HDF spreading and HDF attachment was inhibited by EDTA, suggesting that the peptides interact with integrins. Immunostaining analyses revealed that B67 induced well-organized actin stress fibers and focal contacts containing vinculin, however, B34, B2-105, and B3-19 did not exhibit stress fiber formation or focal contacts. The inhibition assay using anti-integrin antibodies indicated that B67 interacts with α3, α6, and β1 integrins, and B34 and B3-19 interact with β1 integrin. Based on adhesion analysis of peptides modified with an alanine scan and on switching analysis with the homologous inactive sequence B2-64 (LPRAMDYDLLLRW, mouse laminin β2 chain, 618-630), the Glu(8) residue in the B67 peptide was critical for HDF adhesion. These findings are useful for identifying an integrin binding motif. The B67 peptide

  14. Evaluation on the Risks of Agricultural Industrial Chain Based on FAHP——A Case of Regions Inhabited by Ethnic Groups in Wuling Mountain

    Institute of Scientific and Technical Information of China (English)


    Through recognizing the risking factors of industrial chain and selecting appropriate evaluation method, the index system on evaluating risking factors including market risk, natural risk, contact risk and efficiency risk in industrial chain is constructed,26 weighting indicators under the four layers are set up. Taking regions inhabited by ethnic groups in Wuling Mountain as an example, the risking factors of agricultural industrial chain in the area are analyzed by adopting the FAHP. The influencing degree of each risking factor on credit risks is analyzed. The results assume that with the market risk, contract risk, natural risk and efficiency risk. The natural risks become the principal risks of agricultural industrial chain and it should be paid much attention to. The low credit risk is a major factor that causes the contract between enterprise and rural households. The flood, pests, diseases and disasters also should be paid high attention to that is regarded as risking factors. The risking factors that come from the efficiency risk layer, for example, the unequal profit distribution among enterprises has little effect on enterprises in industrial chain. The research results provide evidence for stipulating risk prevention measures.

  15. Regional mean and variability characteristics of temperature and precipitation over Thailand in 1961-2000 by a regional climate model and their evaluation (United States)

    Torsri, Kritanai; Octaviani, Mega; Manomaiphiboon, Kasemsan; Towprayoon, Sirintornthep


    This study presents the characterization of regional means and variability of temperature and precipitation in 1961-2000 for Thailand using regional climate model RegCM3. Two fine-resolution (20 km) simulations forced by ERA-40 reanalysis data were performed, with the default land covers and with a land-cover modification strategy suggested by a previous work. The strategy was shown to substantially alleviate the problem of systematic underestimation of temperature given by the default simulation, for most part of Thailand in both dry and wet seasons. The degree of bias in precipitation tends to vary differently in every sub-region and season considered. The patterns of seasonal variation of both climatic variables are acceptably reproduced. Simulated 850-hPa winds have general agreement with those of ERA-40, but wind speed is overestimated over the Gulf of Thailand during the dry months, potentially bringing excessive moisture to and causing more rain than actual in the south. Long-term trends in temperature are reasonably predicted by the model while those in observed and simulated precipitations for upper Thailand are in the opposite directions. Apart from the conventional methods used in characterization, spectral decomposition using Kolmogorov-Zurbenko filters was applied to inspect the model's capability of accounting for variability (here, in terms of variance) in both climatic variables on three temporal scales (short term, seasonal, and long term). The model was found to closely estimate the total variances in the original time series and fairly predict the relative variance contributions on all temporal scales. The latter finding is in line with the results from an additional spectral coherence analysis. Overall, the model was shown to be acceptably adequate for use in support of further climate studies for Thailand, and its evident strength is the capability of reproducing seasonal characteristics and, to a lesser degree, trends.

  16. Modelling regional variability of irrigation requirements due to climate change in Northern Germany. (United States)

    Riediger, Jan; Breckling, Broder; Svoboda, Nikolai; Schröder, Winfried


    The question whether global climate change invalidates the efficiency of established land use practice cannot be answered without systemic considerations on a region specific basis. In this context plant water availability and irrigation requirements, respectively, were investigated in Northern Germany. The regions under investigation--Diepholz, Uelzen, Fläming and Oder-Spree--represent a climatic gradient with increasing continentality from West to East. Besides regional climatic variation and climate change, soil conditions and crop management differ on the regional scale. In the model regions, temporal seasonal droughts influence crop success already today, but on different levels of intensity depending mainly on climate conditions. By linking soil water holding capacities, crop management data and calculations of evapotranspiration and precipitation from the climate change scenario RCP 8.5 irrigation requirements for maintaining crop productivity were estimated for the years 1991 to 2070. Results suggest that water requirement for crop irrigation is likely to increase with considerable regional variation. For some of the regions, irrigation requirements might increase to such an extent that the established regional agricultural practice might be hard to retain. Where water availability is limited, agricultural practice, like management and cultivated crop spectrum, has to be changed to deal with the new challenges.

  17. Morphological variability of Carex dioica L. (Cyperaceae Juss. in Polissya region

    Directory of Open Access Journals (Sweden)

    Svetlana V. Izmestieva


    Full Text Available Morphological variability of Carex dioica L. generative individuals in 4 habitats on the territory of Polissya has analysed. It is established that antropogenic influence and biotope heterogenity determine the highest level of morphological changeability of individuals in one of the localities on the bog Koza. The length of leaves and stems are the most variable traits which depend on the environmental conditions. Stability of such characteristics, as a width of leaves and a length of spikes are determined by their important diagnostic value and application in the systematic of sedges.

  18. Predicting Climate Variability over the Indian Region Using Data Mining Strategies

    CERN Document Server

    Mallenahalli, Naresh Kumar


    In this paper an approach based on expectation maximization (EM) clustering to find the climate regions and a support vector machine to build a predictive model for each of these regions is proposed. To minimize the biases in the estimations a ten cross fold validation is adopted both for obtaining clusters and building the predictive models. The EM clustering could identify all the zones as per the Koppen classification over Indian region. The proposed strategy when employed for predicting temperature has resulted in an RMSE of $1.19$ in the Montane climate region and $0.89$ in the Humid Sub Tropical region as compared to $2.9$ and $0.95$ respectively predicted using k-means and linear regression method.

  19. Consensus and Variable Region PCR Analysis of Helicobacter pylori 3′ Region of cagA Gene in Isolates from Individuals with or without Peptic Ulcer (United States)

    Rota, Cláudia Augustin; Pereira-Lima, Júlio C.; Blaya, Carolina; Nardi, Nance Beyer


    The clinical outcome of Helicobacter pylori infection may be associated with the cagA bacterial genotype. To investigate the cagA status of H. pylori-infected patients and the relationship between cagA and peptic ulcer disease, gastric biopsy specimens from 103 Caucasian patients in Brazil were analyzed by PCR. Since allelic variation in cagA exists and distinct H. pylori subgenotypes may circulate in different regions, PCR using primers for a variable 3′ region of the cagA gene according to a Japanese methodology and for a consensus cagA 3′ region used in Western methods was used for cagA detection. cagA was present in 53 (71%) of 75 H. pylori-positive cases when analyzed by the consensus region method and was associated with duodenal ulcer disease (P = 0.02), but not with gastric ulcer (P = 0.26), when compared to patients with duodenitis or gastritis. The variable region PCR method was able to detect 43 (57%) cagA-positive cases within the same group of H. pylori-positive patients and showed three subtypes of cagA (A, B/D, and C) that were not associated with clinical outcome. However, in 8 (18%) of the cases, more than one subtype was present, and an association between patients with multiple subtypes and disease outcome was observed when compared to patients with isolated subtypes (P = 0.048). cagA was a marker of H. pylori strains for duodenal ulcer disease in our population, and in spite of the differences in the 3′ region of the cagA gene, the Japanese methodology was able to detect the cagA status in most cases. The presence of multiple subgenotypes of cagA was associated with gastric ulcer. PMID:11158115

  20. Heatwaves in Europe: areas of homogeneous variability and links with the regional to large-scale atmospheric and SSTs anomalies

    Energy Technology Data Exchange (ETDEWEB)

    Carril, Andrea F.; Gualdi, Silvio; Cherchi, Annalisa; Navarra, Antonio [Istituto Nazionale di Geofisica e Vulcanologia, INGV, Centro Euro-Mediterraneo per i Cambiamenti Climatici, CMCC, Bologna (Italy)


    This work presents a methodology to study the interannual variability associated with summertime months in which extremely hot temperatures are frequent. Daily time series of maximum and minimum temperature fields (T{sub max} and T{sub min}, respectively) are used to define indexes of extreme months based on the number of days crossing thresholds. An empirical orthogonal function (EOF) analysis is applied to the monthly indexes. EOF loadings give information about the geographical areas where the number of days per month with extreme temperatures has the largest variability. Correlations between the EOF principal components and the time series of other fields allow plotting maps highlighting the anomalies in the large scale circulation and in the SSTs that are associated with the occurrence of extreme events. The methodology is used to construct the ''climatology'' of the extremely hot summertime months over Europe. In terms of both interannual and intraseasonal variability, there are three regions in which the frequency of the extremely hot days per month homogeneously varies: north-west Europe, Euro-Mediterranean and Eurasia region. Although extremes over those regions occur during the whole summer (June to August), the anomalous climatic conditions associated with frequent heatwaves present some intraseasonal variability. Extreme climate events over the north-west Europe and Eurasia are typically related to the occurrence of blocking situations. The intraseasonal variability of those patterns is related to the amplitude of the blocking, the relative location of the action centre and the wavetrain of anomalies downstream or upstream of the blocking. During June and July, blocking situations which give extremely hot climate conditions over north-west Europe are also associated with cold conditions over the eastern Mediterranean sector. The Euro-Mediterranean region is a transition area in which extratropical and tropical systems compete

  1. Transforming p21 ras protein: flexibility in the major variable region linking the catalytic and membrane-anchoring domains

    DEFF Research Database (Denmark)

    Willumsen, B M; Papageorge, A G; Hubbert, N;


    that is required for post-translational processing, membrane localization and transforming activity of the proteins. We have now used the viral oncogene (v-rasH) of Harvey sarcoma virus to study the major variable region by deleting or duplicating parts of the gene. Reducing this region to five amino acids...... or increasing it to 50 amino acids has relatively little effect on the capacity of the gene to induce morphological transformation of NIH 3T3 cells. Assays of GTP binding, GTPase and autophosphorylating activities of such mutant v-rasH-encoded proteins synthesized in bacteria indicated that the sequences...

  2. Multispecies Fisheries in the Lower Amazon River and Its Relationship with the Regional and Global Climate Variability (United States)

    Buss de Souza, Ronald; Freire, Juan; Isaac, Victoria Judith


    This paper aims to describe the spatial-temporal variability in catch of the main fishery resources of the Amazon River and floodplain lakes of the Lower Amazon, as well as relating the Catch per Unit of Effort with anomalies of some of the Amazon River, atmosphere and Atlantic Ocean system variables, determining the influence of the environment on the Amazonian fishery resources. Finfish landings data from the towns and villages of the Lower Amazon for the fisheries of three sites (Óbidos, Santarém and Monte Alegre), were obtained for the period between January 1993 and December 2004. Analysis of variance, detrended correspondence analysis, redundancy analysis and multiple regression techniques were used for the statistical analysis of the distinct time series. Fisheries production in the Lower Amazon presents differences between the Amazon River and the floodplain lakes. Production in the Amazon River is approximately half of the one of the floodplain lakes. This variability occurs both along the Lower Amazon River region (longitudinal gradient) and laterally (latitudinal gradient) for every fishing ground studied here. The distinct environmental variables alone or in association act differently on the fishery stocks and the success of catches in each fishery group studied here. Important variables are the flooding events; the soil the sea surface temperatures; the humidity; the wind and the occurence of El Niño-Southern Oscillation events. Fishery productivity presents a large difference in quantity and distribution patterns between the river and floodplain lakes. This variability occurs in the region of the Lower Amazon as well as laterally for each fishery group studied, being dependent on the ecological characteristics and life strategies of each fish group considered here. PMID:27314951

  3. Multispecies Fisheries in the Lower Amazon River and Its Relationship with the Regional and Global Climate Variability. (United States)

    Pinaya, Walter Hugo Diaz; Lobon-Cervia, Francisco Javier; Pita, Pablo; Buss de Souza, Ronald; Freire, Juan; Isaac, Victoria Judith


    This paper aims to describe the spatial-temporal variability in catch of the main fishery resources of the Amazon River and floodplain lakes of the Lower Amazon, as well as relating the Catch per Unit of Effort with anomalies of some of the Amazon River, atmosphere and Atlantic Ocean system variables, determining the influence of the environment on the Amazonian fishery resources. Finfish landings data from the towns and villages of the Lower Amazon for the fisheries of three sites (Óbidos, Santarém and Monte Alegre), were obtained for the period between January 1993 and December 2004. Analysis of variance, detrended correspondence analysis, redundancy analysis and multiple regression techniques were used for the statistical analysis of the distinct time series. Fisheries production in the Lower Amazon presents differences between the Amazon River and the floodplain lakes. Production in the Amazon River is approximately half of the one of the floodplain lakes. This variability occurs both along the Lower Amazon River region (longitudinal gradient) and laterally (latitudinal gradient) for every fishing ground studied here. The distinct environmental variables alone or in association act differently on the fishery stocks and the success of catches in each fishery group studied here. Important variables are the flooding events; the soil the sea surface temperatures; the humidity; the wind and the occurence of El Niño-Southern Oscillation events. Fishery productivity presents a large difference in quantity and distribution patterns between the river and floodplain lakes. This variability occurs in the region of the Lower Amazon as well as laterally for each fishery group studied, being dependent on the ecological characteristics and life strategies of each fish group considered here.

  4. Variability of morphological characteristics of bream Abramis brama in water basins of upper Volga region

    Directory of Open Access Journals (Sweden)

    I. A. Stolbunov


    Full Text Available Data on variability of morphological readings of bream in the Rybinsk reservoir, and also in the system of reservoirs and water-currents (lake Galichskoe – river Kostroma – river Sot’ – the Kostroma expansion – Gorki reservoir were generalized.


    Water retention of mineral soil is often well predicted using algorithms (pedotransfer functions) with basic soil properties but the spatial variability of these properties has not been well characterized. A further source of uncertainty is that water retention by volcanic soils...

  6. A new insight into the innermost jet regions: probing extreme jet variability with LOFT

    CERN Document Server

    Donnarumma, I; Turriziani, S; Costamante, L; Campana, R; De Rosa, A; Bozzo, E


    Blazars are highly variable sources over timescales that can be as low as minutes. This is the case of the High Energy Peaked BL Lac (HBL) objects showing strong variability in X-rays, which highly correlate with that of the TeV emission. The degree of this correlation is still debated, particularly when the flaring activity is followed down to very short time scales. This correlation could challenge the synchrotron-self-Compton scenario in which one relativistic electron population dominates the entire radiative output. We argue that the LOFT Large Area Detector (10 m$^2$, LAD), thanks to its unprecedented timing capability, will allow us to detect the X-ray counterpart (2-50 keV) of the very fast variability observed at TeV energies, sheding light on the nature of X-TeV connection. We will discuss the test case of PKS 2155-304, showing as it would be possible to look for any X-ray variability occurring at very short timescales, never explored so far. This will put strong constraints on the size and the loca...

  7. Validation of EURO-CORDEX regional climate models in reproducing the variability of precipitation extremes in Romania (United States)

    Dumitrescu, Alexandru; Busuioc, Aristita


    EURO-CORDEX is the European branch of the international CORDEX initiative that aims to provide improved regional climate change projections for Europe. The main objective of this paper is to document the performance of the individual models in reproducing the variability of precipitation extremes in Romania. Here three EURO-CORDEX regional climate models (RCMs) ensemble (scenario RCP4.5) are analysed and inter-compared: DMI-HIRHAM5, KNMI-RACMO2.2 and MPI-REMO. Compared to previous studies, when the RCM validation regarding the Romanian climate has mainly been made on mean state and at station scale, a more quantitative approach of precipitation extremes is proposed. In this respect, to have a more reliable comparison with observation, a high resolution daily precipitation gridded data set was used as observational reference (CLIMHYDEX project). The comparison between the RCM outputs and observed grid point values has been made by calculating three extremes precipitation indices, recommended by the Expert Team on Climate Change Detection Indices (ETCCDI), for the 1976-2005 period: R10MM, annual count of days when precipitation ≥10mm; RX5DAY, annual maximum 5-day precipitation and R95P%, precipitation fraction of annual total precipitation due to daily precipitation > 95th percentile. The RCMs capability to reproduce the mean state for these variables, as well as the main modes of their spatial variability (given by the first three EOF patterns), are analysed. The investigation confirms the ability of RCMs to simulate the main features of the precipitation extreme variability over Romania, but some deficiencies in reproducing of their regional characteristics were found (for example, overestimation of the mea state, especially over the extra Carpathian regions). This work has been realised within the research project "Changes in climate extremes and associated impact in hydrological events in Romania" (CLIMHYDEX), code PN II-ID-2011-2-0073, financed by the Romanian

  8. 16S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads. (United States)

    Tokajian, Sima; Issa, Nahla; Salloum, Tamara; Ibrahim, Joe; Farah, Maya


    Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S-23S rDNA intergenic spacer (ITS) sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S-23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 and 849 bp, while their G+C content was 42.2-57.9 mol%. Five distinct ITS types were identified: ITS(none) (without tRNA genes), ITS(Ala(TGC)), ITS(Ala(TGC)+Ile(GAT)), ITS(Ile(GAT)+Ala(TGC)), and ITS (Ile(GAT)+Pseudo). All of the identified tRNA(Ala(TGC)) molecules consisted of 73 bases, and all of the tRNA(Ile(GAT)) molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2. The importance of this study is that this is the first comparison of the 16S-23S rDNA ITS sequence similarities and tRNA genes from sphingomonads. Collectively the data obtained in this study revealed the heterogeneity and extent of variability within the ITS region compared to the 16S rRNA gene within closely related isolates. Sequence and length polymorphisms within the ITS region along with the ITS types (tRNA-containing or lacking and the type of tRNA) and ITS-2 size and sequence similarities allowed us to overcome the limitation we previously encountered in resolving closely related isolates based on the 16S rRNA gene sequence.


    Institute of Scientific and Technical Information of China (English)

    何凤田; 聂勇战; 陈宝军; 乔太东; 韩者艺; 樊代明


    Objective. To generate phage-displayed anti-idiotypic antibody single chain variable fragments (anti -Id ScFv) to MG7 monoclonal antibody (McAb) directed against gastric carcinoma so as to lay a foundation for developing anti-Id ScFv vaccine of the cancer.Methods. Balb/c mice were immunized i. p. with MG7 McAb conjugated with keyhole limpet hemocyanin (KLH), and mRNA was isolated from the spleens of the immunized mice. Heavy and light chain (VH and VL)genes of antibody were amplified separately and assembled into ScFv genes with a linker DNA by PCR. The ScFv genes were ligated into the phagemid vector pCANTAB5E and the ligated sample was transformed into competent E. coli TG1. The transformants were infected with M13KO7 helper phage to yield recombinant phages displaying ScFv on the tips of M13 phage. After 4 rounds of panning with MG7, the MG7-positive clones were selected by ELISA from the enriched phages. Thetypesoftheanti-IdScFvdisplayedontheselectedphagecloneswerepreliminarily identified by competition ELISA.Results. The VH, VL and ScFv DNAs were about 340 bp, 320 bp and 750 bp respectively. Twenty-four MG7-positive clones were selected from 60 enriched phage clones, among which 5 displayed β or γtype anti-Id ScFv.Conclsion. The anti-Id ScFv to MG7 McAb can be successfully selected by recombinant phage antibody technique, which paves a way for the study of prevention and cure of gastric carcinoma by using anti-Id ScFv.

  10. Regional Variability and Uncertainty of Electric Vehicle Life Cycle CO₂ Emissions across the United States. (United States)

    Tamayao, Mili-Ann M; Michalek, Jeremy J; Hendrickson, Chris; Azevedo, Inês M L


    We characterize regionally specific life cycle CO2 emissions per mile traveled for plug-in hybrid electric vehicles (PHEVs) and battery electric vehicles (BEVs) across the United States under alternative assumptions for regional electricity emission factors, regional boundaries, and charging schemes. We find that estimates based on marginal vs average grid emission factors differ by as much as 50% (using National Electricity Reliability Commission (NERC) regional boundaries). Use of state boundaries versus NERC region boundaries results in estimates that differ by as much as 120% for the same location (using average emission factors). We argue that consumption-based marginal emission factors are conceptually appropriate for evaluating the emissions implications of policies that increase electric vehicle sales or use in a region. We also examine generation-based marginal emission factors to assess robustness. Using these two estimates of NERC region marginal emission factors, we find the following: (1) delayed charging (i.e., starting at midnight) leads to higher emissions in most cases due largely to increased coal in the marginal generation mix at night; (2) the Chevrolet Volt has higher expected life cycle emissions than the Toyota Prius hybrid electric vehicle (the most efficient U.S. gasoline vehicle) across the U.S. in nearly all scenarios; (3) the Nissan Leaf BEV has lower life cycle emissions than the Prius in the western U.S. and in Texas, but the Prius has lower emissions in the northern Midwest regardless of assumed charging scheme and marginal emissions estimation method; (4) in other regions the lowest emitting vehicle depends on charge timing and emission factor estimation assumptions.

  11. Drought Variability and Land Degradation in Semiarid Regions: Assessment Using Remote Sensing Data and Drought Indices (1982–2011)

    KAUST Repository

    Vicente-Serrano, Sergio


    We analyzed potential land degradation processes in semiarid regions worldwide using long time series of remote sensing images and the Normalized Difference Vegetation Index (NDVI) for the period 1981 to 2011. The objectives of the study were to identify semiarid regions showing a marked decrease in potential vegetation activity, indicative of the occurrence of land degradation processes, and to assess the possible influence of the observed drought trends quantified using the Standardized Precipitation Evapotranspiration Index (SPEI). We found that the NDVI values recorded during the period of maximum vegetation activity (NDVImax) predominantly showed a positive evolution in the majority of the semiarid regions assessed, but NDVImax was highly correlated with drought variability, and the trends of drought events influenced trends in NDVImax at the global scale. The semiarid regions that showed most increase in NDVImax (the Sahel, northern Australia, South Africa) were characterized by a clear positive trend in the SPEI values, indicative of conditions of greater humidity and lesser drought conditions. While changes in drought severity may be an important driver of NDVI trends and land degradation processes in semiarid regions worldwide, drought did not apparently explain some of the observed changes in NDVImax. This reflects the complexity of vegetation activity processes in the world’s semiarid regions, and the difficulty of defining a universal response to drought in these regions, where a number of factors (natural and anthropogenic) may also affect on land degradation.

  12. Drought Variability and Land Degradation in Semiarid Regions: Assessment Using Remote Sensing Data and Drought Indices (1982–2011

    Directory of Open Access Journals (Sweden)

    Sergio M. Vicente-Serrano


    Full Text Available We analyzed potential land degradation processes in semiarid regions worldwide using long time series of remote sensing images and the Normalized Difference Vegetation Index (NDVI for the period 1981 to 2011. The objectives of the study were to identify semiarid regions showing a marked decrease in potential vegetation activity, indicative of the occurrence of land degradation processes, and to assess the possible influence of the observed drought trends quantified using the Standardized Precipitation Evapotranspiration Index (SPEI. We found that the NDVI values recorded during the period of maximum vegetation activity (NDVImax predominantly showed a positive evolution in the majority of the semiarid regions assessed, but NDVImax was highly correlated with drought variability, and the trends of drought events influenced trends in NDVImax at the global scale. The semiarid regions that showed most increase in NDVImax (the Sahel, northern Australia, South Africa were characterized by a clear positive trend in the SPEI values, indicative of conditions of greater humidity and lesser drought conditions. While changes in drought severity may be an important driver of NDVI trends and land degradation processes in semiarid regions worldwide, drought did not apparently explain some of the observed changes in NDVImax. This reflects the complexity of vegetation activity processes in the world’s semiarid regions, and the difficulty of defining a universal response to drought in these regions, where a number of factors (natural and anthropogenic may also affect on land degradation.

  13. Exploring the crowded central region of 10 Galactic globular clusters using EMCCDs. Variable star searches and new discoveries

    CERN Document Server

    Jaimes, R Figuera; Skottfelt, J; Kains, N; Jørgensen, U G; Horne, K; Dominik, M; Alsubai, K A; Bozza, V; Novati, S Calchi; Ciceri, S; D'Ago, G; Galianni, P; Gu, S -H; Harpsøe, K B W; Haugbølle, T; Hinse, T C; Hundertmark, M; Juncher, D; Korhonen, H; Liebig, C; Mancini, L; Popovas, A; Rabus, M; Rahvar, S; Scarpetta, G; Schmidt, R W; Snodgrass, C; Southworth, J; Starkey, D; Street, R A; Surdej, J; Wang, X -B; Wertz, O


    Obtain time-series photometry of the very crowded central regions of Galactic globular clusters with better angular resolution than previously achieved with conventional CCDs on ground-based telescopes to complete, or improve, the census of the variable star population in those stellar systems. Images were taken using the Danish 1.54-m Telescope at the ESO observatory at La Silla in Chile. The telescope was equipped with an electron-multiplying CCD and the short-exposure-time images obtained (10 images per second) were stacked using the shift-and-add technique to produce the normal-exposure-time images (minutes). Photometry was performed via difference image analysis. Automatic detection of variable stars in the field was attempted. The light curves of 12541 stars in the cores of 10 globular clusters were statistically analysed in order to automatically extract the variable stars. We obtained light curves for 31 previously known variable stars (3 L, 2 SR, 20 RR Lyrae, 1 SX Phe, 3 cataclysmic variables, 1 EW a...

  14. Spatial variability of air temperature in a free-stall in the Northeastern semi-arid region of Brazil

    Directory of Open Access Journals (Sweden)

    Indira C. M. Gonçalves


    Full Text Available ABSTRACT The knowledge on the spatial variability of climatic attributes and the building of Kriging maps can assist in the design and management of confined animal facilities, by allowing a spatial visualization that is helpful for the planning and control of information from the production environment. The study aimed to characterize the spatial variability of air temperature in a free-stall barn used for dairy cattle confinement located in Petrolina-PE, Brazil, in different seasons and at different times. The variable air temperature was recorded at 136 points distributed in the areas under the shed and the shade cloth for the study of spatial variability and the construction of maps by Kriging. Air temperature data was collected in the winter and in the summer, in the months of July and August (2013 and January and February (2014, at different times (9 and 15 h. According to the results, the use of geostatistics enabled to define areas with different spatial variabilities in air temperature and specific areas in the free-stall with values higher than the recommended levels for thermal comfort. In addition, the central part of the facility is the region with the lowest values of air temperatures, due to the presence of a ridge vent.

  15. Identification of human rotavirus serotype by hybridization to polymerase chain reaction-generated probes derived from a hyperdivergent region of the gene encoding outer capsid protein VP7

    Energy Technology Data Exchange (ETDEWEB)

    Flores, J.; Sears, J.; Schael, I.P.; White, L.; Garcia, D.; Lanata, C.; Kapikian, A.Z. (National Institutes of Health, Bethesda, MD (USA))


    We have synthesized {sup 32}P-labeled hybridization probes from a hyperdivergent region (nucleotides 51 to 392) of the rotavirus gene encoding the VP7 glycoprotein by using the polymerase chain reaction method. Both RNA (after an initial reverse transcription step) and cloned cDNA from human rotavirus serotypes 1 through 4 could be used as templates to amplify this region. High-stringency hybridization of each of the four probes to rotavirus RNAs dotted on nylon membranes allowed the specific detection of corresponding sequences and thus permitted identification of the serotype of the strains dotted. The procedure was useful when applied to rotaviruses isolated from field studies.

  16. Efficient expression of single chain variable fragment antibody against paclitaxel using the Bombyx mori nucleopolyhedrovirus bacmid DNA system and its characterizations. (United States)

    Yusakul, Gorawit; Sakamoto, Seiichi; Tanaka, Hiroyuki; Morimoto, Satoshi


    A single chain variable fragment (scFv), the smallest unit of functional recombinant antibody, is an attractive format of recombinant antibodies for various applications due to its small fragment and possibility of genetic engineering. Hybridoma clone 3A3 secreting anti-paclitaxel monoclonal antibody was used to construct genes encoding its variable domains of heavy (VH) and light (VL) chains. The VH and VL domains were linked to be the PT-scFv3A3 using flexible peptide linker in a format of VH-(GGGGS)5-VL. The PT-scFv3A3 was primarily expressed using the pET28a(+) vector in the Escherichia coli system, and was then further expressed by using the Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system. Interestingly, the reactivity of PT-scFv3A3 expressed in the hemolymph of B. mori using the BmNPV bacmid DNA system was much higher than that expressed in the E. coli system. Using indirect competitive enzyme-linked immunosorbent assay (icELISA), the PT-scFv3A3 (B. mori) reacted not only with immobilized paclitaxel, but also with free paclitaxel in a concentration-dependent manner, with the linear range of free paclitaxel between 0.156 and 5.00 µg/ml. The PT-scFv3A3 (B. mori) exhibited less cross-reactivity (%) than its parental MAb clone 3A3 against paclitaxel-related compounds, including docetaxel (31.1 %), 7-xylosyltaxol (22.1 %), baccatin III (<0.68 %), 10-deacetylbaccatin III (<0.68 %), 1-hydroxybaccatin I (<0.68 %), and 1-acetoxy-5-deacetylbaccatin I (<0.68 %). With the exception of cephalomannine, the cross-reactivity was slightly increased to 8.50 %. The BmNPV bacmid DNA system was a highly efficient expression system of active PT-scFv3A3, which is applicable for PT-scFv3A3-based immunoassay of paclitaxel. In addition, the PT-scFv3A3 can be applied to evaluate its neutralizing property of paclitaxel or docetaxel toxicity.

  17. Molecular Variability Within and Among Verticillium dahliae Vegetative Compatibility Groups Determined by Fluorescent Amplified Fragment Length Polymorphism and Polymerase Chain Reaction Markers. (United States)

    Collado-Romero, Melania; Mercado-Blanco, Jesús; Olivares-García, Concepción; Valverde-Corredor, Antonio; Jiménez-Díaz, Rafael M


    ABSTRACT A degree of genetic diversity may exist among Verticillium dahliae isolates within vegetative compatibility groups (VCGs) that bears phytopathological significance and is worth investigating using molecular tools of a higher resolution than VCG characterization. The molecular variability within and among V. dahliae VCGs was studied using 53 artichoke isolates from eastern-central Spain, 96 isolates from cotton, 7 from cotton soil, and 45 from olive trees in countries of the Mediterranean Basin. Isolates were selected to represent the widest available diversity in cotton- and olive-defoliating (D) and -nondefoliating (ND) pathotypes, as well as for VCG. The VCG of 96 cotton and olive isolates was determined in this present study. Molecular variability among V. dahliae isolates was assessed by fluorescent amplified fragment length polymorphism (AFLP) analysis and by polymerase chain reaction (PCR) assays for DNA fragments associated with the D (462 bp) and ND (824 bp) pathotypes, as well as a 334-bp amplicon associated with D pathotype isolates but also present in some VCG2B isolates. Isolates from cotton were in VCG1A, VCG1B, VCG2A, VCG2B, and VCG4B and those from olive trees were in VCG1A, VCG2A, and VCG4B. Artichoke isolates included representatives of VCG1A, VCG2A, VCG2B (including a newly identified VCG2Ba), and VCG4B. AFLP data were used to generate matrixes of genetic distance among isolates for cluster analysis using the neighbor-joining method and for analysis of molecular variance. Results demonstrated that V. dahliae isolates within a VCG subgroup are molecularly similar, to the extent that clustering of isolates correlated with VCG subgroups regardless of the host source and geographic origin. VCGs differed in molecular variability, with the variability being highest in VCG2B and VCG2A. For some AFLP/VCG subgroup clusterings, V. dahliae isolates from artichoke grouped in subclusters clearly distinct from those comprising isolates from cotton and

  18. Making the best of climatic variability: options for upgrading rainfed farming in water scarce regions. (United States)

    Rockström, J


    Coping with climatic variability for livelihood security is part of everyday life for rural communities in semi-arid and dry sub-humid savannas. Water scarcity caused by rainfall fluctuations is common, causing meteorological droughts and dry spells. However, this paper indicates, based on experiences in sub-Saharan Africa and India, that the social impact on rural societies of climatically induced droughts is exaggerated. Instead, water scarcity causing food deficits is more often caused by management induced droughts and dry spells. A conceptual framework to distinguish between manageable and unmanageable droughts is presented. It is suggested that climatic droughts require focus on social resilience building instead of land and water resource management. Focus is then set on the manageable part of climatic variability, namely the almost annual occurrence of dry spells, short 2-4 week periods of no rainfall, affecting farmer yields. On-farm experiences in savannas of sub-Saharan Africa of water harvesting systems for dry spell mitigation are presented. It is shown that bridging dry spells combined with soil fertility management can double and even triple on-farm yield levels. Combined with innovative systems to ensure maximum plant water availability and water uptake capacity, through adoption of soil fertility improvement and conservation tillage systems, there is a clear opportunity to upgrade rainfed farming systems in vulnerable savanna environments, through appropriate local management of climatic variability.

  19. Spatial-temporal variability of the microbial respiration at the regional scale: comparison of field and laboratory approaches (United States)

    Vasenev, Viacheslav; Stoorvogel, Jetse; Ananyeva, Nadezhda D.; Valentini, Riccardo


    Regional carbon assessments are increasingly important. Soil respiration is a predominant carbon efflux of terrestrial ecosystems. The total carbon efflux from soils includes autotrophic respiration of root systems and heterotrophic microbial respiration (MR). MR usually refers to 60-80% of the total efflux and thus plays a key role in regional carbon balance. Quite a few studies report high sensitivity of MR to climate conditions and land-use. Different approaches to analyze MR exist. The methods differ in the procedures to consider space and time variability. We evaluated two approaches to assess MR variability. One approach uses field measurements on a limited number of locations with chambers. The other approach samples more intensively and derives basal respiration (BR) from measurements under standard conditions in the laboratory. The chamber approach includes periodic measurements at a limited number of sites. As such, the methodology provides appropriate information on temporal dynamics. Spatial variability although, is underrepresented .. In our case chambers were mounted in forest, cropland and urban sites (n=48) located in the north of Moscow city. Roots were removed and geotextile (1 micron mesh) bags were inserted in soil to segregate MR. The flux was measured weekly by Li-6400-XT from July till September 2012. In contrast, standardized BR techniques minimize the diversity of initial conditions. This allows to increase the number of observations considerably. However, the temporal variance is avoided. BR was analyzed in mixed topsoil (0-10 cm) and subsoil (10-150 cm) samples (n=182) collected in forest, cropland and urban sites from different bioclimatic zones of Moscow region. After preincubation (T=22°C, 55% water content, 7 days) soil MR (in μg ?O2-? g-1) was measured after incubating 2g soil with 0.2 μl distilled water as the rate of ?O2 production (22° ?, 24 h) by gas chromatography. Both approaches can be used to describe MR variability in

  20. Key environmental challenges for food groups and regions representing the variation within the EU, Ch.3 Salmon Aquaculture Supply Chain

    DEFF Research Database (Denmark)

    G., Ólafsdóttir; Andrade, Grace Patricia Viera; Nielsen, Thorkild


    The report is aimed to give a thorough review of different environmental impacts that the food and drink sector are producing along the whole chain, from fork to farm and to assess which of them are the key environmental challenges for Europe. A representative range of product groups have been...

  1. Quantifying regional vegetation cover variability in North China during the Holocene: implications for climate feedback. (United States)

    Liu, Guo; Yin, Yi; Liu, Hongyan; Hao, Qian


    Validating model simulations of vegetation-climate feedback needs information not only on changes in past vegetation types as reconstructed by palynologists, but also on other proxies such as vegetation cover. We present here a quantitative regional vegetation cover reconstruction for North China during the Holocene. The reconstruction was based on 15 high-quality lake sediment profiles selected from 55 published sites in North China, along with their modern remote sensing vegetation index. We used the surface soil pollen percentage to build three pollen-vegetation cover transfer models, and used lake surface sediment pollen data to validate their accuracy. Our results showed that vegetation cover in North China increased slightly before its maximum at 6.5 cal ka BP and has since declined significantly. The vegetation decline since 6.5 cal ka BP has likely induced a regional albedo change and aerosol increase. Further comparison with paleoclimate and paleovegetation dynamics in South China reproduced the regional cooling effect of vegetation cover decline in North China modelled in previous work. Our discussion demonstrates that, instead of reconstructing vegetation type from a single site, reconstructing quantitative regional vegetation cover could offer a broader understanding of regional vegetation-climate feedback.

  2. Quantifying regional vegetation cover variability in North China during the Holocene: implications for climate feedback.

    Directory of Open Access Journals (Sweden)

    Guo Liu

    Full Text Available Validating model simulations of vegetation-climate feedback needs information not only on changes in past vegetation types as reconstructed by palynologists, but also on other proxies such as vegetation cover. We present here a quantitative regional vegetation cover reconstruction for North China during the Holocene. The reconstruction was based on 15 high-quality lake sediment profiles selected from 55 published sites in North China, along with their modern remote sensing vegetation index. We used the surface soil pollen percentage to build three pollen-vegetation cover transfer models, and used lake surface sediment pollen data to validate their accuracy. Our results showed that vegetation cover in North China increased slightly before its maximum at 6.5 cal ka BP and has since declined significantly. The vegetation decline since 6.5 cal ka BP has likely induced a regional albedo change and aerosol increase. Further comparison with paleoclimate and paleovegetation dynamics in South China reproduced the regional cooling effect of vegetation cover decline in North China modelled in previous work. Our discussion demonstrates that, instead of reconstructing vegetation type from a single site, reconstructing quantitative regional vegetation cover could offer a broader understanding of regional vegetation-climate feedback.

  3. Variability of sunspot cycle QBO and total ozone over high altitude western Himalayan regions (United States)

    Ningombam, Shantikumar Singh


    Long-term trend of total column ozone at high altitude region in Ladakh is studied, using a total ozone mapping spectrometer and an ozone monitoring instrument during 1979-2008. In the region, total ozone exhibits seasonality with maximum in spring and minimum in autumn. The decreasing trend of total ozone was found as -2.51±0.45% per decade with 95% confidence level in the region. Ozone deficiency in the Ladakh region is strongest (-33.9 DU at Hanle) in May and weakest (-11.5 DU at Hanle) in January-February. In the study, the solar maximum in 1990 is in phase with ozone maximum, while ozone variation lags in phase with the 1980 and 2000 solar maxima. However, a significant correlation between total ozone and sunspot number is achieved in the westerly phase of quasi-biennial oscillation during spring season. Decreasing trend of ozone in the region is correlating well with the cooling rate in the lower stratosphere.

  4. Structural repertoire of immunoglobulin λ light chains

    KAUST Repository

    Chailyan, Anna


    The immunoglobulin λ isotype is present in nearly all vertebrates and plays an important role in the human immune system. Despite its importance, few systematic studies have been performed to analyze the structural conformation of its variable regions, contrary to what is the case for κ and heavy chains. We show here that an analysis of the structures of λ chains allows the definition of a discrete set of recurring conformations (canonical structures) of their hypervariable loops and, most importantly, the identification of sequence constraints that can be used to predict their structure. We also show that the structural repertoire of λ chains is different and more varied than that of the κ chains, consistently with the current view of the involvement of the two major light-chain families in complementary strategies of the immune system to ensure a fine tuning between diversity and stability in antigen recognition. © 2011 Wiley-Liss, Inc.

  5. A Novel Variable Number of Tandem Repeat of the Natriuretic Peptide Precursor B gene's 5'-Flanking Region is Associated with Essential Hypertension among Japanese Females

    Directory of Open Access Journals (Sweden)

    Kotoko Kosuge, Masayoshi Soma, Tomohiro Nakayama, Noriko Aoi, Mikano Sato, Yoichi Izumi, Koichi Matsumoto


    Full Text Available Background: Brain natriuretic peptide (BNP acts primarily as a cardiac hormone; it is produced by the ventricle and has both vasodilatory and natriuretic actions. Therefore, the BNP gene is thought to be a candidate gene for essential hypertension (EH. The present study identified variants in the 5'-flanking region of natriuretic peptide precursor B (NPPB gene and assessed the relationship between gene variants and EH. Methods: The polymerase chain reaction-single strand conformation polymorphism method and nucleotide sequencing were used to identify variants. Results: A novel variable number of tandem repeat (VNTR polymorphism in the 5'-flanking region (-1241 nucleotides from the major transcriptional initiation site was discovered. This VNTR polymorphism is a tandem repeat of the 4-nucleotide sequence TTTC. There were 8 alleles, ranging from 9-repeat to 19-repeat. An association study was done involving 317 EH patients and 262 age-matched normotensive (NT subjects. The 11-repeat allele was the most frequent (88.2%; the 16-repeat allele was the second most frequent (10.5% in the NT group. The observed and expected genotypes were in agreement with the predicted Hardy-Weinberg equilibrium values (P=0.972. Among females, the overall distribution of genotypes was significantly different between the EH and NT groups (p=0.039. The frequency of the 16-repeat allele was significantly lower in the female EH group (6.5% than in the female NT group (12.2%, p=0.046. Conclusions: The 16-repeat allele of the VNTR in the 5'-flanking region of NPPB appears to be a useful genetic marker of EH in females.

  6. A Search for Interstellar Carbon Chain Alcohol HC4OH in Star-Forming Region L1527 and Dark Cloud TMC-1

    CERN Document Server

    Araki, Mitsunori; Yamabe, Hiromichi; Koshikawa, Naohiro; Tsukiyama, Koichi; Nakane, Aya; Okabayashi, Toshiaki; Kunimatsu, Arisa; Kuze, Nobuhiko


    We report a sensitive search for the rotational transitions of the carbon chain alcohol HC4OH in the frequency range of 21.2-46.7 GHz in the star-forming region L1527 and the dark cloud TMC-1. The motivation was laboratory detection of HC4OH by microwave spectroscopy. Despite achieving rms noise levels of several millikelvin in the antenna temperature using the 45 m telescope at Nobeyama Radio Observatory, the detection was not successful, leading to 3 sigma upper limits corresponding to the column densities of 2.0 \\times 1012 and 5.6 \\times 1012 cm-2 in L1527 and TMC-1, respectively. These upper limits indicate that [HC4OH]/[HC5N] ratios are less than 0.3 and 0.1 in L1527 and TMC-1, respectively, where HC5N is an HC4-chain cyanide and HC4OH is a hydroxide. These ratios suggest that the cyano carbon chain molecule dominates the hydroxyl carbon chain molecule in L1527 and TMC-1. This is contrary to the case of saturated compounds in hot cores, e.g., CH3OH and CH3CN, and can be a chemical feature of carbon chai...

  7. Partial-reflection studies of D-region winter variability. [electron density measurements (United States)

    Denny, B. W.; Bowhill, S. A.


    D-region electron densities were measured from December, 1972, to July, 1973, at Urbana, Illinois (latitude 40.2N) using the partial-reflection technique. During the winter, electron densities at altitudes of 72, 76.5, and 81 km show cyclical changes with a period of about 5 days that are highly correlated between these altitudes, suggesting that the mechanism responsible for the winter anomaly in D-region ionization applies throughout this height region. From January 13 to February 3, a pronounced wave-like variation occurred in the partial-reflection measurements, apparently associated with a major stratospheric warming that developed in that period. During the same time period, a traveling periodic variation is observed in the 10-mb height; it is highly correlated with the partial-reflection measurements. Electron density enhancements occur approximately at the same time as increases in the 10-mb height. Comparison of AL and A3 absorption measurements with electron density measurements below 82 km indicates that the winter anomaly in D-region ionization is divided into two types. Type 1, above about 82 km, extends horizontally for about 200 km while type 2, below about 82 km, extends for a horizontal scale of at least 1000 km.

  8. USDA Northern Plains Regional Climate Hub assessment of climate change variability and adaptation and mitigation strategies (United States)

    Ranchers, farmers and forest land owners in the Northern Plains have experienced warmer temperatures (1 to 1.5 degrees F), longer growing seasons (about a week and a half) and generally more precipitation (5 to >15% increases over the eastern 2/3 of this region) over the past twenty years compared t...

  9. Quantitative remote sensing for monitoring forest canopy structural variables in the Three Gorges region of China

    NARCIS (Netherlands)

    Zeng, Y.


    Bridging various scales ranging from local to regional and global, remote sensing has facilitated extraordinary advances in modeling and mapping ecosystems and their functioning. Since forests are one of the most important natural resources on the terrestrial Earth surface, accurate and up-to-date i

  10. Single chain Fab (scFab fragment

    Directory of Open Access Journals (Sweden)

    Brenneis Mariam


    Full Text Available Abstract Background The connection of the variable part of the heavy chain (VH and and the variable part of the light chain (VL by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv was a breakthrough for the functional production of antibody fragments in Escherichia coli. Being double the size of fragment variable (Fv fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields in E. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody in E. coli and antibody phage display. Results Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd and the light chain (LC, resulting in the formation of a single chain Fab fragment (scFab, can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC connecting the constant part 1 of the heavy chain (CH1 and the constant part of the light chain (CL were best suited for phage display and production of soluble antibody fragments. Beside the expression system E. coli, the new antibody format was also expressed in Pichia pastoris. Monovalent and divalent fragments (DiFabodies as well as multimers were characterised. Conclusion A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of

  11. Study of the influence of solar variability on a regional (Indian) climate: 1901-2007

    CERN Document Server

    Aslam, O P M


    We use Indian temperature data of more than 100 years to study the influence of solar activity on climate. We study the Sun-climate relationship by averaging solar and climate data at various time scales; decadal, solar activity and solar magnetic cycles. We also consider the minimum and maximum values of sunspot number (SSN) during each solar cycle. This parameter SSN is correlated better with Indian temperature when these data are averaged over solar magnetic polarity epochs (SSN maximum to maximum). Our results indicate that the solar variability may still be contributing to ongoing climate change and suggest for more investigations.

  12. Regional variability of imaging biomarkers in autosomal dominant Alzheimer’s disease (United States)

    Benzinger, Tammie L. S.; Blazey, Tyler; Jack, Clifford R.; Koeppe, Robert A.; Su, Yi; Xiong, Chengjie; Raichle, Marcus E.; Snyder, Abraham Z.; Ances, Beau M.; Bateman, Randall J.; Cairns, Nigel J.; Fagan, Anne M.; Goate, Alison; Marcus, Daniel S.; Aisen, Paul S.; Christensen, Jon J.; Ercole, Lindsay; Hornbeck, Russ C.; Farrar, Angela M.; Aldea, Patricia; Jasielec, Mateusz S.; Owen, Christopher J.; Xie, Xianyun; Mayeux, Richard; Brickman, Adam; McDade, Eric; Klunk, William; Mathis, Chester A.; Ringman, John; Thompson, Paul M.; Ghetti, Bernardino; Saykin, Andrew J.; Sperling, Reisa A.; Johnson, Keith A.; Salloway, Stephen; Correia, Stephen; Schofield, Peter R.; Masters, Colin L.; Rowe, Christopher; Villemagne, Victor L.; Martins, Ralph; Ourselin, Sebastien; Rossor, Martin N.; Fox, Nick C.; Cash, David M.; Weiner, Michael W.; Holtzman, David M.; Buckles, Virginia D.; Moulder, Krista; Morris, John C.


    Major imaging biomarkers of Alzheimer’s disease include amyloid deposition [imaged with [11C]Pittsburgh compound B (PiB) PET], altered glucose metabolism (imaged with [18F]fluro-deoxyglucose PET), and structural atrophy (imaged by MRI). Recently we published the initial subset of imaging findings for specific regions in a cohort of individuals with autosomal dominant Alzheimer’s disease. We now extend this work to include a larger cohort, whole-brain analyses integrating all three imaging modalities, and longitudinal data to examine regional differences in imaging biomarker dynamics. The anatomical distribution of imaging biomarkers is described in relation to estimated years from symptom onset. Autosomal dominant Alzheimer’s disease mutation carrier individuals have elevated PiB levels in nearly every cortical region 15 y before the estimated age of onset. Reduced cortical glucose metabolism and cortical thinning in the medial and lateral parietal lobe appeared 10 and 5 y, respectively, before estimated age of onset. Importantly, however, a divergent pattern was observed subcortically. All subcortical gray-matter regions exhibited elevated PiB uptake, but despite this, only the hippocampus showed reduced glucose metabolism. Similarly, atrophy was not observed in the caudate and pallidum despite marked amyloid accumulation. Finally, before hypometabolism, a hypermetabolic phase was identified for some cortical regions, including the precuneus and posterior cingulate. Additional analyses of individuals in which longitudinal data were available suggested that an accelerated appearance of volumetric declines approximately coincides with the onset of the symptomatic phase of the disease. PMID:24194552

  13. Expression of anti-tumor necrosis factor alpha (TNFα) single-chain variable fragment (scFv) in Spirodela punctata plants transformed with Agrobacterium tumefaciens. (United States)

    Balaji, Parthasarathy; Satheeshkumar, P K; Venkataraman, Krishnan; Vijayalakshmi, M A


    Therapeutic antibodies against tumor necrosis factor alpha (TNFα) have been considered effective for some of the autoimmune diseases such as rheumatoid arthritis, Crohn's diseases, and so on. But associated limitations of the current therapeutics in terms of cost, availability, and immunogenicity have necessitated the need for alternative candidates. Single-chain variable fragment (scFv) can negate the limitations tagged with the anti-TNFα therapeutics to a greater extent. In the present study, Spirodela punctata plants were transformed with anti-TNFα through in planta transformation using Agrobacterium tumefaciens strain, EHA105. Instead of cefotaxime, garlic extract (1 mg/mL) was used to remove the agrobacterial cells after cocultivation. To the best of our knowledge, this report shows for the first time the application of plant extracts in transgenic plant development. 95% of the plants survived screening under hygromycin. ScFv cDNA integration in the plant genomic DNA was confirmed at the molecular level by PCR. The transgenic protein expression was followed up to 10 months. Expression of scFv was confirmed by immunodot blot. Protein expression levels of up to 6.3% of total soluble protein were observed. β-Glucuronidase and green fluorescent protein expressions were also detected in the antibiotic resistant plants. The paper shows the generation of transgenic Spirodela punctuata plants through in planta transformation.

  14. Single Chain Variable Fragments Produced in Escherichia coli against Heat-Labile and Heat-Stable Toxins from Enterotoxigenic E. coli.

    Directory of Open Access Journals (Sweden)

    Christiane Y Ozaki

    Full Text Available Diarrhea is a prevalent pathological condition frequently associated to the colonization of the small intestine by enterotoxigenic Escherichia coli (ETEC strains, known to be endemic in developing countries. These strains can produce two enterotoxins associated with the manifestation of clinical symptoms that can be used to detect these pathogens. Although several detection tests have been developed, minimally equipped laboratories are still in need of simple and cost-effective methods. With the aim to contribute to the development of such diagnostic approaches, we describe here two mouse hybridoma-derived single chain fragment variable (scFv that were produced in E. coli against enterotoxins of ETEC strains.Recombinant scFv were developed against ETEC heat-labile toxin (LT and heat-stable toxin (ST, from previously isolated hybridoma clones. This work reports their design, construction, molecular and functional characterization against LT and ST toxins. Both antibody fragments were able to recognize the cell-interacting toxins by immunofluorescence, the purified toxins by ELISA and also LT-, ST- and LT/ST-producing ETEC strains.The developed recombinant scFvs against LT and ST constitute promising starting point for simple and cost-effective ETEC diagnosis.

  15. Modeling of Surface Tension and Viscosity for Non-electrolyte Systems by Means of the Equation of State for Square-well Chain Fluids with Variable Interaction Range

    Institute of Scientific and Technical Information of China (English)

    LI Jinlong; HE Changchun; MA Jun; PENG Changjun; LIU Honglai; HU Ying


    The equation of state(EOS)for square-well chain fluid with variable range(SWCF-VR) developed in our previous work based on statistical mechanical theory for chemical association is employed for the correlations of surface tension and viscosity of common fluids and ionic liquids(ILs).A model of surface tension for multi-component mixtures is presented by combining the SWCF-VR EOS and the scaled particle theory and used to produce the surface tension of binary and ternary mixtures.The predicted surface tensions are in excellent agreement with the experimental data with an overall average absolute relative deviation(AAD)of 0.36%.A method for the calculation of dynamic viscosity of common fluids and ILs at high pressure is presented by combining Eyring’s rate theory of viscosity and the SWCF-VR EOS.The calculated viscosities are in good agreement with the experimental data with the overall AAD of 1.44% for 14 fluids in 84 cases.The salient feature is that the molecular parameters used in these models are self-consistent and can be applied to calculate different thermodynamic properties such as pVT,vapor-liquid equilibrium,caloric properties,surface tension,and viscosity.

  16. A rice-based soluble form of a murine TNF-specific llama variable domain of heavy-chain antibody suppresses collagen-induced arthritis in mice. (United States)

    Abe, Michiyo; Yuki, Yoshikazu; Kurokawa, Shiho; Mejima, Mio; Kuroda, Masaharu; Park, Eun Jeong; Scheller, Jürgen; Nakanishi, Ushio; Kiyono, Hiroshi


    Tumor necrosis factor alpha (TNF) plays a pivotal role in chronic inflammatory diseases such as rheumatoid arthritis and Crohn's disease. Although anti-TNF antibody therapy is now commonly used to treat patients suffering from these inflammatory conditions, the cost of treatment continues to be a concern. Here, we developed a rice transgenic system for the production of a llama variable domain of a heavy-chain antibody fragment (VHH) specific for mouse TNF in rice seeds (MucoRice-mTNF-VHH). MucoRice-mTNF-VHH was produced at high levels in the rice seeds when we used our most recent transgene-overexpression system with RNA interference technology that suppresses the production of major rice endogenous storage proteins while enhancing the expression of the transgene-derived protein. Production levels of mTNF-VHH in rice seeds reached an average of 1.45% (w/w). Further, approximately 91% of mTNF-VHH was released easily when the powder form of MucoRice-mTNF-VHH was mixed with PBS. mTNF-VHH purified by means of single-step gel filtration from rice PBS extract showed high neutralizing activity in an in vitro mTNF cytotoxicity assay using WEHI164 cells. In addition, purified mTNF-VHH suppressed progression of collagen-induced arthritis in mice. These results show that this rice-expression system is useful for the production of neutralizing VHH antibody specific for mTNF.

  17. Random frog: an efficient reversible jump Markov Chain Monte Carlo-like approach for variable selection with applications to gene selection and disease classification. (United States)

    Li, Hong-Dong; Xu, Qing-Song; Liang, Yi-Zeng


    The identification of disease-relevant genes represents a challenge in microarray-based disease diagnosis where the sample size is often limited. Among established methods, reversible jump Markov Chain Monte Carlo (RJMCMC) methods have proven to be quite promising for variable selection. However, the design and application of an RJMCMC algorithm requires, for example, special criteria for prior distributions. Also, the simulation from joint posterior distributions of models is computationally extensive, and may even be mathematically intractable. These disadvantages may limit the applications of RJMCMC algorithms. Therefore, the development of algorithms that possess the advantages of RJMCMC methods and are also efficient and easy to follow for selecting disease-associated genes is required. Here we report a RJMCMC-like method, called random frog that possesses the advantages of RJMCMC methods and is much easier to implement. Using the colon and the estrogen gene expression datasets, we show that random frog is effective in identifying discriminating genes. The top 2 ranked genes for colon and estrogen are Z50753, U00968, and Y10871_at, Z22536_at, respectively. (The source codes with GNU General Public License Version 2.0 are freely available to non-commercial users at:

  18. Single Chain Variable Fragments Produced in Escherichia coli against Heat-Labile and Heat-Stable Toxins from Enterotoxigenic E. coli (United States)

    Andrade, Fernanda B.; Nepomuceno, Roberto; Silva, Anderson; Munhoz, Danielle D.; Yamamoto, Bruno B.; Luz, Daniela; Abreu, Patrícia A. E.; Horton, Denise S. P. Q.; Elias, Waldir P.; Ramos, Oscar H. P.; Piazza, Roxane M. F.


    Background Diarrhea is a prevalent pathological condition frequently associated to the colonization of the small intestine by enterotoxigenic Escherichia coli (ETEC) strains, known to be endemic in developing countries. These strains can produce two enterotoxins associated with the manifestation of clinical symptoms that can be used to detect these pathogens. Although several detection tests have been developed, minimally equipped laboratories are still in need of simple and cost-effective methods. With the aim to contribute to the development of such diagnostic approaches, we describe here two mouse hybridoma-derived single chain fragment variable (scFv) that were produced in E. coli against enterotoxins of ETEC strains. Methods and Findings Recombinant scFv were developed against ETEC heat-labile toxin (LT) and heat-stable toxin (ST), from previously isolated hybridoma clones. This work reports their design, construction, molecular and functional characterization against LT and ST toxins. Both antibody fragments were able to recognize the cell-interacting toxins by immunofluorescence, the purified toxins by ELISA and also LT-, ST- and LT/ST-producing ETEC strains. Conclusion The developed recombinant scFvs against LT and ST constitute promising starting point for simple and cost-effective ETEC diagnosis. PMID:26154103

  19. Tidal and sub-tidal sea level variability at the northern shelf of the Brazilian Northeast Region

    Directory of Open Access Journals (Sweden)



    Full Text Available ABSTRACT A characterization of the sea level variability at tidal and sub-tidal frequencies at the northern shore of the Brazilian Northeast shelf for the period 2009-2011 is presented. The sea level data used was obtained from the Permanent Geodetic Tide Network from the Brazilian Institute of Geography and Statistics for the Fortaleza gauge station. Local wind data was also used to assess its effects on the low-frequency sea level variability. The variability of the sea level was investigated by classical harmonic analysis and by morphology assessment over the tidal signal. The low frequencies were obtained by low-pass filtering. The tidal range oscillated with the highest value of 3.3 m during the equinox and the lowest value of 0.7 m during the solstice. Differences between the spring and neap tides were as high as 1 m. A total of 59 tidal constituents were obtained from harmonic analysis, and the regional tide was classified as semi-diurnal pure with a form number of 0.11. An assessment of the monthly variability of the main tidal constituents (M2, S2, N2, O1, and K1 indicated that the main semi-diurnal solar S2 presented the highest variability, ranging from 0.21 to 0.41 m; it was the main element altering the form number through the years. The low frequency sea-level variability is negligible, although there is a persistent signal with an energy peak in the 10-15 day period, and it cannot be explained by the effects of local winds.

  20. Impact of climate variability and anthropogenic activity on streamflow in the Three Rivers Headwater Region, Tibetan Plateau, China (United States)

    Jiang, Chong; Li, Daiqing; Gao, Yanni; Liu, Wenfeng; Zhang, Linbo


    Under the impacts of climate variability and human activities, there is violent fluctuation for streamflow in the large basins in China. Therefore, it is crucial to separate the impacts of climate variability and human activities on streamflow fluctuation for better water resources planning and management. In this study, the Three Rivers Headwater Region (TRHR) was chosen as the study area. Long-term hydrological data for the TRHR were collected in order to investigate the changes in annual runoff during the period of 1956-2012. The nonparametric Mann-Kendall test, moving t test, Pettitt test, Mann-Kendall-Sneyers test, and the cumulative anomaly curve were used to identify trends and change points in the hydro-meteorological variables. Change point in runoff was identified in the three basins, which respectively occurred around the years 1989 and 1993, dividing the long-term runoff series into a natural period and a human-induced period. Then, the hydrologic sensitivity analysis method was employed to evaluate the effects of climate variability and human activities on mean annual runoff for the human-induced period based on precipitation and potential evapotranspiration. In the human-induced period, climate variability was the main factor that increased (reduced) runoff in LRB and YARB (YRB) with contribution of more than 90 %, while the increasing (decreasing) percentage due to human activities only accounted for less than 10 %, showing that runoff in the TRHR is more sensitive to climate variability than human activities. The intra-annual distribution of runoff shifted gradually from a double peak pattern to a single peak pattern, which was mainly influenced by atmospheric circulation in the summer and autumn. The inter-annual variation in runoff was jointly controlled by the East Asian monsoon, the westerly, and Tibetan Plateau monsoons.

  1. 116S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads

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    Sima eTokajian


    Full Text Available Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S-23S rDNA intergenic spacer (ITS sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S-23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 to 849 bp, while their G+C content was 42.2 mol% to 57.9 mol%. Five distinct ITS types were identified: ITSnone (without tRNA genes, ITSAla(TGC, ITSAla (TGC+Ile (GAT, ITSIle (GAT+Ala (TGC and ITS Ile (GAT+Pseudo. All of the identified tRNAAla (TGC molecules consisted of 73 bases, and all of the tRNAIle (GAT molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2.

  2. Water maser variability over 20 years in a large sample of star-forming regions: the complete database (United States)

    Felli, M.; Brand, J.; Cesaroni, R.; Codella, C.; Comoretto, G.; Di Franco, S.; Massi, F.; Moscadelli, L.; Nesti, R.; Olmi, L.; Palagi, F.; Panella, D.; Valdettaro, R.


    Context: Water vapor emission at 22 GHz from masers associated with star-forming regions is highly variable. Aims: We present a database of up to 20 years of monitoring of a sample of 43 masers within star-forming regions. The sample covers a large range of luminosities of the associated IRAS source and is representative of the entire population of H2O masers of this type. The database forms a good starting point for any further study of H2O maser variability. Methods: The observations were obtained with the Medicina 32-m radiotelescope, at a rate of 4-5 observations per year. Results: To provide a database that can be easily accessed through the web, we give for each source: plots of the calibrated spectra, the velocity-time-flux density plot, the light curve of the integrated flux, the lower and upper envelopes of the maser emission, the mean spectrum, and the rate of the maser occurrence as a function of velocity. Figures for just one source are given in the text for representative purposes. Figures for all the sources are given in electronic form the appendix. A discussion of the main properties of the H2O variability in our sample will be presented in a forthcoming paper. Based on observations with the Medicina radiotelescope operated by INAF - Istituto di Radioastronomia.

  3. Variable-density ground-water flow and paleohydrology in the Waste Isolation Pilot Plant (WIPP) region, southeastern New Mexico (United States)

    Davies, P.B.


    Variable-density groundwater flow was studied near the Waste Isolation Pilot Plant in southeastern New Mexico. An analysis of the relative magnitude of pressure-related and density-related flow-driving forces indicates that density-related gravity effects are not significant at the plant and to the west but are significant in areas to the north, northeast, and south. A regional-scale model of variable-density groundwater flow in the Culebra Dolomite member of the Rustler Formation indicates that the flow velocities are relatively rapid (10 to the minus 7th power m/sec) west of the site and extremely slow (10 to the minus 11th power m/sec) east and northeast of the site. In the transition zone between those two extremes, which includes the plant, velocities are highly variable. Sensitivity simulations indicate that the central and western parts of the region, including the plant, are fairly well isolated from the eastern and northeastern boundaries. Vertical-flux simulations indicate that as much as 25% of total inflow to the Culebra could be entering as vertical flow, with most of this flow occurring west of the plant. A simple cross-sectional model was developed to examine the flow system as it drains through time following recharge during a past glacial pluvial. This model indicates that the system as a whole drains very slowly and that it apparently could have sustained flow from purely transient drainage following recharge of the system during the Pleistocene. (USGS)

  4. A search in the COS-B data base for correlated time variability in regions containing objects of interest (United States)

    Caraveo, P. A.; Buccheri, R.; Clear, J.; Foa, O.; Pollock, A. M. T.


    As is well known, association of the gamma-ray sources with celestial objects is, in general, difficult on a pure positional basis, while correlated time variability could obviously provide such proof. This technique can be employed on regions of the gamma-ray sky containing interesting objects of known variability at some wavelength even in the absence of a recognized gamma-ray excess with the aim to extract a weak but predictable signal from the surrounding noise. This technique is applied here on a longer variability time scale, generally of the order of days. Photons coming from the sky regions centered on the various celestial objects considered were selected with energies 100 MeV and with arrival directions within an energy-dependent area of radius of approx 6 deg at 100 MeV. In order to construct a time profile of such photons, their arrival times were grouped in bins of dimensions defined by the available photons number and by the value of the period searched for.

  5. Regional variability in secondary remodeling within long bone cortices of catarrhine primates: the influence of bone growth history. (United States)

    McFarlin, Shannon C; Terranova, Carl J; Zihlman, Adrienne L; Enlow, Donald H; Bromage, Timothy G


    Secondary intracortical remodeling of bone varies considerably among and within vertebrate skeletons. Although prior research has shed important light on its biomechanical significance, factors accounting for this variability remain poorly understood. We examined regional patterning of secondary osteonal bone in an ontogenetic series of wild-collected primates, at the midshaft femur and humerus of Chlorocebus (Cercopithecus) aethiops (n = 32) and Hylobates lar (n = 28), and the midshaft femur of Pan troglodytes (n = 12). Our major objectives were: 1) to determine whether secondary osteonal bone exhibits significant regional patterning across inner, mid-cortical and outer circumferential cortical rings within cross-sections; and if so, 2) to consider the manner in which this regional patterning may reflect the influence of relative tissue age and other circumstances of bone growth. Using same field-of-view images of 100-microm-thick cross-sections acquired in brightfield and circularly polarized light microscopy, we quantified the percent area of secondary osteonal bone (%HAV) for whole cross-sections and across the three circumferential rings within cross-sections. We expected bone areas with inner and middle rings to exhibit higher %HAV than the outer cortical ring within cross-sections, the latter comprising tissues of more recent depositional history. Observations of primary bone microstructural development provided an additional context in which to evaluate regional patterning of intracortical remodeling. Results demonstrated significant regional variability in %HAV within all skeletal sites. As predicted,%HAV was usually lowest in the outer cortical ring within cross-sections. However, regional patterning across inner vs. mid-cortical rings showed a more variable pattern across taxa, age classes, and skeletal sites examined. Observations of primary bone microstructure revealed that the distribution of endosteally deposited bone had an important influence on

  6. Multi-Site and Multi-Variables Statistical Downscaling Technique in the Monsoon Dominated Region of Pakistan (United States)

    Khan, Firdos; Pilz, Jürgen


    South Asia is under the severe impacts of changing climate and global warming. The last two decades showed that climate change or global warming is happening and the first decade of 21st century is considered as the warmest decade over Pakistan ever in history where temperature reached 53 0C in 2010. Consequently, the spatio-temporal distribution and intensity of precipitation is badly effected and causes floods, cyclones and hurricanes in the region which further have impacts on agriculture, water, health etc. To cope with the situation, it is important to conduct impact assessment studies and take adaptation and mitigation remedies. For impact assessment studies, we need climate variables at higher resolution. Downscaling techniques are used to produce climate variables at higher resolution; these techniques are broadly divided into two types, statistical downscaling and dynamical downscaling. The target location of this study is the monsoon dominated region of Pakistan. One reason for choosing this area is because the contribution of monsoon rains in this area is more than 80 % of the total rainfall. This study evaluates a statistical downscaling technique which can be then used for downscaling climatic variables. Two statistical techniques i.e. quantile regression and copula modeling are combined in order to produce realistic results for climate variables in the area under-study. To reduce the dimension of input data and deal with multicollinearity problems, empirical orthogonal functions will be used. Advantages of this new method are: (1) it is more robust to outliers as compared to ordinary least squares estimates and other estimation methods based on central tendency and dispersion measures; (2) it preserves the dependence among variables and among sites and (3) it can be used to combine different types of distributions. This is important in our case because we are dealing with climatic variables having different distributions over different meteorological

  7. Genetic Variability and Microdistribution of Triatoma infestans Genotypes and Trypanosoma cruzi Clones in Arequipa Region (Peru

    Directory of Open Access Journals (Sweden)

    Brenière Simone F


    Full Text Available The genetic variability of Triatoma infestans and Trypanosoma cruzi populations was studied by isoenzyme analysis in two distinct areas of Arequipa province (Peru; one, Santa Rita de Siguas, being an endemic area for Chagas' disease, the second, Arequipa, recently infected. Analysis of T. infestans genetic variability indicates, (i temporal stability of genotypes found in Santa Rita de Siguas, (ii high genetic differences between Arequipa and Santa Rita de Siguas populations suggesting minor contact between them, (iii multiple origin of the T. infestans population in Arequipa, and (iv poor dispersal capacity of T. infestans: the panmictic unit could be reduce to a house. Parasite isoenzyme analysis was performed in 29 Peruvian stocks of T. cruzi, mainly isolated from bugs taken in a single locality, Santa Rita de Siguas. The results show, (i a high genetic polymorphism, (ii nine different multilocus genotypes were detected and clustered in two different clades, (iii most of the parasite isolates pertained to one of the clade and were genetically similar to those analyzed 12 years before. This sample allowed the study of the mating system of T. cruzi in strict sympatic conditions and gave more strength to the hypothesis of the clonal structure of T. cruzi populations

  8. Genetic variability and microdistribution of Triatoma infestans genotypes and Trypanosoma cruzi clones in Arequipa region (Peru). (United States)

    Brenière, S F; Lopez, J; Vargas, F; Barnabé, C


    The genetic variability of Triatoma infestans and Trypanosoma cruzi populations was studied by isoenzyme analysis in two distinct areas of Arequipa province (Peru); one, Santa Rita de Siguas, being an endemic area for Chagas' disease, the second, Arequipa, recently infected. Analysis of T. infestans genetic variability indicates, (i) temporal stability of genotypes found in Santa Rita de Siguas, (ii) high genetic differences between Arequipa and Santa Rita de Siguas populations suggesting minor contact between them, (iii) multiple origin of the T. infestans population in Arequipa, and (iv) poor dispersal capacity of T. infestans: the panmictic unit could be reduce to a house. Parasite isoenzyme analysis was performed in 29 Peruvian stocks of T. cruzi, mainly isolated from bugs taken in a single locality, Santa Rita de Siguas. The results show, (i) a high genetic polymorphism, (ii) nine different multilocus genotypes were detected and clustered in two different clades, (iii) most of the parasite isolates pertained to one of the clade and were genetically similar to those analyzed 12 years before. This sample allowed the study of the mating system of T. cruzi in strict sympathic conditions and gave more strength to the hypothesis of the clonal structure of T. cruzi populations.

  9. The economic viability of value-based food chain for dairy farms in mountain regions: an econometric analysis approach

    Directory of Open Access Journals (Sweden)

    Jernej Prišenk


    Full Text Available The attention of this paper is drawn to analyze the economic potential of involvement of farmers into the small-medium sized value-based food chain (VBFC. The survey represents a solid dana basis from which econometric modelling approach was further developed. Empirical results reveal the positive economic viability on a general level; this means more stable purchase price of raw milk for dairy farms, which are the part of value-based food chain. Results point at inelastic demand for milk and milk related products. Furthermore, there are some accompanying and underlying indirect social benefits, such as production of high-quality food products, more stable and constant demand for raw milk, steady payments and better social situation. The last one is especially important for the farms operating in less-favored mountain areas where the survey was actually conducted.

  10. The Precise Radio Observation of the 13C Isotopic Fractionation for Carbon Chain Molecule HC3N in the Low-Mass Star Forming Region L1527 (United States)

    Araki, Mitsunori; Takano, Shuro; Sakai, Nami; Yamamoto, Satoshi; Oyama, Takahiro; Kuze, Nobuhiko; Tsukiyama, Koichi


    We observed the three 13C isotopic species of HC3N with the high signal-to-noise ratios in L1527 using Green Bank 100 m telescope and Nobeyama 45 m telescope to explore the production scheme of HC3N, where L1527 is the low-mass star forming region in the phase of a warm carbon chain chemistry region. The spectral lines of the J = 5--4, 9--8, 10--9, and 12--11 transitions in the 44-109 GHz region were used to measure isotopic ratios. The abundance of HCCCN was determined from the line intensities of the two weak hyperfine components of the J = 5-4 transition. The isotopic ratios were precisely determined to be 1.00 : 1.01 : 1.35 : 86.4 for [H13CCCN] : [HC13CCN] : [HCC13CN] : [HCCCN]. It was found that the abundance of H13CCCN is equal to that of HC13CCN, and it was implied that HC3N is mainly formed by the reaction schemes via C2H2 and C2H2+ in L1527. This would suggest a universality of dicarbide chemistry producing HC3N irrespective of evolutional phases from a starless dark cloud to a warm carbon chain chemistry region. Sakai, N., Sakai, T., Hirota, T., & Yamamoto, S. 2008, ApJ, 672, 371 Takano, S., Masuda, A., Hirahara, Y., et al. 1998, A&A, 329, 1156

  11. Structural asymmetry of the human cerebral cortex: Regional and between-subject variability of surface area, cortical thickness, and local gyrification. (United States)

    Chiarello, Christine; Vazquez, David; Felton, Adam; McDowell, Alessandra


    Structural asymmetry varies across individuals, brain regions, and metrics of cortical organization. The current study investigated regional differences in asymmetry of cortical surface area, thickness, and local gyrification, and the extent of between-subject variability in these metrics, in a sample of healthy young adults (N=200). Between-subject variability in cortical structure may provide a means to assess the extent of biological flexibility or constraint of brain regions, and we explored the potential influence of this variability on the phenotypic expression of structural asymmetry. The findings demonstrate that structural asymmetries are nearly ubiquitous across the cortex, with differing regional organization for the three cortical metrics. This implies that there are multiple, only partially overlapping, maps of structural asymmetry. The results further indicate that the degree of asymmetry of a brain region can be predicted by the extent of the region's between-subject variability. These findings provide evidence that reduced biological constraint promotes the expression of strong structural asymmetry.

  12. The five factors of personality and regional cortical variability in the Baltimore longitudinal study of aging. (United States)

    Kapogiannis, Dimitrios; Sutin, Angelina; Davatzikos, Christos; Costa, Paul; Resnick, Susan


    Although personality changes have been associated with brain lesions and atrophy caused by neurodegenerative diseases and aging, neuroanatomical correlates of personality in healthy individuals and their stability over time have received relatively little investigation. In this study, we explored regional gray matter (GM) volumetric associations of the five-factor model of personality. Eighty-seven healthy older adults took the NEO Personality Inventory and had brain MRI at two time points 2 years apart. We performed GM segmentation followed by regional analysis of volumes examined in normalized space map creation and voxel based morphometry-type statistical inference in SPM8. We created a regression model including all five factors and important covariates. Next, a conjunction analysis identified associations between personality scores and GM volumes that were replicable across time, also using cluster-level Family-Wise-Error correction. Larger right orbitofrontal and dorsolateral prefrontal cortices and rolandic operculum were associated with lower Neuroticism; larger left temporal, dorsolateral prefrontal, and anterior cingulate cortices with higher Extraversion; larger right frontopolar and smaller orbitofrontal and insular cortices with higher Openness; larger right orbitofrontal cortex with higher Agreeableness; larger dorsolateral prefrontal and smaller frontopolar cortices with higher Conscientiousness. In summary, distinct personality traits were associated with stable individual differences in GM volumes. As expected for higher-order traits, regions performing a large number of cognitive and affective functions were implicated. Our findings highlight personality-related variation that may be related to individual differences in brain structure that merit additional attention in neuroimaging research.

  13. The variability of radiative balance elements and air temperature on the Asian region of Russia

    Directory of Open Access Journals (Sweden)

    E. V. Kharyutkina


    Full Text Available The variability of spatial-temporal distribution of temperature and radiative and heat balances components is investigated for the Asian territory of Russia (45–80° N, 60–180° E using JRA-25, NCEP/DOE AMIP reanalysis data and observational data for the period of current global warming 1979–2008. It is shown that since the beginning of 90s of XX century the increase of back earth-atmosphere short-wave radiation is observed. Such tendency is in conformity with the cloud cover dynamics and downward short-wave radiation at the surface. Annual averaged radiative balance values at the top are negative; it is consistent with negative annual averaged air temperature, averaged over territory. The downward trend of radiative balance is the most obvious after the beginning of 90s of XX century.

  14. Improvement in affinity and HIV-1 neutralization by somatic mutation in the heavy chain first complementarity-determining region of antibodies triggered by HIV-1 infection. (United States)

    Torán, J L; Sánchez-Pulido, L; Kremer, L; del Real, G; Valencia, A; Martínez-A, C


    We assessed the impact of somatic hypermutation in the framework region 1 (FR1) and complementarity-determining region 1 (CDR1) of three clonally-related heavy chains from the human monovalent antigen-binding fragments Fab S19, S8 and S20 on gp120 binding and HIV-1 neutralization capacity. Nucleotide changes were introduced in the heavy chains to revert single and multiple amino acid residues, and two Fab libraries were constructed with the same light chain to express equivalent amounts of parental and reverted phage Fab. We studied the contribution of each amino acid replacement to antigen binding by calculating the frequency of phage Fab retrieval after competitive library selection on gp120. Whereas mutations in FR1 had no effect on antigen binding, somatic replacements in the CDR1 of the heavy chain (HCDR1) appeared to produce significant changes. In S19 HCDR1, somatic mutation of residue 32 reduced gp120 binding. In Fab S20, the Arg(30) and Asp(31) somatically replaced residues in HCDR1 improved antigen binding. Both of these residues are necessary to increase Fab binding to gp120; reversion of either residue alone results in a decrease in binding. The impact of these two replacements was confirmed by the greater neutralization capacity of S20 compared to the other Fab. Molecular modeling of S20 HCDR1 suggests that Arg(30) and Asp(31) are the main interaction sites for gp120, increasing antibody affinity and promoting the enhanced neutralization ability of S20. These findings are consistent with a gp120-driven process, supporting a role for affinity maturation and intraclonal evolution of HIV-1 neutralizing antibodies.

  15. The intraannual variability of land-atmosphere coupling over North America in the Canadian Regional Climate Model (CRCM5) (United States)

    Yang Kam Wing, G.; Sushama, L.; Diro, G. T.


    This study investigates the intraannual variability of soil moisture-temperature coupling over North America. To this effect, coupled and uncoupled simulations are performed with the fifth-generation Canadian Regional Climate Model (CRCM5), driven by ERA-Interim. In coupled simulations, land and atmosphere interact freely; in uncoupled simulations, the interannual variability of soil moisture is suppressed by prescribing climatological values for soil liquid and frozen water contents. The study also explores projected changes to coupling by comparing coupled and uncoupled CRCM5 simulations for current (1981-2010) and future (2071-2100) periods, driven by the Canadian Earth System Model. Coupling differs for the northern and southern parts of North America. Over the southern half, it is persistent throughout the year while for the northern half, strongly coupled regions generally follow the freezing line during the cold months. Detailed analysis of the southern Canadian Prairies reveals seasonal differences in the underlying coupling mechanism. During spring and fall, as opposed to summer, the interactive soil moisture phase impacts the snow depth and surface albedo, which further impacts the surface energy budget and thus the surface air temperature; the air temperature then influences the snow depth in a feedback loop. Projected changes to coupling are also season specific: relatively drier soil conditions strengthen coupling during summer, while changes in soil moisture phase, snow depth, and cloud cover impact coupling during colder months. Furthermore, results demonstrate that soil moisture variability amplifies the frequency of temperature extremes over regions of strong coupling in current and future climates.

  16. Rainfall and temperature changes and variability in the Upper East Region of Ghana (United States)

    Issahaku, Abdul-Rahaman; Campion, Benjamin Betey; Edziyie, Regina


    The aim of the research was to assess the current trend and variation in rainfall and temperature in the Upper East Region, Ghana, using time series moving average analysis and decomposition methods. Meteorological data obtained from the Ghana Meteorological Agency in Accra, Ghana, from 1954 to 2014 were used in the models. The additive decomposition model was used to analyze the rainfall because the seasonal variation was relatively constant over time, while the multiplicative model was used for both the daytime and nighttime temperatures because their seasonal variations increase over time. The monthly maximum and the minimum values for the entire period were as follows: rainfall 455.50 and 0.00 mm, nighttime temperature 29.10°C and 13.25°C and daytime temperature 41.10°C and 26.10°C, respectively. Also, while rainfall was decreasing, nighttime and daytime temperatures were increasing in decadal times. Since both the daytime and nighttime temperatures were increasing and rainfall was decreasing, climate extreme events such as droughts could result and affect agriculture in the region, which is predominantly rain fed. Also, rivers, dams, and dugouts are likely to dry up in the region. It was also observed that there was much variation in rainfall making prediction difficult. Day temperatures were generally high with the months of March and April have been the highest. The months of December recorded the lowest night temperature. Inhabitants are therefore advised to sleep in well-ventilated rooms during the warmest months and wear protective clothing during the cold months to avoid contracting climate-related diseases.

  17. Reliability Measurement for Software with Variable Length Markov Control Transfer Chain%VLMC控制流软件可靠性度量方法

    Institute of Scientific and Technical Information of China (English)

    赵瑞曼; 潘冠华; 方建勇


    The classical software reliability model of Cheung based on architecture analysis is imperfect when applied to soft-ware which has non-uniqueness terminal node because of ideal assumptions. In order to handle this problem, an improved model is established through two improvement as follows:first, probability matrix of control transfer from start node to other inner nodes in a given software is computed independently of control transfer within inner nodes on the assumptions that the start node is inaccessible to control transfer from any inner nodes;and then, probability matrixes of control transfer within in-ner nodes are reconfigured by weaken the difference between inner nodes and ending nodes. In order to measure the reliability of software with VLMC control transfer flow, the variable length Markov control sequence chain is converted to simple Markov chain by node expansion and conditional transfer probability redistribution. By using deductive inference, a formal proof for the new model is given in this essay. In the end, effectiveness and simplicity of the proposed method is verified by a software example.%针对现有软件可靠性模型普遍不适用于实际软件的问题,分析了软件内部模块间控制转移机理,通过分离入口模块,提取一阶控制转移概率矩阵;弱化内部模块与出口模块间差异,重构二阶以上转移概率矩阵,在改进Cheung模型的基础上建立一个更符合软件实际的可靠性度量模型。针对变阶依赖( VLMC)控制转移导致的可靠性度量难问题,通过对导致复杂依赖的多入多出模块进行节点扩展,将VLMC控制流转化为Markov链,利用所建立的软件可靠性模型对VLMC控制流软件进行可靠性度量。研究利用演绎推理对所建立模型进行了正确性形式化证明。最后给出了方法的实例验证。

  18. Characterization of Campylobacter jejuni applying flaA short variable region sequencing, multilocus sequencing and Fourier transform infrared spectroscopy

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Bonnichsen, Lise; Larsson, Jonas;

    flaA short variable region sequencing and phenetic Fourier transform infrared (FTIR) spectroscopy was applied on a collection of 102 Campylobacter jejuni isolated from continuous sampling of organic, free range geese and chickens. FTIR has been shown to serve as a valuable tool in typing...... of thermotolerant Campylobacter. A subset of isolates, initially discriminated by flaA sequencing, was further subjected to multilocus sequence typing (MLST). The findings of this study revealed flaA sequencing to have a slightly higher discriminatory power than FTIR indicated by a Simpsons diversity index of 0...

  19. ESA STSE Project “Sea Surface Temperature Diurnal Variability: Regional Extend – Implications in Atmospheric Modelling”

    DEFF Research Database (Denmark)

    Karagali, Ioanna

    , atmospheric and oceanic modelling, bio-chemical processes and oceanic CO2 studies. The diurnal variability of SST, driven by the coincident occurrence of low enough wind and solar heating, is currently not properly understood. Atmospheric, oceanic and climate models are currently not adequately resolving...... present the final project findings regarding the analysis of hourly SEVIRI SSTs from SEVIRI over the Atlantic Ocean and the European Seas, revealing the regional extend of diurnal warming. As satellite SSTs are representative of the upper centimetre of the water column, they do not provide information...

  20. Construction and characterization of a non-immune Llama variable heavy chain phage display antibody library%羊驼非免疫重链单域抗体库的构建和鉴定

    Institute of Scientific and Technical Information of China (English)

    吴标; 王树军; 夏立亮; 季萍; 葛海良; 赵国屏; 王颖


    本研究旨在通过构建羊驼非免疫重链单域抗体库,完成抗体库多样性的鉴定,为进一步筛选抗原特异性重链抗体奠定基础.我们从未经免疫的羊驼外周血中分离外周血单个核细胞(PBMC),抽提RNA后,用RT-PCR方法特异性扩增羊驼重链抗体可变区(VHH)片段;并采用两步连接方法将重链抗体可变区片段与噬菌粒载体pCANTAB5E连接获得重组子,多次电转感受态大肠杆菌TG1后获得VHH抗体基因库;并采用稀释计数法测定抗体库库容量,随机挑取克隆测序验证抗体库多样性.结果显示,我们所构建的羊驼非免疫重链单域抗体库的库容量为1.5×109,随机克隆测序验证多样性良好,独立克隆所占比例为80%,并显示出和人源抗体较高的同源性.上述结果表明,我们已经成功构建获得大容量的羊驼非免疫重链单域抗体库,为进一步筛选抗原特异性重链抗体奠定基础.%To construct a non-immune Llama variable domain of heavy chain antibody(VHH) phage display antibody library (VHH antibody library). Llama peripheral blood mononuclear lymphocytes were isolated from whole blood by Ficoll-hypaque density gradient centrifugation. Total RNA was extracted from PBMCs and reverse-transcripted into cDNA by using specific primers. VHH were amplified by nested PCR. PCR products of VHH fragments were then purified and ligated with phagemid vector pCANTAB5E by a modified two-step ligation method. Recombinant pCANTAB5E-VHH vectors were electroporated into competent TGI E.coli cells to obtain the primary VHH antibody library. The library capacity was titrated through limited dilution. Recombination efficacy and diversity of VHH antibody library was determined by sequencing analysis. Alignment a-nalysis was performed to compare the homology between Llama VHH domain and human/mouse variable regions of heavy chains. By using a modified strategy, we have constructed a non-immune Llama VHH antibody library with 1. 5

  1. Variability or conservation of hepatitis C virus hypervariable region 1? Implications for immune responses

    Indian Academy of Sciences (India)

    Mario U Mondelli; Antonella Cerino; Annalisa Meola; Alfredo Nicosia


    The hypervariable region 1 (HVR1) of the E2 protein of hepatitis C virus (HCV) is highly heterogeneous in its primary sequence and is responsible for significant inter- and intra-individual variation of the infecting virus, which may represent an important pathogenetic mechanism leading to immune escape and persistent infection. A binding site for neutralizing antibodies (Ab) has also been allegedly identified in this region. Prospective studies of serological responses to synthetic oligopeptides derived from naturally-occurring HVR1 sequences showed promiscuous recognition of HVR1 variants in most patients via binding to C-terminal amino acid residues with conserved physicochemical properties. Monoclonal antibodies generated by immunization of mice with peptides derived from natural HVR1 sequences were shown to recognize several HVR1 variants in line with evidence gathered from studies using human sera. In addition, selected mAbs were able to bind HVR1 in the context of a complete soluble form of the E2 glycoprotein, indicating recognition of correctly folded sequences, and were shown to specifically capture circulating and recombinant HCV particles, suggesting that HVR1 is expressed on intact virus particles and therefore potentially able to interact with cellular receptor(s). These findings suggest that it is possible to induce a broadly reactive clonal immune response to multiple HCV variants and that this mechanism could be used in principle to induce protective immunity for a large repertoire of HCV variants.

  2. Seasonal variability of planktonic copepods (Copepoda: Crustacea in a tropical estuarine region in Brazil

    Directory of Open Access Journals (Sweden)

    Cristina de Oliveira Dias


    Full Text Available The Caravelas River estuary and adjacent coastal region were studied during the rainy and dry seasons of 2003-2004 to assess the copepod community structure. Abiotic and biotic parameters were measured, and the total density, frequency and percentage of copepod taxa were determined for each sampling period. Copepod densities showed significant differences between sampling periods, with higher densities in the rainy seasons (Mean: 90,941.80 ind.m-3; S.D.: 26,364.79. The sampling stations located to the north and south, in the coastal region adjacent to the Caravelas River estuary presented the lowest copepod density values. The copepod assemblage was composed mainly of estuarine and estuarine/coastal copepods. The seasonal variations in temperature and salinity influenced the abundance of species during the rainy and dry seasons, with the following dominant species alternating: Paracalanus quasimodo Bowman, 1971 in the rainy season of 2003, Parvocalanus crassirostris Dahl, 1894 in the dry season of 2003 and Acartia lilljeborgii Giesbrecht, 1892 in the rainy and dry seasons of 2004. Non-parametric multidimensional scaling indicated differences in copepod assemblages between sampling periods, but not between sampling stations.

  3. Haplotypes and variable position detection in the mitochondrial DNA coding region encompassing nucleotide positions 10,716-11,184. (United States)

    Hameed, Imad Hadi; Abdulzahra, Ameer Ibrahim; Jebor, Mohammed Abdullah; Kqueen, Cheah Yoke; Ommer, Aamera Jaber


    This study evaluates the mitochondrial noncoding regions by using the Sanger sequencing method for application in Forensic Science. FTA® Technology (FTA™ paper DNA extraction) was utilized to extract DNA. Portion of coding region encompassing positions from (10,716 to 11,184) amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column were then sequenced and detected using the ABI 3730 × L DNA Analyzer. A new polymorphic positions 10,750 and 10,790 that are described may be suitable sources in future for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence, most promising for identification variants.

  4. Peptides from the variable region of specific antibodies are shared among lung cancer patients.

    Directory of Open Access Journals (Sweden)

    Dominique de Costa

    Full Text Available Late diagnosis of lung cancer is still the main reason for high mortality rates in lung cancer. Lung cancer is a heterogeneous disease which induces an immune response to different tumor antigens. Several methods for searching autoantibodies have been described that are based on known purified antigen panels. The aim of our study is to find evidence that parts of the antigen-binding-domain of antibodies are shared among lung cancer patients. This was investigated by a novel approach based on sequencing antigen-binding-fragments (Fab of immunoglobulins using proteomic techniques without the need of previously known antigen panels. From serum of 93 participants of the NELSON trial IgG was isolated and subsequently digested into Fab and Fc. Fab was purified from the digested mixture by SDS-PAGE. The Fab containing gel-bands were excised, tryptic digested and measured on a nano-LC-Orbitrap-Mass-spectrometry system. Multivariate analysis of the mass spectrometry data by linear canonical discriminant analysis combined with stepwise logistic regression resulted in a 12-antibody-peptide model which was able to distinguish lung cancer patients from controls in a high risk population with a sensitivity of 84% and specificity of 90%. With our Fab-purification combined Orbitrap-mass-spectrometry approach, we found peptides from the variable-parts of antibodies which are shared among lung cancer patients.

  5. DR Tau: Temporal variability of the brightness distribution in the potential planet-forming region

    CERN Document Server

    Brunngräber, Robert; Ratzka, Thorsten; Ober, Florian


    We investigate the variability of the brightness distribution and the changing density structure of the protoplanetary disk around DR Tau, a classical T Tauri star. DR Tau is known for its peculiar variations from the ultraviolet (UV) to the mid-infrared (MIR). Our goal is to constrain the temporal variation of the disk structure based on photometric and MIR interferometric data. We observed DR Tau with the MID-infrared Interferometric instrument (MIDI) at the Very Large Telescope Interferometer (VLTI) at three epochs separated by about nine years, two months, respectively. We fit the spectral energy distribution and the MIR visibilities with radiative transfer simulations. We are able to reproduce the spectral energy distribution as well as the MIR visibility for one of the three epochs (third epoch) with a basic disk model. We were able to reproduce the very different visibility curve obtained nine years earlier with a very similar baseline (first epoch), using the same disk model with a smaller scale heigh...

  6. Load Mitigation and Optimal Power Capture for Variable Speed Wind Turbine in Region 2

    Directory of Open Access Journals (Sweden)

    Saravanakumar Rajendran


    Full Text Available This paper proposes the two nonlinear controllers for variable speed wind turbine (VSWT operating at below rated wind speed. The objective of the controller is to maximize the energy capture from the wind with reduced oscillation on the drive train. The conventional controllers such as aerodynamic torque feedforward (ATF and indirect speed control (ISC are adapted initially, which introduce more power loss, and the dynamic aspects of WT are not considered. In order to overcome the above drawbacks, modified nonlinear static state with feedback estimator (MNSSFE and terminal sliding mode controller (TSMC based on Modified Newton Raphson (MNR wind speed estimator are proposed. The proposed controllers are simulated with nonlinear FAST (fatigue, aerodynamics, structures, and turbulence WT dynamic simulation for different mean wind speeds at below rated wind speed. The frequency analysis of the drive train torque is done by taking the power spectral density (PSD of low speed shaft torque. From the result, it is found that a trade-off is to be maintained between the transient load on the drive train and maximum power capture.

  7. Optical system design with variable working distance for monitoring of environmental contamination in infrared region (United States)

    Romanova, G. E.; Zaitceva, A. S.


    The project is dedicated to a research and development of a compact optical system for an identification of dangerous substances in a surrounding environment using a spectrum of scattered laser radiation. There is a whole class of tasks for diagnostics of environments and substances which are solved by mobile systems on distances of 0.5 - 10 m from the object. The key feature of an optical system in this case is having the highest functionality, to meet this demands it should be able to work on variable distances and provide the minimal light spot. The purpose of the work is a research of the best possible initial system parameters and its components, designing of an optical system with minimum possible number of elements providing acceptable quality of the image in the required dimensions. An image quality criterion for such systems is the size of the light spot, which defines an operation speed of the system. Using the beam diameter and allowable system dimensions as initial parameters of the two components system, relations were found which helps to define optimal component parameters for future design. To provide the possibility of working on various distances the thickness between the components can be varied. An example of a two component system consisted of three lenses with spherical surfaces is presented. The system works with a laser with the wavelength of 0.785 μm and provides the light spot less than 2.3 mm for all working distances within the range of 2 - 5 m.

  8. RFID cryptographic protocol based on two-dimensional region Hash chain%基于二维区间Hash链的RFID安全协议

    Institute of Scientific and Technical Information of China (English)

    熊宛星; 薛开平; 洪佩琳; 麻常莎


    Due to the limitation of relevant devices, a lot of security problems exist in a radio frequency identification (RFID) system, one of the core technologies of the future internet of things (IOT). A new protocol based on the two-dimensional region (TDR) Hash chains was proposed after the core ideas of several typical RFID cryptographic protocols were analyzed. TDR could significantly improve the efficiency of database retrieval by identifying each Hash chain with region division. Moreover, a random number was introduced to further enhance the security of RFID systems.%作为未来物联网(IOT)的核心技术之一,无线射频识别(RFID)系统由于设备的局限性而存在许多安全问题.在分析几种典型安全协议核心思想的基础上,提出了基于二维区间(two-dimensional region,TDR) Hash链的安全协议.该协议以区间划分的方式标识各链,从而提高了数据库的检索效率;同时,由于在协议中引入了随机性,RFID系统的安全性得到了进一步增强.

  9. Demographic variability indicators of somatically healthy men from different administrative and territorial regions of Ukraine

    Directory of Open Access Journals (Sweden)

    Mishalov Volodymyr


    Full Text Available Our work has revealed a rather low level of similarity in regard to the finger dermatoglyphics of somatically healthy men, 19-35 years old, between Ukraine’s north and west, north and south, center and west, center and south, as well as the palmar dermatoglyphics between central regions and the east, center and west, center and south. The obtained finger/palmar dermatoglyphics did not differentiate administrative-territorial local groups of men between the north and the center, south and west (quantitative characteristics; or palmar – between the north and west, north and east, south and west, south and east, north and center. The differences between the administrative and territorial division of dermatoglyphic signs are a reflection of the historical and cultural differences induced by migration, as well as the intensive process of mixing, in addition to the isolation of particular groups.

  10. Ecosystem relevance of variable jellyfish biomass in the Irish Sea between years, regions and water types (United States)

    Bastian, Thomas; Lilley, Martin K. S.; Beggs, Steven E.; Hays, Graeme C.; Doyle, Thomas K.


    Monitoring the abundance and distribution of taxa is essential to assess their contribution to ecosystem processes. For marine taxa that are difficult to study or have long been perceived of little ecological importance, quantitative information is often lacking. This is the case for jellyfish (medusae and other gelatinous plankton). In the present work, 4 years of scyphomedusae by-catch data from the 2007-2010 Irish Sea juvenile gadoid fish survey were analysed with three main objectives: (1) to provide quantitative and spatially-explicit species-specific biomass data, for a region known to have an increasing trend in jellyfish abundance; (2) to investigate whether year-to-year changes in catch-biomass are due to changes in the numbers or in the size of medusa (assessed as the mean mass per individual), and (3) to determine whether inter-annual variation patterns are consistent between species and water masses. Scyphomedusae were present in 97% of samples (N = 306). Their overall annual median catch-biomass ranged from 0.19 to 0.92 g m-3 (or 8.6 to 42.4 g m-2). Aurelia aurita and Cyanea spp. (Cyanea lamarckii and Cyanea capillata) made up 77.7% and 21.5% of the total catch-biomass respectively, but species contributions varied greatly between sub-regions and years. No consistent pattern was detected between the distribution and inter-annual variations of the two genera, and contrasting inter-annual patterns emerged when considering abundance either as biomass or as density. Significantly, A. aurita medusae were heavier in stratified than in mixed waters, which we hypothesize may be linked to differences in timing and yield of primary and secondary productions between water masses. These results show the vulnerability of time-series from bycatch datasets to phenological changes and highlight the importance of taking species- and population-specific distribution patterns into account when integrating jellyfish into ecosystem models.

  11. Prokaryotic expression and purification of anti-AEG-1 single-chain variable antibody%抗 AEG-1单链可变区抗体的原核表达及纯化

    Institute of Scientific and Technical Information of China (English)

    路蔓; 刘昕阳; 龙敏; 王琛; 刘冲; 郜赵伟; 欧阳永日; 陈曦; 张惠中


    Objective To construct anti-astrocyte elevated gene-1(AEG-1)single-chain variable antibody (V23)prokaryotic ex-pression vector,and to conduct the protein purification and immunological activity detection.Methods The Primer5 software was applied to design the primers aiming at the gene sequence of the antibody anti-AEG-1 single-chain variable region for constructing the prokaryotic expression plasmid of PRsetC/V23.After the enzyme digestion by the restriction enzyme Pst1 and correct DNA se-quencing,the prokaryotic expression plasmid was led to E.coli BL21 ,the prokaryotic expression engineering strain containing the V23 gene was constructed.After the induction with IPTG,the interest protein was purified by the magnetic beads with the HIS tag,and the content of interest protein was determined by the SDS-PAGE electrophoresis.Western blot and ELISA were adopted to detect the immune activity of the nti-AEG-1 single-chain variable region antibody.Results For the constructed prokaryotic expres-sion plasmid PRsetC/V23,the single enzyme digestion and sequencing analysis displayed that the constructed V23 gene was com-pletely consistent to the designing sequences.After IPTG induction,SDS-PAGE electrophoresis showed an apparent protein band at 31×103 ,the Western blot detection showed a specific AEG-1 response band at 80 ×103 ,the ELISA test showed the positive re-sults.Conclusion The PRsetC/V23 prokaryotic expression plasmid and the V23 prokaryotic expression engineering strain are suc-cessfully constructed,this engineering strain can express anti-AEG-1 single-chain variable region antibody protein,and the protein has good immune activity.%目的:构建抗星形细胞上调基因1(AEG-1)单链可变区抗体(V23)的原核表达载体,并对表达蛋白进行纯化及免疫活性检测。方法应用 Primer5软件设计针对抗 AEG-1单链可变区抗体基因序列的引物,构建 PRsetC/V23原核表达质粒,经限制性内切酶 Pst1酶切以及 DNA

  12. Measuring the environmental sustainability performance of global supply chains: A multi-regional input-output analysis for carbon, sulphur oxide and water footprints. (United States)

    Acquaye, Adolf; Feng, Kuishuang; Oppon, Eunice; Salhi, Said; Ibn-Mohammed, Taofeeq; Genovese, Andrea; Hubacek, Klaus


    Measuring the performance of environmentally sustainable supply chains instead of chain constitute has become a challenge despite the convergence of the underlining principles of sustainable supply chain management. This challenge is exacerbated by the fact that supply chains are inherently dynamic and complex and also because multiple measures can be used to characterize performances. By identifying some of the critical issues in the literature regarding performance measurements, this paper contributes to the existing body of literature by adopting an environmental performance measurement approach for economic sectors. It uses economic sectors and evaluates them on a sectoral level in specific countries as well as part of the Global Value Chain based on the established multi-regional input-output (MRIO) modeling framework. The MRIO model has been used to calculate direct and indirect (that is supply chain or upstream) environmental effects such as CO2, SO2, biodiversity, water consumption and pollution to name just a few of the applications. In this paper we use MRIO analysis to calculate emissions and resource consumption intensities and footprints, direct and indirect impacts, and net emission flows between countries. These are exemplified by using carbon emissions, sulphur oxide emissions and water use in two highly polluting industries; Electricity production and Chemical industry in 33 countries, including the EU-27, Brazil, India and China, the USA, Canada and Japan from 1995 to 2009. Some of the highlights include: On average, direct carbon emissions in the electricity sector across all 27 member states of the EU was estimated to be 1368 million tons and indirect carbon emissions to be 470.7 million tons per year representing 25.6% of the EU-27 total carbon emissions related to this sector. It was also observed that from 2004, sulphur oxide emissions intensities in electricity production in India and China have remained relatively constant at about 62.8 g

  13. Meteo-marine parameters for highly variable environment in coastal regions from satellite radar images (United States)

    Pleskachevsky, A. L.; Rosenthal, W.; Lehner, S.


    The German Bight of the North Sea is the area with highly variable sea state conditions, intensive ship traffic and with a high density of offshore installations, e.g. wind farms in use and under construction. Ship navigation and the docking on offshore constructions is impeded by significant wave heights HS > 1.3 m. For these reasons, improvements are required in recognition and forecasting of sea state HS in the range 0-3 m. Thus, this necessitates the development of new methods to determine the distribution of meteo-marine parameters from remote sensing data with an accuracy of decimetres for HS. The operationalization of these methods then allows the robust automatic processing in near real time (NRT) to support forecast agencies by providing validations for model results. A new empirical algorithm XWAVE_C (C = coastal) for estimation of significant wave height from X-band satellite-borne Synthetic Aperture Radar (SAR) data has been developed, adopted for coastal applications using TerraSAR-X (TS-X) and Tandem-X (TD-X) satellites in the German Bight and implemented into the Sea Sate Processor (SSP) for fully automatic processing for NRT services. The algorithm is based on the spectral analysis of subscenes and the model function uses integrated image spectra parameters as well as local wind information from the analyzed subscene. The algorithm is able to recognize and remove the influence of non-sea state produced signals in the Wadden Sea areas such as dry sandbars as well as nonlinear SAR image distortions produced by e.g. short wind waves and breaking waves. Also parameters of very short waves, which are not visible in SAR images and produce only unsystematic clutter, can be accurately estimated. The SSP includes XWAVE_C, a pre-filtering procedure for removing artefacts such as ships, seamarks, buoys, offshore constructions and slicks, and an additional procedure performing a check of results based on the statistics of the whole scene. The SSP allows an

  14. Regional Heat Sources and the Active and Break Phases of Boreal Summer Intraseasonal Variability

    Energy Technology Data Exchange (ETDEWEB)

    Annamalai, H; Sperber, K R


    The boreal summer intraseasonal variability (BSISV) associated with the 30-50 day mode is represented by the co-existence of three components, poleward propagation of convection over the Indian and tropical west Pacific longitudes and eastward propagation along the equator. The hypothesis that the three components influence each other has been investigated using observed OLR, NCEP-NCAR reanalysis, and solutions from an idealized linear model. The null hypothesis is that the three components are mutually independent. Cyclostationary EOF (CsEOF) analysis is applied on filtered OLR to extract the life-cycle of the BSISV. The dominant mode of CsEOF is significantly tied to observed rainfall over the Indian subcontinent. The components of the heating patterns from CsEOF analysis serve as prescribed forcings for the linear model. This allows us to ascertain which heat sources and sinks are instrumental in driving the large-scale monsoon circulation during the BSISV life-cycle. We identify three new findings: (1) the circulation anomalies that develop as a Rossby wave response to suppressed convection over the equatorial Indian Ocean associated with the previous break phase of the BSISV precondition the ocean-atmosphere system in the western Indian Ocean and trigger the next active phase of the BSISV, (2) the development of convection over the tropical west Pacific forces descent anomalies to the west. This, in conjunction with the weakened cross-equatorial flow due to suppressed convective anomalies over the equatorial Indian Ocean reduce the tropospheric moisture over the Arabian Sea, and promote westerly wind anomalies that do not recurve over India. As a result the low-level cyclonic vorticity shifts from India to southeast Asia and break conditions are initiated over India, and (3) the circulation anomalies forced by equatorial Indian Ocean convective anomalies significantly influence the active/break phases over the tropical west Pacific. Our model solutions support

  15. Next-Generation Satellite Precipitation Products for Understanding Global and Regional Water Variability (United States)

    Hou, Arthur Y.


    A major challenge in understanding the space-time variability of continental water fluxes is the lack of accurate precipitation estimates over complex terrains. While satellite precipitation observations can be used to complement ground-based data to obtain improved estimates, space-based and ground-based estimates come with their own sets of uncertainties, which must be understood and characterized. Quantitative estimation of uncertainties in these products also provides a necessary foundation for merging satellite and ground-based precipitation measurements within a rigorous statistical framework. Global Precipitation Measurement (GPM) is an international satellite mission that will provide next-generation global precipitation data products for research and applications. It consists of a constellation of microwave sensors provided by NASA, JAXA, CNES, ISRO, EUMETSAT, DOD, NOAA, NPP, and JPSS. At the heart of the mission is the GPM Core Observatory provided by NASA and JAXA to be launched in 2013. The GPM Core, which will carry the first space-borne dual-frequency radar and a state-of-the-art multi-frequency radiometer, is designed to set new reference standards for precipitation measurements from space, which can then be used to unify and refine precipitation retrievals from all constellation sensors. The next-generation constellation-based satellite precipitation estimates will be characterized by intercalibrated radiometric measurements and physical-based retrievals using a common observation-derived hydrometeor database. For pre-launch algorithm development and post-launch product evaluation, NASA supports an extensive ground validation (GV) program in cooperation with domestic and international partners to improve (1) physics of remote-sensing algorithms through a series of focused field campaigns, (2) characterization of uncertainties in satellite and ground-based precipitation products over selected GV testbeds, and (3) modeling of atmospheric processes and

  16. Rotational Variability of Earth's Polar Regions: Implications for Detecting Snowball Planets (United States)

    Cowan, Nicolas B.; Robinson, Tyler; Livengood, Timothy A.; Deming, Drake; Agol, Eric; A'Hearn, Michael F.; Charbonneau, David; Lisse, Carey M.; Meadows, Victoria S.; Seager, Sara; Shields, Aomawa L.; Wellnitz, Dennis D.


    We have obtained the first time-resolved, disk-integrated observations of Earth's poles with the Deep Impact spacecraft as part of the EPOXI mission of opportunity. These data mimic what we will see when we point next-generation space telescopes at nearby exoplanets. We use principal component analysis (PCA) and rotational light curve inversion to characterize color inhomogeneities and map their spatial distribution from these unusual vantage points, as a complement to the equatorial views presented by Cowan et al. in 2009. We also perform the same PCA on a suite of simulated rotational multi-band light curves from NASA's Virtual Planetary Laboratory three-dimensional spectral Earth model. This numerical experiment allows us to understand what sorts of surface features PCA can robustly identify. We find that the EPOXI polar observations have similar broadband colors as the equatorial Earth, but with 20%-30% greater apparent albedo. This is because the polar observations are most sensitive to mid-latitudes, which tend to be more cloudy than the equatorial latitudes emphasized by the original EPOXI Earth observations. The cloudiness of the mid-latitudes also manifests itself in the form of increased variability at short wavelengths in the polar observations and as a dominant gray eigencolor in the south polar observation. We construct a simple reflectance model for a snowball Earth. By construction, our model has a higher Bond albedo than the modern Earth; its surface albedo is so high that Rayleigh scattering does not noticeably affect its spectrum. The rotational color variations occur at short wavelengths due to the large contrast between glacier ice and bare land in those wavebands. Thus, we find that both the broadband colors and diurnal color variations of such a planet would be easily distinguishable from the modern-day Earth, regardless of viewing angle.

  17. Duration of the Arctic sea ice melt season: Regional and interannual variability, 1979-2001 (United States)

    Belchansky, G.I.; Douglas, D.C.; Platonov, N.G.


    Melt onset dates, freeze onset dates, and melt season duration were estimated over Arctic sea ice, 1979–2001, using passive microwave satellite imagery and surface air temperature data. Sea ice melt duration for the entire Northern Hemisphere varied from a 104-day minimum in 1983 and 1996 to a 124-day maximum in 1989. Ranges in melt duration were highest in peripheral seas, numbering 32, 42, 44, and 51 days in the Laptev, Barents-Kara, East Siberian, and Chukchi Seas, respectively. In the Arctic Ocean, average melt duration varied from a 75-day minimum in 1987 to a 103-day maximum in 1989. On average, melt onset in annual ice began 10.6 days earlier than perennial ice, and freeze onset in perennial ice commenced 18.4 days earlier than annual ice. Average annual melt dates, freeze dates, and melt durations in annual ice were significantly correlated with seasonal strength of the Arctic Oscillation (AO). Following high-index AO winters (January–March), spring melt tended to be earlier and autumn freeze later, leading to longer melt season durations. The largest increases in melt duration were observed in the eastern Siberian Arctic, coincident with cyclonic low pressure and ice motion anomalies associated with high-index AO phases. Following a positive AO shift in 1989, mean annual melt duration increased 2–3 weeks in the northern East Siberian and Chukchi Seas. Decreasing correlations between consecutive-year maps of melt onset in annual ice during 1979–2001 indicated increasing spatial variability and unpredictability in melt distributions from one year to the next. Despite recent declines in the winter AO index, recent melt distributions did not show evidence of reestablishing spatial patterns similar to those observed during the 1979–88 low-index AO period. Recent freeze distributions have become increasingly similar to those observed during 1979–88, suggesting a recurrent spatial pattern of freeze chronology under low-index AO conditions.

  18. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya. (United States)

    Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin


    Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; pKenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya.

  19. Three Ingredients for Improved Global Aftershock Forecasts: Tectonic Region, Time-Dependent Catalog Incompleteness, and Inter-Sequence Variability (United States)

    Page, M. T.; Hardebeck, J.; Felzer, K. R.; Michael, A. J.; van der Elst, N.


    Following a large earthquake, seismic hazard can be orders of magnitude higher than the long-term average as a result of aftershock triggering. Due to this heightened hazard, there is a demand from emergency managers and the public for rapid, authoritative, and reliable aftershock forecasts. In the past, USGS aftershock forecasts following large, global earthquakes have been released on an ad-hoc basis with inconsistent methods, and in some cases, aftershock parameters adapted from California. To remedy this, we are currently developing an automated aftershock product that will generate more accurate forecasts based on the Reasenberg and Jones (Science, 1989) method. To better capture spatial variations in aftershock productivity and decay, we estimate regional aftershock parameters for sequences within the Garcia et al. (BSSA, 2012) tectonic regions. We find that regional variations for mean aftershock productivity exceed a factor of 10. The Reasenberg and Jones method combines modified-Omori aftershock decay, Utsu productivity scaling, and the Gutenberg-Richter magnitude distribution. We additionally account for a time-dependent magnitude of completeness following large events in the catalog. We generalize the Helmstetter et al. (2005) equation for short-term aftershock incompleteness and solve for incompleteness levels in the global NEIC catalog following large mainshocks. In addition to estimating average sequence parameters within regions, we quantify the inter-sequence parameter variability. This allows for a more complete quantification of the forecast uncertainties and Bayesian updating of the forecast as sequence-specific information becomes available.

  20. Elongation of the C-terminal domain of an anti-amyloid β single-chain variable fragment increases its thermodynamic stability and decreases its aggregation tendency. (United States)

    Rivera-Hernández, Geovanny; Marin-Argany, Marta; Blasco-Moreno, Bernat; Bonet, Jaume; Oliva, Baldo; Villegas, Sandra


    Amyloid β (Aβ) immunotherapy is considered a promising approach to Alzheimer disease treatment. In contrast to the use of complete antibodies, administration of single-chain variable fragments (scFv) has not been associated with either meningoencephalitis or cerebral hemorrhage. ScFv-h3D6 is known to preclude cytotoxicity of the Aβ 1-42 peptide by removing its oligomers from the amyloid pathway. As is the case for other scFv molecules, the recombinant production of scFv-h3D6 is limited by its folding and stability properties. Here, we show that its urea-induced unfolding pathway is characterized by the presence of an intermediate state composed of the unfolded VL domain and the folded VH domain, which suggests the VL domain as a target for thermodynamic stability redesign. The modeling of the 3D structure revealed that the VL domain, located at the C-terminal of the molecule, was ending before its latest β-strand was completed. Three elongation mutants, beyond VL-K107, showed increased thermodynamic stability and lower aggregation tendency, as determined from urea denaturation experiments and Fourier-transform infrared spectroscopy, respectively. Because the mutants maintained the capability of removing Aβ-oligomers from the amyloid pathway, we expect these traits to increase the half-life of scFv-h3D6 in vivo and, consequently, to decrease the effective doses. Our results led to the improvement of a potential Alzheimer disease treatment and may be extrapolated to other class-I scFv molecules of therapeutic interest.

  1. Anti-CD20 single chain variable antibody fragment-apolipoprotein A-I chimera containing nanodisks promote targeted bioactive agent delivery to CD20-positive lymphomas. (United States)

    Crosby, Natasha M; Ghosh, Mistuni; Su, Betty; Beckstead, Jennifer A; Kamei, Ayako; Simonsen, Jens B; Luo, Bing; Gordon, Leo I; Forte, Trudy M; Ryan, Robert O


    A fusion protein comprising an α-CD20 single chain variable fragment (scFv) antibody, a spacer peptide, and human apolipoprotein (apo) A-I was constructed and expressed in Escherichia coli. The lipid interaction properties intrinsic to apoA-I as well as the antigen recognition properties of the scFv were retained by the chimera. scFv•apoA-I was formulated into nanoscale reconstituted high-density lipoprotein particles (termed nanodisks; ND) and incubated with cultured cells. α-CD20 scFv•apoA-I ND bound to CD20-positive non-Hodgkins lymphoma (NHL) cells (Ramos and Granta) but not to CD20-negative T lymphocytes (i.e., Jurkat). Binding to NHL cells was partially inhibited by pre-incubation with rituximab, a monoclonal antibody directed against CD20. Confocal fluorescence microscopy analysis of Granta cells following incubation with α-CD20 scFv•apoA-I ND formulated with the intrinsically fluorescent hydrophobic polyphenol, curcumin, revealed α-CD20 scFv•apoA-I localizes to the cell surface, while curcumin off-loads and gains entry to the cell. Compared to control incubations, viability of cultured NHL cells was decreased upon incubation with α-CD20 scFv•apoA-I ND harboring curcumin. Thus, formulation of curcumin ND with α-CD20 scFv•apoA-I as the scaffold component confers cell targeting and enhanced bioactive agent delivery, providing a strategy to minimize toxicity associated with chemotherapeutic agents.

  2. Generation of human single-chain variable fragment antibodies specific to dengue virus non-structural protein 1 that interfere with the virus infectious cycle. (United States)

    Poungpair, Ornnuthchar; Bangphoomi, Kunan; Chaowalit, Prapaipit; Sawasdee, Nunghathai; Saokaew, Nichapatr; Choowongkomon, Kiattawee; Chaicumpa, Wanpen; Yenchitsomanus, Pa-thai


    Severe forms of dengue virus (DENV) infection frequently cause high case fatality rate. Currently, there is no effective vaccine against the infection. Clinical cases are given only palliative treatment as specific anti-DENV immunotherapy is not available and it is urgently required. In this study, human single-chain variable fragment (HuScFv) antibodies that bound specifically to the conserved non-structural protein-1 (NS1) of DENV and interfered with the virus replication cycle were produced by using phage display technology. Recombinant NS1 (rNS1) of DENV serotype 2 (DENV2) was used as antigen in phage bio-panning to select phage clones that displayed HuScFv from antibody phage display library. HuScFv from two phagemid transformed E. coli clones, i.e., clones 11 and 13, bound to the rNS1 as well as native NS1 in both secreted and intracellular forms. Culture fluids of the HuScFv11/HuScFv13 exposed DENV2 infected cells had significant reduction of the infectious viral particles, implying that the antibody fragments affected the virus morphogenesis or release. HuScFv epitope mapping by phage mimotope searching revealed that HuScFv11 bound to amino acids 1-14 of NS1, while the HuScFv13 bound to conformational epitope at the C-terminal portion of the NS1. Although the functions of the epitopes and the molecular mechanism of the HuScFv11 and HuScFv13 require further investigations, these small antibodies have high potential for development as anti-DENV biomolecules.

  3. Expression of a single-chain variable-fragment antibody against a Fusarium virguliforme toxin peptide enhances tolerance to sudden death syndrome in transgenic soybean plants. (United States)

    Brar, Hargeet K; Bhattacharyya, Madan K


    Plants do not produce antibodies. However, plants can correctly assemble functional antibody molecules encoded by mammalian antibody genes. Many plant diseases are caused by pathogen toxins. One such disease is the soybean sudden death syndrome (SDS). SDS is a serious disease caused by the fungal pathogen Fusarium virguliforme. The pathogen, however, has never been isolated from diseased foliar tissues. Thus, one or more toxins produced by the pathogen have been considered to cause foliar SDS. One of these possible toxins, FvTox1, was recently identified. We investigated whether expression of anti-FvTox1 single-chain variable-fragment (scFv) antibody in transgenic soybean can confer resistance to foliar SDS. We have created two scFv antibody genes, Anti-FvTox1-1 and Anti-FvTox1-2, encoding anti-FvTox1 scFv antibodies from RNAs of a hybridoma cell line that expresses mouse monoclonal anti-FvTox1 7E8 antibody. Both anti-FvTox1 scFv antibodies interacted with an antigenic site of FvTox1 that binds to mouse monoclonal anti-FvTox1 7E8 antibody. Binding of FvTox1 by the anti-FvTox1 scFv antibodies, expressed in either Escherichia coli or transgenic soybean roots, was initially verified on nitrocellulose membranes. Expression of anti-FvTox1-1 in stable transgenic soybean plants resulted in enhanced foliar SDS resistance compared with that in nontransgenic control plants. Our results suggest that i) FvTox1 is an important pathogenicity factor for foliar SDS development and ii) expression of scFv antibodies against pathogen toxins could be a suitable biotechnology approach for protecting crop plants from toxin-induced diseases.

  4. Predictive value of serum ALT and T-cell receptor beta variable chain for HBeAg seroconversion in chronic hepatitis B patients during tenofovir treatment (United States)

    Yang, Jiezuan; Yan, Dong; Guo, Renyong; Chen, Jiajia; Li, Yongtao; Fan, Jun; Fu, Xuyan; Yao, Xinsheng; Diao, Hongyan; Li, Lanjuan


    Abstract Effective antiviral therapy plays a key role in slowing the progression of chronic hepatitis B (CHB). Identification of serum indices, including hepatitis B e antigen (HBeAg) expression and seroconversion, will facilitate evaluation of the efficacy of antiviral therapy in HBeAg-positive CHB patients. The biochemical, serological, virological parameters, and the frequency of circulating CD4+CD25+ regulatory T cell (Treg) in 32 patients were measured at baseline and every 12 weeks during 96 weeks of tenofovir disoproxil fumarate (TDF) treatment. The relationship between the hepatitis B virus (HBV) deoxyribonucleic acid (DNA) and Treg and alanine aminotransferase (ALT) levels was analyzed, respectively. The molecular profiles of T-cell receptor beta variable chain (TRBV) were determined using gene melting spectral pattern. For the seroconverted 12 patients, ALT declined to normal levels by week 24 and remained at this level in subsequent treatment; moreover, the predictive cutoff value of ALT for HBeAg seroconversion (SC) was 41.5 U/L at week 24. The positive correlation between HBV DNA and Treg and ALT was significant in SC patients, but not in non-SC patients. Six TRBV families (BV3, BV11, BV12, BV14, BV20, and BV24) were predominantly expressed in SC patients at baseline. The decline of ALT could be used to predict HBeAg seroconversion for CHB patients during TDF treatment. In addition, the profile of Tregs and TRBVs may be associated with HBeAg seroconversion and could also be a potential indicator for predicting HBeAg SC and treatment outcome for CHB patients. PMID:28272219

  5. Identification of region-specific yeast artificial chromosomes using pools of Alu element-mediated polymerase chain reaction probes labeled via linear amplification

    Energy Technology Data Exchange (ETDEWEB)

    Cole, C.G.; Bobrow, M.; Bentley, D.R.; Dunham, I. (United Medical and Dental Schools of Guy' s and St. Thomas Hospitals, London Bridge, London, England (United Kingdom)); Patel, K.; Shipley, J.; Sheer, D. (Imperial Cancer Research Fund, London (United Kingdom))


    The ability to identify large numbers of yeast artificial chromosomes (YACS) specific to any given genomic region rapidly and efficiently enhances both the construction of clone maps and the isolation of region-specific landmarks (e.g., polymorphic markers). The authors describe a method of preparing region-specific single-stranded hybridization probes from Alu element-mediated polymerase chain reaction (Alu-PCR) products of somatic cell hybrids for YAC library screening. Pools of up to 50 cloned Alu-PCR products from an irradiation-reduced hybrid containing 22q11.2-q13.1 were labeled to high specific activity by linear amplification using a single vector primer. The resulting single-stranded probes were extensively competed to remove repetitive sequences, while retaining the full complexity of the probe. Extensive coverage of the region by YACs using multiple probe pools was demonstrated as many YACs were detected more than once. In situ analysis using chosen YACs confirmed that the clones were specific for the region. Thus, this pooled probe approach constitutes a rapid method to identify large numbers of YACs relevant to a large chromosomal region. 29 refs., 4 figs.

  6. Identification of region-specific yeast artificial chromosomes using pools of Alu element-mediated polymerase chain reaction probes labeled via linear amplification. (United States)

    Cole, C G; Patel, K; Shipley, J; Sheer, D; Bobrow, M; Bentley, D R; Dunham, I


    The ability to identify large numbers of yeast artificial chromosomes (YACs) specific to any given genomic region rapidly and efficiently enhances both the construction of clone maps and the isolation of region-specific landmarks (e.g., polymorphic markers). We describe a method of preparing region-specific single-stranded hybridization probes from Alu element-mediated polymerase chain reaction (Alu-PCR) products of somatic cell hybrids for YAC library screening. Pools of up to 50 cloned Alu-PCR products from an irradiation-reduced hybrid containing 22q11.2-q13.1 were labeled to high specific activity by linear amplification using a single vector primer. The resulting single-stranded probes were extensively competed to remove repetitive sequences, while retaining the full complexity of the probe. Extensive coverage of the region by YACs using multiple probe pools was demonstrated as many YACs were detected more than once. In situ analysis using chosen YACs confirmed that the clones were specific for the region. Thus, this pooled probe approach constitutes a rapid method to identify large numbers of YACs relevant to a large chromosomal region.

  7. Influence of topographic and environmental variability on model uncertainty: a case study on snow and ground temperatures in mountain regions (United States)

    Gubler, S.; Gruber, S.; Purves, R.; Endrizzi, S.


    A variety of physically based models to predict and understand the spatio-temporal behaviour of snow and ground temperatures have been developed in recent years. Model evaluation including the analysis of model uncertainty and validation is widely accepted as fundamental in enhancing trust in decisions that are based on model simulations. Due to constraints on resources or lack of distributed validation data, model evaluation is often restricted to one or few locations only, even if the model is applied to make predictions for large spatial areas and time periods. Thus, conclusions about model behaviour entail the tacit assumption that validation at one point can inform decisions about model performance in different environmental conditions. The effect of this assumption on model application and development when modeling phenomena in highly variable terrain or over large distances has rarely been studied. This study is focused on a sensitivity and uncertainty analysis of an energy and mass balance model that simulates snow and ground temperatures. It serves as a case study examining the role of topography and soil on parametric model uncertainty and sensitivity. A sensitivity analysis on individual parameters and a Monte Carlo based uncertainty study are performed at a variety of locations covering the range of topographic and environmental variability typically found in mountain regions. The results indicate that model uncertainties and sensitivities vary strongly under differing environmental conditions. This demonstrates that model evaluation (validation, sensitivity and uncertainty analyses) benefits strongly from the consideration of differing variables and, especially, the environmental variation of their behaviour.

  8. Dense water formation and BiOS-induced variability in the Adriatic Sea simulated using an ocean regional circulation model (United States)

    Dunić, Natalija; Vilibić, Ivica; Šepić, Jadranka; Somot, Samuel; Sevault, Florence


    A performance analysis of the NEMOMED8 ocean regional circulation model was undertaken for the Adriatic Sea during the period of 1961-2012, focusing on two mechanisms, dense water formation (DWF) and the Adriatic-Ionian Bimodal Oscillating System (BiOS), which drive interannual and decadal variability in the basin. The model was verified based on sea surface temperature and sea surface height satellite measurements and long-term in situ observations from several key areas. The model qualitatively reproduces basin-scale processes: thermohaline-driven cyclonic circulation and freshwater surface outflow along the western Adriatic coast, dense water dynamics, and the inflow of Ionian and Levantine waters to the Adriatic. Positive temperature and salinity biases are reported; the latter are particularly large along the eastern part of the basin, presumably because of the inappropriate introduction of eastern Adriatic rivers into the model. The highest warm temperature biases in the vertical direction were found in dense-water-collecting depressions in the Adriatic, indicating either an inappropriate quantification of DWF processes or temperature overestimation of modelled dense water. The decadal variability in the thermohaline properties is reproduced better than interannual variability, which is considerably underestimated. The DWF rates are qualitatively well reproduced by the model, being larger when preconditioned by higher basin-wide salinities. Anticyclonic circulation in the northern Ionian Sea was modelled only during the Eastern Mediterranean Transient. No other reversals of circulation that could be linked to BiOS-driven changes were modelled.

  9. Short communication: severe immune suppression in patients infected with R5-tropic HIV-1 strains is associated with increased gp120 net charge at variable regions. (United States)

    Seclén, Eduardo; Soriano, Vincent; del Mar González, María; González-Lahoz, Juan; Poveda, Eva


    CXCR4-tropic viruses have been associated with advanced immune suppression. However, 50% of patients with AIDS exclusively harbor CCR5-tropic viruses. The net charge at HIV-1 envelope gp120 variable regions was examined in 66 HIV-1-infected individuals with CCR5-tropic viruses, of whom 30 had less than 200 cells/mm(3). A positive net charge at gp120 variable regions was significantly associated with lower CD4 counts. Thus, the net charge at gp120 variable regions could influence HIV-1 disease progression in subjects with CCR5-tropic viruses.

  10. Water maser variability over 20 years in a large sample of star-forming regions: the complete database

    CERN Document Server

    Felli, M; Cesaroni, R; Codella, C; Comoretto, G; Di Franco, S; Massi, F; Moscadelli, L; Nesti, R; Olmi, L; Palagi, F; Panella, D; Valdettaro, R


    Context. Water vapor emission at 22 GHz from masers associated with star-forming regions is highly variable. Aims. We present a database of up to 20 years of monitoring of a sample of 43 masers within star-forming regions. The sample covers a large range of luminosities of the associated IRAS source and is representative of the entire population of H2O masers of this type. The database forms a good starting point for any further study of H2O maser variability. Methods. The observations were obtained with the Medicina 32-m radiotelescope, at a rate of 4-5 observations per year. Results. To provide a database that can be easily accessed through the web, we give for each source: plots of the calibrated spectra, the velocity-time-flux density plot, the light curve of the integrated flux, the lower and upper envelopes of the maser emission, the mean spectrum, and the rate of the maser occurrence as a function of velocity. Figures for just one source are given in the text for representative purposes